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Posted to commits@taverna.apache.org by st...@apache.org on 2015/02/17 21:44:21 UTC
[01/16] incubator-taverna-plugin-bioinformatics git commit:
temporarily empty repository
Repository: incubator-taverna-plugin-bioinformatics
Updated Branches:
refs/heads/master 793628502 -> e13e3b741
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-soaplab-activity/src/main/java/net/sf/taverna/t2/activities/soaplab/SoaplabActivity.java
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diff --git a/taverna-soaplab-activity/src/main/java/net/sf/taverna/t2/activities/soaplab/SoaplabActivity.java b/taverna-soaplab-activity/src/main/java/net/sf/taverna/t2/activities/soaplab/SoaplabActivity.java
deleted file mode 100644
index 53091e1..0000000
--- a/taverna-soaplab-activity/src/main/java/net/sf/taverna/t2/activities/soaplab/SoaplabActivity.java
+++ /dev/null
@@ -1,413 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.soaplab;
-
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import javax.xml.namespace.QName;
-import javax.xml.rpc.ServiceException;
-
-import net.sf.taverna.t2.reference.ReferenceService;
-import net.sf.taverna.t2.reference.ReferenceServiceException;
-import net.sf.taverna.t2.reference.T2Reference;
-import net.sf.taverna.t2.workflowmodel.OutputPort;
-import net.sf.taverna.t2.workflowmodel.processor.activity.AbstractAsynchronousActivity;
-import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityConfigurationException;
-import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityInputPort;
-import net.sf.taverna.t2.workflowmodel.processor.activity.AsynchronousActivityCallback;
-
-import org.apache.axis.client.Call;
-import org.apache.axis.client.Service;
-import org.apache.log4j.Logger;
-
-import com.fasterxml.jackson.databind.JsonNode;
-
-/**
- * An Activity providing Soaplab functionality.
- *
- * @author David Withers
- */
-public class SoaplabActivity extends AbstractAsynchronousActivity<JsonNode> {
-
- public static final String URI = "http://ns.taverna.org.uk/2010/activity/soaplab";
-
- private static final Logger logger = Logger
- .getLogger(SoaplabActivity.class);
-
- private static final int INVOCATION_TIMEOUT = 0;
-
- private JsonNode json;
-
-// private Map<String, Class<?>> inputTypeMap = new HashMap<String, Class<?>>();
-
- public SoaplabActivity() {
- }
-
- @Override
- public void configure(JsonNode configurationBean) throws ActivityConfigurationException {
- this.json = configurationBean;
-// generatePorts();
- }
-
- @Override
- public JsonNode getConfiguration() {
- return json;
- }
-
- @Override
- public void executeAsynch(final Map<String, T2Reference> data,
- final AsynchronousActivityCallback callback) {
- callback.requestRun(new Runnable() {
-
- @SuppressWarnings("unchecked")
- public void run() {
- ReferenceService referenceService = callback.getContext().getReferenceService();
-
- Map<String, T2Reference> outputData = new HashMap<String, T2Reference>();
-
- try {
- // Copy the contents of the data set in the input map
- // to a new Map object which just contains the raw data
- // objects
- Map<String, Object> soaplabInputMap = new HashMap<String, Object>();
- for (Map.Entry<String, T2Reference> entry : data
- .entrySet()) {
- Class<?> inputType = getInputType(entry.getKey());
- logger.info("Resolving " + entry.getKey() + " to "
- + inputType);
- soaplabInputMap.put(entry.getKey(), referenceService.renderIdentifier(
- entry.getValue(), inputType, callback.getContext()));
- logger.info(" Value = "
- + soaplabInputMap.get(entry.getKey()));
- }
-
- // Invoke the web service...
- Call call = (Call) new Service().createCall();
- call.setTimeout(new Integer(INVOCATION_TIMEOUT));
- // TODO is there endpoint stored in the configuration as a
- // String or a URL?
- // URL soaplabWSDLURL = new
- // URL(configurationBean.getEndpoint());
- call.setTargetEndpointAddress(json.get("endpoint").textValue());
-
- // Invoke the job and wait for it to complete
- call.setOperationName(new QName("createAndRun"));
- String jobID = (String) call
- .invoke(new Object[] { soaplabInputMap });
- // Get the array of desired outputs to avoid pulling
- // everything back
- // TODO Decide how to get the bound ports for the processor
- // OutputPort[] boundOutputs =
- // this.proc.getBoundOutputPorts();
- OutputPort[] boundOutputs = getOutputPorts().toArray(
- new OutputPort[0]);
- String[] outputPortNames = new String[boundOutputs.length];
- for (int i = 0; i < outputPortNames.length; i++) {
- outputPortNames[i] = boundOutputs[i].getName();
- logger.debug("Adding output : " + outputPortNames[i]);
- }
-
- if (!isPollingDefined()) {
- // If we're not polling then use this behaviour
- call.setOperationName(new QName("waitFor"));
- call.invoke(new Object[] { jobID });
- } else {
- // Wait for the polling interval then request a status
- // and do this until the status is terminal.
- boolean polling = true;
- // Number of milliseconds to wait before the first
- // status request.
- int pollingInterval = json.get("pollingInterval").intValue();
- while (polling) {
- try {
- Thread.sleep(pollingInterval);
- } catch (InterruptedException ie) {
- // do nothing
- }
- call.setOperationName(new QName("getStatus"));
- String statusString = (String) call
- .invoke(new Object[] { jobID });
- logger.info("Polling, status is : " + statusString);
- if (statusString.equals("RUNNING")
- || statusString.equals("CREATED")) {
- pollingInterval = (int) ((double) pollingInterval * json
- .get("pollingBackoff").doubleValue());
- if (pollingInterval > json.get("pollingIntervalMax").intValue()) {
- pollingInterval = json.get("pollingIntervalMax").intValue();
- }
- } else {
- // Either completed with an error or success
- polling = false;
- }
- }
- }
-
- // Get the status code
- call.setOperationName(new QName("getStatus"));
- String statusString = (String) call
- .invoke(new Object[] { jobID });
- if (statusString.equals("TERMINATED_BY_ERROR")) {
- // Get the report
- call.setOperationName(new QName("getSomeResults"));
- HashMap<String, String> temp = new HashMap<String, String>(
- (Map) call.invoke(new Object[] { jobID,
- new String[] { "report" } }));
- String reportText = temp.get("report");
- callback.fail("Soaplab call returned an error : "
- + reportText);
- return;
- }
-
- // Get the results required by downstream processors
- call.setOperationName(new QName("getSomeResults"));
- HashMap<String, Object> outputMap = new HashMap<String, Object>(
- (Map) call.invoke(new Object[] { jobID,
- outputPortNames }));
-
- // Tell soaplab that we don't need this session any more
- call.setOperationName(new QName("destroy"));
- call.invoke(new Object[] { jobID });
-
- // Build the map of DataThing objects
- for (Map.Entry<String, Object> entry : outputMap.entrySet()) {
- String parameterName = entry.getKey();
- Object outputObject = entry.getValue();
- if (logger.isDebugEnabled())
- logger.debug("Soaplab : parameter '"
- + parameterName + "' has type '"
- + outputObject.getClass().getName() + "'");
-
- if (outputObject instanceof String[]) {
- // outputThing = DataThingFactory
- // .bake((String[]) outputObject);
- outputData.put(parameterName, referenceService
- .register(Arrays.asList(outputObject), 1, true, callback.getContext()));
- } else if (outputObject instanceof byte[][]) {
- // Create a List of byte arrays, this will
- // map to l('application/octet-stream') in
- // the output document.
- // outputThing = DataThingFactory
- // .bake((byte[][]) outputObject);
- List<byte[]> list = new ArrayList<byte[]>();
- for (byte[] byteArray : (byte[][]) outputObject) {
- list.add(byteArray);
- }
- outputData.put(parameterName, referenceService
- .register(list, 1, true, callback.getContext()));
- // outputData.put(parameterName, dataFacade
- // .register(Arrays.asList(outputObject)));
- } else if (outputObject instanceof List) {
- List<?> convertedList = convertList((List<?>) outputObject);
- outputData.put(parameterName, referenceService
- .register(convertedList, 1, true, callback.getContext()));
- } else {
- // Fallthrough case, this mostly applies to
- // output of type byte[] or string, both of which
- // are handled perfectly sensibly by default.
- outputData.put(parameterName, referenceService
- .register(outputObject, 0, true, callback.getContext()));
- }
- }
-
- // success
- callback.receiveResult(outputData, new int[0]);
- } catch (ReferenceServiceException e) {
- callback.fail("Error accessing soaplab input/output data", e);
- } catch (IOException e) {
- callback.fail("Failure calling soaplab", e);
- } catch (ServiceException e) {
- callback.fail("Failure calling soaplab", e);
- }
- }
-
- });
-
- }
-
- public boolean isPollingDefined() {
- return json != null
- && (json.get("pollingInterval").intValue() != 0
- || json.get("pollingBackoff").doubleValue() != 1.0 || json
- .get("pollingIntervalMax").intValue() != 0);
- }
-
- private List<?> convertList(List<?> theList) {
- if (theList.size() == 0) {
- return theList;
- }
-
- List<byte[]> listOfBytes = new ArrayList<byte[]>();
- for (Object element : theList) {
- if (element instanceof List) {
- List<?> list = ((List<?>) element);
- if (list.size() > 0 && (list.get(0) instanceof Byte)) {
- byte[] bytes = new byte[list.size()];
- for (int j = 0; j < list.size(); j++) {
- bytes[j] = ((Byte) list.get(j)).byteValue();
- }
- listOfBytes.add(bytes);
- } else {
- // If we can't cope here just return the original
- // object
- return theList;
- }
- } else {
- return theList;
- }
- }
- return listOfBytes;
- }
-
- private Class<?> getInputType(String portName) {
- Class<?> inputType = String.class;
- for (ActivityInputPort inputPort : getInputPorts()) {
- if (inputPort.getName().equals(portName)) {
- return inputPort.getTranslatedElementClass();
- }
- }
- return inputType;
- }
-
-// @SuppressWarnings("unchecked")
-// private void generatePorts() throws ActivityConfigurationException {
-// // Wipe the existing port declarations
-// // ports = new ArrayList();
-// try {
-// // Do web service type stuff[tm]
-// Map<String, String>[] inputs = (Map<String, String>[]) Soap
-// .callWebService(json.get("endpoint").textValue(),
-// "getInputSpec");
-// // Iterate over the inputs
-// for (int i = 0; i < inputs.length; i++) {
-// Map<String, String> input_spec = inputs[i];
-// String input_name = input_spec.get("name");
-// String input_type = input_spec.get("type").toLowerCase();
-// // Could get other properties such as defaults here
-// // but at the moment we've got nowhere to put them
-// // so we don't bother.
-// if (input_type.equals("string")) {
-// addInput(input_name, 0, true,
-// new ArrayList<Class<? extends ExternalReferenceSPI>>(), String.class);
-// inputTypeMap.put(input_name, String.class);
-// } else if (input_type.equals("string[]")) {
-// addInput(input_name, 1, true,
-// new ArrayList<Class<? extends ExternalReferenceSPI>>(), String.class);
-// inputTypeMap.put(input_name, String.class);
-// } else if (input_type.equals("byte[]")) {
-// addInput(input_name, 0, true,
-// new ArrayList<Class<? extends ExternalReferenceSPI>>(), byte[].class);
-// inputTypeMap.put(input_name, byte[].class);
-// } else if (input_type.equals("byte[][]")) {
-// addInput(input_name, 1, true,
-// new ArrayList<Class<? extends ExternalReferenceSPI>>(), byte[].class);
-// inputTypeMap.put(input_name, byte[].class);
-// } else {
-// // Count number of [] to get the arrays right
-// int depth = (input_type.split("\\[\\]", -1).length) -1 ;
-// logger.info("Soaplab input type '" + input_type
-// + "' unknown for input '" + input_name + "' in "
-// + json.get("endpoint").textValue()
-// + ", will attempt to add as String depth " + depth);
-// addInput(input_name, depth, true,
-// new ArrayList<Class<? extends ExternalReferenceSPI>>(), String.class);
-// inputTypeMap.put(input_name, String.class);
-// }
-// }
-//
-// // Get outputs
-// Map<String, String>[] results = (Map<String, String>[]) Soap
-// .callWebService(json.get("endpoint").textValue(),
-// "getResultSpec");
-// // Iterate over the outputs
-// for (int i = 0; i < results.length; i++) {
-// Map<String, String> output_spec = results[i];
-// String output_name = output_spec.get("name");
-// String output_type = output_spec.get("type").toLowerCase();
-// // Check to see whether the output is either report or
-// // detailed_status, in
-// // which cases we ignore it, this is soaplab metadata rather
-// // than application data.
-// if ((!output_name.equalsIgnoreCase("detailed_status"))) {
-//
-// // && (!output_name.equalsIgnoreCase("report"))) {
-// if (output_type.equals("string")) {
-// addOutput(output_name, 0, "text/plain");
-// } else if (output_type.equals("string[]")) {
-// addOutput(output_name, 1, "text/plain");
-// } else if (output_type.equals("byte[]")) {
-// addOutput(output_name, 0, "application/octet-stream");
-// } else if (output_type.equals("byte[][]")) {
-// addOutput(output_name, 1, "application/octet-stream");
-// } else {
-// // Count number of [] to get the arrays right
-// int depth = (output_type.split("\\[\\]", -1).length) -1 ;
-// logger.info("Soaplab output type '" + output_type
-// + "' unknown for output '" + output_name + "' in "
-// + json.get("endpoint").textValue()
-// + ", will add as depth " + depth);
-// addOutput(output_name, depth, null);
-// }
-// }
-// }
-//
-// } catch (ServiceException se) {
-// throw new ActivityConfigurationException(
-// json.get("endpoint").textValue()
-// + ": Unable to create a new call to connect\n to soaplab, error was : "
-// + se.getMessage());
-// } catch (RemoteException re) {
-// throw new ActivityConfigurationException(
-// ": Unable to call the get spec method for\n endpoint : "
-// + json.get("endpoint").textValue()
-// + "\n Remote exception message "
-// + re.getMessage());
-// } catch (NullPointerException npe) {
-// // If we had a null pointer exception, go around again - this is a
-// // bug somewhere between axis and soaplab
-// // that occasionally causes NPEs to happen in the first call or two
-// // to a given soaplab installation. It also
-// // manifests in the Talisman soaplab clients.
-// generatePorts();
-// }
-// }
-
-// protected void addOutput(String portName, int portDepth, String type) {
-// ActivityOutputPort port = edits.createActivityOutputPort(
-// portName, portDepth, portDepth);
-// MimeType mimeType = null;
-// if (type != null) {
-// mimeType = new MimeType();
-// mimeType.setText(type);
-// }
-// try {
-// edits.getAddAnnotationChainEdit(port, mimeType).doEdit();
-// } catch (EditException e) {
-// logger.debug("Error adding MimeType annotation to port", e);
-// }
-// outputPorts.add(port);
-// }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-soaplab-activity/src/main/java/net/sf/taverna/t2/activities/soaplab/SoaplabActivityConfigurationBean.java
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diff --git a/taverna-soaplab-activity/src/main/java/net/sf/taverna/t2/activities/soaplab/SoaplabActivityConfigurationBean.java b/taverna-soaplab-activity/src/main/java/net/sf/taverna/t2/activities/soaplab/SoaplabActivityConfigurationBean.java
deleted file mode 100644
index fa6bdec..0000000
--- a/taverna-soaplab-activity/src/main/java/net/sf/taverna/t2/activities/soaplab/SoaplabActivityConfigurationBean.java
+++ /dev/null
@@ -1,119 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.soaplab;
-
-import net.sf.taverna.t2.workflowmodel.processor.config.ConfigurationBean;
-import net.sf.taverna.t2.workflowmodel.processor.config.ConfigurationProperty;
-
-/**
- * A configuration bean specific to a Soaplab activity. In particular it provides details
- * about the Soaplab service endpoint and the polling settings.
- *
- * @author David Withers
- */
-@ConfigurationBean(uri = SoaplabActivity.URI + "#Config")
-public class SoaplabActivityConfigurationBean {
-
- private String endpoint = null;
-
- private int pollingInterval = 0;
-
- private double pollingBackoff = 1.0;
-
- private int pollingIntervalMax = 0;
-
- /**
- * Returns the endpoint.
- *
- * @return the endpoint
- */
- public String getEndpoint() {
- return endpoint;
- }
-
- /**
- * Sets the endpoint.
- *
- * @param endpoint the new endpoint
- */
- @ConfigurationProperty(name = "endpoint", label = "Soaplab Service Endpoint", description = "The endpoint of the Soaplab service")
- public void setEndpoint(String endpoint) {
- this.endpoint = endpoint;
- }
-
- /**
- * Returns the pollingInterval.
- *
- * @return the pollingInterval
- */
- public int getPollingInterval() {
- return pollingInterval;
- }
-
- /**
- * Sets the pollingInterval.
- *
- * @param pollingInterval the new pollingInterval
- */
- @ConfigurationProperty(name = "pollingInterval", label = "Polling Interval", description = "The polling time interval (in milliseconds)", required = false)
- public void setPollingInterval(int pollingInterval) {
- this.pollingInterval = pollingInterval;
- }
-
- /**
- * Returns the pollingBackoff.
- *
- * @return the pollingBackoff
- */
- public double getPollingBackoff() {
- return pollingBackoff;
- }
-
- /**
- * Sets the pollingBackoff.
- *
- * @param pollingBackoff the new pollingBackoff
- */
- @ConfigurationProperty(name = "pollingBackoff", label = "Polling Backoff", description = "The polling backoff factor", required = false)
- public void setPollingBackoff(double pollingBackoff) {
- this.pollingBackoff = pollingBackoff;
- }
-
- /**
- * Returns the pollingIntervalMax.
- *
- * @return the pollingIntervalMax
- */
- public int getPollingIntervalMax() {
- return pollingIntervalMax;
- }
-
- /**
- * Sets the pollingIntervalMax.
- *
- * @param pollingIntervalMax the new pollingIntervalMax
- */
- @ConfigurationProperty(name = "pollingIntervalMax", label = "Max Polling Interval", description = "The maximum polling time interval (in milliseconds)", required = false)
- public void setPollingIntervalMax(int pollingIntervalMax) {
- this.pollingIntervalMax = pollingIntervalMax;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-soaplab-activity/src/main/java/net/sf/taverna/t2/activities/soaplab/SoaplabActivityFactory.java
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diff --git a/taverna-soaplab-activity/src/main/java/net/sf/taverna/t2/activities/soaplab/SoaplabActivityFactory.java b/taverna-soaplab-activity/src/main/java/net/sf/taverna/t2/activities/soaplab/SoaplabActivityFactory.java
deleted file mode 100644
index 3c62c9d..0000000
--- a/taverna-soaplab-activity/src/main/java/net/sf/taverna/t2/activities/soaplab/SoaplabActivityFactory.java
+++ /dev/null
@@ -1,216 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2011 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.soaplab;
-
-import java.io.IOException;
-import java.net.URI;
-import java.rmi.RemoteException;
-import java.util.HashSet;
-import java.util.Map;
-import java.util.Set;
-
-import javax.xml.rpc.ServiceException;
-
-import net.sf.taverna.t2.annotation.annotationbeans.MimeType;
-import net.sf.taverna.t2.workflowmodel.EditException;
-import net.sf.taverna.t2.workflowmodel.Edits;
-import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityConfigurationException;
-import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityFactory;
-import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityInputPort;
-import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityOutputPort;
-
-import org.apache.log4j.Logger;
-
-import com.fasterxml.jackson.databind.JsonNode;
-import com.fasterxml.jackson.databind.ObjectMapper;
-
-/**
- * An {@link ActivityFactory} for creating <code>SoaplabActivity</code>.
- *
- * @author David Withers
- */
-public class SoaplabActivityFactory implements ActivityFactory {
-
- private static final Logger logger = Logger.getLogger(SoaplabActivityFactory.class);
-
- private Edits edits;
-
- @Override
- public SoaplabActivity createActivity() {
- return new SoaplabActivity();
- }
-
- @Override
- public URI getActivityType() {
- return URI.create(SoaplabActivity.URI);
- }
-
- @Override
- public JsonNode getActivityConfigurationSchema() {
- ObjectMapper objectMapper = new ObjectMapper();
- try {
- return objectMapper.readTree(getClass().getResource("/schema.json"));
- } catch (IOException e) {
- return objectMapper.createObjectNode();
- }
- }
-
- @Override
- public Set<ActivityInputPort> getInputPorts(JsonNode json) throws ActivityConfigurationException {
- Set<ActivityInputPort> inputPorts = new HashSet<>();
- try {
- // Do web service type stuff[tm]
- Map<String, String>[] inputs = (Map<String, String>[]) Soap
- .callWebService(json.get("endpoint").textValue(),
- "getInputSpec");
- // Iterate over the inputs
- for (int i = 0; i < inputs.length; i++) {
- Map<String, String> input_spec = inputs[i];
- String input_name = input_spec.get("name");
- String input_type = input_spec.get("type").toLowerCase();
- // Could get other properties such as defaults here
- // but at the moment we've got nowhere to put them
- // so we don't bother.
- if (input_type.equals("string")) {
- inputPorts.add(edits.createActivityInputPort(input_name, 0, true,
- null, String.class));
- } else if (input_type.equals("string[]")) {
- inputPorts.add(edits.createActivityInputPort(input_name, 1, true,
- null, String.class));
- } else if (input_type.equals("byte[]")) {
- inputPorts.add(edits.createActivityInputPort(input_name, 0, true,
- null, byte[].class));
- } else if (input_type.equals("byte[][]")) {
- inputPorts.add(edits.createActivityInputPort(input_name, 1, true,
- null, byte[].class));
- } else {
- // Count number of [] to get the arrays right
- int depth = (input_type.split("\\[\\]", -1).length) -1 ;
- logger.info("Soaplab input type '" + input_type
- + "' unknown for input '" + input_name + "' in "
- + json.get("endpoint").textValue()
- + ", will attempt to add as String depth " + depth);
- inputPorts.add(edits.createActivityInputPort(input_name, depth, true, null, String.class));
- }
- }
- } catch (ServiceException se) {
- throw new ActivityConfigurationException(
- json.get("endpoint").textValue()
- + ": Unable to create a new call to connect\n to soaplab, error was : "
- + se.getMessage());
- } catch (RemoteException re) {
- throw new ActivityConfigurationException(
- ": Unable to call the get spec method for\n endpoint : "
- + json.get("endpoint").textValue()
- + "\n Remote exception message "
- + re.getMessage());
- } catch (NullPointerException npe) {
- // If we had a null pointer exception, go around again - this is a
- // bug somewhere between axis and soaplab
- // that occasionally causes NPEs to happen in the first call or two
- // to a given soaplab installation. It also
- // manifests in the Talisman soaplab clients.
- return getInputPorts(json);
- }
- return inputPorts;
- }
-
- @Override
- public Set<ActivityOutputPort> getOutputPorts(JsonNode json) throws ActivityConfigurationException {
- Set<ActivityOutputPort> outputPorts = new HashSet<>();
- try {
- // Get outputs
- Map<String, String>[] results = (Map<String, String>[]) Soap
- .callWebService(json.get("endpoint").textValue(),
- "getResultSpec");
- // Iterate over the outputs
- for (int i = 0; i < results.length; i++) {
- Map<String, String> output_spec = results[i];
- String output_name = output_spec.get("name");
- String output_type = output_spec.get("type").toLowerCase();
- // Check to see whether the output is either report or
- // detailed_status, in
- // which cases we ignore it, this is soaplab metadata rather
- // than application data.
- if ((!output_name.equalsIgnoreCase("detailed_status"))) {
-
- // && (!output_name.equalsIgnoreCase("report"))) {
- if (output_type.equals("string")) {
- outputPorts.add(createOutput(output_name, 0, "text/plain"));
- } else if (output_type.equals("string[]")) {
- outputPorts.add(createOutput(output_name, 1, "text/plain"));
- } else if (output_type.equals("byte[]")) {
- outputPorts.add(createOutput(output_name, 0, "application/octet-stream"));
- } else if (output_type.equals("byte[][]")) {
- outputPorts.add(createOutput(output_name, 1, "application/octet-stream"));
- } else {
- // Count number of [] to get the arrays right
- int depth = (output_type.split("\\[\\]", -1).length) -1 ;
- logger.info("Soaplab output type '" + output_type
- + "' unknown for output '" + output_name + "' in "
- + json.get("endpoint").textValue()
- + ", will add as depth " + depth);
- outputPorts.add(createOutput(output_name, depth, null));
- }
- }
- }
-
- } catch (ServiceException se) {
- throw new ActivityConfigurationException(
- json.get("endpoint").textValue()
- + ": Unable to create a new call to connect\n to soaplab, error was : "
- + se.getMessage());
- } catch (RemoteException re) {
- throw new ActivityConfigurationException(
- ": Unable to call the get spec method for\n endpoint : "
- + json.get("endpoint").textValue()
- + "\n Remote exception message "
- + re.getMessage());
- } catch (NullPointerException npe) {
- // If we had a null pointer exception, go around again - this is a
- // bug somewhere between axis and soaplab
- // that occasionally causes NPEs to happen in the first call or two
- // to a given soaplab installation. It also
- // manifests in the Talisman soaplab clients.
- return getOutputPorts(json);
- }
- return outputPorts;
- }
-
- public void setEdits(Edits edits) {
- this.edits = edits;
- }
-
- public ActivityOutputPort createOutput(String portName, int portDepth, String type) {
- ActivityOutputPort port = edits.createActivityOutputPort(portName, portDepth, portDepth);
- if (type != null) {
- MimeType mimeType = new MimeType();
- mimeType.setText(type);
- try {
- edits.getAddAnnotationChainEdit(port, mimeType).doEdit();
- } catch (EditException e) {
- logger.debug("Error adding MimeType annotation to port", e);
- }
- }
- return port;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-soaplab-activity/src/main/java/net/sf/taverna/t2/activities/soaplab/SoaplabActivityHealthChecker.java
----------------------------------------------------------------------
diff --git a/taverna-soaplab-activity/src/main/java/net/sf/taverna/t2/activities/soaplab/SoaplabActivityHealthChecker.java b/taverna-soaplab-activity/src/main/java/net/sf/taverna/t2/activities/soaplab/SoaplabActivityHealthChecker.java
deleted file mode 100644
index 69b910e..0000000
--- a/taverna-soaplab-activity/src/main/java/net/sf/taverna/t2/activities/soaplab/SoaplabActivityHealthChecker.java
+++ /dev/null
@@ -1,66 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.soaplab;
-
-import java.io.IOException;
-import java.net.HttpURLConnection;
-import java.net.MalformedURLException;
-import java.net.SocketTimeoutException;
-import java.net.URL;
-import java.net.URLConnection;
-import java.util.List;
-
-import net.sf.taverna.t2.workflowmodel.Processor;
-import net.sf.taverna.t2.workflowmodel.processor.activity.Activity;
-import net.sf.taverna.t2.workflowmodel.health.HealthCheck;
-import net.sf.taverna.t2.workflowmodel.health.HealthChecker;
-import net.sf.taverna.t2.visit.VisitReport;
-import net.sf.taverna.t2.visit.VisitReport.Status;
-
-import net.sf.taverna.t2.workflowmodel.health.RemoteHealthChecker;
-import net.sf.taverna.t2.workflowmodel.processor.activity.DisabledActivity;
-
-public class SoaplabActivityHealthChecker extends RemoteHealthChecker {
-
- public boolean canVisit(Object subject) {
- if (subject == null) {
- return false;
- }
- if (subject instanceof SoaplabActivity) {
- return true;
- }
- if (subject instanceof DisabledActivity) {
- return (((DisabledActivity) subject).getActivity() instanceof SoaplabActivity);
- }
- return false;
- }
-
- public VisitReport visit(Object o, List<Object> ancestors) {
- SoaplabActivityConfigurationBean configuration = null;
- Activity activity = (Activity) o;
- if (activity instanceof SoaplabActivity) {
- configuration = (SoaplabActivityConfigurationBean) activity.getConfiguration();
- } else if (activity instanceof DisabledActivity) {
- configuration = (SoaplabActivityConfigurationBean) ((DisabledActivity) activity).getActivityConfiguration();
- }
- return contactEndpoint(activity, configuration.getEndpoint());
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-soaplab-activity/src/main/resources/META-INF/services/net.sf.taverna.t2.workflowmodel.health.HealthChecker
----------------------------------------------------------------------
diff --git a/taverna-soaplab-activity/src/main/resources/META-INF/services/net.sf.taverna.t2.workflowmodel.health.HealthChecker b/taverna-soaplab-activity/src/main/resources/META-INF/services/net.sf.taverna.t2.workflowmodel.health.HealthChecker
deleted file mode 100644
index 1e52569..0000000
--- a/taverna-soaplab-activity/src/main/resources/META-INF/services/net.sf.taverna.t2.workflowmodel.health.HealthChecker
+++ /dev/null
@@ -1 +0,0 @@
-net.sf.taverna.t2.activities.soaplab.SoaplabActivityHealthChecker
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-soaplab-activity/src/main/resources/META-INF/spring/soaplab-activity-context-osgi.xml
----------------------------------------------------------------------
diff --git a/taverna-soaplab-activity/src/main/resources/META-INF/spring/soaplab-activity-context-osgi.xml b/taverna-soaplab-activity/src/main/resources/META-INF/spring/soaplab-activity-context-osgi.xml
deleted file mode 100644
index 434f054..0000000
--- a/taverna-soaplab-activity/src/main/resources/META-INF/spring/soaplab-activity-context-osgi.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<beans:beans xmlns="http://www.springframework.org/schema/osgi" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:beans="http://www.springframework.org/schema/beans"
- xsi:schemaLocation="http://www.springframework.org/schema/beans
- http://www.springframework.org/schema/beans/spring-beans.xsd
- http://www.springframework.org/schema/osgi
- http://www.springframework.org/schema/osgi/spring-osgi.xsd">
-
- <service ref="soaplabActivityHealthChecker" interface="net.sf.taverna.t2.workflowmodel.health.HealthChecker" />
-
- <service ref="soaplabActivityFactory" interface="net.sf.taverna.t2.workflowmodel.processor.activity.ActivityFactory" />
-
- <reference id="edits" interface="net.sf.taverna.t2.workflowmodel.Edits" />
-
-</beans:beans>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-soaplab-activity/src/main/resources/META-INF/spring/soaplab-activity-context.xml
----------------------------------------------------------------------
diff --git a/taverna-soaplab-activity/src/main/resources/META-INF/spring/soaplab-activity-context.xml b/taverna-soaplab-activity/src/main/resources/META-INF/spring/soaplab-activity-context.xml
deleted file mode 100644
index 8a6eb40..0000000
--- a/taverna-soaplab-activity/src/main/resources/META-INF/spring/soaplab-activity-context.xml
+++ /dev/null
@@ -1,12 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<beans xmlns="http://www.springframework.org/schema/beans" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://www.springframework.org/schema/beans
- http://www.springframework.org/schema/beans/spring-beans.xsd">
-
- <bean id="soaplabActivityHealthChecker" class="net.sf.taverna.t2.activities.soaplab.SoaplabActivityHealthChecker" />
-
- <bean id="soaplabActivityFactory" class="net.sf.taverna.t2.activities.soaplab.SoaplabActivityFactory">
- <property name="edits" ref="edits" />
- </bean>
-
-</beans>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-soaplab-activity/src/main/resources/schema.json
----------------------------------------------------------------------
diff --git a/taverna-soaplab-activity/src/main/resources/schema.json b/taverna-soaplab-activity/src/main/resources/schema.json
deleted file mode 100644
index d2a908a..0000000
--- a/taverna-soaplab-activity/src/main/resources/schema.json
+++ /dev/null
@@ -1,40 +0,0 @@
-{
- "$schema": "http://json-schema.org/draft-03/schema#",
- "id": "http://ns.taverna.org.uk/2010/activity/soaplab.schema.json",
- "title": "Soaplab consumer activity configuration",
- "type": "object",
- "properties": {
- "@context": {
- "description": "JSON-LD context for interpreting the configuration as RDF",
- "required": true,
- "enum": ["http://ns.taverna.org.uk/2010/activity/soaplab.context.json"]
- },
- "endpoint": {
- "title": "Soaplab Service Endpoint",
- "description": "The endpoint of the Soaplab service",
- "type": "string",
- "required": true
- }
- "pollingInterval": {
- "title": "Polling Interval",
- "description": "The polling time interval (in milliseconds",
- "type": "integer",
- "default": 0,
- "required": true
- }
- "pollingBackoff": {
- "title": "Polling Backoff",
- "description": "The polling backoff factor",
- "type": "number",
- "default": 1.0,
- "required": true
- }
- "pollingIntervalMax": {
- "title": "Max Polling Interval",
- "description": "The maximum polling time interval (in milliseconds)",
- "type": "integer",
- "default": 0,
- "required": true
- }
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-soaplab-activity/src/test/java/net/sf/taverna/t2/activities/soaplab/SoaplabActivityConfigurationBeanTest.java
----------------------------------------------------------------------
diff --git a/taverna-soaplab-activity/src/test/java/net/sf/taverna/t2/activities/soaplab/SoaplabActivityConfigurationBeanTest.java b/taverna-soaplab-activity/src/test/java/net/sf/taverna/t2/activities/soaplab/SoaplabActivityConfigurationBeanTest.java
deleted file mode 100644
index 3dc9ec3..0000000
--- a/taverna-soaplab-activity/src/test/java/net/sf/taverna/t2/activities/soaplab/SoaplabActivityConfigurationBeanTest.java
+++ /dev/null
@@ -1,92 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.soaplab;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNull;
-
-import org.junit.Before;
-import org.junit.Test;
-
-/**
- * Unit tests for SoaplabActivityConfigurationBean.
- *
- * @author David Withers
- */
-public class SoaplabActivityConfigurationBeanTest {
-
- private SoaplabActivityConfigurationBean bean;
-
- private String endpoint = "http://www.ebi.ac.uk/soaplab/emboss4/services/utils_misc.embossversion";
-
- @Before
- public void setUp() throws Exception {
- bean = new SoaplabActivityConfigurationBean();
- }
-
- @Test
- public void testGetEndpoint() {
- assertNull(bean.getEndpoint());
- }
-
- @Test
- public void testSetEndpoint() {
- bean.setEndpoint(endpoint);
- assertEquals(endpoint, bean.getEndpoint());
- bean.setEndpoint(null);
- assertNull(bean.getEndpoint());
-
- }
-
- @Test
- public void testGetPollingInterval() {
- assertEquals(0, bean.getPollingInterval());
- }
-
- @Test
- public void testSetPollingInterval() {
- bean.setPollingInterval(2000);
- assertEquals(2000, bean.getPollingInterval());
- }
-
- @Test
- public void testGetPollingBackoff() {
- assertEquals(1.0, bean.getPollingBackoff(), 0);
- }
-
- @Test
- public void testSetPollingBackoff() {
- bean.setPollingBackoff(1.4);
- assertEquals(1.4, bean.getPollingBackoff(), 0);
- }
-
- @Test
- public void testGetPollingIntervalMax() {
- assertEquals(0, bean.getPollingIntervalMax());
- }
-
- @Test
- public void testSetPollingIntervalMax() {
- bean.setPollingInterval(5000);
- assertEquals(5000, bean.getPollingInterval());
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-soaplab-activity/src/test/java/net/sf/taverna/t2/activities/soaplab/SoaplabActivityTest.java
----------------------------------------------------------------------
diff --git a/taverna-soaplab-activity/src/test/java/net/sf/taverna/t2/activities/soaplab/SoaplabActivityTest.java b/taverna-soaplab-activity/src/test/java/net/sf/taverna/t2/activities/soaplab/SoaplabActivityTest.java
deleted file mode 100644
index e0b0dca..0000000
--- a/taverna-soaplab-activity/src/test/java/net/sf/taverna/t2/activities/soaplab/SoaplabActivityTest.java
+++ /dev/null
@@ -1,127 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.soaplab;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.Map;
-import java.util.Set;
-
-import net.sf.taverna.t2.activities.testutils.ActivityInvoker;
-import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityOutputPort;
-
-import org.junit.Before;
-import org.junit.Ignore;
-import org.junit.Test;
-
-import com.fasterxml.jackson.databind.node.JsonNodeFactory;
-import com.fasterxml.jackson.databind.node.ObjectNode;
-
-/**
- * Unit tests for SoaplabActivity.
- *
- * @author David Withers
- */
-public class SoaplabActivityTest {
-
- private SoaplabActivity activity;
-
- private ObjectNode configurationBean;
-
- @Ignore("Integration test")
- @Before
- public void setUp() throws Exception {
- activity = new SoaplabActivity();
- configurationBean = JsonNodeFactory.instance.objectNode();
- configurationBean.put("endpoint", "http://www.ebi.ac.uk/soaplab/emboss4/services/utils_misc.embossversion");
- }
-
- @Ignore("Integration test")
- @Test
- public void testExecuteAsynch() throws Exception {
- Map<String, Object> inputs = new HashMap<String, Object>();
- // inputs.put("full", "true");
- Map<String, Class<?>> expectedOutputs = new HashMap<String, Class<?>>();
- expectedOutputs.put("report", String.class);
- expectedOutputs.put("outfile", String.class);
-
- activity.configure(configurationBean);
-
- Map<String, Object> outputs = ActivityInvoker.invokeAsyncActivity(
- activity, inputs, expectedOutputs);
- assertTrue(outputs.containsKey("report"));
- // assertTrue(outputs.get("report") instanceof String);
- assertTrue(outputs.containsKey("outfile"));
- assertTrue(outputs.get("outfile") instanceof String);
- System.out.println(outputs.get("outfile"));
-
- // test with polling
- configurationBean.put("pollingInterval", 5);
- configurationBean.put("PollingIntervalMax", 6);
- configurationBean.put("PollingBackoff", 1.2);
- activity.configure(configurationBean);
-
- outputs = ActivityInvoker.invokeAsyncActivity(activity, inputs,
- expectedOutputs);
- assertTrue(outputs.containsKey("report"));
- assertTrue(outputs.containsKey("outfile"));
- }
-
- @Ignore("Integration test")
- @Test
- public void testSoaplabActivity() {
- assertNotNull(new SoaplabActivity());
- }
-
- @Ignore("Integration test")
- @Test
- public void testConfigureSoaplabActivityConfigurationBean()
- throws Exception {
- Set<String> expectedOutputs = new HashSet<String>();
- expectedOutputs.add("report");
- expectedOutputs.add("outfile");
-
- activity.configure(configurationBean);
- Set<ActivityOutputPort> ports = activity.getOutputPorts();
- assertEquals(expectedOutputs.size(), ports.size());
- for (ActivityOutputPort outputPort : ports) {
- assertTrue("Wrong output : " + outputPort.getName(),
- expectedOutputs.remove(outputPort.getName()));
- }
- }
-
- @Ignore("Integration test")
- @Test
- public void testIsPollingDefined() throws Exception {
- assertFalse(activity.isPollingDefined());
- activity.configure(configurationBean);
- assertFalse(activity.isPollingDefined());
- configurationBean.put("pollingInterval", 1000);
- activity.configure(configurationBean);
- assertTrue(activity.isPollingDefined());
- }
-
-}
[04/16] incubator-taverna-plugin-bioinformatics git commit:
temporarily empty repository
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyObjectActivityHealthChecker.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyObjectActivityHealthChecker.java b/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyObjectActivityHealthChecker.java
deleted file mode 100644
index 7db539a..0000000
--- a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyObjectActivityHealthChecker.java
+++ /dev/null
@@ -1,57 +0,0 @@
-/*******************************************************************************
- * This file is a component of the Taverna project, and is licensed under the
- * GNU LGPL. Copyright Edward Kawas, The BioMoby Project
- ******************************************************************************/
-package net.sf.taverna.t2.activities.biomoby;
-
-import java.io.IOException;
-import java.net.HttpURLConnection;
-import java.net.MalformedURLException;
-import java.net.SocketTimeoutException;
-import java.net.URL;
-import java.net.URLConnection;
-import java.util.List;
-
-import net.sf.taverna.t2.workflowmodel.Processor;
-import net.sf.taverna.t2.workflowmodel.processor.activity.Activity;
-import net.sf.taverna.t2.workflowmodel.health.HealthCheck;
-import net.sf.taverna.t2.workflowmodel.health.HealthChecker;
-import net.sf.taverna.t2.visit.VisitReport;
-import net.sf.taverna.t2.visit.VisitReport.Status;
-
-import net.sf.taverna.t2.workflowmodel.health.RemoteHealthChecker;
-import net.sf.taverna.t2.workflowmodel.processor.activity.DisabledActivity;
-
-/**
- * A health checker for the Biomoby Object activity.
- *
- * @author David Withers
- */
-public class BiomobyObjectActivityHealthChecker extends RemoteHealthChecker {
-
- public boolean canVisit(Object subject) {
- if (subject == null) {
- return false;
- }
- if (subject instanceof BiomobyObjectActivity) {
- return true;
- }
- if (subject instanceof DisabledActivity) {
- return (((DisabledActivity) subject).getActivity() instanceof BiomobyObjectActivity);
- }
- return false;
- }
-
- public VisitReport visit(Object o, List<Object> ancestors) {
- Activity activity = (Activity) o;
- BiomobyObjectActivityConfigurationBean configuration = null;
- if (activity instanceof BiomobyObjectActivity) {
- configuration = (BiomobyObjectActivityConfigurationBean) activity.getConfiguration();
- } else if (activity instanceof DisabledActivity) {
- configuration = (BiomobyObjectActivityConfigurationBean) ((DisabledActivity) activity).getActivityConfiguration();
- }
- return contactEndpoint(activity, configuration.getMobyEndpoint());
-
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/ExecuteAsyncCgiService.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/ExecuteAsyncCgiService.java b/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/ExecuteAsyncCgiService.java
deleted file mode 100644
index 552dd34..0000000
--- a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/ExecuteAsyncCgiService.java
+++ /dev/null
@@ -1,517 +0,0 @@
-/*******************************************************************************
- * This file is a component of the Taverna project, and is licensed under the
- * GNU LGPL. Copyright Edward Kawas, The BioMoby Project
- ******************************************************************************/
-package net.sf.taverna.t2.activities.biomoby;
-
-import java.io.BufferedReader;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.io.StringReader;
-import java.io.UnsupportedEncodingException;
-import java.util.ArrayList;
-import java.util.HashMap;
-
-import javax.xml.parsers.DocumentBuilder;
-import javax.xml.parsers.DocumentBuilderFactory;
-
-import org.apache.commons.httpclient.DefaultHttpMethodRetryHandler;
-import org.apache.commons.httpclient.HttpClient;
-import org.apache.commons.httpclient.HttpStatus;
-import org.apache.commons.httpclient.methods.PostMethod;
-import org.apache.commons.httpclient.methods.RequestEntity;
-import org.apache.commons.httpclient.methods.StringRequestEntity;
-import org.apache.commons.httpclient.params.HttpMethodParams;
-import org.apache.log4j.Logger;
-import org.biomoby.shared.MobyException;
-import org.biomoby.shared.MobyPrefixResolver;
-import org.biomoby.shared.parser.MobyTags;
-import org.biomoby.w3c.addressing.EndpointReference;
-import org.jdom.Element;
-import org.jdom.output.Format;
-import org.jdom.output.XMLOutputter;
-import org.omg.lsae.notifications.AnalysisEvent;
-import org.w3c.dom.NodeList;
-import org.xml.sax.InputSource;
-
-/**
- * This class contains one method that is used to execute asynchronous HTTP POST
- * services
- *
- * @author Edward Kawas
- *
- */
-public class ExecuteAsyncCgiService {
-
- private static final String GET_MULTIPLE_RESOURCE_PROPERTIES_ACTION = "http://docs.oasis-open.org/wsrf/rpw-2/GetMultipleResourceProperties/GetMultipleResourcePropertiesRequest";
- private static final String DESTROY_RESOURCE_ACTION = "http://docs.oasis-open.org/wsrf/rlw-2/ImmediateResourceTermination/DestroyRequest";
-
- private static final String RESOURCE_PROPERTIES_NS = "http://docs.oasis-open.org/wsrf/rp-2";
- private static final String RESULT_PREFIX = "result_";
- private static final String STATUS_PREFIX = "status_";
- private static Logger logger = Logger
- .getLogger(ExecuteAsyncCgiService.class);
-
- /**
- *
- * @param url
- * @param serviceName
- * @param xml
- * @return
- */
- public static String executeMobyCgiAsyncService(String url,
- String serviceName, String xml) throws MobyException {
-
- // First, let's get the queryIds
- org.w3c.dom.Document message = null;
-
- try {
- DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
- dbf.setNamespaceAware(true);
- dbf.setValidating(false);
- DocumentBuilder db = dbf.newDocumentBuilder();
-
- message = db.parse(new InputSource(new StringReader(xml)));
- } catch (Throwable t) {
- throw new MobyException("Error while parsing input query", t);
- }
-
- NodeList l_data = message.getElementsByTagNameNS(
- MobyPrefixResolver.MOBY_XML_NAMESPACE, MobyTags.MOBYDATA);
- if (l_data == null || l_data.getLength() == 0) {
- l_data = message.getElementsByTagNameNS(
- MobyPrefixResolver.MOBY_XML_NAMESPACE_INVALID,
- MobyTags.MOBYDATA);
- }
-
- // Freeing resources
- message = null;
-
- if (l_data == null || l_data.getLength() == 0) {
- throw new MobyException("Empty asynchronous MOBY query!");
- }
-
- int nnode = l_data.getLength();
- String[] queryIds = new String[nnode];
- String[] tmpQueryIds = new String[nnode];
- String[] results = new String[nnode];
- for (int inode = 0; inode < nnode; inode++) {
- String queryId = null;
-
- org.w3c.dom.Element mdata = (org.w3c.dom.Element) l_data
- .item(inode);
-
- queryId = mdata.getAttribute(MobyTags.QUERYID);
- if (queryId == null || queryId.length() == 0)
- queryId = mdata
- .getAttributeNS(MobyPrefixResolver.MOBY_XML_NAMESPACE,
- MobyTags.QUERYID);
- if (queryId == null || queryId.length() == 0)
- queryId = mdata.getAttributeNS(
- MobyPrefixResolver.MOBY_XML_NAMESPACE_INVALID,
- MobyTags.QUERYID);
-
- if (queryId == null || queryId.length() == 0) {
- throw new MobyException(
- "Unable to extract queryId for outgoing MOBY message");
- }
-
- tmpQueryIds[inode] = queryIds[inode] = queryId;
- results[inode] = null;
- }
-
- // Freeing resources
- l_data = null;
-
- // Second, let's launch
- EndpointReference epr = launchCgiAsyncService(url, xml);
-
- // Third, waiting for the results
- try {
- // FIXME - add appropriate values here
- long pollingInterval = 1000L;
- double backoff = 1.0;
-
- // Max: one minute pollings
- long maxPollingInterval = 60000L;
-
- // Min: one second
- if (pollingInterval <= 0L)
- pollingInterval = 1000L;
-
- // Backoff: must be bigger than 1.0
- if (backoff <= 1.0)
- backoff = 1.5;
-
- do {
- try {
- Thread.sleep(pollingInterval);
- } catch (InterruptedException ie) {
- // DoNothing(R)
- }
-
- if (pollingInterval != maxPollingInterval) {
- pollingInterval = (long) ((double) pollingInterval * backoff);
- if (pollingInterval > maxPollingInterval) {
- pollingInterval = maxPollingInterval;
- }
- }
- } while (pollAsyncCgiService(serviceName, url, epr, tmpQueryIds,
- results));
- } finally {
-
- // Call destroy on this service ....
- freeCgiAsyncResources(url, epr);
-
- }
-
- // Fourth, assembling back the results
-
- // Results array already contains mobyData
- Element[] mobydatas = new Element[results.length];
- for (int x = 0; x < results.length; x++) {
- // TODO remove the extra wrapping from our result
- try {
- Element inputElement = XMLUtilities.getDOMDocument(results[x])
- .getRootElement();
- if (inputElement.getName().indexOf(
- "GetMultipleResourcePropertiesResponse") >= 0)
- if (inputElement.getChildren().size() > 0)
- inputElement = (Element) inputElement.getChildren()
- .get(0);
- if (inputElement.getName().indexOf("result_") >= 0)
- if (inputElement.getChildren().size() > 0)
- inputElement = (Element) inputElement.getChildren()
- .get(0);
- // replace results[x]
- mobydatas[x] = inputElement;
- } catch (MobyException e) {
- // TODO what should i do?
- }
- }
- Element e = null;
- try {
- e = XMLUtilities.createMultipleInvokations(mobydatas);
- } catch (Exception ex) {
- logger
- .error("There was a problem creating our XML message ...",
- ex);
- }
- // Fifth, returning results
- return e == null ? "" : new XMLOutputter(Format.getPrettyFormat())
- .outputString(e);
- }
-
- private static void freeCgiAsyncResources(String endpoint,
- EndpointReference epr) throws MobyException {
- // construct the Httpclient
- HttpClient client = new HttpClient();
- client.getParams().setParameter("http.useragent", "jMoby/Taverna2");
- // create the post method
- PostMethod method = new PostMethod(endpoint + "/destroy");
-
- // put our data in the request
- RequestEntity entity;
- try {
- entity = new StringRequestEntity(
- "<Destroy xmlns=\"http://docs.oasis-open.org/wsrf/rl-2\"/>",
- "text/xml", null);
- } catch (UnsupportedEncodingException e) {
- throw new MobyException("Problem posting data to webservice", e);
- }
- method.setRequestEntity(entity);
-
- // set the header
- StringBuffer httpheader = new StringBuffer();
- httpheader.append("<moby-wsrf>");
- httpheader
- .append("<wsa:Action xmlns:wsa=\"http://www.w3.org/2005/08/addressing\">"
- + DESTROY_RESOURCE_ACTION + "</wsa:Action>");
- httpheader
- .append("<wsa:To xmlns:wsu=\"http://docs.oasis-open.org/wss/2004/01/oasis-200401-wss-wssecurity-utility-1.0.xsd\" xmlns:wsa=\"http://www.w3.org/2005/08/addressing\" wsu:Id=\"To\">"
- + endpoint + "</wsa:To>");
- httpheader
- .append("<mobyws:ServiceInvocationId xmlns:mobyws=\"http://biomoby.org/\" xmlns:wsa=\"http://www.w3.org/2005/08/addressing\" wsa:IsReferenceParameter=\"true\">"
- + epr.getServiceInvocationId()
- + "</mobyws:ServiceInvocationId>");
- httpheader.append("</moby-wsrf>");
- method.addRequestHeader("moby-wsrf", httpheader.toString().replaceAll(
- "\r\n", ""));
- // retry up to 10 times
- client.getParams().setParameter(HttpMethodParams.RETRY_HANDLER,
- new DefaultHttpMethodRetryHandler(10, true));
-
- // call the method
- try {
- int result = client.executeMethod(method);
- if (result != HttpStatus.SC_OK)
- throw new MobyException(
- "Async HTTP POST service returned code: " + result
- + "\n" + method.getStatusLine());
- } catch (IOException e) {
- throw new MobyException("Problem reading response from webservice",
- e);
- } finally {
- // Release current connection to the connection pool once you are
- // done
- method.releaseConnection();
- }
- }
-
- /**
- *
- * @param endpoint
- * the url to the service to call
- * @param xml
- * the BioMOBY input message
- * @return EndpointReference the EPR returned by the service
- * @throws MobyException
- */
- private static EndpointReference launchCgiAsyncService(String endpoint,
- String xml) throws MobyException {
- // construct the Httpclient
- HttpClient client = new HttpClient();
- client.getParams().setParameter("http.useragent", "jMoby/Taverna2");
- // create the post method
- PostMethod method = new PostMethod(endpoint);
-
- // put our data in the request
- RequestEntity entity;
- try {
- entity = new StringRequestEntity(xml, "text/xml", null);
- } catch (UnsupportedEncodingException e) {
- throw new MobyException("Problem posting data to webservice", e);
- }
- method.setRequestEntity(entity);
-
- // retry up to 10 times
- client.getParams().setParameter(HttpMethodParams.RETRY_HANDLER,
- new DefaultHttpMethodRetryHandler(10, true));
-
- // call the method
- try {
- int result = client.executeMethod(method);
- if (result != HttpStatus.SC_OK)
- throw new MobyException(
- "Async HTTP POST service returned code: " + result
- + "\n" + method.getStatusLine());
- return EndpointReference.createFromXML(method.getResponseHeader(
- "moby-wsrf").getValue());
- } catch (IOException e) {
- throw new MobyException("Problem reading response from webservice",
- e);
- } finally {
- // Release current connection to the connection pool once you are
- // done
- method.releaseConnection();
- }
- }
-
- private static boolean pollAsyncCgiService(String msName, String url,
- EndpointReference epr, String[] queryIds, String[] result)
- throws MobyException {
- // Needed to remap results
- HashMap<String, Integer> queryMap = new HashMap<String, Integer>();
- for (int qi = 0; qi < queryIds.length; qi++) {
- String queryId = queryIds[qi];
- if (queryId != null)
- queryMap.put(queryId, new Integer(qi));
- }
-
- if (queryMap.size() == 0)
- return false;
-
- // construct the GetMultipleResourceProperties XML
- StringBuffer xml = new StringBuffer();
- xml.append("<wsrf-rp:GetMultipleResourceProperties xmlns:wsrf-rp='"
- + RESOURCE_PROPERTIES_NS
- + "' xmlns:mobyws='http://biomoby.org/'>");
- for (String q : queryMap.keySet())
- xml.append("<wsrf-rp:ResourceProperty>mobyws:" + STATUS_PREFIX + q
- + "</wsrf-rp:ResourceProperty>");
- xml.append("</wsrf-rp:GetMultipleResourceProperties>");
-
- StringBuffer httpheader = new StringBuffer();
- httpheader.append("<moby-wsrf>");
- httpheader
- .append("<wsa:Action xmlns:wsa=\"http://www.w3.org/2005/08/addressing\">"
- + GET_MULTIPLE_RESOURCE_PROPERTIES_ACTION
- + "</wsa:Action>");
- httpheader
- .append("<wsa:To xmlns:wsu=\"http://docs.oasis-open.org/wss/2004/01/oasis-200401-wss-wssecurity-utility-1.0.xsd\" xmlns:wsa=\"http://www.w3.org/2005/08/addressing\" wsu:Id=\"To\">"
- + url + "</wsa:To>");
- httpheader
- .append("<mobyws:ServiceInvocationId xmlns:mobyws=\"http://biomoby.org/\" xmlns:wsa=\"http://www.w3.org/2005/08/addressing\" wsa:IsReferenceParameter=\"true\">"
- + epr.getServiceInvocationId()
- + "</mobyws:ServiceInvocationId>");
- httpheader.append("</moby-wsrf>");
-
- AnalysisEvent[] l_ae = null;
- // First, status from queries
- String response = "";
- // construct the Httpclient
- HttpClient client = new HttpClient();
- client.getParams().setParameter("http.useragent", "jMoby/Taverna2");
- // create the post method
- PostMethod method = new PostMethod(url + "/status");
- // add the moby-wsrf header (with no newlines)
- method.addRequestHeader("moby-wsrf", httpheader.toString().replaceAll(
- "\r\n", ""));
-
- // put our data in the request
- RequestEntity entity;
- try {
- entity = new StringRequestEntity(xml.toString(), "text/xml", null);
- } catch (UnsupportedEncodingException e) {
- throw new MobyException("Problem posting data to webservice", e);
- }
- method.setRequestEntity(entity);
-
- // retry up to 10 times
- client.getParams().setParameter(HttpMethodParams.RETRY_HANDLER,
- new DefaultHttpMethodRetryHandler(10, true));
-
- // call the method
- try {
- if (client.executeMethod(method) != HttpStatus.SC_OK)
- throw new MobyException(
- "Async HTTP POST service returned code: "
- + method.getStatusCode() + "\n"
- + method.getStatusLine()
- + "\nduring our polling request");
- response = stream2String(method.getResponseBodyAsStream());
- } catch (IOException e) {
- throw new MobyException("Problem reading response from webservice",
- e);
- } finally {
- // Release current connection to the connection pool once you
- // are
- // done
- method.releaseConnection();
- }
-
- if (response != null) {
- l_ae = AnalysisEvent.createFromXML(response);
- }
-
- if (l_ae == null || l_ae.length == 0) {
- new MobyException(
- "Troubles while checking asynchronous MOBY job status from service "
- + msName);
- }
-
- ArrayList<String> finishedQueries = new ArrayList<String>();
- // Second, gather those finished queries
- for (int iae = 0; iae < l_ae.length; iae++) {
- AnalysisEvent ae = l_ae[iae];
- if (ae.isCompleted()) {
- String queryId = ae.getQueryId();
- if (!queryMap.containsKey(queryId)) {
- throw new MobyException(
- "Invalid result queryId on asynchronous MOBY job status fetched from "
- + msName);
- }
- finishedQueries.add(queryId);
- }
- }
-
- // Third, let's fetch the results from the finished queries
- if (finishedQueries.size() > 0) {
- String[] resQueryIds = finishedQueries.toArray(new String[0]);
- for (int x = 0; x < resQueryIds.length; x++) {
- // construct the GetMultipleResourceProperties XML
- xml = new StringBuffer();
- xml
- .append("<wsrf-rp:GetMultipleResourceProperties xmlns:wsrf-rp='"
- + RESOURCE_PROPERTIES_NS
- + "' xmlns:mobyws='http://biomoby.org/'>");
- for (String q : resQueryIds)
- xml.append("<wsrf-rp:ResourceProperty>mobyws:" + RESULT_PREFIX + q
- + "</wsrf-rp:ResourceProperty>");
- xml.append("</wsrf-rp:GetMultipleResourceProperties>");
-
- httpheader = new StringBuffer();
- httpheader.append("<moby-wsrf>");
- httpheader
- .append("<wsa:Action xmlns:wsa=\"http://www.w3.org/2005/08/addressing\">"
- + GET_MULTIPLE_RESOURCE_PROPERTIES_ACTION
- + "</wsa:Action>");
- httpheader
- .append("<wsa:To xmlns:wsu=\"http://docs.oasis-open.org/wss/2004/01/oasis-200401-wss-wssecurity-utility-1.0.xsd\" xmlns:wsa=\"http://www.w3.org/2005/08/addressing\" wsu:Id=\"To\">"
- + url + "</wsa:To>");
- httpheader
- .append("<mobyws:ServiceInvocationId xmlns:mobyws=\"http://biomoby.org/\" xmlns:wsa=\"http://www.w3.org/2005/08/addressing\" wsa:IsReferenceParameter=\"true\">"
- + epr.getServiceInvocationId()
- + "</mobyws:ServiceInvocationId>");
- httpheader.append("</moby-wsrf>");
- client = new HttpClient();
- client.getParams().setParameter("http.useragent",
- "jMoby/Taverna2");
- // create the post method
- method = new PostMethod(url + "/results");
- // add the moby-wsrf header (with no newlines)
- method.addRequestHeader("moby-wsrf", httpheader.toString()
- .replaceAll("\r\n", ""));
-
- // put our data in the request
- entity = null;
- try {
- entity = new StringRequestEntity(xml.toString(),
- "text/xml", null);
- } catch (UnsupportedEncodingException e) {
- throw new MobyException(
- "Problem posting data to webservice", e);
- }
- method.setRequestEntity(entity);
-
- // retry up to 10 times
- client.getParams().setParameter(HttpMethodParams.RETRY_HANDLER,
- new DefaultHttpMethodRetryHandler(10, true));
-
- // call the method
- try {
- if (client.executeMethod(method) != HttpStatus.SC_OK)
- throw new MobyException(
- "Async HTTP POST service returned code: "
- + method.getStatusCode() + "\n"
- + method.getStatusLine()
- + "\nduring our polling request");
- // place the result in the array
- result[x] = stream2String(method.getResponseBodyAsStream());
- // Marking as null
- queryIds[x] = null;
- } catch (IOException e) {
- logger.warn("Problem getting result from webservice\n"
- + e.getMessage());
- } finally {
- // Release current connection
- method.releaseConnection();
- }
- }
-
- }
- return finishedQueries.size() != queryMap.size();
- }
-
- private static String stream2String(InputStream is) {
- BufferedReader br = new BufferedReader(new InputStreamReader(is));
- StringBuilder sb = new StringBuilder();
- String line = null;
- String newline = System.getProperty("line.separator");
- try {
- while ((line = br.readLine()) != null) {
- sb.append(line + newline);
- }
- } catch (IOException e) {
- logger.warn("Exception reading input stream ...", e);
- } finally {
- try {
- br.close();
- } catch (IOException e) {
- logger.warn("Exception closing input stream ...", e);
- }
- }
- return sb.toString();
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/ExecuteAsyncMobyService.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/ExecuteAsyncMobyService.java b/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/ExecuteAsyncMobyService.java
deleted file mode 100644
index 10c76bc..0000000
--- a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/ExecuteAsyncMobyService.java
+++ /dev/null
@@ -1,695 +0,0 @@
-/*******************************************************************************
- * This file is a component of the Taverna project, and is licensed under the
- * GNU LGPL. Copyright Edward Kawas, The BioMoby Project
- ******************************************************************************/
-package net.sf.taverna.t2.activities.biomoby;
-
-import java.io.StringReader;
-import java.io.StringWriter;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.Map;
-
-import javax.xml.namespace.QName;
-import javax.xml.parsers.DocumentBuilder;
-import javax.xml.parsers.DocumentBuilderFactory;
-import javax.xml.soap.MessageFactory;
-import javax.xml.soap.SOAPBody;
-import javax.xml.soap.SOAPElement;
-import javax.xml.soap.SOAPEnvelope;
-import javax.xml.soap.SOAPException;
-import javax.xml.soap.SOAPHeader;
-import javax.xml.soap.SOAPMessage;
-import javax.xml.soap.SOAPPart;
-import javax.xml.transform.OutputKeys;
-import javax.xml.transform.Transformer;
-import javax.xml.transform.TransformerConfigurationException;
-import javax.xml.transform.TransformerException;
-import javax.xml.transform.TransformerFactory;
-import javax.xml.transform.dom.DOMSource;
-import javax.xml.transform.stream.StreamResult;
-import javax.xml.ws.BindingProvider;
-import javax.xml.ws.Dispatch;
-import javax.xml.ws.Service;
-import javax.xml.ws.soap.SOAPBinding;
-
-import org.apache.log4j.Logger;
-import org.biomoby.shared.MobyException;
-import org.biomoby.shared.MobyPrefixResolver;
-import org.biomoby.shared.MobyService;
-import org.biomoby.shared.parser.MobyTags;
-import org.biomoby.w3c.addressing.EndpointReference;
-import org.omg.lsae.notifications.AnalysisEvent;
-import org.w3c.dom.Node;
-import org.w3c.dom.NodeList;
-import org.xml.sax.InputSource;
-
-
-/**
- * This class contains one method that is used to execute asynchronous moby
- * services
- *
- * @author Edward Kawas
- *
- */
-
-public class ExecuteAsyncMobyService {
-
- /* async constants */
- private static final String GET_MULTIPLE_RESOURCE_PROPERTIES_ACTION = "http://docs.oasis-open.org/wsrf/rpw-2/GetMultipleResourceProperties/GetMultipleResourcePropertiesRequest";
- private static final String DESTROY_RESOURCE_ACTION = "http://docs.oasis-open.org/wsrf/rlw-2/ImmediateResourceTermination/DestroyRequest";
-
- private static final String RESOURCE_PROPERTIES_NS = "http://docs.oasis-open.org/wsrf/rp-2";
- private static final String RESOURCE_LIFETIME_NS = "http://docs.oasis-open.org/wsrf/rl-2";
-
- @SuppressWarnings("unused")
- private static final String XMLNS_NS = "http://www.w3.org/2000/xmlns/";
- private static final String XSD_NS = "http://www.w3.org/2001/XMLSchema";
- private static final String WSA_NS = "http://www.w3.org/2005/08/addressing";
- private static final String WSU_NS = "http://docs.oasis-open.org/wss/2004/01/oasis-200401-wss-wssecurity-utility-1.0.xsd";
- private static final String ANON_URI = WSA_NS + "/anonymous";
- private static final String RESULT_PREFIX = "result_";
- private static final String STATUS_PREFIX = "status_";
-
- private static Logger logger = Logger.getLogger(ExecuteAsyncMobyService.class);
- /**
- * This method does the same as getMultipleResourceProperties, with the
- * difference that it returns an String instead of a SOAPPart object. The
- * result is the serialization of the SOAPPart output obtained from
- * getMultipleResourceProperties.
- *
- * @param msName
- * The MOBY service name
- * @param queryIds
- * The array with the queryIds to use. It may contain null
- * strings
- * @param epr
- * The EndpointReference object which helds the MOBY asynchronous
- * job information
- * @param asResult
- * If this parameter is true, then this call fetches the results
- * associated to the input queryIds. If it is false, then this
- * call only asks for the job status.
- * @return When at least one of the strings from queryIds array was not
- * null, an String with the serialized answer from the service.
- * Otherwise, it returns null.
- * @throws SOAPException
- */
- private static String getMultipleResourcePropertiesAsString(String msName,
- String[] queryIds, EndpointReference epr, boolean asResult)
- throws TransformerConfigurationException, SOAPException,
- TransformerException {
- SOAPPart result = getMultipleResourceProperties(msName, queryIds, epr,
- asResult);
- if (result == null)
- return null;
- Transformer tr = TransformerFactory.newInstance().newTransformer();
- tr.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
-
- DOMSource dombody = new DOMSource(result);
-
- StringWriter sw = new StringWriter();
- tr.transform(dombody, new StreamResult(sw));
-
- return sw.toString();
- }
-
- /**
- * This method does the check and fetch work related to asynchronous
- * services. When all the results are fetched, it returns false. When some
- * recheck must be issued, it returns true.
- *
- * @param msName
- * The MOBY service name
- * @param epr
- * The EndpointReference, used for the queries
- * @param queryIds
- * The array which holds the queryIds to ask for. It can contain
- * null strings.
- * @param result
- * The array which will hold the mobyData results. This one must
- * have the same size as queryIds array.
- * @return true, if we need more checking iterations. Otherwise, false
- * @throws MobyException
- */
- private static boolean checkMobyAsyncJobsStatus(String msName,
- EndpointReference epr, String[] queryIds,
- org.w3c.dom.Element[] result) throws MobyException {
- // Needed to remap results
- HashMap<String, Integer> queryMap = new HashMap<String, Integer>();
- for (int qi = 0; qi < queryIds.length; qi++) {
- String queryId = queryIds[qi];
- if (queryId != null)
- queryMap.put(queryId, new Integer(qi));
- }
-
- if (queryMap.size() == 0)
- return false;
-
- try {
- AnalysisEvent[] l_ae = null;
- // First, status from queries
- String response = getMultipleResourcePropertiesAsString(msName,
- queryIds, epr, false);
- if (response != null) {
- l_ae = AnalysisEvent.createFromXML(response);
- }
-
- if (l_ae == null || l_ae.length == 0) {
- new MobyException(
- "Troubles while checking asynchronous MOBY job status from service "
- + msName);
- }
-
- ArrayList<String> finishedQueries = new ArrayList<String>();
- // Second, gather those finished queries
- for (int iae = 0; iae < l_ae.length; iae++) {
- AnalysisEvent ae = l_ae[iae];
- if (ae.isCompleted()) {
- String queryId = ae.getQueryId();
- if (!queryMap.containsKey(queryId)) {
- throw new MobyException(
- "Invalid result queryId on asynchronous MOBY job status fetched from "
- + msName);
- }
- finishedQueries.add(queryId);
- }
- }
-
- // Third, let's fetch the results from the finished queries
- if (finishedQueries.size() > 0) {
- String[] resQueryIds = finishedQueries.toArray(new String[0]);
- SOAPPart soapDOM = getMultipleResourceProperties(msName,
- resQueryIds, epr, true);
- NodeList l_mul = soapDOM.getElementsByTagNameNS(
- RESOURCE_PROPERTIES_NS,
- "GetMultipleResourcePropertiesResponse");
- if (l_mul == null || l_mul.getLength() == 0) {
- throw new MobyException(
- "Error while fetching asynchronous MOBY results from "
- + msName);
- }
-
- org.w3c.dom.Element mul = (org.w3c.dom.Element) l_mul.item(0);
- for (org.w3c.dom.Node child = mul.getFirstChild(); child != null; child = child
- .getNextSibling()) {
- if (child.getNodeType() == Node.ELEMENT_NODE
- && MobyService.BIOMOBY_SERVICE_URI.equals(child
- .getNamespaceURI())) {
- String preQueryId = child.getLocalName();
- int subpos = preQueryId.indexOf(RESULT_PREFIX);
- if (subpos != 0) {
- throw new MobyException(
- "Invalid result prefix on asynchronous MOBY job results fetched from "
- + msName);
- }
- String queryId = preQueryId.substring(RESULT_PREFIX
- .length());
- if (!queryMap.containsKey(queryId)) {
- throw new MobyException(
- "Invalid result queryId on asynchronous MOBY job results fetched from "
- + msName);
- }
-
- org.w3c.dom.Element elchild = (org.w3c.dom.Element) child;
- NodeList l_moby = elchild.getElementsByTagNameNS(
- MobyPrefixResolver.MOBY_XML_NAMESPACE,
- MobyTags.MOBYDATA);
- if (l_moby == null || l_moby.getLength() == 0)
- l_moby = elchild
- .getElementsByTagNameNS(
- MobyPrefixResolver.MOBY_XML_NAMESPACE_INVALID,
- MobyTags.MOBYDATA);
-
- if (l_moby == null || l_moby.getLength() == 0) {
- throw new MobyException(
- "Recovered empty payload from asynchronous MOBY service "
- + msName);
- }
- Integer queryPos = queryMap.get(queryId);
- result[queryPos] = (org.w3c.dom.Element) l_moby.item(0);
- // Marking as null
- queryIds[queryPos] = null;
- }
- }
- }
-
- return finishedQueries.size() != queryMap.size();
- } catch (SOAPException se) {
- throw new MobyException("Error while querying MOBY job status", se);
- } catch (TransformerConfigurationException tce) {
- throw new MobyException(
- "Error while preparing to parse MOBY job status", tce);
- } catch (TransformerException te) {
- throw new MobyException("Error while parsing MOBY job status", te);
- }
- }
-
- /**
- * This method calls the input MOBY service using the asynchronous protocol.
- *
- * @param endpoint
- * The endpoint of the service.
- * @param msName
- * The MOBY service name.
- * @param mobyXML
- * The MOBY payload to be sent to the service.
- * @return The MOBY payload with the results from the service.
- * @throws MobyException
- */
- public static String executeMobyAsyncService(String endpoint, String msName,
- String mobyXML) throws MobyException {
- // First, let's get the queryIds
- org.w3c.dom.Document message = null;
-
- try {
- DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
- dbf.setNamespaceAware(true);
- dbf.setValidating(false);
- DocumentBuilder db = dbf.newDocumentBuilder();
-
- message = db.parse(new InputSource(new StringReader(mobyXML)));
- } catch (Throwable t) {
- throw new MobyException("Error while parsing input query", t);
- }
-
- NodeList l_data = message.getElementsByTagNameNS(
- MobyPrefixResolver.MOBY_XML_NAMESPACE, MobyTags.MOBYDATA);
- if (l_data == null || l_data.getLength() == 0) {
- l_data = message.getElementsByTagNameNS(
- MobyPrefixResolver.MOBY_XML_NAMESPACE_INVALID,
- MobyTags.MOBYDATA);
- }
-
- // Freeing resources
- message = null;
-
- if (l_data == null || l_data.getLength() == 0) {
- throw new MobyException("Empty asynchronous MOBY query!");
- }
-
- int nnode = l_data.getLength();
- String[] queryIds = new String[nnode];
- String[] tmpQueryIds = new String[nnode];
- org.w3c.dom.Element[] results = new org.w3c.dom.Element[nnode];
- for (int inode = 0; inode < nnode; inode++) {
- String queryId = null;
-
- org.w3c.dom.Element mdata = (org.w3c.dom.Element) l_data
- .item(inode);
-
- queryId = mdata.getAttribute(MobyTags.QUERYID);
- if (queryId == null || queryId.length() == 0)
- queryId = mdata
- .getAttributeNS(MobyPrefixResolver.MOBY_XML_NAMESPACE,
- MobyTags.QUERYID);
- if (queryId == null || queryId.length() == 0)
- queryId = mdata.getAttributeNS(
- MobyPrefixResolver.MOBY_XML_NAMESPACE_INVALID,
- MobyTags.QUERYID);
-
- if (queryId == null || queryId.length() == 0) {
- throw new MobyException(
- "Unable to extract queryId for outgoing MOBY message");
- }
-
- tmpQueryIds[inode] = queryIds[inode] = queryId;
- results[inode] = null;
- }
-
- // Freeing resources
- l_data = null;
-
- // Second, let's launch
- EndpointReference epr = launchMobyAsyncService(endpoint, msName,
- mobyXML);
-
- // Third, waiting for the results
- try {
- // FIXME - add appropriate values here
- long pollingInterval = 1000L; // proc.getRetryDelay();
- double backoff = 1.0;// proc.getBackoff();
-
- // Max: one minute pollings
- long maxPollingInterval = 60000L;
-
- // Min: one second
- if (pollingInterval <= 0L)
- pollingInterval = 1000L;
-
- // Backoff: must be bigger than 1.0
- if (backoff <= 1.0)
- backoff = 1.5;
-
- do {
- try {
- Thread.sleep(pollingInterval);
- } catch (InterruptedException ie) {
- // DoNothing(R)
- }
-
- if (pollingInterval != maxPollingInterval) {
- pollingInterval = (long) ((double) pollingInterval * backoff/*
- * proc.
- * getBackoff
- * (
- * )
- */);
- if (pollingInterval > maxPollingInterval) {
- pollingInterval = maxPollingInterval;
- }
- }
- } while (checkMobyAsyncJobsStatus(msName, epr, tmpQueryIds, results));
- } finally {
- try {
- freeAsyncResources(msName, epr);
- } catch (SOAPException se) {
- logger.info(
- "An error was fired while freeing MOBY asynchronous resources from "
- + msName, se);
- }
- }
-
- // Fourth, assembling back the results
- org.w3c.dom.Document resdoc = null;
- try {
- DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
- dbf.setNamespaceAware(true);
- dbf.setValidating(false);
- DocumentBuilder db = dbf.newDocumentBuilder();
- resdoc = db.newDocument();
-
- org.w3c.dom.Element mobyroot = resdoc.createElementNS(
- MobyPrefixResolver.MOBY_XML_NAMESPACE, MobyTags.MOBY);
- resdoc.appendChild(mobyroot);
- org.w3c.dom.Element mobycontent = resdoc
- .createElementNS(MobyPrefixResolver.MOBY_XML_NAMESPACE,
- MobyTags.MOBYCONTENT);
- mobyroot.appendChild(mobycontent);
-
- // Results array already contains mobyData
-
- for (org.w3c.dom.Element result : results) {
- mobycontent.appendChild(resdoc.importNode(result, true));
- }
- } catch (Throwable t) {
- throw new MobyException("Error while assembling output", t);
- }
-
- // Fifth, returning results
- try {
- Transformer tr = TransformerFactory.newInstance().newTransformer();
- tr.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
-
- DOMSource dombody = new DOMSource(resdoc);
-
- StringWriter sw = new StringWriter();
- tr.transform(dombody, new StreamResult(sw));
-
- return sw.toString();
- } catch (Throwable t) {
- throw new MobyException("Error while assembling output", t);
- }
- }
-
- /**
- * This method free the asynchronous MOBY resources associated to the job
- * identifier tied to the EndpointReference object passed as input.
- *
- * @param msName
- * The MOBY service name
- * @param epr
- * The EndpointReference object which holds the MOBY asynchronous
- * job information
- * @throws SOAPException
- */
- private static void freeAsyncResources(String msName, EndpointReference epr)
- throws SOAPException {
- Service service = Service.create(new QName(
- MobyService.BIOMOBY_SERVICE_URI, msName + "Service"));
- QName mQName = new QName(MobyService.BIOMOBY_SERVICE_URI,
- "WSRF_Operations_Port");
- service.addPort(mQName, SOAPBinding.SOAP11HTTP_BINDING, epr
- .getAddress());
-
- Dispatch<SOAPMessage> dispatch = service.createDispatch(mQName,
- SOAPMessage.class, Service.Mode.MESSAGE);
- Map<String, Object> rc = dispatch.getRequestContext();
- rc.put(BindingProvider.SOAPACTION_USE_PROPERTY, new Boolean(true));
- rc.put(BindingProvider.SOAPACTION_URI_PROPERTY,
- GET_MULTIPLE_RESOURCE_PROPERTIES_ACTION);
-
- MessageFactory mf = MessageFactory.newInstance();
- SOAPMessage request = mf.createMessage();
- SOAPPart part = request.getSOAPPart();
-
- String mobyPrefix = "mobyws";
- String wsaPrefix = "wsa";
- String wsuPrefix = "wsu";
- // Obtain the SOAPEnvelope and header and body elements.
- SOAPEnvelope env = part.getEnvelope();
- SOAPHeader header = env.getHeader();
- SOAPBody body = env.getBody();
-
- header.addNamespaceDeclaration(mobyPrefix,
- MobyService.BIOMOBY_SERVICE_URI);
- header.addNamespaceDeclaration(wsaPrefix, WSA_NS);
- header.addNamespaceDeclaration(wsuPrefix, WSU_NS);
- // This is for the action
- SOAPElement actionRoot = header.addChildElement("Action", wsaPrefix,
- WSA_NS);
- actionRoot.addAttribute(env.createName("Id", wsuPrefix, WSU_NS),
- "Action");
- actionRoot.addTextNode(DESTROY_RESOURCE_ACTION);
-
- // This is for the To
- SOAPElement toRoot = header.addChildElement("To", wsaPrefix, WSA_NS);
- toRoot.addAttribute(env.createName("Id", wsuPrefix, WSU_NS), "To");
- toRoot.addTextNode(epr.getAddress());
-
- // And this is for the mobyws
- SOAPElement mobywsRoot = header.addChildElement("ServiceInvocationId",
- mobyPrefix, MobyService.BIOMOBY_SERVICE_URI);
- mobywsRoot.addNamespaceDeclaration(wsaPrefix, WSA_NS);
- mobywsRoot.addAttribute(env.createName("isReferenceParameter",
- wsaPrefix, WSA_NS), "true");
- mobywsRoot.addTextNode(epr.getServiceInvocationId());
-
- // At last, the replyto
- SOAPElement replyRoot = header.addChildElement("ReplyTo", wsaPrefix,
- WSA_NS);
- replyRoot.addAttribute(env.createName("Id", wsuPrefix, WSU_NS),
- "ReplyTo");
- SOAPElement addr = replyRoot.addChildElement("Address", wsaPrefix,
- WSA_NS);
- addr.addTextNode(ANON_URI);
-
- // Let's disable the headers
- // ((WSBindingProvider)dispatch).setOutboundHeaders(headers);
-
- // Now the SOAP body
- body.addChildElement("Destroy", "rl", RESOURCE_LIFETIME_NS);
-
- request.saveChanges();
- // We don't mind what it is returned
- dispatch.invoke(request);
- }
-
- /**
- * This method is used to launch an asynchronous MOBY job.
- *
- * @param endpoint
- * The endpoint of the service.
- * @param msName
- * The MOBY service name.
- * @param mobyXML
- * The MOBY payload to be sent to the service.
- * @return The EndpointReference object which helds the details of the MOBY
- * asynchronous job.
- * @throws MobyException
- */
- private static EndpointReference launchMobyAsyncService(String endpoint,
- String msName, String mobyXML) throws MobyException {
- try {
- Service service = Service.create(new QName(
- MobyService.BIOMOBY_SERVICE_URI, msName + "Service"));
- QName mQName = new QName(MobyService.BIOMOBY_SERVICE_URI, msName
- + "Port");
-
- service.addPort(mQName, SOAPBinding.SOAP11HTTP_BINDING, endpoint);
- Dispatch<SOAPMessage> dispatch = service.createDispatch(mQName,
- SOAPMessage.class, Service.Mode.MESSAGE);
- Map<String, Object> rc = dispatch.getRequestContext();
- rc.put(BindingProvider.SOAPACTION_USE_PROPERTY, new Boolean(true));
- rc.put(BindingProvider.SOAPACTION_URI_PROPERTY,
- MobyService.BIOMOBY_SERVICE_URI + "#" + msName + "_submit");
-
- MessageFactory mf = MessageFactory.newInstance();
- SOAPMessage request = mf.createMessage();
- SOAPPart part = request.getSOAPPart();
-
- String mobyPrefix = "mobyws";
- String xsiPrefix = "xsi";
-
- // Obtain the SOAPEnvelope and header and body elements.
- SOAPEnvelope env = part.getEnvelope();
- SOAPBody body = env.getBody();
-
- // Now the SOAP body
- body.addNamespaceDeclaration(mobyPrefix,
- MobyService.BIOMOBY_SERVICE_URI);
- SOAPElement rootMessage = body.addChildElement(msName + "_submit",
- mobyPrefix, MobyService.BIOMOBY_SERVICE_URI);
- SOAPElement data = rootMessage.addChildElement("data", mobyPrefix,
- MobyService.BIOMOBY_SERVICE_URI);
- data.addNamespaceDeclaration(xsiPrefix,
- MobyPrefixResolver.XSI_NAMESPACE2001);
- data.addNamespaceDeclaration("xsd", XSD_NS);
- data.addAttribute(env.createName("type", xsiPrefix,
- MobyPrefixResolver.XSI_NAMESPACE2001), "xsd:string");
- data.addTextNode(mobyXML);
-
- request.saveChanges();
- SOAPMessage outputMessage = dispatch.invoke(request);
- DOMSource output = new DOMSource(outputMessage.getSOAPPart()
- .getEnvelope());
-
- StringWriter sw = new StringWriter();
- Transformer tr = TransformerFactory.newInstance().newTransformer();
- tr.setOutputProperty(OutputKeys.OMIT_XML_DECLARATION, "yes");
- tr.transform(output, new StreamResult(sw));
-
- String response = sw.toString();
- return EndpointReference.createFromXML(response);
- } catch (SOAPException pce) {
- throw new MobyException(
- "Unable to create SOAP document builder for MOBY asynchronous call submission",
- pce);
- } catch (TransformerConfigurationException tce) {
- throw new MobyException(
- "Unable to create transformer factory for MOBY asynchronous call response",
- tce);
- } catch (TransformerException te) {
- throw new MobyException(
- "Unable to create transformer for MOBY asynchronous call response",
- te);
- }
- }
-
-
-
- /**
- * This method issues WSRF getMultipleResourceProperties calls. As this call
- * is used in BioMOBY for polling and for result fetching, it has an
- * additional parameter which handles the call mode.
- *
- * @param msName
- * The MOBY service name
- * @param queryIds
- * The array with the queryIds to use. It may contain null
- * strings
- * @param epr
- * The EndpointReference object which helds the MOBY asynchronous
- * job information
- * @param asResult
- * If this parameter is true, then this call fetches the results
- * associated to the input queryIds. If it is false, then this
- * call only asks for the job status.
- * @return When at least one of the strings from queryIds array was not
- * null, a SOAPPart object is returned with the answer for the
- * request issued to the MOBY service. Otherwise, it returns null.
- * @throws SOAPException
- */
- private static SOAPPart getMultipleResourceProperties(String msName,
- String[] queryIds, EndpointReference epr, boolean asResult)
- throws SOAPException {
- String op = asResult ? RESULT_PREFIX : STATUS_PREFIX;
-
- Service service = Service.create(new QName(
- MobyService.BIOMOBY_SERVICE_URI, msName + "Service"));
- QName mQName = new QName(MobyService.BIOMOBY_SERVICE_URI,
- "WSRF_Operations_Port");
- service.addPort(mQName, SOAPBinding.SOAP11HTTP_BINDING, epr
- .getAddress());
-
- Dispatch<SOAPMessage> dispatch = service.createDispatch(mQName,
- SOAPMessage.class, Service.Mode.MESSAGE);
- Map<String, Object> rc = dispatch.getRequestContext();
- rc.put(BindingProvider.SOAPACTION_USE_PROPERTY, new Boolean(true));
- rc.put(BindingProvider.SOAPACTION_URI_PROPERTY,
- GET_MULTIPLE_RESOURCE_PROPERTIES_ACTION);
-
- MessageFactory mf = MessageFactory.newInstance();
- SOAPMessage request = mf.createMessage();
- SOAPPart part = request.getSOAPPart();
-
- String mobyPrefix = "mobyws";
- String wsaPrefix = "wsa";
- String wsuPrefix = "wsu";
- // Obtain the SOAPEnvelope and header and body elements.
- SOAPEnvelope env = part.getEnvelope();
- SOAPHeader header = env.getHeader();
- SOAPBody body = env.getBody();
-
- header.addNamespaceDeclaration(mobyPrefix,
- MobyService.BIOMOBY_SERVICE_URI);
- header.addNamespaceDeclaration(wsaPrefix, WSA_NS);
- header.addNamespaceDeclaration(wsuPrefix, WSU_NS);
- // This is for the action
- SOAPElement actionRoot = header.addChildElement("Action", wsaPrefix,
- WSA_NS);
- actionRoot.addAttribute(env.createName("Id", wsuPrefix, WSU_NS),
- "Action");
- actionRoot.addTextNode(GET_MULTIPLE_RESOURCE_PROPERTIES_ACTION);
-
- // This is for the To
- SOAPElement toRoot = header.addChildElement("To", wsaPrefix, WSA_NS);
- toRoot.addAttribute(env.createName("Id", wsuPrefix, WSU_NS), "To");
- toRoot.addTextNode(epr.getAddress());
-
- // And this is for the mobyws
- SOAPElement mobywsRoot = header.addChildElement("ServiceInvocationId",
- mobyPrefix, MobyService.BIOMOBY_SERVICE_URI);
- mobywsRoot.addNamespaceDeclaration(wsaPrefix, WSA_NS);
- mobywsRoot.addAttribute(env.createName("isReferenceParameter",
- wsaPrefix, WSA_NS), "true");
- mobywsRoot.addTextNode(epr.getServiceInvocationId());
-
- // At last, the replyto
- SOAPElement replyRoot = header.addChildElement("ReplyTo", wsaPrefix,
- WSA_NS);
- replyRoot.addAttribute(env.createName("Id", wsuPrefix, WSU_NS),
- "ReplyTo");
- SOAPElement addr = replyRoot.addChildElement("Address", wsaPrefix,
- WSA_NS);
- addr.addTextNode(ANON_URI);
-
- // Let's disable the headers
- // ((WSBindingProvider)dispatch).setOutboundHeaders(headers);
-
- // Now the SOAP body
- SOAPElement smrp = body.addChildElement(
- "GetMultipleResourceProperties", "rp", RESOURCE_PROPERTIES_NS);
- boolean doSubmit = false;
- for (String queryId : queryIds) {
- if (queryId != null) {
- doSubmit = true;
- SOAPElement sii = smrp.addChildElement("ResourceProperty",
- "rp", RESOURCE_PROPERTIES_NS);
- sii.addNamespaceDeclaration(mobyPrefix,
- MobyService.BIOMOBY_SERVICE_URI);
- sii.addTextNode(mobyPrefix + ":" + op + queryId);
- }
- }
-
- if (doSubmit) {
- request.saveChanges();
- SOAPMessage output = dispatch.invoke(request);
-
- return output.getSOAPPart();
- } else {
- return null;
- }
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/ExecuteCgiService.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/ExecuteCgiService.java b/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/ExecuteCgiService.java
deleted file mode 100644
index a221a8a..0000000
--- a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/ExecuteCgiService.java
+++ /dev/null
@@ -1,70 +0,0 @@
-/*******************************************************************************
- * This file is a component of the Taverna project, and is licensed under the
- * GNU LGPL. Copyright Edward Kawas, The BioMoby Project
- ******************************************************************************/
-package net.sf.taverna.t2.activities.biomoby;
-
-import java.io.BufferedReader;
-import java.io.InputStreamReader;
-/*******************************************************************************
- * This file is a component of the Taverna project, and is licensed under the
- * GNU LGPL. Copyright Edward Kawas, The BioMoby Project
- ******************************************************************************/
-import java.io.OutputStreamWriter;
-import java.net.URL;
-import java.net.URLConnection;
-import java.net.URLEncoder;
-
-import org.biomoby.shared.MobyException;
-
-/**
- * This class contains one method that is used to execute synchronous HTTP POST
- * services
- *
- * @author Edward Kawas
- *
- */
-
-public class ExecuteCgiService {
-
- /**
- *
- * @param serviceEndpoint
- * the URL to the HTTP POST service
- * @param xml
- * the XML to send the service
- * @return a string representing the output from the service
- * @throws MobyException
- * if anything goes wrong (problems reading/writing to the
- * service)
- */
- public static String executeCgiService(String serviceEndpoint, String xml)
- throws MobyException {
- try {
- // Construct data
- String data = "data=" + URLEncoder.encode(xml, "UTF-8");
-
- // Send data
- URL url = new URL(serviceEndpoint);
- URLConnection conn = url.openConnection();
- conn.setDoOutput(true);
- OutputStreamWriter wr = new OutputStreamWriter(conn
- .getOutputStream());
- wr.write(data);
- wr.flush();
- // Get the response
- BufferedReader rd = new BufferedReader(new InputStreamReader(conn
- .getInputStream()));
- String line;
- StringBuffer sb = new StringBuffer();
- while ((line = rd.readLine()) != null) {
- sb.append(line);
- }
- wr.close();
- rd.close();
- return sb.toString();
- } catch (Exception e) {
- throw new MobyException(e.getMessage());
- }
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/ExecuteMobyService.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/ExecuteMobyService.java b/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/ExecuteMobyService.java
deleted file mode 100644
index f494d47..0000000
--- a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/ExecuteMobyService.java
+++ /dev/null
@@ -1,38 +0,0 @@
-/*******************************************************************************
- * This file is a component of the Taverna project, and is licensed under the
- * GNU LGPL. Copyright Edward Kawas, The BioMoby Project
- ******************************************************************************/
-package net.sf.taverna.t2.activities.biomoby;
-
-import org.biomoby.client.CentralImpl;
-import org.biomoby.shared.MobyException;
-
-/**
- * This class contains one method that is used to execute synchronous moby
- * services
- *
- * @author Edward Kawas
- *
- */
-
-public class ExecuteMobyService {
-
- /**
- *
- * @param endpoint
- * the SOAP endpoint of the service to call
- * @param service
- * the name of the service
- * @param xml
- * the XML to send the service
- * @return a string of XML representing the output from the service given
- * our input
- * @throws MobyException
- * if anything goes wrong (SOAP error)
- */
- public static String executeMobyService(String endpoint, String service,
- String xml) throws MobyException {
- return new CentralImpl(endpoint, "http://biomoby.org/").call(service,
- xml);
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/GetOntologyThread.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/GetOntologyThread.java b/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/GetOntologyThread.java
deleted file mode 100644
index e2402e8..0000000
--- a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/GetOntologyThread.java
+++ /dev/null
@@ -1,59 +0,0 @@
-/*******************************************************************************
- * This file is a component of the Taverna project, and is licensed under the
- * GNU LGPL. Copyright Edward Kawas, The BioMoby Project
- ******************************************************************************/
-/*
- * This file is a component of the Taverna project,
- * and is licensed under the GNU LGPL.
- * Copyright Edward Kawas, The BioMoby Project
- */
-
-package net.sf.taverna.t2.activities.biomoby;
-
-
-import org.biomoby.client.CentralImpl;
-
-/**
- * This class is used to speed up the running of workflows. Basically, whenever
- * a new Biomoby activity is added to taverna, a call out to RESOURCES/Objects
- * is made to download the datatype ontology.
- *
- * Uses BiomobyCache to process the registry
- *
- * This should speed up the execution of workflows, since the ontologies will
- * have already been downloaded.
- *
- * @author Eddie Kawas
- * @author Stuart Owen
- *
- * @see BiomobyCache
- *
- */
-public class GetOntologyThread extends Thread {
-
-
- // the registry endpoint
- String worker = null;
-
- /**
- *
- * @param url
- * the registry endpoint URL
- */
- public GetOntologyThread(String url) {
- super("BioMOBY GetOntologyThread");
- if (url == null || url.trim().equals(""))
- url = CentralImpl.getDefaultURL();
- this.worker = url;
- setDaemon(true);
- }
-
- /*
- * (non-Javadoc)
- *
- * @see java.lang.Thread#run()
- */
- public void run() {
- BiomobyCache.cacheForRegistryEndpoint(worker);
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/MobyParseDatatypeActivity.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/MobyParseDatatypeActivity.java b/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/MobyParseDatatypeActivity.java
deleted file mode 100644
index c33a5bf..0000000
--- a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/MobyParseDatatypeActivity.java
+++ /dev/null
@@ -1,417 +0,0 @@
-/*******************************************************************************
- * This file is a component of the Taverna project, and is licensed under the
- * GNU LGPL. Copyright Edward Kawas, The BioMoby Project
- ******************************************************************************/
-package net.sf.taverna.t2.activities.biomoby;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-import java.util.Scanner;
-
-import net.sf.taverna.t2.annotation.annotationbeans.MimeType;
-import net.sf.taverna.t2.reference.ExternalReferenceSPI;
-import net.sf.taverna.t2.reference.ReferenceService;
-import net.sf.taverna.t2.reference.ReferenceServiceException;
-import net.sf.taverna.t2.reference.T2Reference;
-import net.sf.taverna.t2.workflowmodel.EditException;
-import net.sf.taverna.t2.workflowmodel.OutputPort;
-import net.sf.taverna.t2.workflowmodel.processor.activity.AbstractAsynchronousActivity;
-import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityConfigurationException;
-import net.sf.taverna.t2.workflowmodel.processor.activity.AsynchronousActivityCallback;
-
-import org.apache.log4j.Logger;
-import org.biomoby.client.CentralImpl;
-import org.biomoby.shared.Central;
-import org.biomoby.shared.MobyDataType;
-import org.biomoby.shared.MobyException;
-import org.biomoby.shared.MobyRelationship;
-import org.biomoby.shared.NoSuccessException;
-
-/**
- * An Activity that breaks up a Moby datatype into its component parts minus all
- * the moby wrappings.
- *
- * Copied from org.biomoby.client.taverna.plugin.MobyParseDatatypeActivityProcessor and
- * org.biomoby.client.taverna.plugin.MobyParseDatatypeActivityTask and converted to a Taverna 2
- * Activity.
- *
- * @author Edward Kawas
- * @author David Withers
- */
-public class MobyParseDatatypeActivity extends AbstractAsynchronousActivity<MobyParseDatatypeActivityConfigurationBean> {
-
- public static final String URI = "http://ns.taverna.org.uk/2010/activity/biomoby/parser";
-
- private static Logger logger = Logger.getLogger(MobyParseDatatypeActivity.class);
-
- private MobyParseDatatypeActivityConfigurationBean configurationBean = new MobyParseDatatypeActivityConfigurationBean();
-
- private Central central = null;
-
- private MobyDataType datatype = null;
-
- @Override
- public void configure(MobyParseDatatypeActivityConfigurationBean configurationBean) throws ActivityConfigurationException {
- this.configurationBean = configurationBean;
- init();
- }
-
- @Override
- public void executeAsynch(final Map<String, T2Reference> data,
- final AsynchronousActivityCallback callback) {
- callback.requestRun(new Runnable() {
-
- @SuppressWarnings("unchecked")
- public void run() {
- ReferenceService referenceService = callback.getContext().getReferenceService();
-
- Map<String, T2Reference> output = new HashMap<String, T2Reference>();
-
- try {
-
- //cache ontology and namespace if not done so already. Immediately returns if already cached.
- BiomobyCache.cacheForRegistryEndpoint(getConfiguration().getRegistryEndpoint());
-
- String inputMapKey = getInputPorts().iterator().next().getName();
- // inputMap wasnt as expected
- if (!data.containsKey(inputMapKey)) {
- callback.receiveResult(output, new int[0]);
- return;
- }
-
- T2Reference inputId = data.get(inputMapKey);
-
- Object input = referenceService.renderIdentifier(inputId, String.class, callback.getContext());
-
- if (input instanceof String) {
- //logger.error(inputMapKey + " is a string!\n");
- String inputXML = (String) input;
- for (OutputPort outPort : getOutputPorts()) {
- String outputPortName = outPort.getName();
- String[] invocations = XMLUtilities.getSingleInvokationsFromMultipleInvokations(inputXML);
- ArrayList<String> names = new ArrayList<String>();
- int type = 0;
- // get the type, names list, etc
- if (outputPortName.equalsIgnoreCase("namespace")) {
- // extract the namespace from the top element
- names.add(configurationBean.getArticleNameUsedByService());
- type = ParseMobyXML.NAMESPACE;
- } else if (outputPortName.equalsIgnoreCase("id")) {
- // extract the id from the top element
- names.add(configurationBean.getArticleNameUsedByService());
- type = ParseMobyXML.ID;
- } else {
- names = getNames(outputPortName);
- if (outputPortName.endsWith("_ns")) {
- type = ParseMobyXML.NAMESPACE;
- if (names.size() > 1) // added nov15-2007
- names.remove(names.size()-1);
- } else if (outputPortName.endsWith("_id")) {
- type = ParseMobyXML.ID;
- if (names.size() > 1)//added nov15-2007
- names.remove(names.size()-1);
- } else {
- type = ParseMobyXML.VALUE;
- }
- }
- ArrayList<String> stuff = new ArrayList<String>();
- for (int i = 0; i < invocations.length; i++) {
- String invocation = invocations[i];
- if (XMLUtilities.isCollection(invocation)) {
- String[] simples = XMLUtilities.getAllSimplesByArticleName(configurationBean.getArticleNameUsedByService(), invocation);
- for (int j = 0; j < simples.length; j++) {
- ArrayList<String> content = ParseMobyXML.getContentForDataType(names, type, XMLUtilities.createMobyDataElementWrapper(simples[j],"a1", null), configurationBean.getRegistryEndpoint());
- stuff.addAll(content);
- }
- } else {
- ArrayList<String> content = ParseMobyXML.getContentForDataType(names, type, invocations[i],configurationBean.getRegistryEndpoint());
- stuff.addAll(content);
- }
- }
- output.put(outputPortName, referenceService.register(stuff, 1, true, callback.getContext()));
- }
-
- } else if (input instanceof List) {
- //logger.error(inputMapKey + " is a list!\n");
- List<String> list = (List) input;
- // holder contains a list of strings indexed by output port name
- // TODO put stuff in the map and in the end put it in the output map
- HashMap<String, ArrayList<String>> holder = new HashMap<String, ArrayList<String>>();
- for (Iterator<String> it = list.iterator(); it.hasNext();) {
- String inputXML = (String) it.next();
- for (OutputPort outPort : getOutputPorts()) {
- String outputPortName = outPort.getName();
- String[] invocations = XMLUtilities.getSingleInvokationsFromMultipleInvokations(inputXML);
- ArrayList<String> names = new ArrayList<String>();
- int type = 0;
- // get the type, names list, etc
- if (outputPortName.equalsIgnoreCase("namespace")) {
- // extract the namespace from the top element
- names.add(configurationBean.getArticleNameUsedByService());
- type = ParseMobyXML.NAMESPACE;
- } else if (outputPortName.equalsIgnoreCase("id")) {
- // extract the id from the top element
- names.add(configurationBean.getArticleNameUsedByService());
- type = ParseMobyXML.ID;
- } else {
- names = getNames(outputPortName);
- if (outputPortName.endsWith("_ns")) {
- type = ParseMobyXML.NAMESPACE;
- if (names.size() > 1)//added nov-15-07
- names.remove(names.size()-1);
- } else if (outputPortName.endsWith("_id")) {
- type = ParseMobyXML.ID;
- if (names.size() > 1)//added nov-15-07
- names.remove(names.size()-1);
- } else {
- type = ParseMobyXML.VALUE;
- }
- }
- ArrayList<String> stuff = new ArrayList<String>();
- for (int i = 0; i < invocations.length; i++) {
- String invocation = invocations[i];
- if (XMLUtilities.isCollection(invocation)) {
- String[] simples = XMLUtilities.getAllSimplesByArticleName(configurationBean.getArticleNameUsedByService(), invocation);
- for (int j = 0; j < simples.length; j++) {
- ArrayList<String> content = ParseMobyXML.getContentForDataType(names, type, XMLUtilities.createMobyDataElementWrapper(simples[j],"a1", null),configurationBean.getRegistryEndpoint());
- stuff.addAll(content);
- }
- } else {
- ArrayList<String> content = ParseMobyXML.getContentForDataType(names, type, invocations[i],configurationBean.getRegistryEndpoint());
- stuff.addAll(content);
- }
- }
- if (holder.containsKey(outputPortName)) {
- ArrayList<String> al = holder.get(outputPortName);
- al.addAll(stuff);
- holder.put(outputPortName, al);
- } else {
- holder.put(outputPortName, stuff);
- }
- }
- }
- // fill output map
- for (Iterator<String> it = holder.keySet().iterator(); it.hasNext();) {
- String key = it.next();
- output.put(key, referenceService.register(holder.get(key), 1, true, callback.getContext()));
- }
- }
-
- callback.receiveResult(output, new int[0]);
- } catch (ReferenceServiceException e) {
- callback.fail("Error accessing input/output data", e);
- } catch (Exception e) {
- callback.fail("rror parsing moby data", e);
- }
-
- }
- });
- }
-
- @Override
- public MobyParseDatatypeActivityConfigurationBean getConfiguration() {
- return configurationBean;
- }
-
- @SuppressWarnings("unchecked")
- private void init() throws ActivityConfigurationException {
- try {
- central = new CentralImpl(configurationBean.getRegistryEndpoint());
- } catch (MobyException e) {
- throw new ActivityConfigurationException("Couldn't create MobyCentral client for endpoint "
- + configurationBean.getRegistryEndpoint() + System.getProperty("line.separator")
- + e.getLocalizedMessage());
- }
- if (this.datatype == null) {
- try {
- this.datatype = central.getDataType(configurationBean.getDatatypeName());
- } catch (MobyException e) {
- throw new ActivityConfigurationException(
- "There was a problem getting information from the MobyCentral registry at "
- + configurationBean.getRegistryEndpoint() + System.getProperty("line.separator")
- + e.getLocalizedMessage());
- } catch (NoSuccessException e) {
- throw new ActivityConfigurationException(
- "There was no success in getting information from the MobyCentral registry at "
- + configurationBean.getRegistryEndpoint() + System.getProperty("line.separator")
- + e.getLocalizedMessage());
- }
- }
-
-// setDescription("Service to parse the datatype " + this.datatype.getName());
-
- ArrayList list = new ArrayList();
- if (isPrimitive(this.datatype.getName())) {
- list.add(configurationBean.getArticleNameUsedByService() + "_" + this.datatype.getName());
- } else if (this.datatype.getName().equals("Object")) {
- // dont do anything because object has no value
- } else {
- processDatatype(this.datatype, central, configurationBean.getArticleNameUsedByService(), list);
- }
- // add the input port called mobyData('datatypeName')
- addInput("mobyData('" + this.datatype.getName() + "')", 0, true,
- new ArrayList<Class<? extends ExternalReferenceSPI>>(),
- String.class);
- // add the namespace/id ports to the processor
- addOutput("namespace", 1, "text/xml");
- addOutput("id", 1, "text/xml");
-
- // list contains the output ports i have to create
- for (Iterator it = list.iterator(); it.hasNext();) {
- String portName = (String) it.next();
- if (portName.equals(configurationBean.getArticleNameUsedByService()+"_id") || portName.equals(configurationBean.getArticleNameUsedByService()+"_ns"))
- continue;
- addOutput(portName, 1, "text/xml");
- }
- }
-
- private boolean isPrimitive(String name) {
- if (name.equals("Integer") || name.equals("String") || name.equals("Float")
- || name.equals("DateTime") || name.equals("Boolean")
- )
- return true;
- return false;
- }
-
- @SuppressWarnings("unchecked")
- private void processDatatype(MobyDataType dt, Central central, String currentName, List list) throws ActivityConfigurationException {
-
- if (dt.getParentName() == null || dt.getParentName().trim().equals("")) {
- //TODO should we throw an error or just return ...
- return;
- }
-
- if (!dt.getParentName().equals("Object")) {
- flattenChildType(dt.getParentName(), central, currentName, list);
- } else {
- list.add(currentName + "_id");
- list.add(currentName + "_ns");
- }
-
- MobyRelationship[] relations = dt.getChildren();
- for (int i = 0; i < relations.length; i++) {
- MobyRelationship relation = relations[i];
- switch (relation.getRelationshipType()) {
- case CentralImpl.iHAS: {
- // check for object or primitives
- if (isPrimitive(relation.getDataTypeName()) || relation.getDataTypeName().equals("Object")) {
- // object has no value ... only primitives do
- if (!relation.getDataTypeName().equals("Object"))
- list.add(currentName + (currentName.equals("") ? "" : "_'")
- + relation.getName() + (currentName.equals("") ? "" : "'"));
- list.add(currentName + (currentName.equals("") ? "" : "_'")
- + relation.getName() + (currentName.equals("") ? "" : "'")+"_id");
- list.add(currentName + (currentName.equals("") ? "" : "_'")
- + relation.getName() + (currentName.equals("") ? "" : "'")+"_ns");
- }
- else {
- flattenChildType(relation.getDataTypeName(), central, currentName
- + (currentName.equals("") ? "" : "_'") + relation.getName() + (currentName.equals("") ? "" : "'"), list);
- }
- }
- break;
- case CentralImpl.iHASA: {
- // check for object or primitives ...
- if (isPrimitive(relation.getDataTypeName()) || relation.getDataTypeName().equals("Object")) {
- // object has no value ... only primitives do
- if (!relation.getDataTypeName().equals("Object"))
- list.add(currentName + (currentName.equals("") ? "" : "_'")
- + relation.getName()+ (currentName.equals("") ? "" : "'"));
- list.add(currentName + (currentName.equals("") ? "" : "_'")
- + relation.getName() + (currentName.equals("") ? "" : "'")+"_id");
- list.add(currentName + (currentName.equals("") ? "" : "_'")
- + relation.getName() + (currentName.equals("") ? "" : "'")+"_ns");
- }
- else {
-
- flattenChildType(relation.getDataTypeName(), central, currentName
- + (currentName.equals("") ? "" : "_'") + relation.getName() + (currentName.equals("") ? "" : "'"), list);
- }
- }
- break;
- default:
- break;
- }
- }
-
- }
-
- @SuppressWarnings("unchecked")
- private void flattenChildType(String name, Central central, String current, List list) throws ActivityConfigurationException {
- MobyDataType dt = null;
- try {
- dt = central.getDataType(name);
- } catch (MobyException e) {
- throw new ActivityConfigurationException(
- "There was a problem getting information from the MobyCentral registry at "
- + configurationBean.getRegistryEndpoint() + System.getProperty("line.separator")
- + e.getLocalizedMessage());
- } catch (NoSuccessException e) {
- throw new ActivityConfigurationException(
- "There was no success in getting information from the MobyCentral registry at "
- + configurationBean.getRegistryEndpoint() + System.getProperty("line.separator")
- + e.getLocalizedMessage());
- }
- processDatatype(dt, central, current, list);
- }
-
- private ArrayList<String> getNames(String names) {
- ArrayList<String> list = new ArrayList<String>();
- ArrayList<String> temp = new ArrayList<String>();
- if (names == null || names.trim().length() == 0)
- return list;
- Scanner s = new Scanner(names).useDelimiter("_'");
- while (s.hasNext()) {
- temp.add(s.next());
- }
- s.close();
-
- for (String str : temp) {
- if (str.indexOf("'_") >= 0) {
- String[] strings = str.split("'_");
- for (int i = 0; i < strings.length; i++) {
- list.add(strings[i].replaceAll("'", ""));
- }
- } else {
- list.add(str.replaceAll("'", ""));
- }
- }
-
- if (list.size() == 1) {
- if (endsWithPrimitive(list.get(0))) {
- String name = list.remove(0);
- int i = name.lastIndexOf("_");
- name = name.substring(0, i);
- list.add(name);
- }
- } else if (isPrimitive(list.get(list.size()-1))) {
- // remove the last entry if its a primitive ... legacy reasons
- list.remove(list.size()-1);
- }
- return list;
- }
-
- private static boolean endsWithPrimitive(String name) {
- if (name.endsWith("_Integer") || name.endsWith("_String") || name.endsWith("_Float")
- || name.endsWith("_DateTime") || name.endsWith("_Boolean"))
- return true;
- return false;
- }
-
- protected void addOutput(String portName, int portDepth, String type) {
- OutputPort port = edits.createActivityOutputPort(
- portName, portDepth, portDepth);
- MimeType mimeType = new MimeType();
- mimeType.setText(type);
- try {
- edits.getAddAnnotationChainEdit(port, mimeType).doEdit();
- } catch (EditException e) {
- logger.debug("Error adding MimeType annotation to port", e);
- }
- outputPorts.add(port);
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/MobyParseDatatypeActivityConfigurationBean.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/MobyParseDatatypeActivityConfigurationBean.java b/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/MobyParseDatatypeActivityConfigurationBean.java
deleted file mode 100644
index 1f02e7e..0000000
--- a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/MobyParseDatatypeActivityConfigurationBean.java
+++ /dev/null
@@ -1,81 +0,0 @@
-/*******************************************************************************
- * This file is a component of the Taverna project, and is licensed under the
- * GNU LGPL. Copyright Edward Kawas, The BioMoby Project
- ******************************************************************************/
-package net.sf.taverna.t2.activities.biomoby;
-
-import net.sf.taverna.t2.workflowmodel.processor.config.ConfigurationBean;
-import net.sf.taverna.t2.workflowmodel.processor.config.ConfigurationProperty;
-
-/**
- * A configuration bean specific to the Moby Parse Datatype activity.
- *
- * @author David Withers
- */
-@ConfigurationBean(uri = MobyParseDatatypeActivity.URI + "#Config")
-public class MobyParseDatatypeActivityConfigurationBean {
-
- private String datatypeName="";
-
- private String registryEndpoint="";
-
- private String articleNameUsedByService="";
-
- /**
- * Returns the datatypeName.
- *
- * @return the datatypeName
- */
- public String getDatatypeName() {
- return datatypeName;
- }
-
- /**
- * Sets the datatypeName.
- *
- * @param datatypeName the new datatypeName
- */
- @ConfigurationProperty(name = "datatypeName", label = "Datatype Name", description = "")
- public void setDatatypeName(String datatypeName) {
- this.datatypeName = datatypeName;
- }
-
- /**
- * Returns the registryEndpoint.
- *
- * @return the registryEndpoint
- */
- public String getRegistryEndpoint() {
- return registryEndpoint;
- }
-
- /**
- * Sets the registryEndpoint.
- *
- * @param registryEndpoint the new registryEndpoint
- */
- @ConfigurationProperty(name = "registryEndpoint", label = "Registry Endpoint", description = "")
- public void setRegistryEndpoint(String registryEndpoint) {
- this.registryEndpoint = registryEndpoint;
- }
-
- /**
- * Returns the articleNameUsedByService.
- *
- * @return the articleNameUsedByService
- */
- public String getArticleNameUsedByService() {
- return articleNameUsedByService;
- }
-
- /**
- * Sets the articleNameUsedByService.
- *
- * @param articleNameUsedByService the new articleNameUsedByService
- */
- @ConfigurationProperty(name = "articleNameUsedByService", label = "Article Name Used By Service", description = "")
- public void setArticleNameUsedByService(String articleNameUsedByService) {
- this.articleNameUsedByService = articleNameUsedByService;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/MobyParseDatatypeActivityFactory.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/MobyParseDatatypeActivityFactory.java b/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/MobyParseDatatypeActivityFactory.java
deleted file mode 100644
index 8da531e..0000000
--- a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/MobyParseDatatypeActivityFactory.java
+++ /dev/null
@@ -1,49 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2011 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.biomoby;
-
-import java.net.URI;
-
-import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityFactory;
-
-/**
- * An {@link ActivityFactory} for creating <code>MobyParseDatatypeActivity</code>.
- *
- * @author David Withers
- */
-public class MobyParseDatatypeActivityFactory implements ActivityFactory {
-
- @Override
- public MobyParseDatatypeActivity createActivity() {
- return new MobyParseDatatypeActivity();
- }
-
- @Override
- public URI getActivityURI() {
- return URI.create(MobyParseDatatypeActivity.URI);
- }
-
- @Override
- public Object createActivityConfiguration() {
- return new MobyParseDatatypeActivityConfigurationBean();
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/MobyParseDatatypeActivityHealthChecker.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/MobyParseDatatypeActivityHealthChecker.java b/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/MobyParseDatatypeActivityHealthChecker.java
deleted file mode 100644
index 0ca0d38..0000000
--- a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/MobyParseDatatypeActivityHealthChecker.java
+++ /dev/null
@@ -1,58 +0,0 @@
-/*******************************************************************************
- * This file is a component of the Taverna project, and is licensed under the
- * GNU LGPL. Copyright Edward Kawas, The BioMoby Project
- ******************************************************************************/
-package net.sf.taverna.t2.activities.biomoby;
-
-import java.io.IOException;
-import java.net.HttpURLConnection;
-import java.net.MalformedURLException;
-import java.net.SocketTimeoutException;
-import java.net.URL;
-import java.net.URLConnection;
-import java.util.List;
-
-import net.sf.taverna.t2.workflowmodel.Processor;
-import net.sf.taverna.t2.workflowmodel.processor.activity.Activity;
-import net.sf.taverna.t2.workflowmodel.health.HealthCheck;
-import net.sf.taverna.t2.workflowmodel.health.HealthChecker;
-import net.sf.taverna.t2.visit.VisitReport;
-import net.sf.taverna.t2.visit.VisitReport.Status;
-
-import net.sf.taverna.t2.workflowmodel.health.RemoteHealthChecker;
-import net.sf.taverna.t2.workflowmodel.processor.activity.DisabledActivity;
-
-
-/**
- * A health checker for the Moby Parse Datatype activity.
- *
- * @author David Withers
- */
-public class MobyParseDatatypeActivityHealthChecker extends RemoteHealthChecker {
-
-
- public boolean canVisit(Object subject) {
- if (subject == null) {
- return false;
- }
- if (subject instanceof MobyParseDatatypeActivity) {
- return true;
- }
- if (subject instanceof DisabledActivity) {
- return (((DisabledActivity) subject).getActivity() instanceof MobyParseDatatypeActivity);
- }
- return false;
- }
-
- public VisitReport visit(Object o, List<Object> ancestors) {
- Activity activity = (Activity) o;
- MobyParseDatatypeActivityConfigurationBean configuration = null;
- if (activity instanceof MobyParseDatatypeActivity) {
- configuration = (MobyParseDatatypeActivityConfigurationBean) activity.getConfiguration();
- } else if (activity instanceof DisabledActivity) {
- configuration = (MobyParseDatatypeActivityConfigurationBean) ((DisabledActivity) activity).getActivityConfiguration();
- }
- return contactEndpoint(activity, configuration.getRegistryEndpoint());
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/ParseMobyXML.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/ParseMobyXML.java b/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/ParseMobyXML.java
deleted file mode 100644
index 042b6e8..0000000
--- a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/ParseMobyXML.java
+++ /dev/null
@@ -1,192 +0,0 @@
-/*
- * This file is a component of the Taverna project,
- * and is licensed under the GNU LGPL.
- * Copyright Edward Kawas, The BioMoby Project
- */
-package net.sf.taverna.t2.activities.biomoby;
-
-import java.io.ByteArrayInputStream;
-import java.util.ArrayList;
-import java.util.Iterator;
-import java.util.List;
-
-import org.apache.log4j.Logger;
-import org.biomoby.shared.MobyNamespace;
-import org.biomoby.shared.data.MobyContentInstance;
-import org.biomoby.shared.data.MobyDataBoolean;
-import org.biomoby.shared.data.MobyDataComposite;
-import org.biomoby.shared.data.MobyDataFloat;
-import org.biomoby.shared.data.MobyDataInstance;
-import org.biomoby.shared.data.MobyDataInt;
-import org.biomoby.shared.data.MobyDataJob;
-import org.biomoby.shared.data.MobyDataObject;
-import org.biomoby.shared.data.MobyDataObjectVector;
-import org.biomoby.shared.data.MobyDataString;
-import org.biomoby.shared.data.MobyDataUtils;
-import org.biomoby.registry.meta.Registry;
-
-/**
- * This class is used to help parse BioMOBY messages.
- *
- * @author Edward Kawas
- *
- */
-public class ParseMobyXML {
-
- private static Logger logger = Logger.getLogger(ParseMobyXML.class);
-
- public static final int NAMESPACE = -10;
-
- public static final int ID = -20;
-
- public static final int VALUE = -30;
-
- private static final List<Integer> allowables;
-
- static {
- allowables = new ArrayList<Integer>();
- allowables.add(NAMESPACE);
- allowables.add(ID);
- allowables.add(VALUE);
- }
-
- /**
- * PRECONDITION: XML is valid MOBY xml and contains exactly 1 invocation
- * message containing our simple element
- *
- * @param names
- * an array of article names in the order that we will
- * extract our information
- * @param type
- * one of {NAMESPACE | ID | VALUE} denoting what exactly it
- * is that you would like returned
- * @param xml
- * the MOBY xml containing the data to extract
- * @param endpoint
- * the BioMOBY registry endpoint to use
- * @return a list of strings representing what it is you asked for
- */
- public static ArrayList<String> getContentForDataType(
- ArrayList<String> names, int type, String xml, String endpoint) {
- if (!allowables.contains(type) || names == null || names.size() == 0
- || xml == null || xml.trim().length() == 0) {
- // nothing to return
- logger.warn("Parser invoked on an empty message ...");
- return new ArrayList<String>();
- }
- MobyContentInstance contents;
- try {
- contents = MobyDataUtils.fromXMLDocument(new ByteArrayInputStream(
- xml.getBytes("UTF8")), new Registry(endpoint, endpoint,
- "http://domain.com/MOBY/Central"));
- } catch (Exception e) {
- logger.error("There was a problem parsing the input XML:\n" + xml
- + "\n", e);
- return new ArrayList<String>();
- }
- if (contents.keySet().size() != 1) {
- return new ArrayList<String>();
- }
-
- ArrayList<String> clone = new ArrayList<String>();
- clone.addAll(names);
- ArrayList<String> output = new ArrayList<String>();
- // should be exactly 1 job!
- Iterator<String> jobIDs = contents.keySet().iterator();
- while (jobIDs.hasNext()) {
- MobyDataJob job = (MobyDataJob) contents.get(jobIDs.next());
- // get the instance
- MobyDataInstance data = job.get(clone.remove(0));
- if (data == null)
- return output;
- recurse(clone, data, output, type);
- }
- return output;
- }
-
- @SuppressWarnings("unchecked")
- private static void recurse(ArrayList<String> names, MobyDataInstance data,
- ArrayList<String> output, int type) {
- // base case => we have finally found the element of interest
- if (names.isEmpty()) {
- baseCase(data, output, type);
- return;
- }
- if (data instanceof MobyDataObjectVector) {
- // recurse on the children -- the recursion will extract by
- // articlename
- MobyDataObjectVector vector = (MobyDataObjectVector) data;
- // recurse on the has relationship
- for (Iterator i = vector.iterator(); i.hasNext();) {
- recurse((ArrayList) (names.clone()), (MobyDataInstance) i
- .next(), output, type);
- }
-
- } else if (data instanceof MobyDataComposite) {
- // recurse on the child given by name.get(0)
- MobyDataInstance d = ((MobyDataComposite) data).remove(names
- .remove(0));
- recurse((ArrayList) (names.clone()), d, output, type);
- } else if (data instanceof MobyDataBoolean) {
- baseCase(data, output, type);
- } else if (data instanceof MobyDataFloat) {
- baseCase(data, output, type);
- } else if (data instanceof MobyDataInt) {
- baseCase(data, output, type);
- } else if (data instanceof MobyDataString) {
- baseCase(data, output, type);
- }
-
- }
-
- private static void baseCase(MobyDataInstance data,
- ArrayList<String> output, int type) {
- if (data == null)
- return;
- switch (type) {
- case NAMESPACE: {
- if (data instanceof MobyDataObjectVector) {
- MobyDataObjectVector vector = (MobyDataObjectVector) data;
- for (Iterator i = vector.iterator(); i.hasNext();) {
- MobyNamespace[] namespaces = ((MobyDataObject) i.next())
- .getNamespaces();
- for (int j = 0; j < namespaces.length; j++) {
- output.add(namespaces[j].getName());
- }
- }
- } else {
- MobyNamespace[] namespaces = ((MobyDataObject) data)
- .getNamespaces();
- for (int j = 0; j < namespaces.length; j++) {
- output.add(namespaces[j].getName());
- }
- }
- }
- break;
- case ID: {
- if (data instanceof MobyDataObjectVector) {
- MobyDataObjectVector vector = (MobyDataObjectVector) data;
- for (Iterator i = vector.iterator(); i.hasNext();) {
- output.add(((MobyDataObject) i.next()).getId());
- }
- } else {
- output.add(((MobyDataObject) data).getId());
- }
- }
- break;
- case VALUE: {
- if (data instanceof MobyDataObjectVector) {
- MobyDataObjectVector vector = (MobyDataObjectVector) data;
- for (Iterator i = vector.iterator(); i.hasNext();) {
- output.add(((MobyDataObject) i.next()).getValue());
- }
- } else {
- output.add(((MobyDataObject) data).getValue());
- }
- }
- break;
- default:
- break;
- }
- }
-}
[06/16] incubator-taverna-plugin-bioinformatics git commit:
temporarily empty repository
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/ui/BiomobyObjectTree.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/ui/BiomobyObjectTree.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/ui/BiomobyObjectTree.java
deleted file mode 100644
index 7ca2578..0000000
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/ui/BiomobyObjectTree.java
+++ /dev/null
@@ -1,635 +0,0 @@
-/*
- * This file is a component of the Taverna project,
- * and is licensed under the GNU LGPL.
- * Copyright Edward Kawas, The BioMoby Project
- */
-package net.sf.taverna.t2.activities.biomoby.ui;
-
-import java.awt.BorderLayout;
-import java.awt.Component;
-import java.awt.Dimension;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.FocusEvent;
-import java.awt.event.FocusListener;
-import java.awt.event.KeyEvent;
-import java.awt.event.KeyListener;
-import java.awt.event.MouseEvent;
-import java.awt.event.MouseListener;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-
-import javax.swing.ImageIcon;
-import javax.swing.JFrame;
-import javax.swing.JLabel;
-import javax.swing.JMenuItem;
-import javax.swing.JPanel;
-import javax.swing.JPopupMenu;
-import javax.swing.JScrollPane;
-import javax.swing.JSeparator;
-import javax.swing.JTextField;
-import javax.swing.JTree;
-import javax.swing.ToolTipManager;
-import javax.swing.tree.DefaultMutableTreeNode;
-import javax.swing.tree.DefaultTreeCellRenderer;
-import javax.swing.tree.DefaultTreeModel;
-import javax.swing.tree.TreePath;
-import javax.swing.tree.TreeSelectionModel;
-
-import net.sf.taverna.t2.activities.biomoby.BiomobyObjectActivity;
-import net.sf.taverna.t2.activities.biomoby.BiomobyObjectActivityConfigurationBean;
-import net.sf.taverna.t2.activities.biomoby.actions.MobyPanel;
-import net.sf.taverna.t2.activities.biomoby.datatypedescriptions.BiomobyDatatypeDescription;
-import net.sf.taverna.t2.activities.biomoby.edits.AddUpstreamObjectEdit;
-import net.sf.taverna.t2.activities.biomoby.query.BiomobyObjectActivityItem;
-import net.sf.taverna.t2.activities.biomoby.query.BiomobyQueryHelper;
-import net.sf.taverna.t2.workbench.edits.EditManager;
-import net.sf.taverna.t2.workbench.file.FileManager;
-import net.sf.taverna.t2.workflowmodel.CompoundEdit;
-import net.sf.taverna.t2.workflowmodel.Dataflow;
-import net.sf.taverna.t2.workflowmodel.Edit;
-import net.sf.taverna.t2.workflowmodel.Edits;
-import net.sf.taverna.t2.workflowmodel.utils.Tools;
-
-import org.apache.log4j.Logger;
-import org.biomoby.client.CentralImpl;
-import org.biomoby.shared.MobyException;
-
-/**
- * Creates a Datatype tree for any BioMOBY registry. The tree allows the user to
- * add nodes to the workflow. Includes the ability to search for datatypes too.
- *
- * @author Eddie Kawas, The BioMoby Project
- *
- */
-public class BiomobyObjectTree {
-
- private static Logger logger = Logger
- .getLogger(BiomobyObjectTree.class);
-
- private JTree tree;
- private String registryEndpoint = "";
- private String registryNamespace = "";
- private static String SEARCH_DATATYPE_TEXT = "Type to search!";
- private FilterTreeModel model;
- private final EditManager editManager;
- private final FileManager fileManager;
-
- /**
- * Default constructor. Creates a BiomobyObjectTree for the default Biomoby
- * registry
- */
- public BiomobyObjectTree(EditManager editManager, FileManager fileManager) {
- this(CentralImpl.DEFAULT_ENDPOINT, CentralImpl.DEFAULT_NAMESPACE, editManager, fileManager);
- }
-
- /**
- *
- * @param url
- * the Biomoby registry endpoint URL to build a tree for
- * @param uri
- * the Biomoby registry namespace URI to build a tree for
- */
- public BiomobyObjectTree(String url, String uri, EditManager editManager, FileManager fileManager) {
- this.registryEndpoint = url;
- this.registryNamespace = uri;
- this.editManager = editManager;
- this.fileManager = fileManager;
- }
-
- /*
- * method that inserts our BiomobyDatatypeDescription object into our tree
- */
- private void insertDescriptionIntoTree(
- BiomobyDatatypeDescription description,
- HashMap<String, FilterTreeNode> nodeMap,
- HashMap<String, BiomobyDatatypeDescription> descriptionMap) {
- FilterTreeNode node = nodeMap.containsKey(description.getName()) ? nodeMap
- .get(description.getName())
- : new FilterTreeNode(description);
-
- String parent = description.getParent();
- if (parent.equals(""))
- parent = "Object";
- FilterTreeNode pNode = nodeMap.containsKey(parent) ? nodeMap
- .get(parent) : new FilterTreeNode(descriptionMap.get(parent));
- pNode.add(node);
- nodeMap.put(description.getName(), node);
- nodeMap.put(parent, pNode);
- }
-
- /**
- *
- * @return a Tree containing the datatype ontology for the specified biomoby
- * registry
- * @throws MobyException
- * if there is a problem comunicating with the specified biomoby
- * registry
- */
- public Component getDatatypeTree() throws MobyException {
- BiomobyQueryHelper bqh = new BiomobyQueryHelper(getRegistryEndpoint(),
- getRegistryNamespace());
- List<BiomobyDatatypeDescription> descriptions = bqh
- .findDatatypeDescriptions();
-
- // create a tree from all of the nodes
- HashMap<String, BiomobyDatatypeDescription> descriptionMap = new HashMap<String, BiomobyDatatypeDescription>();
- HashMap<String, FilterTreeNode> nodeMap = new HashMap<String, FilterTreeNode>();
- for (BiomobyDatatypeDescription d : descriptions) {
- // PRECONDITION: datatype names are unique across the ontology
- descriptionMap.put(d.getDatatypeName(), d);
- }
-
- nodeMap.put("Object", new FilterTreeNode(descriptionMap.get("Object")));
- for (BiomobyDatatypeDescription d : descriptions) {
- if (!d.getName().equals("Object"))
- insertDescriptionIntoTree(d, nodeMap, descriptionMap);
- }
- // construct a new tree with our root node
- tree = new JTree(nodeMap.get("Object"));
-
- // only allow one node to be selected at once
- tree.getSelectionModel().setSelectionMode(
- TreeSelectionModel.SINGLE_TREE_SELECTION);
- model = new FilterTreeModel((FilterTreeNode) tree.getModel().getRoot());
- tree.setModel(model);
-
- // set up the icon and tooltips for the nodes in the tree
- ImageIcon icon = new ImageIcon(BiomobyObjectActivityItem.class
- .getResource("/biomoby_object.png"));
- if (icon != null) {
- DefaultTreeCellRenderer renderer = new DatatypeTreeRenderer();
- renderer.setLeafIcon(icon);
- renderer.setOpenIcon(icon);
- renderer.setClosedIcon(icon);
- renderer.setIcon(icon);
- tree.setCellRenderer(renderer);
- }
-
- // add a mouse listener to catch context clicks
- // the listener adds the selected datatype to the workflow
- // it also adds the datatype's container relationships
- tree.addMouseListener(new BiomobyObjectTreeMouseListener());
- // clear the hashmaps to clear some memory
- nodeMap.clear();
- descriptionMap.clear();
- // register our tree for tool tips
- ToolTipManager.sharedInstance().registerComponent(tree);
- // insert the tree into a scrollpane
- JScrollPane treeView = new JScrollPane(tree);
- treeView.setSize(getFrameSize());
-
- // create a new panel to hold the scrollpane and a search box
- JPanel panel = new JPanel(new BorderLayout());
- panel.add(treeView, BorderLayout.CENTER);
- JTextField search = new JTextField(SEARCH_DATATYPE_TEXT);
- panel.add(search, BorderLayout.PAGE_END);
- search.addKeyListener(new KeyListener() {
- public void keyPressed(KeyEvent e) {
- if (e.getSource() instanceof JTextField) {
- JTextField field = (JTextField) e.getSource();
- if (field.getText().trim().equals(
- BiomobyObjectTree.SEARCH_DATATYPE_TEXT)) {
- field.setText("");
- }
- }
- }
-
- public void keyReleased(KeyEvent e) {
- if (e.getSource() instanceof JTextField) {
- JTextField field = (JTextField) e.getSource();
- if (e.getKeyCode() == KeyEvent.VK_ESCAPE) {
- field.setText(SEARCH_DATATYPE_TEXT);
- model.setFilter(null);
- return;
- }
- // filter our tree
- if (!field.getText().trim().equals(
- BiomobyObjectTree.SEARCH_DATATYPE_TEXT)) {
- // does our filter tree model exist yet?
- model.setFilter(field.getText().trim());
- }
- }
- }
-
- public void keyTyped(KeyEvent e) {
-
- }
- });
- search.addFocusListener(new FocusListener() {
-
- public void focusGained(FocusEvent e) {
- if (e.getSource() instanceof JTextField) {
- JTextField field = (JTextField) e.getSource();
- if (field.getText().trim().equals(
- BiomobyObjectTree.SEARCH_DATATYPE_TEXT)) {
- field.setText("");
- }
- }
- }
-
- public void focusLost(FocusEvent e) {
- if (e.getSource() instanceof JTextField) {
- JTextField field = (JTextField) e.getSource();
- if (field.getText().trim().equals("")) {
- field.setText(SEARCH_DATATYPE_TEXT);
- }
- }
- }
- });
- // done
- panel.setToolTipText("Datatype Viewer for " + getRegistryEndpoint().toString());
- return panel;
- }
-
- /**
- *
- * @param registryEndpoint
- * the endpoint to set
- */
- public void setRegistryEndpoint(String registryEndpoint) {
- this.registryEndpoint = registryEndpoint;
- }
-
- /**
- *
- * @param registryNamespace
- * the namespace to set
- */
- public void setRegistryNamespace(String registryNamespace) {
- this.registryNamespace = registryNamespace;
- }
-
- /**
- *
- * @return the registry endpoint that this tree is using
- */
- public String getRegistryEndpoint() {
- return registryEndpoint;
- }
-
- /**
- *
- * @return the registry namespace that this tree is using
- */
- public String getRegistryNamespace() {
- return registryNamespace;
- }
-
- /**
- * returns the frame size as a dimension for the content pane housing this
- * action
- */
- public Dimension getFrameSize() {
- return new Dimension(550, 450);
- }
-
- /*
- * A mouse listener for our datatype tree
- */
- private class BiomobyObjectTreeMouseListener implements MouseListener {
- public void mouseClicked(MouseEvent me) {
- }
-
- public void mousePressed(MouseEvent me) {
- mouseReleased(me);
- }
-
- public void mouseReleased(MouseEvent me) {
- if (me.isPopupTrigger()) // right click, show popup menu
- {
- TreePath path = tree.getPathForLocation(me.getX(), me.getY());
- if (path == null)
- return;
-
- DefaultMutableTreeNode node = (DefaultMutableTreeNode) tree
- .getLastSelectedPathComponent();
- if (node == null)
- return;
-
- final String selectedObject = node.toString();
- final BiomobyDatatypeDescription bdd = (BiomobyDatatypeDescription) node
- .getUserObject();
- final JPopupMenu menu = new JPopupMenu();
- // Create and add a menu item for adding to the
- // item to the workflow
- JMenuItem item = new JMenuItem("Add Datatype - '"
- + selectedObject + "' to the workflow?");
-
- item.addActionListener(new ActionListener() {
-
- public void actionPerformed(ActionEvent ae) {
-
- try {
- Dataflow dataflow = fileManager.getCurrentDataflow();
- List<Edit<?>> compoundEdits = new ArrayList<Edit<?>>();
- List<Edit<?>> editList = new ArrayList<Edit<?>>();
-
- String name = Tools.uniqueProcessorName(
- selectedObject, dataflow);
-
- BiomobyObjectActivityConfigurationBean configBean = new BiomobyObjectActivityConfigurationBean();
- configBean.setMobyEndpoint(bdd
- .getActivityConfiguration()
- .getMobyEndpoint());
- configBean.setAuthorityName("");
- configBean.setServiceName(selectedObject);
-
- Edits edits = editManager.getEdits();
- net.sf.taverna.t2.workflowmodel.Processor sourceProcessor = edits
- .createProcessor(name);
- BiomobyObjectActivity boActivity = new BiomobyObjectActivity();
- Edit<?> configureActivityEdit = edits
- .getConfigureActivityEdit(boActivity,
- configBean);
- editList.add(configureActivityEdit);
-
- editList
- .add(edits
- .getDefaultDispatchStackEdit(sourceProcessor));
-
- Edit<?> addActivityToProcessorEdit = edits
- .getAddActivityEdit(sourceProcessor,
- boActivity);
- editList.add(addActivityToProcessorEdit);
-
- editList.add(edits.getAddProcessorEdit(dataflow,
- sourceProcessor));
-
- CompoundEdit compoundEdit = new CompoundEdit(
- editList);
- compoundEdits.add(compoundEdit);
- compoundEdit.doEdit();
-
- // process relationships
- Edit<?> edit = new AddUpstreamObjectEdit(dataflow,
- sourceProcessor, boActivity, edits);
- editManager.doDataflowEdit(dataflow, edit);
-
- } catch (Exception e) {
- logger.error("Could not add datatype", e);
- }
- }
- });
- item.setIcon(MobyPanel.getIcon("/Add24.gif"));
-
- // add the components to the menus
- menu.add(new JLabel("Add to workflow ... ", JLabel.CENTER));
- menu.add(new JSeparator());
- menu.add(item);
- // show the window
- menu.show(me.getComponent(), me.getX(), me.getY());
- }
- }
-
- public void mouseEntered(MouseEvent me) {
- }
-
- public void mouseExited(MouseEvent me) {
- }
- }
-
- private static class DatatypeTreeRenderer extends DefaultTreeCellRenderer {
-
- private static final long serialVersionUID = 7287097980554656834L;
-
- // the max tool tip length
- private static int MAX_TOOLTIP_LENGTH = 300;
-
- @Override
- public Component getTreeCellRendererComponent(JTree tree, Object value,
- boolean sel, boolean expanded, boolean leaf, int row,
- boolean hasFocus) {
- if (value instanceof DefaultMutableTreeNode) {
- if (((DefaultMutableTreeNode) value).getUserObject() instanceof BiomobyDatatypeDescription) {
- BiomobyDatatypeDescription desc = (BiomobyDatatypeDescription) ((DefaultMutableTreeNode) value)
- .getUserObject();
- String d = desc.getDescription().trim();
- // we only keep MAX_TOOLTIP_LENGTH characters of the string
- if (d.length() > MAX_TOOLTIP_LENGTH)
- d = d.substring(0, MAX_TOOLTIP_LENGTH) + "...";
- setToolTipText("<html><body><div style='width:200px;'><span>"
- + d + "</span></div></body></html>");
-
- ToolTipManager.sharedInstance().setDismissDelay(
- Integer.MAX_VALUE);
- }
- }
- return super.getTreeCellRendererComponent(tree, value, sel,
- expanded, leaf, row, hasFocus);
- }
- }
-
- /*
- * Shamelessly stolen from t2. Made the Filter a simple string filter and
- * modified the code a bit to make it relevant to my tree
- */
- private final class FilterTreeModel extends DefaultTreeModel {
-
- private static final long serialVersionUID = 8446366558654481274L;
- String currentFilter;
-
- /**
- *
- * @param node
- * the node to apply filtering to
- */
- public FilterTreeModel(FilterTreeNode node) {
- this(node, null);
- }
-
- /**
- *
- * @param node
- * the node to apply filtering to
- * @param filter
- * the actual filter we will apply
- */
- public FilterTreeModel(FilterTreeNode node, String filter) {
- super(node);
- currentFilter = filter;
- node.setFilter(filter);
- }
-
- /**
- *
- * @param filter
- * the filter to set and apply to our node
- */
- public void setFilter(String filter) {
- if (root != null) {
- currentFilter = filter;
- ((FilterTreeNode) root).setFilter(filter);
- Object[] path = { root };
- fireTreeStructureChanged(this, path, null, null);
- }
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * javax.swing.tree.DefaultTreeModel#getChildCount(java.lang.Object)
- */
- public int getChildCount(Object parent) {
- if (parent instanceof FilterTreeNode) {
- return (((FilterTreeNode) parent).getChildCount());
- }
- return 0;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see javax.swing.tree.DefaultTreeModel#getChild(java.lang.Object,
- * int)
- */
- public Object getChild(Object parent, int index) {
- if (parent instanceof FilterTreeNode) {
- return (((FilterTreeNode) parent).getChildAt(index));
- }
- return null;
- }
-
- /**
- * Getter
- *
- * @return the filter that we are currently using
- */
- public String getCurrentFilter() {
- return currentFilter;
- }
- }
-
- private class FilterTreeNode extends DefaultMutableTreeNode {
-
- private static final long serialVersionUID = -5269485070471940445L;
- private String filter;
- private boolean passed = true;
- private List<FilterTreeNode> filteredChildren = new ArrayList<FilterTreeNode>();
-
- public FilterTreeNode(Object userObject) {
- super(userObject);
- }
-
- public String getFilter() {
- return filter;
- }
-
- public void setFilter(String filter) {
- this.filter = filter == null ? "" : filter;
- passed = false;
- filteredChildren.clear();
- if (filter == null) {
- passed = true;
- passFilterDown(null);
- } else if (pass(this)) {
- passed = true;
- passFilterDown(filter);
- } else {
- passFilterDown(filter);
- passed = filteredChildren.size() != 0;
- }
- }
-
- private boolean pass(FilterTreeNode node) {
- if (getFilter().trim().equals("")) {
- return true;
- }
- return node.getUserObject().toString().toLowerCase().trim()
- .contains(getFilter().toLowerCase().trim());
- }
-
- private void passFilterDown(String filter) {
- int realChildCount = super.getChildCount();
- for (int i = 0; i < realChildCount; i++) {
- FilterTreeNode realChild = (FilterTreeNode) super.getChildAt(i);
- realChild.setFilter(filter);
- if (realChild.isPassed()) {
- filteredChildren.add(realChild);
- }
- }
- }
-
- public void add(FilterTreeNode node) {
- super.add(node);
- node.setFilter(filter);
- if (node.isPassed()) {
- filteredChildren.add(node);
- }
- }
-
- /*
- * (non-Javadoc)
- *
- * @see javax.swing.tree.DefaultMutableTreeNode#remove(int)
- */
- public void remove(int childIndex) {
- if (filter != null) {
- // as child indexes might be inconsistent..
- throw new IllegalStateException(
- "Can't remove while the filter is active");
- }
- super.remove(childIndex);
- }
-
- /*
- * (non-Javadoc)
- *
- * @see javax.swing.tree.DefaultMutableTreeNode#getChildCount()
- */
- public int getChildCount() {
- if (filter == null) {
- return super.getChildCount();
- }
- return (filteredChildren.size());
- }
-
- /*
- * (non-Javadoc)
- *
- * @see javax.swing.tree.DefaultMutableTreeNode#getChildAt(int)
- */
- public FilterTreeNode getChildAt(int index) {
- if (filter == null) {
- return (FilterTreeNode) super.getChildAt(index);
- }
- return filteredChildren.get(index);
- }
-
- /**
- *
- * @return
- */
- public boolean isPassed() {
- return passed;
- }
- }
-
- public static void main(String[] args) throws Exception {
- // Create a frame
- String title = "TeST";
- JFrame frame = new JFrame(title);
-
- // Create a component to add to the frame
-/* Component comp = new BiomobyObjectTree(CentralImpl.DEFAULT_ENDPOINT,
- CentralImpl.DEFAULT_NAMESPACE).getDatatypeTree();*/
-
- Component comp = new BiomobyObjectTree("http://cropwiki.irri.org/cgi-bin/MOBY-Central.pl",
- CentralImpl.DEFAULT_NAMESPACE, null, null).getDatatypeTree();
-
- // Add the component to the frame's content pane;
- // by default, the content pane has a border layout
- frame.getContentPane().add(comp, BorderLayout.CENTER);
-
- // Show the frame
- int width = 300;
- int height = 300;
- frame.setSize(width, height);
- frame.setVisible(true);
-
- // Set to exit on close
- frame.setDefaultCloseOperation(JFrame.EXIT_ON_CLOSE);
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/ui/DatatypeMenuItem.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/ui/DatatypeMenuItem.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/ui/DatatypeMenuItem.java
deleted file mode 100644
index c5a7468..0000000
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/ui/DatatypeMenuItem.java
+++ /dev/null
@@ -1,196 +0,0 @@
-/*
- * This file is a component of the Taverna project,
- * and is licensed under the GNU LGPL.
- * Copyright Edward Kawas, The BioMoby Project
- */
-package net.sf.taverna.t2.activities.biomoby.ui;
-
-import java.awt.BorderLayout;
-import java.awt.Component;
-import java.awt.Frame;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-
-import javax.swing.BorderFactory;
-import javax.swing.ImageIcon;
-import javax.swing.JDialog;
-import javax.swing.JLabel;
-import javax.swing.JMenuItem;
-import javax.swing.JPanel;
-import javax.swing.JProgressBar;
-
-import net.sf.taverna.t2.activities.biomoby.actions.MobyPanel;
-import net.sf.taverna.t2.activities.biomoby.query.BiomobyObjectActivityItem;
-import net.sf.taverna.t2.workbench.MainWindow;
-import net.sf.taverna.t2.workbench.edits.EditManager;
-import net.sf.taverna.t2.workbench.file.FileManager;
-import net.sf.taverna.t2.workbench.helper.HelpEnabledDialog;
-
-import org.apache.log4j.Logger;
-import org.biomoby.client.CentralImpl;
-import org.biomoby.shared.MobyException;
-
-import com.sun.java.help.impl.SwingWorker;
-
-/**
- * DatatypeMenuItem is a JMenuItem that onClick produces a biomoby datatype tree
- * that workbench users can utilize to add datatypes to any workflow.
- *
- * @author Edward Kawas
- *
- */
-public class DatatypeMenuItem extends JMenuItem {
-
- private static Logger logger = Logger.getLogger(DatatypeMenuItem.class);
- private static final long serialVersionUID = -1010828167358361441L;
-
- private String endpoint;
- private String namespace;
-
- private final EditManager editManager;
- private final FileManager fileManager;
-
- /**
- * Default constructor; Creates a menu item for the default registry
- */
- public DatatypeMenuItem(EditManager editManager, FileManager fileManager) {
- this(CentralImpl.DEFAULT_ENDPOINT, CentralImpl.DEFAULT_NAMESPACE, editManager, fileManager);
- }
-
- /**
- * Create a Datatype menu item for a biomoby registry given a specific
- * endpoint and namespace
- *
- * @param endpoint
- * the registry endpoint
- * @param namespace
- * the registry namespace
- */
- public DatatypeMenuItem(String endpoint, String namespace, EditManager editManager, FileManager fileManager) {
- this(endpoint, namespace, endpoint, editManager, fileManager);
- }
-
- /*
- * A private constructor. Every constructor ends up here
- */
- private DatatypeMenuItem(String endpoint, String namespace, String label, EditManager editManager, FileManager fileManager) {
- // set up some specifics
- this.endpoint = endpoint;
- this.namespace = namespace;
- this.editManager = editManager;
- this.fileManager = fileManager;
- // set up the name, label and icon for this menu item
- setName(label);
- setText(label);
- setIcon(new ImageIcon(BiomobyObjectActivityItem.class
- .getResource("/biomoby_object.png")));
- // enable the item
- setEnabled(true);
- // create an action listener to catch clicks
- addActionListener(new ActionListener() {
- public void actionPerformed(ActionEvent e) {
- if (e.getSource() instanceof DatatypeMenuItem) {
- final DatatypeMenuItem item = (DatatypeMenuItem) e
- .getSource();
- // create a swing worker that creates our tree
- SwingWorker worker = new SwingWorker() {
- @Override
- public Object construct() {
- // create a progress bar ...
- JProgressBar bar = new JProgressBar();
- bar.setIndeterminate(true);
- bar.setString("Creating datatype tree ...");
- bar.setStringPainted(true);
- // a dialog frame hold the bar
- String title = "Datatype Tree Builder";
- JDialog frame = new HelpEnabledDialog(MainWindow.getMainWindow(), title, false, null);
- JLabel label = new JLabel(
- "Constructing tree for:\n\t"
- + item.getEndpoint());
- JPanel panel = new JPanel();
- panel.add(bar);
- // the panel that holds the label and bar
- JPanel panel1 = new JPanel();
- panel1.setLayout(new BorderLayout());
- panel1.add(panel, BorderLayout.NORTH);
- panel1.add(label, BorderLayout.CENTER);
- panel1.setBorder(BorderFactory.createEmptyBorder(
- 20, 20, 20, 20));
- frame.setContentPane(panel1);
- frame.setResizable(false);
- frame.pack();
- frame.setVisible(true);
- // do our task
- getTreeForRegistry(item.getEndpoint(), item
- .getNamespace());
- // hide the progress bar ...
- frame.setVisible(false);
- frame.removeAll();
- frame = null;
- return null;
- }
- };
- worker.start();
- }
- }
- });
- }
-
- /**
- * Set the registry namespace
- *
- * @param namespace
- * the registry namespace that this menu item will use
- */
- public void setNamespace(String namespace) {
- this.namespace = namespace;
- }
-
- /**
- * Set the registry endpoint
- *
- * @param endpoint
- * the registry endpoint that this menu item will use
- */
- public void setEndpoint(String endpoint) {
- this.endpoint = endpoint;
- }
-
- /**
- * Get the registry endpoint
- *
- * @return the registry endpoint that this menu item is using
- */
- public String getEndpoint() {
- return endpoint;
- }
-
- /**
- * Get the registry namespace
- *
- * @return the registry namespace that this menu item is using
- */
- public String getNamespace() {
- return namespace;
- }
-
- /*
- * Creates a tree for a given registry
- */
- private void getTreeForRegistry(String endpoint, String namespace) {
- Frame f = MobyPanel.CreateFrame("Datatype Viewer for " + endpoint);
- try {
- Component c = new BiomobyObjectTree(endpoint, namespace, editManager, fileManager)
- .getDatatypeTree();
- f.add(c);
- f.setPreferredSize(c.getPreferredSize());
- f.setMinimumSize(c.getPreferredSize());
- f.pack();
- } catch (MobyException e) {
- logger.error(
- "Error encountered while constructing datatype viewer:\n",
- e);
- }
- f.setVisible(true);
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyActivityContextualView.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyActivityContextualView.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyActivityContextualView.java
deleted file mode 100644
index 4911721..0000000
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyActivityContextualView.java
+++ /dev/null
@@ -1,106 +0,0 @@
-/*******************************************************************************
- * This file is a component of the Taverna project, and is licensed under the
- * GNU LGPL. Copyright Edward Kawas, The BioMoby Project
- ******************************************************************************/
-package net.sf.taverna.t2.activities.biomoby.view;
-
-import java.awt.BorderLayout;
-import java.awt.FlowLayout;
-import java.awt.Frame;
-import java.util.Map.Entry;
-
-import javax.swing.Action;
-import javax.swing.JButton;
-import javax.swing.JComponent;
-import javax.swing.JPanel;
-
-import net.sf.taverna.t2.activities.biomoby.BiomobyActivity;
-import net.sf.taverna.t2.activities.biomoby.BiomobyActivityConfigurationBean;
-import net.sf.taverna.t2.activities.biomoby.actions.BiomobyActivityConfigurationAction;
-import net.sf.taverna.t2.activities.biomoby.actions.MobyParserAction;
-import net.sf.taverna.t2.activities.biomoby.actions.MobyServiceDetailsAction;
-import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
-import net.sf.taverna.t2.workbench.configuration.colour.ColourManager;
-import net.sf.taverna.t2.workbench.edits.EditManager;
-import net.sf.taverna.t2.workbench.file.FileManager;
-import net.sf.taverna.t2.workbench.ui.actions.activity.HTMLBasedActivityContextualView;
-import net.sf.taverna.t2.workflowmodel.processor.activity.Activity;
-
-@SuppressWarnings("serial")
-public class BiomobyActivityContextualView extends
- HTMLBasedActivityContextualView<BiomobyActivityConfigurationBean> {
-
- private EditManager editManager;
- private final FileManager fileManager;
- private final ActivityIconManager activityIconManager;
-
- @Override
- public Action getConfigureAction(Frame owner) {
- BiomobyActivity activity = (BiomobyActivity) getActivity();
- if (activity.getMobyService() != null && activity.containsSecondaries()) {
- return new BiomobyActivityConfigurationAction((BiomobyActivity) getActivity(), owner,
- editManager, fileManager, activityIconManager);
- } else {
- return null;
- }
- }
-
- public BiomobyActivityContextualView(Activity<?> activity, EditManager editManager,
- FileManager fileManager, ActivityIconManager activityIconManager,
- ColourManager colourManager) {
- super(activity, colourManager);
- this.editManager = editManager;
- this.editManager = editManager;
- this.fileManager = fileManager;
- this.activityIconManager = activityIconManager;
- }
-
- @Override
- protected String getRawTableRowsHtml() {
- String html = "<tr><td>Endpoint</td><td>" + getConfigBean().getMobyEndpoint()
- + "</td></tr>";
- html += "<tr><td>Authority</td><td>" + getConfigBean().getAuthorityName() + "</td></tr>";
- html += "<tr><td>Service</td><td>" + getConfigBean().getServiceName() + "</td></tr>";
- if (getConfigBean().getSecondaries().size() > 0) {
- html += "<tr><th colspan='2' align='left'>Secondaries</th></tr>";
- for (Entry<String, String> entry : getConfigBean().getSecondaries().entrySet()) {
- html += "<tr><td>" + entry.getKey() + "</td><td>" + entry.getValue() + "</td></tr>";
- }
- }
- return html;
- }
-
- @Override
- public String getViewTitle() {
- return "Biomoby service";
- }
-
- /**
- * Gets the component from the {@link HTMLBasedActivityContextualView} and adds buttons to it
- * allowing Moby service details
- */
- @Override
- public JComponent getMainFrame() {
- final JComponent mainFrame = super.getMainFrame();
- JPanel flowPanel = new JPanel(new FlowLayout());
-
- BiomobyActivity activity = (BiomobyActivity) getActivity();
-
- JButton button = new JButton(new MobyServiceDetailsAction(activity, null, editManager,
- fileManager));
- flowPanel.add(button);
- if (activity.getMobyService() != null) {
- JButton button2 = new JButton(new MobyParserAction(activity, null, editManager,
- fileManager));
- flowPanel.add(button2);
- }
- mainFrame.add(flowPanel, BorderLayout.SOUTH);
- return mainFrame;
- }
-
- @Override
- public int getPreferredPosition() {
- return 100;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyActivityContextualViewFactory.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyActivityContextualViewFactory.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyActivityContextualViewFactory.java
deleted file mode 100644
index 942e52c..0000000
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyActivityContextualViewFactory.java
+++ /dev/null
@@ -1,50 +0,0 @@
-/*******************************************************************************
- * This file is a component of the Taverna project, and is licensed under the
- * GNU LGPL. Copyright Edward Kawas, The BioMoby Project
- ******************************************************************************/
-package net.sf.taverna.t2.activities.biomoby.view;
-
-import java.util.Arrays;
-import java.util.List;
-
-import net.sf.taverna.t2.activities.biomoby.BiomobyActivity;
-import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
-import net.sf.taverna.t2.workbench.configuration.colour.ColourManager;
-import net.sf.taverna.t2.workbench.edits.EditManager;
-import net.sf.taverna.t2.workbench.file.FileManager;
-import net.sf.taverna.t2.workbench.ui.views.contextualviews.ContextualView;
-import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory;
-
-public class BiomobyActivityContextualViewFactory implements ContextualViewFactory<BiomobyActivity> {
-
- private EditManager editManager;
- private FileManager fileManager;
- private ActivityIconManager activityIconManager;
- private ColourManager colourManager;
-
- public boolean canHandle(Object activity) {
- return activity instanceof BiomobyActivity;
- }
-
- public List<ContextualView> getViews(BiomobyActivity activity) {
- return Arrays.asList(new ContextualView[] { new BiomobyActivityContextualView(activity,
- editManager, fileManager, activityIconManager, colourManager) });
- }
-
- public void setEditManager(EditManager editManager) {
- this.editManager = editManager;
- }
-
- public void setFileManager(FileManager fileManager) {
- this.fileManager = fileManager;
- }
-
- public void setActivityIconManager(ActivityIconManager activityIconManager) {
- this.activityIconManager = activityIconManager;
- }
-
- public void setColourManager(ColourManager colourManager) {
- this.colourManager = colourManager;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyConfigView.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyConfigView.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyConfigView.java
deleted file mode 100644
index 0e08e0b..0000000
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyConfigView.java
+++ /dev/null
@@ -1,108 +0,0 @@
-/**
- *
- */
-package net.sf.taverna.t2.activities.biomoby.view;
-
-import java.awt.BorderLayout;
-import java.util.Map;
-
-import javax.swing.JComponent;
-
-import net.sf.taverna.t2.activities.biomoby.BiomobyActivity;
-import net.sf.taverna.t2.activities.biomoby.BiomobyActivityConfigurationBean;
-import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ActivityConfigurationPanel;
-
-import org.apache.log4j.Logger;
-import org.biomoby.service.dashboard.data.ParametersTable;
-
-/**
- * @author alanrw
- *
- */
-public class BiomobyConfigView extends ActivityConfigurationPanel<BiomobyActivity, BiomobyActivityConfigurationBean> {
-
- private BiomobyActivity activity;
- private BiomobyActivityConfigurationBean configuration;
- private boolean changed = false;
-
- private static Logger logger = Logger
- .getLogger(BiomobyConfigView.class);
- private ParametersTable parameterTable;
-
- public BiomobyConfigView(BiomobyActivity activity) {
- this.activity = activity;
- initialise();
- }
-
- private void initialise() {
- configuration = activity.getConfiguration();
- this.setLayout(new BorderLayout());
- parameterTable = activity.getParameterTable();
- JComponent component = parameterTable.scrollable();
- this.add(component, BorderLayout.NORTH);
- validate();
- }
-
- /* (non-Javadoc)
- * @see net.sf.taverna.t2.workbench.ui.views.contextualviews.ActivityConfigurationPanel#getConfiguration()
- */
- @Override
- public BiomobyActivityConfigurationBean getConfiguration() {
- return configuration;
- }
-
- /* (non-Javadoc)
- * @see net.sf.taverna.t2.workbench.ui.views.contextualviews.ActivityConfigurationPanel#isConfigurationChanged()
- */
- @Override
- public boolean isConfigurationChanged() {
- Map<String,String> secondaries = configuration.getSecondaries();
- int rows = parameterTable.getModel().getRowCount();
- for (int i = 0; i < rows; i++) {
- String key = (String)parameterTable.getModel().getValueAt(i,0);
- String newValue = parameterTable.getModel().getValueAt(i,1).toString();
- String currentValue = secondaries.get(key);
- if (!currentValue.equals(newValue)) {
- return true;
- }
- }
- return false;
- }
-
- /* (non-Javadoc)
- * @see net.sf.taverna.t2.workbench.ui.views.contextualviews.ActivityConfigurationPanel#noteConfiguration()
- */
- @Override
- public void noteConfiguration() {
- BiomobyActivityConfigurationBean newConfiguration =
- (BiomobyActivityConfigurationBean) cloneBean(configuration);
- Map<String,String> secondaries = newConfiguration.getSecondaries();
- int rows = parameterTable.getModel().getRowCount();
- for (int i = 0; i < rows; i++) {
- String key = (String)parameterTable.getModel().getValueAt(i,0);
- String value = parameterTable.getModel().getValueAt(i,1).toString();
- secondaries.put(key, value);
- }
-// logger.info(convertBeanToString(configuration));
-// logger.info("COnfiguration was " + configuration.hashCode());
-// logger.info(convertBeanToString(newConfiguration));
-// logger.info("New configuration is " + newConfiguration.hashCode());
- configuration = newConfiguration;
- }
-
- @Override
- public void refreshConfiguration() {
- logger.info(convertBeanToString(activity.getConfiguration()));
- removeAll();
- initialise();
- }
-
- @Override
- public boolean checkValues() {
- // TODO Not yet implemented
- return true;
- }
-
-
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyObjectActivityContextualView.java
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diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyObjectActivityContextualView.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyObjectActivityContextualView.java
deleted file mode 100644
index 4ceed9b..0000000
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyObjectActivityContextualView.java
+++ /dev/null
@@ -1,95 +0,0 @@
-/**
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- */
-package net.sf.taverna.t2.activities.biomoby.view;
-
-import java.awt.BorderLayout;
-import java.awt.FlowLayout;
-
-import javax.swing.JButton;
-import javax.swing.JComponent;
-import javax.swing.JPanel;
-
-import net.sf.taverna.t2.activities.biomoby.BiomobyObjectActivity;
-import net.sf.taverna.t2.activities.biomoby.BiomobyObjectActivityConfigurationBean;
-import net.sf.taverna.t2.activities.biomoby.actions.MobyObjectDetailsAction;
-import net.sf.taverna.t2.workbench.configuration.colour.ColourManager;
-import net.sf.taverna.t2.workbench.edits.EditManager;
-import net.sf.taverna.t2.workbench.file.FileManager;
-import net.sf.taverna.t2.workbench.ui.actions.activity.HTMLBasedActivityContextualView;
-import net.sf.taverna.t2.workflowmodel.processor.activity.Activity;
-
-/**
- * @author Stuart Owen
- *
- */
-@SuppressWarnings("serial")
-public class BiomobyObjectActivityContextualView extends
- HTMLBasedActivityContextualView<BiomobyObjectActivityConfigurationBean> {
-
- private EditManager editManager;
- private final FileManager fileManager;
-
- public BiomobyObjectActivityContextualView(Activity<?> activity, EditManager editManager,
- FileManager fileManager, ColourManager colourManager) {
- super(activity, colourManager);
- this.editManager = editManager;
- this.fileManager = fileManager;
- }
-
- @Override
- protected String getRawTableRowsHtml() {
- String html = "<tr><td>Endpoint</td><td>" + getConfigBean().getMobyEndpoint()
- + "</td></tr>";
- html += "<tr><td>Authority</td><td>" + getConfigBean().getAuthorityName() + "</td></tr>";
- html += "<tr><td>Datatype</td><td>" + getConfigBean().getServiceName() + "</td></tr>";
- return html;
- }
-
- @Override
- public String getViewTitle() {
- return "Biomoby Object service";
- }
-
- /**
- * Gets the component from the {@link HTMLBasedActivityContextualView} and adds buttons to it
- * allowing Moby object details
- */
- @Override
- public JComponent getMainFrame() {
- final JComponent mainFrame = super.getMainFrame();
- BiomobyObjectActivity activity = (BiomobyObjectActivity) getActivity();
- if (activity.getMobyObject() != null) {
- JPanel flowPanel = new JPanel(new FlowLayout());
- JButton button = new JButton(new MobyObjectDetailsAction(activity, null, editManager,
- fileManager));
- flowPanel.add(button);
- mainFrame.add(flowPanel, BorderLayout.SOUTH);
- }
- return mainFrame;
- }
-
- @Override
- public int getPreferredPosition() {
- return 100;
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyObjectActivityContextualViewFactory.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyObjectActivityContextualViewFactory.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyObjectActivityContextualViewFactory.java
deleted file mode 100644
index 0e6ea55..0000000
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyObjectActivityContextualViewFactory.java
+++ /dev/null
@@ -1,67 +0,0 @@
-/**
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- */
-package net.sf.taverna.t2.activities.biomoby.view;
-
-import java.util.Arrays;
-import java.util.List;
-
-import net.sf.taverna.t2.activities.biomoby.BiomobyObjectActivity;
-import net.sf.taverna.t2.workbench.configuration.colour.ColourManager;
-import net.sf.taverna.t2.workbench.edits.EditManager;
-import net.sf.taverna.t2.workbench.file.FileManager;
-import net.sf.taverna.t2.workbench.ui.views.contextualviews.ContextualView;
-import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory;
-
-/**
- * @author Stuart Owen
- *
- */
-public class BiomobyObjectActivityContextualViewFactory implements
- ContextualViewFactory<BiomobyObjectActivity> {
-
- private EditManager editManager;
- private FileManager fileManager;
- private ColourManager colourManager;
-
- public boolean canHandle(Object activity) {
- return activity instanceof BiomobyObjectActivity;
- }
-
- public List<ContextualView> getViews(BiomobyObjectActivity activity) {
- return Arrays.asList(new ContextualView[] { new BiomobyObjectActivityContextualView(
- activity, editManager, fileManager, colourManager) });
- }
-
- public void setEditManager(EditManager editManager) {
- this.editManager = editManager;
- }
-
- public void setFileManager(FileManager fileManager) {
- this.fileManager = fileManager;
- }
-
- public void setColourManager(ColourManager colourManager) {
- this.colourManager = colourManager;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/MobyParseDatatypeContextualView.java
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diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/MobyParseDatatypeContextualView.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/MobyParseDatatypeContextualView.java
deleted file mode 100644
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--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/MobyParseDatatypeContextualView.java
+++ /dev/null
@@ -1,62 +0,0 @@
-/**
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- */
-package net.sf.taverna.t2.activities.biomoby.view;
-
-import net.sf.taverna.t2.activities.biomoby.MobyParseDatatypeActivityConfigurationBean;
-import net.sf.taverna.t2.workbench.configuration.colour.ColourManager;
-import net.sf.taverna.t2.workbench.ui.actions.activity.HTMLBasedActivityContextualView;
-import net.sf.taverna.t2.workflowmodel.processor.activity.Activity;
-
-/**
- * @author Stuart Owen
- *
- */
-@SuppressWarnings("serial")
-public class MobyParseDatatypeContextualView extends
- HTMLBasedActivityContextualView<MobyParseDatatypeActivityConfigurationBean> {
-
- public MobyParseDatatypeContextualView(Activity<?> activity, ColourManager colourManager) {
- super(activity, colourManager);
- }
-
- @Override
- protected String getRawTableRowsHtml() {
- String html = "<tr><td>Article name used by service</td><td>"
- + getConfigBean().getArticleNameUsedByService() + "</td></tr>";
- html += "<tr><td>Datatype</td><td>" + getConfigBean().getDatatypeName() + "</td></tr>";
- html += "<tr><td>Registry endpoint</td><td>" + getConfigBean().getRegistryEndpoint()
- + "</td></tr>";
- return html;
- }
-
- @Override
- public String getViewTitle() {
- return "Moby parse datatype service";
- }
-
- @Override
- public int getPreferredPosition() {
- return 100;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/MobyParseDatatypeContextualViewFactory.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/MobyParseDatatypeContextualViewFactory.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/MobyParseDatatypeContextualViewFactory.java
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--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/view/MobyParseDatatypeContextualViewFactory.java
+++ /dev/null
@@ -1,69 +0,0 @@
-/**
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- */
-package net.sf.taverna.t2.activities.biomoby.view;
-
-import java.util.Arrays;
-import java.util.List;
-
-import net.sf.taverna.t2.activities.biomoby.MobyParseDatatypeActivity;
-import net.sf.taverna.t2.workbench.configuration.colour.ColourManager;
-import net.sf.taverna.t2.workbench.ui.views.contextualviews.ContextualView;
-import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory;
-
-/**
- * @author Stuart Owen
- *
- */
-public class MobyParseDatatypeContextualViewFactory implements
- ContextualViewFactory<MobyParseDatatypeActivity> {
-
- private ColourManager colourManager;
-
- /*
- * (non-Javadoc)
- *
- * @see
- * net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory#canHandle
- * (java.lang.Object)
- */
- public boolean canHandle(Object activity) {
- return activity instanceof MobyParseDatatypeActivity;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory#getView
- * (java.lang.Object)
- */
- public List<ContextualView> getViews(MobyParseDatatypeActivity activity) {
- return Arrays.asList(new ContextualView[] { new MobyParseDatatypeContextualView(activity,
- colourManager) });
- }
-
- public void setColourManager(ColourManager colourManager) {
- this.colourManager = colourManager;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/resources/Add24.gif
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diff --git a/taverna-biomoby-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.partition.PartitionAlgorithmSetSPI b/taverna-biomoby-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.partition.PartitionAlgorithmSetSPI
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--- a/taverna-biomoby-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.partition.PartitionAlgorithmSetSPI
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@@ -1 +0,0 @@
-net.sf.taverna.t2.activities.biomoby.partition.BiomobyPartitionAlgorithmSetSPI
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.partition.PropertyExtractorSPI
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diff --git a/taverna-biomoby-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.partition.PropertyExtractorSPI b/taverna-biomoby-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.partition.PropertyExtractorSPI
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+++ /dev/null
@@ -1 +0,0 @@
-net.sf.taverna.t2.activities.biomoby.partition.BiomobyPropertyExtractor
\ No newline at end of file
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diff --git a/taverna-biomoby-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.partition.QueryFactory b/taverna-biomoby-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.partition.QueryFactory
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+++ /dev/null
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-net.sf.taverna.t2.activities.biomoby.query.BiomobyQueryFactory
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider
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diff --git a/taverna-biomoby-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider b/taverna-biomoby-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider
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+++ /dev/null
@@ -1 +0,0 @@
-net.sf.taverna.t2.activities.biomoby.servicedescriptions.BiomobyServiceProvider
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent
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diff --git a/taverna-biomoby-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent b/taverna-biomoby-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent
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+++ /dev/null
@@ -1,5 +0,0 @@
-net.sf.taverna.t2.activities.biomoby.menu.BiomobyActivityDetailsMenuAction
-net.sf.taverna.t2.activities.biomoby.menu.BiomobyActivityParserMenuAction
-#net.sf.taverna.t2.activities.biomoby.actions.BiomobyAdvancedMenuAction
-net.sf.taverna.t2.activities.biomoby.menu.ConfigureBiomobyMenuAction
-
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI
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diff --git a/taverna-biomoby-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI b/taverna-biomoby-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI
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--- a/taverna-biomoby-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI
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@@ -1,2 +0,0 @@
-net.sf.taverna.t2.activities.biomoby.query.BiomobyActivityIcon
-net.sf.taverna.t2.activities.biomoby.query.BiomobyObjectActivityIcon
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory
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diff --git a/taverna-biomoby-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory b/taverna-biomoby-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory
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-net.sf.taverna.t2.activities.biomoby.view.BiomobyActivityContextualViewFactory
-net.sf.taverna.t2.activities.biomoby.view.BiomobyObjectActivityContextualViewFactory
-net.sf.taverna.t2.activities.biomoby.view.MobyParseDatatypeContextualViewFactory
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/resources/META-INF/spring/biomoby-activity-ui-context-osgi.xml
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diff --git a/taverna-biomoby-activity-ui/src/main/resources/META-INF/spring/biomoby-activity-ui-context-osgi.xml b/taverna-biomoby-activity-ui/src/main/resources/META-INF/spring/biomoby-activity-ui-context-osgi.xml
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-<?xml version="1.0" encoding="UTF-8"?>
-<beans:beans xmlns="http://www.springframework.org/schema/osgi" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:beans="http://www.springframework.org/schema/beans"
- xsi:schemaLocation="http://www.springframework.org/schema/beans
- http://www.springframework.org/schema/beans/spring-beans.xsd
- http://www.springframework.org/schema/osgi
- http://www.springframework.org/schema/osgi/spring-osgi.xsd">
-
- <service ref="BiomobyActivityIcon" interface="net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI" />
- <service ref="BiomobyObjectActivityIcon" interface="net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI" />
-
- <service ref="BiomobyServiceProvider" interface="net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider" />
-
- <service ref="BiomobyActivityDetailsMenuAction" auto-export="interfaces" />
- <service ref="BiomobyActivityParserMenuAction" auto-export="interfaces" />
- <service ref="ConfigureBiomobyMenuAction" auto-export="interfaces" />
-
- <service ref="BiomobyActivityContextualViewFactory" interface="net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory" />
- <service ref="BiomobyObjectActivityContextualViewFactory" interface="net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory" />
- <service ref="MobyParseDatatypeContextualViewFactory" interface="net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory" />
-
- <reference id="editManager" interface="net.sf.taverna.t2.workbench.edits.EditManager" />
- <reference id="fileManager" interface="net.sf.taverna.t2.workbench.file.FileManager" />
- <reference id="activityIconManager" interface="net.sf.taverna.t2.workbench.activityicons.ActivityIconManager" />
- <reference id="colourManager" interface="net.sf.taverna.t2.workbench.configuration.colour.ColourManager" />
- <reference id="serviceDescriptionRegistry" interface="net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry" />
-
-</beans:beans>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/resources/META-INF/spring/biomoby-activity-ui-context.xml
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diff --git a/taverna-biomoby-activity-ui/src/main/resources/META-INF/spring/biomoby-activity-ui-context.xml b/taverna-biomoby-activity-ui/src/main/resources/META-INF/spring/biomoby-activity-ui-context.xml
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-<?xml version="1.0" encoding="UTF-8"?>
-<beans xmlns="http://www.springframework.org/schema/beans" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://www.springframework.org/schema/beans
- http://www.springframework.org/schema/beans/spring-beans.xsd">
-
- <bean id="BiomobyActivityIcon" class="net.sf.taverna.t2.activities.biomoby.query.BiomobyActivityIcon" />
- <bean id="BiomobyObjectActivityIcon" class="net.sf.taverna.t2.activities.biomoby.query.BiomobyObjectActivityIcon" />
-
- <bean id="BiomobyServiceProvider" class="net.sf.taverna.t2.activities.biomoby.servicedescriptions.BiomobyServiceProvider">
- <property name="serviceDescriptionRegistry" ref="serviceDescriptionRegistry" />
- </bean>
-
- <bean id="BiomobyActivityDetailsMenuAction" class="net.sf.taverna.t2.activities.biomoby.menu.BiomobyActivityDetailsMenuAction">
- <property name="editManager" ref="editManager" />
- <property name="fileManager" ref="fileManager" />
- </bean>
- <bean id="BiomobyActivityParserMenuAction" class="net.sf.taverna.t2.activities.biomoby.menu.BiomobyActivityParserMenuAction">
- <property name="editManager" ref="editManager" />
- <property name="fileManager" ref="fileManager" />
- </bean>
- <bean id="ConfigureBiomobyMenuAction" class="net.sf.taverna.t2.activities.biomoby.menu.ConfigureBiomobyMenuAction">
- <property name="editManager" ref="editManager" />
- <property name="fileManager" ref="fileManager" />
- <property name="activityIconManager" ref="activityIconManager" />
- </bean>
-
- <bean id="BiomobyActivityContextualViewFactory" class="net.sf.taverna.t2.activities.biomoby.view.BiomobyActivityContextualViewFactory">
- <property name="editManager" ref="editManager" />
- <property name="fileManager" ref="fileManager" />
- <property name="activityIconManager" ref="activityIconManager" />
- <property name="colourManager" ref="colourManager" />
- </bean>
- <bean id="BiomobyObjectActivityContextualViewFactory" class="net.sf.taverna.t2.activities.biomoby.view.BiomobyObjectActivityContextualViewFactory">
- <property name="editManager" ref="editManager" />
- <property name="fileManager" ref="fileManager" />
- <property name="colourManager" ref="colourManager" />
- </bean>
- <bean id="MobyParseDatatypeContextualViewFactory" class="net.sf.taverna.t2.activities.biomoby.view.MobyParseDatatypeContextualViewFactory">
- <property name="colourManager" ref="colourManager" />
- </bean>
-
-</beans>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/resources/Search24.gif
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http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/test/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyContextualViewFactoryTest.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/test/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyContextualViewFactoryTest.java b/taverna-biomoby-activity-ui/src/test/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyContextualViewFactoryTest.java
deleted file mode 100644
index a9c51c6..0000000
--- a/taverna-biomoby-activity-ui/src/test/java/net/sf/taverna/t2/activities/biomoby/view/BiomobyContextualViewFactoryTest.java
+++ /dev/null
@@ -1,49 +0,0 @@
-/*******************************************************************************
- * This file is a component of the Taverna project, and is licensed under the
- * GNU LGPL. Copyright Edward Kawas, The BioMoby Project
- ******************************************************************************/
-package net.sf.taverna.t2.activities.biomoby.view;
-
-import static org.junit.Assert.assertNull;
-import static org.junit.Assert.assertTrue;
-
-import java.util.List;
-
-import net.sf.taverna.t2.activities.biomoby.BiomobyActivity;
-import net.sf.taverna.t2.activities.biomoby.BiomobyActivityConfigurationBean;
-import net.sf.taverna.t2.workbench.ui.views.contextualviews.ContextualView;
-import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory;
-import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactoryRegistry;
-import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityConfigurationException;
-
-import org.junit.Before;
-import org.junit.Test;
-
-public class BiomobyContextualViewFactoryTest {
- BiomobyActivity activity;
- @Before
- public void setup() throws ActivityConfigurationException {
- activity=new BiomobyActivity() { //need to prevent the activity trying to configure itself, but store a copy of the config bean
-
- @Override
- public void configure(
- BiomobyActivityConfigurationBean configurationBean)
- throws ActivityConfigurationException {
- this.configurationBean=configurationBean;
- }
-
- };
- BiomobyActivityConfigurationBean b = new BiomobyActivityConfigurationBean();
- b.setAuthorityName("a");
- b.setMobyEndpoint("e");
- b.setServiceName("s");
- activity.configure(b);
- }
-
- @Test
- public void testGetConfigureAction() throws Exception {
- ContextualView view = new BiomobyActivityContextualView(activity, null, null, null, null);
- //will be null because its not a valid activity so therefore has no secondaries
- assertNull("The action should be null",view.getConfigureAction(null));
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity/pom.xml
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diff --git a/taverna-biomoby-activity/pom.xml b/taverna-biomoby-activity/pom.xml
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--- a/taverna-biomoby-activity/pom.xml
+++ /dev/null
@@ -1,142 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
- <modelVersion>4.0.0</modelVersion>
- <parent>
- <groupId>net.sf.taverna</groupId>
- <artifactId>taverna-parent</artifactId>
- <version>3.0.1-SNAPSHOT</version>
- </parent>
- <groupId>net.sf.taverna.t2.activities</groupId>
- <artifactId>biomoby-activity</artifactId>
- <version>2.0.1-SNAPSHOT</version>
- <packaging>bundle</packaging>
- <name>Taverna 2 Biomoby Activity</name>
- <build>
- <plugins>
- <plugin>
- <groupId>org.apache.felix</groupId>
- <artifactId>maven-bundle-plugin</artifactId>
- <configuration>
- <instructions>
- <Embed-Transitive>true</Embed-Transitive>
- <Embed-Dependency>jmoby;jmoby-dashboard</Embed-Dependency>
- </instructions>
- </configuration>
- </plugin>
- </plugins>
- </build>
- <dependencies>
- <dependency>
- <groupId>net.sf.taverna.t2.core</groupId>
- <artifactId>workflowmodel-api</artifactId>
- <version>${t2.core.version}</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.core</groupId>
- <artifactId>reference-api</artifactId>
- <version>${t2.core.version}</version>
- </dependency>
- <dependency>
- <groupId>org.biomoby</groupId>
- <artifactId>jmoby</artifactId>
- <version>${jmoby.version}</version>
- <exclusions>
- <exclusion>
- <groupId>org.biomoby</groupId>
- <artifactId>taverna-for-moby</artifactId>
- </exclusion>
- <exclusion>
- <groupId>log4j</groupId>
- <artifactId>log4j</artifactId>
- </exclusion>
- <exclusion>
- <groupId>xml-apis</groupId>
- <artifactId>xml-apis</artifactId>
- </exclusion>
- <exclusion>
- <groupId>stax</groupId>
- <artifactId>stax-api</artifactId>
- </exclusion>
- <exclusion>
- <groupId>xerces</groupId>
- <artifactId>xmlParserAPIs</artifactId>
- </exclusion>
- <exclusion>
- <groupId>javax.xml.ws</groupId>
- <artifactId>jaxws-api</artifactId>
- </exclusion>
- <exclusion>
- <groupId>javax.xml.soap</groupId>
- <artifactId>saaj-api</artifactId>
- </exclusion>
- </exclusions>
- </dependency>
- <dependency>
- <groupId>org.biomoby</groupId>
- <artifactId>jmoby-dashboard</artifactId>
- <version>${jmoby.version}</version>
- </dependency>
- <dependency>
- <groupId>org.jdom</groupId>
- <artifactId>com.springsource.org.jdom</artifactId>
- <version>${jdom.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.commons</groupId>
- <artifactId>com.springsource.org.apache.commons.httpclient</artifactId>
- <version>${commons.httpclient.version}</version>
- </dependency>
- <!--<dependency> <groupId>org.apache.xmlcommons</groupId> <artifactId>com.springsource.org.apache.xmlcommons</artifactId>
- <version>1.3.4</version> </dependency> -->
- <!--<dependency> <groupId>javax.xml.ws</groupId> <artifactId>jaxws-api</artifactId>
- <version>2.1</version> </dependency> -->
- <!--<dependency> <groupId>com.sun.org.apache</groupId> <artifactId>jaxp-ri</artifactId>
- <version>1.4</version> </dependency> -->
- <dependency>
- <groupId>org.apache.log4j</groupId>
- <artifactId>com.springsource.org.apache.log4j</artifactId>
- <version>${log4j.version}</version>
- </dependency>
-
- <dependency>
- <groupId>junit</groupId>
- <artifactId>junit</artifactId>
- <version>${junit.version}</version>
- <scope>test</scope>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.activities</groupId>
- <artifactId>activity-test-utils</artifactId>
- <version>${t2.activities.version}</version>
- <scope>test</scope>
- </dependency>
- </dependencies>
- <repositories>
- <repository>
- <releases />
- <snapshots>
- <enabled>false</enabled>
- </snapshots>
- <id>mygrid-repository</id>
- <name>myGrid Repository</name>
- <url>http://www.mygrid.org.uk/maven/repository</url>
- </repository>
- <repository>
- <releases>
- <enabled>false</enabled>
- </releases>
- <snapshots />
- <id>mygrid-snapshot-repository</id>
- <name>myGrid Snapshot Repository</name>
- <url>http://www.mygrid.org.uk/maven/snapshot-repository</url>
- </repository>
- </repositories>
- <scm>
- <connection>scm:git:https://github.com/taverna/taverna-biomoby-activity.git</connection>
- <developerConnection>scm:git:ssh://git@github.com/taverna/taverna-biomoby-activity.git</developerConnection>
- <url>https://github.com/taverna/taverna-biomoby-activity/</url>
- <tag>HEAD</tag>
- </scm>
-
-</project>
[07/16] incubator-taverna-plugin-bioinformatics git commit:
temporarily empty repository
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/edits/AddMobyParseDatatypeEdit.java
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diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/edits/AddMobyParseDatatypeEdit.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/edits/AddMobyParseDatatypeEdit.java
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--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/edits/AddMobyParseDatatypeEdit.java
+++ /dev/null
@@ -1,220 +0,0 @@
-/**
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- */
-package net.sf.taverna.t2.activities.biomoby.edits;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import net.sf.taverna.t2.activities.biomoby.BiomobyActivity;
-import net.sf.taverna.t2.activities.biomoby.MobyParseDatatypeActivity;
-import net.sf.taverna.t2.activities.biomoby.MobyParseDatatypeActivityConfigurationBean;
-import net.sf.taverna.t2.workflowmodel.CompoundEdit;
-import net.sf.taverna.t2.workflowmodel.Dataflow;
-import net.sf.taverna.t2.workflowmodel.Edit;
-import net.sf.taverna.t2.workflowmodel.EditException;
-import net.sf.taverna.t2.workflowmodel.Edits;
-import net.sf.taverna.t2.workflowmodel.EventForwardingOutputPort;
-import net.sf.taverna.t2.workflowmodel.EventHandlingInputPort;
-import net.sf.taverna.t2.workflowmodel.InputPort;
-import net.sf.taverna.t2.workflowmodel.OutputPort;
-import net.sf.taverna.t2.workflowmodel.Processor;
-import net.sf.taverna.t2.workflowmodel.ProcessorInputPort;
-import net.sf.taverna.t2.workflowmodel.ProcessorOutputPort;
-import net.sf.taverna.t2.workflowmodel.impl.AbstractDataflowEdit;
-import net.sf.taverna.t2.workflowmodel.impl.DataflowImpl;
-import net.sf.taverna.t2.workflowmodel.processor.activity.Activity;
-import net.sf.taverna.t2.workflowmodel.utils.Tools;
-
-/**
- * @author Stuart Owen
- *
- */
-public class AddMobyParseDatatypeEdit extends AbstractDataflowEdit {
-
- private final BiomobyActivity activity;
- private final String objectName;
- private final boolean isCollection;
- private final String potentialCollectionString;
-
- private Edit<?> compoundEdit = null;
- private Edit<?> linkEdit = null;
-
- private Edits edits;
-
- /**
- * @param dataflow
- */
- public AddMobyParseDatatypeEdit(Dataflow dataflow,
- BiomobyActivity activity, String objectName, boolean isCollection,
- String potentialCollectionString, Edits edits) {
- super(dataflow);
- this.activity = activity;
- this.objectName = objectName;
- this.isCollection = isCollection;
- this.potentialCollectionString = potentialCollectionString;
- this.edits = edits;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * net.sf.taverna.t2.workflowmodel.impl.AbstractEdit#doEditAction(java.lang
- * .Object)
- */
- @Override
- protected void doEditAction(DataflowImpl dataflow) throws EditException {
-
- List<Edit<?>> editList = new ArrayList<Edit<?>>();
-
- String defaultName = objectName;
- if (defaultName.indexOf("(") > 0)
- defaultName = defaultName.substring(0, defaultName.indexOf("("));
-
- String name = Tools
- .uniqueProcessorName("Parse Moby Data(" + defaultName + ")",
- dataflow);
-
- String articlename = "";
- if (isCollection) {
- articlename = potentialCollectionString.substring(
- potentialCollectionString.indexOf("('") + 2,
- potentialCollectionString.lastIndexOf("'"));
- } else {
- articlename = objectName.substring(objectName.indexOf("'") + 1,
- objectName.lastIndexOf("'"));
- }
-
- MobyParseDatatypeActivityConfigurationBean bean = new MobyParseDatatypeActivityConfigurationBean();
- bean.setArticleNameUsedByService(articlename);
- bean.setRegistryEndpoint(activity.getConfiguration().getMobyEndpoint());
- bean.setDatatypeName(defaultName);
- MobyParseDatatypeActivity mobyDatatypeActivity = new MobyParseDatatypeActivity();
-
- editList
- .add(edits.getConfigureActivityEdit(mobyDatatypeActivity, bean));
-
- net.sf.taverna.t2.workflowmodel.Processor sinkProcessor = edits
- .createProcessor(name);
-
- editList.add(edits.getDefaultDispatchStackEdit(sinkProcessor));
-
- Edit<?> addActivityToProcessorEdit = edits.getAddActivityEdit(
- sinkProcessor, mobyDatatypeActivity);
- editList.add(addActivityToProcessorEdit);
-
- editList.add(edits.getAddProcessorEdit(dataflow, sinkProcessor));
-
- compoundEdit = new CompoundEdit(editList);
- compoundEdit.doEdit();
-
- Processor sourceProcessor = Tools.getProcessorsWithActivity(dataflow,
- activity).iterator().next();
-
- List<Edit<?>> linkEditList = new ArrayList<Edit<?>>();
-
- String inputName = mobyDatatypeActivity.getInputPorts().iterator()
- .next().getName();
- EventHandlingInputPort sinkPort = getSinkPort(sinkProcessor,
- mobyDatatypeActivity, inputName, linkEditList);
-
-
- String outputPortName;
- if (isCollection) {
- outputPortName = defaultName + "(Collection - '"
- + (articlename.equals("") ? "MobyCollection" : articlename)
- + "' As Simples)";
- }
- else {
- outputPortName = defaultName +"(" + articlename + ")";
- }
- EventForwardingOutputPort sourcePort = getSourcePort(sourceProcessor,
- activity, outputPortName, linkEditList);
- linkEditList.add(Tools.getCreateAndConnectDatalinkEdit(dataflow,
- sourcePort, sinkPort, edits));
- linkEdit = new CompoundEdit(linkEditList);
- linkEdit.doEdit();
-
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * net.sf.taverna.t2.workflowmodel.impl.AbstractEdit#undoEditAction(java
- * .lang.Object)
- */
- @Override
- protected void undoEditAction(DataflowImpl subjectImpl) {
- if (linkEdit != null && linkEdit.isApplied())
- linkEdit.undo();
- if (compoundEdit != null && compoundEdit.isApplied())
- compoundEdit.undo();
- }
-
- private EventHandlingInputPort getSinkPort(
- net.sf.taverna.t2.workflowmodel.Processor processor,
- Activity<?> activity, String portName, List<Edit<?>> editList) {
- InputPort activityPort = net.sf.taverna.t2.workflowmodel.utils.Tools
- .getActivityInputPort(activity, portName);
- // check if processor port exists
- EventHandlingInputPort input = net.sf.taverna.t2.workflowmodel.utils.Tools
- .getProcessorInputPort(processor, activity, activityPort);
- if (input == null) {
- // port doesn't exist so create a processor port and map it
- ProcessorInputPort processorInputPort = edits
- .createProcessorInputPort(processor,
- activityPort.getName(), activityPort.getDepth());
- editList.add(edits.getAddProcessorInputPortEdit(processor,
- processorInputPort));
- editList.add(edits.getAddActivityInputPortMappingEdit(activity,
- activityPort.getName(), activityPort.getName()));
- input = processorInputPort;
- }
- return input;
- }
-
- private EventForwardingOutputPort getSourcePort(
- net.sf.taverna.t2.workflowmodel.Processor processor,
- Activity<?> activity, String portName, List<Edit<?>> editList) {
- OutputPort activityPort = net.sf.taverna.t2.workflowmodel.utils.Tools
- .getActivityOutputPort(activity, portName);
- // check if processor port exists
- EventForwardingOutputPort output = net.sf.taverna.t2.workflowmodel.utils.Tools
- .getProcessorOutputPort(processor, activity, activityPort);
- if (output == null) {
- // port doesn't exist so create a processor port and map it
- ProcessorOutputPort processorOutputPort = edits
- .createProcessorOutputPort(processor, activityPort
- .getName(), activityPort.getDepth(), activityPort
- .getGranularDepth());
- editList.add(edits.getAddProcessorOutputPortEdit(processor,
- processorOutputPort));
- editList.add(edits.getAddActivityOutputPortMappingEdit(activity,
- activityPort.getName(), activityPort.getName()));
- output = processorOutputPort;
- }
- return output;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/edits/AddUpstreamObjectEdit.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/edits/AddUpstreamObjectEdit.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/edits/AddUpstreamObjectEdit.java
deleted file mode 100644
index fea1860..0000000
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/edits/AddUpstreamObjectEdit.java
+++ /dev/null
@@ -1,216 +0,0 @@
-/**
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- */
-package net.sf.taverna.t2.activities.biomoby.edits;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import net.sf.taverna.t2.activities.biomoby.BiomobyObjectActivity;
-import net.sf.taverna.t2.activities.biomoby.BiomobyObjectActivityConfigurationBean;
-import net.sf.taverna.t2.workflowmodel.CompoundEdit;
-import net.sf.taverna.t2.workflowmodel.Dataflow;
-import net.sf.taverna.t2.workflowmodel.Edit;
-import net.sf.taverna.t2.workflowmodel.EditException;
-import net.sf.taverna.t2.workflowmodel.Edits;
-import net.sf.taverna.t2.workflowmodel.EventForwardingOutputPort;
-import net.sf.taverna.t2.workflowmodel.EventHandlingInputPort;
-import net.sf.taverna.t2.workflowmodel.InputPort;
-import net.sf.taverna.t2.workflowmodel.OutputPort;
-import net.sf.taverna.t2.workflowmodel.Processor;
-import net.sf.taverna.t2.workflowmodel.ProcessorInputPort;
-import net.sf.taverna.t2.workflowmodel.ProcessorOutputPort;
-import net.sf.taverna.t2.workflowmodel.impl.AbstractDataflowEdit;
-import net.sf.taverna.t2.workflowmodel.impl.DataflowImpl;
-import net.sf.taverna.t2.workflowmodel.processor.activity.Activity;
-import net.sf.taverna.t2.workflowmodel.utils.Tools;
-
-import org.apache.log4j.Logger;
-
-/**
- * @author Stuart Owen
- *
- */
-public class AddUpstreamObjectEdit extends AbstractDataflowEdit {
-
- private static Logger logger = Logger.getLogger(AddUpstreamObjectEdit.class);
-
- private final Processor sinkProcessor;
- private final BiomobyObjectActivity activity;
- private Edits edits;
-
- private List<Edit<?>> subEdits = new ArrayList<Edit<?>>();
-
- /**
- * @param dataflow
- */
- public AddUpstreamObjectEdit(Dataflow dataflow, Processor sinkProcessor,
- BiomobyObjectActivity activity, Edits edits) {
- super(dataflow);
- this.sinkProcessor = sinkProcessor;
- this.activity = activity;
- this.edits = edits;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * net.sf.taverna.t2.workflowmodel.impl.AbstractDataflowEdit#doEditAction
- * (net.sf.taverna.t2.workflowmodel.impl.DataflowImpl)
- */
- @Override
- protected void doEditAction(DataflowImpl dataflow) throws EditException {
- subEdits.clear();
-
- for (InputPort inputPort : activity.getInputPorts()) {
- // ignore article name, id, namespace, value
- if (inputPort.getName().equals("namespace")
- || inputPort.getName().equals("id")
- || inputPort.getName().equals("article name")
- || inputPort.getName().equals("value")) {
- continue;
- }
- List<Edit<?>> editList = new ArrayList<Edit<?>>();
- String defaultName = inputPort.getName().split("\\(")[0];
-
- String name = Tools
- .uniqueProcessorName(inputPort.getName(), dataflow);
-
- BiomobyObjectActivityConfigurationBean configBean = new BiomobyObjectActivityConfigurationBean();
- configBean.setMobyEndpoint(activity.getConfiguration()
- .getMobyEndpoint());
- configBean.setAuthorityName("");
- configBean.setServiceName(defaultName);
-
- net.sf.taverna.t2.workflowmodel.Processor sourceProcessor = edits
- .createProcessor(name);
- BiomobyObjectActivity boActivity = new BiomobyObjectActivity();
- Edit<?> configureActivityEdit = edits.getConfigureActivityEdit(
- boActivity, configBean);
- editList.add(configureActivityEdit);
-
- editList.add(edits.getDefaultDispatchStackEdit(sourceProcessor));
-
- Edit<?> addActivityToProcessorEdit = edits.getAddActivityEdit(
- sourceProcessor, boActivity);
- editList.add(addActivityToProcessorEdit);
-
-
-
- editList.add(edits.getAddProcessorEdit(dataflow, sourceProcessor));
-
- CompoundEdit compoundEdit = new CompoundEdit(editList);
- subEdits.add(compoundEdit);
- compoundEdit.doEdit();
-
-
- List<Edit<?>> linkEditList = new ArrayList<Edit<?>>();
-
- EventForwardingOutputPort sourcePort = getSourcePort(
- sourceProcessor, boActivity, "mobyData", linkEditList);
- EventHandlingInputPort sinkPort = getSinkPort(sinkProcessor, activity, inputPort.getName(), linkEditList);
- linkEditList.add(Tools.getCreateAndConnectDatalinkEdit(dataflow,
- sourcePort, sinkPort, edits));
- CompoundEdit linkEdit = new CompoundEdit(linkEditList);
- subEdits.add(linkEdit);
- linkEdit.doEdit();
-
- if (!(defaultName.equalsIgnoreCase("Object")
- || name.equalsIgnoreCase("String")
- || name.equalsIgnoreCase("Integer") || name
- .equalsIgnoreCase("DateTime"))) {
- Edit upstreamObjectEdit = new AddUpstreamObjectEdit(dataflow,
- sourceProcessor, boActivity, edits);
- subEdits.add(upstreamObjectEdit);
- upstreamObjectEdit.doEdit();
- }
- }
-
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * net.sf.taverna.t2.workflowmodel.impl.AbstractDataflowEdit#undoEditAction
- * (net.sf.taverna.t2.workflowmodel.impl.DataflowImpl)
- */
- @Override
- protected void undoEditAction(DataflowImpl dataflow) {
- if (subEdits != null && subEdits.size() > 0) {
- for (int i = subEdits.size() - 1; i >= 0; i--) {
- Edit<?> edit = subEdits.get(i);
- if (edit.isApplied())
- edit.undo();
- }
- }
-
-
- }
-
- private EventHandlingInputPort getSinkPort(
- net.sf.taverna.t2.workflowmodel.Processor processor,
- Activity<?> activity, String portName, List<Edit<?>> editList) {
- InputPort activityPort = net.sf.taverna.t2.workflowmodel.utils.Tools
- .getActivityInputPort(activity, portName);
- // check if processor port exists
- EventHandlingInputPort input = net.sf.taverna.t2.workflowmodel.utils.Tools
- .getProcessorInputPort(processor, activity, activityPort);
- if (input == null) {
- // port doesn't exist so create a processor port and map it
- ProcessorInputPort processorInputPort = edits
- .createProcessorInputPort(processor,
- activityPort.getName(), activityPort.getDepth());
- editList.add(edits.getAddProcessorInputPortEdit(processor,
- processorInputPort));
- editList.add(edits.getAddActivityInputPortMappingEdit(activity,
- activityPort.getName(), activityPort.getName()));
- input = processorInputPort;
- }
- return input;
- }
-
- private EventForwardingOutputPort getSourcePort(
- net.sf.taverna.t2.workflowmodel.Processor processor,
- Activity<?> activity, String portName, List<Edit<?>> editList) {
- OutputPort activityPort = net.sf.taverna.t2.workflowmodel.utils.Tools
- .getActivityOutputPort(activity, portName);
- // check if processor port exists
- EventForwardingOutputPort output = net.sf.taverna.t2.workflowmodel.utils.Tools
- .getProcessorOutputPort(processor, activity, activityPort);
- if (output == null) {
- // port doesn't exist so create a processor port and map it
- ProcessorOutputPort processorOutputPort = edits
- .createProcessorOutputPort(processor, activityPort
- .getName(), activityPort.getDepth(), activityPort
- .getGranularDepth());
- editList.add(edits.getAddProcessorOutputPortEdit(processor,
- processorOutputPort));
- editList.add(edits.getAddActivityOutputPortMappingEdit(activity,
- activityPort.getName(), activityPort.getName()));
- output = processorOutputPort;
- }
- return output;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/menu/BiomobyActivityDetailsMenuAction.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/menu/BiomobyActivityDetailsMenuAction.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/menu/BiomobyActivityDetailsMenuAction.java
deleted file mode 100644
index cee5420..0000000
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/menu/BiomobyActivityDetailsMenuAction.java
+++ /dev/null
@@ -1,40 +0,0 @@
-package net.sf.taverna.t2.activities.biomoby.menu;
-
-import javax.swing.Action;
-
-import net.sf.taverna.t2.activities.biomoby.BiomobyActivity;
-import net.sf.taverna.t2.activities.biomoby.actions.MobyServiceDetailsAction;
-import net.sf.taverna.t2.workbench.activitytools.AbstractConfigureActivityMenuAction;
-import net.sf.taverna.t2.workbench.edits.EditManager;
-import net.sf.taverna.t2.workbench.file.FileManager;
-import net.sf.taverna.t2.workflowmodel.Edits;
-
-public class BiomobyActivityDetailsMenuAction extends
- AbstractConfigureActivityMenuAction<BiomobyActivity> {
-
- private static final String CONFIGURE_BIOMOBY_DETAILS = "Browse Biomoby service details";
- private EditManager editManager;
- private FileManager fileManager;
-
- public BiomobyActivityDetailsMenuAction() {
- super(BiomobyActivity.class);
- }
-
- @Override
- protected Action createAction() {
- MobyServiceDetailsAction configAction = new MobyServiceDetailsAction(
- findActivity(), getParentFrame(), editManager, fileManager);
- configAction.putValue(Action.NAME, CONFIGURE_BIOMOBY_DETAILS);
- addMenuDots(configAction);
- return configAction;
- }
-
- public void setEditManager(EditManager editManager) {
- this.editManager = editManager;
- }
-
- public void setFileManager(FileManager fileManager) {
- this.fileManager = fileManager;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/menu/BiomobyActivityParserMenuAction.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/menu/BiomobyActivityParserMenuAction.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/menu/BiomobyActivityParserMenuAction.java
deleted file mode 100644
index b760bbc..0000000
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/menu/BiomobyActivityParserMenuAction.java
+++ /dev/null
@@ -1,41 +0,0 @@
-package net.sf.taverna.t2.activities.biomoby.menu;
-
-import javax.swing.Action;
-
-import net.sf.taverna.t2.activities.biomoby.BiomobyActivity;
-import net.sf.taverna.t2.activities.biomoby.actions.MobyParserAction;
-import net.sf.taverna.t2.workbench.activitytools.AbstractConfigureActivityMenuAction;
-import net.sf.taverna.t2.workbench.edits.EditManager;
-import net.sf.taverna.t2.workbench.file.FileManager;
-
-public class BiomobyActivityParserMenuAction extends
- AbstractConfigureActivityMenuAction<BiomobyActivity> {
-
- private static final String ADD_BIOMOBY_PARSER = "Add Biomoby parser";
-
- private EditManager editManager;
-
- private FileManager fileManager;
-
- public BiomobyActivityParserMenuAction() {
- super(BiomobyActivity.class);
- }
-
- @Override
- protected Action createAction() {
- MobyParserAction configAction = new MobyParserAction(
- findActivity(), getParentFrame(), editManager, fileManager);
- configAction.putValue(Action.NAME, ADD_BIOMOBY_PARSER);
- addMenuDots(configAction);
- return configAction;
- }
-
- public void setEditManager(EditManager editManager) {
- this.editManager = editManager;
- }
-
- public void setFileManager(FileManager fileManager) {
- this.fileManager = fileManager;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/menu/ConfigureBiomobyMenuAction.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/menu/ConfigureBiomobyMenuAction.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/menu/ConfigureBiomobyMenuAction.java
deleted file mode 100644
index b86df2a..0000000
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/menu/ConfigureBiomobyMenuAction.java
+++ /dev/null
@@ -1,52 +0,0 @@
-package net.sf.taverna.t2.activities.biomoby.menu;
-
-import javax.swing.Action;
-
-import net.sf.taverna.t2.activities.biomoby.BiomobyActivity;
-import net.sf.taverna.t2.activities.biomoby.actions.BiomobyActivityConfigurationAction;
-import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
-import net.sf.taverna.t2.workbench.activitytools.AbstractConfigureActivityMenuAction;
-import net.sf.taverna.t2.workbench.edits.EditManager;
-import net.sf.taverna.t2.workbench.file.FileManager;
-
-public class ConfigureBiomobyMenuAction extends
- AbstractConfigureActivityMenuAction<BiomobyActivity> {
-
- private EditManager editManager;
- private FileManager fileManager;
- private ActivityIconManager activityIconManager;
-
- public ConfigureBiomobyMenuAction() {
- super(BiomobyActivity.class);
- }
-
- @Override
- protected Action createAction() {
- BiomobyActivity a = findActivity();
- Action result = null;
- result = new BiomobyActivityConfigurationAction(a, getParentFrame(), editManager,
- fileManager, activityIconManager);
- result.putValue(Action.NAME, "Configure");
- addMenuDots(result);
- return result;
- }
-
- public boolean isEnabled() {
- BiomobyActivity activity = findActivity();
- return (super.isEnabled() && (activity.getMobyService() != null) && activity
- .containsSecondaries());
- }
-
- public void setEditManager(EditManager editManager) {
- this.editManager = editManager;
- }
-
- public void setFileManager(FileManager fileManager) {
- this.fileManager = fileManager;
- }
-
- public void setActivityIconManager(ActivityIconManager activityIconManager) {
- this.activityIconManager = activityIconManager;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyActivityIcon.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyActivityIcon.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyActivityIcon.java
deleted file mode 100644
index 2c28c32..0000000
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyActivityIcon.java
+++ /dev/null
@@ -1,36 +0,0 @@
-/*******************************************************************************
- * This file is a component of the Taverna project, and is licensed under the
- * GNU LGPL. Copyright Edward Kawas, The BioMoby Project
- ******************************************************************************/
-package net.sf.taverna.t2.activities.biomoby.query;
-
-import javax.swing.Icon;
-import javax.swing.ImageIcon;
-
-import net.sf.taverna.t2.activities.biomoby.BiomobyActivity;
-import net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI;
-import net.sf.taverna.t2.workflowmodel.processor.activity.Activity;
-
-/**
- *
- * @author Alex Nenadic
- *
- */
-public class BiomobyActivityIcon implements ActivityIconSPI{
-
- public int canProvideIconScore(Activity<?> activity) {
- if (activity.getClass().getName().equals(BiomobyActivity.class.getName()))
- return DEFAULT_ICON + 1;
- else
- return NO_ICON;
- }
-
- public Icon getIcon(Activity<?> activity) {
- return getBiomobyIcon();
- }
-
- public static Icon getBiomobyIcon() {
- return new ImageIcon(BiomobyActivityIcon.class.getResource("/registry.gif"));
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyActivityItem.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyActivityItem.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyActivityItem.java
deleted file mode 100644
index a799280..0000000
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyActivityItem.java
+++ /dev/null
@@ -1,94 +0,0 @@
-/*******************************************************************************
- * This file is a component of the Taverna project, and is licensed under the
- * GNU LGPL. Copyright Edward Kawas, The BioMoby Project
- ******************************************************************************/
-package net.sf.taverna.t2.activities.biomoby.query;
-
-
-public class BiomobyActivityItem /*extends AbstractActivityItem */{
-
- String registryUrl;
- String serviceName;
- String authorityName;
- String registryUri;
- String category;
- String serviceType;
-
- public String getRegistryUri() {
- return registryUri;
- }
-
- public void setRegistryUri(String registryUri) {
- this.registryUri = registryUri;
- }
-
- public String getRegistryUrl() {
- return registryUrl;
- }
-
- public void setRegistryUrl(String registryUrl) {
- this.registryUrl = registryUrl;
- }
-
- public String getServiceName() {
- return serviceName;
- }
-
- public void setServiceName(String serviceName) {
- this.serviceName = serviceName;
- }
-
- public String getAuthorityName() {
- return authorityName;
- }
-
- public void setAuthorityName(String authorityName) {
- this.authorityName = authorityName;
- }
-
-// @Override
-// public Object getConfigBean() {
-// BiomobyActivityConfigurationBean bean = new BiomobyActivityConfigurationBean();
-// bean.setAuthorityName(getAuthorityName());
-// bean.setServiceName(getServiceName());
-// bean.setMobyEndpoint(getRegistryUrl());
-// return bean;
-// }
-//
-// @Override
-// public Icon getIcon() {
-// return BiomobyActivityIcon.getBiomobyIcon();
-// }
-//
-// @Override
-// public Activity<?> getUnconfiguredActivity() {
-// return new BiomobyActivity();
-// }
-
- public String getType() {
- return "Biomoby";
- }
-
- @Override
- public String toString() {
- return getServiceName();
- }
-
- public String getCategory() {
- return category;
- }
-
- public void setCategory(String category) {
- this.category = category;
- }
-
- public String getServiceType() {
- return serviceType;
- }
-
- public void setServiceType(String serviceType) {
- this.serviceType = serviceType;
- }
-
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyObjectActivityIcon.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyObjectActivityIcon.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyObjectActivityIcon.java
deleted file mode 100644
index f4575e4..0000000
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyObjectActivityIcon.java
+++ /dev/null
@@ -1,32 +0,0 @@
-/*******************************************************************************
- * This file is a component of the Taverna project, and is licensed under the
- * GNU LGPL. Copyright Edward Kawas, The BioMoby Project
- ******************************************************************************/
-package net.sf.taverna.t2.activities.biomoby.query;
-
-import javax.swing.Icon;
-import javax.swing.ImageIcon;
-
-import net.sf.taverna.t2.activities.biomoby.BiomobyObjectActivity;
-import net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI;
-import net.sf.taverna.t2.workflowmodel.processor.activity.Activity;
-
-/**
- *
- * @author Alex Nenadic
- *
- */
-public class BiomobyObjectActivityIcon implements ActivityIconSPI{
-
- public int canProvideIconScore(Activity<?> activity) {
- if (activity.getClass().getName().equals(BiomobyObjectActivity.class.getName()))
- return DEFAULT_ICON + 1;
- else
- return NO_ICON;
- }
-
- public Icon getIcon(Activity<?> activity) {
- return new ImageIcon(BiomobyObjectActivityIcon.class.getResource("/biomoby_object.png"));
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyObjectActivityItem.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyObjectActivityItem.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyObjectActivityItem.java
deleted file mode 100644
index 1e50d37..0000000
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyObjectActivityItem.java
+++ /dev/null
@@ -1,76 +0,0 @@
-/*******************************************************************************
- * This file is a component of the Taverna project, and is licensed under the
- * GNU LGPL. Copyright Edward Kawas, The BioMoby Project
- ******************************************************************************/
-package net.sf.taverna.t2.activities.biomoby.query;
-
-
-/**
- *
- * @author Alex Nenadic
- * @author Stuart Owen
- *
- */
-public class BiomobyObjectActivityItem /*extends AbstractActivityItem*/ {
-
- String registryUrl;
- String serviceName;
- String authorityName;
- String registryUri;
-
- public String getRegistryUri() {
- return registryUri;
- }
-
- public void setRegistryUri(String registryUri) {
- this.registryUri = registryUri;
- }
-
- public String getRegistryUrl() {
- return registryUrl;
- }
-
- public void setRegistryUrl(String registryUrl) {
- this.registryUrl = registryUrl;
- }
-
- public String getServiceName() {
- return serviceName;
- }
-
- public void setServiceName(String serviceName) {
- this.serviceName = serviceName;
- }
-
- public String getAuthorityName() {
- return authorityName;
- }
-
- public void setAuthorityName(String authorityName) {
- this.authorityName = authorityName;
- }
-
-// @Override
-// public Object getConfigBean() {
-// BiomobyObjectActivityConfigurationBean bean = new BiomobyObjectActivityConfigurationBean();
-// bean.setAuthorityName(getAuthorityName());
-// bean.setServiceName(getServiceName());
-// bean.setMobyEndpoint(getRegistryUrl());
-// return bean;
-// }
-//
-// @Override
-// public Icon getIcon() {
-// return new ImageIcon(BiomobyObjectActivityItem.class.getResource("/biomoby_object.png"));
-// }
-//
-// @Override
-// public Activity<?> getUnconfiguredActivity() {
-// return new BiomobyObjectActivity();
-// }
-
- public String getType() {
- return "Biomoby Object";
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyQueryHelper.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyQueryHelper.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyQueryHelper.java
deleted file mode 100644
index e22b78c..0000000
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/BiomobyQueryHelper.java
+++ /dev/null
@@ -1,270 +0,0 @@
-/*******************************************************************************
- * This file is a component of the Taverna project, and is licensed under the
- * GNU LGPL. Copyright Edward Kawas, The BioMoby Project
- ******************************************************************************/
-package net.sf.taverna.t2.activities.biomoby.query;
-
-import java.io.File;
-import java.io.InputStream;
-import java.net.URI;
-import java.util.ArrayList;
-import java.util.Comparator;
-import java.util.List;
-import java.util.SortedMap;
-import java.util.SortedSet;
-import java.util.TreeMap;
-import java.util.TreeSet;
-
-import javax.xml.parsers.DocumentBuilder;
-import javax.xml.parsers.DocumentBuilderFactory;
-
-import net.sf.taverna.raven.appconfig.ApplicationRuntime;
-import net.sf.taverna.t2.activities.biomoby.GetOntologyThread;
-import net.sf.taverna.t2.activities.biomoby.datatypedescriptions.BiomobyDatatypeDescription;
-import net.sf.taverna.t2.activities.biomoby.servicedescriptions.BiomobyServiceDescription;
-import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider.FindServiceDescriptionsCallBack;
-
-import org.apache.log4j.Logger;
-import org.biomoby.client.CentralDigestCachedImpl;
-import org.biomoby.client.CentralImpl;
-import org.biomoby.shared.MobyDataType;
-import org.biomoby.shared.MobyException;
-import org.biomoby.shared.MobyService;
-import org.w3c.dom.Document;
-
-public class BiomobyQueryHelper {
-
- private static Logger log = Logger.getLogger(BiomobyQueryHelper.class);
-
- private String registryNamespace;
- private String registryEndpoint;
-
- private CentralDigestCachedImpl central;
-
- private String DEFAULT_REGISTRY_ENDPOINT = CentralImpl.DEFAULT_ENDPOINT;
-
- private String DEFAULT_REGISTRY_NAMESPACE = CentralImpl.DEFAULT_NAMESPACE;
-
- private String remoteDatatypeRdfUrl = null;
-
- private String remoteServiceRdfUrl = null;
-
- private static final String CACHE_NAME = "moby-cache";
-
- private ApplicationRuntime applicationRuntime = ApplicationRuntime
- .getInstance();
-
- public BiomobyQueryHelper(String registryEndpoint, String registryNamespace)
- throws MobyException {
- try {
- if (registryNamespace != null)
- this.registryNamespace = registryNamespace;
- else
- this.registryNamespace = DEFAULT_REGISTRY_NAMESPACE;
- if (registryEndpoint != null)
- this.registryEndpoint = registryEndpoint;
- else
- this.registryEndpoint = DEFAULT_REGISTRY_ENDPOINT;
- String tavernaHome = null;
- if (applicationRuntime.getApplicationHomeDir() != null) {
- tavernaHome = applicationRuntime.getApplicationHomeDir()
- .getAbsolutePath();
- }
- String cacheLoc = tavernaHome;
- if (cacheLoc == null || cacheLoc.trim().length() == 0)
- cacheLoc = "";
- if (!cacheLoc.endsWith(System.getProperty("file.separator")))
- cacheLoc += File.separator;
-
- central = new CentralDigestCachedImpl(this.registryEndpoint,
- this.registryNamespace, cacheLoc + CACHE_NAME);
-
- } catch (MobyException e) {
- //
- log.warn("There was a problem in initializing the caching agent, therefor caching is disabled.",
- e);
- }
- // now we try to speed up the loading of the datatypes ontology
- try {
- new GetOntologyThread(central.getRegistryEndpoint()).start();
- } catch (Exception e) {
- /* don't care if an exception occurs here ... */
- }
- // just call this to ensure that the registry is valid
- // throws exception if it isnt
- central.getResourceRefs();
- }
-
- /**
- *
- * @return an ArrayList of BiomobyActivityItem
- * @throws MobyException
- * if something goes wrong
- */
- public synchronized ArrayList<BiomobyActivityItem> getServices()
- throws MobyException {
- central.updateCache(CentralDigestCachedImpl.CACHE_PART_SERVICES);
- MobyService[] services = central.getServices();
- SortedMap<String, SortedSet<MobyService>> map = new TreeMap<String, SortedSet<MobyService>>();
- for (MobyService service : services) {
- String authority = service.getAuthority();
- SortedSet<MobyService> set;
- if (map.containsKey(authority)) {
- set = map.remove(authority);
- set.add(service);
- map.put(authority, set);
- } else {
- set = new TreeSet<MobyService>(new Comparator<MobyService>() {
- public int compare(MobyService o1, MobyService o2) {
- return o1.getName().compareTo(o2.getName());
- }
- });
- set.add(service);
- map.put(authority, set);
- }
- }
- ArrayList<BiomobyActivityItem> authorityList = new ArrayList<BiomobyActivityItem>();
- for (String authority_name : map.keySet()) {
- for (MobyService service : map.get(authority_name)) {
- String serviceName = service.getName();
- // if (service.getStatus() != MobyService.UNCHECKED) {
- // f.setAlive((service.getStatus() & MobyService.ALIVE) == 2);
- // }
- BiomobyActivityItem item = makeActivityItem(registryEndpoint,
- registryNamespace, authority_name, serviceName);
- item.setCategory(service.getCategory());
- item.setServiceType(service.getServiceType() == null ? "Service"
- : service.getServiceType().getName());
- authorityList.add(item);
- }
- }
- return authorityList;
-
- }
-
- private BiomobyActivityItem makeActivityItem(String url, String uri,
- String authorityName, String serviceName) {
- BiomobyActivityItem item = new BiomobyActivityItem();
- item.setAuthorityName(authorityName);
- item.setServiceName(serviceName);
- item.setRegistryUrl(url);
- item.setRegistryUri(uri);
- return item;
- }
-
- public String getRemoteDatatypeRdfUrl() {
- return remoteDatatypeRdfUrl;
- }
-
- public String getRemoteServiceRdfUrl() {
- return remoteServiceRdfUrl;
- }
-
- public static Document loadDocument(InputStream input) throws MobyException {
- try {
- DocumentBuilderFactory dbf = (DocumentBuilderFactory) DOCUMENT_BUILDER_FACTORIES
- .get();
- DocumentBuilder db = dbf.newDocumentBuilder();
- return (db.parse(input));
- } catch (Exception e) {
- throw new MobyException("Problem with reading XML input: "
- + e.toString(), e);
- }
- }
-
- public static ThreadLocal<DocumentBuilderFactory> DOCUMENT_BUILDER_FACTORIES = new ThreadLocal<DocumentBuilderFactory>() {
- protected synchronized DocumentBuilderFactory initialValue() {
- DocumentBuilderFactory dbf = DocumentBuilderFactory.newInstance();
- dbf.setNamespaceAware(true);
- return dbf;
- }
- };
-
- public void findServiceDescriptionsAsync(
- FindServiceDescriptionsCallBack callBack) {
- try {
- central.updateCache(CentralDigestCachedImpl.CACHE_PART_SERVICES);
- } catch (MobyException ex) {
- callBack.fail("Can't update the Biomoby cache", ex);
- return;
- }
- MobyService[] services;
- try {
- services = central.getServices();
- } catch (MobyException ex) {
- callBack.fail("Can't get BioMoby services", ex);
- return;
- }
- List<BiomobyServiceDescription> serviceDescriptions = new ArrayList<BiomobyServiceDescription>();
- for (MobyService service : services) {
- BiomobyServiceDescription serviceDesc = new BiomobyServiceDescription();
- serviceDesc.setEndpoint(URI.create(registryEndpoint));
- serviceDesc.setNamespace(URI.create(registryNamespace));
- serviceDesc.setAuthorityName(service.getAuthority());
- serviceDesc.setServiceName(service.getName());
- serviceDesc.setCategory(service.getCategory());
- serviceDesc.setDescription(service.getDescription());
- String lsid = service.getLSID();
- if (lsid != null && lsid.length() > 0) {
- serviceDesc.setLSID(URI.create(lsid));
- }
- serviceDesc.setEmailContact(service.getEmailContact());
- serviceDesc.setServiceType(service.getServiceType() == null ? "Service"
- : service.getServiceType().getName());
- String signatureURL = service.getSignatureURL();
- if (signatureURL != null && signatureURL.length() > 0) {
- serviceDesc.setSignatureURI(URI.create(signatureURL));
- }
- serviceDescriptions.add(serviceDesc);
- }
- callBack.partialResults(serviceDescriptions);
- callBack.partialResults(findDatatypeDescriptions());
- callBack.finished();
- }
-
- public List<BiomobyDatatypeDescription> findDatatypeDescriptions() {
- try {
- central.updateCache(CentralDigestCachedImpl.CACHE_PART_DATATYPES);
- } catch (MobyException ex) {
-
- return new ArrayList<BiomobyDatatypeDescription>();
- }
- MobyDataType[] datatypes;
- try {
- datatypes = central.getDataTypes();
- } catch (MobyException ex) {
-
- return new ArrayList<BiomobyDatatypeDescription>();
- }
- List<BiomobyDatatypeDescription> datatypeDescriptions = new ArrayList<BiomobyDatatypeDescription>();
- for (MobyDataType datatype : datatypes) {
- BiomobyDatatypeDescription dataDesc = new BiomobyDatatypeDescription();
- dataDesc.setAuthorityName(datatype.getAuthority());
- dataDesc.setDatatypeName(datatype.getName());
- dataDesc.setEmailContact(datatype.getEmailContact());
- dataDesc.setEndpoint(URI.create(registryEndpoint));
- dataDesc.setNamespace(URI.create(registryNamespace));
- dataDesc.setParent(datatype.getParentName());
- dataDesc.setDescription(datatype.getDescription());
- String lsid = datatype.getLSID();
- if (lsid != null && lsid.length() > 0) {
- try {
- dataDesc.setLsid(URI.create(lsid));
- } catch (Exception e) {
-
- }
- }
- ArrayList<String> lineage = new ArrayList<String>();
- if (datatype.getParent() == null && !datatype.getName().equals("Object")) {
- lineage.add("Object");
- lineage.add(datatype.getName());
- } else
- for (MobyDataType d : datatype.getLineage())
- if (!d.getName().equals(datatype.getName()))
- lineage.add(d.getName());
- dataDesc.setLineage(lineage.toArray(new String[]{}));
- datatypeDescriptions.add(dataDesc);
- }
- return datatypeDescriptions;
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/CacheImpl.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/CacheImpl.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/CacheImpl.java
deleted file mode 100644
index 37d677e..0000000
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/query/CacheImpl.java
+++ /dev/null
@@ -1,568 +0,0 @@
-/*******************************************************************************
- * This file is a component of the Taverna project, and is licensed under the
- * GNU LGPL. Copyright Edward Kawas, The BioMoby Project
- ******************************************************************************/
-/*
- * This file is a component of the Taverna project,
- * and is licensed under the GNU LGPL.
- * Copyright Edward Kawas, Martin Senger, The BioMoby Project
- */
-
-package net.sf.taverna.t2.activities.biomoby.query;
-
-import java.io.BufferedOutputStream;
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileOutputStream;
-import java.io.FileReader;
-import java.io.IOException;
-import java.io.InputStreamReader;
-import java.io.PrintWriter;
-import java.net.ConnectException;
-import java.net.HttpURLConnection;
-import java.net.URL;
-import java.util.Comparator;
-
-import org.apache.log4j.Logger;
-import org.biomoby.shared.MobyException;
-
-/**
- * An implementation of {@link org.biomoby.shared.CentralAll}, allowing to
- * cache locally results of the cumulative methods so it does not need to access
- * Moby registry all the time. The other methods of the Central interface do not
- * use the results of the cached cumulative results (their implementation is
- * just passed to the parent class).
- * <p>
- *
- * The caching is done in the file system, not in memory, so the results are
- * permanent (until someone removes the caching directory, or calls
- * {@link #removeFromCache}).
- * <p>
- *
- * This class can be used also without caching - just instantiate it with
- * 'cacheDir' set to null in the constructor.
- * <p>
- *
- * @author <A HREF="mailto:martin.senger@gmail.com">Martin Senger</A>
- * @version $Id: CacheImpl.java,v 1.2 2008/09/04 13:42:16 sowen70 Exp $
- */
-
-public class CacheImpl {
-
- private static Logger log = Logger.getLogger(CacheImpl.class);
-
- // filename for a list of cached entities
- protected static final String LIST_FILE = "__L__S__I__D__S__";
-
- /** An ID used in {@link #removeFromCache} indicating data types part. */
- public static final String CACHE_PART_DATATYPES = "c1";
-
- /** An ID used in {@link #removeFromCache} indicating services part. */
- public static final String CACHE_PART_SERVICES = "c2";
-
- public static final String CACHE_PROP_NAME = "cache-name";
-
- public static final String CACHE_PROP_COUNT = "cache-count";
-
- public static final String CACHE_PROP_OLDEST = "cache-oldest";
-
- public static final String CACHE_PROP_YOUNGEST = "cache-youngest";
-
- public static final String CACHE_PROP_SIZE = "cache-size";
-
- public static final String CACHE_PROP_LOCATION = "cache-loc";
-
- // DEFAULT registry
- private String MOBYCENTRAL_REGISTRY_URL = "http://moby.ucalgary.ca/moby/MOBY-Central.pl";
-
- // Default Endpoint
- private String MOBYCENTRAL_REGISTRY_URI = "http://moby.ucalgary.ca/MOBY/Central";
-
- // cache location
- private String cacheDir; // as defined in the constructor
-
- protected File dataTypesCache;
-
- protected File servicesCache;
-
- public static final String SERVICE_INSTANCE_FILENAME = "SERVICE_INSTANCE.rdf";
-
- private String serviceInstanceRDFLocation = SERVICE_INSTANCE_FILENAME;
-
- public static final String DATATYPE_FILENAME = "DATATYPES.rdf";
-
- private String datatypeRDFLocation = DATATYPE_FILENAME;
-
- // for optimalization
- private String fileSeparator;
-
- /***************************************************************************
- * Create an instance that will access a default Moby registry and will
- * cache results in the 'cacheDir' directory.
- * <p>
- **************************************************************************/
- public CacheImpl(String cacheDir) throws MobyException {
- this(null, null, cacheDir);
- }
-
- /***************************************************************************
- * Create an instance that will access a Moby registry defined by its
- * 'endpoint' and 'namespace', and will cache results in the 'cacheDir'
- * directory. Note that the same 'cacheDir' can be safely used for more Moby
- * registries.
- * <p>
- **************************************************************************/
- public CacheImpl(String endpoint, String namespace, String cacheDir)
- throws MobyException {
- if (endpoint != null && !endpoint.trim().equals(""))
- this.MOBYCENTRAL_REGISTRY_URL = endpoint;
- if (namespace != null && !namespace.trim().equals(""))
- this.MOBYCENTRAL_REGISTRY_URI = namespace;
- fileSeparator = System.getProperty("file.separator");
- this.cacheDir = cacheDir;
- initCache();
- }
-
- // it makes all necessary directories for cache given in the
- // constructor (which is now in global 'cacheDir'); it is
- // separated here because it can be called either from the
- // constructor, or everytime a cache is going to be used but it is
- // not there (somebody removed it)
- protected void initCache() throws MobyException {
- if (cacheDir != null) {
- File cache = createCacheDir(cacheDir, MOBYCENTRAL_REGISTRY_URL);
- dataTypesCache = createSubCacheDir(cache, "datatype_rdf");
- servicesCache = createSubCacheDir(cache, "service_rdf");
- serviceInstanceRDFLocation = servicesCache.getPath()
- + fileSeparator + SERVICE_INSTANCE_FILENAME;
- datatypeRDFLocation = dataTypesCache.getPath() + fileSeparator
- + DATATYPE_FILENAME;
- }
- }
-
- /***************************************************************************
- * Return a directory name representing the current cache. This is the same
- * name as given in constructors.
- * <p>
- *
- * @return current cache directory name
- **************************************************************************/
- public String getCacheDir() {
- return cacheDir;
- }
-
- /***************************************************************************
- * Removes object groups from the cache. If 'id' is null it removes the
- * whole cache (for that Moby registry this instance was initiated for).
- * Otherwise 'id' indicates which part of the cache that will be removed.
- * <p>
- *
- * @param id
- * should be either null, or one of the following:
- * {@link #CACHE_PART_DATATYPES}, {@link #CACHE_PART_SERVICES},
- * {@link #CACHE_PART_SERVICETYPES}, and {@link
- * #CACHE_PART_NAMESPACES}.
- **************************************************************************/
- public void removeFromCache(String id) {
- try {
- if (cacheDir != null) {
- String[] parts = null;
- if (id == null)
- parts = new String[] { "datatype_rdf", "service_rdf" };
- else if (id.equals(CACHE_PART_SERVICES))
- parts = new String[] { "service_rdf" };
- else if (id.equals(CACHE_PART_DATATYPES))
- parts = new String[] { "datatype_rdf" };
- if (parts != null) {
- removeCacheDir(cacheDir, MOBYCENTRAL_REGISTRY_URL, parts);
- }
- }
- } catch (MobyException e) {
- log.error("Removing cache failed: " + e.getMessage());
- }
- }
-
- /**
- * Create a cache directory from 'cacheDirectory' and 'registryId' if it
- * does not exist yet. Make sure that it is writable. Return a File
- * representing created directory.
- *
- * 'registryId' (which may be null) denotes what registry this cache is
- * going to be created for. If null, an endpoint of a default Moby registry
- * is used.
- */
- protected File createCacheDir(String cacheDirectory, String registryId)
- throws MobyException {
- if (registryId == null || registryId.equals(""))
- registryId = MOBYCENTRAL_REGISTRY_URL;
- File cache = new File(cacheDirectory + fileSeparator
- + clean(registryId));
- try {
- if (!cache.exists())
- if (!cache.mkdirs())
- throw new MobyException("Cannot create '"
- + cache.getAbsolutePath() + "'.");
- if (!cache.isDirectory())
- throw new MobyException("Cache location '"
- + cache.getAbsolutePath()
- + "' exists but it is not a directory.");
- if (!cache.canWrite())
- throw new MobyException("Cache location '"
- + cache.getAbsolutePath() + "' is not writable for me.");
- return cache;
- } catch (SecurityException e) {
- throw new MobyException("Cannot handle cache location '"
- + cache.getAbsolutePath() + "'. " + e.toString());
- }
- }
-
- /**
- * Remove cache and all (but given in 'subCacheDirNames') its
- * subdirectories.
- */
- protected void removeCacheDir(String cacheDirectory, String registryId,
- String[] subCacheDirNames) throws MobyException {
- if (registryId == null || registryId.equals(""))
- registryId = MOBYCENTRAL_REGISTRY_URL;
- File cache = new File(cacheDirectory + fileSeparator
- + clean(registryId));
- try {
- if (!cache.exists())
- return;
- if (!cache.isDirectory())
- throw new MobyException("Cache location '"
- + cache.getAbsolutePath()
- + "' exists but it is not a directory.");
- if (!cache.canWrite())
- throw new MobyException("Cache location '"
- + cache.getAbsolutePath() + "' is not writable for me.");
- for (int i = 0; i < subCacheDirNames.length; i++) {
- File cacheSubDir = new File(cache.getAbsolutePath()
- + fileSeparator + clean(subCacheDirNames[i]));
- File[] files = cacheSubDir.listFiles();
- for (int f = 0; f < files.length; f++) {
- if (files[f].isDirectory())
- throw new MobyException("Found a directory '"
- + files[f].getAbsolutePath()
- + "' where no directory should be");
- if (!files[f].delete())
- log.error("Can't delete file '" + files[f] + "'.");
- }
- cacheSubDir.delete();
- }
- cache.delete();
-
- } catch (SecurityException e) {
- throw new MobyException("Cannot handle cache location '"
- + cache.getAbsolutePath() + "'. " + e.toString());
- }
- }
-
- //
- protected File createSubCacheDir(File mainCache, String subCacheDirName)
- throws MobyException {
- File cache = new File(mainCache.getAbsolutePath() + fileSeparator
- + clean(subCacheDirName));
- try {
- if (!cache.exists())
- if (!cache.mkdirs())
- throw new MobyException("Cannot create '"
- + cache.getAbsolutePath() + "'.");
- return cache;
- } catch (SecurityException e) {
- throw new MobyException("Cannot handle cache location '"
- + cache.getAbsolutePath() + "'. " + e.toString());
- }
- }
-
- /***************************************************************************
- * Replace non digit/letter characters in 'toBeCleaned' by their numeric
- * value. If there are more such numeric values side by side, put a dot
- * between them. Return the cleaned string.
- **************************************************************************/
- protected static String clean(String toBeCleaned) {
-
- char[] chars = toBeCleaned.toCharArray();
- int len = chars.length;
- int i = -1;
- while (++i < len) {
- char c = chars[i];
- if (!Character.isLetterOrDigit(c) && c != '_')
- break;
- }
- if (i < len) {
- StringBuffer buf = new StringBuffer(len * 2);
- for (int j = 0; j < i; j++) {
- buf.append(chars[j]);
- }
- boolean lastOneWasDigitalized = false;
- while (i < len) {
- char c = chars[i];
- if (Character.isLetterOrDigit(c) || c == '_') {
- buf.append(c);
- lastOneWasDigitalized = false;
- } else {
- if (lastOneWasDigitalized)
- buf.append('.');
- buf.append((int) c);
- lastOneWasDigitalized = true;
- }
- i++;
- }
- return new String(buf);
- }
- return toBeCleaned;
- }
-
- // create a file and put into it data to be cached
- protected static void store(File cache, String name, String data)
- throws MobyException {
- // File outputFile = new File (cache.getAbsolutePath() + fileSeparator +
- // clean (name));
- File outputFile = new File(cache.getAbsolutePath()
- + System.getProperty("file.separator") + name);
- try {
- PrintWriter fileout = new PrintWriter(new BufferedOutputStream(
- new FileOutputStream(outputFile)));
- fileout.write(data);
- fileout.close();
- } catch (IOException e) {
- throw new MobyException("Cannot write to '"
- + outputFile.getAbsolutePath() + ". " + e.toString());
- }
- }
-
- // create a file from a url
- protected void storeURL(File cache, String name, String url)
- throws MobyException {
- File outputFile = new File(cache.getAbsolutePath() + fileSeparator
- + name);
- try {
- StringBuffer sb = new StringBuffer();
- String newline = System.getProperty("line.separator");
- HttpURLConnection urlConnection = null;
-
- URL rdf_url = new URL(url);
- urlConnection = (HttpURLConnection) rdf_url.openConnection();
- urlConnection.setDefaultUseCaches(false);
- urlConnection.setUseCaches(false);
- urlConnection.setRequestProperty ( "User-agent", "Taverna_BioMOBY/1.5");
- urlConnection.setConnectTimeout(1000*60*5);
-
- BufferedReader in = new BufferedReader(new InputStreamReader(
- urlConnection.getInputStream()));
- String inputLine;
- while ((inputLine = in.readLine()) != null)
- sb.append(inputLine + newline);
- in.close();
-
- PrintWriter fileout = new PrintWriter(new BufferedOutputStream(
- new FileOutputStream(outputFile)));
- fileout.write(sb.toString());
- fileout.close();
- } catch (ConnectException e) {
- throw new MobyException("Cannot read from url '"
- + url + "'. " + e.toString());
- } catch (IOException e) {
- throw new MobyException("Cannot write to '"
- + outputFile.getAbsolutePath() + "'. " + e.toString());
- } catch (Exception e) {
- throw new MobyException("Unexpected Exception caught: " + e.toString());
- }
- }
-
- // remove a file from a cache
- protected void remove(File cache, String name) {
- File file = new File(cache, name);
- // do not throw here an exception because a missing file
- // can be a legitimate status (e.g. for LIST_FILE when we
- // are updating)
- file.delete();
- }
-
- /***************************************************************************
- * Read a cached file
- **************************************************************************/
- protected static String load(File file) throws MobyException {
- try {
- StringBuffer buf = new StringBuffer();
- BufferedReader in = new BufferedReader(new FileReader(file));
- char[] buffer = new char[1024];
- int charsRead;
-
- while ((charsRead = in.read(buffer, 0, 1024)) != -1) {
- buf.append(buffer, 0, charsRead);
- }
-
- return new String(buf);
-
- } catch (Throwable e) { // be prepare for "out-of-memory" error
- throw new MobyException("Serious error when reading from cache. "
- + e.toString());
-
- }
- }
-
- /***************************************************************************
- * Is the given cache empty (meaning: cache directory does not exist, is
- * empty, or contains only files to be ignored)?
- **************************************************************************/
- protected boolean isCacheEmpty(File cache) throws MobyException {
- if (cache == null)
- return true;
- String[] list = cache.list();
- if (list == null || list.length == 0)
- return true;
- for (int i = 0; i < list.length; i++) {
- if (!ignoredForEmptiness(new File(list[i])))
- return false;
- }
- return true;
- }
-
- /***************************************************************************
- * A LIST_FILE is a TOC of a cache object (each cache part has its own
- * LIST_FILE). Read it and return it. If it does not exist, return null.
- **************************************************************************/
- protected static String getListFile(File cache) throws MobyException {
- File listFile = new File(cache, LIST_FILE);
- if (!listFile.exists())
- return null;
- return load(listFile);
- }
-
- /***************************************************************************
- * A LIST_FILE is a TOC of a cache object (each cache part has its own
- * LIST_FILE). Read it and return it. If it does not exist, return null.
- **************************************************************************/
- protected static void storeListFile(File cache, String data)
- throws MobyException {
- CacheImpl.store(cache, LIST_FILE, data);
- }
-
- /***************************************************************************
- * Return a comparator for Files that compares in case-insensitive way.
- **************************************************************************/
- protected static Comparator getFileComparator() {
- return new Comparator() {
- public int compare(Object o1, Object o2) {
- return o1.toString().compareToIgnoreCase(o2.toString());
- }
- };
- }
-
- /***************************************************************************
- * Some file (when being read from a cache directory) are ignored.
- **************************************************************************/
- protected static boolean ignored(File file) {
- String path = file.getPath();
- return path.endsWith("~") || path.endsWith(LIST_FILE);
- }
-
- /***************************************************************************
- * Some file (when a cache is being tested fir emptyness) are ignored.
- **************************************************************************/
- protected static boolean ignoredForEmptiness(File file) {
- String path = file.getPath();
- return path.endsWith("~");
- }
-
- /***************************************************************************
- *
- **************************************************************************/
- protected static String MSG_CACHE_NOT_DIR(File cache) {
- return "Surprisingly, '" + cache.getAbsolutePath()
- + "' is not a directory. Strange...";
- }
-
- /***************************************************************************
- *
- **************************************************************************/
- protected static String MSG_CACHE_BAD_FILE(File file, Exception e) {
- return "Ignoring '" + file.getPath()
- + "'. It should not be in the cache directory:"
- + e.getMessage();
- }
-
- /***************************************************************************
- * Return age of the current (whole) cache in millis from the beginning of
- * the Epoch; or -1 if cache is empty, or the age is unknown.
- * <p>
- *
- * @return the cache age which is taken as the oldest (but filled) cache
- * part (part is considered e.g. 'services', or 'data types', not
- * their individual entities)
- **************************************************************************/
- public long getCacheAge() {
- try {
- long dataTypesCacheAge = (isCacheEmpty(dataTypesCache) ? Long.MAX_VALUE
- : dataTypesCache.lastModified());
- long servicesCacheAge = (isCacheEmpty(servicesCache) ? Long.MAX_VALUE
- : servicesCache.lastModified());
- long age = Math.min(dataTypesCacheAge, servicesCacheAge);
- return (age == Long.MAX_VALUE ? -1 : age);
- } catch (MobyException e) {
- return -1;
- }
- }
-
- /**
- * @return the serviceInstanceRDFLocation
- */
- public String getServiceInstanceRDFLocation() {
- return serviceInstanceRDFLocation;
- }
-
- /**
- * @param serviceInstanceRDFLocation
- * the serviceInstanceRDFLocation to set
- */
- public void setServiceInstanceRDFLocation(String serviceInstanceRDFLocation) {
- this.serviceInstanceRDFLocation = serviceInstanceRDFLocation;
- }
-
- /**
- * @return the mOBYCENTRAL_REGISTRY_URI
- */
- public String getMOBYCENTRAL_REGISTRY_URI() {
- return MOBYCENTRAL_REGISTRY_URI;
- }
-
- /**
- * @param mobycentral_registry_uri
- * the mOBYCENTRAL_REGISTRY_URI to set
- */
- public void setMOBYCENTRAL_REGISTRY_URI(String mobycentral_registry_uri) {
- MOBYCENTRAL_REGISTRY_URI = mobycentral_registry_uri;
- }
-
- /**
- * @return the MOBYCENTRAL_REGISTRY_URL
- */
- public String getMOBYCENTRAL_REGISTRY_URL() {
- return MOBYCENTRAL_REGISTRY_URL;
- }
-
- /**
- * @param mobycentral_registry_url
- * the MOBYCENTRAL_REGISTRY_URL to set
- */
- public void setMOBYCENTRAL_REGISTRY_URL(String mobycentral_registry_url) {
- MOBYCENTRAL_REGISTRY_URL = mobycentral_registry_url;
- }
-
- /**
- * @return the datatypeRDFLocation
- */
- public String getDatatypeRDFLocation() {
- return datatypeRDFLocation;
- }
-
- /**
- * @param datatypeRDFLocation the datatypeRDFLocation to set
- */
- public void setDatatypeRDFLocation(String datatypeRDFLocation) {
- this.datatypeRDFLocation = datatypeRDFLocation;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/servicedescriptions/BiomobyServiceDescription.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/servicedescriptions/BiomobyServiceDescription.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/servicedescriptions/BiomobyServiceDescription.java
deleted file mode 100644
index f327e96..0000000
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/servicedescriptions/BiomobyServiceDescription.java
+++ /dev/null
@@ -1,137 +0,0 @@
-package net.sf.taverna.t2.activities.biomoby.servicedescriptions;
-
-import java.net.URI;
-import java.util.Arrays;
-import java.util.List;
-
-import javax.swing.Icon;
-
-import net.sf.taverna.t2.activities.biomoby.BiomobyActivity;
-import net.sf.taverna.t2.activities.biomoby.BiomobyActivityConfigurationBean;
-import net.sf.taverna.t2.activities.biomoby.query.BiomobyActivityIcon;
-import net.sf.taverna.t2.servicedescriptions.ServiceDescription;
-import net.sf.taverna.t2.workflowmodel.processor.activity.Activity;
-
-public class BiomobyServiceDescription extends
- ServiceDescription<BiomobyActivityConfigurationBean> {
-
- private String authorityName;
- private String category;
- private String emailContact;
- private URI endpoint;
-
- private URI lsid;
-
- private URI namespace;
- private String serviceName;
- private String serviceType;
- private URI signatureURI;
-
- @Override
- public Class<? extends Activity<BiomobyActivityConfigurationBean>> getActivityClass() {
- return BiomobyActivity.class;
- }
-
- @Override
- public BiomobyActivityConfigurationBean getActivityConfiguration() {
- BiomobyActivityConfigurationBean bean = new BiomobyActivityConfigurationBean();
- bean.setAuthorityName(getAuthorityName());
- bean.setServiceName(getServiceName());
- bean.setMobyEndpoint(getEndpoint().toASCIIString());
- return bean;
- }
-
- public String getAuthorityName() {
- return authorityName;
- }
-
- public String getCategory() {
- return category;
- }
-
- public String getEmailContact() {
- return emailContact;
- }
-
- public URI getEndpoint() {
- return endpoint;
- }
-
- @Override
- public Icon getIcon() {
- return BiomobyActivityIcon.getBiomobyIcon();
- }
-
- public URI getLSID() {
- return lsid;
- }
-
- @Override
- public String getName() {
- return getServiceName();
- }
-
- public URI getNamespace() {
- return namespace;
- }
-
- @Override
- public List<String> getPath() {
- return Arrays.asList("Biomoby @ " + getEndpoint(), getServiceType(), getAuthorityName());
- }
-
- public String getServiceName() {
- return serviceName;
- }
-
- public String getServiceType() {
- return serviceType;
- }
-
- public URI getSignatureURI() {
- return signatureURI;
- }
-
- public void setAuthorityName(String authorityName) {
- this.authorityName = authorityName;
- }
-
- public void setCategory(String category) {
- this.category = category;
- }
-
- public void setEmailContact(String emailContact) {
- this.emailContact = emailContact;
- }
-
- public void setEndpoint(URI endpoint) {
- this.endpoint = endpoint;
- }
-
- public void setLSID(URI lsid) {
- this.lsid = lsid;
- }
-
- public void setNamespace(URI namespace) {
- this.namespace = namespace;
- }
-
- public void setServiceName(String serviceName) {
- this.serviceName = serviceName;
- }
-
- public void setServiceType(String serviceType) {
- this.serviceType = serviceType;
- }
-
- public void setSignatureURI(URI signatureURI) {
- this.signatureURI = signatureURI;
- }
-
- @Override
- protected List<Object> getIdentifyingData() {
- return Arrays.<Object>asList(getNamespace(), getEndpoint(), getAuthorityName(), getServiceName());
- }
-
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/servicedescriptions/BiomobyServiceProvider.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/servicedescriptions/BiomobyServiceProvider.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/servicedescriptions/BiomobyServiceProvider.java
deleted file mode 100644
index a80c5fb..0000000
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/servicedescriptions/BiomobyServiceProvider.java
+++ /dev/null
@@ -1,121 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.biomoby.servicedescriptions;
-
-import java.net.URI;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-
-import javax.swing.Icon;
-
-import net.sf.taverna.t2.activities.biomoby.query.BiomobyActivityIcon;
-import net.sf.taverna.t2.activities.biomoby.query.BiomobyQueryHelper;
-import net.sf.taverna.t2.activities.biomoby.ui.AddBiomobyDialogue;
-import net.sf.taverna.t2.servicedescriptions.AbstractConfigurableServiceProvider;
-import net.sf.taverna.t2.servicedescriptions.CustomizedConfigurePanelProvider;
-import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
-
-import org.biomoby.client.CentralImpl;
-import org.biomoby.shared.MobyException;
-
-public class BiomobyServiceProvider extends
- AbstractConfigurableServiceProvider<BiomobyServiceProviderConfig> implements
- CustomizedConfigurePanelProvider<BiomobyServiceProviderConfig> {
-
- private static final URI providerId = URI
- .create("http://taverna.sf.net/2010/service-provider/biomoby");
- private ServiceDescriptionRegistry serviceDescriptionRegistry;
-
- public BiomobyServiceProvider() {
- super(new BiomobyServiceProviderConfig());
- }
-
- public void findServiceDescriptionsAsync(FindServiceDescriptionsCallBack callBack) {
- try {
- // constructor throws exception if it cannot communicate
- // with the registry
- BiomobyQueryHelper helper = new BiomobyQueryHelper(getConfiguration().getEndpoint()
- .toASCIIString(), getConfiguration().getNamespace().toASCIIString());
- helper.findServiceDescriptionsAsync(callBack);
- } catch (MobyException ex) {
- callBack.fail("Could not connect to Biomoby endpoint "
- + getConfiguration().getEndpoint(), ex);
- }
- }
-
- @Override
- public List<BiomobyServiceProviderConfig> getDefaultConfigurations() {
-
- List<BiomobyServiceProviderConfig> defaults = new ArrayList<BiomobyServiceProviderConfig>();
-
- // If defaults have failed to load from a configuration file then load them here.
- if (!serviceDescriptionRegistry.isDefaultSystemConfigurableProvidersLoaded()) {
- defaults.add(new BiomobyServiceProviderConfig(CentralImpl.DEFAULT_ENDPOINT,
- CentralImpl.DEFAULT_NAMESPACE));
- } // else return an empty list
-
- return defaults;
- }
-
- public String getName() {
- return "Biomoby service";
- }
-
- public Icon getIcon() {
- return BiomobyActivityIcon.getBiomobyIcon();
- }
-
- @Override
- public String toString() {
- return getName() + " " + getConfiguration().getEndpoint();
- }
-
- @SuppressWarnings("serial")
- public void createCustomizedConfigurePanel(
- final CustomizedConfigureCallBack<BiomobyServiceProviderConfig> callBack) {
- AddBiomobyDialogue addBiomobyDialogue = new AddBiomobyDialogue() {
- @Override
- protected void addRegistry(String registryEndpoint, String registryURI) {
- BiomobyServiceProviderConfig providerConfig = new BiomobyServiceProviderConfig(
- registryEndpoint, registryURI);
- callBack.newProviderConfiguration(providerConfig);
- }
- };
- addBiomobyDialogue.setVisible(true);
- }
-
- @Override
- protected List<? extends Object> getIdentifyingData() {
- List<String> result;
- result = Arrays.asList(getConfiguration().getEndpoint().toString());
- return result;
- }
-
- public String getId() {
- return providerId.toString();
- }
-
- public void setServiceDescriptionRegistry(ServiceDescriptionRegistry serviceDescriptionRegistry) {
- this.serviceDescriptionRegistry = serviceDescriptionRegistry;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/servicedescriptions/BiomobyServiceProviderConfig.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/servicedescriptions/BiomobyServiceProviderConfig.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/servicedescriptions/BiomobyServiceProviderConfig.java
deleted file mode 100644
index 3f568c7..0000000
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/servicedescriptions/BiomobyServiceProviderConfig.java
+++ /dev/null
@@ -1,37 +0,0 @@
-package net.sf.taverna.t2.activities.biomoby.servicedescriptions;
-
-import java.net.URI;
-
-import net.sf.taverna.t2.lang.beans.PropertyAnnotated;
-
-public class BiomobyServiceProviderConfig extends PropertyAnnotated {
-
- private URI endpoint;
-
- private URI namespace;
-
- public BiomobyServiceProviderConfig() {
- }
-
- public BiomobyServiceProviderConfig(String endpoint, String namespace) {
- this.endpoint = URI.create(endpoint.trim());
- this.namespace = URI.create(namespace.trim());
- }
-
- public URI getEndpoint() {
- return endpoint;
- }
-
- public URI getNamespace() {
- return namespace;
- }
-
- public void setEndpoint(URI endpoint) {
- this.endpoint = endpoint;
- }
-
- public void setNamespace(URI namespace) {
- this.namespace = namespace;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/ui/AddBiomobyDialogue.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/ui/AddBiomobyDialogue.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/ui/AddBiomobyDialogue.java
deleted file mode 100644
index 99b82f9..0000000
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/ui/AddBiomobyDialogue.java
+++ /dev/null
@@ -1,94 +0,0 @@
-package net.sf.taverna.t2.activities.biomoby.ui;
-
-import java.awt.event.ActionEvent;
-
-import javax.swing.AbstractAction;
-import javax.swing.JButton;
-
-import net.sf.taverna.t2.activities.biomoby.actions.BiomobyScavengerDialog;
-import net.sf.taverna.t2.workbench.MainWindow;
-import net.sf.taverna.t2.workbench.helper.HelpEnabledDialog;
-
-import org.apache.log4j.Logger;
-import org.biomoby.client.CentralImpl;
-
-@SuppressWarnings("serial")
-public abstract class AddBiomobyDialogue extends HelpEnabledDialog {
-
- @SuppressWarnings("unused")
- private static Logger logger = Logger.getLogger(AddBiomobyDialogue.class);
-
- private String endpoint = CentralImpl.DEFAULT_ENDPOINT;
-
- private String uri = CentralImpl.DEFAULT_NAMESPACE;
-
- public AddBiomobyDialogue() {
- super(MainWindow.getMainWindow(), "Add BioMoby Registry", true, null);
- initialize();
- setLocationRelativeTo(getParent());
- }
- public void initialize() {
- final BiomobyScavengerDialog msp = new BiomobyScavengerDialog();
- getContentPane().add(msp);
- JButton accept = new JButton(new OKAction(msp));
- JButton cancel = new JButton(new CancelAction());
- msp.add(accept);
- msp.add(cancel);
- setResizable(false);
- getContentPane().add(msp);
- setLocationRelativeTo(null);
- pack();
- }
-
- protected abstract void addRegistry(String registryEndpoint,
- String registryURI);
-
- public class CancelAction extends AbstractAction {
- public CancelAction() {
- super("Cancel");
- }
-
- public void actionPerformed(ActionEvent ae2) {
- if (isVisible()) {
- setVisible(false);
- dispose();
- }
- }
- }
-
- public class OKAction extends AbstractAction {
- private final BiomobyScavengerDialog scavengerDialogue;
-
- private OKAction(BiomobyScavengerDialog msp) {
- super("OK");
- this.scavengerDialogue = msp;
- }
-
- public void actionPerformed(ActionEvent ae2) {
- if (isVisible()) {
- String registryEndpoint = "";
- String registryNamespace = "";
-
- if (scavengerDialogue.getRegistryEndpoint().equals("")) {
- registryEndpoint = endpoint;
- } else {
- registryEndpoint = scavengerDialogue.getRegistryEndpoint();
- }
-
- if (scavengerDialogue.getRegistryEndpoint().equals("")) {
- registryNamespace = uri;
- } else {
- registryNamespace = scavengerDialogue.getRegistryURI();
- }
-
- try {
- addRegistry(registryEndpoint.trim(), registryNamespace.trim());
- } finally {
- setVisible(false);
- dispose();
- }
- }
- }
- }
-
-}
[16/16] incubator-taverna-plugin-bioinformatics git commit:
temporarily empty repository
Posted by st...@apache.org.
temporarily empty repository
... as Software Grant is not yet formally on gfile
Project: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/repo
Commit: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/commit/e13e3b74
Tree: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/tree/e13e3b74
Diff: http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/diff/e13e3b74
Branch: refs/heads/master
Commit: e13e3b7419f7c67ddf3c3e4184a59686639484cd
Parents: 7936285
Author: Stian Soiland-Reyes <st...@apache.org>
Authored: Tue Feb 17 20:44:04 2015 +0000
Committer: Stian Soiland-Reyes <st...@apache.org>
Committed: Tue Feb 17 20:44:04 2015 +0000
----------------------------------------------------------------------
pom.xml | 41 -
taverna-biomart-activity-ui/pom.xml | 94 -
.../BiomartActivityConfigurationAction.java | 74 -
.../actions/BiomartConfigurationPanel.java | 134 -
.../menu/BiomartConfigurationMenuAction.java | 68 -
.../BiomartActivityIcon.java | 59 -
.../BiomartServiceDescription.java | 146 -
.../BiomartServiceProvider.java | 147 -
.../BiomartServiceProviderConfig.java | 36 -
.../views/BiomartActivityContextualView.java | 117 -
.../views/BiomartActivityViewFactory.java | 86 -
...rvicedescriptions.ServiceDescriptionProvider | 1 -
.../net.sf.taverna.t2.ui.menu.MenuComponent | 1 -
...a.t2.workbench.activityicons.ActivityIconSPI | 1 -
...ntextualviews.activity.ContextualViewFactory | 1 -
.../spring/biomart-activity-ui-context-osgi.xml | 30 -
.../spring/biomart-activity-ui-context.xml | 29 -
.../src/main/resources/biomart.png | Bin 3175 -> 0 bytes
.../TestBiomartActivityContextualView.java | 94 -
.../src/test/resources/biomart-query.xml | 24 -
taverna-biomart-activity/pom.xml | 77 -
.../t2/activities/biomart/BiomartActivity.java | 351 --
.../BiomartActivityConfigurationBean.java | 47 -
.../biomart/BiomartActivityFactory.java | 144 -
.../biomart/BiomartActivityHealthChecker.java | 76 -
...averna.t2.workflowmodel.health.HealthChecker | 1 -
.../spring/biomart-activity-context-osgi.xml | 15 -
.../spring/biomart-activity-context.xml | 13 -
.../src/main/resources/schema.json | 19 -
.../biomart/BiomartActivityFactoryTest.java | 65 -
.../src/test/resources/biomart-query.xml | 17 -
taverna-biomart-martservice/pom.xml | 105 -
.../org/biomart/martservice/DatasetLink.java | 220 --
.../org/biomart/martservice/MartDataset.java | 342 --
.../java/org/biomart/martservice/MartQuery.java | 436 ---
.../org/biomart/martservice/MartRegistry.java | 96 -
.../org/biomart/martservice/MartService.java | 709 ----
.../martservice/MartServiceException.java | 86 -
.../biomart/martservice/MartServiceUtils.java | 725 ----
.../martservice/MartServiceXMLHandler.java | 390 --
.../biomart/martservice/MartURLLocation.java | 422 ---
.../org/biomart/martservice/ResultReceiver.java | 61 -
.../martservice/ResultReceiverException.java | 85 -
.../config/QueryConfigController.java | 388 --
.../martservice/config/QueryConfigUtils.java | 598 ---
.../config/event/QueryComponentAdapter.java | 109 -
.../config/event/QueryComponentEvent.java | 120 -
.../config/event/QueryComponentListener.java | 104 -
.../config/ui/ConfigDisplayObject.java | 125 -
.../martservice/config/ui/ExpandableBox.java | 204 -
.../martservice/config/ui/MartServiceIcons.java | 104 -
.../ui/MartServiceQueryConfigUIFactory.java | 3543 ------------------
.../martservice/config/ui/MinimalLayout.java | 158 -
.../martservice/config/ui/QueryComponent.java | 342 --
.../config/ui/QueryConfigUIFactory.java | 345 --
.../biomart/martservice/query/Attribute.java | 198 -
.../org/biomart/martservice/query/Dataset.java | 309 --
.../org/biomart/martservice/query/Filter.java | 243 --
.../org/biomart/martservice/query/Link.java | 181 -
.../org/biomart/martservice/query/Query.java | 555 ---
.../martservice/query/QueryListener.java | 108 -
.../martservice/query/QueryXMLHandler.java | 332 --
.../biomart/martservice/config/ui/contract.gif | Bin 90 -> 0 bytes
.../biomart/martservice/config/ui/expand.gif | Bin 93 -> 0 bytes
.../martservice/config/ui/gene_schematic.gif | Bin 734 -> 0 bytes
.../config/ui/gene_schematic_3utr.gif | Bin 717 -> 0 bytes
.../config/ui/gene_schematic_5utr.gif | Bin 722 -> 0 bytes
.../config/ui/gene_schematic_cdna.gif | Bin 743 -> 0 bytes
.../config/ui/gene_schematic_coding.gif | Bin 760 -> 0 bytes
.../ui/gene_schematic_coding_gene_flank.gif | Bin 715 -> 0 bytes
.../gene_schematic_coding_transcript_flank.gif | Bin 765 -> 0 bytes
.../config/ui/gene_schematic_gene_exon.gif | Bin 504 -> 0 bytes
.../ui/gene_schematic_gene_exon_intron.gif | Bin 710 -> 0 bytes
.../config/ui/gene_schematic_gene_flank.gif | Bin 710 -> 0 bytes
.../config/ui/gene_schematic_peptide.gif | Bin 760 -> 0 bytes
.../ui/gene_schematic_transcript_exon.gif | Bin 920 -> 0 bytes
.../gene_schematic_transcript_exon_intron.gif | Bin 716 -> 0 bytes
.../ui/gene_schematic_transcript_flank.gif | Bin 751 -> 0 bytes
.../biomart/martservice/MartDatasetTest.java | 335 --
.../biomart/martservice/MartRegistryTest.java | 113 -
.../martservice/MartServiceUtilsTest.java | 65 -
.../martservice/MartServiceXMLHandlerTest.java | 218 --
.../martservice/MartURLLocationTest.java | 255 --
.../config/event/QueryComponentEventTest.java | 131 -
.../config/ui/MartServiceIconsTest.java | 77 -
.../martservice/query/AttributeTest.java | 164 -
.../biomart/martservice/query/DatasetTest.java | 308 --
.../biomart/martservice/query/FilterTest.java | 242 --
.../biomart/martservice/query/QueryTest.java | 303 --
taverna-biomoby-activity-ui/pom.xml | 86 -
.../biomoby/actions/AddParserActionHelper.java | 280 --
.../BioMobyObjectTreeCustomRenderer.java | 97 -
.../BioMobyServiceTreeCustomRenderer.java | 86 -
.../biomoby/actions/BiomobyActionHelper.java | 852 -----
.../BiomobyActivityConfigurationAction.java | 60 -
.../actions/BiomobyObjectActionHelper.java | 787 ----
.../biomoby/actions/BiomobyScavengerDialog.java | 136 -
.../actions/MobyObjectDetailsAction.java | 83 -
.../biomoby/actions/MobyObjectTreeNode.java | 50 -
.../activities/biomoby/actions/MobyPanel.java | 136 -
.../biomoby/actions/MobyParserAction.java | 70 -
.../actions/MobyServiceDetailsAction.java | 65 -
.../biomoby/actions/MobyServiceTreeNode.java | 42 -
.../activities/biomoby/actions/PopupThread.java | 34 -
.../biomoby/actions/SimpleActionFrame.java | 46 -
.../BiomobyDatatypeDescription.java | 143 -
.../edits/AddBiomobyCollectionDataTypeEdit.java | 60 -
.../edits/AddBiomobyConsumingServiceEdit.java | 236 --
.../biomoby/edits/AddBiomobyDataTypeEdit.java | 207 -
.../biomoby/edits/AddMobyParseDatatypeEdit.java | 220 --
.../biomoby/edits/AddUpstreamObjectEdit.java | 216 --
.../menu/BiomobyActivityDetailsMenuAction.java | 40 -
.../menu/BiomobyActivityParserMenuAction.java | 41 -
.../menu/ConfigureBiomobyMenuAction.java | 52 -
.../biomoby/query/BiomobyActivityIcon.java | 36 -
.../biomoby/query/BiomobyActivityItem.java | 94 -
.../query/BiomobyObjectActivityIcon.java | 32 -
.../query/BiomobyObjectActivityItem.java | 76 -
.../biomoby/query/BiomobyQueryHelper.java | 270 --
.../t2/activities/biomoby/query/CacheImpl.java | 568 ---
.../BiomobyServiceDescription.java | 137 -
.../BiomobyServiceProvider.java | 121 -
.../BiomobyServiceProviderConfig.java | 37 -
.../biomoby/ui/AddBiomobyDialogue.java | 94 -
.../biomoby/ui/BiomobyObjectTree.java | 635 ----
.../activities/biomoby/ui/DatatypeMenuItem.java | 196 -
.../view/BiomobyActivityContextualView.java | 106 -
.../BiomobyActivityContextualViewFactory.java | 50 -
.../biomoby/view/BiomobyConfigView.java | 108 -
.../BiomobyObjectActivityContextualView.java | 95 -
...mobyObjectActivityContextualViewFactory.java | 67 -
.../view/MobyParseDatatypeContextualView.java | 62 -
.../MobyParseDatatypeContextualViewFactory.java | 69 -
.../src/main/resources/Add24.gif | Bin 470 -> 0 bytes
.../src/main/resources/Cut24.gif | Bin 1193 -> 0 bytes
.../src/main/resources/Information24.gif | Bin 1328 -> 0 bytes
...averna.t2.partition.PartitionAlgorithmSetSPI | 1 -
...sf.taverna.t2.partition.PropertyExtractorSPI | 1 -
.../net.sf.taverna.t2.partition.QueryFactory | 1 -
...rvicedescriptions.ServiceDescriptionProvider | 1 -
.../net.sf.taverna.t2.ui.menu.MenuComponent | 5 -
...a.t2.workbench.activityicons.ActivityIconSPI | 2 -
...ntextualviews.activity.ContextualViewFactory | 3 -
.../spring/biomoby-activity-ui-context-osgi.xml | 28 -
.../spring/biomoby-activity-ui-context.xml | 42 -
.../src/main/resources/Search24.gif | Bin 820 -> 0 bytes
.../src/main/resources/authority.png | Bin 481 -> 0 bytes
.../src/main/resources/biomoby_object.png | Bin 981 -> 0 bytes
.../src/main/resources/collection.png | Bin 628 -> 0 bytes
.../src/main/resources/input.png | Bin 489 -> 0 bytes
.../src/main/resources/moby.png | Bin 981 -> 0 bytes
.../src/main/resources/moby_small.gif | Bin 787 -> 0 bytes
.../src/main/resources/output.png | Bin 511 -> 0 bytes
.../src/main/resources/parse.png | Bin 227 -> 0 bytes
.../src/main/resources/registry.gif | Bin 935 -> 0 bytes
.../src/main/resources/service.png | Bin 441 -> 0 bytes
.../view/BiomobyContextualViewFactoryTest.java | 49 -
taverna-biomoby-activity/pom.xml | 142 -
.../t2/activities/biomoby/BiomobyActivity.java | 1319 -------
.../BiomobyActivityConfigurationBean.java | 142 -
.../biomoby/BiomobyActivityFactory.java | 49 -
.../biomoby/BiomobyActivityHealthChecker.java | 45 -
.../t2/activities/biomoby/BiomobyCache.java | 78 -
.../biomoby/BiomobyObjectActivity.java | 545 ---
.../BiomobyObjectActivityConfigurationBean.java | 81 -
.../biomoby/BiomobyObjectActivityFactory.java | 49 -
.../BiomobyObjectActivityHealthChecker.java | 57 -
.../biomoby/ExecuteAsyncCgiService.java | 517 ---
.../biomoby/ExecuteAsyncMobyService.java | 695 ----
.../activities/biomoby/ExecuteCgiService.java | 70 -
.../activities/biomoby/ExecuteMobyService.java | 38 -
.../activities/biomoby/GetOntologyThread.java | 59 -
.../biomoby/MobyParseDatatypeActivity.java | 417 ---
...yParseDatatypeActivityConfigurationBean.java | 81 -
.../MobyParseDatatypeActivityFactory.java | 49 -
.../MobyParseDatatypeActivityHealthChecker.java | 58 -
.../t2/activities/biomoby/ParseMobyXML.java | 192 -
.../activities/biomoby/RetrieveWsdlThread.java | 57 -
.../t2/activities/biomoby/XMLUtilities.java | 1927 ----------
...averna.t2.workflowmodel.health.HealthChecker | 3 -
.../spring/biomoby-activity-context-osgi.xml | 17 -
.../spring/biomoby-activity-context.xml | 14 -
.../BiomobyActivityHealthCheckerTest.java | 45 -
.../BiomobyObjectActivityHealthCheckerTest.java | 45 -
...yParseDatatypeActivityHealthCheckerTest.java | 45 -
taverna-ncbi-activity-ui/pom.xml | 49 -
.../spring/ncbi-activity-ui-context-osgi.xml | 9 -
.../spring/ncbi-activity-ui-context.xml | 6 -
.../src/main/resources/ncbi_services | 0
.../src/main/resources/wsdl.png | Bin 748 -> 0 bytes
taverna-soaplab-activity-ui/pom.xml | 103 -
.../SoaplabActivityConfigurationAction.java | 68 -
.../actions/SoaplabConfigurationPanel.java | 183 -
.../ConfigureSoaplabActivityMenuAction.java | 54 -
.../MissingSoaplabException.java | 63 -
.../SoaplabActivityIcon.java | 60 -
.../servicedescriptions/SoaplabCategory.java | 80 -
.../SoaplabScavengerAgent.java | 144 -
.../SoaplabServiceDescription.java | 131 -
.../SoaplabServiceProvider.java | 183 -
.../SoaplabServiceProviderConfig.java | 38 -
.../views/SoaplabActivityContextualView.java | 156 -
.../views/SoaplabActivityViewFactory.java | 73 -
...rvicedescriptions.ServiceDescriptionProvider | 1 -
.../net.sf.taverna.t2.ui.menu.MenuComponent | 1 -
...a.t2.workbench.activityicons.ActivityIconSPI | 1 -
...ntextualviews.activity.ContextualViewFactory | 1 -
.../spring/soaplab-activity-ui-context-osgi.xml | 28 -
.../spring/soaplab-activity-ui-context.xml | 27 -
.../main/resources/analysis_metadata_2_html.xsl | 96 -
.../src/main/resources/soaplab.png | Bin 701 -> 0 bytes
.../TestSoaplabActivityContextualView.java | 61 -
taverna-soaplab-activity/pom.xml | 80 -
.../sf/taverna/t2/activities/soaplab/Soap.java | 82 -
.../t2/activities/soaplab/SoaplabActivity.java | 413 --
.../SoaplabActivityConfigurationBean.java | 119 -
.../soaplab/SoaplabActivityFactory.java | 216 --
.../soaplab/SoaplabActivityHealthChecker.java | 66 -
...averna.t2.workflowmodel.health.HealthChecker | 1 -
.../spring/soaplab-activity-context-osgi.xml | 15 -
.../spring/soaplab-activity-context.xml | 12 -
.../src/main/resources/schema.json | 40 -
.../SoaplabActivityConfigurationBeanTest.java | 92 -
.../activities/soaplab/SoaplabActivityTest.java | 127 -
224 files changed, 32788 deletions(-)
----------------------------------------------------------------------
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/pom.xml
----------------------------------------------------------------------
diff --git a/pom.xml b/pom.xml
deleted file mode 100644
index 5102f18..0000000
--- a/pom.xml
+++ /dev/null
@@ -1,41 +0,0 @@
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/xsd/maven-4.0.0.xsd">
- <modelVersion>4.0.0</modelVersion>
- <parent>
- <groupId>org.apache.taverna</groupId>
- <artifactId>taverna-parent</artifactId>
- <version>1-incubating-SNAPSHOT</version>
- </parent>
- <groupId>org.apache.taverna.bioinformatics</groupId>
- <artifactId>taverna-plugin-bioinformatics</artifactId>
- <version>3.1.0-incubating-SNAPSHOT</version>
- <packaging>pom</packaging>
- <name>Apache Taverna Plugin for Bioinformatics</name>
- <properties>
- <taverna.language.version>0.15.0-incubating-SNAPSHOT</taverna.language.version>
- <taverna.osgi.version>0.2.0-incubating-SNAPSHOT</taverna.osgi.version>
- <taverna.engine.version>3.1.0-incubating-SNAPSHOT</taverna.engine.version>
- <taverna.commonactivities.version>2.1.0-incubating-SNAPSHOT</taverna.commonactivities.version>
- </properties>
- <modules>
- <module>taverna-biomart-activity</module>
- <module>taverna-biomart-activity-ui</module>
- <module>taverna-biomart-martservice</module>
- <module>taverna-biomoby-activity</module>
- <module>taverna-biomoby-activity-ui</module>
- <module>taverna-ncbi-activity-ui</module>
- <module>taverna-soaplab-activity</module>
- <module>taverna-soaplab-activity-ui</module>
- </modules>
- <repositories>
- <repository>
- <id>taverna-incubating</id>
- <name>Apache Taverna incubating Repository</name>
- <url>http://repository.mygrid.org.uk/artifactory/incubator-snapshot-local/</url>
- <releases>
- <enabled>false</enabled>
- </releases>
- <snapshots />
- </repository>
- </repositories>
-</project>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-activity-ui/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-biomart-activity-ui/pom.xml b/taverna-biomart-activity-ui/pom.xml
deleted file mode 100644
index 8465101..0000000
--- a/taverna-biomart-activity-ui/pom.xml
+++ /dev/null
@@ -1,94 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
- <modelVersion>4.0.0</modelVersion>
- <parent>
- <groupId>net.sf.taverna</groupId>
- <artifactId>taverna-parent</artifactId>
- <version>3.0.1-SNAPSHOT</version>
- </parent>
- <groupId>net.sf.taverna.t2.ui-activities</groupId>
- <artifactId>biomart-activity-ui</artifactId>
- <version>2.0-SNAPSHOT</version>
- <packaging>bundle</packaging>
- <name>Taverna 2 Biomart Activity UI</name>
- <build>
- <plugins>
- <plugin>
- <groupId>org.apache.felix</groupId>
- <artifactId>maven-bundle-plugin</artifactId>
- <configuration>
- <instructions>
- <Import-Package>net.sf.taverna.t2.ui.menu,*</Import-Package>
- </instructions>
- </configuration>
- </plugin>
- </plugins>
- </build>
- <dependencies>
- <dependency>
- <groupId>net.sf.taverna.t2.activities</groupId>
- <artifactId>biomart-activity</artifactId>
- <version>${t2.activities.version}</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.ui-api</groupId>
- <artifactId>activity-icons-api</artifactId>
- <version>${t2.ui.api.version}</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.ui-api</groupId>
- <artifactId>activity-palette-api</artifactId>
- <version>${t2.ui.api.version}</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.ui-api</groupId>
- <artifactId>contextual-views-api</artifactId>
- <version>${t2.ui.api.version}</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.ui-api</groupId>
- <artifactId>activity-tools</artifactId>
- <version>${t2.ui.api.version}</version>
- </dependency>
- <dependency>
- <groupId>uk.org.taverna.configuration</groupId>
- <artifactId>taverna-app-configuration-api</artifactId>
- <version>${taverna.configuration.version}</version>
- </dependency>
-
- <dependency>
- <groupId>junit</groupId>
- <artifactId>junit</artifactId>
- <version>${junit.version}</version>
- <scope>test</scope>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.ui-impl</groupId>
- <artifactId>configuration-impl</artifactId>
- <version>${t2.ui.impl.version}</version>
- <scope>test</scope>
- </dependency>
- </dependencies>
- <repositories>
- <repository>
- <releases />
- <snapshots>
- <enabled>false</enabled>
- </snapshots>
- <id>mygrid-repository</id>
- <name>myGrid Repository</name>
- <url>http://www.mygrid.org.uk/maven/repository
- </url>
- </repository>
- <repository>
- <releases>
- <enabled>false</enabled>
- </releases>
- <snapshots />
- <id>mygrid-snapshot-repository</id>
- <name>myGrid Snapshot Repository</name>
- <url>http://www.mygrid.org.uk/maven/snapshot-repository</url>
- </repository>
- </repositories>
-</project>
-
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/actions/BiomartActivityConfigurationAction.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/actions/BiomartActivityConfigurationAction.java b/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/actions/BiomartActivityConfigurationAction.java
deleted file mode 100644
index a0b51e7..0000000
--- a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/actions/BiomartActivityConfigurationAction.java
+++ /dev/null
@@ -1,74 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.biomart.actions;
-
-import java.awt.Frame;
-import java.awt.event.ActionEvent;
-
-import javax.swing.Action;
-
-import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
-import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
-import net.sf.taverna.t2.workbench.edits.EditManager;
-import net.sf.taverna.t2.workbench.file.FileManager;
-import net.sf.taverna.t2.workbench.ui.actions.activity.ActivityConfigurationAction;
-import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ActivityConfigurationDialog;
-import uk.org.taverna.commons.services.ServiceRegistry;
-import uk.org.taverna.configuration.app.ApplicationConfiguration;
-import uk.org.taverna.scufl2.api.activity.Activity;
-
-@SuppressWarnings("serial")
-public class BiomartActivityConfigurationAction extends ActivityConfigurationAction {
-
- public static final String CONFIGURE_BIOMART = "Configure Biomart query";
- private final EditManager editManager;
- private final FileManager fileManager;
- private final ApplicationConfiguration applicationConfiguration;
- private final ServiceRegistry serviceRegistry;
-
- public BiomartActivityConfigurationAction(Activity activity, Frame owner,
- EditManager editManager, FileManager fileManager, ActivityIconManager activityIconManager,
- ApplicationConfiguration applicationConfiguration, ServiceDescriptionRegistry serviceDescriptionRegistry,
- ServiceRegistry serviceRegistry) {
- super(activity, activityIconManager, serviceDescriptionRegistry);
- this.editManager = editManager;
- this.fileManager = fileManager;
- this.applicationConfiguration = applicationConfiguration;
- this.serviceRegistry = serviceRegistry;
- putValue(Action.NAME, CONFIGURE_BIOMART);
- }
-
- public void actionPerformed(ActionEvent action) {
- ActivityConfigurationDialog currentDialog = ActivityConfigurationAction.getDialog(getActivity());
- if (currentDialog != null) {
- currentDialog.toFront();
- return;
- }
-
- final BiomartConfigurationPanel configurationPanel = new BiomartConfigurationPanel(
- getActivity(), applicationConfiguration, serviceRegistry);
- final ActivityConfigurationDialog dialog = new ActivityConfigurationDialog(
- getActivity(), configurationPanel, editManager);
-
- ActivityConfigurationAction.setDialog(getActivity(), dialog, fileManager);
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/actions/BiomartConfigurationPanel.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/actions/BiomartConfigurationPanel.java b/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/actions/BiomartConfigurationPanel.java
deleted file mode 100644
index 2b6f662..0000000
--- a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/actions/BiomartConfigurationPanel.java
+++ /dev/null
@@ -1,134 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.biomart.actions;
-
-import java.awt.Dimension;
-import java.io.File;
-import java.io.IOException;
-import java.io.StringReader;
-import java.net.URI;
-
-import javax.swing.Box;
-import javax.swing.BoxLayout;
-import javax.swing.JLabel;
-
-import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ActivityConfigurationPanel;
-
-import org.apache.log4j.Logger;
-import org.biomart.martservice.MartQuery;
-import org.biomart.martservice.MartService;
-import org.biomart.martservice.MartServiceException;
-import org.biomart.martservice.MartServiceXMLHandler;
-import org.biomart.martservice.config.QueryConfigController;
-import org.biomart.martservice.config.ui.MartServiceQueryConfigUIFactory;
-import org.biomart.martservice.config.ui.QueryConfigUIFactory;
-import org.jdom.Document;
-import org.jdom.Element;
-import org.jdom.JDOMException;
-import org.jdom.input.SAXBuilder;
-import org.jdom.output.XMLOutputter;
-
-import uk.org.taverna.commons.services.ServiceRegistry;
-import uk.org.taverna.configuration.app.ApplicationConfiguration;
-import uk.org.taverna.scufl2.api.activity.Activity;
-
-public class BiomartConfigurationPanel extends ActivityConfigurationPanel {
- private static Logger logger = Logger.getLogger(BiomartConfigurationPanel.class);
-
- private static final long serialVersionUID = 1884045346293327621L;
-
- public static final URI ACTIVITY_TYPE = URI.create("http://ns.taverna.org.uk/2010/activity/biomart");
-
- private String configurationString;
-
- private MartQuery biomartQuery;
-
- private static XMLOutputter outputter = new XMLOutputter();
-
- private final ApplicationConfiguration applicationConfiguration;
-
- private final ServiceRegistry serviceRegistry;
-
- public BiomartConfigurationPanel(Activity activity, ApplicationConfiguration applicationConfiguration,
- ServiceRegistry serviceRegistry) {
- super(activity);
- this.applicationConfiguration = applicationConfiguration;
- this.serviceRegistry = serviceRegistry;
- initialise();
- }
-
- protected void initialise() {
- super.initialise();
- removeAll();
-
- configurationString = getProperty("martQuery");
- Element martQuery = null;
- try {
- martQuery = new SAXBuilder().build(new StringReader(configurationString)).getRootElement();
- } catch (JDOMException | IOException e) {
- logger.warn(e);
- }
- setLayout(new BoxLayout(this,BoxLayout.Y_AXIS));
-
- biomartQuery = MartServiceXMLHandler.elementToMartQuery(martQuery, null);
- MartService service = biomartQuery.getMartService();
-
- File homeRoot=applicationConfiguration.getApplicationHomeDir();
- if (homeRoot==null) {
- logger.error("unable to determine application home for biomart cache");
- homeRoot=new File(System.getProperty("java.io.tmpdir"));
- }
- File cache=new File(homeRoot,"t2-biomart-activity");
- service.setCacheDirectory(new File(cache,"cache"));
- logger.info("Biomart is using cache directory:"+cache.getAbsolutePath());
-
- QueryConfigController controller = new QueryConfigController(biomartQuery);
- try {
- QueryConfigUIFactory queryConfigUIFactory = new MartServiceQueryConfigUIFactory(
- service, controller, biomartQuery.getMartDataset());
- add(queryConfigUIFactory.getDatasetConfigUI());
- add(Box.createGlue());
- } catch (MartServiceException e) {
- add(new JLabel("Error reading configuration properties"));
- add(new JLabel(e.getMessage()));
- add(Box.createGlue());
- }
- this.setPreferredSize(new Dimension(900,500));
- this.validate();
- }
-
- public Element getQuery() {
- return MartServiceXMLHandler.martQueryToElement(biomartQuery, null);
- }
-
- @Override
- public void noteConfiguration() {
- setProperty("martQuery", outputter.outputString(new Document(getQuery())));
- configureInputPorts(serviceRegistry);
- configureOutputPorts(serviceRegistry);
- }
-
- @Override
- public boolean checkValues() {
- // TODO Not yet done
- return true;
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/menu/BiomartConfigurationMenuAction.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/menu/BiomartConfigurationMenuAction.java b/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/menu/BiomartConfigurationMenuAction.java
deleted file mode 100644
index 775ce95..0000000
--- a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/menu/BiomartConfigurationMenuAction.java
+++ /dev/null
@@ -1,68 +0,0 @@
-package net.sf.taverna.t2.activities.biomart.menu;
-
-import java.net.URI;
-
-import javax.swing.Action;
-
-import net.sf.taverna.t2.activities.biomart.actions.BiomartActivityConfigurationAction;
-import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
-import net.sf.taverna.t2.ui.menu.ContextualMenuComponent;
-import net.sf.taverna.t2.ui.menu.MenuComponent;
-import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
-import net.sf.taverna.t2.workbench.activitytools.AbstractConfigureActivityMenuAction;
-import net.sf.taverna.t2.workbench.edits.EditManager;
-import net.sf.taverna.t2.workbench.file.FileManager;
-import uk.org.taverna.commons.services.ServiceRegistry;
-import uk.org.taverna.configuration.app.ApplicationConfiguration;
-
-public class BiomartConfigurationMenuAction extends AbstractConfigureActivityMenuAction implements
- MenuComponent, ContextualMenuComponent {
-
- private static final URI BIOMART_ACTIVITY = URI
- .create("http://ns.taverna.org.uk/2010/activity/biomart");
- private EditManager editManager;
- private FileManager fileManager;
- private ActivityIconManager activityIconManager;
- private ApplicationConfiguration applicationConfiguration;
- private ServiceDescriptionRegistry serviceDescriptionRegistry;
- private ServiceRegistry serviceRegistry;
-
- public BiomartConfigurationMenuAction() {
- super(BIOMART_ACTIVITY);
- }
-
- @Override
- protected Action createAction() {
- BiomartActivityConfigurationAction configAction = new BiomartActivityConfigurationAction(
- findActivity(), getParentFrame(), editManager, fileManager, activityIconManager,
- applicationConfiguration, serviceDescriptionRegistry, serviceRegistry);
- configAction.putValue(Action.NAME, BiomartActivityConfigurationAction.CONFIGURE_BIOMART);
- addMenuDots(configAction);
- return configAction;
- }
-
- public void setEditManager(EditManager editManager) {
- this.editManager = editManager;
- }
-
- public void setFileManager(FileManager fileManager) {
- this.fileManager = fileManager;
- }
-
- public void setActivityIconManager(ActivityIconManager activityIconManager) {
- this.activityIconManager = activityIconManager;
- }
-
- public void setApplicationConfiguration(ApplicationConfiguration applicationConfiguration) {
- this.applicationConfiguration = applicationConfiguration;
- }
-
- public void setServiceDescriptionRegistry(ServiceDescriptionRegistry serviceDescriptionRegistry) {
- this.serviceDescriptionRegistry = serviceDescriptionRegistry;
- }
-
- public void setServiceRegistry(ServiceRegistry serviceRegistry) {
- this.serviceRegistry = serviceRegistry;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartActivityIcon.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartActivityIcon.java b/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartActivityIcon.java
deleted file mode 100644
index 845665e..0000000
--- a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartActivityIcon.java
+++ /dev/null
@@ -1,59 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.biomart.servicedescriptions;
-
-import java.net.URI;
-
-import javax.swing.Icon;
-import javax.swing.ImageIcon;
-
-import net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI;
-
-/**
- *
- * @author Alex Nenadic
- * @author Alan R Williams
- *
- */
-public class BiomartActivityIcon implements ActivityIconSPI {
-
- private static final URI BIOMART_ACTIVITY = URI.create("http://ns.taverna.org.uk/2010/activity/biomart");
-
- static Icon icon = null;
-
- public int canProvideIconScore(URI activityType) {
- if (BIOMART_ACTIVITY.equals(activityType))
- return DEFAULT_ICON + 1;
- else
- return NO_ICON;
- }
-
- public Icon getIcon(URI activityType) {
- return getBiomartIcon();
- }
-
- public static Icon getBiomartIcon() {
- if (icon == null) {
- icon = new ImageIcon(BiomartActivityIcon.class.getResource("/biomart.png"));
- }
- return icon;
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartServiceDescription.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartServiceDescription.java b/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartServiceDescription.java
deleted file mode 100644
index ca50019..0000000
--- a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartServiceDescription.java
+++ /dev/null
@@ -1,146 +0,0 @@
-/* Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.biomart.servicedescriptions;
-
-import java.net.URI;
-import java.util.Arrays;
-import java.util.List;
-
-import javax.swing.Icon;
-
-import net.sf.taverna.t2.servicedescriptions.ServiceDescription;
-
-import org.jdom.Document;
-import org.jdom.Element;
-import org.jdom.output.XMLOutputter;
-
-import uk.org.taverna.scufl2.api.configurations.Configuration;
-
-import com.fasterxml.jackson.databind.node.ObjectNode;
-
-/**
- * @author alanrw
- * @author David Withers
- */
-public class BiomartServiceDescription extends ServiceDescription {
-
- public static final URI ACTIVITY_TYPE = URI.create("http://ns.taverna.org.uk/2010/activity/biomart");
-
- private String url;
- private String dataset;
- private String location;
-
- private static final String BIOMART = "Biomart @ ";
- private Element martQuery;
-
- public Element getMartQuery() {
- return martQuery;
- }
-
- /**
- * @return the url
- */
- public String getUrl() {
- return url;
- }
-
- /**
- * @param url
- * the url to set
- */
- public void setUrl(String url) {
- this.url = url;
- }
-
- /**
- * @return the dataset
- */
- public String getDataset() {
- return dataset;
- }
-
- /**
- * @param dataset
- * the dataset to set
- */
- public void setDataset(String dataset) {
- this.dataset = dataset;
- }
-
- /**
- * @return the location
- */
- public String getLocation() {
- return location;
- }
-
- /**
- * @param location
- * the location to set
- */
- public void setLocation(String location) {
- this.location = location;
- }
-
- public void setMartQuery(Element martQuery) {
- this.martQuery = martQuery;
- }
-
- @Override
- public URI getActivityType() {
- return ACTIVITY_TYPE;
- }
-
- @Override
- public Configuration getActivityConfiguration() {
- Configuration configuration = new Configuration();
- configuration.setType(ACTIVITY_TYPE.resolve("#Config"));
- String queryText = new XMLOutputter().outputString(new Document(martQuery));
- ((ObjectNode) configuration.getJson()).put("martQuery", queryText);
- return configuration;
- }
-
- @Override
- public Icon getIcon() {
- return BiomartActivityIcon.getBiomartIcon();
- }
-
- @Override
- public String getName() {
- return dataset;
- }
-
- @Override
- public List<? extends Comparable<?>> getPath() {
- List<String> result;
- result = Arrays.asList(BIOMART + url, location);
- return result;
- }
-
- @Override
- protected List<Object> getIdentifyingData() {
- return Arrays.<Object> asList(getUrl(), getLocation(), getDataset());
- }
-
- @Override
- public boolean isTemplateService() {
- return true;
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartServiceProvider.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartServiceProvider.java b/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartServiceProvider.java
deleted file mode 100644
index 712e8d8..0000000
--- a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartServiceProvider.java
+++ /dev/null
@@ -1,147 +0,0 @@
-/**
- *
- */
-package net.sf.taverna.t2.activities.biomart.servicedescriptions;
-
-import java.net.URI;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-
-import javax.swing.Icon;
-
-import net.sf.taverna.t2.servicedescriptions.AbstractConfigurableServiceProvider;
-import net.sf.taverna.t2.servicedescriptions.ServiceDescription;
-import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
-
-import org.biomart.martservice.MartDataset;
-import org.biomart.martservice.MartQuery;
-import org.biomart.martservice.MartRegistry;
-import org.biomart.martservice.MartService;
-import org.biomart.martservice.MartServiceException;
-import org.biomart.martservice.MartServiceXMLHandler;
-import org.biomart.martservice.MartURLLocation;
-
-/**
- * @author alanrw
- * @author David Withers
- */
-public class BiomartServiceProvider extends AbstractConfigurableServiceProvider<BiomartServiceProviderConfig> {
-
- private static final String TAVERNA = "taverna";
- private static final String BIOMART_SERVICE = "Biomart service";
-
- private static final URI providerId = URI
- .create("http://taverna.sf.net/2010/service-provider/biomart");
-
- private ServiceDescriptionRegistry serviceDescriptionRegistry;
-
- public BiomartServiceProvider() {
- super(new BiomartServiceProviderConfig("http://somehost/biomart"));
- }
-
- public void findServiceDescriptionsAsync(
- FindServiceDescriptionsCallBack callBack) {
- List<ServiceDescription> descriptions = new ArrayList<ServiceDescription>();
- String url = serviceProviderConfig.getUrl();
- callBack.status("About to parse biomart:" + url);
- try {
- MartService martService = MartService
- .getMartService(getBiomartServiceLocation(url));
- martService.setRequestId(TAVERNA);
- MartRegistry registry = martService.getRegistry();
- MartURLLocation[] martURLLocations = registry.getMartURLLocations();
- for (MartURLLocation martURLLocation : martURLLocations) {
- if (martURLLocation.isVisible()) {
-
- MartDataset[] datasets = martService
- .getDatasets(martURLLocation);
- Arrays.sort(datasets, MartDataset.getDisplayComparator());
- for (MartDataset dataset : datasets) {
- if (dataset.isVisible()) {
- BiomartServiceDescription item = new BiomartServiceDescription();
- item.setUrl(martService.getLocation());
- item.setLocation(martURLLocation.getDisplayName());
- item.setDataset(dataset.getName());
- item.setDescription(dataset.getDisplayName());
- MartQuery biomartQuery = new MartQuery(martService,
- dataset, TAVERNA);
- item.setMartQuery(MartServiceXMLHandler.martQueryToElement(biomartQuery, null));
- descriptions.add(item);
- }
- }
- if (descriptions.size() > 0) {
- callBack.partialResults(descriptions);
- descriptions.clear();
- }
- }
- }
- callBack.finished();
- }
- catch (MartServiceException e) {
- callBack.fail("Failed to load Biomart from " + url, e);
- }
- }
-
- public Icon getIcon() {
- return BiomartActivityIcon.getBiomartIcon();
- }
-
- public String getName() {
- return BIOMART_SERVICE;
- }
-
- /**
- * Attempts to construct a valid MartService URL from the location given.
- *
- * @param biomartLocation
- * @return a (hopefully) valid MartService URL
- */
- private String getBiomartServiceLocation(String biomartLocation) {
- StringBuffer sb = new StringBuffer();
- if (biomartLocation.endsWith("martservice")) {
- sb.append(biomartLocation);
- } else if (biomartLocation.endsWith("martview")) {
- sb.append(biomartLocation.substring(0, biomartLocation
- .lastIndexOf("martview")));
- sb.append("martservice");
- } else if (biomartLocation.endsWith("/")) {
- sb.append(biomartLocation);
- sb.append("martservice");
- } else {
- sb.append(biomartLocation);
- sb.append("/martservice");
- }
- return sb.toString();
- }
-
- public List<BiomartServiceProviderConfig> getDefaultConfigurations() {
-
- List<BiomartServiceProviderConfig> defaults = new ArrayList<BiomartServiceProviderConfig>();
-
- // If defaults have failed to load from a configuration file then load them here.
- if (!serviceDescriptionRegistry.isDefaultSystemConfigurableProvidersLoaded()){
- defaults.add(new BiomartServiceProviderConfig(
- "http://www.biomart.org/biomart/martservice"));
- } // else return an empty list
-
- return defaults;
-
- }
-
- @Override
- protected List<? extends Object> getIdentifyingData() {
- List<String> result;
- result = Arrays.asList(getConfiguration().getUrl());
- return result;
- }
-
- public String getId() {
- return providerId.toString();
- }
-
- public void setServiceDescriptionRegistry(ServiceDescriptionRegistry serviceDescriptionRegistry) {
- this.serviceDescriptionRegistry = serviceDescriptionRegistry;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartServiceProviderConfig.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartServiceProviderConfig.java b/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartServiceProviderConfig.java
deleted file mode 100644
index 9891fae..0000000
--- a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/servicedescriptions/BiomartServiceProviderConfig.java
+++ /dev/null
@@ -1,36 +0,0 @@
-/**
- *
- */
-package net.sf.taverna.t2.activities.biomart.servicedescriptions;
-
-import net.sf.taverna.t2.lang.beans.PropertyAnnotated;
-import net.sf.taverna.t2.lang.beans.PropertyAnnotation;
-
-/**
- * @author alanrw
- *
- */
-public class BiomartServiceProviderConfig extends PropertyAnnotated {
-
- private String url;
-
- public BiomartServiceProviderConfig() {
- }
-
- public BiomartServiceProviderConfig(String url) {
- this.url = url.trim();
- }
-
- @PropertyAnnotation(displayName = "Biomart location", preferred = true)
- public String getUrl() {
- return url;
- }
-
- public void setUrl(String url) {
- this.url = url.trim();
- }
-
- public String toString() {
- return getUrl();
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/views/BiomartActivityContextualView.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/views/BiomartActivityContextualView.java b/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/views/BiomartActivityContextualView.java
deleted file mode 100644
index 87a2294..0000000
--- a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/views/BiomartActivityContextualView.java
+++ /dev/null
@@ -1,117 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.biomart.views;
-
-import java.awt.Frame;
-import java.io.IOException;
-import java.io.StringReader;
-
-import javax.swing.Action;
-
-import net.sf.taverna.t2.activities.biomart.actions.BiomartActivityConfigurationAction;
-import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
-import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
-import net.sf.taverna.t2.workbench.configuration.colour.ColourManager;
-import net.sf.taverna.t2.workbench.edits.EditManager;
-import net.sf.taverna.t2.workbench.file.FileManager;
-import net.sf.taverna.t2.workbench.ui.actions.activity.HTMLBasedActivityContextualView;
-
-import org.biomart.martservice.MartQuery;
-import org.biomart.martservice.MartServiceXMLHandler;
-import org.biomart.martservice.query.Attribute;
-import org.biomart.martservice.query.Filter;
-import org.jdom.Element;
-import org.jdom.JDOMException;
-import org.jdom.input.SAXBuilder;
-
-import uk.org.taverna.commons.services.ServiceRegistry;
-import uk.org.taverna.configuration.app.ApplicationConfiguration;
-import uk.org.taverna.scufl2.api.activity.Activity;
-
-@SuppressWarnings("serial")
-public class BiomartActivityContextualView extends HTMLBasedActivityContextualView {
-
- private final EditManager editManager;
- private final FileManager fileManager;
- private final ActivityIconManager activityIconManager;
- private final ApplicationConfiguration applicationConfiguration;
- private final ServiceDescriptionRegistry serviceDescriptionRegistry;
- private final ServiceRegistry serviceRegistry;
-
- public BiomartActivityContextualView(Activity activity, EditManager editManager,
- FileManager fileManager, ActivityIconManager activityIconManager,
- ColourManager colourManager, ApplicationConfiguration applicationConfiguration,
- ServiceDescriptionRegistry serviceDescriptionRegistry, ServiceRegistry serviceRegistry) {
- super(activity, colourManager);
- this.editManager = editManager;
- this.fileManager = fileManager;
- this.activityIconManager = activityIconManager;
- this.applicationConfiguration = applicationConfiguration;
- this.serviceDescriptionRegistry = serviceDescriptionRegistry;
- this.serviceRegistry = serviceRegistry;
- }
-
- @Override
- protected String getRawTableRowsHtml() {
- String queryText = getConfigBean().getJson().get("martQuery").textValue();
- Element martQuery = null;
- try {
- martQuery = new SAXBuilder().build(new StringReader(queryText)).getRootElement();
- } catch (JDOMException | IOException e) {
- }
- MartQuery q = MartServiceXMLHandler.elementToMartQuery(martQuery, null);
- String html = "<tr><td>URL</td><td>" + q.getMartService().getLocation() + "</td></tr>";
- html += "<tr><td>Location</td><td>"
- + q.getMartDataset().getMartURLLocation().getDisplayName() + "</td></tr>";
- boolean firstFilter = true;
- for (Filter filter : q.getQuery().getFilters()) {
- html += firstFilter ? "<tr><td>Filter</td><td>" : "<tr><td></td></td>";
- firstFilter = false;
- html += filter.getName() + "</td></tr>";
- }
- boolean firstAttribute = true;
- for (Attribute attribute : q.getQuery().getAttributes()) {
- html += firstAttribute ? "<tr><td>Attribute</td><td>" : "<tr><td></td><td>";
- firstAttribute = false;
- html += attribute.getName() + "</td></tr>";
- }
- html += "<tr><td>Dataset</td><td>" + q.getMartDataset().getDisplayName() + "</td></tr>";
- return html;
- }
-
- @Override
- public String getViewTitle() {
- return "Biomart service";
- }
-
- @Override
- public Action getConfigureAction(Frame owner) {
- return new BiomartActivityConfigurationAction(getActivity(), owner, editManager,
- fileManager, activityIconManager, applicationConfiguration,
- serviceDescriptionRegistry, serviceRegistry);
- }
-
- @Override
- public int getPreferredPosition() {
- return 100;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/views/BiomartActivityViewFactory.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/views/BiomartActivityViewFactory.java b/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/views/BiomartActivityViewFactory.java
deleted file mode 100644
index ad8321a..0000000
--- a/taverna-biomart-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomart/views/BiomartActivityViewFactory.java
+++ /dev/null
@@ -1,86 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.biomart.views;
-
-import java.util.Arrays;
-import java.util.List;
-
-import net.sf.taverna.t2.activities.biomart.servicedescriptions.BiomartServiceDescription;
-import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
-import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
-import net.sf.taverna.t2.workbench.configuration.colour.ColourManager;
-import net.sf.taverna.t2.workbench.edits.EditManager;
-import net.sf.taverna.t2.workbench.file.FileManager;
-import net.sf.taverna.t2.workbench.ui.views.contextualviews.ContextualView;
-import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory;
-import uk.org.taverna.commons.services.ServiceRegistry;
-import uk.org.taverna.configuration.app.ApplicationConfiguration;
-import uk.org.taverna.scufl2.api.activity.Activity;
-
-public class BiomartActivityViewFactory implements ContextualViewFactory<Activity> {
-
- private EditManager editManager;
- private FileManager fileManager;
- private ActivityIconManager activityIconManager;
- private ColourManager colourManager;
- private ApplicationConfiguration applicationConfiguration;
- private ServiceDescriptionRegistry serviceDescriptionRegistry;
- private ServiceRegistry serviceRegistry;
-
- public boolean canHandle(Object object) {
- return object instanceof Activity && ((Activity) object).getType().equals(BiomartServiceDescription.ACTIVITY_TYPE);
- }
-
- public List<ContextualView> getViews(Activity activity) {
- return Arrays.asList(new ContextualView[] { new BiomartActivityContextualView(activity,
- editManager, fileManager, activityIconManager, colourManager,
- applicationConfiguration, serviceDescriptionRegistry, serviceRegistry) });
- }
-
- public void setEditManager(EditManager editManager) {
- this.editManager = editManager;
- }
-
- public void setFileManager(FileManager fileManager) {
- this.fileManager = fileManager;
- }
-
- public void setActivityIconManager(ActivityIconManager activityIconManager) {
- this.activityIconManager = activityIconManager;
- }
-
- public void setColourManager(ColourManager colourManager) {
- this.colourManager = colourManager;
- }
-
- public void setApplicationConfiguration(ApplicationConfiguration applicationConfiguration) {
- this.applicationConfiguration = applicationConfiguration;
- }
-
- public void setServiceDescriptionRegistry(ServiceDescriptionRegistry serviceDescriptionRegistry) {
- this.serviceDescriptionRegistry = serviceDescriptionRegistry;
- }
-
- public void setServiceRegistry(ServiceRegistry serviceRegistry) {
- this.serviceRegistry = serviceRegistry;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider
----------------------------------------------------------------------
diff --git a/taverna-biomart-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider b/taverna-biomart-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider
deleted file mode 100644
index 637d76a..0000000
--- a/taverna-biomart-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider
+++ /dev/null
@@ -1 +0,0 @@
-net.sf.taverna.t2.activities.biomart.servicedescriptions.BiomartServiceProvider
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent
----------------------------------------------------------------------
diff --git a/taverna-biomart-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent b/taverna-biomart-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent
deleted file mode 100644
index dbff4b7..0000000
--- a/taverna-biomart-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent
+++ /dev/null
@@ -1 +0,0 @@
-net.sf.taverna.t2.activities.biomart.menu.BiomartConfigurationMenuAction
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI
----------------------------------------------------------------------
diff --git a/taverna-biomart-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI b/taverna-biomart-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI
deleted file mode 100644
index e8506ef..0000000
--- a/taverna-biomart-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI
+++ /dev/null
@@ -1 +0,0 @@
-net.sf.taverna.t2.activities.biomart.servicedescriptions.BiomartActivityIcon
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory
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diff --git a/taverna-biomart-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory b/taverna-biomart-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory
deleted file mode 100644
index 355b9ef..0000000
--- a/taverna-biomart-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory
+++ /dev/null
@@ -1 +0,0 @@
-net.sf.taverna.t2.activities.biomart.views.BiomartActivityViewFactory
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-activity-ui/src/main/resources/META-INF/spring/biomart-activity-ui-context-osgi.xml
----------------------------------------------------------------------
diff --git a/taverna-biomart-activity-ui/src/main/resources/META-INF/spring/biomart-activity-ui-context-osgi.xml b/taverna-biomart-activity-ui/src/main/resources/META-INF/spring/biomart-activity-ui-context-osgi.xml
deleted file mode 100644
index e5ea96b..0000000
--- a/taverna-biomart-activity-ui/src/main/resources/META-INF/spring/biomart-activity-ui-context-osgi.xml
+++ /dev/null
@@ -1,30 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<beans:beans xmlns="http://www.springframework.org/schema/osgi" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:beans="http://www.springframework.org/schema/beans"
- xsi:schemaLocation="http://www.springframework.org/schema/beans
- http://www.springframework.org/schema/beans/spring-beans.xsd
- http://www.springframework.org/schema/osgi
- http://www.springframework.org/schema/osgi/spring-osgi.xsd">
-
- <service ref="BiomartActivityIcon" interface="net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI" />
-
- <service ref="BiomartServiceProvider">
- <interfaces>
- <beans:value>net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider</beans:value>
- <beans:value>net.sf.taverna.t2.servicedescriptions.ConfigurableServiceProvider</beans:value>
- </interfaces>
- </service>
-
- <service ref="BiomartConfigurationMenuAction" auto-export="interfaces" />
-
- <service ref="BiomartActivityViewFactory" interface="net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory" />
-
- <reference id="editManager" interface="net.sf.taverna.t2.workbench.edits.EditManager" />
- <reference id="fileManager" interface="net.sf.taverna.t2.workbench.file.FileManager" />
- <reference id="activityIconManager" interface="net.sf.taverna.t2.workbench.activityicons.ActivityIconManager" />
- <reference id="colourManager" interface="net.sf.taverna.t2.workbench.configuration.colour.ColourManager" />
- <reference id="serviceDescriptionRegistry" interface="net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry"/>
- <reference id="applicationConfiguration" interface="uk.org.taverna.configuration.app.ApplicationConfiguration" />
- <reference id="serviceRegistry" interface="uk.org.taverna.commons.services.ServiceRegistry" />
-
-</beans:beans>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-activity-ui/src/main/resources/META-INF/spring/biomart-activity-ui-context.xml
----------------------------------------------------------------------
diff --git a/taverna-biomart-activity-ui/src/main/resources/META-INF/spring/biomart-activity-ui-context.xml b/taverna-biomart-activity-ui/src/main/resources/META-INF/spring/biomart-activity-ui-context.xml
deleted file mode 100644
index 21b43b2..0000000
--- a/taverna-biomart-activity-ui/src/main/resources/META-INF/spring/biomart-activity-ui-context.xml
+++ /dev/null
@@ -1,29 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<beans xmlns="http://www.springframework.org/schema/beans" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://www.springframework.org/schema/beans
- http://www.springframework.org/schema/beans/spring-beans.xsd">
-
- <bean id="BiomartActivityIcon" class="net.sf.taverna.t2.activities.biomart.servicedescriptions.BiomartActivityIcon" />
-
- <bean id="BiomartServiceProvider" class="net.sf.taverna.t2.activities.biomart.servicedescriptions.BiomartServiceProvider">
- <property name="serviceDescriptionRegistry" ref="serviceDescriptionRegistry" />
- </bean>
-
- <bean id="BiomartConfigurationMenuAction" class="net.sf.taverna.t2.activities.biomart.menu.BiomartConfigurationMenuAction">
- <property name="editManager" ref="editManager" />
- <property name="fileManager" ref="fileManager" />
- <property name="activityIconManager" ref="activityIconManager" />
- <property name="applicationConfiguration" ref="applicationConfiguration" />
- <property name="serviceRegistry" ref="serviceRegistry" />
- </bean>
-
- <bean id="BiomartActivityViewFactory" class="net.sf.taverna.t2.activities.biomart.views.BiomartActivityViewFactory">
- <property name="editManager" ref="editManager" />
- <property name="fileManager" ref="fileManager" />
- <property name="activityIconManager" ref="activityIconManager" />
- <property name="colourManager" ref="colourManager" />
- <property name="applicationConfiguration" ref="applicationConfiguration" />
- <property name="serviceRegistry" ref="serviceRegistry" />
- </bean>
-
-</beans>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-activity-ui/src/main/resources/biomart.png
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diff --git a/taverna-biomart-activity-ui/src/main/resources/biomart.png b/taverna-biomart-activity-ui/src/main/resources/biomart.png
deleted file mode 100644
index a969908..0000000
Binary files a/taverna-biomart-activity-ui/src/main/resources/biomart.png and /dev/null differ
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-activity-ui/src/test/java/net/sf/taverna/t2/biomart/views/TestBiomartActivityContextualView.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-activity-ui/src/test/java/net/sf/taverna/t2/biomart/views/TestBiomartActivityContextualView.java b/taverna-biomart-activity-ui/src/test/java/net/sf/taverna/t2/biomart/views/TestBiomartActivityContextualView.java
deleted file mode 100644
index 04ad076..0000000
--- a/taverna-biomart-activity-ui/src/test/java/net/sf/taverna/t2/biomart/views/TestBiomartActivityContextualView.java
+++ /dev/null
@@ -1,94 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.biomart.views;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-
-import java.io.IOException;
-import java.io.InputStream;
-import java.net.URI;
-
-import net.sf.taverna.t2.activities.biomart.actions.BiomartActivityConfigurationAction;
-import net.sf.taverna.t2.activities.biomart.views.BiomartActivityContextualView;
-
-import org.jdom.Document;
-import org.jdom.Element;
-import org.jdom.input.SAXBuilder;
-import org.jdom.output.XMLOutputter;
-import org.junit.Before;
-import org.junit.Ignore;
-import org.junit.Test;
-
-import uk.org.taverna.scufl2.api.activity.Activity;
-import uk.org.taverna.scufl2.api.configurations.Configuration;
-import uk.org.taverna.scufl2.api.profiles.Profile;
-
-import com.fasterxml.jackson.databind.node.ObjectNode;
-
-public class TestBiomartActivityContextualView {
- Activity activity;
-
- @Before
- public void setup() throws Exception {
- activity = new Activity();
- activity.setParent(new Profile());
-
- Element el = getQueryElement("biomart-query.xml");
-
- Configuration configuration = new Configuration();
- configuration.setType(URI.create("http://ns.taverna.org.uk/2010/activity/biomart").resolve("#Config"));
- String queryText = new XMLOutputter().outputString(new Document(el));
- ((ObjectNode) configuration.getJson()).put("martQuery", queryText);
-
- configuration.setConfigures(activity);
- }
-
- @Test @Ignore
- public void testConfigurationAction() throws Exception {
- BiomartActivityContextualView view = new BiomartActivityContextualView(activity, null, null, null, null, null, null, null);
- assertNotNull("The view should provide a configuration action",view.getConfigureAction(null));
- assertTrue("The configuration action should be an instance of BiomartActivityConfigurationAction",view.getConfigureAction(null) instanceof BiomartActivityConfigurationAction);
- }
-
- private Element getQueryElement(String resourceName) throws Exception {
- InputStream inStream = TestBiomartActivityContextualView.class
- .getResourceAsStream("/"+resourceName);
-
- if (inStream == null)
- throw new IOException(
- "Unable to find resource for:"
- + resourceName);
- SAXBuilder builder = new SAXBuilder();
- return builder.build(inStream).detachRootElement();
- }
-
- private void run() throws Exception {
- setup();
- BiomartActivityContextualView view = new BiomartActivityContextualView(activity, null, null, null, null, null, null, null);
- view.setVisible(true);
- }
-
- public static void main(String[] args) throws Exception {
- new TestBiomartActivityContextualView().run();
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-activity-ui/src/test/resources/biomart-query.xml
----------------------------------------------------------------------
diff --git a/taverna-biomart-activity-ui/src/test/resources/biomart-query.xml b/taverna-biomart-activity-ui/src/test/resources/biomart-query.xml
deleted file mode 100644
index 0e52a23..0000000
--- a/taverna-biomart-activity-ui/src/test/resources/biomart-query.xml
+++ /dev/null
@@ -1,24 +0,0 @@
-<biomart:MartQuery
- xmlns:biomart="http://org.embl.ebi.escience/xscufl-biomart/0.1alpha">
- <biomart:MartService
- location="http://www.biomart.org/biomart/martservice" />
- <biomart:MartDataset displayName="Homo sapiens genes (NCBI36)"
- name="hsapiens_gene_ensembl" type="TableSet" initialBatchSize="10"
- maximumBatchSize="50000" visible="false" interface="default"
- modified="2006-11-27 12:49:27">
- <biomart:MartURLLocation database="ensembl_mart_41" default="1"
- displayName="ENSEMBL 41 (SANGER)" host="www.biomart.org"
- includeDatasets="" martUser="" name="ensembl"
- path="/biomart/martservice" port="80" serverVirtualSchema="default"
- virtualSchema="default" visible="1" />
- </biomart:MartDataset>
- <biomart:Query virtualSchemaName="default" count="0" uniqueRows="0"
- softwareVersion="0.5" requestId="taverna">
- <biomart:Dataset name="hsapiens_gene_ensembl">
- <biomart:Attribute name="coding_gene_flank" />
- <biomart:Attribute name="gene_stable_id" />
- <biomart:Filter name="ensembl_gene_id" value="" list="true" />
- <biomart:Filter name="upstream_flank" value="100" />
- </biomart:Dataset>
- </biomart:Query>
-</biomart:MartQuery>
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-activity/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-biomart-activity/pom.xml b/taverna-biomart-activity/pom.xml
deleted file mode 100644
index 2662e59..0000000
--- a/taverna-biomart-activity/pom.xml
+++ /dev/null
@@ -1,77 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
- <modelVersion>4.0.0</modelVersion>
- <parent>
- <groupId>net.sf.taverna</groupId>
- <artifactId>taverna-parent</artifactId>
- <version>3.0.1-SNAPSHOT</version>
- </parent>
- <groupId>net.sf.taverna.t2.activities</groupId>
- <version>2.0.1-SNAPSHOT</version>
- <artifactId>biomart-activity</artifactId>
- <packaging>bundle</packaging>
- <name>Taverna 2 Biomart Activity.</name>
- <dependencies>
- <dependency>
- <groupId>org.biomart</groupId>
- <artifactId>martservice</artifactId>
- <version>2.0.1-SNAPSHOT</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.core</groupId>
- <artifactId>workflowmodel-api</artifactId>
- <version>${t2.core.version}</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.core</groupId>
- <artifactId>reference-api</artifactId>
- <version>${t2.core.version}</version>
- </dependency>
- <dependency>
- <groupId>com.fasterxml.jackson.core</groupId>
- <artifactId>jackson-databind</artifactId>
- <version>${jackson-databind.version}</version>
- </dependency>
- <dependency>
- <groupId>junit</groupId>
- <artifactId>junit</artifactId>
- <version>${junit.version}</version>
- <scope>test</scope>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.activities</groupId>
- <artifactId>activity-test-utils</artifactId>
- <version>${t2.activities.version}</version>
- <scope>test</scope>
- </dependency>
- </dependencies>
-
- <repositories>
- <repository>
- <releases />
- <snapshots>
- <enabled>false</enabled>
- </snapshots>
- <id>mygrid-repository</id>
- <name>myGrid Repository</name>
- <url>http://www.mygrid.org.uk/maven/repository</url>
- </repository>
- <repository>
- <releases>
- <enabled>false</enabled>
- </releases>
- <snapshots />
- <id>mygrid-snapshot-repository</id>
- <name>myGrid Snapshot Repository</name>
- <url>http://www.mygrid.org.uk/maven/snapshot-repository</url>
- </repository>
- </repositories>
- <scm>
- <connection>scm:git:https://github.com/taverna/taverna-biomart-activity.git</connection>
- <developerConnection>scm:git:ssh://git@github.com/taverna/taverna-biomart-activity.git</developerConnection>
- <url>https://github.com/taverna/taverna-biomart-activity/</url>
- <tag>HEAD</tag>
- </scm>
-</project>
-
[13/16] incubator-taverna-plugin-bioinformatics git commit:
temporarily empty repository
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/QueryConfigController.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/QueryConfigController.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/QueryConfigController.java
deleted file mode 100644
index 450b2ba..0000000
--- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/QueryConfigController.java
+++ /dev/null
@@ -1,388 +0,0 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: QueryConfigController.java,v $
- * Revision $Revision: 1.4 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/12/13 11:38:57 $
- * by $Author: davidwithers $
- * Created on 27-Mar-2006
- *****************************************************************/
-package org.biomart.martservice.config;
-
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.Map;
-
-import org.apache.log4j.Logger;
-import org.biomart.martservice.MartQuery;
-import org.biomart.martservice.config.event.QueryComponentEvent;
-import org.biomart.martservice.config.event.QueryComponentListener;
-import org.biomart.martservice.config.ui.QueryComponent;
-import org.biomart.martservice.query.Attribute;
-import org.biomart.martservice.query.Dataset;
-import org.biomart.martservice.query.Filter;
-import org.biomart.martservice.query.Query;
-import org.biomart.martservice.query.QueryListener;
-import org.ensembl.mart.lib.config.FilterDescription;
-
-/**
- * Controls the interaction between graphical <code>QueryComponent</code>s
- * and <code>Query</code>s.
- *
- * @author David Withers
- */
-public class QueryConfigController {
- private static Logger logger = Logger
- .getLogger("org.biomart.martservice.config");
-
- private static QueryListener queryListener = new QueryHandler();
-
- private MartQuery martQuery;
-
- private Query query;
-
- private Map<String, Attribute> initialAttributeMap = new HashMap<String, Attribute>();
-
- private Map<String, Filter> initialFilterMap = new HashMap<String, Filter>();
-
- private Map<String, Attribute> nameToAttributeMap = new HashMap<String, Attribute>();
-
- private Map <String, Filter> nameToFilterMap = new HashMap<String, Filter>();
-
- private QueryComponentHandler queryComponenHandler = new QueryComponentHandler();
-
- /**
- * Constructs an instance of a <code>QueryConfigController</code>.
- *
- * @param martQuery
- */
- public QueryConfigController(MartQuery martQuery) {
- this.martQuery = martQuery;
- query = martQuery.getQuery();
- query.addQueryListener(queryListener);
-
- for (Attribute attribute : query.getAttributes()) {
- initialAttributeMap.put(attribute.getQualifiedName(), attribute);
- nameToAttributeMap.put(attribute.getQualifiedName(), attribute);
- }
- for (Filter filter : query.getFilters()) {
- initialFilterMap.put(filter.getQualifiedName(), filter);
- nameToFilterMap.put(filter.getQualifiedName(), filter);
- }
- }
-
- /*
- * (non-Javadoc)
- *
- * @see java.lang.Object#finalize()
- */
- protected void finalize() throws Throwable {
- super.finalize();
- query.removeQueryListener(queryListener);
- }
-
- /**
- * Returns the <code>MartQuery</code> under control.
- *
- * @return the <code>MartQuery</code> under control
- */
- public MartQuery getMartQuery() {
- return martQuery;
- }
-
- /**
- * Removes a <code>QueryComponent</code> from the controller.
- *
- * @param queryComponent
- * the <code>QueryComponent</code> to remove
- */
- public void deregister(QueryComponent queryComponent) {
- queryComponent.removeQueryComponentListener(queryComponenHandler);
- }
-
- /**
- * Registers a <code>QueryComponent</code> with the controller.
- *
- * If the <code>Query</code> already contains an <code>Attribute</code>
- * or <code>Filter</code> with the corresponding name the
- * <code>QueryComponent</code> is set as selected.
- *
- * @param queryComponent
- * the <code>QueryComponent</code> to register
- */
- public void register(QueryComponent queryComponent) {
- if (queryComponent.getType() == QueryComponent.ATTRIBUTE) {
- getAttribute(queryComponent);
-
- // if query already contains attribute then set the component as
- // selected
- if (initialAttributeMap.containsKey(queryComponent
- .getQualifiedName())) {
- queryComponent.setSelected(true);
- }
-
- } else if (queryComponent.getType() == QueryComponent.FILTER) {
- Filter filter = getFilter(queryComponent);
-
- String value = filter.getValue();
- if (value != null) {
- if (filter.isBoolean()) {
- if ("excluded".equals(value)) {
- queryComponent.setValue("excluded");
- } else {
- queryComponent.setValue("only");
- }
- } else {
- queryComponent.setValue(value);
- }
- }
-
- if (initialFilterMap.containsKey(queryComponent.getQualifiedName())) {
- queryComponent.setSelected(true);
- }
- } else if (queryComponent.getType() == QueryComponent.LINK) {
- Iterator<String> linkedDatasets = martQuery.getLinkedDatasets().iterator();
- // only one linked dataset allowed for now
- if (linkedDatasets.hasNext()) {
- String dataset = linkedDatasets.next();
- queryComponent.setName(dataset);
- queryComponent.setValue(martQuery.getLink(dataset));
- }
- }
-
- queryComponent.addQueryComponentListener(queryComponenHandler);
-
- }
-
- /**
- * Returns the <code>Attribute</code> mapped to the
- * <code>QueryComponent</code>. If no <code>Attribute</code> is mapped
- * a new <code>Attribute</code> is created and added to the map.
- *
- * @param queryComponent
- * @return
- */
- private Attribute getAttribute(QueryComponent queryComponent) {
- String internalName = queryComponent.getQualifiedName();
- Attribute attribute = null;
- if (nameToAttributeMap.containsKey(internalName)) {
- attribute = (Attribute) nameToAttributeMap.get(internalName);
- } else {
- attribute = new Attribute(queryComponent.getName());
- if (queryComponent.getValue() != null) {
- attribute.setAttributes(queryComponent.getValue());
- }
- nameToAttributeMap.put(internalName, attribute);
- }
- return attribute;
- }
-
- /**
- * Returns the <code>Filter</code> mapped to the
- * <code>QueryComponent</code>. If no <code>Filter</code> is mapped a
- * new <code>Filter</code> is created and added to the map.
- *
- * @param queryComponent
- * @return
- */
- private Filter getFilter(QueryComponent queryComponent) {
- FilterDescription filterDescription = (FilterDescription) queryComponent
- .getConfigObject();
- String internalName = queryComponent.getQualifiedName();
- Filter filter;
- if (nameToFilterMap.containsKey(internalName)) {
- filter = (Filter) nameToFilterMap.get(internalName);
- } else {
- if ("boolean".equals(filterDescription.getType())) {
- if ("excluded".equals(queryComponent.getValue())) {
- filter = new Filter(queryComponent.getName(), "excluded", true);
- } else {
- filter = new Filter(queryComponent.getName(), "only", true);
- }
- } else {
- String defaultValue = filterDescription.getDefaultValue();
- if (defaultValue == null
- && !QueryConfigUtils.isNestedList(filterDescription)) {
- // if there is no default value but there are options then
- // choose the first option as the filter value
-// Option[] options = filterDescription.getOptions();
-// if (options != null && options.length > 0) {
-// defaultValue = options[0].getValue();
-// } else {
- defaultValue = queryComponent.getValue();
-// }
- }
- filter = new Filter(queryComponent.getName(), defaultValue);
- if ("id_list".equals(filterDescription.getType())) {
- filter.setList(true);
- }
- }
- nameToFilterMap.put(internalName, filter);
- }
- return filter;
- }
-
- class QueryComponentHandler implements QueryComponentListener {
-
- /*
- * (non-Javadoc)
- *
- * @see org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponentListener#attributeAdded(org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponentEvent)
- */
- public void attributeAdded(QueryComponentEvent event) {
- Attribute attribute = (Attribute) nameToAttributeMap.get(event
- .getDataset().getName()
- + "." + event.getName());
- synchronized (query) {
- martQuery.addAttribute(event.getDataset().getName(), attribute);
- }
- }
-
- /*
- * (non-Javadoc)
- *
- * @see org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponentListener#attributeRemoved(org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponentEvent)
- */
- public void attributeRemoved(QueryComponentEvent event) {
- Attribute attribute = (Attribute) nameToAttributeMap.get(event
- .getDataset().getName()
- + "." + event.getName());
- synchronized (query) {
- martQuery.removeAttribute(attribute);
- }
- }
-
- /*
- * (non-Javadoc)
- *
- * @see org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponentListener#filterAdded(org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponentEvent)
- */
- public void filterAdded(QueryComponentEvent event) {
- Filter filter = (Filter) nameToFilterMap.get(event.getDataset()
- .getName()
- + "." + event.getName());
- synchronized (query) {
- martQuery.addFilter(event.getDataset().getName(), filter);
- }
- }
-
- /*
- * (non-Javadoc)
- *
- * @see org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponentListener#filterRemoved(org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponentEvent)
- */
- public void filterRemoved(QueryComponentEvent event) {
- Filter filter = (Filter) nameToFilterMap.get(event.getDataset()
- .getName()
- + "." + event.getName());
- synchronized (query) {
- martQuery.removeFilter(filter);
- }
- }
-
- /*
- * (non-Javadoc)
- *
- * @see org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponentListener#filterChanged(org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponentEvent)
- */
- public void filterChanged(QueryComponentEvent event) {
- Filter filter = (Filter) nameToFilterMap.get(event.getDataset()
- .getName()
- + "." + event.getName());
- synchronized (query) {
- filter.setValue(event.getValue());
- }
- }
-
- /*
- * (non-Javadoc)
- *
- * @see org.biomart.martservice.config.event.QueryComponentListener#linkAdded(org.biomart.martservice.config.event.QueryComponentEvent)
- */
- public void linkAdded(QueryComponentEvent event) {
- martQuery.addLinkedDataset(event.getName(), event.getValue());
- }
-
- /*
- * (non-Javadoc)
- *
- * @see org.biomart.martservice.config.event.QueryComponentListener#linkRemoved(org.biomart.martservice.config.event.QueryComponentEvent)
- */
- public void linkRemoved(QueryComponentEvent event) {
- martQuery.removeLinkedDataset(event.getName());
- }
-
- /*
- * (non-Javadoc)
- *
- * @see org.biomart.martservice.config.QueryComponentListener#linkChanged(org.biomart.martservice.config.QueryComponentEvent)
- */
- public void linkChanged(QueryComponentEvent event) {
- martQuery.changeLinkedDataset(event.getName(), event.getValue());
- }
-
- }
-
- static class QueryHandler implements QueryListener {
-
- public void attributeAdded(Attribute attribute, Dataset dataset) {
- logger.info("Attribute Added " + attribute.getQualifiedName());
- }
-
- public void attributeRemoved(Attribute attribute, Dataset dataset) {
- logger.info("Attribute Removed " + attribute.getQualifiedName());
- }
-
- public void filterAdded(Filter filter, Dataset dataset) {
- logger.info("Filter Added " + filter.getQualifiedName() + " "
- + filter.getValue());
- }
-
- public void filterRemoved(Filter filter, Dataset dataset) {
- logger.info("Filter Removed " + filter.getQualifiedName());
- }
-
- public void filterChanged(Filter filter, Dataset dataset) {
- logger.info("Filter Changed " + filter.getQualifiedName() + " "
- + filter.getValue());
- }
-
- public void formatterAdded(String formatter) {
- logger.info("Formatter Added " + formatter);
- }
-
- public void formatterRemoved(String formatter) {
- logger.info("Formatter Removed " + formatter);
- }
-
- public void formatterChanged(String formatter) {
- logger.info("Formatter Changed to " + formatter);
- }
-
- }
-
-}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/QueryConfigUtils.java
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diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/QueryConfigUtils.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/QueryConfigUtils.java
deleted file mode 100644
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--- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/QueryConfigUtils.java
+++ /dev/null
@@ -1,598 +0,0 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: QueryConfigUtils.java,v $
- * Revision $Revision: 1.3 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/12/13 11:38:57 $
- * by $Author: davidwithers $
- * Created on 30-Mar-2006
- *****************************************************************/
-package org.biomart.martservice.config;
-
-import java.awt.Component;
-import java.awt.Font;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.util.ArrayList;
-import java.util.Iterator;
-import java.util.List;
-
-import javax.swing.JMenu;
-import javax.swing.JMenuBar;
-import javax.swing.JMenuItem;
-import javax.swing.border.EtchedBorder;
-
-import org.biomart.martservice.MartDataset;
-import org.biomart.martservice.MartService;
-import org.biomart.martservice.MartServiceException;
-import org.biomart.martservice.config.ui.QueryComponent;
-import org.ensembl.mart.lib.config.AttributeDescription;
-import org.ensembl.mart.lib.config.AttributePage;
-import org.ensembl.mart.lib.config.BaseNamedConfigurationObject;
-import org.ensembl.mart.lib.config.DatasetConfig;
-import org.ensembl.mart.lib.config.FilterDescription;
-import org.ensembl.mart.lib.config.Option;
-
-/**
- * Utility class for configuration objects.
- *
- * @author David Withers
- */
-public abstract class QueryConfigUtils {
- public static final String LINE_END = System.getProperty("line.separator");
-
- private static int DISPLAY_WIDTH = 35;
-
- public static String splitSentence(String sentence) {
- return splitSentence(sentence, DISPLAY_WIDTH);
- }
-
- public static String splitSentence(String sentence, int limit) {
- StringBuffer sb = new StringBuffer();
- sb.append("<html>");
-
- int width = 0;
- String[] split = sentence.split(" ");
- for (int i = 0; i < split.length; i++) {
- if (width == 0) {
- sb.append(split[i]);
- width += split[i].length();
- } else if (width + split[i].length() + 1 > limit) {
- sb.append("<br>");
- sb.append(split[i]);
- width = split[i].length();
- } else {
- sb.append(" ");
- sb.append(split[i]);
- width += split[i].length() + 1;
- }
- }
-
- return sb.toString();
- }
-
- /**
- * Returns name truncated to DISPLAY_WIDTH.
- *
- * @param name
- * @return
- */
- public static String truncateName(String name) {
- if (name.length() > DISPLAY_WIDTH) {
- return name.substring(0, DISPLAY_WIDTH);
- } else {
- return name;
- }
- }
-
- public static List<String> getOutputFormats(AttributePage attributePage) {
- List<String> outputFormats = new ArrayList<String>();
-
- String[] formats = attributePage.getOutFormats().split(",");
- for (int i = 0; i < formats.length; i++) {
- outputFormats.add(formats[i]);
- }
- return outputFormats;
- }
-
- /**
- * Returns true if filterDescription has no options.
- *
- * @param filterDescription
- * @return true if filterDescription has no options
- */
- public static boolean isList(FilterDescription filterDescription) {
- return filterDescription.getOptions().length > 0;
- }
-
- /**
- * Returns true if filterDescription has options and at least one option
- * also has options.
- *
- * @param filterDescription
- * @return true if filterDescription has options and at least one option
- * also has options
- */
- public static boolean isNestedList(FilterDescription filterDescription) {
- Option[] options = filterDescription.getOptions();
- for (int i = 0; i < options.length; i++) {
- if (options[i].getOptions().length > 0) {
- return true;
- }
- }
- return false;
- }
-
- /**
- * Returns true if filterDescription has options and the first option has a
- * type equal to "boolean".
- *
- * @param filterDescription
- * @return true if filterDescription has options and the first option has a
- * type equal to "boolean"
- */
- public static boolean isBooleanList(FilterDescription filterDescription) {
- Option[] options = filterDescription.getOptions();
- if (options.length > 0) {
- if ("boolean".equals(options[0].getType())) {
- return true;
- }
- }
- return false;
- }
-
- /**
- * Returns true if filterDescription has options and the first option has a
- * value equal to null.
- *
- * @param filterDescription
- * @return true if filterDescription has options and the first option has a
- * value equal to null
- */
- public static boolean isIdList(FilterDescription filterDescription) {
- Option[] options = filterDescription.getOptions();
- if (options.length > 0) {
- if (options[0].getValue() == null) {
- return true;
- }
- }
- return false;
- }
-
- public static Option[] fixOptionLength(Option[] options, int length) {
- if (options.length > length) {
- Option[] firstOptions = new Option[length];
- Option[] otherOptions = new Option[options.length - (length - 1)];
- for (int i = 0; i < length - 1; i++) {
- firstOptions[i] = options[i];
- fixOptionLength(options[i].getOptions(), length);
- }
- for (int i = length - 1; i < options.length; i++) {
- otherOptions[i - (length - 1)] = options[i];
- }
- Option newOption = new Option();
- newOption.setInternalName("more");
- newOption.setDisplayName("more");
- newOption.addOptions(fixOptionLength(otherOptions, length));
- firstOptions[length - 1] = newOption;
- return firstOptions;
- } else {
- return options;
- }
- }
-
- public static Component getOptionButton(
- FilterDescription filterDescription, QueryComponent queryComponent) {
- JMenuBar menuBar = new JMenuBar();
- menuBar.setBorder(new EtchedBorder());
- JMenu menu = new JMenu("browse");
- menu.setFont(menu.getFont().deriveFont(Font.PLAIN));
- menuBar.add(menu);
- Option[] options = fixOptionLength(filterDescription.getOptions(), 20);
- for (int i = 0; i < options.length; i++) {
- menu.add(getMenuItem(options[i], queryComponent));
- }
- return menuBar;
- }
-
- public static JMenuItem getMenuItem(final Option option,
- final QueryComponent queryComponent) {
- JMenuItem menuItem;
-
- Option[] options = option.getOptions();
- if (options.length > 0) {
- JMenu menu = new JMenu(option.getDisplayName());
- menu.setFont(menu.getFont().deriveFont(Font.PLAIN));
- for (int i = 0; i < options.length; i++) {
- menu.add(getMenuItem(options[i], queryComponent));
- }
- menuItem = menu;
- } else {
- menuItem = new JMenuItem(option.getDisplayName());
- menuItem.setFont(menuItem.getFont().deriveFont(Font.PLAIN));
- menuItem.addActionListener(new ActionListener() {
-
- public void actionPerformed(ActionEvent e) {
- queryComponent.setValue(option.getValue());
- }
-
- });
- }
-
- return menuItem;
- }
-
- /**
- * Returns the dataset referenced by a configuration object or null if the
- * configuration object does not reference a dataset.
- *
- * @param martService
- * the MartService to fetch the referenced dataset from
- * @param referencedFromDataset
- * the datset containing the configuration object
- * @param bnco
- * the configuration object
- * @return the dataset referenced by a configuration object or null if the
- * configuration object does not reference a dataset.
- * @throws MartServiceException
- * if and exception occurs while fetching the dataset
- */
- public static MartDataset getReferencedDataset(MartService martService,
- MartDataset referencedFromDataset,
- BaseNamedConfigurationObject bnco, String softwareVersion)
- throws MartServiceException {
- if ("0.5".equals(softwareVersion)) {
- String pointerDataset = bnco.getAttribute("pointerDataset");
- if (pointerDataset != null) {
- return martService.getDataset(referencedFromDataset
- .getVirtualSchema(), pointerDataset);
- } else {
- return null;
- }
- } else {
- String[] splitName = bnco.getInternalName().split("\\.");
- if (splitName.length > 1) {
- return martService.getDataset(referencedFromDataset
- .getVirtualSchema(), splitName[0]);
- } else {
- return null;
- }
- }
- }
-
- /**
- * Returns the filter description referenced by the filter description.
- *
- * @param martService
- * the MartService to fetch the referenced filter description
- * from
- * @param dataset
- * the datset containing the referenced filter description
- * @param filterDescription
- * the filter description
- * @return the filter description referenced by the filter description
- * @throws MartServiceException
- * if and exception occurs while fetching the filter description
- */
- public static FilterDescription getReferencedFilterDescription(
- MartService martService, MartDataset dataset,
- FilterDescription filterDescription, String softwareVersion)
- throws MartServiceException {
- if ("0.5".equals(softwareVersion)) {
- String pointerFilter = filterDescription
- .getAttribute("pointerFilter");
- if (pointerFilter != null) {
- return getReferencedFilterDescription(martService, dataset,
- pointerFilter);
- } else {
- return null;
- }
- } else {
- String[] splitName = filterDescription.getInternalName().split(
- "\\.");
- FilterDescription ref = getReferencedFilterDescription(martService,
- dataset, splitName[1]);
- return ref;
- }
- }
-
- /**
- * Returns the filter description referenced by the attribute description.
- *
- * @param martService
- * the MartService to fetch the referenced filter description
- * from
- * @param dataset
- * the datset containing the referenced filter description
- * @param attributeDescription
- * the attribute description
- * @return the filter description referenced by the attribute description
- * @throws MartServiceException
- * if and exception occurs while fetching the filter description
- */
- public static FilterDescription getReferencedFilterDescription(
- MartService martService, MartDataset dataset,
- AttributeDescription attributeDescription, String softwareVersion)
- throws MartServiceException {
- if ("0.5".equals(softwareVersion)) {
- String pointerFilter = attributeDescription
- .getAttribute("pointerFilter");
- if (pointerFilter != null) {
- return getReferencedFilterDescription(martService, dataset,
- pointerFilter);
- } else {
- return null;
- }
- } else {
- String[] splitName = attributeDescription.getInternalName().split(
- "\\.");
- return getReferencedFilterDescription(martService, dataset,
- splitName[2]);
- }
- }
-
- public static FilterDescription getReferencedFilterDescription(
- MartService martService, MartDataset dataset, String filterName)
- throws MartServiceException {
- FilterDescription referencedFilter = null;
- DatasetConfig datasetConfig = martService.getDatasetConfig(dataset);
- List<FilterDescription> filterDescriptions = datasetConfig.getAllFilterDescriptions();
- for (FilterDescription filterDescription : filterDescriptions) {
- if (filterName.equals(filterDescription.getInternalName())) {
- if (!"true".equals(filterDescription.getHidden())) {
- referencedFilter = filterDescription;
- break;
- }
- }
- }
- return referencedFilter;
- }
-
- public static FilterDescription getReferencedFilterDescription(
- AttributeDescription attributeDescription, String softwareVersion) {
- FilterDescription filterDescription = new FilterDescription();
- if ("0.5".equals(softwareVersion)) {
- filterDescription.setInternalName(attributeDescription
- .getInternalName());
- filterDescription.setAttribute(attributeDescription
- .getAttribute("pointerDataset"));
- filterDescription.setAttribute(attributeDescription
- .getAttribute("pointerFilter"));
- filterDescription.setAttribute(attributeDescription
- .getAttribute("pointerInterface"));
- } else {
- String[] splitName = attributeDescription.getInternalName().split(
- "\\.");
- filterDescription
- .setInternalName(splitName[0] + "." + splitName[2]);
- }
- return filterDescription;
- }
-
- public static AttributeDescription getReferencedAttributeDescription(
- MartService martService, MartDataset dataset,
- AttributeDescription attributeDescription, String softwareVersion)
- throws MartServiceException {
- AttributeDescription referencedAttributeDescription = null;
- String attributeName = null;
- if ("0.5".equals(softwareVersion)) {
- attributeName = attributeDescription
- .getAttribute("pointerAttribute");
- } else {
- String internalName = attributeDescription.getInternalName();
- String[] splitName = internalName.split("\\.");
- if (splitName.length == 2) {
- attributeName = splitName[1];
- }
- }
- if (attributeName != null) {
- DatasetConfig datasetConfig = martService.getDatasetConfig(dataset);
- if (datasetConfig.containsAttributeDescription(attributeName)) {
- referencedAttributeDescription = datasetConfig
- .getAttributeDescriptionByInternalName(attributeName);
- }
- }
- return referencedAttributeDescription;
- }
-
- /**
- * Returns true if the internal name of the configuration object contains a
- * '.' character.
- *
- * @param bnco
- * the configuration object
- * @return true if the internal name of the configuration object contains a
- * '.' character
- */
- public static boolean isReference(BaseNamedConfigurationObject bnco,
- String softwareVersion) {
- if ("0.5".equals(softwareVersion)) {
- return bnco.getAttribute("pointerDataset") != null
- && (bnco.getAttribute("pointerAttribute") != null || bnco.getAttribute("pointerFilter") != null);
- } else {
- return bnco.getInternalName().indexOf(".") != -1;
- }
- }
-
- /**
- * Returns true if the internal name of the AttributeDescription has the
- * format "[datasetName].[attributeName]".
- *
- * @param attributeDescription
- * @return true if the internal name of the AttributeDescription has the
- * format "[datasetName].[attributeName]"
- */
- public static boolean isAttributeReference(
- AttributeDescription attributeDescription, String softwareVersion) {
- if ("0.5".equals(softwareVersion)) {
- return attributeDescription.getAttribute("pointerAttribute") != null;
- } else {
- return attributeDescription.getInternalName().split("\\.").length == 2;
- }
- }
-
- /**
- * Returns true if the internal name of the AttributeDescription has the
- * format "[datasetName].filter.[filterName]".
- *
- * @param attributeDescription
- * @return true if the internal name of the AttributeDescription has the
- * format "[datasetName].filter.[filterName]"
- */
- public static boolean isFilterReference(
- AttributeDescription attributeDescription, String softwareVersion) {
- if ("0.5".equals(softwareVersion)) {
- return attributeDescription.getAttribute("pointerFilter") != null;
- } else {
- return attributeDescription.getInternalName().split("\\.").length == 3;
- }
- }
-
-// /**
-// * Returns the qualified name of the AttributeDescription in the format
-// * "[datasetName].[attributeName]".
-// *
-// * @param dataset
-// * @param attributeDescription
-// * @return true if the qualified name of the AttributeDescription in the
-// * format "[datasetName].[attributeName]"
-// */
-// public static String getQualifiedName(MartDataset dataset,
-// AttributeDescription attributeDescription, String softwareVersion) {
-// if ("0.5".equals(softwareVersion)) {
-// if (isAttributeReference(attributeDescription, softwareVersion)) {
-// return attributeDescription.getAttribute("pointerDataset")
-// + "."
-// + attributeDescription.getAttribute("pointerAttribute");
-// } else if (isFilterReference(attributeDescription, softwareVersion)) {
-// return attributeDescription.getAttribute("pointerDataset")
-// + "."
-// + attributeDescription.getAttribute("pointerFilter");
-// } else {
-// return dataset.getName()
-// + attributeDescription.getInternalName();
-// }
-// } else {
-// if (isAttributeReference(attributeDescription, softwareVersion)) {
-// return attributeDescription.getInternalName();
-// } else if (isFilterReference(attributeDescription, softwareVersion)) {
-// String[] splitName = attributeDescription.getInternalName()
-// .split("\\.");
-// return splitName[0] + "." + splitName[2];
-// } else {
-// return dataset.getName()
-// + attributeDescription.getInternalName();
-// }
-// }
-// }
-
- public static String csvToValuePerLine(String csv) {
- StringBuffer list = new StringBuffer();
-
- String[] splitString = csv.split(",");
- for (int i = 0; i < splitString.length; i++) {
- if (i > 0) {
- list.append(LINE_END);
- }
- list.append(splitString[i].trim());
- }
-
- return list.toString();
- }
-
- public static String valuePerLineToCsv(String list) {
- return list.trim().replaceAll("\\s", ",");
- }
-
- public static List<String> csvToList(String csv) {
- List<String> list = new ArrayList<String>();
-
- String[] splitString = csv.split(",");
- for (int i = 0; i < splitString.length; i++) {
- list.add(splitString[i].trim());
- }
-
- return list;
- }
-
- /**
- * Converts a List of objects to a comma separated string of the objects'
- * string representations in the order given by the List's iterator. For
- * example:
- *
- * <blockquote>
- *
- * <pre>
- * List list = Arrays.toList(new String[] {"one", "two", "three"};
- * System.out.println(listToCsv(list));
- * </pre>
- *
- * </blockquote> would return the string "one,two,three".
- *
- * @param list
- * @return a List of objects to a comma separated string of the object's
- * string representations
- */
- public static String listToCsv(List<?> list) {
- StringBuffer sb = new StringBuffer();
- for (Iterator<?> iter = list.iterator(); iter.hasNext();) {
- sb.append(iter.next().toString());
- if (iter.hasNext()) {
- sb.append(',');
- }
- }
- return sb.toString();
- }
-
- /**
- * Returns true iff the 'display' or 'hidden' value of the configuration
- * object is not "true".
- *
- * @param bnco
- * the configuration object
- * @return true iff the 'display' or 'hidden' value of configuration object
- * is "true"
- */
- public static boolean display(BaseNamedConfigurationObject bnco) {
- boolean display = true;
- String hideDisplay = bnco.getDisplay();
- if (hideDisplay != null) {
- if (hideDisplay.equals("true")) {
- display = false;
- }
- } else {
- String hidden = bnco.getHidden();
- if (hidden != null) {
- if (hidden.equals("true")) {
- display = false;
- }
- }
- }
- return display;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/event/QueryComponentAdapter.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/event/QueryComponentAdapter.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/event/QueryComponentAdapter.java
deleted file mode 100644
index 201cc1d..0000000
--- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/event/QueryComponentAdapter.java
+++ /dev/null
@@ -1,109 +0,0 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: QueryComponentAdapter.java,v $
- * Revision $Revision: 1.1 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/01/31 14:12:06 $
- * by $Author: davidwithers $
- * Created on 04-Apr-2006
- *****************************************************************/
-package org.biomart.martservice.config.event;
-
-/**
- * An abstract adapter class for receiving <code>QueryComponent</code> events.
- * The methods in this class are empty. This class exists as convenience for
- * creating listener objects.
- *
- * @author David Withers
- */
-public class QueryComponentAdapter implements QueryComponentListener {
-
- /*
- * (non-Javadoc)
- *
- * @see org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponentListener#attributeAdded(org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponentEvent)
- */
- public void attributeAdded(QueryComponentEvent event) {
- }
-
- /*
- * (non-Javadoc)
- *
- * @see org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponentListener#attributeRemoved(org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponentEvent)
- */
- public void attributeRemoved(QueryComponentEvent event) {
- }
-
- /*
- * (non-Javadoc)
- *
- * @see org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponentListener#filterAdded(org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponentEvent)
- */
- public void filterAdded(QueryComponentEvent event) {
- }
-
- /*
- * (non-Javadoc)
- *
- * @see org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponentListener#filterRemoved(org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponentEvent)
- */
- public void filterRemoved(QueryComponentEvent event) {
- }
-
- /*
- * (non-Javadoc)
- *
- * @see org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponentListener#filterChanged(org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponentEvent)
- */
- public void filterChanged(QueryComponentEvent event) {
- }
-
- /*
- * (non-Javadoc)
- *
- * @see org.biomart.martservice.config.event.QueryComponentListener#linkAdded(org.biomart.martservice.config.event.QueryComponentEvent)
- */
- public void linkAdded(QueryComponentEvent event) {
- }
-
- /*
- * (non-Javadoc)
- *
- * @see org.biomart.martservice.config.event.QueryComponentListener#linkRemoved(org.biomart.martservice.config.event.QueryComponentEvent)
- */
- public void linkRemoved(QueryComponentEvent event) {
- }
-
- /*
- * (non-Javadoc)
- *
- * @see org.biomart.martservice.config.QueryComponentListener#linkChanged(org.biomart.martservice.config.QueryComponentEvent)
- */
- public void linkChanged(QueryComponentEvent event) {
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/event/QueryComponentEvent.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/event/QueryComponentEvent.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/event/QueryComponentEvent.java
deleted file mode 100644
index 6fc5d18..0000000
--- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/event/QueryComponentEvent.java
+++ /dev/null
@@ -1,120 +0,0 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: QueryComponentEvent.java,v $
- * Revision $Revision: 1.1 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/01/31 14:12:06 $
- * by $Author: davidwithers $
- * Created on 03-Apr-2006
- *****************************************************************/
-package org.biomart.martservice.config.event;
-
-import java.util.EventObject;
-
-import org.biomart.martservice.MartDataset;
-
-/**
- * An event which indicates that a <code>QueryComponent</code> has been
- * selected, deselected or its value has been modified.
- *
- * @author David Withers
- */
-public class QueryComponentEvent extends EventObject {
- private static final long serialVersionUID = -7576317475836030298L;
-
- private String name;
-
- private MartDataset dataset;
-
- private String value;
-
- /**
- * Constructs a new <code>QueryComponentEvent</code> instance.
- *
- * @param source
- * the source of the event
- * @param name
- * the name of the attribute or filter affected by this event
- * @param dataset
- * the dataset containing the attribute or filter affected by
- * this event
- */
- public QueryComponentEvent(Object source, String name, MartDataset dataset) {
- this(source, name, dataset, null);
- }
-
- /**
- * Constructs a new <code>QueryComponentEvent</code> instance.
- *
- * @param source
- * the source of the event
- * @param name
- * the name of the attribute or filter affected by this event
- * @param dataset
- * the dataset containing the attribute or filter affected by
- * this event
- * @param value
- * the value of the filter affected by this event
- */
- public QueryComponentEvent(Object source, String name, MartDataset dataset,
- String value) {
- super(source);
- this.name = name;
- this.dataset = dataset;
- this.value = value;
- }
-
- /**
- * Returns the name of the attribute or filter affected by this event.
- *
- * @return the name of the attribute or filter affected by this event.
- */
- public String getName() {
- return name;
- }
-
- /**
- * Returns the dataset containing the attribute or filter affected by this
- * event.
- *
- * @return the dataset containing the attribute or filter affected by this
- * event.
- */
- public MartDataset getDataset() {
- return dataset;
- }
-
- /**
- * Returns the value of the filter affected by this event.
- *
- * @return the value of the filter affected by this event.
- */
- public String getValue() {
- return value;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/event/QueryComponentListener.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/event/QueryComponentListener.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/event/QueryComponentListener.java
deleted file mode 100644
index af63326..0000000
--- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/event/QueryComponentListener.java
+++ /dev/null
@@ -1,104 +0,0 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: QueryComponentListener.java,v $
- * Revision $Revision: 1.1 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/01/31 14:12:06 $
- * by $Author: davidwithers $
- * Created on 03-Apr-2006
- *****************************************************************/
-package org.biomart.martservice.config.event;
-
-import java.util.EventListener;
-
-/**
- * The listener interface for receiving QueryComponent events.
- *
- * @author David Withers
- */
-public interface QueryComponentListener extends EventListener {
-
- /**
- * Invoked when a <code>QueryComponent</code> for an attribute is
- * selected.
- *
- * @param event the query component event
- */
- public void attributeAdded(QueryComponentEvent event);
-
- /**
- * Invoked when a <code>QueryComponent</code> for an attribute is
- * deselected.
- *
- * @param event the query component event
- */
- public void attributeRemoved(QueryComponentEvent event);
-
- /**
- * Invoked when a <code>QueryComponent</code> for a filter is selected.
- *
- * @param event the query component event
- */
- public void filterAdded(QueryComponentEvent event);
-
- /**
- * Invoked when a <code>QueryComponent</code> for a filter is deselected.
- *
- * @param event the query component event
- */
- public void filterRemoved(QueryComponentEvent event);
-
- /**
- * Invoked when a <code>QueryComponent</code> for a filter is changed.
- *
- * @param event the query component event
- */
- public void filterChanged(QueryComponentEvent event);
-
- /**
- * Invoked when a <code>QueryComponent</code> for a link is selected.
- *
- * @param event the query component event
- */
- public void linkAdded(QueryComponentEvent event);
-
- /**
- * Invoked when a <code>QueryComponent</code> for a link is deselected.
- *
- * @param event the query component event
- */
- public void linkRemoved(QueryComponentEvent event);
-
- /**
- * Invoked when a <code>QueryComponent</code> for a dataset link id is
- * changed.
- *
- * @param event the query component event
- */
- public void linkChanged(QueryComponentEvent event);
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/ConfigDisplayObject.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/ConfigDisplayObject.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/ConfigDisplayObject.java
deleted file mode 100644
index 89820d3..0000000
--- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/ConfigDisplayObject.java
+++ /dev/null
@@ -1,125 +0,0 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: ConfigDisplayObject.java,v $
- * Revision $Revision: 1.1 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/01/31 14:12:09 $
- * by $Author: davidwithers $
- * Created on 17-Mar-2006
- *****************************************************************/
-package org.biomart.martservice.config.ui;
-
-import java.awt.Component;
-
-import org.ensembl.mart.lib.config.BaseNamedConfigurationObject;
-
-/**
- * An object containing a configuration object and it's graphical component.
- *
- * @author David Withers
- */
-public class ConfigDisplayObject {
- private BaseNamedConfigurationObject configObject;
-
- private Component component;
-
- /**
- * Constructs an instance of a <code>ConfigDisplayObject</code> with the
- * specified configuration object and a <code>null</code> component.
- *
- * @param configObject
- * the configuration object; must not be <code>null</code>
- */
- public ConfigDisplayObject(BaseNamedConfigurationObject configObject) {
- this(configObject, null);
- }
-
- /**
- * Constructs an instance of a <code>ConfigDisplayObject</code> with the
- * specified configuration object and component.
- *
- * @param configObject
- * the configuration object; must not be <code>null</code>
- * @param component
- * the component
- */
- public ConfigDisplayObject(BaseNamedConfigurationObject configObject,
- Component component) {
- if (configObject == null) {
- throw new IllegalArgumentException(
- "Parameter 'configObject' must not be null");
- }
- this.configObject = configObject;
- this.component = component;
- }
-
- /**
- * Returns the display name.
- *
- * @return the display name
- */
- public String getDisplayName() {
- return configObject.getDisplayName();
- }
-
- /**
- * Returns the internal name.
- *
- * @return the internal name
- */
- public String getInternalName() {
- return configObject.getInternalName();
- }
-
- /**
- * Returns the display name.
- *
- * @return the display name
- */
- public String toString() {
- return getDisplayName();
- }
-
- /**
- * Returns the configuration object.
- *
- * @return the configuration object
- */
- public BaseNamedConfigurationObject getConfigObject() {
- return configObject;
- }
-
- /**
- * Returns the component.
- *
- * @return the component.
- */
- public Component getComponent() {
- return component;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/ExpandableBox.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/ExpandableBox.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/ExpandableBox.java
deleted file mode 100644
index d5ff0dd..0000000
--- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/ExpandableBox.java
+++ /dev/null
@@ -1,204 +0,0 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: ExpandableBox.java,v $
- * Revision $Revision: 1.2 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/12/13 11:38:56 $
- * by $Author: davidwithers $
- * Created on Jun 22, 2007
- *****************************************************************/
-package org.biomart.martservice.config.ui;
-
-import java.awt.Color;
-import java.awt.Component;
-import java.awt.Dimension;
-import java.awt.Insets;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-
-import javax.swing.Box;
-import javax.swing.BoxLayout;
-import javax.swing.JButton;
-import javax.swing.JPanel;
-import javax.swing.Timer;
-import javax.swing.border.CompoundBorder;
-import javax.swing.border.EmptyBorder;
-import javax.swing.border.LineBorder;
-
-/**
- * A component that when collapsed only shows a title and when expanded shows
- * the title and contained components.
- *
- * @author David Withers
- *
- */
-public class ExpandableBox extends JPanel {
- private static final long serialVersionUID = -5678399632577606442L;
-
- private JButton expandButton;
-
- private JPanel labelBox;
-
- private boolean expanded = true;
-
- private boolean animated = false;
-
- private Timer timer = new Timer(1, null);
-
- private Dimension minSize;
-
- private Dimension maxSize;
-
- private int height;
-
- private final int increment = 10;
-
- private ActionListener openAction = new ActionListener() {
- public void actionPerformed(ActionEvent evt) {
- if (height <= maxSize.height) {
- setPreferredSize(new Dimension(maxSize.width, height));
- revalidate();
- repaint();
- height += increment;
- } else {
- timer.removeActionListener(this);
- timer.stop();
- setPreferredSize(new Dimension(maxSize.width, maxSize.height));
- revalidate();
- repaint();
- }
- }
- };
-
- private ActionListener closeAction = new ActionListener() {
- public void actionPerformed(ActionEvent evt) {
- if (height >= minSize.height) {
- setPreferredSize(new Dimension(minSize.width, height));
- revalidate();
- repaint();
- height -= increment;
- } else {
- timer.removeActionListener(this);
- timer.stop();
- height = minSize.height;
- setPreferredSize(new Dimension(minSize.width, height));
- revalidate();
- repaint();
- }
- }
- };
-
- public ExpandableBox(Component titleComponent, Color backgroundColor,
- Color borderColor) {
- this(titleComponent, backgroundColor, borderColor, new Insets(10, 10,
- 10, 10), false);
- }
-
- public ExpandableBox(Component titleComponent, Color backgroundColor,
- Color borderColor, Insets borderInsets) {
- this(titleComponent, backgroundColor, borderColor, borderInsets, false);
- }
-
- public ExpandableBox(Component titleComponent, Color backgroundColor,
- Color borderColor, boolean animated) {
- this(titleComponent, backgroundColor, borderColor, new Insets(10, 10,
- 10, 10), animated);
- }
-
- public ExpandableBox(Component titleComponent, Color backgroundColor,
- Color borderColor, Insets borderInsets, boolean animated) {
- this.animated = animated;
- setLayout(new BoxLayout(this, BoxLayout.Y_AXIS));
- setBackground(backgroundColor);
- setBorder(new CompoundBorder(new LineBorder(borderColor, 1),
- new EmptyBorder(borderInsets)));
-
- labelBox = new JPanel();
- labelBox.setLayout(new BoxLayout(labelBox, BoxLayout.X_AXIS));
- labelBox.setBackground(backgroundColor);
-
- expandButton = new JButton(MartServiceIcons.getIcon("contract"));
- expandButton.setActionCommand("contract");
- expandButton.setBackground(backgroundColor);
- expandButton.setBorder(new EmptyBorder(0, 0, 0, 0));
- expandButton.addActionListener(new ActionListener() {
-
- public void actionPerformed(ActionEvent e) {
- if ("contract".equals(e.getActionCommand())) {
- setExpanded(false);
- } else {
- setExpanded(true);
- }
- }
-
- });
- labelBox.add(expandButton);
- labelBox.add(Box.createHorizontalStrut(5));
- labelBox.add(titleComponent);
- labelBox.add(Box.createHorizontalGlue());
- add(labelBox);
- minSize = getPreferredSize();
- }
-
- public void setExpanded(boolean expanded) {
- if (maxSize == null || maxSize.height <= minSize.height) {
- maxSize = getLayout().preferredLayoutSize(this);
- }
- if (this.expanded != expanded) {
- this.expanded = expanded;
- if (expanded) {
- expandButton.setIcon(MartServiceIcons.getIcon("contract"));
- expandButton.setActionCommand("contract");
- if (animated) {
- timer.stop();
- timer.removeActionListener(closeAction);
- timer.addActionListener(openAction);
- timer.start();
- } else {
- setPreferredSize(new Dimension(maxSize.width,
- maxSize.height));
- }
- } else {
- expandButton.setIcon(MartServiceIcons.getIcon("expand"));
- expandButton.setActionCommand("expand");
- if (animated) {
- timer.stop();
- timer.removeActionListener(openAction);
- timer.addActionListener(closeAction);
- timer.start();
- } else {
- setPreferredSize(new Dimension(minSize.width,
- minSize.height));
- }
- }
- revalidate();
- repaint();
- }
- expandButton.setSelected(expanded);
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/MartServiceIcons.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/MartServiceIcons.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/MartServiceIcons.java
deleted file mode 100644
index 15f294a..0000000
--- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/MartServiceIcons.java
+++ /dev/null
@@ -1,104 +0,0 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: MartServiceIcons.java,v $
- * Revision $Revision: 1.2 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/12/13 11:38:56 $
- * by $Author: davidwithers $
- * Created on 24-Aug-2006
- *****************************************************************/
-package org.biomart.martservice.config.ui;
-
-import java.util.HashMap;
-import java.util.Map;
-
-import javax.swing.Icon;
-import javax.swing.ImageIcon;
-
-/**
- *
- * @author witherd5
- */
-public class MartServiceIcons {
- private static Map<String, Icon> nameToIcon = new HashMap<String, Icon>();
-
- private static final String imageLocation = "org/biomart/martservice/config/ui/";
-
- static {
- ClassLoader loader = MartServiceQueryConfigUIFactory.class
- .getClassLoader();
- if (loader == null) {
- loader = Thread.currentThread().getContextClassLoader();
- }
-
- nameToIcon.put("gene_schematic", new ImageIcon(loader
- .getResource(imageLocation + "gene_schematic.gif")));
- nameToIcon.put("gene_schematic_3utr", new ImageIcon(loader
- .getResource(imageLocation + "gene_schematic_3utr.gif")));
- nameToIcon.put("gene_schematic_5utr", new ImageIcon(loader
- .getResource(imageLocation + "gene_schematic_5utr.gif")));
- nameToIcon.put("gene_schematic_cdna", new ImageIcon(loader
- .getResource(imageLocation + "gene_schematic_cdna.gif")));
- nameToIcon.put("gene_schematic_coding_gene_flank", new ImageIcon(loader
- .getResource(imageLocation
- + "gene_schematic_coding_gene_flank.gif")));
- nameToIcon.put("gene_schematic_coding_transcript_flank", new ImageIcon(
- loader.getResource(imageLocation
- + "gene_schematic_coding_transcript_flank.gif")));
- nameToIcon.put("gene_schematic_coding", new ImageIcon(loader
- .getResource(imageLocation + "gene_schematic_coding.gif")));
- nameToIcon.put("gene_schematic_gene_exon_intron", new ImageIcon(loader
- .getResource(imageLocation
- + "gene_schematic_gene_exon_intron.gif")));
- nameToIcon.put("gene_schematic_gene_exon", new ImageIcon(loader
- .getResource(imageLocation + "gene_schematic_gene_exon.gif")));
- nameToIcon.put("gene_schematic_gene_flank", new ImageIcon(loader
- .getResource(imageLocation + "gene_schematic_gene_flank.gif")));
- nameToIcon.put("gene_schematic_peptide", new ImageIcon(loader
- .getResource(imageLocation + "gene_schematic_peptide.gif")));
- nameToIcon.put("gene_schematic_transcript_exon_intron", new ImageIcon(
- loader.getResource(imageLocation
- + "gene_schematic_transcript_exon_intron.gif")));
- nameToIcon.put("gene_schematic_transcript_exon", new ImageIcon(
- loader.getResource(imageLocation
- + "gene_schematic_transcript_exon.gif")));
- nameToIcon.put("gene_schematic_transcript_flank", new ImageIcon(loader
- .getResource(imageLocation
- + "gene_schematic_transcript_flank.gif")));
- nameToIcon.put("contract", new ImageIcon(loader
- .getResource(imageLocation
- + "contract.gif")));
- nameToIcon.put("expand", new ImageIcon(loader
- .getResource(imageLocation
- + "expand.gif")));
- }
-
- public static Icon getIcon(String name) {
- return (Icon) nameToIcon.get(name);
- }
-
-}
[08/16] incubator-taverna-plugin-bioinformatics git commit:
temporarily empty repository
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BiomobyObjectActionHelper.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BiomobyObjectActionHelper.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BiomobyObjectActionHelper.java
deleted file mode 100644
index 9ff9d67..0000000
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BiomobyObjectActionHelper.java
+++ /dev/null
@@ -1,787 +0,0 @@
-/*
- * This file is a component of the Taverna project, and is licensed under the
- * GNU LGPL. Copyright Edward Kawas, The BioMoby Project
- */
-package net.sf.taverna.t2.activities.biomoby.actions;
-
-import java.awt.BorderLayout;
-import java.awt.Dimension;
-import java.awt.Frame;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.MouseEvent;
-import java.awt.event.MouseListener;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Enumeration;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.Set;
-import java.util.SortedSet;
-import java.util.TreeMap;
-import java.util.TreeSet;
-import java.util.Vector;
-
-import javax.swing.ImageIcon;
-import javax.swing.JButton;
-import javax.swing.JComponent;
-import javax.swing.JLabel;
-import javax.swing.JMenuItem;
-import javax.swing.JOptionPane;
-import javax.swing.JPanel;
-import javax.swing.JPopupMenu;
-import javax.swing.JProgressBar;
-import javax.swing.JScrollPane;
-import javax.swing.JSeparator;
-import javax.swing.JTree;
-import javax.swing.ToolTipManager;
-import javax.swing.tree.DefaultMutableTreeNode;
-import javax.swing.tree.MutableTreeNode;
-import javax.swing.tree.TreePath;
-import javax.swing.tree.TreeSelectionModel;
-
-import net.sf.taverna.t2.activities.biomoby.BiomobyObjectActivity;
-import net.sf.taverna.t2.activities.biomoby.edits.AddBiomobyConsumingServiceEdit;
-import net.sf.taverna.t2.workbench.edits.EditManager;
-import net.sf.taverna.t2.workbench.file.FileManager;
-import net.sf.taverna.t2.workflowmodel.Dataflow;
-import net.sf.taverna.t2.workflowmodel.Edit;
-import net.sf.taverna.t2.workflowmodel.Edits;
-import net.sf.taverna.t2.workflowmodel.OutputPort;
-
-import org.apache.log4j.Logger;
-import org.biomoby.client.CentralImpl;
-import org.biomoby.registry.meta.Registry;
-import org.biomoby.shared.Central;
-import org.biomoby.shared.MobyData;
-import org.biomoby.shared.MobyDataType;
-import org.biomoby.shared.MobyException;
-import org.biomoby.shared.MobyNamespace;
-import org.biomoby.shared.MobyPrimaryDataSet;
-import org.biomoby.shared.MobyPrimaryDataSimple;
-import org.biomoby.shared.MobyService;
-import org.biomoby.shared.data.MobyDataInstance;
-import org.biomoby.shared.data.MobyDataObject;
-import org.biomoby.shared.data.MobyDataObjectSet;
-
-public class BiomobyObjectActionHelper {
-
- private static Logger logger = Logger
- .getLogger(BiomobyObjectActionHelper.class);
-
- private boolean searchParentTypes = false;
-
- private OutputPort outputPort = null;
-
- private MobyNamespace[] namespaces = null;
-
- private EditManager editManager;
-
- private final FileManager fileManager;
-
- public BiomobyObjectActionHelper(boolean searchParentTypes, EditManager editManager, FileManager fileManager) {
- super();
- this.searchParentTypes = searchParentTypes;
- this.editManager = editManager;
- this.fileManager = fileManager;
- }
-
- public BiomobyObjectActionHelper(OutputPort outputPort, boolean searchParentTypes, EditManager editManager, FileManager fileManager) {
- super();
- this.searchParentTypes = searchParentTypes;
- this.outputPort = outputPort;
- this.editManager = editManager;
- this.fileManager = fileManager;
- }
-
- public BiomobyObjectActionHelper(EditManager editManager, FileManager fileManager) {
- super();
- this.editManager = editManager;
- this.fileManager = fileManager;
- }
-
- private class Worker extends Thread {
- private BiomobyObjectActivity activity;
-
- private BiomobyObjectActionHelper action;
-
- private JPanel panel = new JPanel(new BorderLayout());
-
- private JPanel namespacePanel = new JPanel(new BorderLayout());
-
- private JProgressBar bar = new JProgressBar();
-
- private JTree namespaceList = null;
-
- public Worker(BiomobyObjectActivity activity, BiomobyObjectActionHelper object) {
- super("Biomoby object action worker");
- this.activity = activity;
- this.action = object;
- }
-
- /*
- * method to show the progress bar
- */
- private void setUpProgressBar(String text) {
- bar = new JProgressBar();
- bar.setIndeterminate(true);
- bar.setValue(0);
- bar.setStringPainted(true);
- bar.setVisible(true);
- bar.setString(text);
- if (panel != null){
- panel.add(bar, BorderLayout.PAGE_END);
- panel.updateUI();
- }
- }
-
- private void takeDownProgressBar() {
- if (panel != null) {
- panel.remove(bar);
- panel.updateUI();
- }
-
- }
-
- public JPanel getPanel() {
- return this.panel;
- }
-
- public void run() {
- Central central = activity.getCentral();
- // ask if we should restrict query by namespace
- // only do this if we dont have an output port
- if (action.outputPort == null) {
- if (JOptionPane.YES_OPTION ==
- JOptionPane.showConfirmDialog(null, "Would you like to restrict your search by based upon a namespace?\n" +
- "This can allow you to find only those services that operate on a specific kind of data.",
- "Restrict query space", JOptionPane.YES_NO_OPTION)) {
- // create a JList chooser with a done button here
- setUpProgressBar("Getting namespaces list");
- try {
- namespacePanel = new JPanel(new BorderLayout());
- createNamespaceList(central.getFullNamespaces());
- JButton button = new JButton("Done");
- button.addActionListener(new ActionListener(){
- @SuppressWarnings("unchecked")
- public void actionPerformed(
- ActionEvent e) {
- ArrayList<MobyNamespace> chosen = new ArrayList<MobyNamespace>();
- TreePath[] paths = namespaceList.getSelectionPaths();
- for (TreePath p : paths) {
- if (p.getLastPathComponent() instanceof DefaultMutableTreeNode) {
- DefaultMutableTreeNode node = (DefaultMutableTreeNode)p.getLastPathComponent();
- if (node.isRoot()) {
- chosen = new ArrayList<MobyNamespace>();
- break;
- }
- if (!node.isLeaf()) {
- // get the children and add them to chosen
- Enumeration<DefaultMutableTreeNode> children = node.children();
- while (children.hasMoreElements() )
- chosen.add(new MobyNamespace(children.nextElement().toString()));
- } else {
- // is a leaf ... add to chosen
- chosen.add(new MobyNamespace(node.toString()));
- }
- }
- }
- // set the namespaces that were selected
- setNamespaces(chosen.toArray(new MobyNamespace[]{}));
- // get the tree - in a new thread
- Thread t = new Thread(){
- public void run() {
- namespacePanel.setVisible(false);
- setUpProgressBar("Getting BioMOBY details for " + activity.getConfiguration().getServiceName() + " ...");
- getSemanticServiceTree();
- }};
- t.setDaemon(true);
- t.start();
-
- }});
- // add the list and button to the panel
- namespacePanel.add(new JScrollPane(namespaceList), BorderLayout.CENTER);
- namespacePanel.add(button, BorderLayout.PAGE_END);
- panel.add(namespacePanel, BorderLayout.CENTER);
- panel.updateUI();
- } catch (MobyException e) {
- logger.error("", e);
- takeDownProgressBar();
- }
- takeDownProgressBar();
- // once done is pressed, insert selected namespace into the namespaces array
- // show the progress bar
-
- } else {
- // start our search
- setNamespaces(null);
- setUpProgressBar("Getting BioMOBY details for " + activity.getConfiguration().getServiceName() + " ...");
- getSemanticServiceTree();
- }
- } else {
- // search only for those services that consume the correct namespaces
- if (this.action != null && this.action.getNamespaces() != null) {
- setNamespaces(this.action.getNamespaces());
- } else {
- setNamespaces(null);
- }
- setUpProgressBar("Getting BioMOBY details for " + activity.getConfiguration().getServiceName() + " ...");
- // start our search
- getSemanticServiceTree();
- }
-
-
- }
-
- /**
- * @param central
- */
- private void getSemanticServiceTree() {
- Central central = activity.getCentral();
- MobyDataType object = activity.getMobyObject();
- MobyService template = new MobyService("dummy");
-
- // strip the lsid portion of the name
- String name = object.getName();
- if (name.indexOf(":") > 0) {
- name = name.substring(name.lastIndexOf(":") + 1);
- }
- // initialize a data object to pass into the service template
- Registry mRegistry = new Registry(central.getRegistryEndpoint(),central.getRegistryEndpoint(),"http://domain.com/MOBY/Central");
- MobyDataObject data = new MobyDataObject("", mRegistry);
- data.setDataType(new MobyDataType(name));
- data.setXmlMode(MobyDataInstance.CENTRAL_XML_MODE);
- if (action.namespaces != null)
- data.setNamespaces(action.namespaces);
- // create the nodes for the tree
- MutableTreeNode parent = new DefaultMutableTreeNode(name);
- MutableTreeNode inputNode = new DefaultMutableTreeNode("Feeds into");
- MutableTreeNode outputNode = new DefaultMutableTreeNode("Produced by");
-
- // what services does this object feed into?
- template.setInputs(new MobyData[] { data });
- template.setCategory("");
- MobyService[] services = null;
- Set<MobyService> theServices = new TreeSet<MobyService>();
- try {
- services = central.findService(template, null, true, action.searchParentTypes);
-
- theServices.addAll(Arrays.asList(services));
- MobyDataObjectSet set = new MobyDataObjectSet("");
- set.add(data);
- template.setInputs(null);
- template.setInputs(new MobyData[]{set});
- services = central.findService(template, null, true, action.searchParentTypes);
- theServices.addAll(Arrays.asList(services));
- } catch (MobyException e) {
- panel.add(new JTree(new String[] { "Error finding services",
- "TODO: create a better Error" }), BorderLayout.CENTER);
- panel.updateUI();
- return;
- }
- createTreeNodes(inputNode, theServices.toArray(new MobyService[]{}));
- if (inputNode.getChildCount() == 0)
- inputNode.insert(new DefaultMutableTreeNode(
- "Object Doesn't Currently Feed Into Any Services"), 0);
-
- // what services return this object?
- template = null;
- template = new MobyService("dummy");
- template.setCategory("");
- template.setOutputs(new MobyData[] { data });
- services = null;
- theServices = new TreeSet<MobyService>();
- try {
- services = central.findService(template, null, true, action.searchParentTypes);
- theServices.addAll(Arrays.asList(services));
- MobyDataObjectSet set = new MobyDataObjectSet("");
- set.add(data);
- template.setOutputs(null);
- template.setOutputs(new MobyData[]{set});
- services = central.findService(template, null, true, action.searchParentTypes);
- theServices.addAll(Arrays.asList(services));
- } catch (MobyException e) {
- panel.add(new JTree(new String[] { "Error finding services",
- "TODO: create a better Error" }), BorderLayout.CENTER);
- panel.updateUI();
- return;
- }
- createTreeNodes(outputNode, theServices.toArray(new MobyService[]{}));
- if (outputNode.getChildCount() == 0)
- outputNode.insert(new DefaultMutableTreeNode(
- "Object Isn't Produced By Any Services"), 0);
- // what kind of object is this?
-
- // set up the nodes
- parent.insert(inputNode, 0);
- parent.insert(outputNode, 1);
-
- // finally return a tree describing the object
- final JTree tree = new JTree(parent);
- tree.setCellRenderer(new BioMobyObjectTreeCustomRenderer());
- ToolTipManager.sharedInstance().registerComponent(tree);
- tree.addMouseListener(new MouseListener() {
- public void mouseClicked(MouseEvent me) {
- }
-
- public void mousePressed(MouseEvent me) {
- mouseReleased(me);
- }
-
- public void mouseReleased(MouseEvent me) {
- if (me.isPopupTrigger()) // right click, show popup menu
- {
- TreePath path = tree.getPathForLocation(me.getX(), me.getY());
- if (path == null)
- return;
- if (path.getPathCount() == 4) {
- if (path.getParentPath().getParentPath().getLastPathComponent()
- .toString().equals("Feeds into")) {
-
- DefaultMutableTreeNode node = (DefaultMutableTreeNode) tree
- .getLastSelectedPathComponent();
- if (node == null)
- return;
- final String selectedService = node.toString();
- // ensure that the last selected item is a
- // service!
- if (!selectedService.equals(path.getLastPathComponent().toString()))
- return;
- final String selectedAuthority = path.getParentPath()
- .getLastPathComponent().toString();
- final JPopupMenu menu = new JPopupMenu();
- // Create and add a menu item for adding to the
- // item
- // to the workflow
- JMenuItem item = new JMenuItem("Add service - " + selectedService
- + " to the workflow?");
- item
- .setIcon(MobyPanel.getIcon("/Add24.gif"));
- item.addActionListener(new ActionListener() {
- public void actionPerformed(ActionEvent ae) {
-
- try {
- if (outputPort==null) {
- outputPort = activity.getOutputPorts().iterator().next();
- }
- Dataflow currentDataflow = fileManager.getCurrentDataflow();
- Edit<?> edit = new AddBiomobyConsumingServiceEdit(
- currentDataflow, activity,
- selectedService,selectedAuthority,outputPort, editManager.getEdits());
- editManager.doDataflowEdit(
- currentDataflow, edit);
-
- } catch (Exception e) {
- logger.error("Could not perform action", e);
- }
- }
- });
- // Create and add a menu item for service
- // details
- JMenuItem details = new JMenuItem("Find out about "
- + selectedService);
- details
- .setIcon(MobyPanel.getIcon("/Information24.gif"));
- details.addActionListener(new ActionListener() {
- public void actionPerformed(ActionEvent ae) {
- // Create a frame
- Frame frame = MobyPanel.CreateFrame("A BioMoby Service Description");
- frame.setSize(getFrameSize());
- JPanel panel = new MobyPanel(selectedService,"A BioMoby Service Description",
- createServiceDescription(selectedService,
- selectedAuthority, activity.getConfiguration().getMobyEndpoint()));
- frame.add(panel);
- frame.pack();
- frame.setVisible(true);
- }
-
- @SuppressWarnings("unchecked")
- private String createServiceDescription(String selectedService,
- String selectedAuthority, String endpoint) {
- StringBuffer sb = new StringBuffer();
- String newline = System.getProperty("line.separator");
- MobyService service = new MobyService(selectedService);
- try {
- Central central = new CentralImpl(endpoint);
- service.setAuthority(selectedAuthority);
- service.setCategory("");
- MobyService[] services = central.findService(service);
- if (services == null || services.length != 1) {
- return "Couldn't retrieve a description on the BioMoby service '"
- + selectedService + "'";
- }
- service = services[0];
-
- } catch (MobyException e) {
- logger.error("Could not retrieve a description on the BioMoby service "
- + selectedService, e);
- return "Couldn't retrieve a description on the BioMoby service '"
- + selectedService + "'";
- }
- sb.append("Service Contact: " + newline + "\t"
- + service.getEmailContact() + newline);
- sb.append("Service Category: " + newline + "\t"
- + service.getCategory() + newline);
- sb.append("Service Authority: " + newline + "\t"
- + service.getAuthority() + newline);
- sb.append("Service Type: " + newline + "\t"
- + service.getType() + newline);
- sb.append("Service Description: " + newline + "\t"
- + service.getDescription() + newline);
- sb.append("Location of Service: " + newline + "\t"
- + service.getURL() + newline);
- sb.append("Service Signature RDF Document is located at: "
- + newline + "\t" + service.getSignatureURL()
- + newline);
- MobyData[] data = service.getPrimaryInputs();
- Vector primaryDataSimples = new Vector();
- Vector primaryDataSets = new Vector();
- for (int x = 0; x < data.length; x++) {
- if (data[x] instanceof MobyPrimaryDataSimple)
- primaryDataSimples.add(data[x]);
- else
- primaryDataSets.add(data[x]);
- }
- // describe inputs simple then
- // collections
- sb.append("Inputs:" + newline);
- if (primaryDataSimples.size() == 0) {
- sb.append("\t\tNo Simple input datatypes consumed."
- + newline);
- } else {
- Iterator it = primaryDataSimples.iterator();
- sb
- .append("\t\tService consumes the following Simple(s):"
- + newline);
- while (it.hasNext()) {
- MobyPrimaryDataSimple simple = (MobyPrimaryDataSimple) it
- .next();
- MobyNamespace[] namespaces = simple.getNamespaces();
- sb.append("\t\tData type: "
- + simple.getDataType().getName() + newline);
- sb.append("\t\t\tArticle name: " + simple.getName()
- + newline);
- if (namespaces.length == 0) {
- sb.append("\t\t\tValid Namespaces: ANY"
- + newline);
- } else {
- sb.append("\t\t\tValid Namespaces: ");
- for (int x = 0; x < namespaces.length; x++)
- sb.append(namespaces[x].getName() + " ");
- sb.append(newline);
- }
- }
- }
- if (primaryDataSets.size() == 0) {
- sb.append(newline
- + "\t\tNo Collection input datatypes consumed."
- + newline);
- } else {
- Iterator it = primaryDataSets.iterator();
- sb
- .append(newline
- + "\t\tService consumes the following collection(s) of datatypes:"
- + newline);
- while (it.hasNext()) {
- MobyPrimaryDataSet set = (MobyPrimaryDataSet) it
- .next();
- MobyPrimaryDataSimple simple = null;
- sb.append("\t\tCollection Name:" + set.getName()
- + newline);
- MobyPrimaryDataSimple[] simples = set.getElements();
- for (int i = 0; i < simples.length; i++) {
- simple = simples[i];
- MobyNamespace[] namespaces = simple
- .getNamespaces();
- // iterate through set and
- // do
- // the following
- sb.append("\t\tData type: "
- + simple.getDataType().getName()
- + newline);
- sb.append("\t\t\tArticle name: "
- + simple.getName() + newline);
- if (namespaces.length == 0) {
- sb.append("\t\t\tValid Namespaces: ANY"
- + newline);
- } else {
- sb.append("\t\t\tValid Namespaces: ");
- for (int x = 0; x < namespaces.length; x++)
- sb
- .append(namespaces[x].getName()
- + " ");
- sb.append(newline);
- }
- }
- }
- }
- // describe secondary inputs
- // describe outputs simple then
- // collections
- data = service.getPrimaryOutputs();
- primaryDataSimples = new Vector();
- primaryDataSets = new Vector();
- for (int x = 0; x < data.length; x++) {
- if (data[x] instanceof MobyPrimaryDataSimple)
- primaryDataSimples.add(data[x]);
- else
- primaryDataSets.add(data[x]);
- }
- sb.append("Outputs:" + newline);
- if (primaryDataSimples.size() == 0) {
- sb.append("\t\tNo Simple output datatypes produced."
- + newline);
- } else {
- Iterator it = primaryDataSimples.iterator();
- sb
- .append("\t\tService produces the following Simple(s):"
- + newline);
- while (it.hasNext()) {
- MobyPrimaryDataSimple simple = (MobyPrimaryDataSimple) it
- .next();
- MobyNamespace[] namespaces = simple.getNamespaces();
- sb.append("\t\tData type: "
- + simple.getDataType().getName() + newline);
- sb.append("\t\t\tArticle name: " + simple.getName()
- + newline);
- if (namespaces.length == 0) {
- sb.append("\t\t\tValid Namespaces: ANY"
- + newline);
- } else {
- sb.append("\t\t\tValid Namespaces: ");
- for (int x = 0; x < namespaces.length; x++)
- sb.append(namespaces[x].getName() + " ");
- sb.append(newline);
- }
- }
- }
- if (primaryDataSets.size() == 0) {
- sb
- .append(newline
- + "\t\tNo Collection output datatypes produced."
- + newline);
- } else {
- Iterator it = primaryDataSets.iterator();
- sb
- .append(newline
- + "\t\tService produces the following collection(s) of datatypes:"
- + newline);
- while (it.hasNext()) {
- MobyPrimaryDataSet set = (MobyPrimaryDataSet) it
- .next();
- MobyPrimaryDataSimple simple = null;
- sb.append("\t\tCollection Name:" + set.getName()
- + newline);
- MobyPrimaryDataSimple[] simples = set.getElements();
- for (int i = 0; i < simples.length; i++) {
- simple = simples[i];
- MobyNamespace[] namespaces = simple
- .getNamespaces();
- // iterate through set and
- // do
- // the following
- sb.append("\t\tData type: "
- + simple.getDataType().getName()
- + newline);
- sb.append("\t\t\tArticle name: "
- + simple.getName() + newline);
- if (namespaces.length == 0) {
- sb.append("\t\t\tValid Namespaces: ANY"
- + newline);
- } else {
- sb.append("\t\t\tValid Namespaces: ");
- for (int x = 0; x < namespaces.length; x++)
- sb
- .append(namespaces[x].getName()
- + " ");
- sb.append(newline);
- }
- }
- }
- }
- sb.append((service.isAuthoritative()) ? newline
- + "The service belongs to this author." + newline
- : newline
- + "The service was wrapped by it's author."
- + newline);
- return sb.toString();
- }
- });
- // add the components to the menus
- menu.add(new JLabel("Add to workflow ... ", JLabel.CENTER));
- menu.add(new JSeparator());
- menu.add(item);
- menu.add(new JSeparator());
- menu.add(new JLabel("Service Details ... ", JLabel.CENTER));
- menu.add(new JSeparator());
- menu.add(details);
- // show the window
- menu.show(me.getComponent(), me.getX(), me.getY());
- }
- }
- }
- }
-
- public void mouseEntered(MouseEvent me) {
- }
-
- public void mouseExited(MouseEvent me) {
- }
- });
- tree.getSelectionModel().setSelectionMode(TreeSelectionModel.SINGLE_TREE_SELECTION);
- panel.add(new JScrollPane(tree), BorderLayout.CENTER);
- takeDownProgressBar();
- }
-
- private void createNamespaceList(MobyNamespace[] fullNamespaces) {
- // sort the namespaces alphabetically
- DefaultMutableTreeNode root = new DefaultMutableTreeNode("ANY");
- // assuming that they increment by one ...
- TreeMap<String, TreeSet<String>> sorted = new TreeMap<String, TreeSet<String>>();
- for (MobyNamespace n : fullNamespaces) {
- String name = n.getName();
- String key = name.toUpperCase().substring(0, 1);
- if (sorted.get(key) == null) {
- sorted.put(key, new TreeSet<String>());
- }
- sorted.get(key).add(name);
- }
- for (String o : sorted.keySet()) {
- if (sorted.get(o) == null)
- continue;
- TreeSet<String> set = sorted.get(o);
- String first = set.first().toUpperCase().charAt(0) + "";
- DefaultMutableTreeNode node = new DefaultMutableTreeNode(first);
- for (String s : set) {
- node.add(new DefaultMutableTreeNode(s));
- }
- root.add(node);
- }
- namespaceList = new JTree(root);
- }
- }
-
- /*
- * (non-Javadoc)
- *
- * @see org.embl.ebi.escience.scuflui.processoractions.AbstractProcessorAction#getComponent(org.embl.ebi.escience.scufl.Processor)
- */
- public JComponent getComponent(BiomobyObjectActivity activity) {
-
- // this was done so that for longer requests, something is shown visually and the user then wont think that nothing happened.
- Worker worker = new Worker(activity, this);
- worker.start();
- return worker.getPanel();
- }
-
- /*
- * method that processes the services returned by findService and adds them
- * to the TreeNode parentNode, sorted by authority
- */
- @SuppressWarnings("unchecked")
- private void createTreeNodes(MutableTreeNode parentNode, MobyService[] services) {
- HashMap inputHash;
- inputHash = new HashMap();
- for (int x = 0; x < services.length; x++) {
- DefaultMutableTreeNode authorityNode = null;
- if (!inputHash.containsKey(services[x].getAuthority())) {
- authorityNode = new DefaultMutableTreeNode(services[x].getAuthority());
- } else {
- authorityNode = (DefaultMutableTreeNode) inputHash.get(services[x].getAuthority());
- }
- MobyServiceTreeNode serv = new MobyServiceTreeNode(services[x].getName(), services[x]
- .getDescription());
- MutableTreeNode temp = new DefaultMutableTreeNode(serv);
- DefaultMutableTreeNode objects = new DefaultMutableTreeNode("Produces");
- // add to this node the MobyObjectTreeNodes that it produces!
- MobyData[] outputs = services[x].getPrimaryOutputs();
- for (int i = 0; i < outputs.length; i++) {
- if (outputs[i] instanceof MobyPrimaryDataSimple) {
- MobyPrimaryDataSimple simple = (MobyPrimaryDataSimple) outputs[i];
- StringBuffer sb = new StringBuffer("Namespaces used by this object: ");
- MobyNamespace[] namespaces = simple.getNamespaces();
- for (int j = 0; j < namespaces.length; j++) {
- sb.append(namespaces[j].getName() + " ");
- }
- if (namespaces.length == 0)
- sb.append("ANY ");
- MobyObjectTreeNode mobyObjectTreeNode = new MobyObjectTreeNode(simple
- .getDataType().getName()
- + "('" + simple.getName() + "')", sb.toString());
- objects.insert(new DefaultMutableTreeNode(mobyObjectTreeNode), objects
- .getChildCount());
- } else {
- // we have a collection
- MobyPrimaryDataSet collection = (MobyPrimaryDataSet) outputs[i];
- DefaultMutableTreeNode collectionNode = new DefaultMutableTreeNode(
- "Collection('" + collection.getName() + "')");
- objects.insert(collectionNode, objects.getChildCount());
- MobyPrimaryDataSimple[] simples = collection.getElements();
- for (int j = 0; j < simples.length; j++) {
- MobyPrimaryDataSimple simple = simples[j];
- StringBuffer sb = new StringBuffer("Namespaces used by this object: ");
- MobyNamespace[] namespaces = simple.getNamespaces();
- for (int k = 0; k < namespaces.length; k++) {
- sb.append(namespaces[k].getName() + " ");
- }
- if (namespaces.length == 0)
- sb.append("ANY ");
- MobyObjectTreeNode mobyObjectTreeNode = new MobyObjectTreeNode(simple
- .getDataType().getName()
- + "('" + simple.getName() + "')", sb.toString());
- collectionNode.insert(new DefaultMutableTreeNode(mobyObjectTreeNode),
- collectionNode.getChildCount());
- }
-
- }
- }
-
- temp.insert(objects, temp.getChildCount());
-
- authorityNode.insert(temp, authorityNode.getChildCount());
- inputHash.put(services[x].getAuthority(), authorityNode);
-
- }
- Set set = inputHash.keySet();
- SortedSet sortedset = new TreeSet(set);
- for (Iterator it = sortedset.iterator(); it.hasNext();) {
- parentNode.insert((DefaultMutableTreeNode) inputHash.get((String) it.next()),
- parentNode.getChildCount());
- }
- }
-
-
- /*
- * (non-Javadoc)
- *
- * @see org.embl.ebi.escience.scuflui.processoractions.ProcessorActionSPI#getDescription()
- */
- public String getDescription() {
- return "Moby Object Details";
- }
-
- /*
- *
- */
- public ImageIcon getIcon() {
- return MobyPanel.getIcon("/moby_small.gif");
- }
-
- /**
- * returns the frame size as a dimension for the content pane housing this
- * action
- */
- public Dimension getFrameSize() {
- return new Dimension(450, 450);
- }
-
- public void setNamespaces(MobyNamespace[] namespaces) {
- if (namespaces != null && namespaces.length == 0)
- this.namespaces = null;
- else
- this.namespaces = namespaces;
- }
- public MobyNamespace[] getNamespaces() {
- return this.namespaces == null ? new MobyNamespace[]{} : this.namespaces;
- }
-}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BiomobyScavengerDialog.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BiomobyScavengerDialog.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BiomobyScavengerDialog.java
deleted file mode 100644
index 4419bf9..0000000
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BiomobyScavengerDialog.java
+++ /dev/null
@@ -1,136 +0,0 @@
-/*******************************************************************************
- * This file is a component of the Taverna project, and is licensed under the
- * GNU LGPL. Copyright Edward Kawas, The BioMoby Project
- ******************************************************************************/
-/*
- * This file is a component of the Taverna project,
- * and is licensed under the GNU LGPL.
- * Copyright Edward Kawas, The BioMoby Project
- */
-package net.sf.taverna.t2.activities.biomoby.actions;
-
-import java.awt.GridLayout;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-
-import javax.swing.JComboBox;
-import javax.swing.JPanel;
-import javax.swing.JTextField;
-
-import org.biomoby.registry.meta.Registries;
-import org.biomoby.registry.meta.RegistriesList;
-import org.biomoby.shared.MobyException;
-
-import net.sf.taverna.t2.lang.ui.ShadedLabel;
-
-/**
- * a dialog for helping create scavengers for BioMoby registries that are not
- * the default registry.
- *
- */
-public class BiomobyScavengerDialog extends JPanel {
-
- private static final String CUSTOM = "Custom";
- private static final long serialVersionUID = -57047613557546674L;
- private JTextField registryEndpoint = new JTextField(
- "http://moby.ucalgary.ca/moby/MOBY-Central.pl");
- private JTextField registryURI = new JTextField(
- "http://moby.ucalgary.ca/MOBY/Central");
-
- /**
- * Default constructor.
- *
- */
- /**
- * Default constructor.
- *
- */
- public BiomobyScavengerDialog() {
- super();
- GridLayout layout = new GridLayout(5, 2);
- setLayout(layout);
-
- registryEndpoint.setEnabled(false);
- registryURI.setEnabled(false);
-
- // a combo box showing known registries
- final Registries regs = RegistriesList.getInstance();
- List<String> choices = new ArrayList<String>(Arrays.asList(regs.list()));
- choices.add(CUSTOM);
-
- JComboBox regList = new JComboBox(choices.toArray());
- regList.setToolTipText("A selection will fill text fields below");
- regList.setSelectedItem(Registries.DEFAULT_REGISTRY_SYNONYM);
- regList.addActionListener(new ActionListener() {
- public void actionPerformed(ActionEvent e) {
- String contents = (String) ((JComboBox) e.getSource())
- .getSelectedItem();
-
- if (contents.equals(CUSTOM)) {
- registryEndpoint.setEnabled(true);
- registryURI.setEnabled(true);
- return;
- } else {
- registryEndpoint.setEnabled(false);
- registryURI.setEnabled(false);
- }
- org.biomoby.registry.meta.Registry theReg = null;
- try {
- theReg = regs.get(contents);
- } catch (MobyException ee) {
- try {
- theReg = regs.get(null);
- } catch (MobyException ee2) {
-
- }
- }
- if (theReg != null) {
- registryEndpoint.setText(theReg.getEndpoint());
- registryURI.setText(theReg.getNamespace());
-
- }
- }
- });
- add(new ShadedLabel("Choose a registry from the list: ",
- ShadedLabel.BLUE, true));
- add(regList);
- add(new ShadedLabel("Or select '" + CUSTOM + "' to enter your own below,", ShadedLabel.BLUE, true));
- add(new ShadedLabel("", ShadedLabel.BLUE, true));
- add(new ShadedLabel(
- "Location (URL) of your BioMoby central registry: ",
- ShadedLabel.BLUE, true));
- registryEndpoint
- .setToolTipText("BioMoby Services will be retrieved from the endpoint that you specify here!");
- add(registryEndpoint);
- add(new ShadedLabel(
- "Namespace (URI) of your BioMoby central registry: ",
- ShadedLabel.BLUE, true));
- registryURI
- .setToolTipText("BioMoby Services will be retrieved from the endpoint/URI that you specify here!");
- add(registryURI);
- // add(Box.createHorizontalGlue());add(Box.createHorizontalGlue());
- setPreferredSize(this.getPreferredSize());
- setMinimumSize(this.getPreferredSize());
- setMaximumSize(this.getPreferredSize());
-
- }
-
- /**
- *
- * @return the string representation of the BioMoby Registry endpoint
- */
- public String getRegistryEndpoint() {
- return registryEndpoint.getText();
- }
-
- /**
- *
- * @return the string representation of the BioMoby Registry endpoint
- */
- public String getRegistryURI() {
- return registryURI.getText();
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyObjectDetailsAction.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyObjectDetailsAction.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyObjectDetailsAction.java
deleted file mode 100644
index 803fde3..0000000
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyObjectDetailsAction.java
+++ /dev/null
@@ -1,83 +0,0 @@
-/**
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- */
-package net.sf.taverna.t2.activities.biomoby.actions;
-
-import java.awt.Component;
-import java.awt.Dimension;
-import java.awt.Frame;
-import java.awt.event.ActionEvent;
-
-import javax.swing.AbstractAction;
-import javax.swing.JDialog;
-
-import net.sf.taverna.t2.activities.biomoby.BiomobyObjectActivity;
-import net.sf.taverna.t2.workbench.edits.EditManager;
-import net.sf.taverna.t2.workbench.file.FileManager;
-import net.sf.taverna.t2.workbench.helper.HelpEnabledDialog;
-
-/**
- * @author Stuart Owen
- *
- */
-@SuppressWarnings("serial")
-public class MobyObjectDetailsAction extends AbstractAction {
-
- private final BiomobyObjectActivity activity;
- private final Frame owner;
- private EditManager editManager;
-
- private static final String MOBY_OBJECT_DETAILS_ACTION = "Datatype registry query";
- private final FileManager fileManager;
-
- public MobyObjectDetailsAction(BiomobyObjectActivity activity, Frame owner, EditManager editManager, FileManager fileManager) {
- this.activity = activity;
- this.owner = owner;
- this.editManager = editManager;
- this.fileManager = fileManager;
- putValue(NAME, MOBY_OBJECT_DETAILS_ACTION);
-
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * java.awt.event.ActionListener#actionPerformed(java.awt.event.ActionEvent)
- */
- public void actionPerformed(ActionEvent e) {
- BiomobyObjectActionHelper helper = new BiomobyObjectActionHelper(editManager, fileManager);
- Dimension size = helper.getFrameSize();
-
- Component component = helper.getComponent(activity);
-
- final JDialog dialog = new HelpEnabledDialog(owner, helper.getDescription(), false, null);
- dialog.getContentPane().add(component);
- dialog.pack();
- // dialog.setTitle(helper.getDescription());
- dialog.setSize(size);
- // dialog.setModal(false);
- dialog.setVisible(true);
-
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyObjectTreeNode.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyObjectTreeNode.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyObjectTreeNode.java
deleted file mode 100644
index f58efc6..0000000
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyObjectTreeNode.java
+++ /dev/null
@@ -1,50 +0,0 @@
-/*
- * This file is a component of the Taverna project,
- * and is licensed under the GNU LGPL.
- * Copyright Edward Kawas, The BioMoby Project
- */
-package net.sf.taverna.t2.activities.biomoby.actions;
-
-import org.biomoby.shared.MobyNamespace;
-
-public class MobyObjectTreeNode {
-
- // name of the object == node name
- private String name = "";
-
- // description of object == tool tip text
- private String description = "";
-
- private MobyNamespace[] ns = null;
- /**
- *
- * @param name - the name of the Moby Object
- * @param description - the description of the Moby Service
- */
- public MobyObjectTreeNode(String name, String description) {
- this.name = name;
- this.description = description;
- }
- /*
- * over-ride the toString method in order to print node values
- * that make sense.
- */
- public String toString() {
- return name;
- }
-
- public void setNamespaces(MobyNamespace[] namespaces) {
- if (namespaces != null && namespaces.length == 0)
- this.ns = null;
- else
- this.ns = namespaces;
- }
-
- public MobyNamespace[] getNamespaces() {
- return this.ns;
- }
-
- public String getDescription() {
- return this.description;
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyPanel.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyPanel.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyPanel.java
deleted file mode 100644
index a2e0a70..0000000
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyPanel.java
+++ /dev/null
@@ -1,136 +0,0 @@
-/*
- * Created on Sep 9, 2005
- *
- * TODO To change the template for this generated file go to
- * Window - Preferences - Java - Code Style - Code Templates
- */
-package net.sf.taverna.t2.activities.biomoby.actions;
-
-import java.awt.BorderLayout;
-import java.awt.Frame;
-import java.awt.event.WindowAdapter;
-import java.awt.event.WindowEvent;
-
-import javax.swing.ImageIcon;
-
-import javax.swing.JLabel;
-import javax.swing.JPanel;
-
-import net.sf.taverna.t2.lang.ui.DialogTextArea;
-
-/**
- * @author Eddie Kawas
- *
- *
- */
-public class MobyPanel extends JPanel {
-
-
- private static final long serialVersionUID = 1L;
- private DialogTextArea textArea = null;
- private String text = "";
- private String name = "";
- private JLabel jLabel = new JLabel();
-
- /**
- * This is the default constructor
- */
- public MobyPanel(String label, String name, String text) {
- super(new BorderLayout());
- jLabel.setText(label);
- this.text = text;
- this.name = name;
- initialize();
- }
-
- public MobyPanel(String label) {
- super(new BorderLayout());
- jLabel.setText(label);
- initialize();
- }
- /**
- * This method initializes this
- *
- * @return void
- */
- private void initialize() {
- this.setSize(450, 450);
- jLabel.setHorizontalAlignment(JLabel.CENTER);
- add(jLabel, BorderLayout.NORTH);
- add(getTextArea(), BorderLayout.CENTER);
- }
-
- /**
- * This method initializes jTextArea
- *
- * @return DialogTextArea
- */
- private DialogTextArea getTextArea() {
- if (textArea == null) {
- textArea = new DialogTextArea();
- }
- textArea.setLineWrap(true);
- textArea.setWrapStyleWord(true);
- textArea.setText(this.text);
- textArea.setEditable(false);
- textArea.setEnabled(true);
- textArea.setAutoscrolls(true);
- textArea.setCaretPosition(0);
- return textArea;
- }
-
- public void setText(String text) {
- this.text = text;
- if (textArea == null) {
- textArea = new DialogTextArea(this.text);
- }
- textArea.setText(text);
- }
-
- /* (non-Javadoc)
- * @see org.embl.ebi.escience.scuflui.ScuflUIComponent#getIcon()
- */
- public ImageIcon getIcon() {
- return new ImageIcon(MobyPanel.class.getResource("/moby_small.png"));
- }
-
- /**
- *
- * @param icon a relative path to an icon to get
- * @return the ImageIcon at icon
- */
- public static ImageIcon getIcon(String icon) {
- return new ImageIcon(MobyPanel.class.getResource(icon));
- }
-
- public String getName(){
- if (name==null) return "";
- else return name;
- }
-
- public void onDisplay() {
- // TODO Auto-generated method stub
-
- }
-
- public void onDispose() {
- // TODO Auto-generated method stub
-
- }
-
- public static Frame CreateFrame(String title) {
- // Create a frame
- Frame frame = new Frame(title);
- // Add a listener for the close event
- frame.addWindowListener(new WindowAdapter() {
- public void windowClosing(WindowEvent evt) {
- Frame frame = (Frame)evt.getSource();
- // Hide the frame
- frame.setVisible(false);
- // If the frame is no longer needed, call dispose
- frame.dispose();
- }
- });
- return frame;
- }
- }
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyParserAction.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyParserAction.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyParserAction.java
deleted file mode 100644
index 865c1f1..0000000
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyParserAction.java
+++ /dev/null
@@ -1,70 +0,0 @@
-/**
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- */
-package net.sf.taverna.t2.activities.biomoby.actions;
-
-import java.awt.Component;
-import java.awt.Frame;
-import java.awt.event.ActionEvent;
-
-import javax.swing.AbstractAction;
-import javax.swing.JDialog;
-
-import net.sf.taverna.t2.activities.biomoby.BiomobyActivity;
-import net.sf.taverna.t2.workbench.edits.EditManager;
-import net.sf.taverna.t2.workbench.file.FileManager;
-import net.sf.taverna.t2.workbench.helper.HelpEnabledDialog;
-
-/**
- * @author Stuart Owen
- *
- */
-@SuppressWarnings("serial")
-public class MobyParserAction extends AbstractAction {
-
- private final BiomobyActivity activity;
- private final Frame owner;
- private EditManager editManager;
- private final FileManager fileManager;
-
- public MobyParserAction(BiomobyActivity activity, Frame owner, EditManager editManager, FileManager fileManager) {
- this.activity = activity;
- this.owner = owner;
- this.editManager = editManager;
- this.fileManager = fileManager;
- putValue(NAME, "Add Biomoby parser");
-
- }
- public void actionPerformed(ActionEvent e) {
- AddParserActionHelper helper = new AddParserActionHelper(editManager, fileManager);
- Component component = helper.getComponent(activity);
-
- final JDialog dialog = new HelpEnabledDialog(owner, helper.getDescription(), false, null);
- dialog.getContentPane().add(component);
- dialog.pack();
-// dialog.setSize(helper.getFrameSize());
- dialog.setTitle(helper.getDescription());
-// dialog.setModal(false);
- dialog.setVisible(true);
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyServiceDetailsAction.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyServiceDetailsAction.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyServiceDetailsAction.java
deleted file mode 100644
index 5000986..0000000
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyServiceDetailsAction.java
+++ /dev/null
@@ -1,65 +0,0 @@
-/*******************************************************************************
- * This file is a component of the Taverna project, and is licensed under the
- * GNU LGPL. Copyright Edward Kawas, The BioMoby Project
- ******************************************************************************/
-package net.sf.taverna.t2.activities.biomoby.actions;
-
-import java.awt.Component;
-import java.awt.Dimension;
-import java.awt.Frame;
-import java.awt.event.ActionEvent;
-
-import javax.swing.AbstractAction;
-import javax.swing.JDialog;
-
-import net.sf.taverna.t2.activities.biomoby.BiomobyActivity;
-import net.sf.taverna.t2.workbench.edits.EditManager;
-import net.sf.taverna.t2.workbench.file.FileManager;
-import net.sf.taverna.t2.workbench.helper.HelpEnabledDialog;
-
-/**
- * @author Stuart Owen
- *
- */
-@SuppressWarnings("serial")
-public class MobyServiceDetailsAction extends AbstractAction {
-
- private final BiomobyActivity activity;
- private final Frame owner;
- private EditManager editManager;
-
- private static final String MOBY_SERVICE_DETAILS_ACTION = "Browse Biomoby service details";
- private final FileManager fileManager;
- public MobyServiceDetailsAction(BiomobyActivity activity, Frame owner, EditManager editManager, FileManager fileManager) {
- this.activity = activity;
- this.owner = owner;
- this.editManager = editManager;
- this.fileManager = fileManager;
- putValue(NAME, MOBY_SERVICE_DETAILS_ACTION);
-
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * java.awt.event.ActionListener#actionPerformed(java.awt.event.ActionEvent)
- */
- public void actionPerformed(ActionEvent e) {
-
- BiomobyActionHelper helper = new BiomobyActionHelper(editManager, fileManager);
- Dimension size = helper.getFrameSize();
-
- Component component = helper.getComponent(activity);
- final JDialog dialog = new HelpEnabledDialog(owner, helper.getDescription(), false, null);
-
- dialog.getContentPane().add(component);
- dialog.pack();
-// dialog.setTitle(helper.getDescription());
- dialog.setSize(size);
-// dialog.setModal(false);
- dialog.setVisible(true);
-
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyServiceTreeNode.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyServiceTreeNode.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyServiceTreeNode.java
deleted file mode 100644
index c957a1f..0000000
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/MobyServiceTreeNode.java
+++ /dev/null
@@ -1,42 +0,0 @@
-/*
- * This file is a component of the Taverna project,
- * and is licensed under the GNU LGPL.
- * Copyright Edward Kawas, The BioMoby Project
- */
-package net.sf.taverna.t2.activities.biomoby.actions;
-import java.util.ArrayList;
-
-public class MobyServiceTreeNode {
-
- // name of the service == node name
- private String name = "";
-
- // list of objects that service produces
- @SuppressWarnings("unused")
- private ArrayList<MobyObjectTreeNode> mobyObjectTreeNodes = null;
-
- // description of object == tool tip text
- private String description = "";
-
-
- /**
- *
- * @param name - the name of the Moby Service
- * @param description - the description of the Moby Service
- */
- public MobyServiceTreeNode(String name, String description) {
- this.name = name;
- this.description = description;
- }
- /*
- * over-ride the toString method in order to print node values
- * that make sense.
- */
- public String toString() {
- return name;
- }
-
- public String getDescription() {
- return this.description;
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/PopupThread.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/PopupThread.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/PopupThread.java
deleted file mode 100644
index 0c8b9fc..0000000
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/PopupThread.java
+++ /dev/null
@@ -1,34 +0,0 @@
-package net.sf.taverna.t2.activities.biomoby.actions;
-
-import java.awt.Component;
-
-import net.sf.taverna.t2.activities.biomoby.BiomobyObjectActivity;
-
-
-public class PopupThread extends Thread {
-
- Object object = null;
-
- BiomobyObjectActivity objectActivity = null;
-
- BiomobyObjectActionHelper objectAction = null;
-
- boolean done = false;
-
- PopupThread(BiomobyObjectActivity bop, BiomobyObjectActionHelper boa) {
- super("Biomoby popup");
- this.objectAction = boa;
- this.objectActivity = bop;
- setDaemon(true);
- }
-
- public void run() {
- object = objectAction.getComponent(objectActivity);
- this.done = true;
- }
-
- // call after you check if done!
- public Component getComponent() {
- return (Component) object;
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/SimpleActionFrame.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/SimpleActionFrame.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/SimpleActionFrame.java
deleted file mode 100644
index a85b50b..0000000
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/SimpleActionFrame.java
+++ /dev/null
@@ -1,46 +0,0 @@
-/*
- * This file is a component of the Taverna project,
- * and is licensed under the GNU LGPL.
- * Copyright Edward Kawas, The BioMoby Project
- */
-package net.sf.taverna.t2.activities.biomoby.actions;
-
-import java.awt.BorderLayout;
-import java.awt.Component;
-
-import javax.swing.JPanel;
-
-
-/**
- * This class contains some methods that are useful in creating a consistent JPanel
- * for displaying information or actions for biomoby services and datatypes.
- *
- * @author Edward Kawas
- * @author Stuart Owen = initial port from T1 to T2
- *
- */
-public class SimpleActionFrame extends JPanel {
-
- private static final long serialVersionUID = -6611234116434482238L;
-
-
- private String name = "";
- public SimpleActionFrame(Component c, String name) {
- super(new BorderLayout());
- add(c, BorderLayout.CENTER);
-
- this.name = name;
- }
-
-
-
- public String getName() {
- return name;
- }
-
- public void onDisplay() {
-
- }
-
-
- }
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/datatypedescriptions/BiomobyDatatypeDescription.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/datatypedescriptions/BiomobyDatatypeDescription.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/datatypedescriptions/BiomobyDatatypeDescription.java
deleted file mode 100644
index 35df9b8..0000000
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/datatypedescriptions/BiomobyDatatypeDescription.java
+++ /dev/null
@@ -1,143 +0,0 @@
-package net.sf.taverna.t2.activities.biomoby.datatypedescriptions;
-
-import java.net.URI;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-
-import javax.swing.Icon;
-
-import net.sf.taverna.t2.activities.biomoby.BiomobyObjectActivity;
-import net.sf.taverna.t2.activities.biomoby.BiomobyObjectActivityConfigurationBean;
-import net.sf.taverna.t2.activities.biomoby.query.BiomobyObjectActivityIcon;
-import net.sf.taverna.t2.servicedescriptions.ServiceDescription;
-import net.sf.taverna.t2.workflowmodel.processor.activity.Activity;
-
-public class BiomobyDatatypeDescription extends
- ServiceDescription<BiomobyObjectActivityConfigurationBean> {
-
- private String authorityName;
- private String emailContact;
- private String datatypeName;
- private URI lsid;
- private String parent;
- private String[] lineage;
-
- private URI endpoint;
- private URI namespace;
-
- @Override
- public Class<? extends Activity<BiomobyObjectActivityConfigurationBean>> getActivityClass() {
- return BiomobyObjectActivity.class;
- }
-
- @Override
- public BiomobyObjectActivityConfigurationBean getActivityConfiguration() {
- BiomobyObjectActivityConfigurationBean bean = new BiomobyObjectActivityConfigurationBean();
- bean.setAuthorityName(getAuthorityName());
- bean.setServiceName(getDatatypeName());
- bean.setMobyEndpoint(getEndpoint().toASCIIString());
- return bean;
- }
-
- public String getAuthorityName() {
- return authorityName;
- }
-
- public void setAuthorityName(String authorityName) {
- this.authorityName = authorityName;
- }
-
- public String getEmailContact() {
- return emailContact;
- }
-
- public void setEmailContact(String emailContact) {
- this.emailContact = emailContact;
- }
-
- public String getDatatypeName() {
- return datatypeName;
- }
-
- public void setDatatypeName(String datatypeName) {
- this.datatypeName = datatypeName;
- }
-
- public URI getLsid() {
- return lsid;
- }
-
- public void setLsid(URI lsid) {
- this.lsid = lsid;
- }
-
- public String getParent() {
- return parent;
- }
-
- public void setParent(String parent) {
- this.parent = parent;
- }
-
- public URI getEndpoint() {
- return endpoint;
- }
-
- public void setEndpoint(URI endpoint) {
- this.endpoint = endpoint;
- }
-
- public URI getNamespace() {
- return namespace;
- }
-
- public void setNamespace(URI namespace) {
- this.namespace = namespace;
- }
-
- public String[] getLineage() {
- return lineage;
- }
-
- public void setLineage(String[] lineage) {
- this.lineage = lineage;
- }
-
- @Override
- public String getName() {
- return getDatatypeName();
- }
-
- @Override
- protected List<Object> getIdentifyingData() {
- return Arrays.<Object> asList(getNamespace(), getEndpoint(), getAuthorityName(),
- getDatatypeName());
- }
-
- @Override
- public List<String> getPath() {
- ArrayList<String> list = new ArrayList<String>();
- list.add("Biomoby @ " + getEndpoint());
- list.add("MOBY Objects");
- list.addAll(Arrays.asList(getLineage()));
- return list;
- }
-
- @Override
- public Icon getIcon() {
- return new BiomobyObjectActivityIcon().getIcon(new BiomobyObjectActivity());
- }
-
- @Override
- public String toString() {
- return getName();
- }
-
- // public Edit getInsertionEdit(Dataflow dataflow, Processor p, Activity a) {
- // if (a instanceof BiomobyObjectActivity) {
- // return new AddUpstreamObjectEdit(dataflow, p, (BiomobyObjectActivity) a);
- // }
- // return null;
- // }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/edits/AddBiomobyCollectionDataTypeEdit.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/edits/AddBiomobyCollectionDataTypeEdit.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/edits/AddBiomobyCollectionDataTypeEdit.java
deleted file mode 100644
index 8e02195..0000000
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/edits/AddBiomobyCollectionDataTypeEdit.java
+++ /dev/null
@@ -1,60 +0,0 @@
-/**
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- */
-package net.sf.taverna.t2.activities.biomoby.edits;
-
-import net.sf.taverna.t2.activities.biomoby.BiomobyActivity;
-import net.sf.taverna.t2.workflowmodel.Dataflow;
-import net.sf.taverna.t2.workflowmodel.Edits;
-
-/**
- * @author Stuart Owen
- *
- */
-public class AddBiomobyCollectionDataTypeEdit extends
- AddBiomobyDataTypeEdit {
-
- private final String theCollectionName;
-
- /**
- * @param dataflow
- * @param activity
- * @param objectName
- */
- public AddBiomobyCollectionDataTypeEdit(Dataflow dataflow,
- BiomobyActivity activity, String objectName, String theCollectionName, Edits edits) {
- super(dataflow, activity, objectName, edits);
- this.theCollectionName = theCollectionName;
- }
-
- @Override
- protected String determineInputPortName(String defaultName,String objectName) {
- return defaultName
- + "(Collection - '"
- + (theCollectionName.equals("") ? "MobyCollection"
- : theCollectionName)
- + "')";
- }
-
-
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/edits/AddBiomobyConsumingServiceEdit.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/edits/AddBiomobyConsumingServiceEdit.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/edits/AddBiomobyConsumingServiceEdit.java
deleted file mode 100644
index e13c208..0000000
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/edits/AddBiomobyConsumingServiceEdit.java
+++ /dev/null
@@ -1,236 +0,0 @@
-/**
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- */
-package net.sf.taverna.t2.activities.biomoby.edits;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import org.biomoby.registry.meta.Registry;
-import org.biomoby.shared.MobyDataType;
-
-import net.sf.taverna.t2.activities.biomoby.BiomobyActivity;
-import net.sf.taverna.t2.activities.biomoby.BiomobyActivityConfigurationBean;
-import net.sf.taverna.t2.activities.biomoby.BiomobyObjectActivity;
-import net.sf.taverna.t2.workflowmodel.CompoundEdit;
-import net.sf.taverna.t2.workflowmodel.Dataflow;
-import net.sf.taverna.t2.workflowmodel.Edit;
-import net.sf.taverna.t2.workflowmodel.EditException;
-import net.sf.taverna.t2.workflowmodel.Edits;
-import net.sf.taverna.t2.workflowmodel.EventForwardingOutputPort;
-import net.sf.taverna.t2.workflowmodel.EventHandlingInputPort;
-import net.sf.taverna.t2.workflowmodel.InputPort;
-import net.sf.taverna.t2.workflowmodel.OutputPort;
-import net.sf.taverna.t2.workflowmodel.ProcessorInputPort;
-import net.sf.taverna.t2.workflowmodel.ProcessorOutputPort;
-import net.sf.taverna.t2.workflowmodel.impl.AbstractDataflowEdit;
-import net.sf.taverna.t2.workflowmodel.impl.DataflowImpl;
-import net.sf.taverna.t2.workflowmodel.processor.activity.Activity;
-import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityInputPort;
-import net.sf.taverna.t2.workflowmodel.utils.Tools;
-
-/**
- * @author Stuart Owen
- *
- */
-public class AddBiomobyConsumingServiceEdit extends AbstractDataflowEdit {
-
- private final BiomobyObjectActivity activity;
- private final String serviceName;
- private Edits edits;
- Edit<?> compoundEdit = null;
- Edit<?> linkEdit = null;
- private final String authority;
- private final OutputPort outputPort;
-
- /**
- * @param dataflow
- */
- public AddBiomobyConsumingServiceEdit(Dataflow dataflow,
- BiomobyObjectActivity activity, String serviceName,String authority,OutputPort outputPort, Edits edits) {
- super(dataflow);
-
- this.activity = activity;
- this.serviceName = serviceName;
- this.authority = authority;
- this.outputPort = outputPort;
- this.edits = edits;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * net.sf.taverna.t2.workflowmodel.impl.AbstractEdit#doEditAction(java.lang
- * .Object)
- */
- @Override
- protected void doEditAction(DataflowImpl dataflow) throws EditException {
- String defaultName = serviceName;
- String name = Tools
- .uniqueProcessorName(defaultName, dataflow);
-
- List<Edit<?>> editList = new ArrayList<Edit<?>>();
-
- net.sf.taverna.t2.workflowmodel.Processor sinkProcessor = edits
- .createProcessor(name);
-
- BiomobyActivityConfigurationBean bean = new BiomobyActivityConfigurationBean();
- bean.setAuthorityName(authority);
- bean.setServiceName(serviceName);
- bean.setMobyEndpoint(activity.getConfiguration().getMobyEndpoint());
- BiomobyActivity boActivity = new BiomobyActivity();
- editList.add(edits.getConfigureActivityEdit(boActivity, bean));
-
- editList.add(edits.getDefaultDispatchStackEdit(sinkProcessor));
-
- Edit<?> addActivityToProcessorEdit = edits.getAddActivityEdit(
- sinkProcessor, boActivity);
- editList.add(addActivityToProcessorEdit);
-
- editList.add(edits.getAddProcessorEdit(dataflow, sinkProcessor));
-
- compoundEdit = new CompoundEdit(editList);
- compoundEdit.doEdit();
-
- net.sf.taverna.t2.workflowmodel.Processor sourceProcessor = Tools.getProcessorsWithActivityOutputPort(dataflow, outputPort).iterator().next();
-
- List<Edit<?>> linkEditList = new ArrayList<Edit<?>>();
-
- EventForwardingOutputPort sourcePort = null;
- //FIXME: there is an assumption here that the processor will contain only 1 activity.
- if (outputPort != null) {
- sourcePort = getSourcePort(sourceProcessor, sourceProcessor.getActivityList().get(0), outputPort.getName(), linkEditList);
- }
- else {
- sourcePort = getSourcePort(sourceProcessor, sourceProcessor.getActivityList().get(0), sourceProcessor.getOutputPorts().get(0).getName(), linkEditList);
- }
- // get the input port that isnt called 'input'
- String inputPortName = "";
- for (ActivityInputPort aip : sinkProcessor.getActivityList().get(0).getInputPorts()) {
- if (!aip.getName().equalsIgnoreCase("input")) {
- // try to match the datatype to an input port
- String dtName = activity.getMobyObject().getName();
- String sinkDtname = aip.getName();
- if (sinkDtname.indexOf("(") > 0)
- sinkDtname = sinkDtname.substring(0, sinkDtname.indexOf("("));
- // are the datatype names exactly the same?
- if (dtName.equals(sinkDtname)) {
- inputPortName = aip.getName();
- break;
- }
- // check for the name in the datatypes lineage
- MobyDataType sinkDt = MobyDataType.getDataType(dtName,
- new Registry(
- activity.getCentral().getRegistryEndpoint(),
- activity.getCentral().getRegistryEndpoint(),
- activity.getCentral().getRegistryNamespace())
- );
- // check the lineage of the sinkdt for dtname
- for (MobyDataType lineage : sinkDt.getLineage()) {
- if (lineage.getName().equals(sinkDtname)) {
- inputPortName = aip.getName();
- break;
- }
- }
- // are we done?
- if (!inputPortName.trim().equals(""))
- break;
- }
- }
- // if inputPortName is not set, then just pick the first one
- if (inputPortName.trim().equals("")) {
- inputPortName = sinkProcessor.getActivityList().get(0).getInputPorts().iterator().next().getName();
- }
- EventHandlingInputPort sinkPort = getSinkPort(sinkProcessor, boActivity, inputPortName, linkEditList);
- if (sinkPort==null) {
- throw new EditException("No valid input called '"+inputPortName+"' found for Biomoby consuming service");
- }
- linkEditList.add(Tools
- .getCreateAndConnectDatalinkEdit(
- dataflow,
- sourcePort, sinkPort, edits));
- linkEdit = new CompoundEdit(linkEditList);
- linkEdit.doEdit();
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * net.sf.taverna.t2.workflowmodel.impl.AbstractEdit#undoEditAction(java
- * .lang.Object)
- */
- @Override
- protected void undoEditAction(DataflowImpl subjectImpl) {
- if (linkEdit!=null && linkEdit.isApplied())
- linkEdit.undo();
- if (compoundEdit!=null && compoundEdit.isApplied())
- compoundEdit.undo();
- }
-
- private EventHandlingInputPort getSinkPort(
- net.sf.taverna.t2.workflowmodel.Processor processor,
- Activity<?> activity, String portName, List<Edit<?>> editList) {
- InputPort activityPort = net.sf.taverna.t2.workflowmodel.utils.Tools
- .getActivityInputPort(activity, portName);
- // check if processor port exists
- EventHandlingInputPort input = net.sf.taverna.t2.workflowmodel.utils.Tools
- .getProcessorInputPort(processor, activity, activityPort);
- if (input == null) {
- // port doesn't exist so create a processor port and map it
- ProcessorInputPort processorInputPort = edits
- .createProcessorInputPort(processor,
- activityPort.getName(), activityPort.getDepth());
- editList.add(edits.getAddProcessorInputPortEdit(processor,
- processorInputPort));
- editList.add(edits.getAddActivityInputPortMappingEdit(activity,
- activityPort.getName(), activityPort.getName()));
- input = processorInputPort;
- }
- return input;
- }
-
- private EventForwardingOutputPort getSourcePort(
- net.sf.taverna.t2.workflowmodel.Processor processor,
- Activity<?> activity, String portName, List<Edit<?>> editList) {
- OutputPort activityPort = net.sf.taverna.t2.workflowmodel.utils.Tools
- .getActivityOutputPort(activity, portName);
- // check if processor port exists
- EventForwardingOutputPort output = net.sf.taverna.t2.workflowmodel.utils.Tools
- .getProcessorOutputPort(processor, activity, activityPort);
- if (output == null) {
- // port doesn't exist so create a processor port and map it
- ProcessorOutputPort processorOutputPort = edits
- .createProcessorOutputPort(processor, activityPort
- .getName(), activityPort.getDepth(), activityPort
- .getGranularDepth());
- editList.add(edits.getAddProcessorOutputPortEdit(processor,
- processorOutputPort));
- editList.add(edits.getAddActivityOutputPortMappingEdit(activity,
- activityPort.getName(), activityPort.getName()));
- output = processorOutputPort;
- }
- return output;
- }
-
-}
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diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/edits/AddBiomobyDataTypeEdit.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/edits/AddBiomobyDataTypeEdit.java
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--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/edits/AddBiomobyDataTypeEdit.java
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@@ -1,207 +0,0 @@
-/*******************************************************************************
- * This file is a component of the Taverna project, and is licensed under the
- * GNU LGPL. Copyright Edward Kawas, The BioMoby Project
- ******************************************************************************/
-package net.sf.taverna.t2.activities.biomoby.edits;
-
-import java.util.ArrayList;
-import java.util.List;
-
-import net.sf.taverna.t2.activities.biomoby.BiomobyActivity;
-import net.sf.taverna.t2.activities.biomoby.BiomobyObjectActivity;
-import net.sf.taverna.t2.activities.biomoby.BiomobyObjectActivityConfigurationBean;
-import net.sf.taverna.t2.workflowmodel.CompoundEdit;
-import net.sf.taverna.t2.workflowmodel.Dataflow;
-import net.sf.taverna.t2.workflowmodel.Edit;
-import net.sf.taverna.t2.workflowmodel.EditException;
-import net.sf.taverna.t2.workflowmodel.Edits;
-import net.sf.taverna.t2.workflowmodel.EventForwardingOutputPort;
-import net.sf.taverna.t2.workflowmodel.EventHandlingInputPort;
-import net.sf.taverna.t2.workflowmodel.InputPort;
-import net.sf.taverna.t2.workflowmodel.OutputPort;
-import net.sf.taverna.t2.workflowmodel.ProcessorInputPort;
-import net.sf.taverna.t2.workflowmodel.ProcessorOutputPort;
-import net.sf.taverna.t2.workflowmodel.impl.AbstractDataflowEdit;
-import net.sf.taverna.t2.workflowmodel.impl.DataflowImpl;
-import net.sf.taverna.t2.workflowmodel.processor.activity.Activity;
-import net.sf.taverna.t2.workflowmodel.utils.Tools;
-
-/**
- * @author Stuart Owen
- *
- */
-public class AddBiomobyDataTypeEdit extends AbstractDataflowEdit {
-
- private final BiomobyActivity activity;
- private Edits edits;
- private final String objectName;
-
- private Edit<?> compoundEdit = null;
- private Edit<?> linkEdit = null;
- private Edit<?> upstreamObjectEdit = null;
-
-
- public AddBiomobyDataTypeEdit(Dataflow dataflow,BiomobyActivity activity,String objectName, Edits edits) {
- super(dataflow);
- this.activity = activity;
- this.objectName = objectName;
- this.edits = edits;
-
- }
-
-
-
-
-
- /* (non-Javadoc)
- * @see net.sf.taverna.t2.workflowmodel.impl.AbstractDataflowEdit#doEditAction(net.sf.taverna.t2.workflowmodel.impl.DataflowImpl)
- */
- @Override
- protected void doEditAction(DataflowImpl dataflow) throws EditException {
- List<Edit<?>> editList = new ArrayList<Edit<?>>();
-
-
- String defaultName = objectName;
- defaultName = defaultName.split("\\(")[0];
- String name = Tools.uniqueProcessorName(objectName, dataflow);
-
- BiomobyObjectActivityConfigurationBean configBean = new BiomobyObjectActivityConfigurationBean();
- configBean.setMobyEndpoint(activity
- .getConfiguration()
- .getMobyEndpoint());
- configBean.setAuthorityName("");
- configBean.setServiceName(defaultName);
-
-
- net.sf.taverna.t2.workflowmodel.Processor sourceProcessor = edits
- .createProcessor(name);
- BiomobyObjectActivity boActivity = new BiomobyObjectActivity();
- Edit<?> configureActivityEdit = edits
- .getConfigureActivityEdit(
- boActivity, configBean);
- editList.add(configureActivityEdit);
-
- editList
- .add(edits
- .getDefaultDispatchStackEdit(sourceProcessor));
-
- Edit<?> addActivityToProcessorEdit = edits
- .getAddActivityEdit(
- sourceProcessor,
- boActivity);
- editList
- .add(addActivityToProcessorEdit);
-
- String inputPortName = determineInputPortName(defaultName,objectName);
-
- editList.add(edits.getAddProcessorEdit(
- dataflow,
- sourceProcessor));
-
- compoundEdit = new CompoundEdit(
- editList);
- compoundEdit.doEdit();
-
- net.sf.taverna.t2.workflowmodel.Processor sinkProcessor = Tools
- .getProcessorsWithActivity(
- dataflow,
- activity).iterator()
- .next();
-
- List<Edit<?>> linkEditList = new ArrayList<Edit<?>>();
- EventHandlingInputPort sinkPort = getSinkPort(
- sinkProcessor, activity,
- inputPortName, linkEditList);
- EventForwardingOutputPort sourcePort = getSourcePort(
- sourceProcessor, boActivity,
- "mobyData", linkEditList);
-
- linkEditList.add(Tools
- .getCreateAndConnectDatalinkEdit(
- dataflow,
- sourcePort, sinkPort, edits));
- linkEdit = new CompoundEdit(linkEditList);
- linkEdit.doEdit();
-
- if (!(defaultName.equalsIgnoreCase("Object")
- || defaultName.equalsIgnoreCase("String")
- || defaultName.equalsIgnoreCase("Integer")
- || defaultName.equalsIgnoreCase("Float")
- || defaultName.equalsIgnoreCase("DateTime"))) {
- upstreamObjectEdit=new AddUpstreamObjectEdit(dataflow,sourceProcessor,boActivity, edits);
- upstreamObjectEdit.doEdit();
-
- }
- }
-
- protected String determineInputPortName(String defaultName,String objectName) {
- String inputPortName = objectName
- .replaceAll("'", "");
- if (inputPortName.indexOf("()") > 0)
- inputPortName = inputPortName
- .replaceAll("\\(\\)",
- "\\(_ANON_\\)");
- return inputPortName;
- }
-
- /* (non-Javadoc)
- * @see net.sf.taverna.t2.workflowmodel.impl.AbstractDataflowEdit#undoEditAction(net.sf.taverna.t2.workflowmodel.impl.DataflowImpl)
- */
- @Override
- protected void undoEditAction(DataflowImpl dataflow) {
- if (linkEdit!=null && linkEdit.isApplied())
- linkEdit.undo();
- if (compoundEdit!=null && compoundEdit.isApplied())
- compoundEdit.undo();
- if (upstreamObjectEdit!=null && upstreamObjectEdit.isApplied()) {
- upstreamObjectEdit.undo();
- }
-
- }
-
- private EventHandlingInputPort getSinkPort(
- net.sf.taverna.t2.workflowmodel.Processor processor,
- Activity<?> activity, String portName, List<Edit<?>> editList) {
- InputPort activityPort = net.sf.taverna.t2.workflowmodel.utils.Tools
- .getActivityInputPort(activity, portName);
- // check if processor port exists
- EventHandlingInputPort input = net.sf.taverna.t2.workflowmodel.utils.Tools
- .getProcessorInputPort(processor, activity, activityPort);
- if (input == null) {
- // port doesn't exist so create a processor port and map it
- ProcessorInputPort processorInputPort = edits
- .createProcessorInputPort(processor,
- activityPort.getName(), activityPort.getDepth());
- editList.add(edits.getAddProcessorInputPortEdit(processor,
- processorInputPort));
- editList.add(edits.getAddActivityInputPortMappingEdit(activity,
- activityPort.getName(), activityPort.getName()));
- input = processorInputPort;
- }
- return input;
- }
-
- private EventForwardingOutputPort getSourcePort(
- net.sf.taverna.t2.workflowmodel.Processor processor,
- Activity<?> activity, String portName, List<Edit<?>> editList) {
- OutputPort activityPort = net.sf.taverna.t2.workflowmodel.utils.Tools
- .getActivityOutputPort(activity, portName);
- // check if processor port exists
- EventForwardingOutputPort output = net.sf.taverna.t2.workflowmodel.utils.Tools
- .getProcessorOutputPort(processor, activity, activityPort);
- if (output == null) {
- // port doesn't exist so create a processor port and map it
- ProcessorOutputPort processorOutputPort = edits
- .createProcessorOutputPort(processor, activityPort
- .getName(), activityPort.getDepth(), activityPort
- .getGranularDepth());
- editList.add(edits.getAddProcessorOutputPortEdit(processor,
- processorOutputPort));
- editList.add(edits.getAddActivityOutputPortMappingEdit(activity,
- activityPort.getName(), activityPort.getName()));
- output = processorOutputPort;
- }
- return output;
- }
-
-}
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diff --git a/taverna-biomart-martservice/src/test/java/org/biomart/martservice/MartDatasetTest.java b/taverna-biomart-martservice/src/test/java/org/biomart/martservice/MartDatasetTest.java
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--- a/taverna-biomart-martservice/src/test/java/org/biomart/martservice/MartDatasetTest.java
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@@ -1,335 +0,0 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: MartDatasetTest.java,v $
- * Revision $Revision: 1.1 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/01/31 14:12:14 $
- * by $Author: davidwithers $
- * Created on 4 Aug 2006
- *****************************************************************/
-package org.biomart.martservice;
-
-import junit.framework.TestCase;
-
-/**
- *
- * @author David Withers
- */
-public class MartDatasetTest extends TestCase {
-
- private String displayName;
-
- private String name;
-
- private String type;
-
- private int initialBatchSize;
-
- private int maximumBatchSize;
-
- private boolean visible;
-
- private String interfaceValue;
-
- private String modified;
-
- private MartURLLocation martUrlLocation;
-
- private MartDataset martDataset;
-
- /*
- * (non-Javadoc)
- *
- * @see junit.framework.TestCase#setUp()
- */
- protected void setUp() throws Exception {
- super.setUp();
- displayName = "dataset-display-name";
- name = "dataset-name";
- type = "type";
- initialBatchSize = 1;
- maximumBatchSize = 2;
- visible = true;
- interfaceValue = "interface";
- modified = "modified";
- martUrlLocation = new MartURLLocation();
- martUrlLocation.setDefault(true);
- martUrlLocation.setDisplayName("location-display-name");
- martUrlLocation.setHost("host");
- martUrlLocation.setName("location-name");
- martUrlLocation.setPort(42);
- martUrlLocation.setServerVirtualSchema("server-virtual-schema");
- martUrlLocation.setVirtualSchema("virtual-schema");
- martUrlLocation.setVisible(false);
- martDataset = new MartDataset();
- martDataset.setDisplayName(displayName);
- martDataset.setInitialBatchSize(initialBatchSize);
- martDataset.setMartURLLocation(martUrlLocation);
- martDataset.setMaximumBatchSize(maximumBatchSize);
- martDataset.setName(name);
- martDataset.setType(type);
- martDataset.setVisible(visible);
- martDataset.setInterface(interfaceValue);
- martDataset.setModified(modified);
- }
-
- /**
- * Test method for {@link org.biomart.martservice.MartDataset#hashCode()}.
- */
- public void testHashCode() {
- assertEquals(martDataset.hashCode(), martDataset.hashCode());
- }
-
- /**
- * Test method for
- * {@link org.biomart.martservice.MartDataset#getDisplayName()}.
- */
- public void testGetDisplayName() {
- assertEquals(martDataset.getDisplayName(), displayName);
- }
-
- /**
- * Test method for
- * {@link org.biomart.martservice.MartDataset#setDisplayName(java.lang.String)}.
- */
- public void testSetDisplayName() {
- martDataset.setDisplayName("new" + displayName);
- assertEquals(martDataset.getDisplayName(), "new" + displayName);
- martDataset.setDisplayName(null);
- assertNull(martDataset.getDisplayName());
- }
-
- /**
- * Test method for
- * {@link org.biomart.martservice.MartDataset#getInitialBatchSize()}.
- */
- public void testGetInitialBatchSize() {
- assertEquals(martDataset.getInitialBatchSize(), initialBatchSize);
- }
-
- /**
- * Test method for
- * {@link org.biomart.martservice.MartDataset#setInitialBatchSize(long)}.
- */
- public void testSetInitialBatchSize() {
- martDataset.setInitialBatchSize(1 + initialBatchSize);
- assertEquals(martDataset.getInitialBatchSize(), 1 + initialBatchSize);
- }
-
- /**
- * Test method for
- * {@link org.biomart.martservice.MartDataset#getMaximumBatchSize()}.
- */
- public void testGetMaximumBatchSize() {
- assertEquals(martDataset.getMaximumBatchSize(), maximumBatchSize);
- }
-
- /**
- * Test method for
- * {@link org.biomart.martservice.MartDataset#setMaximumBatchSize(long)}.
- */
- public void testSetMaximumBatchSize() {
- martDataset.setMaximumBatchSize(1 + maximumBatchSize);
- assertEquals(martDataset.getMaximumBatchSize(), 1 + maximumBatchSize);
- }
-
- /**
- * Test method for {@link org.biomart.martservice.MartDataset#getName()}.
- */
- public void testGetName() {
- assertEquals(martDataset.getName(), name);
- }
-
- /**
- * Test method for
- * {@link org.biomart.martservice.MartDataset#setName(java.lang.String)}.
- */
- public void testSetName() {
- martDataset.setName("new" + name);
- assertEquals(martDataset.getName(), "new" + name);
- martDataset.setName(null);
- assertNull(martDataset.getName());
- }
-
- /**
- * Test method for {@link org.biomart.martservice.MartDataset#getType()}.
- */
- public void testGetType() {
- assertEquals(martDataset.getType(), type);
- }
-
- /**
- * Test method for
- * {@link org.biomart.martservice.MartDataset#setType(java.lang.String)}.
- */
- public void testSetType() {
- martDataset.setType("new" + type);
- assertEquals(martDataset.getType(), "new" + type);
- martDataset.setType(null);
- assertNull(martDataset.getType());
- }
-
- /**
- * Test method for {@link org.biomart.martservice.MartDataset#isVisible()}.
- */
- public void testIsVisible() {
- assertEquals(martDataset.isVisible(), visible);
- }
-
- /**
- * Test method for
- * {@link org.biomart.martservice.MartDataset#setVisible(boolean)}.
- */
- public void testSetVisible() {
- martDataset.setVisible(!visible);
- assertEquals(martDataset.isVisible(), !visible);
- }
-
- /**
- * Test method for {@link org.biomart.martservice.MartDataset#getInterface()}.
- */
- public void testGetInterface() {
- assertEquals(martDataset.getInterface(), interfaceValue);
- }
-
- /**
- * Test method for
- * {@link org.biomart.martservice.MartDataset#setInterface(java.lang.String)}.
- */
- public void testSetInterface() {
- martDataset.setInterface("new" + interfaceValue);
- assertEquals(martDataset.getInterface(), "new" + interfaceValue);
- martDataset.setInterface(null);
- assertNull(martDataset.getInterface());
- }
-
- /**
- * Test method for {@link org.biomart.martservice.MartDataset#getModified()}.
- */
- public void testGetModified() {
- assertEquals(martDataset.getModified(), modified);
- }
-
- /**
- * Test method for
- * {@link org.biomart.martservice.MartDataset#setModified(java.lang.String)}.
- */
- public void testSetModified() {
- martDataset.setModified("new" + modified);
- assertEquals(martDataset.getModified(), "new" + modified);
- martDataset.setModified(null);
- assertNull(martDataset.getModified());
- }
-
- /**
- * Test method for
- * {@link org.biomart.martservice.MartDataset#getMartURLLocation()}.
- */
- public void testGetMartURLLocation() {
- assertEquals(martDataset.getMartURLLocation(), martUrlLocation);
- }
-
- /**
- * Test method for
- * {@link org.biomart.martservice.MartDataset#setMartURLLocation(org.biomart.martservice.MartURLLocation)}.
- */
- public void testSetMartURLLocation() {
- martUrlLocation = new MartURLLocation();
- martDataset.setMartURLLocation(martUrlLocation);
- assertEquals(martDataset.getMartURLLocation(), martUrlLocation);
- martDataset.setMartURLLocation(null);
- assertNull(martDataset.getMartURLLocation());
- }
-
- /**
- * Test method for
- * {@link org.biomart.martservice.MartDataset#getVirtualSchema()}.
- */
- public void testGetVirtualSchema() {
- assertEquals(martDataset.getVirtualSchema(), martDataset
- .getMartURLLocation().getVirtualSchema());
- martDataset.setMartURLLocation(null);
- assertNull(martDataset.getVirtualSchema());
- }
-
- /**
- * Test method for
- * {@link org.biomart.martservice.MartDataset#getQualifiedName()}.
- */
- public void testGetQualifiedName() {
- assertEquals(martDataset.getQualifiedName(), martDataset
- .getVirtualSchema()
- + "." + name);
- martDataset.setMartURLLocation(null);
- assertEquals(martDataset.getQualifiedName(), name);
- }
-
- /**
- * Test method for {@link org.biomart.martservice.MartDataset#toString()}.
- */
- public void testToString() {
- assertEquals(martDataset.toString(), martDataset.getDisplayName());
- }
-
- /**
- * Test method for
- * {@link org.biomart.martservice.MartDataset#equals(java.lang.Object)}.
- */
- public void testEqualsObject() {
- MartDataset martDataset2 = new MartDataset();
- martDataset2.setDisplayName(displayName);
- martDataset2.setInitialBatchSize(initialBatchSize);
- martDataset2.setMartURLLocation(martUrlLocation);
- martDataset2.setMaximumBatchSize(maximumBatchSize);
- martDataset2.setName(name);
- martDataset2.setType(type);
- martDataset2.setVisible(visible);
-
- assertTrue(martDataset.equals(martDataset));
- assertTrue(martDataset.equals(martDataset2));
- assertTrue(martDataset2.equals(martDataset));
- assertFalse(martDataset.equals(null));
- assertFalse(martDataset.equals(new Object()));
- assertFalse(martDataset.equals(new MartRegistry()));
- martDataset2.setName("new" + name);
- assertFalse(martDataset.equals(martDataset2));
- assertFalse(martDataset2.equals(martDataset));
- }
-
- /**
- * Test method for
- * {@link org.biomart.martservice.MartDataset#getDisplayComparator()}.
- */
- public void testGetDisplayComparator() {
- MartDataset martDataset2 = new MartDataset();
- martDataset2.setDisplayName(displayName);
- assertEquals(MartDataset.getDisplayComparator().compare(martDataset, martDataset2), 0);
- martDataset2.setDisplayName("new" + displayName);
- assertTrue(MartDataset.getDisplayComparator().compare(martDataset, martDataset2) != 0);
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-martservice/src/test/java/org/biomart/martservice/MartRegistryTest.java
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diff --git a/taverna-biomart-martservice/src/test/java/org/biomart/martservice/MartRegistryTest.java b/taverna-biomart-martservice/src/test/java/org/biomart/martservice/MartRegistryTest.java
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--- a/taverna-biomart-martservice/src/test/java/org/biomart/martservice/MartRegistryTest.java
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@@ -1,113 +0,0 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: MartRegistryTest.java,v $
- * Revision $Revision: 1.1 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/01/31 14:12:14 $
- * by $Author: davidwithers $
- * Created on 4 Aug 2006
- *****************************************************************/
-package org.biomart.martservice;
-
-import junit.framework.TestCase;
-
-/**
- *
- * @author David Withers
- */
-public class MartRegistryTest extends TestCase {
-
- private MartURLLocation martUrlLocation;
-
- private MartRegistry martRegistry;
-
- /* (non-Javadoc)
- * @see junit.framework.TestCase#setUp()
- */
- protected void setUp() throws Exception {
- super.setUp();
- martUrlLocation = new MartURLLocation();
- martUrlLocation.setDefault(true);
- martUrlLocation.setDisplayName("location-display-name");
- martUrlLocation.setHost("host");
- martUrlLocation.setName("location-name");
- martUrlLocation.setPort(42);
- martUrlLocation.setServerVirtualSchema("server-virtual-schema");
- martUrlLocation.setVirtualSchema("virtual-schema");
- martUrlLocation.setVisible(false);
- martRegistry = new MartRegistry();
- }
-
- /**
- * Test method for {@link org.biomart.martservice.MartRegistry#hashCode()}.
- */
- public void testHashCode() {
- MartRegistry martRegistry2 = new MartRegistry();
- martRegistry.addMartURLLocation(martUrlLocation);
- martRegistry2.addMartURLLocation(martUrlLocation);
- assertEquals(martRegistry.hashCode(), martRegistry.hashCode());
- assertEquals(martRegistry.hashCode(), martRegistry2.hashCode());
- }
-
- /**
- * Test method for {@link org.biomart.martservice.MartRegistry#getMartURLLocations()}.
- */
- public void testGetMartURLLocations() {
- assertEquals(martRegistry.getMartURLLocations().length, 0);
- martRegistry.addMartURLLocation(martUrlLocation);
- assertEquals(martRegistry.getMartURLLocations()[0], martUrlLocation);
- }
-
- /**
- * Test method for {@link org.biomart.martservice.MartRegistry#addMartURLLocation(org.biomart.martservice.MartURLLocation)}.
- */
- public void testAddMartURLLocation() {
- martRegistry.addMartURLLocation(martUrlLocation);
- MartURLLocation[] martURLLocations = martRegistry.getMartURLLocations();
- assertEquals(martURLLocations[martURLLocations.length - 1], martUrlLocation);
- }
-
- /**
- * Test method for {@link org.biomart.martservice.MartRegistry#equals(java.lang.Object)}.
- */
- public void testEqualsObject() {
- MartRegistry martRegistry2 = new MartRegistry();
- martRegistry.addMartURLLocation(martUrlLocation);
- martRegistry2.addMartURLLocation(martUrlLocation);
-
- assertTrue(martRegistry.equals(martRegistry));
- assertTrue(martRegistry.equals(martRegistry2));
- assertTrue(martRegistry2.equals(martRegistry));
- assertFalse(martRegistry.equals(null));
- assertFalse(martRegistry.equals(new Object()));
- assertFalse(martRegistry.equals(new MartRegistry()));
- martRegistry2.addMartURLLocation(martUrlLocation);
- assertFalse(martRegistry.equals(martRegistry2));
- assertFalse(martRegistry2.equals(martRegistry));
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-martservice/src/test/java/org/biomart/martservice/MartServiceUtilsTest.java
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diff --git a/taverna-biomart-martservice/src/test/java/org/biomart/martservice/MartServiceUtilsTest.java b/taverna-biomart-martservice/src/test/java/org/biomart/martservice/MartServiceUtilsTest.java
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--- a/taverna-biomart-martservice/src/test/java/org/biomart/martservice/MartServiceUtilsTest.java
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@@ -1,65 +0,0 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: MartServiceUtilsTest.java,v $
- * Revision $Revision: 1.1 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/02/22 18:31:56 $
- * by $Author: davidwithers $
- * Created on 22 Feb 2007
- *****************************************************************/
-package org.biomart.martservice;
-
-import static org.junit.Assert.*;
-
-import org.junit.Test;
-
-/**
- *
- * @author David Withers
- */
-public class MartServiceUtilsTest {
-
- /**
- * Test method for {@link org.biomart.martservice.MartServiceUtils#isProxyHost(java.lang.String)}.
- */
- @Test
- public void testIsProxyHost() {
- System.setProperty("http.nonProxyHosts", "localhost|127.0.0.1|*.mydomain.com|192.168.1.*");
- assertFalse(MartServiceUtils.isProxyHost("http://localhost/"));
- assertFalse(MartServiceUtils.isProxyHost("http://localhost:8080/"));
- assertFalse(MartServiceUtils.isProxyHost("http://127.0.0.1/"));
- assertFalse(MartServiceUtils.isProxyHost("http://www.mydomain.com/"));
- assertFalse(MartServiceUtils.isProxyHost("http://www.sub.mydomain.com/"));
- assertFalse(MartServiceUtils.isProxyHost("http://192.168.1.1/"));
- assertFalse(MartServiceUtils.isProxyHost("http://192.168.1.2/"));
- assertTrue(MartServiceUtils.isProxyHost("http://www.mydomain.co.uk/"));
- assertTrue(MartServiceUtils.isProxyHost("http://192.168.2.1/"));
- assertTrue(MartServiceUtils.isProxyHost("http://127.0.0.2/"));
- assertTrue(MartServiceUtils.isProxyHost("http://nonlocalhost/"));
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-martservice/src/test/java/org/biomart/martservice/MartServiceXMLHandlerTest.java
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diff --git a/taverna-biomart-martservice/src/test/java/org/biomart/martservice/MartServiceXMLHandlerTest.java b/taverna-biomart-martservice/src/test/java/org/biomart/martservice/MartServiceXMLHandlerTest.java
deleted file mode 100644
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--- a/taverna-biomart-martservice/src/test/java/org/biomart/martservice/MartServiceXMLHandlerTest.java
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@@ -1,218 +0,0 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: MartServiceXMLHandlerTest.java,v $
- * Revision $Revision: 1.2 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/10/04 14:16:00 $
- * by $Author: davidwithers $
- * Created on 02-Jun-2006
- *****************************************************************/
-package org.biomart.martservice;
-
-import java.io.IOException;
-import java.io.StringReader;
-
-import junit.framework.TestCase;
-import org.jdom.Element;
-import org.jdom.JDOMException;
-import org.jdom.Namespace;
-import org.jdom.input.SAXBuilder;
-import org.jdom.output.XMLOutputter;
-
-/**
- *
- * @author David Withers
- */
-public class MartServiceXMLHandlerTest extends TestCase {
- private XMLOutputter xmlOutputter;
-
- private SAXBuilder saxBuilder;
-
- private Namespace namespace;
-
- private MartService martService;
-
- private String martServiceXML;
-
- private MartURLLocation martUrlLocation;
-
- private String martUrlLocationXML;
-
- private MartDataset martDataset;
-
- private String martDatasetXML;
-
- private MartRegistry martRegistry;
-
- private String martRegistryXML;
-
- private String martRegistryXML2;
-
- /*
- * @see TestCase#setUp()
- */
- protected void setUp() throws Exception {
- super.setUp();
- xmlOutputter = new XMLOutputter();
- saxBuilder = new SAXBuilder();
- namespace = Namespace.getNamespace("test-namespace");
- martService = MartService.getMartService("url-location");
- martServiceXML = "<MartService xmlns=\"test-namespace\" location=\"url-location\" />";
- martUrlLocation = new MartURLLocation();
- martUrlLocation.setDefault(true);
- martUrlLocation.setDisplayName("location-display-name");
- martUrlLocation.setHost("host");
- martUrlLocation.setName("location-name");
- martUrlLocation.setPort(42);
- martUrlLocation.setServerVirtualSchema("server-virtual-schema");
- martUrlLocation.setVirtualSchema("virtual-schema");
- martUrlLocation.setVisible(false);
- martUrlLocation.setRedirect(true);
- martUrlLocationXML = "<MartURLLocation xmlns=\"test-namespace\" default=\"1\" displayName=\"location-display-name\" host=\"host\" name=\"location-name\" port=\"42\" serverVirtualSchema=\"server-virtual-schema\" virtualSchema=\"virtual-schema\" visible=\"0\" redirect=\"1\" />";
- martDataset = new MartDataset();
- martDataset.setDisplayName("dataset-display-name");
- martDataset.setInitialBatchSize(1);
- martDataset.setMartURLLocation(martUrlLocation);
- martDataset.setMaximumBatchSize(2);
- martDataset.setName("dataset-name");
- martDataset.setType("type");
- martDataset.setVisible(true);
- martDataset.setInterface("interface");
- martDataset.setModified("modified");
- martDatasetXML = "<MartDataset xmlns=\"test-namespace\" displayName=\"dataset-display-name\" name=\"dataset-name\" type=\"type\" initialBatchSize=\"1\" maximumBatchSize=\"2\" visible=\"true\" interface=\"interface\" modified=\"modified\"><MartURLLocation default=\"1\" displayName=\"location-display-name\" host=\"host\" name=\"location-name\" port=\"42\" serverVirtualSchema=\"server-virtual-schema\" virtualSchema=\"virtual-schema\" visible=\"0\" redirect=\"1\" /></MartDataset>";
- martRegistry = new MartRegistry();
- martRegistry.addMartURLLocation(martUrlLocation);
- martRegistryXML = "<MartRegistry xmlns=\"test-namespace\" ><virtualSchema xmlns=\"test-namespace\" name=\"virtual-schema\" visible=\"0\"><MartURLLocation xmlns=\"test-namespace\" default=\"1\" displayName=\"location-display-name\" host=\"host\" name=\"location-name\" port=\"42\" serverVirtualSchema=\"server-virtual-schema\" visible=\"0\" redirect=\"1\" /></virtualSchema></MartRegistry>";
- martRegistryXML2 = "<MartRegistry xmlns=\"test-namespace\" ><virtualSchema xmlns=\"test-namespace\" name=\"default\" visible=\"0\"><MartURLLocation xmlns=\"test-namespace\" default=\"1\" displayName=\"location-display-name\" host=\"host\" name=\"location-name\" port=\"42\" serverVirtualSchema=\"server-virtual-schema\" visible=\"0\" redirect=\"1\" /></virtualSchema></MartRegistry>";
- }
-
- /*
- * Test method for
- * 'org.biomart.martservice.MartServiceXMLHandler.martServiceToElement(MartService,
- * Namespace)'
- */
- public void testMartServiceToElement() {
- Element element = MartServiceXMLHandler.martServiceToElement(
- martService, namespace);
- assertEquals(xmlOutputter.outputString(element), martServiceXML);
- }
-
- /*
- * Test method for
- * 'org.biomart.martservice.MartServiceXMLHandler.elementToMartService(Element)'
- */
- public void testElementToMartService() throws JDOMException, IOException {
- Element element = saxBuilder.build(new StringReader(martServiceXML))
- .getRootElement();
- assertEquals(MartServiceXMLHandler.elementToMartService(element),
- martService);
- }
-
- /*
- * Test method for
- * 'org.biomart.martservice.MartServiceXMLHandler.datasetToElement(MartDataset,
- * Namespace)'
- */
- public void testDatasetToElement() {
- Element element = MartServiceXMLHandler.datasetToElement(martDataset,
- namespace);
- assertEquals(xmlOutputter.outputString(element), martDatasetXML);
-// System.out.println(new XMLOutputter().outputString(element));
- }
-
- /*
- * Test method for
- * 'org.biomart.martservice.MartServiceXMLHandler.elementToDataset(Element,
- * Namespace)'
- */
- public void testElementToDataset() throws JDOMException, IOException {
- Element element = saxBuilder.build(new StringReader(martDatasetXML))
- .getRootElement();
- assertEquals(
- MartServiceXMLHandler.elementToDataset(element, namespace),
- martDataset);
- }
-
- /*
- * Test method for
- * 'org.biomart.martservice.MartServiceXMLHandler.elementToRegistry(Element,
- * Namespace)'
- */
- public void testElementToRegistry() throws JDOMException, IOException {
- Element element = saxBuilder.build(new StringReader(martRegistryXML))
- .getRootElement();
- assertEquals(MartServiceXMLHandler
- .elementToRegistry(element, namespace), martRegistry);
-
- martUrlLocation.setVirtualSchema("default");
- element = saxBuilder.build(new StringReader(martRegistryXML2))
- .getRootElement();
- assertEquals(MartServiceXMLHandler
- .elementToRegistry(element, namespace), martRegistry);
- }
-
- /*
- * Test method for
- * 'org.biomart.martservice.MartServiceXMLHandler.locationToElement(MartURLLocation,
- * Namespace)'
- */
- public void testLocationToElement() {
- Element element = MartServiceXMLHandler.locationToElement(
- martUrlLocation, namespace);
- assertEquals(xmlOutputter.outputString(element), martUrlLocationXML);
- }
-
- /*
- * Test method for
- * 'org.biomart.martservice.MartServiceXMLHandler.elementToLocation(Element)'
- */
- public void testElementToLocation() throws JDOMException, IOException {
- Element element = saxBuilder
- .build(new StringReader(martUrlLocationXML)).getRootElement();
- assertEquals(MartServiceXMLHandler.elementToLocation(element),
- martUrlLocation);
- }
-
- /*
- * Test method for
- * 'org.biomart.martservice.MartServiceXMLHandler.elementToMartQuery(Element,
- * Namespace)'
- */
- public void testElementToMartQuery() {
-
- }
-
- /*
- * Test method for
- * 'org.biomart.martservice.MartServiceXMLHandler.martQueryToElement(MartQuery,
- * Namespace)'
- */
- public void testMartQueryToElement() {
-
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-martservice/src/test/java/org/biomart/martservice/MartURLLocationTest.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/test/java/org/biomart/martservice/MartURLLocationTest.java b/taverna-biomart-martservice/src/test/java/org/biomart/martservice/MartURLLocationTest.java
deleted file mode 100644
index aa5ad8a..0000000
--- a/taverna-biomart-martservice/src/test/java/org/biomart/martservice/MartURLLocationTest.java
+++ /dev/null
@@ -1,255 +0,0 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: MartURLLocationTest.java,v $
- * Revision $Revision: 1.1 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/01/31 14:12:14 $
- * by $Author: davidwithers $
- * Created on 02-Jun-2006
- *****************************************************************/
-package org.biomart.martservice;
-
-import junit.framework.TestCase;
-
-/**
- *
- * @author David Withers
- */
-public class MartURLLocationTest extends TestCase {
- private MartURLLocation martURLLocation;
- /*
- * @see TestCase#setUp()
- */
- protected void setUp() throws Exception {
- super.setUp();
- martURLLocation = new MartURLLocation();
- }
-
- /*
- * Test method for 'org.biomart.martservice.MartURLLocation.isDefault()'
- */
- public void testIsDefault() {
- assertFalse(martURLLocation.isDefault());
- martURLLocation.setDefault(true);
- assertTrue(martURLLocation.isDefault());
- }
-
- /*
- * Test method for 'org.biomart.martservice.MartURLLocation.setDefault(boolean)'
- */
- public void testSetDefault() {
- martURLLocation.setDefault(true);
- assertTrue(martURLLocation.isDefault());
- martURLLocation.setDefault(false);
- assertFalse(martURLLocation.isDefault());
- }
-
- /*
- * Test method for 'org.biomart.martservice.MartURLLocation.getDisplayName()'
- */
- public void testGetDisplayName() {
- assertNull(martURLLocation.getDisplayName());
- martURLLocation.setDisplayName("DisplayName");
- assertEquals(martURLLocation.getDisplayName(), "DisplayName");
- }
-
- /*
- * Test method for 'org.biomart.martservice.MartURLLocation.setDisplayName(String)'
- */
- public void testSetDisplayName() {
- martURLLocation.setDisplayName("DisplayName");
- assertEquals(martURLLocation.getDisplayName(), "DisplayName");
- martURLLocation.setDisplayName(null);
- assertNull(martURLLocation.getDisplayName());
- }
-
- /*
- * Test method for 'org.biomart.martservice.MartURLLocation.getHost()'
- */
- public void testGetHost() {
- assertNull(martURLLocation.getHost());
- martURLLocation.setHost("Host");
- assertEquals(martURLLocation.getHost(), "Host");
- }
-
- /*
- * Test method for 'org.biomart.martservice.MartURLLocation.setHost(String)'
- */
- public void testSetHost() {
- martURLLocation.setHost("Host");
- assertEquals(martURLLocation.getHost(), "Host");
- martURLLocation.setHost(null);
- assertNull(martURLLocation.getHost());
- }
-
- /*
- * Test method for 'org.biomart.martservice.MartURLLocation.getName()'
- */
- public void testGetName() {
- assertNull(martURLLocation.getName());
- martURLLocation.setName("Name");
- assertEquals(martURLLocation.getName(), "Name");
- }
-
- /*
- * Test method for 'org.biomart.martservice.MartURLLocation.setName(String)'
- */
- public void testSetName() {
- martURLLocation.setName("Name");
- assertEquals(martURLLocation.getName(), "Name");
- martURLLocation.setName(null);
- assertNull(martURLLocation.getName());
- }
-
- /*
- * Test method for 'org.biomart.martservice.MartURLLocation.getPort()'
- */
- public void testGetPort() {
- assertEquals(martURLLocation.getPort(), 0);
- martURLLocation.setPort(-1);
- assertEquals(martURLLocation.getPort(), -1);
- }
-
- /*
- * Test method for 'org.biomart.martservice.MartURLLocation.setPort(int)'
- */
- public void testSetPort() {
- martURLLocation.setPort(-1);
- assertEquals(martURLLocation.getPort(), -1);
- martURLLocation.setPort(0);
- assertEquals(martURLLocation.getPort(), 0);
- martURLLocation.setPort(1);
- assertEquals(martURLLocation.getPort(), 1);
- }
-
- /*
- * Test method for 'org.biomart.martservice.MartURLLocation.getServerVirtualSchema()'
- */
- public void testGetServerVirtualSchema() {
- assertNull(martURLLocation.getServerVirtualSchema());
- martURLLocation.setServerVirtualSchema("ServerVirtualSchema");
- assertEquals(martURLLocation.getServerVirtualSchema(), "ServerVirtualSchema");
- }
-
- /*
- * Test method for 'org.biomart.martservice.MartURLLocation.setServerVirtualSchema(String)'
- */
- public void testSetServerVirtualSchema() {
- martURLLocation.setServerVirtualSchema("ServerVirtualSchema");
- assertEquals(martURLLocation.getServerVirtualSchema(), "ServerVirtualSchema");
- martURLLocation.setServerVirtualSchema(null);
- assertNull(martURLLocation.getServerVirtualSchema());
- }
-
- /*
- * Test method for 'org.biomart.martservice.MartURLLocation.getVirtualSchema()'
- */
- public void testGetVirtualSchema() {
- assertNull(martURLLocation.getVirtualSchema());
- martURLLocation.setVirtualSchema("VirtualSchema");
- assertEquals(martURLLocation.getVirtualSchema(), "VirtualSchema");
-
- }
-
- /*
- * Test method for 'org.biomart.martservice.MartURLLocation.setVirtualSchema(String)'
- */
- public void testSetVirtualSchema() {
- martURLLocation.setVirtualSchema("VirtualSchema");
- assertEquals(martURLLocation.getVirtualSchema(), "VirtualSchema");
- martURLLocation.setVirtualSchema(null);
- assertNull(martURLLocation.getVirtualSchema());
- }
-
- /*
- * Test method for 'org.biomart.martservice.MartURLLocation.isVisible()'
- */
- public void testIsVisible() {
- assertFalse(martURLLocation.isVisible());
- martURLLocation.setVisible(true);
- assertTrue(martURLLocation.isVisible());
- }
-
- /*
- * Test method for 'org.biomart.martservice.MartURLLocation.setVisible(boolean)'
- */
- public void testSetVisible() {
- martURLLocation.setVisible(true);
- assertTrue(martURLLocation.isVisible());
- martURLLocation.setVisible(false);
- assertFalse(martURLLocation.isVisible());
- }
-
- /*
- * Test method for 'org.biomart.martservice.MartURLLocation.getType()'
- */
- public void testGetType() {
- assertEquals(martURLLocation.getType(), "URL");
- }
-
- /*
- * Test method for 'org.biomart.martservice.MartURLLocation.toString()'
- */
- public void testToString() {
- martURLLocation.setDisplayName("DisplayName");
- assertEquals(martURLLocation.toString(), "DisplayName");
- }
-
- public void testHashCode() {
- MartURLLocation martURLLocation2 = new MartURLLocation();
- assertEquals(martURLLocation.hashCode(), martURLLocation2.hashCode());
- martURLLocation.setDefault(true);
- martURLLocation2.setDefault(true);
- assertEquals(martURLLocation.hashCode(), martURLLocation2.hashCode());
- martURLLocation.setDisplayName("DisplayName");
- martURLLocation2.setDisplayName("DisplayName");
- assertEquals(martURLLocation.hashCode(), martURLLocation2.hashCode());
- martURLLocation.setHost("Host");
- martURLLocation2.setHost("Host");
- assertEquals(martURLLocation.hashCode(), martURLLocation2.hashCode());
- martURLLocation.setName("Name");
- martURLLocation2.setName("Name");
- assertEquals(martURLLocation.hashCode(), martURLLocation2.hashCode());
- martURLLocation.setPort(-1);
- martURLLocation2.setPort(-1);
- assertEquals(martURLLocation.hashCode(), martURLLocation2.hashCode());
- martURLLocation.setServerVirtualSchema("ServerVirtualSchema");
- martURLLocation2.setServerVirtualSchema("ServerVirtualSchema");
- assertEquals(martURLLocation.hashCode(), martURLLocation2.hashCode());
- martURLLocation.setVirtualSchema("VirtualSchema");
- martURLLocation2.setVirtualSchema("VirtualSchema");
- assertEquals(martURLLocation.hashCode(), martURLLocation2.hashCode());
- martURLLocation.setVisible(true);
- martURLLocation2.setVisible(true);
- assertEquals(martURLLocation.hashCode(), martURLLocation2.hashCode());
- martURLLocation.setVisible(true);
- martURLLocation2.setVisible(true);
- assertEquals(martURLLocation.hashCode(), martURLLocation2.hashCode());
-
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-martservice/src/test/java/org/biomart/martservice/config/event/QueryComponentEventTest.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/test/java/org/biomart/martservice/config/event/QueryComponentEventTest.java b/taverna-biomart-martservice/src/test/java/org/biomart/martservice/config/event/QueryComponentEventTest.java
deleted file mode 100644
index c22d8e2..0000000
--- a/taverna-biomart-martservice/src/test/java/org/biomart/martservice/config/event/QueryComponentEventTest.java
+++ /dev/null
@@ -1,131 +0,0 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: QueryComponentEventTest.java,v $
- * Revision $Revision: 1.1 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/01/31 14:12:15 $
- * by $Author: davidwithers $
- * Created on 06-Jun-2006
- *****************************************************************/
-package org.biomart.martservice.config.event;
-
-import org.biomart.martservice.MartDataset;
-
-import junit.framework.TestCase;
-
-/**
- *
- * @author David Withers
- */
-public class QueryComponentEventTest extends TestCase {
- private QueryComponentEvent queryComponentEvent;
-
- private QueryComponentEvent nullQueryComponentEvent;
-
- private Object source;
-
- private String name;
-
- private MartDataset martDataset;
-
- private String value;
-
- /*
- * @see TestCase#setUp()
- */
- protected void setUp() throws Exception {
- super.setUp();
- source = "source";
- name = "name";
- martDataset = new MartDataset();
- value = "value";
- queryComponentEvent = new QueryComponentEvent(source, name, martDataset, value);
- nullQueryComponentEvent = new QueryComponentEvent(source, null, null, null);
- }
-
- /*
- * Test method for
- * 'org.biomart.martservice.config.event.QueryComponentEvent.QueryComponentEvent(Object,
- * String, MartDataset)'
- */
- public void testQueryComponentEventObjectStringMartDataset() {
- QueryComponentEvent event = new QueryComponentEvent(source, name, martDataset);
- assertSame(event.getSource(), source);
- assertEquals(event.getName(), name);
- assertEquals(event.getDataset(), martDataset);
- assertNull(event.getValue());
- }
-
- /*
- * Test method for
- * 'org.biomart.martservice.config.event.QueryComponentEvent.QueryComponentEvent(Object,
- * String, MartDataset, String)'
- */
- public void testQueryComponentEventObjectStringMartDatasetString() {
- QueryComponentEvent event = new QueryComponentEvent(source, name, martDataset, value);
- assertSame(event.getSource(), source);
- assertEquals(event.getName(), name);
- assertEquals(event.getDataset(), martDataset);
- assertEquals(event.getValue(), value);
- }
-
- /*
- * Test method for
- * 'org.biomart.martservice.config.event.QueryComponentEvent.getName()'
- */
- public void testGetName() {
- assertEquals(queryComponentEvent.getName(), name);
- assertNull(nullQueryComponentEvent.getName());
- }
-
- /*
- * Test method for
- * 'org.biomart.martservice.config.event.QueryComponentEvent.getDataset()'
- */
- public void testGetDataset() {
- assertEquals(queryComponentEvent.getDataset(), martDataset);
- assertNull(nullQueryComponentEvent.getDataset());
- }
-
- /*
- * Test method for
- * 'org.biomart.martservice.config.event.QueryComponentEvent.getValue()'
- */
- public void testGetValue() {
- assertEquals(queryComponentEvent.getValue(), value);
- assertNull(nullQueryComponentEvent.getValue());
- }
-
- /*
- * Test method for 'java.util.EventObject.getSource()'
- */
- public void testGetSource() {
- assertSame(queryComponentEvent.getSource(), source);
- assertSame(nullQueryComponentEvent.getSource(), source);
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-martservice/src/test/java/org/biomart/martservice/config/ui/MartServiceIconsTest.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/test/java/org/biomart/martservice/config/ui/MartServiceIconsTest.java b/taverna-biomart-martservice/src/test/java/org/biomart/martservice/config/ui/MartServiceIconsTest.java
deleted file mode 100644
index 2236f37..0000000
--- a/taverna-biomart-martservice/src/test/java/org/biomart/martservice/config/ui/MartServiceIconsTest.java
+++ /dev/null
@@ -1,77 +0,0 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: MartServiceIconsTest.java,v $
- * Revision $Revision: 1.1 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/01/31 14:12:16 $
- * by $Author: davidwithers $
- * Created on 24-Aug-2006
- *****************************************************************/
-package org.biomart.martservice.config.ui;
-
-import junit.framework.TestCase;
-
-/**
- *
- * @author witherd5
- */
-public class MartServiceIconsTest extends TestCase {
-
- /* (non-Javadoc)
- * @see junit.framework.TestCase#setUp()
- */
- protected void setUp() throws Exception {
- super.setUp();
- }
-
- /**
- * Test method for {@link org.biomart.martservice.config.ui.MartServiceIcons#getIcon(java.lang.String)}.
- */
- public void testGetIcon() {
- assertNotNull(MartServiceIcons.getIcon("gene_schematic"));
- assertNotNull(MartServiceIcons.getIcon("gene_schematic"));
- assertNotNull(MartServiceIcons.getIcon("gene_schematic_3utr"));
- assertNotNull(MartServiceIcons.getIcon("gene_schematic_5utr"));
- assertNotNull(MartServiceIcons.getIcon("gene_schematic_cdna"));
- assertNotNull(MartServiceIcons.getIcon("gene_schematic_coding_gene_flank"));
- assertNotNull(MartServiceIcons.getIcon("gene_schematic_coding_transcript_flank"));
- assertNotNull(MartServiceIcons.getIcon("gene_schematic_coding"));
- assertNotNull(MartServiceIcons.getIcon("gene_schematic_gene_exon_intron"));
- assertNotNull(MartServiceIcons.getIcon("gene_schematic_gene_exon"));
- assertNotNull(MartServiceIcons.getIcon("gene_schematic_gene_flank"));
- assertNotNull(MartServiceIcons.getIcon("gene_schematic_peptide"));
- assertNotNull(MartServiceIcons.getIcon("gene_schematic_transcript_exon_intron"));
- assertNotNull(MartServiceIcons.getIcon("gene_schematic_transcript_exon"));
- assertNotNull(MartServiceIcons.getIcon("gene_schematic_transcript_flank"));
- assertNotNull(MartServiceIcons.getIcon("expand"));
- assertNotNull(MartServiceIcons.getIcon("contract"));
- assertNull(MartServiceIcons.getIcon("something else"));
- assertNull(MartServiceIcons.getIcon(""));
- assertNull(MartServiceIcons.getIcon(null));
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-martservice/src/test/java/org/biomart/martservice/query/AttributeTest.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/test/java/org/biomart/martservice/query/AttributeTest.java b/taverna-biomart-martservice/src/test/java/org/biomart/martservice/query/AttributeTest.java
deleted file mode 100644
index 5ac4c9e..0000000
--- a/taverna-biomart-martservice/src/test/java/org/biomart/martservice/query/AttributeTest.java
+++ /dev/null
@@ -1,164 +0,0 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: AttributeTest.java,v $
- * Revision $Revision: 1.2 $
- * Release status $State: Exp $
- * Last modified on $Date: 2008/03/04 16:43:40 $
- * by $Author: davidwithers $
- * Created on 02-May-2006
- *****************************************************************/
-package org.biomart.martservice.query;
-
-import org.junit.Test;
-import org.junit.Before;
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNull;
-
-/**
- *
- * @author David Withers
- */
-public class AttributeTest {
- private String attributeName;
-
- private String attributes;
-
- private Dataset dataset;
-
- private Attribute attribute;
-
- @Before
- public void setUp() throws Exception {
- attributeName = "attribute name";
- attributes = "attributes";
- dataset = new Dataset("dataset name");
- attribute = new Attribute(attributeName);
- }
-
- @Test
- public void AttributeString() {
- Attribute attribute = new Attribute(attributeName);
- assertEquals("Name should be '" + attributeName + "'", attribute
- .getName(), attributeName);
- }
-
- @Test
- public void AttributeAttribute() {
- attribute.setContainingDataset(dataset);
- Attribute copy = new Attribute(attribute);
- assertEquals(attribute.getName(), copy.getName());
- assertNull(copy.getContainingDataset());
- }
-
- @Test
- public final void getName() {
- assertEquals("Name should be '" + attributeName + "'", attribute
- .getName(), attributeName);
- }
-
- @Test (expected=IllegalArgumentException.class)
- public final void setName() {
- String newName = "new attribute name";
- attribute.setName(newName);
- assertEquals("Name should be '" + newName + "'", attribute.getName(),
- newName);
- attribute.setName(null);
- }
-
- @Test
- public final void getQualifiedName() {
- assertEquals("Qualified name should be '" + attributeName + "'",
- attribute.getQualifiedName(), attributeName);
-
- String qualifiedName = dataset.getName() + "." + attributeName;
- attribute.setContainingDataset(dataset);
- assertEquals("Qualified name should be '" + qualifiedName + "'",
- attribute.getQualifiedName(), qualifiedName);
-
- dataset.setName("new dataset name");
- qualifiedName = dataset.getName() + "." + attributeName;
- attribute.setContainingDataset(dataset);
- assertEquals("Qualified name should be '" + qualifiedName + "'",
- attribute.getQualifiedName(), qualifiedName);
-
- attribute.setContainingDataset(null);
- assertEquals("Qualified name should be '" + attributeName + "'",
- attribute.getQualifiedName(), attributeName);
- }
-
- @Test
- public void getAttributes() {
- assertNull(attribute.getAttributes());
- attribute.setAttributes(attributes);
- assertEquals("Attributes should be '" + attributes + "'", attribute
- .getAttributes(), attributes);
- }
-
- @Test
- public void setAttributes() {
- String newAttributes = "new attributes";
- attribute.setAttributes(newAttributes);
- assertEquals("Attributes should be '" + newAttributes + "'", attribute.getAttributes(),
- newAttributes);
- attribute.setAttributes(null);
- assertNull(attribute.getAttributes());
- }
-
- @Test
- public void testGetAttributesCount() {
- assertEquals(attribute.getAttributesCount(), 0);
- attribute.setAttributes("a");
- assertEquals(attribute.getAttributesCount(), 1);
- attribute.setAttributes("a,b,c");
- assertEquals(attribute.getAttributesCount(), 3);
- attribute.setAttributes(null);
- assertEquals(attribute.getAttributesCount(), 0);
- }
-
- @Test
- public void getContainingDataset() {
- assertNull(attribute.getContainingDataset());
- dataset.addAttribute(attribute);
- assertEquals(attribute.getContainingDataset(), dataset);
- }
-
- @Test
- public void setContainingDataset() {
- attribute.setContainingDataset(dataset);
- assertEquals(attribute.getContainingDataset(), dataset);
- attribute.setContainingDataset(null);
- assertNull(attribute.getContainingDataset());
- }
-
- @Test
- public void hashCodeTest() {
- Attribute attribute2 = new Attribute(attributeName);
- assertEquals(attribute.hashCode(), attribute.hashCode());
- assertEquals(attribute.hashCode(), attribute2.hashCode());
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-martservice/src/test/java/org/biomart/martservice/query/DatasetTest.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/test/java/org/biomart/martservice/query/DatasetTest.java b/taverna-biomart-martservice/src/test/java/org/biomart/martservice/query/DatasetTest.java
deleted file mode 100644
index 374ce5d..0000000
--- a/taverna-biomart-martservice/src/test/java/org/biomart/martservice/query/DatasetTest.java
+++ /dev/null
@@ -1,308 +0,0 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: DatasetTest.java,v $
- * Revision $Revision: 1.1 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/01/31 14:12:10 $
- * by $Author: davidwithers $
- * Created on 03-May-2006
- *****************************************************************/
-package org.biomart.martservice.query;
-
-import junit.framework.TestCase;
-
-/**
- *
- * @author David Withers
- */
-public class DatasetTest extends TestCase {
- private String attributeName;
-
- private Attribute attribute;
-
- private String filterName;
-
- private String filterValue;
-
- private Filter filter;
-
-// private Link link;
-
- private String datasetName;
-
- private Dataset dataset;
-
- private Query query;
-
- /*
- * @see TestCase#setUp()
- */
- protected void setUp() throws Exception {
- super.setUp();
- attributeName = "attribute name";
- attribute = new Attribute(attributeName);
-
- filterName = "filter name";
- filterValue = "filter value";
- filter = new Filter(filterName, filterValue);
-
-// link = new Link("source", "target", "id");
-
- datasetName = "dataset name";
- dataset = new Dataset(datasetName);
-
- query = new Query("default");
- }
-
- /*
- * Test method for 'org.biomart.martservice.query.Dataset.Dataset(String)'
- */
- public final void testDatasetString() {
- Dataset dataset = new Dataset(datasetName);
- assertEquals("Name should be '" + datasetName + "'", dataset.getName(),
- datasetName);
- }
-
- /*
- * Test method for 'org.biomart.martservice.query.Dataset.Dataset(Dataset)'
- */
- public final void testDatasetDataset() {
- dataset.addAttribute(attribute);
- dataset.addFilter(filter);
- Dataset copy = new Dataset(dataset);
- assertEquals("Name should be '" + datasetName + "'", copy.getName(),
- datasetName);
- assertEquals(copy.getAttributes().size(), 1);
- assertEquals(((Attribute) copy.getAttributes().get(0)).getName(),
- attribute.getName());
- assertEquals(copy.getFilters().size(), 1);
- assertEquals(((Filter) copy.getFilters().get(0)).getName(), filter
- .getName());
- }
-
- /*
- * Test method for 'org.biomart.martservice.query.Dataset.getName()'
- */
- public final void testGetName() {
- assertEquals("Name should be '" + datasetName + "'", dataset.getName(),
- datasetName);
- }
-
- /*
- * Test method for 'org.biomart.martservice.query.Dataset.setName(String)'
- */
- public final void testSetName() {
- String newName = "new dataset name";
- filter.setName(newName);
- assertEquals("Name should be '" + newName + "'", filter.getName(),
- newName);
- }
-
- /*
- * Test method for 'org.biomart.martservice.query.Dataset.getAttributes()'
- */
- public final void testGetAttributes() {
- assertEquals(dataset.getAttributes().size(), 0);
- dataset.addAttribute(attribute);
- assertEquals(dataset.getAttributes().size(), 1);
- assertEquals(dataset.getAttributes().get(0), attribute);
- }
-
- /*
- * Test method for
- * 'org.biomart.martservice.query.Dataset.addAttribute(Attribute)'
- */
- public final void testAddAttribute() {
- assertTrue(dataset.addAttribute(attribute));
- assertFalse(dataset.addAttribute(attribute));
- assertEquals(dataset.getAttributes().size(), 1);
- assertEquals(dataset.getAttributes().get(0), attribute);
- query.addDataset(dataset);
- assertTrue(dataset.addAttribute(new Attribute("new attribute")));
- }
-
- /*
- * Test method for
- * 'org.biomart.martservice.query.Dataset.addAttributes(Attribute[])'
- */
- public final void testAddAttributes() {
- dataset.addAttributes(new Attribute[] {});
- assertEquals(dataset.getAttributes().size(), 0);
- dataset.addAttributes(new Attribute[] { attribute });
- assertEquals(dataset.getAttributes().size(), 1);
- assertEquals(dataset.getAttributes().get(0), attribute);
- Attribute anotherAttribute = new Attribute("another attribute");
- dataset.addAttributes(new Attribute[] { attribute, anotherAttribute });
- assertEquals(dataset.getAttributes().size(), 2);
- assertEquals(dataset.getAttributes().get(0), attribute);
- assertEquals(dataset.getAttributes().get(1), anotherAttribute);
- }
-
- /*
- * Test method for
- * 'org.biomart.martservice.query.Dataset.hasAttribute(Attribute)'
- */
- public final void testHasAttribute() {
- assertFalse(dataset.hasAttribute(attribute));
- dataset.addAttribute(attribute);
- assertTrue(dataset.hasAttribute(attribute));
- }
-
- /*
- * Test method for 'org.biomart.martservice.query.Dataset.hasAttributes()'
- */
- public final void testHasAttributes() {
- assertFalse(dataset.hasAttributes());
- dataset.addAttribute(attribute);
- assertTrue(dataset.hasAttributes());
- dataset.removeAttribute(attribute);
- assertFalse(dataset.hasAttributes());
- }
-
- /*
- * Test method for
- * 'org.biomart.martservice.query.Dataset.removeAttribute(Attribute)'
- */
- public final void testRemoveAttribute() {
- assertFalse(dataset.removeAttribute(attribute));
- dataset.addAttribute(attribute);
- assertTrue(dataset.removeAttribute(attribute));
- assertEquals(dataset.getAttributes().size(), 0);
- query.addDataset(dataset);
- dataset.addAttribute(attribute);
- assertTrue(dataset.removeAttribute(attribute));
- }
-
- public void testRemoveAllAttributes() {
- dataset.removeAllAttributes();
- assertFalse(dataset.hasAttributes());
- dataset.addAttribute(attribute);
- dataset.removeAllAttributes();
- assertFalse(dataset.hasAttributes());
- dataset.addAttributes(new Attribute[] { attribute, new Attribute("new attribute") });
- dataset.removeAllAttributes();
- assertFalse(dataset.hasAttributes());
- }
-
- /*
- * Test method for 'org.biomart.martservice.query.Dataset.getFilters()'
- */
- public final void testGetFilters() {
- assertEquals(dataset.getFilters().size(), 0);
- dataset.addFilter(filter);
- assertEquals(dataset.getFilters().size(), 1);
- assertEquals(dataset.getFilters().get(0), filter);
- }
-
- /*
- * Test method for 'org.biomart.martservice.query.Dataset.addFilter(Filter)'
- */
- public final void testAddFilter() {
- assertTrue(dataset.addFilter(filter));
- assertFalse(dataset.addFilter(filter));
- assertEquals(dataset.getFilters().size(), 1);
- assertEquals(dataset.getFilters().get(0), filter);
- query.addDataset(dataset);
- assertTrue(dataset.addFilter(new Filter("new filter")));
- }
-
- /*
- * Test method for
- * 'org.biomart.martservice.query.Dataset.addFilters(Filter[])'
- */
- public final void testAddFilters() {
- dataset.addFilters(new Filter[] {});
- assertEquals(dataset.getFilters().size(), 0);
- dataset.addFilters(new Filter[] { filter });
- assertEquals(dataset.getFilters().size(), 1);
- assertEquals(dataset.getFilters().get(0), filter);
- Filter anotherFilter = new Filter("another filter");
- dataset.addFilters(new Filter[] { filter, anotherFilter });
- assertEquals(dataset.getFilters().size(), 2);
- assertEquals(dataset.getFilters().get(0), filter);
- assertEquals(dataset.getFilters().get(1), anotherFilter);
- }
-
- /*
- * Test method for 'org.biomart.martservice.query.Dataset.hasFilter(Filter)'
- */
- public final void testHasFilter() {
- assertFalse(dataset.hasFilter(filter));
- dataset.addFilter(filter);
- assertTrue(dataset.hasFilter(filter));
- dataset.removeFilter(filter);
- assertFalse(dataset.hasFilters());
- }
-
- /*
- * Test method for 'org.biomart.martservice.query.Dataset.hasFilters()'
- */
- public final void testHasFilters() {
- assertFalse(dataset.hasFilters());
- dataset.addFilter(filter);
- assertTrue(dataset.hasFilters());
- }
-
- /*
- * Test method for
- * 'org.biomart.martservice.query.Dataset.removeFilter(Filter)'
- */
- public final void testRemoveFilter() {
- assertFalse(dataset.removeFilter(filter));
- dataset.addFilter(filter);
- assertTrue(dataset.removeFilter(filter));
- assertEquals(dataset.getFilters().size(), 0);
- query.addDataset(dataset);
- dataset.addFilter(filter);
- assertTrue(dataset.removeFilter(filter));
- }
-
- public void testRemoveAllFilters() {
- dataset.removeAllFilters();
- assertFalse(dataset.hasFilters());
- dataset.addFilter(filter);
- dataset.removeAllFilters();
- assertFalse(dataset.hasFilters());
- dataset.addFilters(new Filter[] { filter, new Filter("new filter") });
- dataset.removeAllFilters();
- assertFalse(dataset.hasFilters());
- }
-
- public void testGetContainingQuery() {
- assertNull(dataset.getContainingQuery());
- query.addDataset(dataset);
- assertEquals(dataset.getContainingQuery(), query);
- }
-
- public void testSetContainingQuery() {
- dataset.setContainingQuery(query);
- assertEquals(dataset.getContainingQuery(), query);
- dataset.setContainingQuery(null);
- assertNull(dataset.getContainingQuery());
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-martservice/src/test/java/org/biomart/martservice/query/FilterTest.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/test/java/org/biomart/martservice/query/FilterTest.java b/taverna-biomart-martservice/src/test/java/org/biomart/martservice/query/FilterTest.java
deleted file mode 100644
index 2d0be4e..0000000
--- a/taverna-biomart-martservice/src/test/java/org/biomart/martservice/query/FilterTest.java
+++ /dev/null
@@ -1,242 +0,0 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: FilterTest.java,v $
- * Revision $Revision: 1.1 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/01/31 14:12:10 $
- * by $Author: davidwithers $
- * Created on 03-May-2006
- *****************************************************************/
-package org.biomart.martservice.query;
-
-import junit.framework.TestCase;
-
-/**
- *
- * @author David Withers
- */
-public class FilterTest extends TestCase {
- private String filterName;
-
- private String filterValue;
-
- private Dataset dataset;
-
- private Filter filter;
-
- private Query query;
-
- /*
- * @see TestCase#setUp()
- */
- protected void setUp() throws Exception {
- super.setUp();
- filterName = "filter name";
- filterValue = "filter value";
- dataset = new Dataset("dataset name");
- filter = new Filter(filterName, filterValue);
- query = new Query("default");
- }
-
- /*
- * Test method for 'org.biomart.martservice.query.Filter.Filter(String)'
- */
- public final void testFilterString() {
- Filter filter = new Filter(filterName);
- assertEquals("Name should be '" + filterName + "'", filter.getName(),
- filterName);
- }
-
- /*
- * Test method for 'org.biomart.martservice.query.Filter.Filter(String,
- * String)'
- */
- public final void testFilterStringString() {
- Filter filter = new Filter(filterName, filterValue);
- assertEquals("Name should be '" + filterName + "'", filter.getName(),
- filterName);
- assertEquals("Value should be '" + filterValue + "'",
- filter.getValue(), filterValue);
- }
-
- /*
- * Test method for 'org.biomart.martservice.query.Filter.Filter(String,
- * String, boolean)'
- */
- public final void testFilterStringStringBoolean() {
- Filter filter = new Filter(filterName, filterValue, true);
- assertEquals("Name should be '" + filterName + "'", filter.getName(),
- filterName);
- assertEquals("Value should be '" + filterValue + "'",
- filter.getValue(), filterValue);
- assertTrue("isBoolean should be true", filter.isBoolean());
- }
-
- /*
- * Test method for 'org.biomart.martservice.query.Filter.Filter(Filter)'
- */
- public final void testFilterFilter() {
- filter.setContainingDataset(dataset);
- Filter copy = new Filter(filter);
- assertEquals("Name should be '" + filterName + "'", copy.getName(),
- filterName);
- assertEquals("Value should be '" + filterValue + "'", copy.getValue(),
- filterValue);
- assertFalse("isBoolean should be false", copy.isBoolean());
- assertNull(copy.getContainingDataset());
- }
-
- /*
- * Test method for
- * 'org.biomart.martservice.query.Filter.getContainingDataset()'
- */
- public final void testGetContainingDataset() {
- assertNull("Default should be NULL ", filter.getContainingDataset());
- dataset.addFilter(filter);
- assertEquals(filter.getContainingDataset(), dataset);
- }
-
- /*
- * Test method for
- * 'org.biomart.martservice.query.Filter.setContainingDataset(Dataset)'
- */
- public final void testSetContainingDataset() {
- filter.setContainingDataset(dataset);
- assertEquals(filter.getContainingDataset(), dataset);
- filter.setContainingDataset(null);
- assertNull(filter.getContainingDataset());
- }
-
- /*
- * Test method for 'org.biomart.martservice.query.Filter.getName()'
- */
- public final void testGetName() {
- assertEquals("Name should be '" + filterName + "'", filter.getName(),
- filterName);
- }
-
- /*
- * Test method for 'org.biomart.martservice.query.Filter.setName(String)'
- */
- public final void testSetName() {
- String newName = "new filter name";
- filter.setName(newName);
- assertEquals("Name should be '" + newName + "'", filter.getName(),
- newName);
- }
-
- /*
- * Test method for 'org.biomart.martservice.query.Filter.getValue()'
- */
- public final void testGetValue() {
- assertEquals("Value should be '" + filterValue + "'",
- filter.getValue(), filterValue);
- }
-
- /*
- * Test method for 'org.biomart.martservice.query.Filter.setValue(String)'
- */
- public final void testSetValue() {
- String newValue = "new filter value";
- filter.setValue(newValue);
- assertEquals("Value should be '" + newValue + "'", filter.getValue(),
- newValue);
- filter.setValue(null);
- assertNull(filter.getValue());
- filter.setValue(null);
- assertNull(filter.getValue());
- filter.setValue(newValue);
- assertEquals("Value should be '" + newValue + "'", filter.getValue(),
- newValue);
- filter.setValue(newValue);
- assertEquals("Value should be '" + newValue + "'", filter.getValue(),
- newValue);
- dataset.addFilter(filter);
- filter.setValue(null);
- filter.setValue(newValue);
- assertEquals("Value should be '" + newValue + "'", filter.getValue(),
- newValue);
- query.addDataset(dataset);
- filter.setValue(null);
- filter.setValue(newValue);
- assertEquals("Value should be '" + newValue + "'", filter.getValue(),
- newValue);
- }
-
- /*
- * Test method for 'org.biomart.martservice.query.Filter.isBoolean()'
- */
- public final void testIsBoolean() {
- assertFalse("Default should be false", filter.isBoolean());
- }
-
- /*
- * Test method for
- * 'org.biomart.martservice.query.Filter.setBoolean(boolean)'
- */
- public final void testSetBoolean() {
- filter.setBoolean(true);
- assertTrue("isBoolean should be true", filter.isBoolean());
- }
-
- /*
- * Test method for 'org.biomart.martservice.query.Filter.getQualifiedName()'
- */
- public final void testGetQualifiedName() {
- assertEquals("Qualified name should be '" + filterName + "'", filter
- .getQualifiedName(), filterName);
-
- String qualifiedName = dataset.getName() + "." + filterName;
- filter.setContainingDataset(dataset);
- assertEquals("Qualified name should be '" + qualifiedName + "'", filter
- .getQualifiedName(), qualifiedName);
-
- dataset.setName("new dataset name");
- qualifiedName = dataset.getName() + "." + filterName;
- filter.setContainingDataset(dataset);
- assertEquals("Qualified name should be '" + qualifiedName + "'", filter
- .getQualifiedName(), qualifiedName);
-
- filter.setContainingDataset(null);
- assertEquals("Qualified name should be '" + filterName + "'", filter
- .getQualifiedName(), filterName);
- }
-
- public void testIsList() {
- assertFalse(filter.isList());
- filter.setList(true);
- assertTrue(filter.isList());
- }
-
- public void testSetList() {
- filter.setList(false);
- assertFalse(filter.isList());
- filter.setList(true);
- assertTrue(filter.isList());
- }
-
-}
[14/16] incubator-taverna-plugin-bioinformatics git commit:
temporarily empty repository
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartService.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartService.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartService.java
deleted file mode 100644
index c02bbb5..0000000
--- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartService.java
+++ /dev/null
@@ -1,709 +0,0 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: MartService.java,v $errors/failure.html
- * Revision $Revision: 1.7 $
- * Release status $State: Exp $
- * Last modified on $Date: 2008/08/11 12:48:29 $
- * by $Author: davidwithers $
- * Created on 17-Mar-2006
- *****************************************************************/
-package org.biomart.martservice;
-
-import java.io.File;
-import java.io.FileInputStream;
-import java.io.FileOutputStream;
-import java.io.IOException;
-import java.lang.ref.SoftReference;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.LinkedList;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-import java.util.zip.GZIPInputStream;
-import java.util.zip.GZIPOutputStream;
-
-import org.apache.log4j.Logger;
-import org.biomart.martservice.query.Query;
-import org.ensembl.mart.lib.config.ConfigurationException;
-import org.ensembl.mart.lib.config.DatasetConfig;
-import org.ensembl.mart.lib.config.DatasetConfigXMLUtils;
-import org.ensembl.mart.lib.config.Exportable;
-import org.ensembl.mart.lib.config.Importable;
-import org.jdom.Document;
-import org.jdom.JDOMException;
-import org.jdom.input.SAXBuilder;
-import org.xml.sax.InputSource;
-
-/**
- * A class for interacting with a BioMart web service.
- *
- * @author David Withers
- */
-public class MartService {
- private static Logger logger = Logger.getLogger(MartServiceUtils.class);
-
- private String location;
-
- private String requestId;
-
- private File cacheDirectory;
-
- private MartRegistry registry;
-
- private Map<MartURLLocation, String> versionMap = new HashMap<MartURLLocation, String>();
-
- private Map<String, MartDataset[]> datasetsMap = new HashMap<String, MartDataset[]>();
-
- private Map<String, SoftReference<DatasetConfig>> datasetConfigMap = new HashMap<String, SoftReference<DatasetConfig>>();
-
- private Map<String, Importable[]> importablesMap = new HashMap<String, Importable[]>();
-
- private Map<String, Exportable[]> exportablesMap = new HashMap<String, Exportable[]>();
-
- private Map<MartDataset, List<DatasetLink>> linkableDatasetsMap = new HashMap<MartDataset, List<DatasetLink>>();
-
- private Map<MartDataset, Set<DatasetLink>> datasetToLinkSetMap = new HashMap<MartDataset, Set<DatasetLink>>();
-
- private Map<MartDataset, Map<MartDataset, MartDataset>> datasetsToPathMap = new HashMap<MartDataset, Map<MartDataset, MartDataset>>();
-
- private static final Map<String, MartService> martServiceMap = new HashMap<String, MartService>();
-
- private static final String fs = System.getProperty("file.separator");
-
- private boolean linksCalculated = false;
-
- /**
- * Constructs an instance of a <code>MartService</code> with the specified
- * location.
- *
- * The location must be the URL of a valid BioMart MartService, e.g.
- * http://www.biomart.org/biomart/martservice
- *
- * @param location
- * the URL of the MartService
- */
- private MartService(String location) {
- this.location = location;
- }
-
- /**
- * Returns a <code>MartService</code> for the specified location. If a
- * <code>MartService</code> does not exist for the location a new one is
- * constructed.
- *
- * The location must be the URL of a valid BioMart MartService, e.g.
- * http://www.biomart.org/biomart/martservice
- *
- * @param location
- * the URL of the MartService
- */
- public static MartService getMartService(String location) {
- if (!martServiceMap.containsKey(location)) {
- martServiceMap.put(location, new MartService(location));
- }
- return martServiceMap.get(location);
- }
-
- /**
- * Returns the requestId.
- *
- * @return the requestId
- */
- public String getRequestId() {
- return requestId;
- }
-
- /**
- * Sets the requestId.
- *
- * @param requestId
- * the new requestId
- */
- public void setRequestId(String requestId) {
- this.requestId = requestId;
- }
-
- /**
- * Returns the cacheDirectory.
- *
- * @return the cacheDirectory
- */
- public File getCacheDirectory() {
- return cacheDirectory;
- }
-
- /**
- * Sets the cacheDirectory.
- *
- * @param cacheDirectory
- * the new cacheDirectory
- */
- public void setCacheDirectory(File cacheDirectory) {
- this.cacheDirectory = cacheDirectory;
- }
-
- /**
- * Returns the URL of the MartService.
- *
- * @return the URL of the MartService
- */
- public String getLocation() {
- return location;
- }
-
- /**
- * Removes any cached items.
- */
- public void clearCache() {
- registry = null;
- datasetsMap.clear();
- datasetConfigMap.clear();
- importablesMap.clear();
- exportablesMap.clear();
- }
-
- /**
- * Returns the MartRegistry for this MartService.
- *
- * @return the MartRegistry for this MartService
- * @throws MartServiceException
- * if the MartService returns an error or is unavailable
- */
- public MartRegistry getRegistry() throws MartServiceException {
- if (registry == null) {
- registry = MartServiceUtils.getRegistry(location, requestId);
- }
- return registry;
- }
-
- public String getVersion(MartURLLocation martURLLocation)
- throws MartServiceException {
- if (!versionMap.containsKey(martURLLocation)) {
- versionMap.put(martURLLocation, MartServiceUtils.getVersion(
- location, requestId, martURLLocation));
- }
- return versionMap.get(martURLLocation);
- }
-
- /**
- * Returns all the datasets available from this MartService.
- *
- * @return all the datasets available from this MartService.
- * @throws MartServiceException
- * if the MartService returns an error or is unavailable
- */
- public MartDataset[] getDatasets() throws MartServiceException {
- List<MartDataset> datasets = new ArrayList<MartDataset>();
- MartURLLocation[] locations = getRegistry().getMartURLLocations();
- for (int i = 0; i < locations.length; i++) {
- datasets.addAll(Arrays.asList(getDatasets(locations[i])));
- }
- return datasets.toArray(new MartDataset[datasets.size()]);
- }
-
- /**
- * Returns the datasets belonging to the virtualSchema.
- *
- * @param virtualSchema
- * the virtual schema to include datasets from.
- * @return the datasets belonging to the virtualSchema.
- * @throws MartServiceException
- * if the MartService returns an error or is unavailable
- */
- public MartDataset[] getDatasets(String virtualSchema)
- throws MartServiceException {
- List<MartDataset> datasets = new ArrayList<MartDataset>();
- MartURLLocation[] locations = getRegistry().getMartURLLocations();
- for (int i = 0; i < locations.length; i++) {
- if (virtualSchema == null
- || virtualSchema.equals(locations[i].getVirtualSchema())) {
- datasets.addAll(Arrays.asList(getDatasets(locations[i])));
- }
- }
- return datasets.toArray(new MartDataset[datasets.size()]);
- }
-
- /**
- * Returns the datasets specified by martURLLocation.
- *
- * @param martURLLocation
- * where to find the datasets.
- * @return the datasets specified by martURLLocation.
- * @throws MartServiceException
- * if the MartService returns an error or is unavailable
- */
- public MartDataset[] getDatasets(MartURLLocation martURLLocation)
- throws MartServiceException {
- String name = martURLLocation.getName();
- if (!datasetsMap.containsKey(name)) {
- datasetsMap.put(name, MartServiceUtils.getDatasets(location,
- requestId, martURLLocation));
- }
- return datasetsMap.get(name);
- }
-
- /**
- * Returns the dataset specified by a virtualSchema and a dataset name.
- *
- * @param virtualSchema
- * the virtualSchema containing the dataset
- * @param datasetName
- * the name of the dataset to return
- * @return a dataset
- * @throws MartServiceException
- * if the MartService returns an error or is unavailable
- */
- public MartDataset getDataset(String virtualSchema, String datasetName)
- throws MartServiceException {
- MartDataset result = null;
- MartDataset[] datasets = getDatasets(virtualSchema);
- for (int i = 0; i < datasets.length; i++) {
- if (datasetName.equals(datasets[i].getName())) {
- result = datasets[i];
- break;
- }
- }
- return result;
- }
-
- /**
- * Returns the configuration for a dataset.
- *
- * @param dataset
- * the dataset to get the configuration for
- * @return the configuration for a dataset
- * @throws MartServiceException
- * if the MartService returns an error or is unavailable
- */
- public DatasetConfig getDatasetConfig(MartDataset dataset)
- throws MartServiceException {
- String qualifiedName = dataset.getQualifiedName();
- DatasetConfig datasetConfig;
- if (!datasetConfigMap.containsKey(qualifiedName)) {
- if (dataset.getModified() != null && cacheDirectory != null) {
- datasetConfig = getDatasetConfigFromCache(dataset);
- } else {
- datasetConfig = MartServiceUtils.getDatasetConfig(location,
- requestId, dataset);
- }
- datasetConfigMap.put(qualifiedName,
- new SoftReference<DatasetConfig>(datasetConfig));
- } else {
- datasetConfig = datasetConfigMap.get(qualifiedName).get();
- if (datasetConfig == null) {
- if (dataset.getModified() != null && cacheDirectory != null) {
- datasetConfig = getDatasetConfigFromCache(dataset);
- } else {
- datasetConfig = MartServiceUtils.getDatasetConfig(location,
- requestId, dataset);
- }
- datasetConfigMap.put(qualifiedName,
- new SoftReference<DatasetConfig>(datasetConfig));
- }
-
- }
- return datasetConfig;
- }
-
- private DatasetConfig getDatasetConfigFromCache(MartDataset dataset)
- throws MartServiceException {
- DatasetConfig datasetConfig = null;
- MartURLLocation mart = dataset.getMartURLLocation();
- String path = mart.getHost() + fs + mart.getName() + fs
- + mart.getVirtualSchema();
- File martCacheDir = new File(cacheDirectory, path);
- martCacheDir.mkdirs();
- File cache = new File(martCacheDir, dataset.getName() + ".cfg");
- DatasetConfigXMLUtils datasetConfigXMLUtils = new DatasetConfigXMLUtils(
- true);
- if (cache.exists()) {
- try {
- SAXBuilder builder = new SAXBuilder();
- Document doc = builder.build(new InputSource(
- new GZIPInputStream(new FileInputStream(cache))));
-
- // Document doc =
- // datasetConfigXMLUtils.getDocumentForXMLStream(new
- // FileInputStream(cache));
-
- datasetConfig = datasetConfigXMLUtils
- .getDatasetConfigForDocument(doc);
- datasetConfigXMLUtils.loadDatasetConfigWithDocument(
- datasetConfig, doc);
- if (!datasetConfig.getModified().trim().equals(
- dataset.getModified().trim())) {
- logger.info(" " + datasetConfig.getModified().trim()
- + " != " + dataset.getModified().trim());
- logger.info(" Database: "
- + dataset.getMartURLLocation().getDatabase()
- + ", Dataset: " + dataset.getName());
- datasetConfig = null;
- }
- } catch (IOException e) {
- logger.debug("error reading cache from " + cache.getPath(), e);
- datasetConfig = null;
- } catch (ConfigurationException e) {
- logger.debug("error parsing from " + cache.getPath(), e);
- datasetConfig = null;
- } catch (JDOMException e) {
- logger.debug("error parsing from " + cache.getPath(), e);
- datasetConfig = null;
- }
- }
- if (datasetConfig == null) {
- datasetConfig = MartServiceUtils.getDatasetConfig(location,
- requestId, dataset);
- try {
- GZIPOutputStream zipOutputStream = new GZIPOutputStream(
- new FileOutputStream(cache));
- datasetConfigXMLUtils.writeDatasetConfigToOutputStream(
- datasetConfig, zipOutputStream);
- zipOutputStream.flush();
- zipOutputStream.close();
- } catch (IOException e) {
- logger.debug("error writing cache to " + cache.getPath(), e);
- } catch (ConfigurationException e) {
- logger.debug("error writing cache to " + cache.getPath(), e);
- }
- }
- return datasetConfig;
- }
-
- /**
- * Returns the importables for a dataset.
- *
- * @param dataset
- * @return the importables for a dataset
- * @throws MartServiceException
- * if the MartService returns an error or is unavailable
- */
- public Importable[] getImportables(MartDataset dataset)
- throws MartServiceException {
- String qualifiedName = dataset.getQualifiedName();
- if (!importablesMap.containsKey(qualifiedName)) {
- try {
- importablesMap.put(qualifiedName, getDatasetConfig(dataset)
- .getImportables());
- } catch (MartServiceException e) {
- return new Importable[0];
- }
- }
- return importablesMap.get(qualifiedName);
- }
-
- /**
- * Returns the exportables for a dataset.
- *
- * @param dataset
- * @return the exportables for a dataset
- * @throws MartServiceException
- * if the MartService returns an error or is unavailable
- */
- public Exportable[] getExportables(MartDataset dataset)
- throws MartServiceException {
- String qualifiedName = dataset.getQualifiedName();
- if (!exportablesMap.containsKey(qualifiedName)) {
- try {
- exportablesMap.put(qualifiedName, getDatasetConfig(dataset)
- .getExportables());
- } catch (MartServiceException e) {
- return new Exportable[0];
- }
- }
- return exportablesMap.get(qualifiedName);
- }
-
- /**
- * Sends a <code>Query</code> to the MartService and returns the results
- * of executing the query.
- *
- * The results are returned as an array of lists; one list for each
- * attribute specified in the query.
- *
- * @param query
- * the query to execute
- * @return the results of executing the query
- * @throws MartServiceException
- * if the MartService returns an error or is unavailable
- */
- public Object[] executeQuery(Query query) throws MartServiceException {
- // logger.info(MartServiceUtils.queryToXML(query));
- return MartServiceUtils.getResults(location, requestId, query);
- }
-
- /**
- * Sends a <code>Query</code> to the MartService and writes the results to
- * the <code>ResultReceiver</code> as each line of the result stream is
- * read.
- *
- * @param query
- * @param resultReceiver
- * @throws MartServiceException
- * if the MartService returns an error or is unavailable
- * @throws ResultReceiverException
- * if the ResultReceiver cannot receive the result
- * @see ResultReceiver
- */
- public void executeQuery(Query query, ResultReceiver resultReceiver)
- throws MartServiceException, ResultReceiverException {
- MartServiceUtils.putResults(location, requestId, query, resultReceiver);
- }
-
- /**
- * Returns a list of datasets that can be linked to the specified dataset.
- *
- * @param martDataset
- * @return datasets that can be linked to the specified dataset
- * @throws MartServiceException
- */
- public List<DatasetLink> getLinkableDatasets(MartDataset martDataset)
- throws MartServiceException {
- if (!linkableDatasetsMap.containsKey(martDataset)) {
- List<DatasetLink> linkableDatasets = new ArrayList<DatasetLink>();
-
- Set<String> importableSet = new HashSet<String>();
- Importable[] importables = getImportables(martDataset);
- for (int i = 0; i < importables.length; i++) {
- importableSet.add(importables[i].getLinkName());
- }
-
- MartDataset[] datasets = getDatasets(martDataset.getVirtualSchema());
- for (int j = 0; j < datasets.length; j++) {
- if (datasets[j].isVisible()
- && !datasets[j].getName().equals(martDataset.getName())) {
- DatasetLink datasetLink = new DatasetLink(datasets[j],
- martDataset);
- Exportable[] exportables = getExportables(datasets[j]);
- for (int k = 0; k < exportables.length; k++) {
- String link = exportables[k].getLinkName();
- if (importableSet.contains(link)) {
- datasetLink.addLink(link);
- }
- }
- if (datasetLink.hasLinks()) {
- linkableDatasets.add(datasetLink);
- }
- }
- }
- linkableDatasetsMap.put(martDataset, linkableDatasets);
- }
-
- return linkableDatasetsMap.get(martDataset);
- }
-
- /*
- * (non-Javadoc)
- *
- * @see java.lang.Object#equals(java.lang.Object)
- */
- public boolean equals(Object obj) {
- boolean result = false;
- if (obj != null) {
- MartService other = (MartService) obj;
- if (location == null) {
- result = other.location == null;
- } else {
- result = location.equals(other.location);
- }
- }
- return result;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see java.lang.Object#hashCode()
- */
- public int hashCode() {
- return location.hashCode();
- }
-
- public boolean linksCalculated() {
- return linksCalculated;
- }
-
- // java implementation of the perl stuff that calculates links.
- // all this should go for the next version of biomart.
-
- public void calculateLinks() throws MartServiceException {
- synchronized (location) {
- if (!linksCalculated) {
- datasetToLinkSetMap.clear();
- datasetsToPathMap.clear();
-
- MartDataset[] allDatasets = getDatasets();
- for (int i = 0; i < allDatasets.length; i++) {
- MartDataset[] datasets = getDatasets(allDatasets[i]
- .getVirtualSchema());
- for (int j = 0; j < datasets.length; j++) {
- if (!allDatasets[i].getName().equals(
- datasets[j].getName())) {
- linkDatasets(allDatasets[i], datasets[j]);
- }
- }
- }
- for (int i = 0; i < allDatasets.length; i++) {
- datasetsToPathMap.put(allDatasets[i],
- dijkstra(allDatasets[i]));
- }
- linksCalculated = true;
- }
- }
- }
-
- public List<MartDataset> getPath(MartDataset source, MartDataset target) {
- List<MartDataset> path = new ArrayList<MartDataset>();
-
- Map<MartDataset, MartDataset> pathMap = datasetsToPathMap.get(source);
-
- MartDataset currentDataset = target;
-
- while (currentDataset != null) {
- path.add(0, currentDataset);
- currentDataset = (MartDataset) pathMap.get(currentDataset);
- }
-
- if (path.size() < 2 || !path.get(0).equals(source)
- || !path.get(path.size() - 1).equals(target)) {
- return null;
- }
-
- return path;
- }
-
- public DatasetLink getLinkBetween(MartDataset exportingDataset,
- MartDataset importingDataset) {
- Set<DatasetLink> links = datasetToLinkSetMap.get(exportingDataset);
- for (DatasetLink link : links) {
- MartDataset targetDataset = link.getTargetDataset();
- if (importingDataset.equals(targetDataset)) {
- return link;
- }
- }
-
- return null;
- }
-
- public List<DatasetLink> getLinksFrom(MartDataset dataset) {
- List<DatasetLink> linksFrom = new ArrayList<DatasetLink>();
- Set<DatasetLink> links = datasetToLinkSetMap.get(dataset);
- if (links != null) {
- for (DatasetLink link : links) {
- if (link.getSourceDataset().equals(dataset)) {
- linksFrom.add(link);
- }
- }
- }
- return linksFrom;
- }
-
- public void linkDatasets(MartDataset source, MartDataset target)
- throws MartServiceException {
- DatasetLink datasetLink = new DatasetLink(source, target);
- Importable[] importables = getImportables(target);
- for (int i = 0; i < importables.length; i++) {
- Exportable[] exportables = getExportables(source);
- for (int j = 0; j < exportables.length; j++) {
- if (importables[i].getLinkName().equals(
- exportables[j].getLinkName())) {
- String importVersion = importables[i].getLinkVersion();
- String exportVersion = exportables[j].getLinkVersion();
- if (importVersion != null && exportVersion != null) {
- if (importVersion.equals(exportVersion)) {
- datasetLink.addLink(importables[i].getLinkName());
- }
- } else {
- datasetLink.addLink(importables[i].getLinkName());
- }
- }
- }
- }
- if (datasetLink.hasLinks()) {
- if (!datasetToLinkSetMap.containsKey(source)) {
- datasetToLinkSetMap.put(source, new HashSet<DatasetLink>());
- }
- if (!datasetToLinkSetMap.containsKey(target)) {
- datasetToLinkSetMap.put(target, new HashSet<DatasetLink>());
- }
- datasetToLinkSetMap.get(source).add(datasetLink);
- datasetToLinkSetMap.get(target).add(datasetLink);
- }
- }
-
- public Map<MartDataset, MartDataset> dijkstra(MartDataset dataset)
- throws MartServiceException {
- Map<MartDataset, MartDataset> path = new HashMap<MartDataset, MartDataset>();
- LinkedList<MartDataset> vertices = new LinkedList<MartDataset>(Arrays
- .asList(getDatasets(dataset.getVirtualSchema())));
- Map<MartDataset, Integer> dist = new HashMap<MartDataset, Integer>();
- for (MartDataset vertex : vertices) {
- dist.put(vertex, new Integer(10000));
- }
-
- dist.put(dataset, new Integer(0));
-
- while (vertices.size() > 0) {
- int min_vert_idx = 0;
- MartDataset min_vert = (MartDataset) vertices.get(min_vert_idx);
- int min_dist = ((Integer) dist.get(min_vert)).intValue();
-
- for (int vertex_idx = 0; vertex_idx < vertices.size(); vertex_idx++) {
- MartDataset vertex = (MartDataset) vertices.get(vertex_idx);
- if (((Integer) dist.get(vertex)).intValue() < min_dist) {
- min_vert_idx = vertex_idx;
- min_vert = vertex;
- min_dist = ((Integer) dist.get(vertex)).intValue();
- }
- }
-
- if (min_dist == 10000) {
- // Exhausted a disjoint set of datasets.
- break;
- }
-
- vertices.remove(min_vert_idx);
-
- List<DatasetLink> edges = getLinksFrom(min_vert);
- for (DatasetLink edge : edges) {
- MartDataset vertex = edge.getTargetDataset();
-
- if (((Integer) dist.get(vertex)).intValue() > ((Integer) dist
- .get(min_vert)).intValue() + 1) {
- dist.put(vertex, new Integer(((Integer) dist.get(min_vert))
- .intValue() + 1));
- path.put(vertex, min_vert);
- }
- }
- }
-
- return path;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartServiceException.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartServiceException.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartServiceException.java
deleted file mode 100644
index f1f0639..0000000
--- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartServiceException.java
+++ /dev/null
@@ -1,86 +0,0 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: MartServiceException.java,v $
- * Revision $Revision: 1.1 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/01/31 14:12:05 $
- * by $Author: davidwithers $
- * Created on 05-May-2006
- *****************************************************************/
-package org.biomart.martservice;
-
-/**
- * Thrown when a MartService is inaccessable or returns an error.
- *
- * @author David Withers
- */
-public class MartServiceException extends Exception {
- private static final long serialVersionUID = 5535008907746588537L;
-
- /**
- * Constructs a new exception with no detail message.
- *
- */
- public MartServiceException() {
- super();
- }
-
- /**
- * Constructs a new exception with the specified detail message.
- *
- * @param message
- * the detail message
- * @param cause
- * the cause (a null value is permitted, and indicates that the
- * cause is nonexistent or unknown)
- */
- public MartServiceException(String message, Throwable cause) {
- super(message, cause);
- }
-
- /**
- * Constructs a new exception with the specified detail message and cause.
- *
- * @param message
- * the detail message
- */
- public MartServiceException(String message) {
- super(message);
- }
-
- /**
- * Constructs a new exception with the specified cause.
- *
- * @param cause
- * the cause (a null value is permitted, and indicates that the
- * cause is nonexistent or unknown)
- */
- public MartServiceException(Throwable cause) {
- super(cause);
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartServiceUtils.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartServiceUtils.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartServiceUtils.java
deleted file mode 100644
index cdcb400..0000000
--- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartServiceUtils.java
+++ /dev/null
@@ -1,725 +0,0 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: MartServiceUtils.java,v $
- * Revision $Revision: 1.12 $
- * Release status $State: Exp $
- * Last modified on $Date: 2008/07/31 15:06:49 $
- * by $Author: davidwithers $
- * Created on 17-Mar-2006
- *****************************************************************/
-package org.biomart.martservice;
-
-import java.io.BufferedReader;
-import java.io.IOException;
-import java.io.InputStream;
-import java.io.InputStreamReader;
-import java.io.Reader;
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.util.ArrayList;
-import java.util.List;
-
-import org.apache.commons.httpclient.DefaultHttpMethodRetryHandler;
-import org.apache.commons.httpclient.HttpClient;
-import org.apache.commons.httpclient.HttpMethod;
-import org.apache.commons.httpclient.HttpStatus;
-import org.apache.commons.httpclient.NameValuePair;
-import org.apache.commons.httpclient.UsernamePasswordCredentials;
-import org.apache.commons.httpclient.auth.AuthScope;
-import org.apache.commons.httpclient.methods.GetMethod;
-import org.apache.commons.httpclient.methods.PostMethod;
-import org.apache.commons.httpclient.params.HttpMethodParams;
-import org.apache.commons.io.IOUtils;
-import org.apache.log4j.Logger;
-import org.biomart.martservice.query.Attribute;
-import org.biomart.martservice.query.Dataset;
-import org.biomart.martservice.query.Query;
-import org.biomart.martservice.query.QueryXMLHandler;
-import org.ensembl.mart.lib.config.ConfigurationException;
-import org.ensembl.mart.lib.config.DatasetConfig;
-import org.ensembl.mart.lib.config.DatasetConfigXMLUtils;
-import org.jdom.DocType;
-import org.jdom.Document;
-import org.jdom.Element;
-import org.jdom.JDOMException;
-import org.jdom.Namespace;
-import org.jdom.input.SAXBuilder;
-import org.jdom.output.XMLOutputter;
-import org.xml.sax.InputSource;
-
-/**
- * Utility class for interacting with a BioMart web service.
- *
- * @author David Withers
- */
-public class MartServiceUtils {
- private static Logger logger = Logger.getLogger(MartServiceUtils.class);
-
- private static String lineSeparator = System.getProperty("line.separator");
-
- public static final String QUERY_ATTRIBUTE = "query";
-
- public static final String DATASET_ATTRIBUTE = "dataset";
-
- public static final String MART_ATTRIBUTE = "mart";
-
- public static final String SCHEMA_ATTRIBUTE = "virtualschema";
-
- public static final String TYPE_ATTRIBUTE = "type";
-
- public static final String MART_USER_ATTRIBUTE = "martuser";
-
- public static final String INTERFACE_ATTRIBUTE = "interface";
-
- public static final String REQUEST_ID_ATTRIBUTE = "requestid";
-
- public static final String REGISTRY_VALUE = "registry";
-
- public static final String VERSION_VALUE = "version";
-
- public static final String DATASETS_VALUE = "datasets";
-
- public static final String DATASET_VALUE = "dataset";
-
- public static final String CONFIGURATION_VALUE = "configuration";
-
- /**
- * Sends a registry request to the Biomart webservice and constructs a
- * MartRegistry from the XML returned by the webservice.
- *
- * @param martServiceLocation
- * the URL of the Biomart webservice
- * @return a MartRegistry
- * @throws MartServiceException
- * if the Biomart webservice returns an error or is unavailable
- */
- public static MartRegistry getRegistry(String martServiceLocation,
- String requestId) throws MartServiceException {
- List<NameValuePair> data = new ArrayList<NameValuePair>();
- data.add(new NameValuePair(TYPE_ATTRIBUTE, REGISTRY_VALUE));
- if (requestId != null) {
- data.add(new NameValuePair(REQUEST_ID_ATTRIBUTE, requestId));
- }
- HttpMethod method = new GetMethod(martServiceLocation);
- method.setQueryString(data
- .toArray(new NameValuePair[data.size()]));
- try {
- InputStream in = executeMethod(method, martServiceLocation);
- Document document = new SAXBuilder().build(in);
- Element root = document.getRootElement();
- return MartServiceXMLHandler.elementToRegistry(root,
- Namespace.NO_NAMESPACE);
- } catch (IOException e) {
- String errorMessage = "Error getting registry from "
- + martServiceLocation;
- throw new MartServiceException(errorMessage, e);
- } catch (JDOMException e) {
- String errorMessage = "Error getting registry from "
- + martServiceLocation;
- throw new MartServiceException(errorMessage, e);
- } finally {
- method.releaseConnection();
- }
-
- }
-
- public static String getVersion(String martServiceLocation,
- String requestId, MartURLLocation mart) throws MartServiceException {
- String errorMessage = "Error getting version from " + martServiceLocation;
-
- List<NameValuePair> data = new ArrayList<NameValuePair>();
- data.add(new NameValuePair(TYPE_ATTRIBUTE, VERSION_VALUE));
- if (mart.getVirtualSchema() != null) {
- data.add(new NameValuePair(SCHEMA_ATTRIBUTE, mart
- .getVirtualSchema()));
- }
- data.add(new NameValuePair(MART_ATTRIBUTE, mart.getName()));
- if (requestId != null) {
- data.add(new NameValuePair(REQUEST_ID_ATTRIBUTE, requestId));
- }
- if (requestId != null) {
- data.add(new NameValuePair(REQUEST_ID_ATTRIBUTE, requestId));
- }
- HttpMethod method = new GetMethod(martServiceLocation);
- method.setQueryString(data
- .toArray(new NameValuePair[data.size()]));
- try {
- InputStream in = executeMethod(method, martServiceLocation);
- BufferedReader bufferedReader = new BufferedReader(
- new InputStreamReader(in));
- String version = bufferedReader.readLine();
- if (version == null) {
- throw new MartServiceException(errorMessage + ": No version returned");
- }
- version = version.trim();
- // fix for biomart's 'let's add a blank line' thing
- if ("".equals(version)) {
- version = bufferedReader.readLine();
- if (version == null) {
- throw new MartServiceException(errorMessage + ": No version returned");
- }
- version = version.trim();
- }
- bufferedReader.close();
- return version;
- } catch (IOException e) {
- throw new MartServiceException(errorMessage, e);
- } finally {
- method.releaseConnection();
- }
- }
-
- /**
- * Sends a datasets request to the Biomart webservice and constructs an
- * array of MartDataset from the tab separated rows of data returned by the
- * webservice.
- *
- * @param martServiceLocation
- * the URL of the Biomart webservice
- * @param mart
- * the mart to get datasets from
- * @return an array of MartDataset
- * @throws MartServiceException
- * if the Biomart webservice returns an error or is unavailable
- */
- public static MartDataset[] getDatasets(String martServiceLocation,
- String requestId, MartURLLocation mart) throws MartServiceException {
- List<NameValuePair> data = new ArrayList<NameValuePair>();
- data.add(new NameValuePair(TYPE_ATTRIBUTE, DATASETS_VALUE));
- if (mart.getVirtualSchema() != null) {
- data.add(new NameValuePair(SCHEMA_ATTRIBUTE, mart
- .getVirtualSchema()));
- }
- data.add(new NameValuePair(MART_ATTRIBUTE, mart.getName()));
- if (mart.getMartUser() != null) {
- data
- .add(new NameValuePair(MART_USER_ATTRIBUTE, mart
- .getMartUser()));
- }
- if (requestId != null) {
- data.add(new NameValuePair(REQUEST_ID_ATTRIBUTE, requestId));
- }
- HttpMethod method = new GetMethod(martServiceLocation);
- method.setQueryString(data
- .toArray(new NameValuePair[data.size()]));
- try {
- InputStream in = executeMethod(method, martServiceLocation);
-
- MartDataset[] datasets = tabSeparatedReaderToDatasets(
- new InputStreamReader(in), mart);
- in.close();
- return datasets;
- } catch (IOException e) {
- String errorMessage = "Error getting datasets from "
- + martServiceLocation;
- throw new MartServiceException(errorMessage, e);
- } finally {
- method.releaseConnection();
- }
- }
-
- /**
- * Sends a configuration request to the Biomart webservice and constructs a
- * DatasetConfig from the XML returned by the webservice.
- *
- * @param martServiceLocation
- * the URL of the Biomart webservice
- * @param dataset
- * the dataset to get the configuration for
- * @return a DatasetConfig
- * @throws MartServiceException
- * if the Biomart webservice returns an error or is unavailable
- */
- public static DatasetConfig getDatasetConfig(String martServiceLocation,
- String requestId, MartDataset dataset) throws MartServiceException {
- List<NameValuePair> data = new ArrayList<NameValuePair>();
- data.add(new NameValuePair(TYPE_ATTRIBUTE, CONFIGURATION_VALUE));
- MartURLLocation mart = dataset.getMartURLLocation();
- // if the dataset has a location specify the virtual schema to uniquely
- // identify the dataset
- if (mart != null && mart.getVirtualSchema() != null) {
- data.add(new NameValuePair(SCHEMA_ATTRIBUTE, mart
- .getVirtualSchema()));
- }
- data.add(new NameValuePair(DATASET_VALUE, dataset.getName()));
-// if (dataset.getInterface() != null) {
-// data.add(new NameValuePair(INTERFACE_ATTRIBUTE, dataset
-// .getInterface()));
-// }
- if (mart != null && mart.getMartUser() != null) {
- data
- .add(new NameValuePair(MART_USER_ATTRIBUTE, mart
- .getMartUser()));
- }
- if (requestId != null) {
- data.add(new NameValuePair(REQUEST_ID_ATTRIBUTE, requestId));
- }
- HttpMethod method = new GetMethod(martServiceLocation);
- method.setQueryString(data
- .toArray(new NameValuePair[data.size()]));
-
- try {
- InputStream in = executeMethod(method, martServiceLocation);
-
- DatasetConfigXMLUtils datasetConfigXMLUtils = new DatasetConfigXMLUtils(
- true);
- SAXBuilder builder = new SAXBuilder();
- Document doc = builder.build(new InputSource(in));
- // Document doc = datasetConfigXMLUtils.getDocumentForXMLStream(in);
-
- DatasetConfig datasetConfig = datasetConfigXMLUtils
- .getDatasetConfigForDocument(doc);
- datasetConfigXMLUtils.loadDatasetConfigWithDocument(datasetConfig,
- doc);
- return datasetConfig;
- } catch (ConfigurationException e) {
- String errorMessage = "Error parsing configuration from "
- + martServiceLocation;
- logger.debug(errorMessage, e);
- throw new MartServiceException(errorMessage, e);
- } catch (JDOMException e) {
- String errorMessage = "Error parsing configuration from "
- + martServiceLocation;
- logger.debug(errorMessage, e);
- throw new MartServiceException(errorMessage, e);
- } catch (IOException e) {
- String errorMessage = "Error getting configuration from "
- + martServiceLocation;
- logger.debug(errorMessage, e);
- throw new MartServiceException(errorMessage, e);
- } finally {
- method.releaseConnection();
- }
- }
-
- /**
- * Sends a query to the Biomart webservice and constructs an array of List
- * of String results from the tab separated rows of data returned by the
- * webservice.
- *
- * @param martServiceLocation
- * the URL of the Biomart webservice
- * @param query
- * the query to send to the webservice
- * @return an array of List of String
- * @throws MartServiceException
- * if the Biomart webservice returns an error or is unavailable
- */
- public static Object[] getResults(String martServiceLocation,
- String requestId, Query query) throws MartServiceException {
- Object[] results = new Object[0];
- // int attributes = query.getAttributes().size();
- int attributes = getAttributeCount(query.getAttributes());
- boolean count = query.getCount() == 1;
- // if there are no attributes and we're not doing a count there's no
- // point in doing the query
- if (attributes > 0 || count) {
- // The 'new' 0.5 server now resolves the attribute lists so there's
- // no need to do the split here any more
- // String queryXml = queryToXML(splitAttributeLists(query));
- String queryXml = queryToXML(query);
- logger.info(queryXml);
- NameValuePair[] data = { new NameValuePair(QUERY_ATTRIBUTE,
- queryXml) };
- PostMethod method = new PostMethod(martServiceLocation);
- method.setRequestBody(data);
-
- try {
- InputStream in = executeMethod(method, martServiceLocation);
- if (query.getFormatter() == null) {
- results = tabSeparatedReaderToResults(
- new InputStreamReader(in), count ? 1 : attributes);
- if (!count) {
- results = reassembleAttributeLists(results, query);
- }
- } else {
- results = readResult(in, query.getFormatter());
- }
- in.close();
- } catch (IOException e) {
- String errorMessage = "Error reading data from "
- + martServiceLocation;
- throw new MartServiceException(errorMessage, e);
- } finally {
- method.releaseConnection();
- }
-
- }
-
- return results;
- }
-
- public static void putResults(String martServiceLocation, String requestId,
- Query query, ResultReceiver resultReceiver) throws MartServiceException, ResultReceiverException {
- int attributeCount = getAttributeCount(query.getAttributes());
- boolean count = query.getCount() == 1;
- // if there are no attributes and we're not doing a count there's no
- // point in doing the query
- if (attributeCount > 0 || count) {
- String queryXml = queryToXML(query);
- logger.info(queryXml);
- NameValuePair[] data = { new NameValuePair(QUERY_ATTRIBUTE,
- queryXml) };
- PostMethod method = new PostMethod(martServiceLocation);
- method.setRequestBody(data);
-
- try {
- InputStream in = executeMethod(method, martServiceLocation);
- if (query.getFormatter() == null) {
- if (count) {
- resultReceiver.receiveResult(tabSeparatedReaderToResults(new InputStreamReader(in), 1), 0);
- } else {
- List<Attribute> attributes = query.getAttributes();
- Object[] result = new Object[attributes.size()];
- BufferedReader bufferedReader = new BufferedReader(new InputStreamReader(in));
- String line = bufferedReader.readLine();
- for (long i = 0; line != null; line = bufferedReader.readLine(), i++) {
- String[] tokens = line.split("\t", -1);
- if (attributeCount == tokens.length) {
- for (int ri = 0, ti = 0; ri < result.length && ti < tokens.length; ri++) {
- Attribute attribute = attributes.get(ri);
- if (attribute.getAttributes() == null) {
- result[ri] = tokens[ti];
- ti++;
- } else {
- int nestedAttributeCount = attribute.getAttributesCount();
- List<Object> list = new ArrayList<Object>();
- for (int j = 0; j < nestedAttributeCount; j++) {
- list.add(tokens[ti]);
- ti++;
- }
- result[ri] = list;
- }
- }
- resultReceiver.receiveResult(result, i);
- } else {
- resultReceiver.receiveError(line, i);
- }
- }
- }
- } else {
- resultReceiver.receiveResult(readResult(in, query.getFormatter()), 0);
- }
- in.close();
- } catch (IOException e) {
- String errorMessage = "Error reading data from "
- + martServiceLocation;
- throw new MartServiceException(errorMessage, e);
- } finally {
- method.releaseConnection();
- }
-
- }
- }
-
-// private static String getLocation(MartURLLocation martUrlLocation) {
-// StringBuffer location = new StringBuffer("http://");
-// location.append(martUrlLocation.getHost());
-// location.append(":" + martUrlLocation.getPort());
-// location.append(martUrlLocation.getPath());
-// return location.toString();
-// }
-
- private static int getAttributeCount(List<Attribute> attributeList) {
- int result = 0;
- for (Attribute attribute : attributeList) {
- if (attribute.getAttributes() == null) {
- result++;
- } else {
- result += attribute.getAttributesCount();
- }
- }
- return result;
- }
-
- private static Object[] reassembleAttributeLists(Object[] lists, Query query) {
- int index = 0;
- List<Object> result = new ArrayList<Object>();
- for (Attribute attribute : query.getAttributes()) {
- if (attribute.getAttributes() == null) {
- result.add(lists[index]);
- index++;
- } else {
- int attributesCount = attribute.getAttributesCount();
- List<Object> list = new ArrayList<Object>();
- for (int i = 0; i < attributesCount; i++) {
- list.add(lists[index]);
- index++;
- }
- result.add(list);
- }
- }
- return result.toArray();
- }
-
- public static Query splitAttributeLists(Query query) {
- Query result = new Query(query);
- for (Dataset dataset : result.getDatasets()) {
- List<Attribute> attributeList = dataset.getAttributes();
- dataset.removeAllAttributes();
- for (Attribute attribute : attributeList) {
- if (attribute.getAttributes() == null) {
- dataset.addAttribute(attribute);
- } else {
- String[] attributes = attribute.getAttributes().split(",");
- for (int i = 0; i < attributes.length; i++) {
- dataset.addAttribute(new Attribute(attributes[i]));
- }
- }
- }
- }
- return result;
- }
-
- public static String getMimeTypeForFormatter(String formatter) {
- String mimeType = "'text/plain'";
- if ("ADF".equals(formatter)) {
- mimeType = "'text/plain'";
- } else if ("AXT".equals(formatter)) {
- mimeType = "'text/plain'";
- } else if ("AXTPLUS".equals(formatter)) {
- mimeType = "'text/plain'";
- } else if ("CSV".equals(formatter)) {
- mimeType = "'text/plain'";
- } else if ("FASTA".equals(formatter)) {
- mimeType = "'text/plain'";
- } else if ("FASTACDNA".equals(formatter)) {
- mimeType = "'text/plain'";
- } else if ("GFF".equals(formatter)) {
- mimeType = "'text/plain'";
- } else if ("HTML".equals(formatter)) {
- mimeType = "'text/html'";
- } else if ("MAF".equals(formatter)) {
- mimeType = "'text/plain'";
- } else if ("MFA".equals(formatter)) {
- mimeType = "'text/plain'";
- } else if ("MFASTA".equals(formatter)) {
- mimeType = "'text/plain'";
- } else if ("TSV".equals(formatter)) {
- mimeType = "'text/tab-separeted-values'";
- } else if ("TXT".equals(formatter)) {
- mimeType = "'text/plain'";
- } else if ("XLS".equals(formatter)) {
- mimeType = "'application/excel'";
- }
-
- return mimeType;
- }
-
- private static List<String>[] tabSeparatedReaderToResults(Reader reader,
- int resultsCount) throws IOException {
- List<String>[] results = new List[resultsCount];
- for (int i = 0; i < results.length; i++) {
- results[i] = new ArrayList<String>();
- }
- BufferedReader bufferedReader = new BufferedReader(reader);
- String line = bufferedReader.readLine();
- while (line != null) {
- String[] tokens = line.split("\t", -1);
- for (int i = 0; i < results.length && i < tokens.length; i++) {
- results[i].add(tokens[i]);
- }
- line = bufferedReader.readLine();
- }
- return results;
- }
-
- private static Object[] readResult(InputStream inputStream, String formatter) throws IOException {
- Object[] result = new Object[1];
-
- if (getMimeTypeForFormatter(formatter).contains("application/")) {
- result[0] = IOUtils.toByteArray(inputStream);
- } else {
- result[0] = IOUtils.toString(inputStream);
- }
- return result;
- }
-
- private static MartDataset[] tabSeparatedReaderToDatasets(Reader reader,
- MartURLLocation martURLLocation) throws IOException {
- List<MartDataset> datasetList = new ArrayList<MartDataset>();
- BufferedReader bufferedReader = new BufferedReader(reader);
- String line = bufferedReader.readLine();
- while (line != null) {
- String[] tokens = line.split("\t");
-
- if (tokens.length >= 7) {
- MartDataset dataset = new MartDataset();
-
- dataset.setType(tokens[0]);
- dataset.setName(tokens[1]);
- dataset.setDisplayName(tokens[2]);
- if (tokens[3].equals("1")) {
- dataset.setVisible(true);
- } else {
- dataset.setVisible(false);
- }
- // value at position 4 is not documented so it's skipped
- try {
- dataset.setInitialBatchSize(Long.parseLong(tokens[5]));
- } catch (NumberFormatException e) {
- dataset.setInitialBatchSize(0);
- }
- try {
- dataset.setMaximumBatchSize(Long.parseLong(tokens[6]));
- } catch (NumberFormatException e) {
- dataset.setMaximumBatchSize(0);
- }
-
- if (tokens.length > 7) {
- dataset.setInterface(tokens[7]);
- dataset.setModified(tokens[8]);
- }
-
- dataset.setMartURLLocation(martURLLocation);
-
- datasetList.add(dataset);
- }
- line = bufferedReader.readLine();
- }
- return datasetList.toArray(new MartDataset[datasetList.size()]);
- }
-
- /**
- * Creates an XML string from a query
- *
- * @param query
- * @return an XML string
- */
- public static String queryToXML(Query query) {
- Document document = new Document(QueryXMLHandler.queryToElement(query,
- Namespace.NO_NAMESPACE), new DocType("Query"));
- return new XMLOutputter().outputString(document);
- }
-
- /**
- * @param martServiceLocation
- * @param data
- * @return
- * @throws MartServiceException
- */
- private static InputStream executeMethod(HttpMethod method,
- String martServiceLocation) throws MartServiceException {
- HttpClient client = new HttpClient();
- if (isProxyHost(martServiceLocation)) {
- setProxy(client);
- }
-
- method.getParams().setParameter(HttpMethodParams.RETRY_HANDLER,
- new DefaultHttpMethodRetryHandler(3, false));
-// method.getParams().setSoTimeout(60000);
- try {
- int statusCode = client.executeMethod(method);
- if (statusCode != HttpStatus.SC_OK) {
- throw constructException(method, martServiceLocation, null);
- }
- return method.getResponseBodyAsStream();
- } catch (IOException e) {
- throw constructException(method, martServiceLocation, e);
- }
- }
-
- /**
- *
- * @param client
- */
- public static void setProxy(HttpClient client) {
- String host = System.getProperty("http.proxyHost");
- String port = System.getProperty("http.proxyPort");
- String user = System.getProperty("http.proxyUser");
- String password = System.getProperty("http.proxyPassword");
-
- if (host != null && port != null) {
- try {
- int portInteger = Integer.parseInt(port);
- client.getHostConfiguration().setProxy(host, portInteger);
- if (user != null && password != null) {
- client.getState().setProxyCredentials(
- new AuthScope(host, portInteger),
- new UsernamePasswordCredentials(user, password));
- }
- } catch (NumberFormatException e) {
- logger.error("Proxy port not an integer", e);
- }
- }
- }
-
- public static boolean isProxyHost(String location) {
- String httpNonProxyHosts = System.getProperty("http.nonProxyHosts");
- if (httpNonProxyHosts != null) {
- try {
- String host = new URL(location).getHost();
- String[] nonProxyHosts = httpNonProxyHosts.split("\\|");
- for (int i = 0; i < nonProxyHosts.length; i++) {
- if (nonProxyHosts[i].startsWith("*")) {
- if (host.endsWith(nonProxyHosts[i].substring(1))) {
- return false;
- }
- } else if (nonProxyHosts[i].endsWith("*")) {
- if (host.startsWith(nonProxyHosts[i].substring(0,
- nonProxyHosts[i].length() - 1))) {
- return false;
- }
- } else {
- if (host.equals(nonProxyHosts[i])) {
- return false;
- }
- }
- }
- } catch (MalformedURLException e) {
- logger.warn("'" + location + "' is not a valid URL. "
- + "Cannot compare host with http.nonProxyHosts", e);
- }
- }
- return true;
- }
-
- private static MartServiceException constructException(HttpMethod method,
- String martServiceLocation, Exception cause) {
- StringBuffer errorMessage = new StringBuffer();
- errorMessage.append("Error posting to " + martServiceLocation
- + lineSeparator);
- if (cause == null) {
- errorMessage.append(" " + method.getStatusLine()
- + lineSeparator);
- }
- if (method instanceof PostMethod) {
- PostMethod postMethod = (PostMethod) method;
- NameValuePair[] data = postMethod.getParameters();
- for (int i = 0; i < data.length; i++) {
- errorMessage.append(" " + data[i].getName() + " = "
- + data[i].getValue()
- + lineSeparator);
- }
-
- } else {
- errorMessage.append(method.getQueryString());
- }
- return new MartServiceException(errorMessage.toString(), cause);
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartServiceXMLHandler.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartServiceXMLHandler.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartServiceXMLHandler.java
deleted file mode 100644
index e8a5189..0000000
--- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartServiceXMLHandler.java
+++ /dev/null
@@ -1,390 +0,0 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: MartServiceXMLHandler.java,v $
- * Revision $Revision: 1.4 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/12/13 11:38:55 $
- * by $Author: davidwithers $
- * Created on 28-Apr-2006
- *****************************************************************/
-package org.biomart.martservice;
-
-import java.util.Iterator;
-import java.util.List;
-import java.util.Set;
-
-import org.biomart.martservice.query.QueryXMLHandler;
-import org.jdom.Element;
-import org.jdom.Namespace;
-
-/**
- * Utility class for serializing mart service classes to XML.
- *
- * @author David Withers
- */
-public class MartServiceXMLHandler {
- public static final String MART_SERVICE_ELEMENT = "MartService";
-
- public static final String MART_URL_LOCATION_ELEMENT = "MartURLLocation";
-
- public static final String MART_DATASET_ELEMENT = "MartDataset";
-
- public static final String MART_QUERY_ELEMENT = "MartQuery";
-
- public static final String LINKED_DATASETS_ELEMENT = "LinkedDatasets";
-
- public static final String LINKED_DATASET_ELEMENT = "LinkedDataset";
-
- public static final String VIRTUAL_SCHEMA_ELEMENT = "virtualSchema";
-
- public static final String LOCATION_ATTRIBUTE = "location";
-
- public static final String DATABASE_ATTRIBUTE = "database";
-
- public static final String DEFAULT_ATTRIBUTE = "default";
-
- public static final String DEFAULT_VALUE_ATTRIBUTE = "defaultValue";
-
- public static final String DISPLAY_NAME_ATTRIBUTE = "displayName";
-
- public static final String HOST_ATTRIBUTE = "host";
-
- public static final String INCLUDE_DATASETS_ATTRIBUTE = "includeDatasets";
-
- public static final String LINK_ATTRIBUTE = "LINK";
-
- public static final String MART_USER_ATTRIBUTE = "martUser";
-
- public static final String NAME_ATTRIBUTE = "name";
-
- public static final String PATH_ATTRIBUTE = "path";
-
- public static final String PORT_ATTRIBUTE = "port";
-
- public static final String TYPE_ATTRIBUTE = "type";
-
- public static final String INITIAL_BATCH_SIZE_ATTRIBUTE = "initialBatchSize";
-
- public static final String MAXIMUM_BATCH_SIZE_ATTRIBUTE = "maximumBatchSize";
-
- public static final String VIRTUAL_SCHEMA_ATTRIBUTE = "virtualSchema";
-
- public static final String SERVER_VIRTUAL_SCHEMA_ATTRIBUTE = "serverVirtualSchema";
-
- public static final String VISIBLE_ATTRIBUTE = "visible";
-
- public static final String REDIRECT_ATTRIBUTE = "redirect";
-
- public static final String INTERFACE_ATTRIBUTE = "interface";
-
- public static final String MODIFIED_ATTRIBUTE = "modified";
-
- /**
- * Converts a <code>MartService</code> to an XML element.
- *
- * @param martService
- * the <code>MartService</code> to serialize
- * @param namespace
- * the <code>Namespace</code> to use when constructing the
- * <code>Element</code>
- * @return an XML serialization of the <code>MartService</code>
- */
- public static Element martServiceToElement(MartService martService,
- Namespace namespace) {
- Element element = new Element(MART_SERVICE_ELEMENT, namespace);
- element.setAttribute(LOCATION_ATTRIBUTE, martService.getLocation());
- return element;
- }
-
- /**
- * Creates a <code>MartService</code> from an XML element.
- *
- * @param element
- * the <code>Element</code> to deserialize
- * @return a deserialized <code>MartService</code>
- */
- public static MartService elementToMartService(Element element) {
- return MartService.getMartService(element
- .getAttributeValue(LOCATION_ATTRIBUTE));
- }
-
- /**
- * Converts a <code>MartDataset</code> to an XML element.
- *
- * @param dataset
- * the <code>MartDataset</code> to serialize
- * @param namespace
- * the <code>Namespace</code> to use when constructing the
- * <code>Element</code>
- * @return an XML serialization of the <code>MartDataset</code>
- */
- public static Element datasetToElement(MartDataset dataset,
- Namespace namespace) {
- Element element = new Element(MART_DATASET_ELEMENT, namespace);
- element.setAttribute(DISPLAY_NAME_ATTRIBUTE, dataset.getDisplayName());
- element.setAttribute(NAME_ATTRIBUTE, dataset.getName());
- element.setAttribute(TYPE_ATTRIBUTE, dataset.getType());
- element.setAttribute(INITIAL_BATCH_SIZE_ATTRIBUTE, String
- .valueOf(dataset.getInitialBatchSize()));
- element.setAttribute(MAXIMUM_BATCH_SIZE_ATTRIBUTE, String
- .valueOf(dataset.getMaximumBatchSize()));
- element.setAttribute(VISIBLE_ATTRIBUTE, String.valueOf(dataset
- .isVisible()));
- if (dataset.getInterface() != null) {
- element.setAttribute(INTERFACE_ATTRIBUTE, dataset.getInterface());
- }
- if (dataset.getModified() != null) {
- element.setAttribute(MODIFIED_ATTRIBUTE, dataset.getModified());
- }
- element.addContent(locationToElement(dataset.getMartURLLocation(),
- namespace));
- return element;
- }
-
- /**
- * Creates a <code>MartDataset</code> from an XML element.
- *
- * @param element
- * the <code>Element</code> to deserialize
- * @param namespace
- * the <code>Namespace</code> containing the
- * <code>Element</code>
- * @return a deserialized <code>MartDataset</code>
- */
- public static MartDataset elementToDataset(Element element,
- Namespace namespace) {
- MartDataset dataset = new MartDataset();
- dataset.setDisplayName(element
- .getAttributeValue(DISPLAY_NAME_ATTRIBUTE));
- dataset.setName(element.getAttributeValue(NAME_ATTRIBUTE));
- dataset.setType(element.getAttributeValue(TYPE_ATTRIBUTE));
- dataset.setInitialBatchSize(Long.parseLong(element
- .getAttributeValue(INITIAL_BATCH_SIZE_ATTRIBUTE)));
- dataset.setMaximumBatchSize(Long.parseLong(element
- .getAttributeValue(MAXIMUM_BATCH_SIZE_ATTRIBUTE)));
- dataset.setVisible(Boolean.getBoolean(element
- .getAttributeValue(VISIBLE_ATTRIBUTE)));
- dataset.setInterface(element.getAttributeValue(INTERFACE_ATTRIBUTE));
- dataset.setModified(element.getAttributeValue(MODIFIED_ATTRIBUTE));
- dataset.setMartURLLocation(elementToLocation(element.getChild(
- MART_URL_LOCATION_ELEMENT, namespace)));
- return dataset;
- }
-
- /**
- * Creates a <code>MartRegistry</code> from an XML element.
- *
- * @param element
- * the <code>Element</code> to deserialize
- * @param namespace
- * the <code>Namespace</code> containing the
- * <code>Element</code>
- * @return a deserialized <code>MartRegistry</code>
- */
- public static MartRegistry elementToRegistry(Element root,
- Namespace namespace) {
- MartRegistry registry = new MartRegistry();
- List<Element> children = root.getChildren();
- for (Element childElement : children) {
- if (childElement.getNamespace().equals(namespace)) {
- if (childElement.getName().equals(MART_URL_LOCATION_ELEMENT)) {
- MartURLLocation martURLLocation = MartServiceXMLHandler
- .elementToLocation(childElement);
- martURLLocation.setVirtualSchema("default");
- registry.addMartURLLocation(martURLLocation);
- } else if (childElement.getName()
- .equals(VIRTUAL_SCHEMA_ELEMENT)) {
- String virtualSchema = childElement
- .getAttributeValue(NAME_ATTRIBUTE);
- List<Element> locations = childElement.getChildren(
- MART_URL_LOCATION_ELEMENT, namespace);
- for (Element location : locations) {
- MartURLLocation martURLLocation = MartServiceXMLHandler
- .elementToLocation(location);
- martURLLocation.setVirtualSchema(virtualSchema);
- registry.addMartURLLocation(martURLLocation);
- }
- }
- }
- }
- return registry;
- }
-
- /**
- * Converts a <code>MartURLLocation</code> to an XML element.
- *
- * @param location
- * the <code>MartURLLocation</code> to serialize
- * @param namespace
- * the <code>Namespace</code> to use when constructing the
- * <code>Element</code>
- * @return an XML serialization of the <code>MartURLLocation</code>
- */
- public static Element locationToElement(MartURLLocation location,
- Namespace namespace) {
- Element element = new Element(MART_URL_LOCATION_ELEMENT, namespace);
- if (location.getDatabase() != null) {
- element.setAttribute(DATABASE_ATTRIBUTE, location.getDatabase());
- }
- element.setAttribute(DEFAULT_ATTRIBUTE, location.isDefault() ? "1"
- : "0");
- element.setAttribute(DISPLAY_NAME_ATTRIBUTE, location.getDisplayName());
- element.setAttribute(HOST_ATTRIBUTE, location.getHost());
- if (location.getIncludeDatasets() != null) {
- element.setAttribute(INCLUDE_DATASETS_ATTRIBUTE, location
- .getIncludeDatasets());
- }
- if (location.getMartUser() != null) {
- element.setAttribute(MART_USER_ATTRIBUTE, location.getMartUser());
- }
- element.setAttribute(NAME_ATTRIBUTE, location.getName());
- if (location.getPath() != null) {
- element.setAttribute(PATH_ATTRIBUTE, location.getPath());
- }
- element
- .setAttribute(PORT_ATTRIBUTE, String
- .valueOf(location.getPort()));
- element.setAttribute(SERVER_VIRTUAL_SCHEMA_ATTRIBUTE, location
- .getServerVirtualSchema());
- if (location.getVirtualSchema() != null) {
- element.setAttribute(VIRTUAL_SCHEMA_ATTRIBUTE, location
- .getVirtualSchema());
- }
- element.setAttribute(VISIBLE_ATTRIBUTE, location.isVisible() ? "1"
- : "0");
- element.setAttribute(REDIRECT_ATTRIBUTE, location.isRedirect() ? "1"
- : "0");
- return element;
- }
-
- /**
- * Creates a <code>MartURLLocation</code> from an XML element.
- *
- * @param element
- * the <code>Element</code> to deserialize
- * @return a deserialized <code>MartURLLocation</code>
- */
- public static MartURLLocation elementToLocation(Element element) {
- MartURLLocation location = new MartURLLocation();
- location.setDatabase(element.getAttributeValue(DATABASE_ATTRIBUTE));
- location.setDefault("1".equals(element
- .getAttributeValue(DEFAULT_ATTRIBUTE)));
- location.setDisplayName(element
- .getAttributeValue(DISPLAY_NAME_ATTRIBUTE));
- location.setHost(element.getAttributeValue(HOST_ATTRIBUTE));
- location.setIncludeDatasets(element
- .getAttributeValue(INCLUDE_DATASETS_ATTRIBUTE));
- location.setMartUser(element.getAttributeValue(MART_USER_ATTRIBUTE));
- location.setName(element.getAttributeValue(NAME_ATTRIBUTE));
- location.setPath(element.getAttributeValue(PATH_ATTRIBUTE));
- try {
- location.setPort(Integer.parseInt(element
- .getAttributeValue(PORT_ATTRIBUTE)));
- } catch (NumberFormatException e) {
- location.setPort(80);
- }
- location.setServerVirtualSchema(element
- .getAttributeValue(SERVER_VIRTUAL_SCHEMA_ATTRIBUTE));
- location.setVirtualSchema(element
- .getAttributeValue(VIRTUAL_SCHEMA_ATTRIBUTE));
- location.setVisible("1".equals(element
- .getAttributeValue(VISIBLE_ATTRIBUTE)));
- location.setRedirect("1".equals(element
- .getAttributeValue(REDIRECT_ATTRIBUTE)));
- return location;
- }
-
- /**
- * Creates a <code>MartQuery</code> from an XML element.
- *
- * @param element
- * the <code>Element</code> to deserialize
- * @param namespace
- * the <code>Namespace</code> containing the
- * <code>Element</code>
- * @return a deserialized <code>MartQuery</code>
- */
- public static MartQuery elementToMartQuery(Element element,
- Namespace namespace) {
- MartQuery martQuery = new MartQuery();
- martQuery.setMartService(MartServiceXMLHandler
- .elementToMartService(element.getChild(MART_SERVICE_ELEMENT,
- namespace)));
- martQuery.setMartDataset(elementToDataset(element.getChild(
- MART_DATASET_ELEMENT, namespace), namespace));
- martQuery.setQuery(QueryXMLHandler.elementToQuery(element.getChild(
- QueryXMLHandler.QUERY_ELEMENT, namespace), namespace));
- Element linksElement = element.getChild(LINKED_DATASETS_ELEMENT, namespace);
- if (linksElement != null) {
- List linkedDatasets = linksElement.getChildren(LINKED_DATASETS_ELEMENT,
- namespace);
- for (Iterator iter = linkedDatasets.iterator(); iter.hasNext();) {
- Element datasetElement = (Element) iter.next();
- String datasetName = datasetElement.getAttributeValue(NAME_ATTRIBUTE);
- String linkId = datasetElement.getAttributeValue(LINK_ATTRIBUTE);
- martQuery.addLinkedDataset(datasetName, linkId);
- }
- }
- return martQuery;
- }
-
- /**
- * Converts a <code>MartQuery</code> to an XML element.
- *
- * @param martQuery
- * the <code>MartQuery</code> to serialize
- * @param namespace
- * the <code>Namespace</code> to use when constructing the
- * <code>Element</code>
- * @return an XML serialization of the <code>MartQuery</code>
- */
- public static Element martQueryToElement(MartQuery martQuery,
- Namespace namespace) {
- Element element = new Element(MART_QUERY_ELEMENT, namespace);
- element.addContent(martServiceToElement(martQuery.getMartService(),
- namespace));
- element.addContent(datasetToElement(martQuery.getMartDataset(),
- namespace));
- element.addContent(QueryXMLHandler.queryToElement(martQuery.getQuery(),
- namespace));
- Set linkedDatasets = martQuery.getLinkedDatasets();
- if (linkedDatasets.size() > 0) {
- Element linksElement = new Element(LINKED_DATASETS_ELEMENT, namespace);
- for (Iterator iter = linkedDatasets.iterator(); iter.hasNext();) {
- String datasetName = (String) iter.next();
- Element datasetElement = new Element(LINKED_DATASETS_ELEMENT, namespace);
- datasetElement.setAttribute(NAME_ATTRIBUTE, datasetName);
- datasetElement.setAttribute(LINK_ATTRIBUTE, martQuery
- .getLink(datasetName));
- linksElement.addContent(datasetElement);
- }
- element.addContent(linksElement);
- }
- return element;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartURLLocation.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartURLLocation.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartURLLocation.java
deleted file mode 100644
index 476956d..0000000
--- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartURLLocation.java
+++ /dev/null
@@ -1,422 +0,0 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: MartURLLocation.java,v $
- * Revision $Revision: 1.2 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/10/04 14:15:59 $
- * by $Author: davidwithers $
- * Created on 17-Mar-2006
- *****************************************************************/
-package org.biomart.martservice;
-
-import org.ensembl.mart.lib.config.MartLocation;
-
-/**
- * The MartURLLocation contained by the MartRegistry returned by a BioMart web
- * service.
- *
- * @author David Withers
- */
-public class MartURLLocation implements MartLocation {
- private static final String URL_TYPE = "URL";
-
- private String database;
-
- private boolean defaultValue;
-
- private String displayName;
-
- private String host;
-
- private String includeDatasets;
-
- private String martUser;
-
- private String name;
-
- private String path;
-
- private int port;
-
- private String serverVirtualSchema;
-
- private String virtualSchema;
-
- private boolean visible;
-
- private boolean redirect;
-
- /**
- * Returns the database.
- *
- * @return the database
- */
- public String getDatabase() {
- return database;
- }
-
- /**
- * Sets the database.
- *
- * @param database the new database
- */
- public void setDatabase(String database) {
- this.database = database;
- }
-
- /**
- * Returns true if the default flag is set.
- *
- * @return true if the default flag is set
- */
- public boolean isDefault() {
- return defaultValue;
- }
-
- /**
- * Sets the default flag.
- *
- * @param defaultValue
- * the value of the default flag
- */
- public void setDefault(boolean defaultValue) {
- this.defaultValue = defaultValue;
- }
-
- /**
- * Returns the displayName.
- *
- * @return the displayName.
- */
- public String getDisplayName() {
- return displayName;
- }
-
- /**
- * Sets the displayName.
- *
- * @param displayName
- * the displayName to set.
- */
- public void setDisplayName(String displayName) {
- this.displayName = displayName;
- }
-
- /**
- * Returns the host.
- *
- * @return the host.
- */
- public String getHost() {
- return host;
- }
-
- /**
- * Sets the host.
- *
- * @param host
- * the host to set.
- */
- public void setHost(String host) {
- this.host = host;
- }
-
- /**
- * Returns the includeDatasets.
- *
- * @return the includeDatasets
- */
- public String getIncludeDatasets() {
- return includeDatasets;
- }
-
- /**
- * Sets the includeDatasets.
- *
- * @param includeDatasets the new includeDatasets
- */
- public void setIncludeDatasets(String includeDatasets) {
- this.includeDatasets = includeDatasets;
- }
-
- /**
- * Returns the martUser.
- *
- * @return the martUser
- */
- public String getMartUser() {
- return martUser;
- }
-
- /**
- * Sets the martUser.
- *
- * @param martUser the new martUser
- */
- public void setMartUser(String martUser) {
- this.martUser = martUser;
- }
-
- /**
- * Returns the name
- *
- * @return the name.
- */
- public String getName() {
- return name;
- }
-
- /**
- * Sets the name.
- *
- * @param name
- * the name to set.
- */
- public void setName(String name) {
- this.name = name;
- }
-
- /**
- * Returns the path.
- *
- * @return the path
- */
- public String getPath() {
- return path;
- }
-
- /**
- * Sets the path.
- *
- * @param path the new path
- */
- public void setPath(String path) {
- this.path = path;
- }
-
- /**
- * Returns the port.
- *
- * @return the port.
- */
- public int getPort() {
- return port;
- }
-
- /**
- * Sets the port.
- *
- * @param port
- * the port to set.
- */
- public void setPort(int port) {
- this.port = port;
- }
-
- /**
- * Returns the serverVirtualSchema.
- *
- * @return the serverVirtualSchema.
- */
- public String getServerVirtualSchema() {
- return serverVirtualSchema;
- }
-
- /**
- * Sets the serverVirtualSchema.
- *
- * @param serverVirtualSchema
- * the serverVirtualSchema to set.
- */
- public void setServerVirtualSchema(String serverVirtualSchema) {
- this.serverVirtualSchema = serverVirtualSchema;
- }
-
- /**
- * Returns the virtualSchema.
- *
- * @return the virtualSchema.
- */
- public String getVirtualSchema() {
- return virtualSchema;
- }
-
- /**
- * Sets the virtualSchema.
- *
- * @param virtualSchema
- * the virtualSchema to set.
- */
- public void setVirtualSchema(String virtualSchema) {
- this.virtualSchema = virtualSchema;
- }
-
- /**
- * Returns true if the location is visible.
- *
- * @return Returns the visible.
- */
- public boolean isVisible() {
- return visible;
- }
-
- /**
- * @param visible
- * The visible to set.
- */
- public void setVisible(boolean visible) {
- this.visible = visible;
- }
-
- /**
- * Returns true if this location is redirected.
- *
- * @return the redirect
- */
- public boolean isRedirect() {
- return redirect;
- }
-
- /**
- * @param redirect the redirect to set
- */
- public void setRedirect(boolean redirect) {
- this.redirect = redirect;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see org.ensembl.mart.lib.config.MartLocation#getType()
- */
- public String getType() {
- return URL_TYPE;
- }
-
- /**
- * Returns the display name.
- *
- * @return the display name
- */
- public String toString() {
- return getDisplayName();
- }
-
- @Override
- public int hashCode() {
- final int prime = 31;
- int result = 1;
- result = prime * result
- + ((database == null) ? 0 : database.hashCode());
- result = prime * result + (defaultValue ? 1231 : 1237);
- result = prime * result
- + ((displayName == null) ? 0 : displayName.hashCode());
- result = prime * result + ((host == null) ? 0 : host.hashCode());
- result = prime * result
- + ((includeDatasets == null) ? 0 : includeDatasets.hashCode());
- result = prime * result
- + ((martUser == null) ? 0 : martUser.hashCode());
- result = prime * result + ((name == null) ? 0 : name.hashCode());
- result = prime * result + ((path == null) ? 0 : path.hashCode());
- result = prime * result + port;
- result = prime * result + (redirect ? 1231 : 1237);
- result = prime
- * result
- + ((serverVirtualSchema == null) ? 0 : serverVirtualSchema
- .hashCode());
- result = prime * result
- + ((virtualSchema == null) ? 0 : virtualSchema.hashCode());
- result = prime * result + (visible ? 1231 : 1237);
- return result;
- }
-
- @Override
- public boolean equals(Object obj) {
- if (this == obj)
- return true;
- if (obj == null)
- return false;
- if (getClass() != obj.getClass())
- return false;
- final MartURLLocation other = (MartURLLocation) obj;
- if (database == null) {
- if (other.database != null)
- return false;
- } else if (!database.equals(other.database))
- return false;
- if (defaultValue != other.defaultValue)
- return false;
- if (displayName == null) {
- if (other.displayName != null)
- return false;
- } else if (!displayName.equals(other.displayName))
- return false;
- if (host == null) {
- if (other.host != null)
- return false;
- } else if (!host.equals(other.host))
- return false;
- if (includeDatasets == null) {
- if (other.includeDatasets != null)
- return false;
- } else if (!includeDatasets.equals(other.includeDatasets))
- return false;
- if (martUser == null) {
- if (other.martUser != null)
- return false;
- } else if (!martUser.equals(other.martUser))
- return false;
- if (name == null) {
- if (other.name != null)
- return false;
- } else if (!name.equals(other.name))
- return false;
- if (path == null) {
- if (other.path != null)
- return false;
- } else if (!path.equals(other.path))
- return false;
- if (port != other.port)
- return false;
- if (redirect != other.redirect)
- return false;
- if (serverVirtualSchema == null) {
- if (other.serverVirtualSchema != null)
- return false;
- } else if (!serverVirtualSchema.equals(other.serverVirtualSchema))
- return false;
- if (virtualSchema == null) {
- if (other.virtualSchema != null)
- return false;
- } else if (!virtualSchema.equals(other.virtualSchema))
- return false;
- if (visible != other.visible)
- return false;
- return true;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-martservice/src/main/java/org/biomart/martservice/ResultReceiver.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/ResultReceiver.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/ResultReceiver.java
deleted file mode 100644
index cc1d062..0000000
--- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/ResultReceiver.java
+++ /dev/null
@@ -1,61 +0,0 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: ResultReceiver.java,v $
- * Revision $Revision: 1.2 $
- * Release status $State: Exp $
- * Last modified on $Date: 2008/07/31 15:06:49 $
- * by $Author: davidwithers $
- * Created on Jan 18, 2008
- *****************************************************************/
-package org.biomart.martservice;
-
-/**
- * An interface for receiving results of a Query.
- *
- * @author David Withers
- */
-public interface ResultReceiver {
-
- /**
- * Receives a single row from the results of executing a Query.
- *
- * This method will be called frequently and should not block.
- *
- * @param resultRow
- */
- public void receiveResult(Object[] resultRow, long index) throws ResultReceiverException;
-
- /**
- * Receives an error for a single row from the results of executing a Query.
- *
- * This method will be called frequently and should not block.
- *
- * @param resultRow
- */
- public void receiveError(String errorMessage, long index) throws ResultReceiverException;
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-martservice/src/main/java/org/biomart/martservice/ResultReceiverException.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/ResultReceiverException.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/ResultReceiverException.java
deleted file mode 100644
index c3498e6..0000000
--- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/ResultReceiverException.java
+++ /dev/null
@@ -1,85 +0,0 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: ResultReceiverException.java,v $
- * Revision $Revision: 1.1 $
- * Release status $State: Exp $
- * Last modified on $Date: 2008/03/04 16:47:57 $
- * by $Author: davidwithers $
- * Created on 05-May-2006
- *****************************************************************/
-package org.biomart.martservice;
-
-/**
- *
- * @author David Withers
- */
-public class ResultReceiverException extends Exception {
- private static final long serialVersionUID = 7151337259555845771L;
-
- /**
- * Constructs a new exception with no detail message.
- *
- */
- public ResultReceiverException() {
- super();
- }
-
- /**
- * Constructs a new exception with the specified detail message.
- *
- * @param message
- * the detail message
- * @param cause
- * the cause (a null value is permitted, and indicates that the
- * cause is nonexistent or unknown)
- */
- public ResultReceiverException(String message, Throwable cause) {
- super(message, cause);
- }
-
- /**
- * Constructs a new exception with the specified detail message and cause.
- *
- * @param message
- * the detail message
- */
- public ResultReceiverException(String message) {
- super(message);
- }
-
- /**
- * Constructs a new exception with the specified cause.
- *
- * @param cause
- * the cause (a null value is permitted, and indicates that the
- * cause is nonexistent or unknown)
- */
- public ResultReceiverException(Throwable cause) {
- super(cause);
- }
-
-}
[15/16] incubator-taverna-plugin-bioinformatics git commit:
temporarily empty repository
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-activity/src/main/java/net/sf/taverna/t2/activities/biomart/BiomartActivity.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-activity/src/main/java/net/sf/taverna/t2/activities/biomart/BiomartActivity.java b/taverna-biomart-activity/src/main/java/net/sf/taverna/t2/activities/biomart/BiomartActivity.java
deleted file mode 100644
index 7e87939..0000000
--- a/taverna-biomart-activity/src/main/java/net/sf/taverna/t2/activities/biomart/BiomartActivity.java
+++ /dev/null
@@ -1,351 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.biomart;
-
-import java.io.IOException;
-import java.io.StringReader;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.List;
-import java.util.Map;
-
-import net.sf.taverna.t2.reference.ReferenceService;
-import net.sf.taverna.t2.reference.ReferenceServiceException;
-import net.sf.taverna.t2.reference.T2Reference;
-import net.sf.taverna.t2.workflowmodel.processor.activity.AbstractAsynchronousActivity;
-import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityConfigurationException;
-import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityOutputPort;
-import net.sf.taverna.t2.workflowmodel.processor.activity.AsynchronousActivityCallback;
-
-import org.apache.log4j.Logger;
-import org.biomart.martservice.MartQuery;
-import org.biomart.martservice.MartServiceException;
-import org.biomart.martservice.MartServiceXMLHandler;
-import org.biomart.martservice.ResultReceiver;
-import org.biomart.martservice.ResultReceiverException;
-import org.biomart.martservice.config.QueryConfigUtils;
-import org.biomart.martservice.query.Attribute;
-import org.biomart.martservice.query.Dataset;
-import org.biomart.martservice.query.Filter;
-import org.biomart.martservice.query.Query;
-import org.jdom.Document;
-import org.jdom.JDOMException;
-import org.jdom.input.SAXBuilder;
-
-import com.fasterxml.jackson.databind.JsonNode;
-
-/**
- * An Activity providing Biomart functionality.
- *
- * @author David Withers
- */
-public class BiomartActivity extends AbstractAsynchronousActivity<JsonNode> {
-
- public static final String URI = "http://ns.taverna.org.uk/2010/activity/biomart";
-
- static boolean STREAM_RESULTS = true;
-
- private static Logger logger = Logger.getLogger(BiomartActivity.class);
-
- private JsonNode json;
-
- private MartQuery biomartQuery;
-
- @Override
- public void configure(JsonNode json)
- throws ActivityConfigurationException {
- this.json = json;
- String martQueryText = json.get("martQuery").asText();
- SAXBuilder builder = new SAXBuilder();
- try {
- Document document = builder.build(new StringReader(martQueryText));
- biomartQuery = MartServiceXMLHandler.elementToMartQuery(document.getRootElement(), null);
- } catch (JDOMException | IOException e) {
- throw new ActivityConfigurationException(e);
- }
- }
-
- @Override
- public JsonNode getConfiguration() {
- return json;
- }
-
- @Override
- public void executeAsynch(final Map<String, T2Reference> data,
- final AsynchronousActivityCallback callback) {
- callback.requestRun(new Runnable() {
-
- public void run() {
- final ReferenceService referenceService = callback.getContext().getReferenceService();
-
- final Map<String, T2Reference> outputData = new HashMap<String, T2Reference>();
-
- try {
- // Get a query including data source etc, creating
- // a copy so that any filter value settings are not
- // overwritten by input values
- biomartQuery.calculateLinks();
- Query query = new Query(biomartQuery.getQuery());
-
- // Configure any filters
- List<Filter> filters = query.getFilters();
- for (Filter filter : filters) {
- String name = filter.getQualifiedName();
- if (data.containsKey(name + "_filter")) {
- Object filterValue = referenceService.renderIdentifier(data
- .get(name + "_filter"), String.class, callback.getContext());
- if (filterValue instanceof String) {
- filter.setValue((String) filterValue);
- } else if (filterValue instanceof List) {
- List<?> idList = (List<?>) filterValue;
- filter.setValue(QueryConfigUtils
- .listToCsv(idList));
- }
- }
- }
-
- if (biomartQuery.getQuery().getFormatter() == null) {
- if (STREAM_RESULTS) {
- final List<Attribute> attributes = biomartQuery
- .getAttributesInLinkOrder();
- final Map<String, List<T2Reference>> outputLists = new HashMap<String, List<T2Reference>>();
- for (Attribute attribute : attributes) {
- outputLists.put(attribute.getQualifiedName(),
- new ArrayList<T2Reference>());
- }
-
- biomartQuery.getMartService().executeQuery(query,
- new ResultReceiver() {
-
- public void receiveResult(
- Object[] resultLine, long index) throws ResultReceiverException {
- Map<String, T2Reference> partialOutputData = new HashMap<String, T2Reference>();
- for (int i = 0; i < resultLine.length; i++) {
- Attribute attribute = attributes
- .get(i);
- String outputName = attribute
- .getQualifiedName();
- Integer outputDepth = getOutputPortDepth(outputName);
- if (outputDepth == null) {
- logger.warn("Skipping unknown output port " + outputName);
- continue;
- }
- try {
- T2Reference data = referenceService
- .register(resultLine[i], outputDepth - 1, true, callback.getContext());
- partialOutputData.put(
- outputName, data);
- outputLists.get(outputName)
- .add((int) index, data);
- } catch (ReferenceServiceException e) {
- throw new ResultReceiverException(e);
-// callback.fail("Failure when calling the reference service", e);
- }
- }
- callback.receiveResult(
- partialOutputData,
- new int[] { (int) index });
- }
-
- public void receiveError(String message,
- long index) throws ResultReceiverException {
- Map<String, T2Reference> partialOutputData = new HashMap<String, T2Reference>();
- for (Attribute attribute : attributes) {
- String outputName = attribute
- .getQualifiedName();
- Integer outputDepth = getOutputPortDepth(outputName);
- if (outputDepth == null) {
- logger.warn("Skipping unknown output port " + outputName);
- continue;
- }
- try {
- T2Reference error = referenceService.getErrorDocumentService()
- .registerError(message, outputDepth - 1, callback.getContext()).getId();
- partialOutputData.put(
- outputName, error);
- outputLists.get(outputName)
- .add((int) index, error);
- } catch (ReferenceServiceException e) {
- throw new ResultReceiverException(e);
-// callback.fail("Failure when calling the reference service", e);
- }
- }
- callback.receiveResult(
- partialOutputData,
- new int[] { (int) index });
- }
-
- });
-
- for (Attribute attribute : attributes) {
- String outputName = attribute
- .getQualifiedName();
- Integer outputDepth = getOutputPortDepth(outputName);
- if (outputDepth == null) {
- logger.warn("Skipping unknown output port " + outputName);
- continue;
- }
- outputData.put(outputName, referenceService.register(
- outputLists.get(outputName),
- outputDepth, true, callback.getContext()));
- }
-
- } else {
- // shouldn't need to reorder attributes for MartJ
- // 0.5
- Object[] resultList = biomartQuery.getMartService()
- .executeQuery(query);
- List<Attribute> attributes = biomartQuery
- .getAttributesInLinkOrder();
- assert resultList.length == attributes.size();
- for (int i = 0; i < resultList.length; i++) {
- Attribute attribute = attributes.get(i);
- String outputName = attribute
- .getQualifiedName();
- Integer outputDepth = getOutputPortDepth(outputName);
- if (outputDepth == null) {
- logger.warn("Skipping unknown output port " + outputName);
- } else {
- outputData.put(outputName, referenceService.register(
- resultList[i], outputDepth, true, callback.getContext()));
- }
- }
- }
- } else {
- Object[] resultList = biomartQuery.getMartService()
- .executeQuery(query);
- assert resultList.length == 1;
- Dataset dataset = biomartQuery.getQuery().getDatasets()
- .get(0);
- String outputName = dataset.getName();
- Integer outputDepth = getOutputPortDepth(outputName);
- if (outputDepth == null) {
- logger.warn("Skipping unknown output port " + outputName);
- } else {
- outputData.put(outputName, referenceService.register(
- resultList[0], outputDepth, true, callback.getContext()));
- }
- }
-
- callback.receiveResult(outputData, new int[0]);
- } catch (MartServiceException e) {
- callback.fail("Failure calling biomart", e);
- } catch (ReferenceServiceException e) {
- callback.fail("Failure when calling the reference service", e);
- } catch (ResultReceiverException e) {
- callback.fail("Failure when receiving a result from biomart", e);
- }
- }
-
- });
-
- }
-
- private Integer getOutputPortDepth(String portName) {
- for (ActivityOutputPort port : getOutputPorts()) {
- if (port.getName().equals(portName)) {
- return port.getDepth();
- }
- }
- return null;
- }
-
-// private void buildInputPorts(List<Edit<?>> editList) {
-// Map<String, ActivityInputPort> newInputMap = new HashMap<String, ActivityInputPort>();
-// List<Filter> filters = biomartQuery.getQuery().getFilters();
-// // Create new input ports corresponding to filters
-// for (Filter filter : filters) {
-// String name = filter.getQualifiedName() + "_filter";
-// if (inputMap.containsKey(name)) {
-// newInputMap.put(name, inputMap.remove(name));
-// } else {
-// ActivityInputPort inputPort = null;
-// if (filter.isList()) {
-// inputPort = edits.createActivityInputPort(name, 1, true,
-// new ArrayList<Class<? extends ExternalReferenceSPI>>(),
-// String.class);
-// } else {
-// inputPort = edits.createActivityInputPort(name, 0, true,
-// new ArrayList<Class<? extends ExternalReferenceSPI>>(),
-// String.class);
-// }
-// newInputMap.put(name, inputPort);
-// editList.add(edits.getAddActivityInputPortEdit(this, inputPort));
-// editList.add(createAddMimeTypeAnnotationEdit(inputPort, "text/plain"));
-// }
-// }
-// //remove any ports still left in the map
-// for (ActivityInputPort inputPort : inputMap.values()) {
-// editList.add(edits.getRemoveActivityInputPortEdit(this, inputPort));
-// }
-// inputMap = newInputMap;
-// }
-
-// private void buildOutputPorts(List<Edit<?>> editList) {
-// Map<String, ActivityOutputPort> newOutputMap = new HashMap<String, ActivityOutputPort>();
-// Query query = biomartQuery.getQuery();
-// List<Attribute> attributes = query.getAttributes();
-// String formatter = query.getFormatter();
-// if (formatter == null) {
-// // Create new output ports corresponding to attributes
-// for (Attribute attribute : attributes) {
-// String name = attribute.getQualifiedName();
-// if (outputMap.containsKey(name)) {
-// newOutputMap.put(name, outputMap.remove(name));
-// } else {
-// ActivityOutputPort outputPort = null;
-// if (attribute.getAttributes() != null) {
-// outputPort = edits.createActivityOutputPort(name, 2, STREAM_RESULTS?1:2);
-// } else {
-// outputPort = edits.createActivityOutputPort(name, 1, STREAM_RESULTS?0:1);
-// }
-// newOutputMap.put(name, outputPort);
-// editList.add(edits.getAddActivityOutputPortEdit(this, outputPort));
-// editList.add(createAddMimeTypeAnnotationEdit(outputPort, "text/plain"));
-// }
-// }
-// } else if (attributes.size() > 0) {
-// // create one port using the dataset name
-// Attribute attribute = attributes.get(0);
-// String name = attribute.getContainingDataset().getName();
-// if (outputMap.containsKey(name)) {
-// newOutputMap.put(name, outputMap.remove(name));
-// } else {
-// ActivityOutputPort outputPort = edits.createActivityOutputPort(name, 0, 0);
-// newOutputMap.put(name, outputPort);
-// editList.add(edits.getAddActivityOutputPortEdit(this, outputPort));
-// editList.add(createAddMimeTypeAnnotationEdit(outputPort, "text/plain"));
-// }
-// }
-// //remove any ports still left in the map
-// for (ActivityOutputPort outputPort : outputMap.values()) {
-// editList.add(edits.getRemoveActivityOutputPortEdit(this, outputPort));
-// }
-// outputMap = newOutputMap;
-// }
-
-// private Edit<?> createAddMimeTypeAnnotationEdit(Annotated<?> annotated, String type) {
-// MimeType mimeType = new MimeType();
-// mimeType.setText(type);
-// return edits.getAddAnnotationChainEdit(annotated, mimeType);
-// }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-activity/src/main/java/net/sf/taverna/t2/activities/biomart/BiomartActivityConfigurationBean.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-activity/src/main/java/net/sf/taverna/t2/activities/biomart/BiomartActivityConfigurationBean.java b/taverna-biomart-activity/src/main/java/net/sf/taverna/t2/activities/biomart/BiomartActivityConfigurationBean.java
deleted file mode 100644
index 91cc323..0000000
--- a/taverna-biomart-activity/src/main/java/net/sf/taverna/t2/activities/biomart/BiomartActivityConfigurationBean.java
+++ /dev/null
@@ -1,47 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2011 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.biomart;
-
-import net.sf.taverna.t2.workflowmodel.processor.config.ConfigurationBean;
-import net.sf.taverna.t2.workflowmodel.processor.config.ConfigurationProperty;
-
-import org.jdom.Element;
-
-/**
- * Biomart configuration.
- *
- * @author David Withers
- */
-@ConfigurationBean(uri = BiomartActivity.URI + "#Config")
-public class BiomartActivityConfigurationBean {
-
- private Element martQuery;
-
- public Element getMartQuery() {
- return martQuery;
- }
-
- @ConfigurationProperty(name = "martQuery", label = "Mart Query", description = "Biomart query in XML")
- public void setMartQuery(Element martQuery) {
- this.martQuery = martQuery;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-activity/src/main/java/net/sf/taverna/t2/activities/biomart/BiomartActivityFactory.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-activity/src/main/java/net/sf/taverna/t2/activities/biomart/BiomartActivityFactory.java b/taverna-biomart-activity/src/main/java/net/sf/taverna/t2/activities/biomart/BiomartActivityFactory.java
deleted file mode 100644
index 4aaf043..0000000
--- a/taverna-biomart-activity/src/main/java/net/sf/taverna/t2/activities/biomart/BiomartActivityFactory.java
+++ /dev/null
@@ -1,144 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2011 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.biomart;
-
-import java.io.IOException;
-import java.io.StringReader;
-import java.net.URI;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import net.sf.taverna.t2.reference.ExternalReferenceSPI;
-import net.sf.taverna.t2.workflowmodel.Edit;
-import net.sf.taverna.t2.workflowmodel.Edits;
-import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityFactory;
-import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityInputPort;
-import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityOutputPort;
-
-import org.apache.log4j.Logger;
-import org.biomart.martservice.MartQuery;
-import org.biomart.martservice.MartServiceXMLHandler;
-import org.biomart.martservice.query.Attribute;
-import org.biomart.martservice.query.Filter;
-import org.biomart.martservice.query.Query;
-import org.jdom.Document;
-import org.jdom.JDOMException;
-import org.jdom.input.SAXBuilder;
-
-import com.fasterxml.jackson.databind.JsonNode;
-import com.fasterxml.jackson.databind.ObjectMapper;
-
-/**
- * An {@link ActivityFactory} for creating <code>BiomartActivity</code>.
- *
- * @author David Withers
- */
-public class BiomartActivityFactory implements ActivityFactory {
-
- private static Logger logger = Logger.getLogger(BiomartActivityFactory.class);
-
- private Edits edits;
- private SAXBuilder builder = new SAXBuilder();
-
- @Override
- public BiomartActivity createActivity() {
- return new BiomartActivity();
- }
-
- @Override
- public URI getActivityType() {
- return URI.create(BiomartActivity.URI);
- }
-
- @Override
- public JsonNode getActivityConfigurationSchema() {
- ObjectMapper objectMapper = new ObjectMapper();
- try {
- return objectMapper.readTree(getClass().getResource("/schema.json"));
- } catch (IOException e) {
- return objectMapper.createObjectNode();
- }
- }
-
- @Override
- public Set<ActivityInputPort> getInputPorts(JsonNode configuration) {
- Set<ActivityInputPort> inputPorts = new HashSet<>();
- try {
- Query query = getQuery(configuration);
- for (Filter filter : query.getFilters()) {
- String name = filter.getQualifiedName() + "_filter";
- inputPorts.add(edits.createActivityInputPort(name, filter.isList() ? 1 : 0, true,
- new ArrayList<Class<? extends ExternalReferenceSPI>>(), String.class));
- }
- } catch (JDOMException | IOException e) {
- logger.warn("Error caluculating input ports from BioMart configuration", e);
- }
- return inputPorts;
- }
-
- @Override
- public Set<ActivityOutputPort> getOutputPorts(JsonNode configuration) {
- Set<ActivityOutputPort> outputPorts = new HashSet<>();
- try {
- Query query = getQuery(configuration);
- List<Attribute> attributes = query.getAttributes();
- if (query.getFormatter() == null) {
- // Create new output ports corresponding to attributes
- for (Attribute attribute : attributes) {
- String name = attribute.getQualifiedName();
- ActivityOutputPort outputPort = null;
- if (attribute.getAttributes() != null) {
- outputPorts.add(edits.createActivityOutputPort(name, 2,
- BiomartActivity.STREAM_RESULTS ? 1 : 2));
- } else {
- outputPorts.add(edits.createActivityOutputPort(name, 1,
- BiomartActivity.STREAM_RESULTS ? 0 : 1));
- }
- }
- } else if (attributes.size() > 0) {
- // create one port using the dataset name
- Attribute attribute = attributes.get(0);
- String name = attribute.getContainingDataset().getName();
- outputPorts.add(edits.createActivityOutputPort(name, 0, 0));
- }
- } catch (JDOMException | IOException e) {
- logger.warn("Error caluculating output ports from BioMart configuration", e);
- }
- return outputPorts;
- }
-
- public void setEdits(Edits edits) {
- this.edits = edits;
- }
-
- private Query getQuery(JsonNode configuration) throws JDOMException, IOException {
- String martQueryText = configuration.get("martQuery").asText();
- Document document = builder.build(new StringReader(martQueryText));
- MartQuery martQuery = MartServiceXMLHandler.elementToMartQuery(document.getRootElement(),
- null);
- return martQuery.getQuery();
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-activity/src/main/java/net/sf/taverna/t2/activities/biomart/BiomartActivityHealthChecker.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-activity/src/main/java/net/sf/taverna/t2/activities/biomart/BiomartActivityHealthChecker.java b/taverna-biomart-activity/src/main/java/net/sf/taverna/t2/activities/biomart/BiomartActivityHealthChecker.java
deleted file mode 100644
index 8e48635..0000000
--- a/taverna-biomart-activity/src/main/java/net/sf/taverna/t2/activities/biomart/BiomartActivityHealthChecker.java
+++ /dev/null
@@ -1,76 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.biomart;
-
-import java.io.IOException;
-import java.io.StringReader;
-import java.util.List;
-
-import net.sf.taverna.t2.visit.VisitReport;
-
-import net.sf.taverna.t2.workflowmodel.health.RemoteHealthChecker;
-import net.sf.taverna.t2.workflowmodel.processor.activity.Activity;
-import net.sf.taverna.t2.workflowmodel.processor.activity.DisabledActivity;
-
-
-import org.biomart.martservice.MartQuery;
-import org.biomart.martservice.MartServiceXMLHandler;
-import org.jdom.Document;
-import org.jdom.Element;
-import org.jdom.JDOMException;
-import org.jdom.input.SAXBuilder;
-
-public class BiomartActivityHealthChecker extends RemoteHealthChecker {
-
- public boolean canVisit(Object subject) {
- if (subject == null) {
- return false;
- }
- if (subject instanceof BiomartActivity) {
- return true;
- }
- if (subject instanceof DisabledActivity) {
- return (((DisabledActivity) subject).getActivity() instanceof BiomartActivity);
- }
- return false;
- }
-
- public VisitReport visit(Object o, List<Object> ancestors) {
- Element biomartQueryElement = null;
- Activity activity = (Activity) o;
- if (activity instanceof BiomartActivity) {
- String martQueryText = ((BiomartActivity)activity).getConfiguration().get("martQuery").asText();
- SAXBuilder builder = new SAXBuilder();
- try {
- Document document = builder.build(new StringReader(martQueryText));
- biomartQueryElement = document.getRootElement();
- } catch (JDOMException | IOException e) {
- e.printStackTrace();
- }
- } else if (activity instanceof DisabledActivity) {
- biomartQueryElement = (Element) ((DisabledActivity) activity).getActivityConfiguration();
- }
- MartQuery biomartQuery = MartServiceXMLHandler.elementToMartQuery(biomartQueryElement, null);
- return contactEndpoint(activity, biomartQuery.getMartService().getLocation());
- }
-
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-activity/src/main/resources/META-INF/services/net.sf.taverna.t2.workflowmodel.health.HealthChecker
----------------------------------------------------------------------
diff --git a/taverna-biomart-activity/src/main/resources/META-INF/services/net.sf.taverna.t2.workflowmodel.health.HealthChecker b/taverna-biomart-activity/src/main/resources/META-INF/services/net.sf.taverna.t2.workflowmodel.health.HealthChecker
deleted file mode 100644
index 19aae39..0000000
--- a/taverna-biomart-activity/src/main/resources/META-INF/services/net.sf.taverna.t2.workflowmodel.health.HealthChecker
+++ /dev/null
@@ -1 +0,0 @@
-# net.sf.taverna.t2.activities.biomart.BiomartActivityHealthChecker
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-activity/src/main/resources/META-INF/spring/biomart-activity-context-osgi.xml
----------------------------------------------------------------------
diff --git a/taverna-biomart-activity/src/main/resources/META-INF/spring/biomart-activity-context-osgi.xml b/taverna-biomart-activity/src/main/resources/META-INF/spring/biomart-activity-context-osgi.xml
deleted file mode 100644
index d8df086..0000000
--- a/taverna-biomart-activity/src/main/resources/META-INF/spring/biomart-activity-context-osgi.xml
+++ /dev/null
@@ -1,15 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<beans:beans xmlns="http://www.springframework.org/schema/osgi" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:beans="http://www.springframework.org/schema/beans"
- xsi:schemaLocation="http://www.springframework.org/schema/beans
- http://www.springframework.org/schema/beans/spring-beans.xsd
- http://www.springframework.org/schema/osgi
- http://www.springframework.org/schema/osgi/spring-osgi.xsd">
-
- <service ref="biomartActivityHealthChecker" interface="net.sf.taverna.t2.workflowmodel.health.HealthChecker" />
-
- <service ref="biomartActivityFactory" interface="net.sf.taverna.t2.workflowmodel.processor.activity.ActivityFactory" />
-
- <reference id="edits" interface="net.sf.taverna.t2.workflowmodel.Edits" />
-
-</beans:beans>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-activity/src/main/resources/META-INF/spring/biomart-activity-context.xml
----------------------------------------------------------------------
diff --git a/taverna-biomart-activity/src/main/resources/META-INF/spring/biomart-activity-context.xml b/taverna-biomart-activity/src/main/resources/META-INF/spring/biomart-activity-context.xml
deleted file mode 100644
index dcc0538..0000000
--- a/taverna-biomart-activity/src/main/resources/META-INF/spring/biomart-activity-context.xml
+++ /dev/null
@@ -1,13 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<beans xmlns="http://www.springframework.org/schema/beans" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://www.springframework.org/schema/beans
- http://www.springframework.org/schema/beans/spring-beans.xsd">
-
- <bean id="biomartActivityHealthChecker" class="net.sf.taverna.t2.activities.biomart.BiomartActivityHealthChecker" />
-
- <bean id="biomartActivityFactory" class="net.sf.taverna.t2.activities.biomart.BiomartActivityFactory">
- <property name="edits" ref="edits" />
- </bean>
-
-
-</beans>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-activity/src/main/resources/schema.json
----------------------------------------------------------------------
diff --git a/taverna-biomart-activity/src/main/resources/schema.json b/taverna-biomart-activity/src/main/resources/schema.json
deleted file mode 100644
index 99eb9f2..0000000
--- a/taverna-biomart-activity/src/main/resources/schema.json
+++ /dev/null
@@ -1,19 +0,0 @@
-{
- "$schema": "http://json-schema.org/draft-03/schema#",
- "id": "http://ns.taverna.org.uk/2010/activity/biomart.schema.json",
- "title": "Biomart activity configuration",
- "type": "object",
- "properties": {
- "@context": {
- "description": "JSON-LD context for interpreting the configuration as RDF",
- "required": true,
- "enum": ["http://ns.taverna.org.uk/2010/activity/biomart.context.json"]
- },
- "martQuery": {
- "title": "Mart Query",
- "description": "Biomart query in XML",
- "type": "string",
- "required": true,
- }
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-activity/src/test/java/net/sf/taverna/t2/activities/biomart/BiomartActivityFactoryTest.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-activity/src/test/java/net/sf/taverna/t2/activities/biomart/BiomartActivityFactoryTest.java b/taverna-biomart-activity/src/test/java/net/sf/taverna/t2/activities/biomart/BiomartActivityFactoryTest.java
deleted file mode 100644
index 78ed2f6..0000000
--- a/taverna-biomart-activity/src/test/java/net/sf/taverna/t2/activities/biomart/BiomartActivityFactoryTest.java
+++ /dev/null
@@ -1,65 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2011 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.biomart;
-
-import static org.junit.Assert.assertEquals;
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-
-import java.net.URI;
-
-import org.junit.Before;
-import org.junit.Test;
-
-/**
- *
- * @author David Withers
- */
-public class BiomartActivityFactoryTest {
-
- private BiomartActivityFactory factory;
-
- /**
- * @throws java.lang.Exception
- */
- @Before
- public void setUp() throws Exception {
- factory = new BiomartActivityFactory();
- }
-
- /**
- * Test method for {@link net.sf.taverna.t2.activities.biomart.BiomartActivityFactory#createActivity()}.
- */
- @Test
- public void testCreateActivity() {
- BiomartActivity createActivity = factory.createActivity();
- assertNotNull(createActivity);
- }
-
- /**
- * Test method for {@link net.sf.taverna.t2.activities.biomart.BiomartActivityFactory#getActivityType()}.
- */
- @Test
- public void testGetActivityURI() {
- assertEquals(URI.create(BiomartActivity.URI), factory.getActivityType());
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-activity/src/test/resources/biomart-query.xml
----------------------------------------------------------------------
diff --git a/taverna-biomart-activity/src/test/resources/biomart-query.xml b/taverna-biomart-activity/src/test/resources/biomart-query.xml
deleted file mode 100644
index e0b43bd..0000000
--- a/taverna-biomart-activity/src/test/resources/biomart-query.xml
+++ /dev/null
@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<MartQuery xmlns:biomart="http://org.embl.ebi.escience/xscufl-biomart/0.1alpha">
- <MartService location="http://www.biomart.org/biomart/martservice" />
- <MartDataset displayName="Homo sapiens genes (NCBI36)" name="hsapiens_gene_ensembl" type="TableSet" initialBatchSize="100" maximumBatchSize="50000" visible="false">
- <MartURLLocation default="1" displayName="ENSEMBL 41 (SANGER)" host="www.biomart.org" name="ensembl" port="80" serverVirtualSchema="default" virtualSchema="default" visible="1" />
- </MartDataset>
- <Query virtualSchemaName="default" count="0" softwareVersion="0.5">
- <Dataset name="hsapiens_gene_ensembl">
- <Attribute name="chromosome_name" />
- <Attribute name="go_description" />
- <Filter name="chromosome_name" value="1" />
- <Filter name="band_end" value="p36.32" />
- <Filter name="band_start" value="p36.33" />
- </Dataset>
- </Query>
-</MartQuery>
-
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-martservice/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/pom.xml b/taverna-biomart-martservice/pom.xml
deleted file mode 100644
index 582a601..0000000
--- a/taverna-biomart-martservice/pom.xml
+++ /dev/null
@@ -1,105 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
- <modelVersion>4.0.0</modelVersion>
- <parent>
- <groupId>net.sf.taverna</groupId>
- <artifactId>taverna-parent</artifactId>
- <version>3.0.1-SNAPSHOT</version>
- </parent>
- <groupId>org.biomart</groupId>
- <artifactId>martservice</artifactId>
- <packaging>bundle</packaging>
- <name>MartService</name>
- <version>2.0.1-SNAPSHOT</version>
- <description>Biomart webservice API</description>
-
- <build>
- <plugins>
- <plugin>
- <groupId>org.apache.felix</groupId>
- <artifactId>maven-bundle-plugin</artifactId>
- <version>2.3.7</version>
- <extensions>true</extensions>
- <configuration>
- <instructions>
- <Private-Package>org.ensembl.mart.lib,org.ensembl.mart.lib.config,org.ensembl.mart.util</Private-Package>
- <Import-Package>!org.ensembl.util,!org.ensembl.mart.editor,!oracle.sql,!gnu.getopt,!org.ewin.*,*</Import-Package>
- </instructions>
- </configuration>
- </plugin>
- </plugins>
- </build>
-
- <dependencies>
- <dependency>
- <groupId>org.biomart</groupId>
- <artifactId>martj</artifactId>
- <version>0.6</version>
- <scope>provided</scope>
- </dependency>
- <dependency>
- <groupId>org.jdom</groupId>
- <artifactId>com.springsource.org.jdom</artifactId>
- <version>1.1.0</version>
- </dependency>
- <dependency>
- <groupId>org.apache.commons</groupId>
- <artifactId>com.springsource.org.apache.commons.httpclient</artifactId>
- <version>3.1.0</version>
- </dependency>
- <dependency>
- <groupId>org.apache.commons</groupId>
- <artifactId>com.springsource.org.apache.commons.io</artifactId>
- <version>1.4.0</version>
- </dependency>
- <dependency>
- <groupId>org.apache.log4j</groupId>
- <artifactId>com.springsource.org.apache.log4j</artifactId>
- <version>${log4j.version}</version>
- </dependency>
- <dependency>
- <groupId>junit</groupId>
- <artifactId>junit</artifactId>
- <version>${junit.version}</version>
- <scope>test</scope>
- </dependency>
- </dependencies>
-
- <repositories>
- <repository>
- <releases />
- <snapshots>
- <enabled>false</enabled>
- </snapshots>
- <id>mygrid-repository</id>
- <name>myGrid Repository</name>
- <url>http://www.mygrid.org.uk/maven/repository</url>
- </repository>
- <repository>
- <releases>
- <enabled>false</enabled>
- </releases>
- <snapshots />
- <id>mygrid-snapshot-repository</id>
- <name>myGrid Snapshot Repository</name>
- <url>http://www.mygrid.org.uk/maven/snapshot-repository</url>
- </repository>
- <repository>
- <id>com.springsource.repository.bundles.release</id>
- <name>SpringSource Enterprise Bundle Repository - SpringSource Bundle Releases</name>
- <url>http://repository.springsource.com/maven/bundles/release</url>
- </repository>
- <repository>
- <id>com.springsource.repository.bundles.external</id>
- <name>SpringSource Enterprise Bundle Repository - External Bundle Releases</name>
- <url>http://repository.springsource.com/maven/bundles/external</url>
- </repository>
- </repositories>
- <scm>
- <connection>scm:git:https://github.com/taverna/taverna-biomart-martservice.git</connection>
- <developerConnection>scm:git:ssh://git@github.com:taverna/taverna-biomart-martservice.git</developerConnection>
- <url>https://github.com/taverna/taverna-biomart-martservice/</url>
- <tag>HEAD</tag>
- </scm>
-</project>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-martservice/src/main/java/org/biomart/martservice/DatasetLink.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/DatasetLink.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/DatasetLink.java
deleted file mode 100644
index e5dccd4..0000000
--- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/DatasetLink.java
+++ /dev/null
@@ -1,220 +0,0 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: DatasetLink.java,v $
- * Revision $Revision: 1.2 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/12/13 11:38:55 $
- * by $Author: davidwithers $
- * Created on 12-Apr-2006
- *****************************************************************/
-package org.biomart.martservice;
-
-import java.util.Comparator;
-import java.util.HashSet;
-import java.util.Set;
-
-/**
- * The link between two MartDatasets and the list of possible the link IDs that
- * could join the source and target MartDataset.
- *
- * @author David Withers
- */
-public class DatasetLink {
- private static final Comparator<DatasetLink> displayComparator = new DatasetLinkComparator();
-
- private MartDataset sourceDataset;
-
- private MartDataset targetDataset;
-
- private Set<String> links = new HashSet<String>();
-
- /**
- * Constructs an instance of an <code>DatasetLink</code> with the
- * specified source and target.
- *
- * @param sourceDataset
- * the link source
- * @param targetDataset
- * the link target
- */
- public DatasetLink(MartDataset sourceDataset, MartDataset targetDataset) {
- this.sourceDataset = sourceDataset;
- this.targetDataset = targetDataset;
- }
-
- /**
- * Returns the source Dataset.
- *
- * @return the source Dataset
- */
- public MartDataset getSourceDataset() {
- return sourceDataset;
- }
-
- /**
- * Sets the source Dataset.
- *
- * @param sourceDataset
- * the sourceDataset to set
- */
- public void setSourceDataset(MartDataset sourceDataset) {
- this.sourceDataset = sourceDataset;
- }
-
- /**
- * Returns the target Dataset.
- *
- * @return the target Dataset
- */
- public MartDataset getTargetDataset() {
- return targetDataset;
- }
-
- /**
- * Sets the target Dataset.
- *
- * @param targetDataset
- * the target Dataset to set
- */
- public void setTargetDataset(MartDataset targetDataset) {
- this.targetDataset = targetDataset;
- }
-
- /**
- * Returns the link IDs that could join the source and target MartDatasets.
- *
- * @return the link IDs that could join the source and target MartDatasets
- */
- public String[] getLinks() {
- return links.toArray(new String[links.size()]);
- }
-
- /**
- * Adds a link ID.
- *
- * @param link
- * the link ID to add.
- */
- public void addLink(String link) {
- links.add(link);
- }
-
- /**
- * Returns true if this DatasetLink has link IDs.
- *
- * @return true if this DatasetLink has link IDs
- */
- public boolean hasLinks() {
- return !links.isEmpty();
- }
-
- public String toString() {
- return "[" + sourceDataset.getMartURLLocation().getDisplayName() + "] "
- + sourceDataset.getDisplayName();
- }
-
- /* (non-Javadoc)
- * @see java.lang.Object#hashCode()
- */
- public int hashCode() {
- final int PRIME = 31;
- int result = 1;
- result = PRIME * result + ((sourceDataset == null) ? 0 : sourceDataset.hashCode());
- result = PRIME * result + ((targetDataset == null) ? 0 : targetDataset.hashCode());
- return result;
- }
-
- /* (non-Javadoc)
- * @see java.lang.Object#equals(java.lang.Object)
- */
- public boolean equals(Object obj) {
- if (this == obj)
- return true;
- if (obj == null)
- return false;
- if (getClass() != obj.getClass())
- return false;
- final DatasetLink other = (DatasetLink) obj;
- if (sourceDataset == null) {
- if (other.sourceDataset != null)
- return false;
- } else if (!sourceDataset.equals(other.sourceDataset))
- return false;
- if (targetDataset == null) {
- if (other.targetDataset != null)
- return false;
- } else if (!targetDataset.equals(other.targetDataset))
- return false;
- return true;
- }
-
- /**
- * Returns a Comparator that compares DatasetLinks based on the display name
- * of the source dataset and the display name of the MartURLLocation
- * containing the source dataset.
- *
- * @return the display comparator
- */
- public static Comparator<DatasetLink> getDisplayComparator() {
- return displayComparator;
- }
-
-}
-
-/**
- * Comparator that compares DatasetLinks based on the display name of the source
- * MartDataset and the display name of the MartURLLocation containing the source
- * MartDataset.
- *
- * @author David Withers
- */
-class DatasetLinkComparator implements Comparator<DatasetLink> {
-
- /**
- * Compares two DatasetLinks based on the display name of the source dataset
- * and the display name of the MartURLLocation containing the source
- * dataset.
- *
- * @param o1
- * the first DatasetLink to be compared
- * @param o2
- * the second DatasetLink to be compared
- * @return a negative integer, zero, or a positive integer as the first
- * argument is less than, equal to, or greater than the second
- */
- public int compare(DatasetLink o1, DatasetLink o2) {
- MartDataset ds1 = o1.getSourceDataset();
- MartDataset ds2 = o2.getSourceDataset();
- int result = ds1.getDisplayName().compareTo(ds2.getDisplayName());
- if (result == 0) {
- result = ds1.getMartURLLocation().getDisplayName().compareTo(
- ds2.getMartURLLocation().getDisplayName());
- }
- return result;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartDataset.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartDataset.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartDataset.java
deleted file mode 100644
index 8c0f584..0000000
--- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartDataset.java
+++ /dev/null
@@ -1,342 +0,0 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: MartDataset.java,v $
- * Revision $Revision: 1.2 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/10/04 14:17:19 $
- * by $Author: davidwithers $
- * Created on 17-Mar-2006
- *****************************************************************/
-package org.biomart.martservice;
-
-import java.util.Comparator;
-
-/**
- * The dataset returned by a BioMart web service.
- *
- * @author David Withers
- */
-public class MartDataset {
- private static final Comparator<MartDataset> displayComparator = new MartDatasetComparator();
-
- private String type;
-
- private String name;
-
- private String displayName;
-
- private boolean visible;
-
- private long initialBatchSize;
-
- private long maximumBatchSize;
-
- private String interfaceValue;
-
- private String modified;
-
- private MartURLLocation martURLLocation;
-
- /**
- * Returns the displayName.
- *
- * @return the displayName.
- */
- public String getDisplayName() {
- return displayName;
- }
-
- /**
- * Sets the displayName.
- *
- * @param displayName
- * the displayName to set.
- */
- public void setDisplayName(String displayName) {
- this.displayName = displayName;
- }
-
- /**
- * Returns the initialBatchSize.
- *
- * @return the initialBatchSize.
- */
- public long getInitialBatchSize() {
- return initialBatchSize;
- }
-
- /**
- * Sets the initialBatchSize.
- *
- * @param initialBatchSize
- * the initialBatchSize to set.
- */
- public void setInitialBatchSize(long initialBatchSize) {
- this.initialBatchSize = initialBatchSize;
- }
-
- /**
- * Returns the maximumBatchSize.
- *
- * @return the maximumBatchSize.
- */
- public long getMaximumBatchSize() {
- return maximumBatchSize;
- }
-
- /**
- * Sets the maximumBatchSize.
- *
- * @param maximumBatchSize
- * the maximumBatchSize to set.
- */
- public void setMaximumBatchSize(long maximumBatchSize) {
- this.maximumBatchSize = maximumBatchSize;
- }
-
- /**
- * Returns the name.
- *
- * @return the name.
- */
- public String getName() {
- return name;
- }
-
- /**
- * Sets the name.
- *
- * @param name
- * the name to set.
- */
- public void setName(String name) {
- this.name = name;
- }
-
- /**
- * Returns the type.
- *
- * @return the type.
- */
- public String getType() {
- return type;
- }
-
- /**
- * Sets the type.
- *
- * @param type
- * the type to set.
- */
- public void setType(String type) {
- this.type = type;
- }
-
- /**
- * Returns the visible flag.
- *
- * @return the visible flag
- */
- public boolean isVisible() {
- return visible;
- }
-
- /**
- * Sets the visible flag.
- *
- * @param visible
- * the visible flag
- */
- public void setVisible(boolean visible) {
- this.visible = visible;
- }
-
- /**
- * Returns the modified date.
- *
- * @return the modified date
- */
- public String getModified() {
- return modified;
- }
-
- /**
- * Sets the modified date.
- *
- * @param modified the new modified date
- */
- public void setModified(String modified) {
- this.modified = modified;
- }
-
- /**
- * Returns the interface.
- *
- * @return the interface
- */
- public String getInterface() {
- return interfaceValue;
- }
-
- /**
- * Sets the interface.
- *
- * @param interfaceValue the new interface
- */
- public void setInterface(String interfaceValue) {
- this.interfaceValue = interfaceValue;
- }
-
- /**
- * Returns the martURLLocation.
- *
- * @return the martURLLocation
- */
- public MartURLLocation getMartURLLocation() {
- return martURLLocation;
- }
-
- /**
- * Sets the martURLLocation.
- *
- * @param martURLLocation
- * the martURLLocation to set.
- */
- public void setMartURLLocation(MartURLLocation martURLLocation) {
- this.martURLLocation = martURLLocation;
- }
-
- /**
- * Returns the virtualSchema of the martURLLocation. If the martURLLocation
- * is null, null is returned.
- *
- * @return the virtualSchema of the martURLLocation
- */
- public String getVirtualSchema() {
- MartURLLocation martURLLocation = getMartURLLocation();
- if (martURLLocation != null) {
- return martURLLocation.getVirtualSchema();
- } else {
- return null;
- }
- }
-
- /**
- * Returns the qualified name of this dataset in the format
- * 'virtualSchemaName.datasetName'. If there is no virtualSchema the
- * datasetName is returned.
- *
- * @return the qualified name of this dataset
- */
- public String getQualifiedName() {
- String schema = getVirtualSchema();
- if (schema != null) {
- return schema + "." + getName();
- } else {
- return getName();
- }
- }
-
- /**
- * Returns the display name.
- *
- * @return the display name
- */
- public String toString() {
- return getDisplayName();
- }
-
- /*
- * (non-Javadoc)
- *
- * @see java.lang.Object#hashCode()
- */
- public int hashCode() {
- final int PRIME = 31;
- int result = 1;
- result = PRIME
- * result
- + ((getQualifiedName() == null) ? 0 : getQualifiedName()
- .hashCode());
- return result;
- }
-
- /**
- * Tests equality based on the qualified name.
- *
- * @return true if the objects are equal based on the qualified name
- */
- public boolean equals(Object obj) {
- if (this == obj)
- return true;
- if (obj == null)
- return false;
- if (getClass() != obj.getClass())
- return false;
- final MartDataset other = (MartDataset) obj;
- if (getQualifiedName() == null) {
- if (other.getQualifiedName() != null)
- return false;
- } else if (!getQualifiedName().equals(other.getQualifiedName()))
- return false;
- return true;
- }
-
- /**
- * Returns a Comparator that compares MartDatasets based on their display
- * names.
- *
- * @return the display comparator
- */
- public static Comparator<MartDataset> getDisplayComparator() {
- return displayComparator;
- }
-
-}
-
-/**
- * Comparator that compares MartDatasets based on their display names.
- *
- * @author David Withers
- */
-class MartDatasetComparator implements Comparator<MartDataset> {
-
- /**
- * Compares two MartDatasets based on their display names.
- *
- * @param martDataset1
- * the first MartDataset to be compared
- * @param martDataset2
- * the second MartDataset to be compared
- * @return a negative integer, zero, or a positive integer as the first
- * argument is less than, equal to, or greater than the second
- */
- public int compare(MartDataset martDataset1, MartDataset martDataset2) {
- return martDataset1.getDisplayName().compareTo(martDataset2.getDisplayName());
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartQuery.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartQuery.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartQuery.java
deleted file mode 100644
index 9f75566..0000000
--- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartQuery.java
+++ /dev/null
@@ -1,436 +0,0 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: MartQuery.java,v $
- * Revision $Revision: 1.2 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/12/13 11:38:55 $
- * by $Author: davidwithers $
- * Created on 08-May-2006
- *****************************************************************/
-package org.biomart.martservice;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import org.biomart.martservice.query.Attribute;
-import org.biomart.martservice.query.Dataset;
-import org.biomart.martservice.query.Filter;
-import org.biomart.martservice.query.Link;
-import org.biomart.martservice.query.Query;
-import org.ensembl.mart.lib.config.AttributeDescription;
-import org.ensembl.mart.lib.config.DatasetConfig;
-
-/**
- * Class for creating queries to send to a BioMart web service.
- *
- * @author David Withers
- */
-public class MartQuery {
- private MartService martService;
-
- private MartDataset martDataset;
-
- private Query query;
-
- private Map<String, String> linkedDatasets = new HashMap<String, String>();
-
- private String softwareVersion;
-
- public MartQuery() {
-
- }
-
- public MartQuery(MartService martService, MartDataset martDataset, String requestId) {
- String version = null;
- try {
- version = martService.getVersion(martDataset.getMartURLLocation());
- } catch (MartServiceException e) {
- //assume it's a pre 0.5 mart service
- }
- setMartService(martService);
- setMartDataset(martDataset);
- if (version == null || version.equals("0.4")) {
- setQuery(new Query(martDataset.getVirtualSchema(), null, requestId));
- } else {
- setQuery(new Query(martDataset.getVirtualSchema(), version, requestId));
- }
- }
-
- /**
- * @param martService
- * @param martDataset
- * @param query
- */
- public MartQuery(MartService martService, MartDataset martDataset,
- Query query) {
- setMartService(martService);
- setMartDataset(martDataset);
- setQuery(query);
- }
-
- /**
- * Returns the martDataset.
- *
- * @return the martDataset.
- */
- public MartDataset getMartDataset() {
- return martDataset;
- }
-
- /**
- * Sets the martDataset.
- *
- * @param martDataset
- * the martDataset to set.
- */
- public void setMartDataset(MartDataset martDataset) {
- this.martDataset = martDataset;
- }
-
- /**
- * Returns the martService.
- *
- * @return the martService.
- */
- public MartService getMartService() {
- return martService;
- }
-
- /**
- * Sets the martService.
- *
- * @param martService
- * the martService to set.
- */
- public void setMartService(MartService martService) {
- this.martService = martService;
- }
-
- /**
- * Returns the query.
- *
- * @return the query.
- */
- public Query getQuery() {
- return query;
- }
-
- /**
- * Sets the query.
- *
- * @param query
- * the query to set.
- */
- public void setQuery(Query query) {
- this.query = query;
- softwareVersion = query.getSoftwareVersion();
- }
-
- /**
- * Adds the ID that links the specified dataset to the initial dataset.
- *
- * @param datasetName
- * the dataset
- * @param linkId
- * the link ID
- */
- public void addLinkedDataset(String datasetName, String linkId) {
- linkedDatasets.put(datasetName, linkId);
- }
-
- /**
- * Removes a dataset and any datasets linked to it.
- *
- * @param datasetName
- * the dataset to remove
- */
- public void removeLinkedDataset(String datasetName) {
- linkedDatasets.remove(datasetName);
- if (query.containsDataset(datasetName)) {
- Dataset dataset = query.getDataset(datasetName);
- dataset.removeAllAttributes();
- dataset.removeAllFilters();
- query.removeDataset(dataset);
- for (Link link : query.getLinks(datasetName)) {
- removeLinkedDataset(link.getTarget());
- }
-
- }
- if (query.containsLink(datasetName)) {
- query.removeLink(query.getLink(datasetName));
- }
- }
-
- /**
- * Changes the ID that links a dataset. This method performs no function,
- * nor does it throw an exception, if the specified dataset does not exist.
- *
- * @param datasetName
- * the dataset
- * @param linkId
- * the link ID
- */
- public void changeLinkedDataset(String datasetName, String linkId) {
- if (linkedDatasets.containsKey(datasetName)) {
- linkedDatasets.put(datasetName, linkId);
- if (query.containsLink(datasetName)) {
- query.getLink(datasetName).setDefaultLink(linkId);
- }
- }
- }
-
- public Set<String> getLinkedDatasets() {
- return linkedDatasets.keySet();
- }
-
- public String getLink(String datasetName) {
- return (String) linkedDatasets.get(datasetName);
- }
-
- /**
- * Returns the Datasets that this Query contains in the order specified by
- * the links.
- *
- * @return the Datasets that this Query contains in the order specified by
- * the links
- */
- public List<Dataset> getDatasetsInLinkOrder() {
- if (query.getLinks().size() > 0) {
- List<Dataset> datasets = new ArrayList<Dataset>();
- datasets.addAll(getLinkedDatasets(martDataset.getName()));
- // add other datasets
- for (Dataset dataset : query.getDatasets()) {
- if (!datasets.contains(dataset)) {
- datasets.add(dataset);
- }
- }
- return datasets;
- } else {
- return query.getDatasets();
- }
- }
-
- /**
- * @param dataset
- * @return
- */
- private List<Dataset> getLinkedDatasets(String dataset) {
- List<Dataset> datasets = new ArrayList<Dataset>();
- datasets.add(query.getDataset(dataset));
- if (query.containsLink(dataset)) {
- Link link = query.getLink(dataset);
- if (!link.getTarget().equals(martDataset.getName())) {
- datasets.addAll(getLinkedDatasets(link.getTarget()));
- }
- }
- return datasets;
- }
-
- /**
- * Returns all the Attributes from all the Datasets in this Query in the
- * order specified by the links.
- *
- * @return all the Attributes from all the Datasets in this Query in the
- * order specified by the links
- */
- public List<Attribute> getAttributesInLinkOrder() {
- List<Attribute> attributes = new ArrayList<Attribute>();
- List<Dataset> datasets;
- if (softwareVersion == null) {
- datasets = getDatasetsInLinkOrder();
- } else {
- datasets = query.getDatasets();
- }
- for (Dataset dataset : datasets) {
- attributes.addAll(dataset.getAttributes());
- }
- return attributes;
- }
-
- /**
- * Adds an Attribute to the Dataset with the given datasetName. If the Query
- * has no Dataset with the given datasetName then a new Dataset is created.
- *
- * @param datasetName
- * the name of the Dataset to add the Attribute to
- * @param attribute
- * the Attribute to add
- * @throws MartServiceException
- */
- public void addAttribute(String datasetName, Attribute attribute) {
- if (!query.containsDataset(datasetName)) {
- Dataset dataset = new Dataset(datasetName);
- if (datasetName.equals(martDataset.getName())) {
- query.addDataset(0, dataset);
- } else {
- query.addDataset(dataset);
- }
- }
- Dataset dataset = query.getDataset(datasetName);
- dataset.addAttribute(attribute);
- }
-
- /**
- * Removes an Attribute from its containing Dataset.
- *
- * @param attribute
- */
- public void removeAttribute(Attribute attribute) {
- Dataset dataset = attribute.getContainingDataset();
- if (dataset != null) {
- if (dataset.removeAttribute(attribute)) {
- if (!dataset.hasAttributes() && !dataset.hasFilters()) {
- Query query = dataset.getContainingQuery();
- if (query != null) {
- query.removeDataset(dataset);
- }
- }
- }
- }
- }
-
- /**
- * Adds a Filter to the Dataset with the given datasetName. If the Query has
- * no Dataset with the given datasetName then a new Dataset is created.
- *
- * @param datasetName
- * the name of the Dataset to add the Filter to
- * @param filter
- * the Filter to add
- * @throws MartServiceException
- */
- public void addFilter(String datasetName, Filter filter) {
- if (!query.containsDataset(datasetName)) {
- Dataset dataset = new Dataset(datasetName);
- if (datasetName.equals(martDataset.getName())) {
- query.addDataset(0, dataset);
- } else {
- query.addDataset(dataset);
- }
- }
- Dataset dataset = query.getDataset(datasetName);
- dataset.addFilter(filter);
- }
-
- /**
- * Removes a Filter from its containing Dataset.
- *
- * @param filter
- */
- public void removeFilter(Filter filter) {
- Dataset dataset = filter.getContainingDataset();
- if (dataset != null) {
- if (dataset.removeFilter(filter)) {
- if (!dataset.hasAttributes() && !dataset.hasFilters()) {
- Query query = dataset.getContainingQuery();
- if (query != null) {
- query.removeDataset(dataset);
- }
- }
- }
- }
- }
-
- /**
- * @throws MartServiceException
- */
- public void calculateLinks() throws MartServiceException {
- if (softwareVersion == null) {
- if (!martService.linksCalculated()) {
- martService.calculateLinks();
- }
- for (Link link : query.getLinks()) {
- query.removeLink(link);
- }
- for (Dataset dataset : query.getDatasets()) {
- if (!martDataset.getName().equals(dataset.getName())) {
- addLinks(dataset.getName());
- }
- }
- }
- }
-
- /**
- * @param source
- * @throws MartServiceException
- */
- public void addLinks(String source) throws MartServiceException {
- MartDataset sourceDataset = martService.getDataset(martDataset
- .getVirtualSchema(), source);
- MartDataset targetDataset = martDataset;
- List<MartDataset> path = martService.getPath(sourceDataset, targetDataset);
- if (path == null) {
- path = martService.getPath(targetDataset, sourceDataset);
- }
- if (path == null) {
- throw new MartServiceException("No link between " + source
- + " and " + targetDataset.getName());
- }
- Iterator<MartDataset> iter = path.iterator();
- if (iter.hasNext()) {
- MartDataset lastDataset = (MartDataset) iter.next();
- while (iter.hasNext()) {
- MartDataset dataset = (MartDataset) iter.next();
- DatasetLink link = martService.getLinkBetween(lastDataset,
- dataset);
- String linkId = link.getLinks()[0];
- if (link.getLinks().length > 1) {
- if (getLink(source) != null) {
- linkId = getLink(source);
- } else {
- List<Attribute> attributes = query.getDataset(source)
- .getAttributes();
- if (attributes.size() > 0) {
- Attribute attribute = (Attribute) attributes.get(0);
- DatasetConfig config = martService
- .getDatasetConfig(sourceDataset);
- if (config.containsAttributeDescription(attribute
- .getName())) {
- AttributeDescription description = config
- .getAttributeDescriptionByInternalName(attribute
- .getName());
- String datasetLink = description
- .getDatasetLink();
- if (datasetLink != null) {
- linkId = datasetLink;
- }
- }
- }
- }
- }
- query.addLink(new Link(lastDataset.getName(),
- dataset.getName(), linkId));
- lastDataset = dataset;
- }
- }
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartRegistry.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartRegistry.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartRegistry.java
deleted file mode 100644
index 93bf04d..0000000
--- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/MartRegistry.java
+++ /dev/null
@@ -1,96 +0,0 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: MartRegistry.java,v $
- * Revision $Revision: 1.2 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/12/13 11:38:55 $
- * by $Author: davidwithers $
- * Created on 17-Mar-2006
- *****************************************************************/
-package org.biomart.martservice;
-
-import java.util.ArrayList;
-import java.util.List;
-
-/**
- * The MartRegistry returned by a BioMart web service.
- *
- * @author David Withers
- */
-public class MartRegistry {
- private List<MartURLLocation> martURLLocations = new ArrayList<MartURLLocation>();
-
- /**
- * Returns the martURLLocations.
- *
- * @return the martURLLocations.
- */
- public MartURLLocation[] getMartURLLocations() {
- return martURLLocations
- .toArray(new MartURLLocation[martURLLocations.size()]);
- }
-
- /**
- * Adds a martURLLocation to the registry.
- *
- * @param martURLLocations
- * the martURLLocations to add.
- */
- public void addMartURLLocation(MartURLLocation martURLLocation) {
- martURLLocations.add(martURLLocation);
- }
-
- /* (non-Javadoc)
- * @see java.lang.Object#hashCode()
- */
- public int hashCode() {
- final int PRIME = 31;
- int result = 1;
- result = PRIME * result + ((martURLLocations == null) ? 0 : martURLLocations.hashCode());
- return result;
- }
-
- /* (non-Javadoc)
- * @see java.lang.Object#equals(java.lang.Object)
- */
- public boolean equals(Object obj) {
- if (this == obj)
- return true;
- if (obj == null)
- return false;
- if (getClass() != obj.getClass())
- return false;
- final MartRegistry other = (MartRegistry) obj;
- if (martURLLocations == null) {
- if (other.martURLLocations != null)
- return false;
- } else if (!martURLLocations.equals(other.martURLLocations))
- return false;
- return true;
- }
-
-}
[02/16] incubator-taverna-plugin-bioinformatics git commit:
temporarily empty repository
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/actions/SoaplabActivityConfigurationAction.java
----------------------------------------------------------------------
diff --git a/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/actions/SoaplabActivityConfigurationAction.java b/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/actions/SoaplabActivityConfigurationAction.java
deleted file mode 100644
index 43b87f1..0000000
--- a/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/actions/SoaplabActivityConfigurationAction.java
+++ /dev/null
@@ -1,68 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.soaplab.actions;
-
-import java.awt.Frame;
-import java.awt.event.ActionEvent;
-
-import javax.swing.Action;
-
-import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
-import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
-import net.sf.taverna.t2.workbench.edits.EditManager;
-import net.sf.taverna.t2.workbench.file.FileManager;
-import net.sf.taverna.t2.workbench.ui.actions.activity.ActivityConfigurationAction;
-import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ActivityConfigurationDialog;
-import uk.org.taverna.scufl2.api.activity.Activity;
-
-public class SoaplabActivityConfigurationAction extends ActivityConfigurationAction {
-
- private static final long serialVersionUID = 5076721332542691094L;
- private final Frame owner;
- public static final String CONFIGURE_SOAPLAB_ACTIVITY = "Configure Soaplab";
- private final EditManager editManager;
- private final FileManager fileManager;
-
- public SoaplabActivityConfigurationAction(Activity activity, Frame owner,
- EditManager editManager, FileManager fileManager,
- ActivityIconManager activityIconManager, ServiceDescriptionRegistry serviceDescriptionRegistry) {
- super(activity, activityIconManager, serviceDescriptionRegistry);
- this.editManager = editManager;
- this.fileManager = fileManager;
- putValue(Action.NAME, CONFIGURE_SOAPLAB_ACTIVITY);
- this.owner = owner;
- }
-
- public void actionPerformed(ActionEvent action) {
- ActivityConfigurationDialog currentDialog = ActivityConfigurationAction.getDialog(getActivity());
- if (currentDialog != null) {
- currentDialog.toFront();
- return;
- }
-
- final SoaplabConfigurationPanel panel = new SoaplabConfigurationPanel(getActivity());
- final ActivityConfigurationDialog dialog = new ActivityConfigurationDialog(
- getActivity(), panel, editManager);
-
- ActivityConfigurationAction.setDialog(getActivity(), dialog, fileManager);
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/actions/SoaplabConfigurationPanel.java
----------------------------------------------------------------------
diff --git a/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/actions/SoaplabConfigurationPanel.java b/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/actions/SoaplabConfigurationPanel.java
deleted file mode 100644
index 9b4b0c8..0000000
--- a/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/actions/SoaplabConfigurationPanel.java
+++ /dev/null
@@ -1,183 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.soaplab.actions;
-
-import java.awt.BorderLayout;
-import java.awt.event.ActionListener;
-import java.awt.event.ItemEvent;
-import java.awt.event.ItemListener;
-
-import javax.swing.Box;
-import javax.swing.BoxLayout;
-import javax.swing.JCheckBox;
-import javax.swing.JOptionPane;
-import javax.swing.JPanel;
-import javax.swing.JTextField;
-import javax.swing.border.TitledBorder;
-
-import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ActivityConfigurationPanel;
-import uk.org.taverna.scufl2.api.activity.Activity;
-
-@SuppressWarnings("serial")
-public class SoaplabConfigurationPanel extends ActivityConfigurationPanel {
-
-// ActionListener closeClicked;
-// ActionListener applyClicked;
-
- private JTextField intervalMaxField;
- private JTextField intervalField;
- private JTextField backoffField;
- private JCheckBox allowPolling;
-
- public SoaplabConfigurationPanel(Activity activity) {
- super(activity);
- initialise();
- }
-
- public boolean isAllowPolling() {
- return allowPolling.isSelected();
- }
-
- public int getInterval() {
- return Integer.parseInt(intervalField.getText());
- }
-
- public int getIntervalMax() {
- return Integer.parseInt(intervalMaxField.getText());
- }
-
- public double getBackoff() {
- return Double.parseDouble(backoffField.getText());
- }
-
- @Override
- protected void initialise() {
- super.initialise();
- removeAll();
-
- setLayout(new BoxLayout(this, BoxLayout.Y_AXIS));
-
- JPanel interval = new JPanel();
- interval.setLayout(new BorderLayout());
- interval.setBorder(new TitledBorder("Interval"));
-
- JPanel intervalMax = new JPanel();
- intervalMax.setLayout(new BorderLayout());
- intervalMax.setBorder(new TitledBorder("Max interval"));
-
- JPanel backoff = new JPanel();
- backoff.setLayout(new BorderLayout());
- backoff.setBorder(new TitledBorder("Backoff"));
-
- intervalField = new JTextField(getJson().get("pollingInterval").asText());
- intervalMaxField = new JTextField(getJson().get("pollingIntervalMax").asText());
- backoffField = new JTextField(getJson().get("pollingBackoff").asText());
-
- interval.add(intervalField, BorderLayout.CENTER);
- intervalMax.add(intervalMaxField);
- backoff.add(backoffField);
-
- allowPolling = new JCheckBox("Polling?", getJson().get("pollingInterval").intValue() != 0);
- allowPolling.addItemListener(new ItemListener() {
- public void itemStateChanged(ItemEvent e) {
- updateEnableForPollingFlag();
- }
- });
-
- updateEnableForPollingFlag();
- JPanel allowPollingPanel = new JPanel();
- allowPollingPanel.setLayout(new BorderLayout());
- allowPollingPanel.add(allowPolling, BorderLayout.WEST);
- add(allowPollingPanel);
- add(interval);
- add(intervalMax);
- add(backoff);
- add(Box.createGlue());
- validate();
- }
-
- @Override
- public void noteConfiguration() {
- if (validateValues()) {
- int interval = 0;
- int intervalMax = 0;
- double backoff = 1.1;
-
- if (isAllowPolling()) {
- interval = getInterval();
- intervalMax = getIntervalMax();
- backoff = getBackoff();
- }
-
- getJson().put("pollingBackoff", backoff);
- getJson().put("pollingInterval", interval);
- getJson().put("pollingIntervalMax", intervalMax);
- }
- }
-
- @Override
- public boolean checkValues() {
- // TODO Not yet implemented
- return true;
- }
-
- private void updateEnableForPollingFlag() {
- boolean enabled = allowPolling.isSelected();
- intervalField.setEnabled(enabled);
- intervalMaxField.setEnabled(enabled);
- backoffField.setEnabled(enabled);
- }
-
- public boolean validateValues() {
- if (allowPolling.isSelected()) {
- try {
- new Integer(intervalField.getText());
- } catch (Exception e) {
- JOptionPane.showMessageDialog(null, "The interval field must be a valid integer",
- "Invalid value", JOptionPane.ERROR_MESSAGE);
- return false;
-
- }
-
- try {
- new Integer(intervalMaxField.getText());
- } catch (Exception e) {
- JOptionPane.showMessageDialog(null,
- "The maximum interval field must be a valid integer", "Invalid value",
- JOptionPane.ERROR_MESSAGE);
- return false;
-
- }
-
- try {
- new Double(backoffField.getText());
- } catch (Exception e) {
- JOptionPane.showMessageDialog(null, "The backoff field must be a valid float",
- "Invalid value", JOptionPane.ERROR_MESSAGE);
- return false;
-
- }
- }
-
- return true;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/menu/ConfigureSoaplabActivityMenuAction.java
----------------------------------------------------------------------
diff --git a/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/menu/ConfigureSoaplabActivityMenuAction.java b/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/menu/ConfigureSoaplabActivityMenuAction.java
deleted file mode 100644
index f182ecb..0000000
--- a/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/menu/ConfigureSoaplabActivityMenuAction.java
+++ /dev/null
@@ -1,54 +0,0 @@
-package net.sf.taverna.t2.activities.soaplab.menu;
-
-import javax.swing.Action;
-
-import net.sf.taverna.t2.activities.soaplab.actions.SoaplabActivityConfigurationAction;
-import net.sf.taverna.t2.activities.soaplab.servicedescriptions.SoaplabServiceDescription;
-import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
-import net.sf.taverna.t2.ui.menu.ContextualMenuComponent;
-import net.sf.taverna.t2.ui.menu.MenuComponent;
-import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
-import net.sf.taverna.t2.workbench.activitytools.AbstractConfigureActivityMenuAction;
-import net.sf.taverna.t2.workbench.edits.EditManager;
-import net.sf.taverna.t2.workbench.file.FileManager;
-
-public class ConfigureSoaplabActivityMenuAction extends AbstractConfigureActivityMenuAction
- implements MenuComponent, ContextualMenuComponent {
-
- private EditManager editManager;
- private FileManager fileManager;
- private ActivityIconManager activityIconManager;
- private ServiceDescriptionRegistry serviceDescriptionRegistry;
-
- public ConfigureSoaplabActivityMenuAction() {
- super(SoaplabServiceDescription.ACTIVITY_TYPE);
- }
-
- @Override
- protected Action createAction() {
- SoaplabActivityConfigurationAction configAction = new SoaplabActivityConfigurationAction(
- findActivity(), getParentFrame(), editManager, fileManager, activityIconManager,
- serviceDescriptionRegistry);
- configAction.putValue(Action.NAME,
- SoaplabActivityConfigurationAction.CONFIGURE_SOAPLAB_ACTIVITY);
- addMenuDots(configAction);
- return configAction;
- }
-
- public void setEditManager(EditManager editManager) {
- this.editManager = editManager;
- }
-
- public void setFileManager(FileManager fileManager) {
- this.fileManager = fileManager;
- }
-
- public void setActivityIconManager(ActivityIconManager activityIconManager) {
- this.activityIconManager = activityIconManager;
- }
-
- public void setServiceDescriptionRegistry(ServiceDescriptionRegistry serviceDescriptionRegistry) {
- this.serviceDescriptionRegistry = serviceDescriptionRegistry;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/MissingSoaplabException.java
----------------------------------------------------------------------
diff --git a/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/MissingSoaplabException.java b/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/MissingSoaplabException.java
deleted file mode 100644
index 594a7a2..0000000
--- a/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/MissingSoaplabException.java
+++ /dev/null
@@ -1,63 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: MissingSoaplabException.java,v $
- * Revision $Revision: 1.3 $
- * Release status $State: Exp $
- * Last modified on $Date: 2008/11/19 17:33:04 $
- * by $Author: anenadic $
- * Created on 4 Sep 2006
- *****************************************************************/
-package net.sf.taverna.t2.activities.soaplab.servicedescriptions;
-
-@SuppressWarnings("serial")
-public class MissingSoaplabException extends Exception {
-
- public MissingSoaplabException(String msg) {
- super(msg);
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabActivityIcon.java
----------------------------------------------------------------------
diff --git a/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabActivityIcon.java b/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabActivityIcon.java
deleted file mode 100644
index f9d273b..0000000
--- a/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabActivityIcon.java
+++ /dev/null
@@ -1,60 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.soaplab.servicedescriptions;
-
-import java.net.URI;
-
-import javax.swing.Icon;
-import javax.swing.ImageIcon;
-
-import net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI;
-
-/**
- *
- * @author Alex Nenadic
- *
- */
-public class SoaplabActivityIcon implements ActivityIconSPI{
-
- private static Icon icon;
-
- public int canProvideIconScore(URI activityType) {
- if (SoaplabServiceDescription.ACTIVITY_TYPE.equals(activityType))
- return DEFAULT_ICON + 1;
- else
- return NO_ICON;
- }
-
- public Icon getIcon(URI activityType) {
- return getSoaplabIcon();
- }
-
- public static Icon getSoaplabIcon() {
- if (icon == null) {
- icon = new ImageIcon(SoaplabActivityIcon.class
- .getResource("/soaplab.png"));
- }
- return icon;
- }
-
-}
-
-
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabCategory.java
----------------------------------------------------------------------
diff --git a/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabCategory.java b/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabCategory.java
deleted file mode 100644
index 47f994c..0000000
--- a/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabCategory.java
+++ /dev/null
@@ -1,80 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: SoaplabCategory.java,v $
- * Revision $Revision: 1.2 $
- * Release status $State: Exp $
- * Last modified on $Date: 2008/09/04 13:40:38 $
- * by $Author: sowen70 $
- * Created on 4 Sep 2006
- *****************************************************************/
-package net.sf.taverna.t2.activities.soaplab.servicedescriptions;
-
-import java.util.ArrayList;
-import java.util.List;
-
-public class SoaplabCategory {
-
- private String category;
- private List<String> services = new ArrayList<String>();
-
- public SoaplabCategory(String category) {
- this.category=category;
- }
-
- public boolean addService(String service) {
- return services.add(service);
- }
-
- public String getCategory() {
- return category;
- }
-
- public List<String> getServices() {
- return services;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabScavengerAgent.java
----------------------------------------------------------------------
diff --git a/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabScavengerAgent.java b/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabScavengerAgent.java
deleted file mode 100644
index fe428ec..0000000
--- a/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabScavengerAgent.java
+++ /dev/null
@@ -1,144 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: SoaplabScavengerAgent.java,v $
- * Revision $Revision: 1.2 $
- * Release status $State: Exp $
- * Last modified on $Date: 2008/09/04 13:40:37 $
- * by $Author: sowen70 $
- * Created on 4 Sep 2006
- *****************************************************************/
-package net.sf.taverna.t2.activities.soaplab.servicedescriptions;
-
-import java.rmi.RemoteException;
-import java.util.ArrayList;
-import java.util.List;
-
-import javax.xml.rpc.ServiceException;
-
-import org.apache.axis.client.Call;
-import org.apache.axis.client.Service;
-import org.apache.log4j.Logger;
-
-/**
- * An agent to query Soaplab server to determine the available categories and services.
- * @author sowen
- *
- */
-
-public class SoaplabScavengerAgent {
-
- private static Logger logger = Logger.getLogger(SoaplabScavengerAgent.class);
-
- /**
- * Returns a list of soaplab categories, containing a list of their services.
- * Throws MissingSoaplabException if an installation cannot be found.
- */
- public static List<SoaplabCategory> load(String base) throws MissingSoaplabException{
- List<SoaplabCategory> categories=new ArrayList<SoaplabCategory>();
-
- // Get the categories for this installation
- boolean foundAnInstallation = loadCategories(base + "AnalysisFactory",categories);
-
- // Yes, bitwise OR is on purpose, to make sure the second
- // loadCategories() is always run. Do NOT replace with
- // foundInstallation = foundInstallation || getCategories(..)
- foundAnInstallation |= loadCategories(base + "GowlabFactory",categories);
- if (!foundAnInstallation) {
- // Neither Soaplab nor Gowlab were found, probably a fault
- throw new MissingSoaplabException("Unable to locate a soaplab installation at \n" + base);
- }
-
- return categories;
-
- }
-
-
- private static boolean loadCategories(String categoryBase, List<SoaplabCategory>cats) {
- boolean foundSome = false;
- String[] categories;
- try {
- categories = (String[]) callWebService(categoryBase, "getAvailableCategories", new Object[0]);
- } catch (Exception e) {
- logger.debug("Missing category: "+categoryBase, e);
- return false;
- }
- // Iterate over all the categories, creating new child nodes
- for (int i = 0; i < categories.length; i++) {
- String[] services;
- try {
- services = (String[]) callWebService(categoryBase, "getAvailableAnalysesInCategory", new Object[] {categories[i]});
- } catch (Exception e) {
- logger.info("Skipping category " + categories[i], e);
- continue;
- }
- if (services.length == 0) {
- // Avoid creating empty treenodes
- continue;
- }
-
- SoaplabCategory category=new SoaplabCategory(categories[i]);
- cats.add(category);
-
- foundSome = true;
- // Iterate over the services
- for (int j = 0; j < services.length; j++) {
- category.addService(services[j]);
- }
- }
- return foundSome;
- }
-
- public static Object callWebService(String target, String operation,
- Object[] parameters) throws ServiceException, RemoteException {
- Service service = new Service();
- Call call = (Call) service.createCall();
- call.setTargetEndpointAddress(target);
- // No need to do new Qname(operation) with unspecified namespaces
- call.setOperationName(operation);
- return call.invoke(parameters);
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabServiceDescription.java
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diff --git a/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabServiceDescription.java b/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabServiceDescription.java
deleted file mode 100644
index 99a25b3..0000000
--- a/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabServiceDescription.java
+++ /dev/null
@@ -1,131 +0,0 @@
-package net.sf.taverna.t2.activities.soaplab.servicedescriptions;
-
-import java.net.URI;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.List;
-
-import javax.swing.Icon;
-
-import net.sf.taverna.t2.servicedescriptions.ServiceDescription;
-import uk.org.taverna.scufl2.api.configurations.Configuration;
-
-import com.fasterxml.jackson.databind.node.ObjectNode;
-
-public class SoaplabServiceDescription extends ServiceDescription {
-
- public static final URI ACTIVITY_TYPE = URI.create("http://ns.taverna.org.uk/2010/activity/soaplab");
-
- private final static String SOAPLAB = "Soaplab @ ";
-
- private String category;
- private String operation;
- private URI endpoint;
- private List<String> types;
-
- private String name;
-
- public List<String> getTypes() {
- return types;
- }
-
- /**
- * @return the category
- */
- public String getCategory() {
- return category;
- }
-
- /**
- * @param category
- * the category to set
- */
- public void setCategory(String category) {
- this.category = category;
- }
-
- /**
- * @return the operation
- */
- public String getOperation() {
- return operation;
- }
-
- /**
- * @param operation
- * the operation to set
- */
- public void setOperation(final String operation) {
- this.operation = operation;
-
- String name = operation;
- int finalColon = operation.lastIndexOf(":");
- if (finalColon != -1) {
- name = operation.substring(finalColon + 1);
- }
- int finalDot = operation.lastIndexOf(".");
- if (finalDot != -1) {
- name = operation.substring(finalDot + 1);
- }
- setName(name);
- }
-
- public void setName(String name) {
- this.name = name;
- }
-
-
- @Override
- public URI getActivityType() {
- return ACTIVITY_TYPE;
- }
-
- @Override
- public Configuration getActivityConfiguration() {
- Configuration configuration = new Configuration();
- configuration.setType(ACTIVITY_TYPE.resolve("#Config"));
- ((ObjectNode) configuration.getJson()).put("endpoint", getEndpoint().toASCIIString() + getOperation());
- ((ObjectNode) configuration.getJson()).put("pollingInterval", 0);
- ((ObjectNode) configuration.getJson()).put("pollingBackoff", 1.0);
- ((ObjectNode) configuration.getJson()).put("pollingIntervalMax", 0);
- return configuration;
- }
-
- @Override
- public Icon getIcon() {
- return SoaplabActivityIcon.getSoaplabIcon();
- }
-
- @Override
- public String getName() {
- return name;
- }
-
- @Override
- public List<String> getPath() {
- List<String> path = new ArrayList<String>();
- path.add(SOAPLAB + getEndpoint());
- path.add(getCategory());
- // Don't use getTypes() - as we end up
- // with double entries..
- return path;
- }
-
- public void setTypes(List<String> types) {
- this.types = types;
- }
-
- public void setEndpoint(URI endpoint) {
- this.endpoint = endpoint;
- }
-
- public URI getEndpoint() {
- return endpoint;
- }
-
- @Override
- protected List<Object> getIdentifyingData() {
- return Arrays.<Object>asList(getEndpoint(), getOperation());
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabServiceProvider.java
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diff --git a/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabServiceProvider.java b/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabServiceProvider.java
deleted file mode 100644
index 54080c9..0000000
--- a/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabServiceProvider.java
+++ /dev/null
@@ -1,183 +0,0 @@
-package net.sf.taverna.t2.activities.soaplab.servicedescriptions;
-
-import java.net.URI;
-import java.rmi.RemoteException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Date;
-import java.util.List;
-import java.util.Map;
-
-import javax.swing.Icon;
-import javax.xml.rpc.ServiceException;
-
-import net.sf.taverna.t2.activities.soaplab.Soap;
-import net.sf.taverna.t2.servicedescriptions.AbstractConfigurableServiceProvider;
-import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
-
-import org.apache.log4j.Logger;
-
-public class SoaplabServiceProvider extends
- AbstractConfigurableServiceProvider<SoaplabServiceProviderConfig> {
-
- // To avoid hammering the soaplab service
- private static final int DELAY_MS = 100;
- private static final int DESCRIPTION_UPDATE_INTERVAL_MS = 2000;
-
- private static Logger logger = Logger
- .getLogger(SoaplabServiceProvider.class);
-
- private static final String SOAPLAB_SERVICE = "Soaplab service";
- private static final boolean FIND_DETAILS = false;
-
- private static final URI providerId = URI
- .create("http://taverna.sf.net/2010/service-provider/soaplab");
-
- private ServiceDescriptionRegistry serviceDescriptionRegistry;
-
- public SoaplabServiceProvider() {
- super(new SoaplabServiceProviderConfig(
- "http://somehost/soaplab/services/"));
- }
-
- public void findServiceDescriptionsAsync(
- FindServiceDescriptionsCallBack callBack) {
- List<SoaplabServiceDescription> descriptions = findSoaplabServices(callBack);
- if (descriptions == null) {
- return;
- }
- callBack.partialResults(descriptions);
-
- if (FIND_DETAILS) {
- if (findSoaplabDetails(descriptions, callBack)) {
- callBack.finished();
- }
- } else {
- callBack.finished();
- }
- }
-
- public List<SoaplabServiceProviderConfig> getDefaultConfigurations() {
-
- List<SoaplabServiceProviderConfig> defaults = new ArrayList<SoaplabServiceProviderConfig>();
-
- // If defaults have failed to load from a configuration file then load them here.
- if (!serviceDescriptionRegistry.isDefaultSystemConfigurableProvidersLoaded()){
- defaults.add(new SoaplabServiceProviderConfig(
- "http://wsembnet.vital-it.ch/soaplab2-axis/services/"));
- } // else return an empty list
-
- return defaults;
- }
-
- public Icon getIcon() {
- return SoaplabActivityIcon.getSoaplabIcon();
- }
-
- public String getName() {
- return SOAPLAB_SERVICE;
- }
-
- @SuppressWarnings("unchecked")
- protected boolean findSoaplabDetails(
- List<SoaplabServiceDescription> descriptions,
- FindServiceDescriptionsCallBack callBack) {
- Date lastUpdate = new Date();
- // We'll fetch more details and update the descriptions in the
- // background
- List<SoaplabServiceDescription> updatedDescriptions = new ArrayList<SoaplabServiceDescription>();
- for (SoaplabServiceDescription serviceDescription : descriptions) {
- try {
- Date now = new Date();
- if (now.getTime() - lastUpdate.getTime() > DESCRIPTION_UPDATE_INTERVAL_MS) {
- if (!updatedDescriptions.isEmpty()) {
- callBack.partialResults(updatedDescriptions);
- updatedDescriptions = new ArrayList<SoaplabServiceDescription>();
- }
- lastUpdate = now;
- }
- Thread.sleep(DELAY_MS);
- URI soaplabEndpoint = serviceProviderConfig.getEndpoint();
- Map info = (Map) Soap.callWebService(soaplabEndpoint
- .toASCIIString()
- + "/" + serviceDescription.getOperation(),
- "getAnalysisType"); // Get the description element from
- // the map
- String description = (String) info.get("description");
- if (description != null) {
- serviceDescription.setDescription(description);
- }
- updatedDescriptions.add(serviceDescription);
- String type = (String) info.get("type");
- if (type != null) {
- serviceDescription.setTypes(Arrays.asList(type.split(",")));
- }
- } catch (ClassCastException e) {
- logger.warn("Can't read descriptions for soaplab service "
- + serviceDescription, e);
- callBack.warning("Can't read descriptions for soaplab service "
- + serviceDescription.getOperation());
- } catch (ServiceException e) {
- logger.warn("Can't read descriptions for soaplab service "
- + serviceDescription, e);
- callBack.warning("Can't read descriptions for soaplab service "
- + serviceDescription.getOperation());
- } catch (RemoteException e) {
- logger.warn("Can't read descriptions for soaplab service "
- + serviceDescription, e);
- callBack.warning("Can't read descriptions for soaplab service "
- + serviceDescription.getOperation());
- } catch (InterruptedException ex) {
- callBack.fail("Thread was interrupted", ex);
- return false;
- }
- }
- if (!updatedDescriptions.isEmpty()) {
- callBack.partialResults(updatedDescriptions);
- }
- return true;
- }
-
- protected List<SoaplabServiceDescription> findSoaplabServices(
- FindServiceDescriptionsCallBack callBack) {
- List<SoaplabServiceDescription> descriptions = new ArrayList<SoaplabServiceDescription>();
- URI soaplabEndpoint = serviceProviderConfig.getEndpoint();
- callBack.status("Connecting to Soaplab:" + soaplabEndpoint);
- List<SoaplabCategory> categories;
- try {
- categories = SoaplabScavengerAgent.load(soaplabEndpoint
- .toASCIIString());
- } catch (MissingSoaplabException ex) {
- String message = "There was an error with the soaplab: "
- + soaplabEndpoint;
- callBack.fail(message, ex);
- return null;
- }
- for (SoaplabCategory cat : categories) {
- for (String service : cat.getServices()) {
- SoaplabServiceDescription item = new SoaplabServiceDescription();
- item.setCategory(cat.getCategory());
- item.setOperation(service);
- item.setEndpoint(soaplabEndpoint);
- descriptions.add(item);
- }
- }
- return descriptions;
- }
-
- @Override
- protected List<? extends Object> getIdentifyingData() {
- List<String> result;
- result = Arrays.asList(getConfiguration().getEndpoint().toString());
- return result;
- }
-
- public String getId() {
- return providerId.toString();
- }
-
- public void setServiceDescriptionRegistry(ServiceDescriptionRegistry serviceDescriptionRegistry) {
- this.serviceDescriptionRegistry = serviceDescriptionRegistry;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabServiceProviderConfig.java
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diff --git a/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabServiceProviderConfig.java b/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabServiceProviderConfig.java
deleted file mode 100644
index d1e86da..0000000
--- a/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/servicedescriptions/SoaplabServiceProviderConfig.java
+++ /dev/null
@@ -1,38 +0,0 @@
-package net.sf.taverna.t2.activities.soaplab.servicedescriptions;
-
-import java.net.URI;
-
-import net.sf.taverna.t2.lang.beans.PropertyAnnotated;
-import net.sf.taverna.t2.lang.beans.PropertyAnnotation;
-
-public class SoaplabServiceProviderConfig extends PropertyAnnotated {
-
- private URI endpoint;
-
- public SoaplabServiceProviderConfig() {
- }
-
- public SoaplabServiceProviderConfig(String endpointURI) {
- this.setEndpoint(URI.create(endpointURI.trim()));
- }
-
- @PropertyAnnotation(displayName = "Soaplab location", preferred = true)
- public URI getEndpoint() {
- return endpoint;
- }
-
- public String toString() {
- return getEndpoint().toString();
- }
-
- public void setEndpoint(URI endpoint) {
- String uriString = endpoint.toString();
- if (!uriString.endsWith("/")) {
- uriString = uriString + "/";
- this.endpoint = URI.create(uriString);
- } else {
- this.endpoint = endpoint;
- }
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/views/SoaplabActivityContextualView.java
----------------------------------------------------------------------
diff --git a/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/views/SoaplabActivityContextualView.java b/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/views/SoaplabActivityContextualView.java
deleted file mode 100644
index de51f23..0000000
--- a/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/views/SoaplabActivityContextualView.java
+++ /dev/null
@@ -1,156 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.soaplab.views;
-
-import java.awt.Frame;
-import java.io.ByteArrayInputStream;
-import java.io.ByteArrayOutputStream;
-import java.net.URL;
-
-import javax.swing.Action;
-import javax.xml.namespace.QName;
-import javax.xml.transform.Templates;
-import javax.xml.transform.Transformer;
-import javax.xml.transform.TransformerFactory;
-import javax.xml.transform.stream.StreamResult;
-import javax.xml.transform.stream.StreamSource;
-
-import net.sf.taverna.t2.activities.soaplab.actions.SoaplabActivityConfigurationAction;
-import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
-import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
-import net.sf.taverna.t2.workbench.configuration.colour.ColourManager;
-import net.sf.taverna.t2.workbench.edits.EditManager;
-import net.sf.taverna.t2.workbench.file.FileManager;
-import net.sf.taverna.t2.workbench.ui.actions.activity.HTMLBasedActivityContextualView;
-
-import org.apache.axis.client.Call;
-import org.apache.axis.client.Service;
-import org.apache.log4j.Logger;
-
-import uk.org.taverna.scufl2.api.activity.Activity;
-import uk.org.taverna.scufl2.api.configurations.Configuration;
-
-import com.fasterxml.jackson.databind.JsonNode;
-
-public class SoaplabActivityContextualView extends HTMLBasedActivityContextualView {
-
- private static Logger logger = Logger.getLogger(SoaplabActivityContextualView.class);
-
- private static final long serialVersionUID = -6470801873448104509L;
-
- private final EditManager editManager;
-
- private final FileManager fileManager;
-
- private final ActivityIconManager activityIconManager;
-
- private final ServiceDescriptionRegistry serviceDescriptionRegistry;
-
- public SoaplabActivityContextualView(Activity activity, EditManager editManager,
- FileManager fileManager, ActivityIconManager activityIconManager,
- ColourManager colourManager, ServiceDescriptionRegistry serviceDescriptionRegistry) {
- super(activity, colourManager);
- this.editManager = editManager;
- this.fileManager = fileManager;
- this.activityIconManager = activityIconManager;
- this.serviceDescriptionRegistry = serviceDescriptionRegistry;
- }
-
- @Override
- public String getViewTitle() {
- return "Soaplab service";
- }
-
- @Override
- protected String getRawTableRowsHtml() {
- Configuration configuration = getConfigBean();
- JsonNode json = configuration.getJson();
- String html = "<tr><td>Endpoint</td><td>" + json.get("endpoint").textValue() + "</td></tr>";
- html += "<tr><td>Polling interval</td><td>" + json.get("pollingInterval").asText()
- + "</td></tr>";
- html += "<tr><td>Polling backoff</td><td>" + json.get("pollingBackoff").asText()
- + "</td></tr>";
- html += "<tr><td>Polling interval max</td><td>" + json.get("pollingIntervalMax").asText()
- + "</td></tr>";
- // html += "<tr><td>SOAPLAB Metadata</td><td>" + getMetadata()
- // + "</td></tr>";
- return html;
- }
-
- @Override
- public Action getConfigureAction(Frame owner) {
- return new SoaplabActivityConfigurationAction(getActivity(), owner, editManager,
- fileManager, activityIconManager, serviceDescriptionRegistry);
- }
-
- private String getMetadata() {
- try {
- Configuration configuration = getConfigBean();
- JsonNode json = configuration.getJson();
- String endpoint = json.get("endpoint").textValue();
- Call call = (Call) new Service().createCall();
- call.setTimeout(new Integer(0));
- call.setTargetEndpointAddress(endpoint);
- call.setOperationName(new QName("describe"));
- String metadata = (String) call.invoke(new Object[0]);
- logger.info(metadata);
- // Old impl, returns a tree of the XML
- // ColXMLTree tree = new ColXMLTree(metadata);
- URL sheetURL = SoaplabActivityContextualView.class
- .getResource("/analysis_metadata_2_html.xsl");
- TransformerFactory transformerFactory = TransformerFactory.newInstance();
- logger.info(sheetURL.toString());
- Templates stylesheet = transformerFactory.newTemplates(new StreamSource(sheetURL
- .openStream()));
- Transformer transformer = stylesheet.newTransformer();
- StreamSource inputStream = new StreamSource(new ByteArrayInputStream(
- metadata.getBytes()));
- ByteArrayOutputStream transformedStream = new ByteArrayOutputStream();
- StreamResult result = new StreamResult(transformedStream);
- transformer.transform(inputStream, result);
- transformedStream.flush();
- transformedStream.close();
- // String summaryText = "<html><head>"
- // + WorkflowSummaryAsHTML.STYLE_NOBG + "</head>"
- // + transformedStream.toString() + "</html>";
- // JEditorPane metadataPane = new ColJEditorPane("text/html",
- // summaryText);
- // metadataPane.setText(transformedStream.toString());
- // // logger.info(transformedStream.toString());
- // JScrollPane jsp = new JScrollPane(metadataPane,
- // JScrollPane.VERTICAL_SCROLLBAR_AS_NEEDED,
- // JScrollPane.HORIZONTAL_SCROLLBAR_NEVER);
- // jsp.setPreferredSize(new Dimension(0, 0));
- // jsp.getVerticalScrollBar().setValue(0);
- return transformedStream.toString();
- } catch (Exception ex) {
- return "<font color=\"red\">Error</font><p>An exception occured while trying to fetch Soaplab metadata from the server. The error was :<pre>"
- + ex.getMessage() + "</pre>";
-
- }
- }
-
- @Override
- public int getPreferredPosition() {
- return 100;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/views/SoaplabActivityViewFactory.java
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diff --git a/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/views/SoaplabActivityViewFactory.java b/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/views/SoaplabActivityViewFactory.java
deleted file mode 100644
index 23e94d8..0000000
--- a/taverna-soaplab-activity-ui/src/main/java/net/sf/taverna/t2/activities/soaplab/views/SoaplabActivityViewFactory.java
+++ /dev/null
@@ -1,73 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.soaplab.views;
-
-import java.util.Arrays;
-import java.util.List;
-
-import net.sf.taverna.t2.activities.soaplab.servicedescriptions.SoaplabServiceDescription;
-import net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry;
-import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
-import net.sf.taverna.t2.workbench.configuration.colour.ColourManager;
-import net.sf.taverna.t2.workbench.edits.EditManager;
-import net.sf.taverna.t2.workbench.file.FileManager;
-import net.sf.taverna.t2.workbench.ui.views.contextualviews.ContextualView;
-import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory;
-import uk.org.taverna.scufl2.api.activity.Activity;
-
-public class SoaplabActivityViewFactory implements ContextualViewFactory<Activity> {
-
- private EditManager editManager;
- private FileManager fileManager;
- private ActivityIconManager activityIconManager;
- private ColourManager colourManager;
- private ServiceDescriptionRegistry serviceDescriptionRegistry;
-
- public boolean canHandle(Object object) {
- return object instanceof Activity && ((Activity) object).getType().equals(SoaplabServiceDescription.ACTIVITY_TYPE);
- }
-
- public List<ContextualView> getViews(Activity activity) {
- return Arrays.asList(new ContextualView[] { new SoaplabActivityContextualView(activity,
- editManager, fileManager, activityIconManager, colourManager, serviceDescriptionRegistry) });
- }
-
- public void setEditManager(EditManager editManager) {
- this.editManager = editManager;
- }
-
- public void setFileManager(FileManager fileManager) {
- this.fileManager = fileManager;
- }
-
- public void setActivityIconManager(ActivityIconManager activityIconManager) {
- this.activityIconManager = activityIconManager;
- }
-
- public void setColourManager(ColourManager colourManager) {
- this.colourManager = colourManager;
- }
-
- public void setServiceDescriptionRegistry(ServiceDescriptionRegistry serviceDescriptionRegistry) {
- this.serviceDescriptionRegistry = serviceDescriptionRegistry;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-soaplab-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider
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diff --git a/taverna-soaplab-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider b/taverna-soaplab-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider
deleted file mode 100644
index fb73ade..0000000
--- a/taverna-soaplab-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider
+++ /dev/null
@@ -1 +0,0 @@
-net.sf.taverna.t2.activities.soaplab.servicedescriptions.SoaplabServiceProvider
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-soaplab-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent
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diff --git a/taverna-soaplab-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent b/taverna-soaplab-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent
deleted file mode 100644
index 1eeb850..0000000
--- a/taverna-soaplab-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.ui.menu.MenuComponent
+++ /dev/null
@@ -1 +0,0 @@
-net.sf.taverna.t2.activities.soaplab.menu.ConfigureSoaplabActivityMenuAction
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-soaplab-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI
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diff --git a/taverna-soaplab-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI b/taverna-soaplab-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI
deleted file mode 100644
index 0bb5227..0000000
--- a/taverna-soaplab-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI
+++ /dev/null
@@ -1 +0,0 @@
-net.sf.taverna.t2.activities.soaplab.servicedescriptions.SoaplabActivityIcon
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-soaplab-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory
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diff --git a/taverna-soaplab-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory b/taverna-soaplab-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory
deleted file mode 100644
index ea7da0b..0000000
--- a/taverna-soaplab-activity-ui/src/main/resources/META-INF/services/net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory
+++ /dev/null
@@ -1 +0,0 @@
-net.sf.taverna.t2.activities.soaplab.views.SoaplabActivityViewFactory
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-soaplab-activity-ui/src/main/resources/META-INF/spring/soaplab-activity-ui-context-osgi.xml
----------------------------------------------------------------------
diff --git a/taverna-soaplab-activity-ui/src/main/resources/META-INF/spring/soaplab-activity-ui-context-osgi.xml b/taverna-soaplab-activity-ui/src/main/resources/META-INF/spring/soaplab-activity-ui-context-osgi.xml
deleted file mode 100644
index f7e486e..0000000
--- a/taverna-soaplab-activity-ui/src/main/resources/META-INF/spring/soaplab-activity-ui-context-osgi.xml
+++ /dev/null
@@ -1,28 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<beans:beans xmlns="http://www.springframework.org/schema/osgi" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:beans="http://www.springframework.org/schema/beans"
- xsi:schemaLocation="http://www.springframework.org/schema/beans
- http://www.springframework.org/schema/beans/spring-beans.xsd
- http://www.springframework.org/schema/osgi
- http://www.springframework.org/schema/osgi/spring-osgi.xsd">
-
- <service ref="SoaplabActivityIcon" interface="net.sf.taverna.t2.workbench.activityicons.ActivityIconSPI" />
-
- <service ref="SoaplabServiceProvider">
- <interfaces>
- <beans:value>net.sf.taverna.t2.servicedescriptions.ServiceDescriptionProvider</beans:value>
- <beans:value>net.sf.taverna.t2.servicedescriptions.ConfigurableServiceProvider</beans:value>
- </interfaces>
- </service>
-
- <service ref="ConfigureSoaplabActivityMenuAction" auto-export="interfaces" />
-
- <service ref="SoaplabActivityViewFactory" interface="net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ContextualViewFactory" />
-
- <reference id="editManager" interface="net.sf.taverna.t2.workbench.edits.EditManager" />
- <reference id="fileManager" interface="net.sf.taverna.t2.workbench.file.FileManager" />
- <reference id="activityIconManager" interface="net.sf.taverna.t2.workbench.activityicons.ActivityIconManager" />
- <reference id="colourManager" interface="net.sf.taverna.t2.workbench.configuration.colour.ColourManager" />
- <reference id="serviceDescriptionRegistry" interface="net.sf.taverna.t2.servicedescriptions.ServiceDescriptionRegistry" />
-
-</beans:beans>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-soaplab-activity-ui/src/main/resources/META-INF/spring/soaplab-activity-ui-context.xml
----------------------------------------------------------------------
diff --git a/taverna-soaplab-activity-ui/src/main/resources/META-INF/spring/soaplab-activity-ui-context.xml b/taverna-soaplab-activity-ui/src/main/resources/META-INF/spring/soaplab-activity-ui-context.xml
deleted file mode 100644
index 7f99ff2..0000000
--- a/taverna-soaplab-activity-ui/src/main/resources/META-INF/spring/soaplab-activity-ui-context.xml
+++ /dev/null
@@ -1,27 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<beans xmlns="http://www.springframework.org/schema/beans" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://www.springframework.org/schema/beans
- http://www.springframework.org/schema/beans/spring-beans.xsd">
-
- <bean id="SoaplabActivityIcon" class="net.sf.taverna.t2.activities.soaplab.servicedescriptions.SoaplabActivityIcon" />
-
- <bean id="SoaplabServiceProvider" class="net.sf.taverna.t2.activities.soaplab.servicedescriptions.SoaplabServiceProvider">
- <property name="serviceDescriptionRegistry" ref="serviceDescriptionRegistry" />
- </bean>
-
- <bean id="ConfigureSoaplabActivityMenuAction" class="net.sf.taverna.t2.activities.soaplab.menu.ConfigureSoaplabActivityMenuAction">
- <property name="editManager" ref="editManager" />
- <property name="fileManager" ref="fileManager" />
- <property name="activityIconManager" ref="activityIconManager" />
- <property name="serviceDescriptionRegistry" ref="serviceDescriptionRegistry" />
- </bean>
-
- <bean id="SoaplabActivityViewFactory" class="net.sf.taverna.t2.activities.soaplab.views.SoaplabActivityViewFactory" >
- <property name="editManager" ref="editManager" />
- <property name="fileManager" ref="fileManager" />
- <property name="activityIconManager" ref="activityIconManager" />
- <property name="colourManager" ref="colourManager" />
- <property name="serviceDescriptionRegistry" ref="serviceDescriptionRegistry" />
- </bean>
-
-</beans>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-soaplab-activity-ui/src/main/resources/analysis_metadata_2_html.xsl
----------------------------------------------------------------------
diff --git a/taverna-soaplab-activity-ui/src/main/resources/analysis_metadata_2_html.xsl b/taverna-soaplab-activity-ui/src/main/resources/analysis_metadata_2_html.xsl
deleted file mode 100644
index 5095e5c..0000000
--- a/taverna-soaplab-activity-ui/src/main/resources/analysis_metadata_2_html.xsl
+++ /dev/null
@@ -1,96 +0,0 @@
-<?xml version="1.0" encoding="utf-8"?>
-
-<!-- ===================================================================== -->
-<!-- Converting analysis metadata returned by Soaplab Web Services to HTML -->
-<!-- (http://www.ebi.ac.uk/soaplab/) -->
-<!-- Author: Martin Senger (senger@ebi.ac.uk) -->
-<!-- ===================================================================== -->
-
-<!-- $Id: analysis_metadata_2_html.xsl,v 1.1 2008/07/14 15:27:42 iandunlop Exp $ -->
-
-<xsl:stylesheet xmlns:xsl="http://www.w3.org/1999/XSL/Transform"
- version="1.0">
- <xsl:output method="html"/>
-
- <!-- the main document body -->
- <xsl:template match="/">
- <body>
- <xsl:apply-templates/>
- </body>
- </xsl:template>
-
- <!-- analysis -->
- <xsl:template match="/DsLSRAnalysis/analysis">
-
- <!-- analysis name -->
- <table border="0" cellpadding="2" cellspacing="3" width="98%" align="center"><tr><th bgcolor="#eeeedd">
- <font size="+1"><xsl:value-of select="@name"/></font>
- </th></tr></table>
-
- <!-- analysis metadata -->
- <table border="0" cellspacing="1" cellpadding="1" width="99%" align="center"><tr>
- <td>
- <table border="0" cellspacing="2">
- <xsl:apply-templates select="description" mode="as-row"/>
- <xsl:apply-templates select="analysis_extension/app_info/@*[local-name != 'help_URL']" mode="as-row"/>
- <xsl:apply-templates select="@*[local-name() != 'name']" mode="as-row"/>
- <tr><td>Help URL</td><td><a href="{analysis_extension/app_info/@help_URL}"><xsl:value-of select="analysis_extension/app_info/@help_URL"/></a></td></tr>
- </table>
- </td></tr></table>
-
- <!-- inputs/outputs metadata -->
- <table border="0" width="98%" cellpadding="2" cellspacing="1" align="center">
- <tr><td colspan="2" bgcolor="#eeeedd"> <b>Outputs</b> </td></tr>
- <xsl:apply-templates select="output"/>
- <tr><td colspan="2" bgcolor="#eeeedd"> <b>Inputs</b> </td></tr>
- <xsl:apply-templates select="input"/>
- </table>
-
- </xsl:template>
-
- <!-- metadata about one input or output -->
- <xsl:template match="input|output">
- <xsl:variable name="param_name" select="@name"/>
- <tr bgcolor="#eae9c2">
- <td valign="top"><b><xsl:value-of select="@name"/></b></td>
- <td><table border="0" cellspacing="1" cellpadding="1" bgcolor="white" width="100%">
- <xsl:apply-templates select="@*[local-name() != 'name']" mode="as-row"/>
- <xsl:apply-templates select="allowed" mode="as-row"/>
- <xsl:apply-templates select="../analysis_extension/parameter/base[@name =$param_name]/*" mode="as-row"/>
- <xsl:apply-templates select="../analysis_extension/parameter/base[concat(@name,'_url') =$param_name]/*" mode="as-row"/>
- <xsl:apply-templates select="../analysis_extension/parameter/base[concat(@name,'_direct_data')=$param_name]/*" mode="as-row"/>
- <xsl:apply-templates select="../analysis_extension/parameter/base[concat(@name,'_usa') =$param_name]/*" mode="as-row"/>
- </table></td>
- </tr>
- </xsl:template>
-
- <!-- attributes and elements expressed as a (bold)name and value -->
- <xsl:template match="@*[local-name() != 'help_URL']|description|default|prompt|help" mode="as-row">
- <tr>
- <td valign="top" width="80"><em><xsl:value-of select="local-name()"/></em></td>
- <td><xsl:value-of select="."/></td>
- </tr>
- </xsl:template>
-
- <!-- more-values elements -->
- <xsl:template match="allowed" mode="as-row">
-
- <xsl:if test="position() = 1">
- <xsl:text disable-output-escaping = "yes"><tr></xsl:text>
- <td valign="top" width="80"><em><xsl:value-of select="local-name()"/></em></td>
- <xsl:text disable-output-escaping = "yes"><td></xsl:text>
- </xsl:if>
-
- <xsl:value-of select="."/>
- <xsl:if test="position() != last()">
- <xsl:text>, </xsl:text>
- </xsl:if>
-
- <xsl:if test="position() = last()">
- <xsl:text disable-output-escaping = "yes"></td></xsl:text>
- <xsl:text disable-output-escaping = "yes"></tr></xsl:text>
- </xsl:if>
-
- </xsl:template>
-
-</xsl:stylesheet>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-soaplab-activity-ui/src/main/resources/soaplab.png
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diff --git a/taverna-soaplab-activity-ui/src/main/resources/soaplab.png b/taverna-soaplab-activity-ui/src/main/resources/soaplab.png
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index b86d848..0000000
Binary files a/taverna-soaplab-activity-ui/src/main/resources/soaplab.png and /dev/null differ
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-soaplab-activity-ui/src/test/java/net/sf/taverna/t2/activities/soaplab/views/TestSoaplabActivityContextualView.java
----------------------------------------------------------------------
diff --git a/taverna-soaplab-activity-ui/src/test/java/net/sf/taverna/t2/activities/soaplab/views/TestSoaplabActivityContextualView.java b/taverna-soaplab-activity-ui/src/test/java/net/sf/taverna/t2/activities/soaplab/views/TestSoaplabActivityContextualView.java
deleted file mode 100644
index c4d683d..0000000
--- a/taverna-soaplab-activity-ui/src/test/java/net/sf/taverna/t2/activities/soaplab/views/TestSoaplabActivityContextualView.java
+++ /dev/null
@@ -1,61 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.soaplab.views;
-
-import static org.junit.Assert.assertNotNull;
-import static org.junit.Assert.assertTrue;
-import net.sf.taverna.t2.activities.soaplab.actions.SoaplabActivityConfigurationAction;
-import net.sf.taverna.t2.workbench.ui.views.contextualviews.ContextualView;
-
-import org.junit.Before;
-import org.junit.Ignore;
-import org.junit.Test;
-
-import uk.org.taverna.scufl2.api.activity.Activity;
-
-public class TestSoaplabActivityContextualView {
-
- Activity a;
-
- @Before
- public void setup() throws Exception {
- a=new Activity();
- }
-
- @Test
- @Ignore("Integration test")
- public void testConfigureAction() throws Exception {
- ContextualView view = new SoaplabActivityContextualView(a, null, null, null, null, null);
- assertNotNull("the action should not be null",view.getConfigureAction(null));
- assertTrue("The action should be a SoaplabAcitivyConfigurationAction",view.getConfigureAction(null) instanceof SoaplabActivityConfigurationAction);
- }
-
- private void run() throws Exception
- {
- setup();
- ContextualView view = new SoaplabActivityContextualView(a, null, null, null, null, null);
- view.setVisible(true);
- }
-
- public static void main(String[] args) throws Exception {
- new TestSoaplabActivityContextualView().run();
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-soaplab-activity/pom.xml
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diff --git a/taverna-soaplab-activity/pom.xml b/taverna-soaplab-activity/pom.xml
deleted file mode 100644
index 5459718..0000000
--- a/taverna-soaplab-activity/pom.xml
+++ /dev/null
@@ -1,80 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
- <modelVersion>4.0.0</modelVersion>
- <parent>
- <groupId>net.sf.taverna</groupId>
- <artifactId>taverna-parent</artifactId>
- <version>3.0.1-SNAPSHOT</version>
- </parent>
- <groupId>net.sf.taverna.t2.activities</groupId>
- <artifactId>soaplab-activity</artifactId>
- <packaging>bundle</packaging>
- <name>Taverna 2 Soaplab Activity</name>
- <dependencies>
- <dependency>
- <groupId>net.sf.taverna.t2.core</groupId>
- <artifactId>workflowmodel-api</artifactId>
- <version>${t2.core.version}</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.core</groupId>
- <artifactId>reference-api</artifactId>
- <version>${t2.core.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.axis</groupId>
- <artifactId>com.springsource.org.apache.axis</artifactId>
- <version>${axis.version}</version>
- </dependency>
- <dependency>
- <groupId>javax.xml.rpc</groupId>
- <artifactId>com.springsource.javax.xml.rpc</artifactId>
- <version>${xml.rpc.version}</version>
- </dependency>
- <dependency>
- <groupId>org.apache.log4j</groupId>
- <artifactId>com.springsource.org.apache.log4j</artifactId>
- <version>${log4j.version}</version>
- </dependency>
- <dependency>
- <groupId>junit</groupId>
- <artifactId>junit</artifactId>
- <version>${junit.version}</version>
- <scope>test</scope>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.activities</groupId>
- <artifactId>activity-test-utils</artifactId>
- <version>${t2.activities.version}</version>
- <scope>test</scope>
- </dependency>
- </dependencies>
- <repositories>
- <repository>
- <releases />
- <snapshots>
- <enabled>false</enabled>
- </snapshots>
- <id>mygrid-repository</id>
- <name>myGrid Repository</name>
- <url>http://www.mygrid.org.uk/maven/repository</url>
- </repository>
- <repository>
- <releases>
- <enabled>false</enabled>
- </releases>
- <snapshots />
- <id>mygrid-snapshot-repository</id>
- <name>myGrid Snapshot Repository</name>
- <url>http://www.mygrid.org.uk/maven/snapshot-repository</url>
- </repository>
- </repositories>
- <scm>
- <connection>scm:git:https://github.com/taverna/taverna-soaplab-activity.git</connection>
- <developerConnection>scm:git:ssh://git@github.com:taverna/taverna-soaplab-activity.git</developerConnection>
- <url>https://github.com/taverna/taverna-soaplab-activity</url>
- <tag>HEAD</tag>
- </scm>
-
-</project>
-
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-soaplab-activity/src/main/java/net/sf/taverna/t2/activities/soaplab/Soap.java
----------------------------------------------------------------------
diff --git a/taverna-soaplab-activity/src/main/java/net/sf/taverna/t2/activities/soaplab/Soap.java b/taverna-soaplab-activity/src/main/java/net/sf/taverna/t2/activities/soaplab/Soap.java
deleted file mode 100644
index ba9cce6..0000000
--- a/taverna-soaplab-activity/src/main/java/net/sf/taverna/t2/activities/soaplab/Soap.java
+++ /dev/null
@@ -1,82 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2007 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.soaplab;
-
-import java.rmi.RemoteException;
-
-import javax.xml.rpc.ServiceException;
-
-import org.apache.axis.client.Call;
-import org.apache.axis.client.Service;
-
-/**
- * Convenience methods for simpler calling of SOAP services using the Axis
- * client.
- *
- * Note that for complex scenarious you might want to construct the Call object
- * yourself.
- *
- * @author Stian Soiland
- *
- */
-public class Soap {
- /**
- * Invoke the web service, passing no parameters, and return the result.
- *
- * @see callWebService(String target, String operation, Object[] parameters)
- *
- */
- public static Object callWebService(String target, String operation)
- throws ServiceException, RemoteException {
- return callWebService(target, operation, new Object[0]);
- }
-
- /**
- * Invoke the web service, passing a single String parameter, and return the result.
- *
- * @see callWebService(String target, String operation, Object[] parameters)
- *
- */
- public static Object callWebService(String target, String operation,
- String parameter) throws ServiceException, RemoteException {
- return callWebService(target, operation, new String[] { parameter });
- }
-
- /**
- * Invoke the web service and return the result.
- *
- * @param target The full URL to the service, example "http://www.ebi.ac.uk/soaplab/services/AnalysisFactory"
- * @param operation The operation name, example "getAvailableCategories"
- * @param parameters A (possibly empty) list of parameters
- * @return The result returned from calling the webservice operation
- * @throws ServiceException If web service facilities are not available
- * @throws RemoteException If remote call failed
- */
- public static Object callWebService(String target, String operation,
- Object[] parameters) throws ServiceException, RemoteException {
- Service service = new Service();
- Call call = (Call) service.createCall();
- call.setTargetEndpointAddress(target);
- // No need to do new Qname(operation) with unspecified namespaces
- call.setOperationName(operation);
- return call.invoke(parameters);
- }
-}
[03/16] incubator-taverna-plugin-bioinformatics git commit:
temporarily empty repository
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/RetrieveWsdlThread.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/RetrieveWsdlThread.java b/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/RetrieveWsdlThread.java
deleted file mode 100644
index a7b873c..0000000
--- a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/RetrieveWsdlThread.java
+++ /dev/null
@@ -1,57 +0,0 @@
-/*******************************************************************************
- * This file is a component of the Taverna project, and is licensed under the
- * GNU LGPL. Copyright Edward Kawas, The BioMoby Project
- ******************************************************************************/
-/*
- * This file is a component of the Taverna project,
- * and is licensed under the GNU LGPL.
- * Copyright Edward Kawas, The BioMoby Project
- */
-
-package net.sf.taverna.t2.activities.biomoby;
-
-import org.biomoby.shared.MobyService;
-import org.biomoby.shared.Central;
-
-/**
- * This class is used to create a threaded call to the Biomoby registry that
- * retrieves WSDL for services. This is done, because the Biomoby API assumes
- * that before calling a service the WSDL is retrieved.
- *
- * @author Eddie Kawas
- *
- */
-public class RetrieveWsdlThread extends Thread {
- // the service to get wsdl document
- MobyService service = null;
-
- // the registry that we will get the document from
- Central worker = null;
-
- /**
- * Constructor
- *
- * @param worker
- * the Central registry that we query for wsdl
- * @param service
- * the service that we want wsdl for
- */
- RetrieveWsdlThread(Central worker, MobyService service) {
- super("BioMOBY RetrieveWsdlThread");
- this.service = service;
- this.worker = worker;
- setDaemon(true);
- }
-
- /*
- * (non-Javadoc)
- * @see java.lang.Thread#run()
- */
- public void run() {
- try {
- worker.getServiceWSDL(service.getName(), service.getAuthority());
- } catch (Exception e) {
-
- }
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/XMLUtilities.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/XMLUtilities.java b/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/XMLUtilities.java
deleted file mode 100644
index d791329..0000000
--- a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/XMLUtilities.java
+++ /dev/null
@@ -1,1927 +0,0 @@
-/*
- * This file is a component of the Taverna project,
- * and is licensed under the GNU LGPL.
- * Copyright Edward Kawas, The BioMoby Project
- */
-package net.sf.taverna.t2.activities.biomoby;
-
-import java.io.IOException;
-import java.io.StringReader;
-import java.util.ArrayList;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Vector;
-
-import org.biomoby.shared.MobyException;
-import org.biomoby.shared.Utils;
-import org.jdom.Document;
-import org.jdom.Element;
-import org.jdom.JDOMException;
-import org.jdom.Namespace;
-import org.jdom.input.SAXBuilder;
-import org.jdom.output.Format;
-import org.jdom.output.XMLOutputter;
-
-/**
- *
- * @author Eddie Kawas
- *
- */
-@SuppressWarnings("unchecked")
-public class XMLUtilities {
-
- // private variables
- // machine independent new line character
- public final static String newline = System.getProperty("line.separator");
-
- // class variable to keep persistant queryIDs
- private static int queryCount = 0;
-
- // the moby namespaces
- public final static Namespace MOBY_NS = Namespace.getNamespace("moby",
- "http://www.biomoby.org/moby");
-
- /**
- *
- * @param message
- * the structurally valid BioMoby message as a String
- * @return true if the message contains multiple invocations, false
- * otherwise.
- * @throws MobyException
- * if the message is null
- */
- public static boolean isMultipleInvocationMessage(String message)
- throws MobyException {
- if (message == null)
- throw new MobyException(
- newline
- + "null 'xml' found where it was not expected in isMultipleInvocationMessage(String message).");
- Element documentElement = getDOMDocument(message).getRootElement();
- return isMultipleInvocationMessage(documentElement);
- }
-
- /**
- *
- * @param message
- * the structurally valid BioMoby message as an Element
- * @return true if the message contains multiple invocations, false
- * otherwise.
- * @throws MobyException
- * if the message is null
- */
- public static boolean isMultipleInvocationMessage(Element message)
- throws MobyException {
- if (message == null)
- throw new MobyException(
- newline
- + "null 'xml' found where it was not expected in isMultipleInvocationMessage(Element message).");
- Element e = (Element) message.clone();
- List list = new ArrayList();
- listChildren(e, "mobyData", list);
- if (list != null)
- if (list.size() > 1)
- return true;
- return false;
- }
-
- /**
- *
- * @param element
- * the element to extract the list of simples from. This method
- * assumes that you are passing in a single invokation and that
- * you wish to extract the Simples not contained in any
- * collections. This method also maintains any past queryIDs.
- * @return an array of elements that are fully 'wrapped' simples.
- * @throws MobyException
- * if the Element isnt structurally valid in terms of Moby
- * message structure
- */
- public static Element[] getListOfSimples(Element element)
- throws MobyException {
- Element temp = (Element) element.clone();
- Element e = (Element) element.clone();
- String queryID = "";
-
- if (isMultipleInvocationMessage(element))
- return new Element[] {};
-
- Element serviceNotes = getServiceNotes(e);
-
- // if the current elements name isnt MOBY, see if its direct child is
- if (!e.getName().equals("MOBY")) {
- if (e.getChild("MOBY") != null)
- temp = e.getChild("MOBY");
- else if (e.getChild("MOBY", MOBY_NS) != null)
- temp = e.getChild("MOBY", MOBY_NS);
- else
- throw new MobyException(newline
- + "Expected 'MOBY' as the local name for the element "
- + newline + "and instead received '" + e.getName()
- + "' (getListOfSimples(Element element).");
- }
- // parse the mobyContent node
- if (temp.getChild("mobyContent") != null)
- temp = temp.getChild("mobyContent");
- else if (temp.getChild("mobyContent", MOBY_NS) != null)
- temp = temp.getChild("mobyContent", MOBY_NS);
- else
- throw new MobyException(
- newline
- + "Expected 'mobyContent' as the local name for the next child element but it "
- + newline
- + "wasn't there. I even tried a qualified name (getListOfSimples(Element element).");
-
- // parse the mobyData node
- if (temp.getChild("mobyData") != null) {
- temp = temp.getChild("mobyData");
- } else if (temp.getChild("mobyData", MOBY_NS) != null) {
- temp = temp.getChild("mobyData", MOBY_NS);
- } else {
- throw new MobyException(
- newline
- + "Expected 'mobyData' as the local name for the next child element but it "
- + newline
- + "wasn't there. I even tried a qualified name (getListOfSimples(Element element).");
- }
-
- // temp == mobyData now we need to get the queryID and save it
- if (temp.getAttribute("queryID") != null) {
- queryID = temp.getAttribute("queryID").getValue();
- } else if (temp.getAttribute("queryID", MOBY_NS) != null) {
- queryID = temp.getAttribute("queryID", MOBY_NS).getValue();
- } else {
- // create a new one -> shouldnt happen very often
- queryID = "a" + queryCount++;
- }
-
- // now we iterate through all of the direct children called Simple, wrap
- // them individually and set the queryID = queryID
- List list = temp.getChildren("Simple", MOBY_NS);
- if (list.isEmpty()) {
- list = temp.getChildren("Simple");
- if (list.isEmpty()) {
- return new Element[] {};
- }
- }
- // non empty list
- Element[] elements = new Element[list.size()];
- int index = 0;
- for (Iterator it = list.iterator(); it.hasNext();) {
- Element next = (Element) it.next();
- elements[index++] = createMobyDataElementWrapper(next, queryID,
- serviceNotes);
- }
- return elements;
- }
-
- /**
- *
- * @param message
- * the String of xml to extract the list of simples from. This
- * method assumes that you are passing in a single invokation and
- * that you wish to extract the Simples not contained in any
- * collections. This method also maintains any past queryIDs.
- * @return an array of Strings that represent fully 'wrapped' simples.
- * @throws MobyException
- * if the String doesnt contain a structurally valid Moby
- * message structure or if an unexpected error occurs
- */
- public static String[] getListOfSimples(String message)
- throws MobyException {
- Element element = getDOMDocument(message).getRootElement();
- Element[] elements = getListOfSimples(element);
- String[] strings = new String[elements.length];
- XMLOutputter outputter = new XMLOutputter(Format.getPrettyFormat()
- .setOmitDeclaration(false));
- for (int count = 0; count < elements.length; count++) {
- try {
- strings[count] = outputter.outputString(elements[count]);
- } catch (Exception e) {
- throw new MobyException(newline
- + "Unexpected error occured while creating String[]:"
- + newline + Utils.format(e.getLocalizedMessage(), 3));
- }
- }
- return strings;
- }
-
- /**
- *
- * @param message
- * the String to extract the list of collections from and assumes
- * that you are passing in a single invocation message.
- * @return an array of Strings representing all of the fully 'wrapped'
- * collections in the message.
- * @throws MobyException
- * if the the element contains an invalid BioMOBY message
- */
- public static String[] getListOfCollections(String message)
- throws MobyException {
- Element element = getDOMDocument(message).getRootElement();
- Element[] elements = getListOfCollections(element);
- String[] strings = new String[elements.length];
- XMLOutputter outputter = new XMLOutputter(Format.getPrettyFormat()
- .setOmitDeclaration(false));
- for (int count = 0; count < elements.length; count++) {
- try {
- strings[count] = outputter.outputString(elements[count]);
- } catch (Exception e) {
- throw new MobyException(newline
- + "Unexpected error occured while creating String[]:"
- + newline + Utils.format(e.getLocalizedMessage(), 3));
- }
- }
- return strings;
- }
-
- /**
- *
- * @param element
- * the element to extract the list of collections from and
- * assumes that you are passing in a single invocation message.
- * @return an array of Elements representing all of the fully 'wrapped'
- * collections in the message
- * @throws MobyException
- * if the element contains an invalid BioMOBY message
- */
- public static Element[] getListOfCollections(Element element)
- throws MobyException {
- Element temp = (Element) element.clone();
- Element e = (Element) element.clone();
- String queryID = "";
-
- if (isMultipleInvocationMessage(e))
- return new Element[] {};
-
- Element serviceNotes = getServiceNotes(e);
-
- // if the current elements name isnt MOBY, see if its direct child is
- if (!e.getName().equals("MOBY")) {
- if (e.getChild("MOBY") != null)
- temp = e.getChild("MOBY");
- else if (e.getChild("MOBY", MOBY_NS) != null)
- temp = e.getChild("MOBY", MOBY_NS);
- else
- throw new MobyException(newline
- + "Expected 'MOBY' as the local name for the element "
- + newline + "and instead received '" + e.getName()
- + "' (getListOfCollections(Element element).");
- }
- // parse the mobyContent node
- if (temp.getChild("mobyContent") != null)
- temp = temp.getChild("mobyContent");
- else if (temp.getChild("mobyContent", MOBY_NS) != null)
- temp = temp.getChild("mobyContent", MOBY_NS);
- else
- throw new MobyException(
- newline
- + "Expected 'mobyContent' as the local name for the next child element but it "
- + newline
- + "wasn't there. I even tried a qualified name (getListOfCollections(Element element).");
-
- // parse the mobyData node
- if (temp.getChild("mobyData") != null) {
- temp = temp.getChild("mobyData");
- } else if (temp.getChild("mobyData", MOBY_NS) != null) {
- temp = temp.getChild("mobyData", MOBY_NS);
- } else {
- throw new MobyException(
- newline
- + "Expected 'mobyData' as the local name for the next child element but it "
- + newline
- + "wasn't there. I even tried a qualified name (getListOfCollections(Element element).");
- }
-
- // temp == mobyData now we need to get the queryID and save it
- if (temp.getAttribute("queryID") != null) {
- queryID = temp.getAttribute("queryID").getValue();
- } else if (temp.getAttribute("queryID", MOBY_NS) != null) {
- queryID = temp.getAttribute("queryID", MOBY_NS).getValue();
- } else {
- // create a new one -> shouldnt happen very often
- queryID = "a" + queryCount++;
- }
-
- // now we iterate through all of the direct children called Simple, wrap
- // them individually and set the queryID = queryID
- List list = temp.getChildren("Collection", MOBY_NS);
- if (list.isEmpty()) {
- list = temp.getChildren("Collection");
- if (list.isEmpty()) {
- return new Element[] {};
- }
- }
- // non empty list
- Element[] elements = new Element[list.size()];
- int index = 0;
- for (Iterator it = list.iterator(); it.hasNext();) {
- Element next = (Element) it.next();
- elements[index++] = createMobyDataElementWrapper(next, queryID,
- serviceNotes);
- }
- return elements;
- }
-
- /**
- * This method assumes a single invocation was passed to it
- * <p>
- *
- * @param name
- * the article name of the simple that you are looking for
- * @param xml
- * the xml that you want to query
- * @return a String object that represent the simple found.
- * @throws MobyException
- * if no simple was found given the article name and/or data
- * type or if the xml was not valid moby xml or if an unexpected
- * error occurs.
- */
- public static String getSimple(String name, String xml)
- throws MobyException {
- Element element = getDOMDocument(xml).getRootElement();
- XMLOutputter outputter = new XMLOutputter(Format.getPrettyFormat()
- .setOmitDeclaration(false));
- Element simples = getSimple(name, element);
- if (simples != null) {
- try {
- return outputter.outputString(simples);
- } catch (Exception e) {
- throw new MobyException(newline
- + "Unexpected error occured while creating String[]:"
- + newline + Utils.format(e.getLocalizedMessage(), 3));
- }
- }
- throw new MobyException(newline + "The simple named '" + name
- + "' was not found in the xml:" + newline + xml + newline);
- }
-
- /**
- * This method assumes a single invocation was passed to it
- * <p>
- *
- * @param name
- * the article name of the simple that you are looking for
- * @param element
- * the Element that you want to query
- * @return an Element that represents the simple found.
- * @throws MobyException
- * if no simple was found given the article name and/or data
- * type or if the xml was not valid moby xml or if an unexpected
- * error occurs.
- */
- public static Element getSimple(String name, Element element)
- throws MobyException {
- Element el = (Element) element.clone();
- Element[] elements = getListOfSimples(el);
- // try matching based on type(less impt) and/or article name (more impt)
- for (int i = 0; i < elements.length; i++) {
- // PRE: elements[i] is a fully wrapped element
- Element e = elements[i];
- if (e.getChild("mobyContent") != null) {
- e = e.getChild("mobyContent");
- } else if (e.getChild("mobyContent", MOBY_NS) != null) {
- e = e.getChild("mobyContent", MOBY_NS);
- } else {
- throw new MobyException(
- newline
- + "Expected 'mobyContent' as the local name for the next child element but it "
- + newline
- + "wasn't there. I even tried a qualified name (getSimple(String name, "
- + "Element element).");
- }
- if (e.getChild("mobyData") != null) {
- e = e.getChild("mobyData");
- } else if (e.getChild("mobyData", MOBY_NS) != null) {
- e = e.getChild("mobyData", MOBY_NS);
- } else {
- throw new MobyException(
- newline
- + "Expected 'mobyData' as the local name for the next child element but it "
- + newline
- + "wasn't there. I even tried a qualified name (getSimple(String name,"
- + " Element element).");
- }
- if (e.getChild("Simple") != null) {
- e = e.getChild("Simple");
- } else if (e.getChild("Simple", MOBY_NS) != null) {
- e = e.getChild("Simple", MOBY_NS);
- } else {
- throw new MobyException(
- newline
- + "Expected 'Simple' as the local name for the next child element but it "
- + newline
- + "wasn't there. I even tried a qualified name (getSimple(String name,"
- + " Element element).");
- }
- // e == Simple -> check its name as long as name != ""
- if (!name.equals(""))
- if (e.getAttributeValue("articleName") != null) {
- String value = e.getAttributeValue("articleName");
- if (value.equals(name)) {
- return e;
- }
- } else if (e.getAttributeValue("articleName", MOBY_NS) != null) {
- String value = e.getAttributeValue("articleName", MOBY_NS);
- if (value.equals(name)) {
- return e;
- }
- }
-
- }
- throw new MobyException(newline
- + "The simple named '"
- + name
- + "' was not found in the xml:"
- + newline
- + (new XMLOutputter(Format.getPrettyFormat()
- .setOmitDeclaration(false))).outputString(element)
- + newline);
- }
-
- /**
- *
- * @param xml
- * a string of xml containing a single invocation message to
- * extract the queryID from
- * @return the queryID contained in the xml or a generated one if one doesnt
- * exist
- * @throws MobyException
- * if the String of xml is invalid or if the message is a
- * multiple invocation message
- */
- public static String getQueryID(String xml) throws MobyException {
- return getQueryID(getDOMDocument(xml).getRootElement());
- }
-
- /**
- *
- * @param xml
- * a single invocation message to extract the queryID from
- * @return the queryID contained in the xml or a generated one if one doesnt
- * exist
- * @throws if
- * the message is a multiple invocation message
- */
- public static String getQueryID(Element xml) throws MobyException {
- Element temp = (Element) xml.clone();
- Element e = (Element) xml.clone();
-
- if (isMultipleInvocationMessage(e))
- throw new MobyException(
- "Unable to retrieve the queryID from the BioMOBY message because a message with greater than one IDs exists.");
-
- if (!e.getName().equals("MOBY")) {
- if (e.getChild("MOBY") != null)
- temp = e.getChild("MOBY");
- else if (e.getChild("MOBY", MOBY_NS) != null)
- temp = e.getChild("MOBY", MOBY_NS);
- }
- // parse the mobyContent node
- if (temp.getChild("mobyContent") != null)
- temp = temp.getChild("mobyContent");
- else if (temp.getChild("mobyContent", MOBY_NS) != null)
- temp = temp.getChild("mobyContent", MOBY_NS);
-
- // parse the mobyData node
- if (temp.getChild("mobyData") != null) {
- temp = temp.getChild("mobyData");
- } else if (temp.getChild("mobyData", MOBY_NS) != null) {
- temp = temp.getChild("mobyData", MOBY_NS);
- }
-
- // temp == mobyData now we need to get the queryID and save it
- if (temp.getAttribute("queryID") != null) {
- return temp.getAttribute("queryID").getValue();
- } else if (temp.getAttribute("queryID", MOBY_NS) != null) {
- return temp.getAttribute("queryID", MOBY_NS).getValue();
- } else {
- // create a new one -> shouldnt happen very often
- return "a" + queryCount++;
- }
- }
-
- /**
- *
- * @param xml
- * a string of xml containing a single invocation message to
- * extract the queryID from
- * @return the element passed in to the method with the queryID set if the
- * message was valid.
- * @throws MobyException
- * if the String of xml is syntatically invalid or if the
- * message is a multiple invocation message
- */
- public static String setQueryID(String xml, String id) throws MobyException {
- return new XMLOutputter(Format.getPrettyFormat().setOmitDeclaration(
- false)).outputString(setQueryID(getDOMDocument(xml)
- .getRootElement(), id));
- }
-
- /**
- *
- * @param xml
- * a single invocation message to extract the queryID from
- * @return the element passed in to the method with the queryID set if the
- * message was valid.
- * @throws MobyException
- * if the message is a multiple invocation message
- */
- public static Element setQueryID(Element xml, String id)
- throws MobyException {
- Element e = (Element) xml.clone();
- Element temp = e;
- if (isMultipleInvocationMessage(e))
- throw new MobyException(
- "Unable to set the queryID, because there are more than one queryID to set!");
- if (!e.getName().equals("MOBY")) {
- if (e.getChild("MOBY") != null)
- temp = e.getChild("MOBY");
- else if (e.getChild("MOBY", MOBY_NS) != null)
- temp = e.getChild("MOBY", MOBY_NS);
- }
- // parse the mobyContent node
- if (temp.getChild("mobyContent") != null)
- temp = temp.getChild("mobyContent");
- else if (temp.getChild("mobyContent", MOBY_NS) != null)
- temp = temp.getChild("mobyContent", MOBY_NS);
-
- // parse the mobyData node
- if (temp.getChild("mobyData") != null) {
- temp = temp.getChild("mobyData");
- } else if (temp.getChild("mobyData", MOBY_NS) != null) {
- temp = temp.getChild("mobyData", MOBY_NS);
- }
-
- temp.removeAttribute("queryID");
- temp.removeAttribute("queryID", MOBY_NS);
- temp.setAttribute("queryID", (id == null || id == "" ? "a"
- + queryCount++ : id), MOBY_NS);
- return e;
- }
-
- /**
- *
- * @param name
- * the articlename of the simple that you wish to extract
- * @param xml
- * the xml message
- * @return the wrapped simple if it exists
- * @throws MobyException
- * if the message is a multiple invocation message or if the xml
- * is syntatically invalid.
- */
- public static String getWrappedSimple(String name, String xml)
- throws MobyException {
- Element element = getWrappedSimple(name, getDOMDocument(xml)
- .getRootElement());
- XMLOutputter outputter = new XMLOutputter(Format.getPrettyFormat()
- .setOmitDeclaration(false));
- return outputter.outputString(element);
- }
-
- /**
- *
- * @param name
- * the articlename of the simple that you wish to extract
- * @param xml
- * the xml message
- * @return the wrapped simple if it exists
- * @throws MobyException
- * if the message is a multiple invocation message.
- */
- public static Element getWrappedSimple(String name, Element element)
- throws MobyException {
- Element e = (Element) element.clone();
- String queryID = getQueryID(e);
- Element serviceNotes = getServiceNotes(e);
- Element simple = getSimple(name, e);
- return createMobyDataElementWrapper(simple, queryID, serviceNotes);
- }
-
- /**
- *
- * @param name
- * the name of the collection to extract
- * @param element
- * the element to extract the collection from
- * @return the collection if found
- * @throws MobyException
- * if the message is invalid
- */
- public static Element getCollection(String name, Element element)
- throws MobyException {
- Element el = (Element) element.clone();
- Element[] elements = getListOfCollections(el);
- for (int i = 0; i < elements.length; i++) {
- // PRE: elements[i] is a fully wrapped element
- Element e = elements[i];
- if (e.getChild("mobyContent") != null) {
- e = e.getChild("mobyContent");
- } else if (e.getChild("mobyContent", MOBY_NS) != null) {
- e = e.getChild("mobyContent", MOBY_NS);
- } else {
- throw new MobyException(
- newline
- + "Expected 'mobyContent' as the local name for the next child element but it "
- + newline
- + "wasn't there. I even tried a qualified name (getCollection(String name, "
- + "Element element).");
- }
- if (e.getChild("mobyData") != null) {
- e = e.getChild("mobyData");
- } else if (e.getChild("mobyData", MOBY_NS) != null) {
- e = e.getChild("mobyData", MOBY_NS);
- } else {
- throw new MobyException(
- newline
- + "Expected 'mobyData' as the local name for the next child element but it "
- + newline
- + "wasn't there. I even tried a qualified name (getCollection(String name,"
- + " Element element).");
- }
- if (e.getChild("Collection") != null) {
- e = e.getChild("Collection");
- } else if (e.getChild("Collection", MOBY_NS) != null) {
- e = e.getChild("Collection", MOBY_NS);
- } else {
- // TODO should i throw exception or continue?
- throw new MobyException(
- newline
- + "Expected 'Collection' as the local name for the next child element but it "
- + newline
- + "wasn't there. I even tried a qualified name (getCollection(String name,"
- + " Element element).");
- }
- // e == collection -> check its name
- if (e.getAttributeValue("articleName") != null) {
- String value = e.getAttributeValue("articleName");
- if (value.equals(name)) {
- return e;
- }
- } else if (e.getAttributeValue("articleName", MOBY_NS) != null) {
- String value = e.getAttributeValue("articleName", MOBY_NS);
- if (value.equals(name)) {
- return e;
- }
- }
- if (elements.length == 1) {
- if (e.getAttributeValue("articleName") != null) {
- String value = e.getAttributeValue("articleName");
- if (value.equals("")) {
- // rename it to make it compatible with moby
- e.setAttribute("articleName", name, MOBY_NS);
- return e;
- }
- } else if (e.getAttributeValue("articleName", MOBY_NS) != null) {
- String value = e.getAttributeValue("articleName", MOBY_NS);
- if (value.equals("")) {
- // rename it to make it compatible with moby
- e.setAttribute("articleName", name, MOBY_NS);
- return e;
- }
- }
- }
- // name didnt match, so too bad ;-)
- }
- throw new MobyException(
- newline
- + "The Collection named '"
- + name
- + "' was not found in the xml:"
- + newline
- + (new XMLOutputter(Format.getPrettyFormat()
- .setOmitDeclaration(false)))
- .outputString(element)
- + newline
- + "Note: A collection of that may exist, but may be contained in a multiple invocation message.");
- }
-
- /**
- *
- * @param name
- * @param xml
- * @return
- * @throws MobyException
- */
- public static String getCollection(String name, String xml)
- throws MobyException {
- Element element = getDOMDocument(xml).getRootElement();
- XMLOutputter outputter = new XMLOutputter(Format.getPrettyFormat()
- .setOmitDeclaration(false));
- Element collection = getCollection(name, element);
- if (collection != null)
- return outputter.outputString(collection);
- return null;
- }
-
- /**
- *
- * @param name
- * @param element
- * @return
- * @throws MobyException
- */
- public static Element getWrappedCollection(String name, Element element)
- throws MobyException {
- Element e = (Element) element.clone();
- String queryID = getQueryID(e);
- Element collection = getCollection(name, e);
- Element serviceNotes = getServiceNotes(e);
- return createMobyDataElementWrapper(collection, queryID, serviceNotes);
- }
-
- /**
- *
- * @param name
- * @param xml
- * @return
- * @throws MobyException
- */
- public static String getWrappedCollection(String name, String xml)
- throws MobyException {
- Element element = getWrappedCollection(name, getDOMDocument(xml)
- .getRootElement());
- XMLOutputter outputter = new XMLOutputter(Format.getPrettyFormat()
- .setOmitDeclaration(false));
- return outputter.outputString(element);
- }
-
- /**
- *
- * @param name
- * the name of the collection to extract the simples from.
- * @param xml
- * the XML to extract from
- * @return an array of String objects that represent the simples
- * @throws MobyException
- */
- public static String[] getSimplesFromCollection(String name, String xml)
- throws MobyException {
- Element[] elements = getSimplesFromCollection(name, getDOMDocument(xml)
- .getRootElement());
- String[] strings = new String[elements.length];
- XMLOutputter output = new XMLOutputter(Format.getPrettyFormat()
- .setOmitDeclaration(false));
- for (int i = 0; i < elements.length; i++) {
- try {
- strings[i] = output.outputString(elements[i]);
- } catch (Exception e) {
- throw new MobyException(newline
- + "Unknown error occured while creating String[]."
- + newline + Utils.format(e.getLocalizedMessage(), 3));
- }
- }
- return strings;
- }
-
- /**
- *
- * @param name
- * the name of the collection to extract the simples from.
- * @param element
- * the Element to extract from
- * @return an array of Elements objects that represent the simples
- * @throws MobyException
- */
- public static Element[] getSimplesFromCollection(String name,
- Element element) throws MobyException {
- Element e = (Element) element.clone();
- // exception thrown if not found
- Element collection = getCollection(name, e);
-
- List list = collection.getChildren("Simple");
- if (list.isEmpty())
- list = collection.getChildren("Simple", MOBY_NS);
- if (list.isEmpty())
- return new Element[] {};
- Vector vector = new Vector();
- for (Iterator it = list.iterator(); it.hasNext();) {
- Object o = it.next();
- if (o instanceof Element) {
- ((Element) o).setAttribute("articleName", name, MOBY_NS);
- if (((Element) o).getChildren().size() > 0)
- vector.add(o);
- }
-
- }
- Element[] elements = new Element[vector.size()];
- vector.copyInto(elements);
- return elements;
- }
-
- /**
- *
- * @param name
- * the name of the simples that you would like to extract. The
- * name can be collection name as well. This method extracts
- * simples from all invocation messages.
- * @param xml
- * the xml to extract the simples from
- * @return a String[] of Simples that you are looking for, taken from
- * collections with your search name as well as simple elements with
- * the search name
- * @throws MobyException
- * if there is a problem with the BioMOBY message
- */
- public static String[] getAllSimplesByArticleName(String name, String xml)
- throws MobyException {
- Element[] elements = getAllSimplesByArticleName(name, getDOMDocument(
- xml).getRootElement());
- String[] strings = new String[elements.length];
- XMLOutputter output = new XMLOutputter(Format.getPrettyFormat()
- .setOmitDeclaration(false));
- for (int i = 0; i < elements.length; i++) {
- try {
- strings[i] = output.outputString(elements[i]);
- } catch (Exception e) {
- throw new MobyException(newline
- + "Unknown error occured while creating String[]."
- + newline + Utils.format(e.getLocalizedMessage(), 3));
- }
- }
- return strings;
- }
-
- /**
- *
- * @param name
- * the name of the simples that you would like to extract. The
- * name can be collection name as well. This method extracts
- * simples from all invocation messages.
- * @param element
- * the xml to extract the simples from
- * @return a String[] of Simples that you are looking for, taken from
- * collections with your search name as well as simple elements with
- * the search name
- * @throws MobyException
- * if there is a problem with the BioMOBY message
- */
- public static Element[] getAllSimplesByArticleName(String name,
- Element element) throws MobyException {
- Element e = (Element) element.clone();
- Element[] invocations = getSingleInvokationsFromMultipleInvokations(e);
- Vector vector = new Vector();
- for (int i = 0; i < invocations.length; i++) {
- Element collection = null;
- try {
- collection = getCollection(name, invocations[i]);
- } catch (MobyException me) {
-
- }
- if (collection != null) {
- List list = collection.getChildren("Simple");
- if (list.isEmpty())
- list = collection.getChildren("Simple", MOBY_NS);
- if (list.isEmpty())
- return new Element[] {};
- for (Iterator it = list.iterator(); it.hasNext();) {
- Object o = it.next();
- if (o instanceof Element) {
- ((Element) o)
- .setAttribute("articleName", name, MOBY_NS);
- }
- vector.add(o);
- }
- }
- collection = null;
-
- Element[] potentialSimples = getListOfSimples(invocations[i]);
- for (int j = 0; j < potentialSimples.length; j++) {
- Element mobyData = extractMobyData(potentialSimples[j]);
- Element simple = mobyData.getChild("Simple");
- if (simple == null)
- simple = mobyData.getChild("Simple", MOBY_NS);
- if (simple != null) {
- if (simple.getAttribute("articleName") != null) {
- if (simple.getAttribute("articleName").getValue()
- .equals(name))
- vector.add(simple);
- } else if (simple.getAttribute("articleName", MOBY_NS) != null) {
- if (simple.getAttribute("articleName", MOBY_NS)
- .getValue().equals(name))
- vector.add(simple);
- }
- }
-
- }
- }
-
- Element[] elements = new Element[vector.size()];
- vector.copyInto(elements);
- return elements;
- }
-
- /**
- *
- * @param xml
- * the XML to extract from
- * @return an array of String objects that represent the simples
- * @throws MobyException
- */
- public static String[] getSimplesFromCollection(String xml)
- throws MobyException {
- Element[] elements = getSimplesFromCollection(getDOMDocument(xml)
- .getRootElement());
- String[] strings = new String[elements.length];
- XMLOutputter output = new XMLOutputter(Format.getPrettyFormat()
- .setOmitDeclaration(false));
- for (int i = 0; i < elements.length; i++) {
- try {
- strings[i] = output.outputString(elements[i]);
- } catch (Exception e) {
- throw new MobyException(newline
- + "Unknown error occured while creating String[]."
- + newline + Utils.format(e.getLocalizedMessage(), 3));
- }
- }
- return strings;
- }
-
- /**
- *
- * @param name
- * the name of the collection to extract the simples from.
- * @param element
- * the Element to extract from
- * @return an array of Elements objects that represent the 'unwrapped'
- * simples
- * @throws MobyException
- */
- public static Element[] getSimplesFromCollection(Element element)
- throws MobyException {
- Element e = (Element) element.clone();
- Element mobyData = extractMobyData(e);
-
- Element collection = mobyData.getChild("Collection");
- if (collection == null)
- collection = mobyData.getChild("Collection", MOBY_NS);
-
- List list = collection.getChildren("Simple");
- if (list.isEmpty())
- list = collection.getChildren("Simple", MOBY_NS);
- if (list.isEmpty())
- return new Element[] {};
- Vector vector = new Vector();
- for (Iterator it = list.iterator(); it.hasNext();) {
- vector.add(it.next());
- }
- Element[] elements = new Element[vector.size()];
- vector.copyInto(elements);
- return elements;
- }
-
- /**
- *
- * @param name
- * the name of the collection to extract the simples from.
- * @param xml
- * the XML to extract from
- * @return an array of String objects that represent the simples, with the
- * name of the collection
- * @throws MobyException
- * if the collection doesnt exist or the xml is invalid
- */
- public static String[] getWrappedSimplesFromCollection(String name,
- String xml) throws MobyException {
- Element[] elements = getWrappedSimplesFromCollection(name,
- getDOMDocument(xml).getRootElement());
- String[] strings = new String[elements.length];
- XMLOutputter output = new XMLOutputter(Format.getPrettyFormat()
- .setOmitDeclaration(false));
- for (int i = 0; i < elements.length; i++) {
- try {
- strings[i] = output.outputString(elements[i]);
- } catch (Exception e) {
- throw new MobyException(newline
- + "Unknown error occured while creating String[]."
- + newline + Utils.format(e.getLocalizedMessage(), 3));
- }
- }
- return strings;
- }
-
- /**
- *
- * @param name
- * the name of the collection to extract the simples from.
- * @param element
- * the Element to extract from
- * @return an array of Elements objects that represent the simples, with the
- * name of the collection
- * @throws MobyException
- * MobyException if the collection doesnt exist or the xml is
- * invalid
- */
- public static Element[] getWrappedSimplesFromCollection(String name,
- Element element) throws MobyException {
- Element el = (Element) element.clone();
- String queryID = getQueryID(el);
- Element collection = getCollection(name, el);
- Element serviceNotes = getServiceNotes(el);
- List list = collection.getChildren("Simple");
- if (list.isEmpty())
- list = collection.getChildren("Simple", MOBY_NS);
- if (list.isEmpty())
- return new Element[] {};
- Vector vector = new Vector();
- for (Iterator it = list.iterator(); it.hasNext();) {
- Element e = (Element) it.next();
- e.setAttribute("articleName", name, MOBY_NS);
- e = createMobyDataElementWrapper(e, queryID + "_split"
- + queryCount++, serviceNotes);
- vector.add(e);
- }
- Element[] elements = new Element[vector.size()];
- vector.copyInto(elements);
- return elements;
- }
-
- /**
- *
- * @param xml
- * the message to extract the invocation messages from
- * @return an array of String objects each representing a distinct BioMOBY
- * invocation message.
- * @throws MobyException
- * if the moby message is invalid or if the xml is syntatically
- * invalid.
- */
- public static String[] getSingleInvokationsFromMultipleInvokations(
- String xml) throws MobyException {
- Element[] elements = getSingleInvokationsFromMultipleInvokations(getDOMDocument(
- xml).getRootElement());
- String[] strings = new String[elements.length];
- XMLOutputter output = new XMLOutputter(Format.getPrettyFormat()
- .setOmitDeclaration(false));
-
- for (int i = 0; i < elements.length; i++) {
- strings[i] = output.outputString(new Document(elements[i]));
- }
- return strings;
- }
-
- /**
- *
- * @param element
- * the message to extract the invocation messages from
- * @return an array of Element objects each representing a distinct
- * invocation message.
- * @throws MobyException
- * if the moby message is invalid.
- */
- public static Element[] getSingleInvokationsFromMultipleInvokations(
- Element element) throws MobyException {
- Element e = (Element) element.clone();
- Element serviceNotes = getServiceNotes(e);
- if (e.getChild("MOBY") != null) {
- e = e.getChild("MOBY");
- } else if (e.getChild("MOBY", MOBY_NS) != null) {
- e = e.getChild("MOBY", MOBY_NS);
- }
-
- if (e.getChild("mobyContent") != null) {
- e = e.getChild("mobyContent");
- } else if (e.getChild("mobyContent", MOBY_NS) != null) {
- e = e.getChild("mobyContent", MOBY_NS);
- } else {
- throw new MobyException(
- newline
- + "Expected a child element called 'mobyContent' and did not receive it in:"
- + newline
- + new XMLOutputter(Format.getPrettyFormat()
- .setOmitDeclaration(false)).outputString(e));
- }
- List invocations = e.getChildren("mobyData");
- if (invocations.isEmpty())
- invocations = e.getChildren("mobyData", MOBY_NS);
- Element[] elements = new Element[] {};
- ArrayList theData = new ArrayList();
- for (Iterator it = invocations.iterator(); it.hasNext();) {
- Element MOBY = new Element("MOBY", MOBY_NS);
- Element mobyContent = new Element("mobyContent", MOBY_NS);
- if (serviceNotes != null)
- mobyContent.addContent(serviceNotes.detach());
- Element mobyData = new Element("mobyData", MOBY_NS);
- Element next = (Element) it.next();
- String queryID = next.getAttributeValue("queryID", MOBY_NS);
- if (queryID == null)
- queryID = next.getAttributeValue("queryID");
-
- mobyData.setAttribute("queryID", (queryID == null ? "a"+queryCount++ : queryID), MOBY_NS);
- mobyData.addContent(next.cloneContent());
- MOBY.addContent(mobyContent);
- mobyContent.addContent(mobyData);
- if (next.getChildren().size() > 0)
- theData.add(MOBY);
- }
- elements = new Element[theData.size()];
- elements = (Element[]) theData.toArray(elements);
- return elements;
- }
-
- /**
- *
- * @param document
- * the string to create a DOM document from
- * @return a Document object that represents the string of XML.
- * @throws MobyException
- * if the xml is invalid syntatically.
- */
- public static Document getDOMDocument(String document) throws MobyException {
- if (document == null)
- throw new MobyException(newline
- + "null found where an XML document was expected.");
- SAXBuilder builder = new SAXBuilder();
- // Create the document
- Document doc = null;
- try {
- doc = builder.build(new StringReader(document));
- } catch (JDOMException e) {
- throw new MobyException(newline + "Error parsing XML:->" + newline
- + document + newline
- + Utils.format(e.getLocalizedMessage(), 3) + ".");
- } catch (IOException e) {
- throw new MobyException(newline + "Error parsing XML:->" + newline
- + Utils.format(e.getLocalizedMessage(), 3) + ".");
- } catch (Exception e) {
- throw new MobyException(newline + "Error parsing XML:->" + newline
- + Utils.format(e.getLocalizedMessage(), 3) + ".");
- }
- return doc;
- }
-
- /**
- *
- * @param elements
- * the fully wrapped moby simples and/or collections to wrap an
- * input message around
- * @param queryID
- * the queryID for this input
- * @return a fully wrapped message with an appropriate queryID and elements
- * added to it
- * @throws MobyException
- * if an element is invalid or if the XML is syntatically
- * invalid.
- */
- public static String createServiceInput(String[] elements, String queryID)
- throws MobyException {
- Element[] element = new Element[elements.length];
- for (int i = 0; i < elements.length; i++) {
- element[i] = getDOMDocument(elements[i]).getRootElement();
- }
- XMLOutputter output = new XMLOutputter(Format.getPrettyFormat()
- .setOmitDeclaration(false));
- return output.outputString(createServiceInput(element, queryID));
- }
-
- /**
- *
- * @param elements
- * the fully wrapped moby simples and/or collections to wrap an
- * input message around
- * @param queryID
- * the queryID for this input
- * @return a fully wrapped message with an appropriate queryID and elements
- * added to it
- * @throws MobyException
- * if an element is invalid.
- */
- public static Element createServiceInput(Element[] elements, String queryID)
- throws MobyException {
- // create the main elements
- Element MOBY = new Element("MOBY", MOBY_NS);
- Element mobyContent = new Element("mobyContent", MOBY_NS);
- Element mobyData = new Element("mobyData", MOBY_NS);
- mobyData.setAttribute("queryID", (queryID == null ? "" : queryID),
- MOBY_NS);
-
- // add the content
- MOBY.addContent(mobyContent);
- mobyContent.addContent(mobyData);
-
- // iterate through elements adding the content of mobyData
- for (int i = 0; i < elements.length; i++) {
- Element e = (Element) elements[i].clone();
- e = extractMobyData(e);
- mobyData.addContent(e.cloneContent());
- }
-
- return MOBY;
- }
-
- /**
- * @param element
- * the element that contains the moby message that you would like
- * to extract the mobyData block from (assumes single invocation,
- * but returns the first mobyData block in a multiple invocation
- * message).
- * @return the mobyData element block.
- * @throws MobyException
- * if the moby message is invalid
- */
- public static Element extractMobyData(Element element) throws MobyException {
- Element e = (Element) element.clone();
- if (e.getChild("MOBY") != null) {
- e = e.getChild("MOBY");
- } else if (e.getChild("MOBY", MOBY_NS) != null) {
- e = e.getChild("MOBY", MOBY_NS);
- }
-
- if (e.getChild("mobyContent") != null) {
- e = e.getChild("mobyContent");
- } else if (e.getChild("mobyContent", MOBY_NS) != null) {
- e = e.getChild("mobyContent", MOBY_NS);
- } else {
- throw new MobyException(
- newline
- + "Expected the child element 'mobyContent' and did not receive it in:"
- + newline
- + new XMLOutputter(Format.getPrettyFormat()
- .setOmitDeclaration(false)).outputString(e));
- }
-
- if (e.getChild("mobyData") != null) {
- e = e.getChild("mobyData");
- } else if (e.getChild("mobyData", MOBY_NS) != null) {
- e = e.getChild("mobyData", MOBY_NS);
- } else {
- throw new MobyException(
- newline
- + "Expected the child element 'mobyData' and did not receive it in:"
- + newline
- + new XMLOutputter(Format.getPrettyFormat()
- .setOmitDeclaration(false)).outputString(e));
- }
- return e;
- }
-
- /**
- *
- * @param newName
- * the new name for this fully wrapped BioMOBY collection
- * @param element
- * the fully wrapped BioMOBY collection
- * @return @return an element 'Collection' representing the renamed collection
- * @throws MobyException
- * if the message is invalid
- */
- public static Element renameCollection(String newName, Element element)
- throws MobyException {
- Element e = (Element) element.clone();
- Element mobyData = extractMobyData(e);
- Element coll = mobyData.getChild("Collection");
- if (coll == null)
- coll = mobyData.getChild("Collection", MOBY_NS);
- if (coll == null)
- return e;
- coll.removeAttribute("articleName");
- coll.removeAttribute("articleName", MOBY_NS);
- coll.setAttribute("articleName", newName, MOBY_NS);
- return coll;
- }
-
- /**
- *
- * @param newName
- * the new name for this fully wrapped BioMOBY collection
- * @param xml
- * the fully wrapped BioMOBY collection
- * @return an element 'Collection' representing the renamed collection
- * @throws MobyException
- * if the BioMOBY message is invalid or the xml is syntatically
- * invalid.
- */
- public static String renameCollection(String newName, String xml)
- throws MobyException {
- return new XMLOutputter(Format.getPrettyFormat().setOmitDeclaration(
- false)).outputString(renameCollection(newName, getDOMDocument(
- xml).getRootElement()));
- }
-
- /**
- *
- * @param oldName
- * @param newName
- * @param type
- * @param xml
- * @return
- * @throws MobyException
- */
- public static String renameSimple(String newName, String type, String xml)
- throws MobyException {
- return new XMLOutputter(Format.getPrettyFormat().setOmitDeclaration(
- false)).outputString(renameSimple(newName, type,
- getDOMDocument(xml).getRootElement()));
- }
-
- /**
- *
- * @param oldName
- * @param newName
- * @param type
- * @param element
- * @return
- * @throws MobyException
- */
- public static Element renameSimple(String newName, String type,
- Element element) throws MobyException {
- Element e = (Element) element.clone();
- Element mobyData = extractMobyData(e);
- String queryID = getQueryID(e);
- Element serviceNotes = getServiceNotes(e);
- Element simple = mobyData.getChild("Simple");
- if (simple == null)
- simple = mobyData.getChild("Simple", MOBY_NS);
- if (simple == null) {
- return e;
- }
- simple.removeAttribute("articleName");
- simple.removeAttribute("articleName", MOBY_NS);
- simple.setAttribute("articleName", newName, MOBY_NS);
- return createMobyDataElementWrapper(simple, queryID, serviceNotes);
- }
-
- /**
- *
- * @return
- * @throws MobyException
- */
- public static Document createDomDocument() throws MobyException {
- Document d = new Document();
- d.setBaseURI(MOBY_NS.getURI());
- return d;
- }
-
- /**
- *
- * @param element
- * @param queryID
- * @param serviceNotes
- * @return
- * @throws MobyException
- */
- public static Element createMobyDataElementWrapper(Element element,
- String queryID, Element serviceNotes) throws MobyException {
- Element e = (Element) element.clone();
- Element MOBY = new Element("MOBY", MOBY_NS);
- Element mobyContent = new Element("mobyContent", MOBY_NS);
- Element mobyData = new Element("mobyData", MOBY_NS);
- mobyData.setAttribute("queryID", queryID, MOBY_NS);
- MOBY.addContent(mobyContent);
- mobyContent.addContent(mobyData);
- // add the serviceNotes if they exist
- if (serviceNotes != null)
- mobyContent.addContent(serviceNotes.detach());
-
- if (e != null) {
- if (e.getName().equals("Simple")) {
- Element simple = new Element("Simple", MOBY_NS);
- simple.setAttribute("articleName", (e
- .getAttributeValue("articleName") == null ? e
- .getAttributeValue("articleName", MOBY_NS, "") : e
- .getAttributeValue("articleName", "")), MOBY_NS);
- simple.addContent(e.cloneContent());
- if (simple.getChildren().size() > 0)
- mobyData.addContent(simple.detach());
- } else if (e.getName().equals("Collection")) {
- Element collection = new Element("Collection", MOBY_NS);
- collection.setAttribute("articleName", (e
- .getAttributeValue("articleName") == null ? e
- .getAttributeValue("articleName", MOBY_NS, "") : e
- .getAttributeValue("articleName", "")), MOBY_NS);
- collection.addContent(e.cloneContent());
- if (collection.getChildren().size() > 0)
- mobyData.addContent(collection.detach());
- }
- }
-
- return MOBY;
- }
-
- public static Element createMobyDataWrapper(String queryID,
- Element serviceNotes) throws MobyException {
-
- Element e = null;
-
- if (serviceNotes != null)
- e = (Element) serviceNotes.clone();
-
- Element MOBY = new Element("MOBY", MOBY_NS);
- Element mobyContent = new Element("mobyContent", MOBY_NS);
- if (e != null)
- mobyContent.addContent(e.detach());
- Element mobyData = new Element("mobyData", MOBY_NS);
- mobyData.setAttribute("queryID", queryID, MOBY_NS);
- MOBY.addContent(mobyContent);
- mobyContent.addContent(mobyData);
- return MOBY;
- }
-
- /**
- *
- * @param xml
- * @return
- * @throws MobyException
- */
- public static String createMobyDataElementWrapper(String xml)
- throws MobyException {
- return createMobyDataElementWrapper(xml, "a" + queryCount++);
- }
-
- /**
- *
- * @param element
- * @return
- * @throws MobyException
- */
- public static Element createMobyDataElementWrapper(Element element)
- throws MobyException {
- Element serviceNotes = getServiceNotes((Element) element.clone());
- return createMobyDataElementWrapper(element, "a" + queryCount++,
- serviceNotes);
- }
-
- /**
- *
- * @param xml
- * @param queryID
- * @return
- * @throws MobyException
- */
- public static String createMobyDataElementWrapper(String xml, String queryID)
- throws MobyException {
- if (xml == null)
- return null;
- Element serviceNotes = getServiceNotes(getDOMDocument(xml)
- .getRootElement());
- Element element = createMobyDataElementWrapper(getDOMDocument(xml)
- .getRootElement(), queryID, serviceNotes);
- XMLOutputter outputter = new XMLOutputter(Format.getPrettyFormat()
- .setOmitDeclaration(false));
- return (element == null ? null : outputter.outputString(element));
- }
-
- public static String createMobyDataElementWrapper(String xml,
- String queryID, Element serviceNotes) throws MobyException {
- if (xml == null)
- return null;
- Element element = createMobyDataElementWrapper(getDOMDocument(xml)
- .getRootElement(), queryID, serviceNotes);
- XMLOutputter outputter = new XMLOutputter(Format.getPrettyFormat()
- .setOmitDeclaration(false));
- return (element == null ? null : outputter.outputString(element));
- }
-
- /**
- *
- * @param elements
- * @return
- * @throws MobyException
- */
- public static Element createMultipleInvokations(Element[] elements)
- throws MobyException {
- Element MOBY = new Element("MOBY", MOBY_NS);
- Element mobyContent = new Element("mobyContent", MOBY_NS);
- Element serviceNotes = null;
- for (int i = 0; i < elements.length; i++) {
- if (serviceNotes == null) {
- serviceNotes = getServiceNotes((Element) elements[i].clone());
- if (serviceNotes != null)
- mobyContent.addContent(serviceNotes.detach());
- }
- Element mobyData = new Element("mobyData", MOBY_NS);
- Element md = extractMobyData((Element) elements[i].clone());
- String queryID = getQueryID((Element) elements[i].clone());
- mobyData.setAttribute("queryID", queryID, MOBY_NS);
- mobyData.addContent(md.cloneContent());
- mobyContent.addContent(mobyData);
- }
- MOBY.addContent(mobyContent);
-
- return MOBY;
- }
-
- /**
- *
- * @param xmls
- * @return
- * @throws MobyException
- */
- public static String createMultipleInvokations(String[] xmls)
- throws MobyException {
- Element[] elements = new Element[xmls.length];
- for (int i = 0; i < elements.length; i++) {
- elements[i] = getDOMDocument(xmls[i]).getRootElement();
- }
- XMLOutputter output = new XMLOutputter(Format.getPrettyFormat()
- .setOmitDeclaration(false));
- return output.outputString(createMultipleInvokations(elements));
- }
-
- /**
- *
- * @param xml
- * a string of xml
- * @return true if the xml contains a full moby message (assumes single
- * invocation, but will return the first mobyData block from a
- * multiple invocation message).
- */
- public static boolean isWrapped(Element element) {
- try {
- extractMobyData((Element) element.clone());
- return true;
- } catch (MobyException e) {
- return false;
- }
- }
-
- /**
- *
- * @param xml
- * a string of xml
- * @return true if the xml contains a full moby message (assumes single
- * invocation, but will return the first mobyData block from a
- * multiple invocation message).
- * @throws MobyException
- * if the xml is syntatically invalid
- */
- public static boolean isWrapped(String xml) throws MobyException {
- Element element = getDOMDocument(xml).getRootElement();
- return isWrapped(element);
- }
-
- /**
- *
- * @param element
- * an Element containing a single invocation
- * @return true if the element contains a moby collection, false otherwise.
- * @throws MobyException
- * if xml is invalid
- */
- public static boolean isCollection(Element element) throws MobyException {
- try {
- return getListOfCollections((Element) element.clone()).length > 0;
-
- } catch (MobyException e) {
- return false;
- }
- }
-
- /**
- *
- * @param xml
- * a string of xml containing a single invocation
- * @return true if the xml contains a moby collection, false otherwise.
- * @throws MobyException
- * if xml is invalid
- */
- public static boolean isCollection(String xml) throws MobyException {
- Element element = getDOMDocument(xml).getRootElement();
- return isCollection(element);
- }
-
- /**
- *
- * @param xml
- * a string of xml to check for emptiness
- * @return true if the element is empty, false otherwise.
- */
- public static boolean isEmpty(String xml) {
- try {
- return isEmpty(getDOMDocument(xml).getRootElement());
- } catch (MobyException e) {
- return true;
- }
- }
-
- /**
- *
- * @param xml
- * an element to check for emptiness
- * @return true if the element is empty, false otherwise.
- */
- public static boolean isEmpty(Element xml) {
- try {
- Element e = extractMobyData((Element) xml.clone());
- if (e.getChild("Collection") != null)
- return false;
- if (e.getChild("Collection", MOBY_NS) != null)
- return false;
- if (e.getChild("Simple") != null)
- return false;
- if (e.getChild("Simple", MOBY_NS) != null)
- return false;
- } catch (MobyException e) {
- }
- return true;
-
- }
-
- /**
- *
- * @param theList
- * a list of Elements that represent collections (wrapped in a
- * MobyData tag
- * @param name
- * the name to set for the collection
- * @return a list containing a single wrapped collection Element that contains all
- * of the simples in the collections in theList
- * @throws MobyException
- *
- */
- public static List mergeCollections(List theList, String name)
- throws MobyException {
- if (theList == null)
- return new ArrayList();
- Element mainCollection = new Element("Collection", MOBY_NS);
- mainCollection.setAttribute("articleName", name, MOBY_NS);
- String queryID = "";
- for (Iterator iter = theList.iterator(); iter.hasNext();) {
- Element mobyData = (Element) iter.next();
- queryID = getQueryID(mobyData);
- Element collection = mobyData.getChild("Collection");
- if (collection == null)
- collection = mobyData.getChild("Collection", MOBY_NS);
- if (collection == null)
- continue;
- mainCollection.addContent(collection.cloneContent());
- }
- theList = new ArrayList();
- theList
- .add((createMobyDataElementWrapper(mainCollection, queryID,
- null)));
- return theList;
- }
-
- /**
- *
- * @param element
- * a full moby message (root element called MOBY) and may be
- * prefixed
- * @return the serviceNotes element if it exists, null otherwise.
- */
- public static Element getServiceNotes(Element element) {
- Element serviceNotes = null;
- Element e = (Element) element.clone();
- Element mobyContent = e.getChild("mobyContent");
- if (mobyContent == null)
- mobyContent = e.getChild("mobyContent", MOBY_NS);
-
- // should throw exception?
- if (mobyContent == null)
- return serviceNotes;
-
- serviceNotes = mobyContent.getChild("serviceNotes");
- if (serviceNotes == null)
- serviceNotes = mobyContent.getChild("serviceNotes", MOBY_NS);
- // note: servicenotes may be null
- return serviceNotes;
- }
-
- /**
- *
- * @param xml
- * a full moby message (root element called MOBY) and may be
- * prefixed
- * @return the serviceNotes element as a string if it exists, null
- * otherwise.
- */
- public static String getServiceNotes(String xml) {
- try {
- Element e = getServiceNotes(getDOMDocument(xml).getRootElement());
- if (e == null)
- return null;
- XMLOutputter out = new XMLOutputter(Format.getPrettyFormat()
- .setOmitDeclaration(false));
- return out.outputString(e);
- } catch (MobyException ex) {
- return null;
- }
- }
-
- /**
- *
- * @param xml
- * a full moby message (root element called MOBY) and may be
- * prefixed
- * @return the serviceNotes element if it exists, null otherwise.
- */
- public static Element getServiceNotesAsElement(String xml) {
- try {
- Element e = getServiceNotes(getDOMDocument(xml).getRootElement());
- return e;
- } catch (MobyException ex) {
- return null;
- }
- }
-
- /**
- *
- * @param element
- * the xml element
- * @param articleName
- * the name of the child to extract
- * @return an element that represents the direct child or null if it wasnt
- * found.
- */
- public static Element getDirectChildByArticleName(Element element,
- String articleName) {
- Element e = (Element) element.clone();
- List list = e.getChildren();
- for (Iterator iter = list.iterator(); iter.hasNext();) {
- Object object = iter.next();
- if (object instanceof Element) {
- Element child = (Element) object;
- if (child.getAttributeValue("articleName") != null) {
- if (child.getAttributeValue("articleName").equals(
- articleName))
- return child;
- } else if (child.getAttributeValue("articleName", MOBY_NS) != null) {
- if (child.getAttributeValue("articleName", MOBY_NS).equals(
- articleName)) {
- return child;
- }
- }
- }
-
- }
- return null;
-
- }
-
- /**
- *
- * @param xml
- * the string of xml
- * @param articleName
- * the name of the child to extract
- * @return an xml string that represents the direct child or null if it
- * wasnt found.
- */
- public static String getDirectChildByArticleName(String xml,
- String articleName) {
- try {
- Element e = getDirectChildByArticleName(getDOMDocument(xml)
- .getRootElement(), articleName);
- if (e == null)
- return null;
- XMLOutputter out = new XMLOutputter(Format.getPrettyFormat()
- .setOmitDeclaration(false));
- return out.outputString(e);
- } catch (MobyException me) {
- return null;
- }
- }
-
- /**
- *
- * @param xml
- * the xml message to test whether or not there is stuff in the
- * mobyData portion of a message.
- * @return true if there is data, false otherwise.
- */
- public static boolean isThereData(Element xml) {
- Element e = null;
- e = (Element) xml.clone();
- try {
- e = extractMobyData(e);
- if (e.getChildren().size() > 0) {
- // make sure we dont have empty collections or simples
- if (e.getChild("Collection") != null) {
- return e.getChild("Collection").getChildren().size() > 0;
- }
- if (e.getChild("Collection", MOBY_NS) != null) {
- return e.getChild("Collection", MOBY_NS).getChildren()
- .size() > 0;
- }
- if (e.getChild("Simple") != null) {
- return e.getChild("Simple").getChildren().size() > 0;
- }
- if (e.getChild("Simple", MOBY_NS) != null) {
- return e.getChild("Simple", MOBY_NS).getChildren().size() > 0;
- }
- return false;
- }
- } catch (MobyException e1) {
- return false;
- }
- return false;
- }
-
- /**
- *
- * @param xml
- * the xml message to test whether or not there is stuff in the
- * mobyData portion of a message.
- * @return true if there is data, false otherwise.
- */
- public static boolean isThereData(String xml) {
- try {
- return isThereData(getDOMDocument(xml).getRootElement());
- } catch (Exception e) {
- return false;
- }
- }
-
- public static void main(String[] args) throws MobyException {
- String msg = "<moby:MOBY xmlns:moby=\"http://www.biomoby.org/moby\">\r\n"
- + " <moby:mobyContent>\r\n"
- + " <moby:mobyData moby:queryID=\"a2_+_s65_+_s165_+_s1290_a2_+_s65_+_s165_+_s1290_+_s1408_a0_+_s3_+_s1409\">\r\n"
- + " <moby:Collection moby:articleName=\"alleles\">\r\n"
- + " <moby:Simple>\r\n"
- + " <Object xmlns=\"http://www.biomoby.org/moby\" namespace=\"DragonDB_Allele\" id=\"def-101\" />\r\n"
- + " </moby:Simple>\r\n"
- + " <moby:Simple>\r\n"
- + " <Object xmlns=\"http://www.biomoby.org/moby\" namespace=\"DragonDB_Allele\" id=\"def-chl\" />\r\n"
- + " </moby:Simple>\r\n"
- + " <moby:Simple>\r\n"
- + " <Object xmlns=\"http://www.biomoby.org/moby\" namespace=\"DragonDB_Allele\" id=\"def-gli\" />\r\n"
- + " </moby:Simple>\r\n"
- + " <moby:Simple>\r\n"
- + " <Object xmlns=\"http://www.biomoby.org/moby\" namespace=\"DragonDB_Allele\" id=\"def-nic\" />\r\n"
- + " </moby:Simple>\r\n"
- + " <moby:Simple>\r\n"
- + " <Object xmlns=\"http://www.biomoby.org/moby\" namespace=\"DragonDB_Allele\" id=\"def-23\" />\r\n"
- + " </moby:Simple>\r\n"
- + " </moby:Collection>\r\n"
- + " </moby:mobyData>\r\n"
- + " </moby:mobyContent>\r\n"
- + "</moby:MOBY>";
- Element inputElement = getDOMDocument(msg).getRootElement();
- String queryID = XMLUtilities.getQueryID(inputElement);
- Element[] simples = XMLUtilities.getSimplesFromCollection(inputElement);
-
- ArrayList list = new ArrayList();
- for (int j = 0; j < simples.length; j++) {
- Element wrappedSimple = XMLUtilities
- .createMobyDataElementWrapper(simples[j]);
- wrappedSimple = XMLUtilities.renameSimple("Allele", "Object",
- wrappedSimple);
- wrappedSimple = XMLUtilities.setQueryID(wrappedSimple, queryID
- + "_+_" + XMLUtilities.getQueryID(wrappedSimple));
- list.add(XMLUtilities.extractMobyData(wrappedSimple));
- }
- }
-
- /*
- *
- * @param current the Element that you would like to search @param name the
- * name of the element that you would like to find @param list the list to
- * put the elements that are found in @return a list containing the elements
- * that are named name
- */
- private static List listChildren(Element current, String name, List list) {
- if (list == null)
- list = new ArrayList();
- if (current.getName().equals(name))
- list.add(current);
- List children = current.getChildren();
- Iterator iterator = children.iterator();
- while (iterator.hasNext()) {
- Element child = (Element) iterator.next();
- if (child instanceof Element)
- listChildren(child, name, list);
- }
- return list;
- }
-
- /**
- *
- * @param collectionName
- * the name you would like the collection to be called
- * @param simples2makeCollection
- * the list of Elements to merge into a collection
- * @return null if a collection wasnt made, otherwise a fully wrapped
- * collection is returned.
- * @throws MobyException
- */
- public static Element createCollectionFromListOfSimples(
- String collectionName, List<Element> simples2makeCollection)
- throws MobyException {
- if (simples2makeCollection.size() > 0) {
- // create a collection from the list of
- // simples
- Element mimCollection = new Element("Collection",
- XMLUtilities.MOBY_NS);
- for (Element simple : simples2makeCollection) {
- Element theSimple = XMLUtilities.extractMobyData(simple);
- if (theSimple.getChild("Simple") != null)
- theSimple = theSimple.getChild("Simple");
- else if (theSimple.getChild("Simple", XMLUtilities.MOBY_NS) != null)
- theSimple = theSimple.getChild("Simple",
- XMLUtilities.MOBY_NS);
- mimCollection.addContent(theSimple.detach());
- }
- String mimQueryID = "merged_" + queryCount++;
-
- mimCollection = XMLUtilities.createMobyDataElementWrapper(
- mimCollection, mimQueryID, null);
- mimCollection = XMLUtilities.renameCollection(collectionName,
- mimCollection);
- mimCollection = XMLUtilities.createMobyDataElementWrapper(
- mimCollection, mimQueryID, null);
- return mimCollection;
- }
- return null;
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity/src/main/resources/META-INF/services/net.sf.taverna.t2.workflowmodel.health.HealthChecker
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity/src/main/resources/META-INF/services/net.sf.taverna.t2.workflowmodel.health.HealthChecker b/taverna-biomoby-activity/src/main/resources/META-INF/services/net.sf.taverna.t2.workflowmodel.health.HealthChecker
deleted file mode 100644
index 7d50ca3..0000000
--- a/taverna-biomoby-activity/src/main/resources/META-INF/services/net.sf.taverna.t2.workflowmodel.health.HealthChecker
+++ /dev/null
@@ -1,3 +0,0 @@
-net.sf.taverna.t2.activities.biomoby.BiomobyActivityHealthChecker
-net.sf.taverna.t2.activities.biomoby.BiomobyObjectActivityHealthChecker
-net.sf.taverna.t2.activities.biomoby.MobyParseDatatypeActivityHealthChecker
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity/src/main/resources/META-INF/spring/biomoby-activity-context-osgi.xml
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity/src/main/resources/META-INF/spring/biomoby-activity-context-osgi.xml b/taverna-biomoby-activity/src/main/resources/META-INF/spring/biomoby-activity-context-osgi.xml
deleted file mode 100644
index 449a31e..0000000
--- a/taverna-biomoby-activity/src/main/resources/META-INF/spring/biomoby-activity-context-osgi.xml
+++ /dev/null
@@ -1,17 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<beans:beans xmlns="http://www.springframework.org/schema/osgi" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:beans="http://www.springframework.org/schema/beans"
- xsi:schemaLocation="http://www.springframework.org/schema/beans
- http://www.springframework.org/schema/beans/spring-beans.xsd
- http://www.springframework.org/schema/osgi
- http://www.springframework.org/schema/osgi/spring-osgi.xsd">
-
- <service ref="biomobyActivityHealthChecker" interface="net.sf.taverna.t2.workflowmodel.health.HealthChecker" />
- <service ref="biomobyObjectActivityHealthChecker" interface="net.sf.taverna.t2.workflowmodel.health.HealthChecker" />
- <service ref="mobyParseDatatypeActivityHealthChecker" interface="net.sf.taverna.t2.workflowmodel.health.HealthChecker" />
-
- <service ref="biomobyActivityFactory" interface="net.sf.taverna.t2.workflowmodel.processor.activity.ActivityFactory" />
- <service ref="biomobyObjectActivityFactory" interface="net.sf.taverna.t2.workflowmodel.processor.activity.ActivityFactory" />
- <service ref="mobyParseDatatypeActivityFactory" interface="net.sf.taverna.t2.workflowmodel.processor.activity.ActivityFactory" />
-
-</beans:beans>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity/src/main/resources/META-INF/spring/biomoby-activity-context.xml
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity/src/main/resources/META-INF/spring/biomoby-activity-context.xml b/taverna-biomoby-activity/src/main/resources/META-INF/spring/biomoby-activity-context.xml
deleted file mode 100644
index 3fbeaaf..0000000
--- a/taverna-biomoby-activity/src/main/resources/META-INF/spring/biomoby-activity-context.xml
+++ /dev/null
@@ -1,14 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<beans xmlns="http://www.springframework.org/schema/beans" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://www.springframework.org/schema/beans
- http://www.springframework.org/schema/beans/spring-beans.xsd">
-
- <bean id="biomobyActivityHealthChecker" class="net.sf.taverna.t2.activities.biomoby.BiomobyActivityHealthChecker" />
- <bean id="biomobyObjectActivityHealthChecker" class="net.sf.taverna.t2.activities.biomoby.BiomobyObjectActivityHealthChecker" />
- <bean id="mobyParseDatatypeActivityHealthChecker" class="net.sf.taverna.t2.activities.biomoby.MobyParseDatatypeActivityHealthChecker" />
-
- <bean id="biomobyActivityFactory" class="net.sf.taverna.t2.activities.biomoby.BiomobyActivityFactory" />
- <bean id="biomobyObjectActivityFactory" class="net.sf.taverna.t2.activities.biomoby.BiomobyObjectActivityFactory" />
- <bean id="mobyParseDatatypeActivityFactory" class="net.sf.taverna.t2.activities.biomoby.MobyParseDatatypeActivityFactory" />
-
-</beans>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity/src/test/java/net/sf/taverna/t2/activities/biomoby/BiomobyActivityHealthCheckerTest.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity/src/test/java/net/sf/taverna/t2/activities/biomoby/BiomobyActivityHealthCheckerTest.java b/taverna-biomoby-activity/src/test/java/net/sf/taverna/t2/activities/biomoby/BiomobyActivityHealthCheckerTest.java
deleted file mode 100644
index 504fdc6..0000000
--- a/taverna-biomoby-activity/src/test/java/net/sf/taverna/t2/activities/biomoby/BiomobyActivityHealthCheckerTest.java
+++ /dev/null
@@ -1,45 +0,0 @@
-/*******************************************************************************
- * This file is a component of the Taverna project, and is licensed under the
- * GNU LGPL. Copyright Edward Kawas, The BioMoby Project
- ******************************************************************************/
-package net.sf.taverna.t2.activities.biomoby;
-
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertTrue;
-import net.sf.taverna.t2.workflowmodel.processor.activity.AbstractActivity;
-import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityConfigurationException;
-
-import org.junit.Before;
-import org.junit.Test;
-
-/**
- * Unit tests for BiomobyActivityHealthChecker.
- *
- */
-public class BiomobyActivityHealthCheckerTest {
-
- private BiomobyActivity activity;
-
- private BiomobyActivityHealthChecker activityHealthChecker;
-
- @Before
- public void setUp() throws Exception {
- activity = new BiomobyActivity();
- activityHealthChecker = new BiomobyActivityHealthChecker();
- }
-
- @Test
- public void testCanHandle() {
- assertFalse(activityHealthChecker.canVisit(null));
- assertFalse(activityHealthChecker.canVisit(new Object()));
- assertFalse(activityHealthChecker.canVisit(new AbstractActivity<Object>() {
- public void configure(Object conf) throws ActivityConfigurationException {
- }
- public Object getConfiguration() {
- return null;
- }
- }));
- assertTrue(activityHealthChecker.canVisit(activity));
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity/src/test/java/net/sf/taverna/t2/activities/biomoby/BiomobyObjectActivityHealthCheckerTest.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity/src/test/java/net/sf/taverna/t2/activities/biomoby/BiomobyObjectActivityHealthCheckerTest.java b/taverna-biomoby-activity/src/test/java/net/sf/taverna/t2/activities/biomoby/BiomobyObjectActivityHealthCheckerTest.java
deleted file mode 100644
index 403d744..0000000
--- a/taverna-biomoby-activity/src/test/java/net/sf/taverna/t2/activities/biomoby/BiomobyObjectActivityHealthCheckerTest.java
+++ /dev/null
@@ -1,45 +0,0 @@
-/*******************************************************************************
- * This file is a component of the Taverna project, and is licensed under the
- * GNU LGPL. Copyright Edward Kawas, The BioMoby Project
- ******************************************************************************/
-package net.sf.taverna.t2.activities.biomoby;
-
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertTrue;
-import net.sf.taverna.t2.workflowmodel.processor.activity.AbstractActivity;
-import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityConfigurationException;
-
-import org.junit.Before;
-import org.junit.Test;
-
-/**
- * Unit tests for BiomobyActivityHealthChecker.
- *
- */
-public class BiomobyObjectActivityHealthCheckerTest {
-
- private BiomobyActivity activity;
-
- private BiomobyActivityHealthChecker activityHealthChecker;
-
- @Before
- public void setUp() throws Exception {
- activity = new BiomobyActivity();
- activityHealthChecker = new BiomobyActivityHealthChecker();
- }
-
- @Test
- public void testCanHandle() {
- assertFalse(activityHealthChecker.canVisit(null));
- assertFalse(activityHealthChecker.canVisit(new Object()));
- assertFalse(activityHealthChecker.canVisit(new AbstractActivity<Object>() {
- public void configure(Object conf) throws ActivityConfigurationException {
- }
- public Object getConfiguration() {
- return null;
- }
- }));
- assertTrue(activityHealthChecker.canVisit(activity));
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity/src/test/java/net/sf/taverna/t2/activities/biomoby/MobyParseDatatypeActivityHealthCheckerTest.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity/src/test/java/net/sf/taverna/t2/activities/biomoby/MobyParseDatatypeActivityHealthCheckerTest.java b/taverna-biomoby-activity/src/test/java/net/sf/taverna/t2/activities/biomoby/MobyParseDatatypeActivityHealthCheckerTest.java
deleted file mode 100644
index 30c8a1d..0000000
--- a/taverna-biomoby-activity/src/test/java/net/sf/taverna/t2/activities/biomoby/MobyParseDatatypeActivityHealthCheckerTest.java
+++ /dev/null
@@ -1,45 +0,0 @@
-/*******************************************************************************
- * This file is a component of the Taverna project, and is licensed under the
- * GNU LGPL. Copyright Edward Kawas, The BioMoby Project
- ******************************************************************************/
-package net.sf.taverna.t2.activities.biomoby;
-
-import static org.junit.Assert.assertFalse;
-import static org.junit.Assert.assertTrue;
-import net.sf.taverna.t2.workflowmodel.processor.activity.AbstractActivity;
-import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityConfigurationException;
-
-import org.junit.Before;
-import org.junit.Test;
-
-/**
- * Unit tests for BiomobyActivityHealthChecker.
- *
- */
-public class MobyParseDatatypeActivityHealthCheckerTest {
-
- private BiomobyActivity activity;
-
- private BiomobyActivityHealthChecker activityHealthChecker;
-
- @Before
- public void setUp() throws Exception {
- activity = new BiomobyActivity();
- activityHealthChecker = new BiomobyActivityHealthChecker();
- }
-
- @Test
- public void testCanHandle() {
- assertFalse(activityHealthChecker.canVisit(null));
- assertFalse(activityHealthChecker.canVisit(new Object()));
- assertFalse(activityHealthChecker.canVisit(new AbstractActivity<Object>() {
- public void configure(Object conf) throws ActivityConfigurationException {
- }
- public Object getConfiguration() {
- return null;
- }
- }));
- assertTrue(activityHealthChecker.canVisit(activity));
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-ncbi-activity-ui/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-ncbi-activity-ui/pom.xml b/taverna-ncbi-activity-ui/pom.xml
deleted file mode 100644
index 0a8a983..0000000
--- a/taverna-ncbi-activity-ui/pom.xml
+++ /dev/null
@@ -1,49 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
- <modelVersion>4.0.0</modelVersion>
- <parent>
- <groupId>net.sf.taverna</groupId>
- <artifactId>taverna-parent</artifactId>
- <version>3.0.1-SNAPSHOT</version>
- </parent>
- <groupId>net.sf.taverna.t2.ui-activities</groupId>
- <artifactId>ncbi-activity-ui</artifactId>
- <name>Taverna 2 NCBI web service Activity UI</name>
- <dependencies>
- <dependency>
- <groupId>junit</groupId>
- <artifactId>junit</artifactId>
- <version>${junit.version}</version>
- <scope>test</scope>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.activities</groupId>
- <artifactId>wsdl-activity</artifactId>
- <version>${t2.activities.version}</version>
- </dependency>
-
- <!-- testing dependencies -->
- </dependencies>
- <repositories>
- <repository>
- <releases />
- <snapshots>
- <enabled>false</enabled>
- </snapshots>
- <id>mygrid-repository</id>
- <name>myGrid Repository</name>
- <url>http://www.mygrid.org.uk/maven/repository</url>
- </repository>
- <repository>
- <releases>
- <enabled>false</enabled>
- </releases>
- <snapshots />
- <id>mygrid-snapshot-repository</id>
- <name>myGrid Snapshot Repository</name>
- <url>http://www.mygrid.org.uk/maven/snapshot-repository</url>
- </repository>
- </repositories>
-
-</project>
-
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-ncbi-activity-ui/src/main/resources/META-INF/spring/ncbi-activity-ui-context-osgi.xml
----------------------------------------------------------------------
diff --git a/taverna-ncbi-activity-ui/src/main/resources/META-INF/spring/ncbi-activity-ui-context-osgi.xml b/taverna-ncbi-activity-ui/src/main/resources/META-INF/spring/ncbi-activity-ui-context-osgi.xml
deleted file mode 100644
index 1c13381..0000000
--- a/taverna-ncbi-activity-ui/src/main/resources/META-INF/spring/ncbi-activity-ui-context-osgi.xml
+++ /dev/null
@@ -1,9 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<beans:beans xmlns="http://www.springframework.org/schema/osgi" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xmlns:beans="http://www.springframework.org/schema/beans"
- xsi:schemaLocation="http://www.springframework.org/schema/beans
- http://www.springframework.org/schema/beans/spring-beans.xsd
- http://www.springframework.org/schema/osgi
- http://www.springframework.org/schema/osgi/spring-osgi.xsd">
-
-</beans:beans>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-ncbi-activity-ui/src/main/resources/META-INF/spring/ncbi-activity-ui-context.xml
----------------------------------------------------------------------
diff --git a/taverna-ncbi-activity-ui/src/main/resources/META-INF/spring/ncbi-activity-ui-context.xml b/taverna-ncbi-activity-ui/src/main/resources/META-INF/spring/ncbi-activity-ui-context.xml
deleted file mode 100644
index 861c878..0000000
--- a/taverna-ncbi-activity-ui/src/main/resources/META-INF/spring/ncbi-activity-ui-context.xml
+++ /dev/null
@@ -1,6 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<beans xmlns="http://www.springframework.org/schema/beans" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"
- xsi:schemaLocation="http://www.springframework.org/schema/beans
- http://www.springframework.org/schema/beans/spring-beans.xsd">
-
-</beans>
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-ncbi-activity-ui/src/main/resources/ncbi_services
----------------------------------------------------------------------
diff --git a/taverna-ncbi-activity-ui/src/main/resources/ncbi_services b/taverna-ncbi-activity-ui/src/main/resources/ncbi_services
deleted file mode 100644
index e69de29..0000000
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-ncbi-activity-ui/src/main/resources/wsdl.png
----------------------------------------------------------------------
diff --git a/taverna-ncbi-activity-ui/src/main/resources/wsdl.png b/taverna-ncbi-activity-ui/src/main/resources/wsdl.png
deleted file mode 100644
index f9fdae8..0000000
Binary files a/taverna-ncbi-activity-ui/src/main/resources/wsdl.png and /dev/null differ
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-soaplab-activity-ui/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-soaplab-activity-ui/pom.xml b/taverna-soaplab-activity-ui/pom.xml
deleted file mode 100644
index 737a13d..0000000
--- a/taverna-soaplab-activity-ui/pom.xml
+++ /dev/null
@@ -1,103 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
- <modelVersion>4.0.0</modelVersion>
- <parent>
- <groupId>net.sf.taverna</groupId>
- <artifactId>taverna-parent</artifactId>
- <version>3.0.1-SNAPSHOT</version>
- </parent>
- <groupId>net.sf.taverna.t2.ui-activities</groupId>
- <artifactId>soaplab-activity-ui</artifactId>
- <version>2.0-SNAPSHOT</version>
- <packaging>bundle</packaging>
- <name>Taverna 2 Soaplab Activity UI</name>
- <dependencies>
- <dependency>
- <groupId>net.sf.taverna.t2.activities</groupId>
- <artifactId>soaplab-activity</artifactId>
- <version>${t2.activities.version}</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.ui-api</groupId>
- <artifactId>activity-icons-api</artifactId>
- <version>${t2.ui.api.version}</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.ui-api</groupId>
- <artifactId>activity-palette-api</artifactId>
- <version>${t2.ui.api.version}</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.ui-api</groupId>
- <artifactId>contextual-views-api</artifactId>
- <version>${t2.ui.api.version}</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.ui-api</groupId>
- <artifactId>activity-tools</artifactId>
- <version>${t2.ui.api.version}</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.ui-api</groupId>
- <artifactId>edits-api</artifactId>
- <version>${t2.ui.api.version}</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.ui-api</groupId>
- <artifactId>file-api</artifactId>
- <version>${t2.ui.api.version}</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.ui-api</groupId>
- <artifactId>menu-api</artifactId>
- <version>${t2.ui.api.version}</version>
- </dependency>
-
- <dependency>
- <groupId>org.apache.axis</groupId>
- <artifactId>com.springsource.org.apache.axis</artifactId>
- <version>${axis.version}</version>
- </dependency>
- <dependency>
- <groupId>javax.xml.rpc</groupId>
- <artifactId>com.springsource.javax.xml.rpc</artifactId>
- <version>${xml.rpc.version}</version>
- </dependency>
-
- <dependency>
- <groupId>junit</groupId>
- <artifactId>junit</artifactId>
- <version>${junit.version}</version>
- <scope>test</scope>
- </dependency>
- </dependencies>
- <repositories>
- <repository>
- <releases />
- <snapshots>
- <enabled>false</enabled>
- </snapshots>
- <id>mygrid-repository</id>
- <name>myGrid Repository</name>
- <url>http://www.mygrid.org.uk/maven/repository
- </url>
- </repository>
- <repository>
- <releases>
- <enabled>false</enabled>
- </releases>
- <snapshots />
- <id>mygrid-snapshot-repository</id>
- <name>myGrid Snapshot Repository</name>
- <url>http://www.mygrid.org.uk/maven/snapshot-repository</url>
- </repository>
- </repositories>
- <scm>
- <connection>scm:git:https://github.com/taverna/taverna-soaplab-activity-ui.git</connection>
- <developerConnection>scm:git:ssh://git@github.com/taverna/taverna-soaplab-activity-ui.git</developerConnection>
- <url>https://github.com/taverna/taverna-soaplab-activity-ui/</url>
- <tag>HEAD</tag>
- </scm>
-
-</project>
-
[11/16] incubator-taverna-plugin-bioinformatics git commit:
temporarily empty repository
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/MinimalLayout.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/MinimalLayout.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/MinimalLayout.java
deleted file mode 100644
index 153b982..0000000
--- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/MinimalLayout.java
+++ /dev/null
@@ -1,158 +0,0 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: MinimalLayout.java,v $
- * Revision $Revision: 1.1 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/06/27 12:49:48 $
- * by $Author: davidwithers $
- * Created on 26 Jun 2007
- *****************************************************************/
-package org.biomart.martservice.config.ui;
-
-import java.awt.Component;
-import java.awt.Container;
-import java.awt.Dimension;
-import java.awt.Insets;
-import java.awt.LayoutManager;
-
-/**
- * A layout manager that lays out components, either horizontally or vertically,
- * according to their minimum size.
- *
- * @author David Withers
- */
-class MinimalLayout implements LayoutManager {
- public static final int HORIZONTAL = 0;
-
- public static final int VERTICAL = 1;
-
- private static final int gap = 5;
-
- private int type;
-
- public MinimalLayout() {
- type = HORIZONTAL;
- }
-
- public MinimalLayout(int type) {
- this.type = type;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see java.awt.LayoutManager#removeLayoutComponent(java.awt.Component)
- */
- public void removeLayoutComponent(Component comp) {
- }
-
- /*
- * (non-Javadoc)
- *
- * @see java.awt.LayoutManager#layoutContainer(java.awt.Container)
- */
- public void layoutContainer(Container parent) {
- Insets insets = parent.getInsets();
- int x = insets.left;
- int y = insets.top;
- if (type == HORIZONTAL) {
- Component[] components = parent.getComponents();
- for (int i = 0; i < components.length; i++) {
- components[i].setLocation(x, y);
- components[i].setSize(getSize(components[i]));
- x = x + gap + components[i].getWidth();
- }
- } else {
- Component[] components = parent.getComponents();
- for (int i = 0; i < components.length; i++) {
- components[i].setLocation(x, y);
- components[i].setSize(getSize(components[i]));
- y = y + gap + components[i].getHeight();
- }
- }
- }
-
- /*
- * (non-Javadoc)
- *
- * @see java.awt.LayoutManager#addLayoutComponent(java.lang.String,
- * java.awt.Component)
- */
- public void addLayoutComponent(String name, Component comp) {
- }
-
- /*
- * (non-Javadoc)
- *
- * @see java.awt.LayoutManager#minimumLayoutSize(java.awt.Container)
- */
- public Dimension minimumLayoutSize(Container parent) {
- Insets insets = parent.getInsets();
- Dimension minimumSize = new Dimension(insets.left, insets.top);
- if (type == HORIZONTAL) {
- int x = insets.left;
- Component[] components = parent.getComponents();
- for (int i = 0; i < components.length; i++) {
- Dimension size = getSize(components[i]);
- if (insets.top + size.height > minimumSize.height) {
- minimumSize.height = insets.top + size.height;
- }
- minimumSize.width = x + size.width;
- x = x + size.width + gap;
- }
- } else {
- int y = insets.top;
- Component[] components = parent.getComponents();
- for (int i = 0; i < components.length; i++) {
- Dimension size = getSize(components[i]);
- if (insets.left + size.width > minimumSize.width) {
- minimumSize.width = insets.left + size.width;
- }
- minimumSize.height = y + size.height;
- y = y + size.height + gap;
- }
- }
- minimumSize.width = minimumSize.width + insets.right;
- minimumSize.height = minimumSize.height + insets.bottom;
-
- return (minimumSize);
- }
-
- /*
- * (non-Javadoc)
- *
- * @see java.awt.LayoutManager#preferredLayoutSize(java.awt.Container)
- */
- public Dimension preferredLayoutSize(Container parent) {
- return minimumLayoutSize(parent);
- }
-
- private Dimension getSize(Component component) {
- return component.getPreferredSize();
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/QueryComponent.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/QueryComponent.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/QueryComponent.java
deleted file mode 100644
index b976684..0000000
--- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/QueryComponent.java
+++ /dev/null
@@ -1,342 +0,0 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: QueryComponent.java,v $
- * Revision $Revision: 1.2 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/12/13 11:38:56 $
- * by $Author: davidwithers $
- * Created on 03-Apr-2006
- *****************************************************************/
-package org.biomart.martservice.config.ui;
-
-import java.awt.event.ItemEvent;
-import java.awt.event.ItemListener;
-import java.util.Vector;
-
-import javax.swing.AbstractButton;
-import javax.swing.JPanel;
-
-import org.biomart.martservice.MartDataset;
-import org.biomart.martservice.config.event.QueryComponentEvent;
-import org.biomart.martservice.config.event.QueryComponentListener;
-import org.ensembl.mart.lib.config.BaseNamedConfigurationObject;
-
-/**
- * Abstract class for creating query configuration UI components.
- *
- * @author David Withers
- */
-public abstract class QueryComponent extends JPanel {
- public static final int ATTRIBUTE = 0;
-
- public static final int FILTER = 1;
-
- public static final int LINK = 2;
-
- private Vector<QueryComponentListener> queryComponentListeners = new Vector<QueryComponentListener>();
-
- private MartDataset dataset;
-
- private String pointerDataset;
-
- private String name;
-
- private String value;
-
- private BaseNamedConfigurationObject configObject;
-
- protected AbstractButton selectorButton;
-
- public abstract int getType();
-
- /**
- * Returns the dataset.
- *
- * @return the dataset.
- */
- public MartDataset getDataset() {
- return dataset;
- }
-
- /**
- * Sets the dataset.
- *
- * @param dataset
- * the dataset to set.
- */
- public void setDataset(MartDataset dataset) {
- this.dataset = dataset;
- }
-
- /**
- * Returns the pointerDataset.
- *
- * @return the pointerDataset
- */
- public String getPointerDataset() {
- return pointerDataset;
- }
-
- /**
- * Sets the pointerDataset.
- *
- * @param pointerDataset the new pointerDataset
- */
- public void setPointerDataset(String pointerDataset) {
- this.pointerDataset = pointerDataset;
- }
-
- /**
- * Returns the name.
- *
- * @return the name.
- */
- public String getName() {
- return name;
- }
-
- /**
- * @param name
- * the name to set.
- */
- public void setName(String name) {
- this.name = name;
- }
-
- public String getQualifiedName() {
- return getDataset().getName() + "." + getName();
- }
-
- public String getOldQualifiedName() {
- if (pointerDataset == null) {
- return getDataset().getName() + "." + getName();
- } else {
- return pointerDataset + "." + getName();
- }
- }
-
- /**
- * Returns the value.
- *
- * @return the value.
- */
- public String getValue() {
- return value;
- }
-
- /**
- * Sets the value.
- *
- * @param value
- * the value to set.
- */
- public void setValue(String value) {
- this.value = value;
- }
-
- /**
- * Returns the configObject.
- *
- * @return the configObject
- */
- public BaseNamedConfigurationObject getConfigObject() {
- return configObject;
- }
-
- /**
- * Sets the configObject.
- *
- * @param configObject
- * the configObject to set.
- */
- public void setConfigObject(BaseNamedConfigurationObject configObject) {
- this.configObject = configObject;
- }
-
- /**
- * Sets the selected state of this component.
- *
- * @param selected
- * <code>true</code> if this component is selected,
- * <code>false</code> otherwise
- */
- public void setSelected(boolean selected) {
- if (selectorButton != null) {
- selectorButton.setSelected(selected);
- }
- }
-
- /**
- * Sets the button used to select/deselect this QueryComponent.
- *
- * This function adds an ItemListener to the button and fires the
- * appropriate QueryComponentEvent when the button is selected or
- * deselected.
- *
- * @param button
- * the button used to select/deselect this QueryComponent.
- */
- public void setSelectorButton(AbstractButton button) {
- selectorButton = button;
- button.addItemListener(new ItemListener() {
- public void itemStateChanged(ItemEvent e) {
- if (e.getStateChange() == ItemEvent.SELECTED) {
- if (getType() == ATTRIBUTE) {
- fireAttributeAdded(new QueryComponentEvent(
- QueryComponent.this, getName(), getDataset()));
- } else {
- fireFilterAdded(new QueryComponentEvent(
- QueryComponent.this, getName(), getDataset()));
- }
- } else if (e.getStateChange() == ItemEvent.DESELECTED) {
- if (getType() == ATTRIBUTE) {
- fireAttributeRemoved(new QueryComponentEvent(
- QueryComponent.this, getName(), getDataset()));
- } else {
- fireFilterRemoved(new QueryComponentEvent(
- QueryComponent.this, getName(), getDataset()));
- }
- }
- }
- });
- }
-
- /**
- * Adds the specified query component listener to receive query component
- * events. If <code>listener</code> is null, no exception is thrown and no
- * action is performed.
- *
- * @param listener
- * the query component listener
- */
- public void addQueryComponentListener(QueryComponentListener listener) {
- queryComponentListeners.add(listener);
- }
-
- /**
- * Removes the specified query component listener so that it no longer
- * receives component query events. This method performs no function, nor
- * does it throw an exception, if <code>listener</code> was not previously
- * added to this component. If <code>listener</code> is null, no exception
- * is thrown and no action is performed.
- *
- * @param listener
- * the query component listener
- */
- public void removeQueryComponentListener(QueryComponentListener listener) {
- queryComponentListeners.remove(listener);
- }
-
- /**
- * Fires an attribute added event.
- *
- * @param event the event to be fired
- */
- protected void fireAttributeAdded(QueryComponentEvent event) {
- for (QueryComponentListener listener : queryComponentListeners) {
- listener.attributeAdded(event);
- }
- }
-
- /**
- * Fires an attribute removed event.
- *
- * @param event the event to be fired
- */
- protected void fireAttributeRemoved(QueryComponentEvent event) {
- for (QueryComponentListener listener : queryComponentListeners) {
- listener.attributeRemoved(event);
- }
- }
-
- /**
- * Fires an filter added event.
- *
- * @param event the event to be fired
- */
- protected void fireFilterAdded(QueryComponentEvent event) {
- for (QueryComponentListener listener : queryComponentListeners) {
- listener.filterAdded(event);
- }
- }
-
- /**
- * Fires an filter removed event.
- *
- * @param event the event to be fired
- */
- protected void fireFilterRemoved(QueryComponentEvent event) {
- for (QueryComponentListener listener : queryComponentListeners) {
- listener.filterRemoved(event);
- }
- }
-
- /**
- * Fires an filter changed event.
- *
- * @param event the event to be fired
- */
- protected void fireFilterChanged(QueryComponentEvent event) {
- for (QueryComponentListener listener : queryComponentListeners) {
- listener.filterChanged(event);
- }
- }
-
- /**
- * Fires an link added event.
- *
- * @param event the event to be fired
- */
- protected void fireLinkAdded(QueryComponentEvent event) {
- for (QueryComponentListener listener : queryComponentListeners) {
- listener.linkAdded(event);
- }
- }
-
- /**
- * Fires an link removed event.
- *
- * @param event the event to be fired
- */
- protected void fireLinkRemoved(QueryComponentEvent event) {
- for (QueryComponentListener listener : queryComponentListeners) {
- listener.linkRemoved(event);
- }
- }
-
- /**
- * Fires an link changed event.
- *
- * @param event the event to be fired
- */
- protected void fireLinkChanged(QueryComponentEvent event) {
- for (QueryComponentListener listener : queryComponentListeners) {
- listener.linkChanged(event);
- }
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/QueryConfigUIFactory.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/QueryConfigUIFactory.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/QueryConfigUIFactory.java
deleted file mode 100644
index d0a740a..0000000
--- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/QueryConfigUIFactory.java
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@@ -1,345 +0,0 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: QueryConfigUIFactory.java,v $
- * Revision $Revision: 1.1 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/01/31 14:12:08 $
- * by $Author: davidwithers $
- * Created on 04-Apr-2006
- *****************************************************************/
-package org.biomart.martservice.config.ui;
-
-import java.awt.Component;
-
-import org.biomart.martservice.MartServiceException;
-import org.ensembl.mart.lib.config.AttributeCollection;
-import org.ensembl.mart.lib.config.AttributeDescription;
-import org.ensembl.mart.lib.config.AttributeGroup;
-import org.ensembl.mart.lib.config.AttributeList;
-import org.ensembl.mart.lib.config.AttributePage;
-import org.ensembl.mart.lib.config.FilterCollection;
-import org.ensembl.mart.lib.config.FilterDescription;
-import org.ensembl.mart.lib.config.FilterGroup;
-import org.ensembl.mart.lib.config.FilterPage;
-
-/**
- * Interface for generating graphical components from <code>DatasetConfig</code>
- * objects.
- *
- * @author David Withers
- */
-public interface QueryConfigUIFactory {
-
- public final static String SINGLE_SELECTION = "SINGLE";
-
- public final static String MULTIPLE_SELECTION = "MULTIPLE";
-
- public final static String LIST_SELECTION = "LIST";
-
- /**
- * Generates a <code>Component</code> for a <code>DatasetConfig</code>.
- *
- * @return the generated <code>Component</code>
- * @throws MartServiceException
- * if the MartService returns an error or is unavailable
- */
- public Component getDatasetConfigUI() throws MartServiceException;
-
- /**
- * Generates a <code>Component</code> for an array of
- * <code>AttributePage</code>.
- *
- * @param attributePages
- * an array of <code>AttributePage</code>
- * @param data
- * extra context information
- * @return the generated <code>Component</code>
- * @throws MartServiceException
- * if the MartService returns an error or is unavailable
- */
- public Component getAttributePagesUI(AttributePage[] attributePages,
- Object data) throws MartServiceException;
-
- /**
- * Generates a <code>Component</code> for an <code>AttributePage</code>.
- *
- * @param attributePage
- * an <code>AttributePage</code>
- * @param data
- * extra context information
- * @return the generated <code>Component</code>
- * @throws MartServiceException
- * if the MartService returns an error or is unavailable
- */
- public Component getAttributePageUI(AttributePage attributePage, Object data)
- throws MartServiceException;
-
- /**
- * Generates a <code>Component</code> for an array of
- * <code>AttributeGroup</code>.
- *
- * @param attributeGroups
- * an array of <code>AttributeGroup</code>
- * @param data
- * extra context information
- * @return the generated <code>Component</code>
- * @throws MartServiceException
- * if the MartService returns an error or is unavailable
- */
- public Component getAttributeGroupsUI(AttributeGroup[] attributeGroups,
- Object data) throws MartServiceException;
-
- /**
- * Generates a <code>Component</code> for an <code>AttributeGroup</code>.
- *
- * @param attributeGroup
- * an <code>AttributeGroup</code>
- * @param data
- * extra context information
- * @return the generated <code>Component</code>
- * @throws MartServiceException
- * if the MartService returns an error or is unavailable
- */
- public Component getAttributeGroupUI(AttributeGroup attributeGroup,
- Object data) throws MartServiceException;
-
- /**
- * Generates a <code>Component</code> for an array of
- * <code>AttributeCollection</code>.
- *
- * @param attributeCollections
- * an array of <code>AttributeCollection</code>
- * @param data
- * extra context information
- * @return the generated <code>Component</code>
- * @throws MartServiceException
- * if the MartService returns an error or is unavailable
- */
- public Component getAttributeCollectionsUI(
- AttributeCollection[] attributeCollections, Object data)
- throws MartServiceException;
-
- /**
- * Generates a <code>Component</code> for an
- * <code>AttributeCollection</code>.
- *
- * @param attributeCollection
- * an <code>AttributeCollection</code>
- * @param data
- * extra context information
- * @return the generated <code>Component</code>
- * @throws MartServiceException
- * if the MartService returns an error or is unavailable
- */
- public Component getAttributeCollectionUI(
- AttributeCollection attributeCollection, Object data)
- throws MartServiceException;
-
- /**
- * Generates a <code>Component</code> for an array of
- * <code>AttributeDescription</code>.
- *
- * @param attributeDescriptions
- * an array of <code>AttributeDescription</code>
- * @param data
- * extra context information
- * @return the generated <code>Component</code>
- * @throws MartServiceException
- * if the MartService returns an error or is unavailable
- */
- public Component getAttributeDescriptionsUI(
- AttributeDescription[] attributeDescriptions, Object data)
- throws MartServiceException;
-
- /**
- * Generates a <code>Component</code> for an
- * <code>AttributeDescription</code>.
- *
- * @param attributeDescription
- * an <code>AttributeDescription</code>
- * @param data
- * extra context information
- * @return the generated <code>Component</code>
- * @throws MartServiceException
- * if the MartService returns an error or is unavailable
- */
- public Component getAttributeDescriptionUI(
- AttributeDescription attributeDescription, Object data)
- throws MartServiceException;
-
- /**
- * Generates a <code>Component</code> for an array of
- * <code>AttributeList</code>.
- *
- * @param attributeLists
- * an array of <code>AttributeList</code>
- * @param data
- * extra context information
- * @return the generated <code>Component</code>
- * @throws MartServiceException
- * if the MartService returns an error or is unavailable
- */
- public Component getAttributeListsUI(
- AttributeList[] attributeLists, Object data)
- throws MartServiceException;
-
- /**
- * Generates a <code>Component</code> for an
- * <code>AttributeList</code>.
- *
- * @param attributeList
- * an <code>AttributeList</code>
- * @param data
- * extra context information
- * @return the generated <code>Component</code>
- * @throws MartServiceException
- * if the MartService returns an error or is unavailable
- */
- public Component getAttributeListUI(
- AttributeList attributeList, Object data)
- throws MartServiceException;
-
- /**
- * Generates a <code>Component</code> for an array of
- * <code>FilterPage</code>.
- *
- * @param filterPages
- * an array of <code>FilterPage</code>
- * @param data
- * extra context information
- * @return the generated <code>Component</code>
- * @throws MartServiceException
- * if the MartService returns an error or is unavailable
- */
- public Component getFilterPagesUI(FilterPage[] filterPages, Object data)
- throws MartServiceException;
-
- /**
- * Generates a <code>Component</code> for a <code>FilterPage</code>.
- *
- * @param filterPage
- * a <code>FilterPage</code>
- * @param data
- * extra context information
- * @return the generated <code>Component</code>
- * @throws MartServiceException
- * if the MartService returns an error or is unavailable
- */
- public Component getFilterPageUI(FilterPage filterPage, Object data)
- throws MartServiceException;
-
- /**
- * Generates a <code>Component</code> for an array of
- * <code>FilterGroup</code>.
- *
- * @param filterGroups
- * an array of <code>FilterGroup</code>
- * @param data
- * extra context information
- * @return the generated <code>Component</code>
- * @throws MartServiceException
- * if the MartService returns an error or is unavailable
- */
- public Component getFilterGroupsUI(FilterGroup[] filterGroups, Object data)
- throws MartServiceException;
-
- /**
- * Generates a <code>Component</code> for a <code>FilterGroup</code>.
- *
- * @param filterGroup
- * a <code>FilterGroup</code>
- * @param data
- * extra context information
- * @return the generated <code>Component</code>
- * @throws MartServiceException
- * if the MartService returns an error or is unavailable
- */
- public Component getFilterGroupUI(FilterGroup filterGroup, Object data)
- throws MartServiceException;
-
- /**
- * Generates a <code>Component</code> for an array of
- * <code>FilterCollection</code>.
- *
- * @param filterCollections
- * an array of <code>FilterCollection</code>
- * @param data
- * extra context information
- * @return the generated <code>Component</code>
- * @throws MartServiceException
- * if the MartService returns an error or is unavailable
- */
- public Component getFilterCollectionsUI(
- FilterCollection[] filterCollections, Object data)
- throws MartServiceException;
-
- /**
- * Generates a <code>Component</code> for a <code>FilterCollection</code>.
- *
- * @param filterCollection
- * a <code>FilterCollection</code>
- * @param data
- * extra context information
- * @return the generated <code>Component</code>
- * @throws MartServiceException
- * if the MartService returns an error or is unavailable
- */
- public Component getFilterCollectionUI(FilterCollection filterCollection,
- Object data) throws MartServiceException;
-
- /**
- * Generates a <code>Component</code> for an array of
- * <code>FilterDescription</code>.
- *
- * @param filterDescriptions
- * an array of <code>FilterDescription</code>
- * @param data
- * extra context information
- * @return the generated <code>Component</code>
- * @throws MartServiceException
- * if the MartService returns an error or is unavailable
- */
- public Component getFilterDescriptionsUI(
- FilterDescription[] filterDescriptions, Object data)
- throws MartServiceException;
-
- /**
- * Generates a <code>Component</code> for a <code>FilterDescription</code>.
- *
- * @param filterDescription
- * a <code>FilterDescription</code>
- * @param data
- * extra context information
- * @return the generated <code>Component</code>
- * @throws MartServiceException
- * if the MartService returns an error or is unavailable
- */
- public Component getFilterDescriptionUI(
- FilterDescription filterDescription, Object data)
- throws MartServiceException;
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Attribute.java
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diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Attribute.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Attribute.java
deleted file mode 100644
index 7ec9932..0000000
--- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Attribute.java
+++ /dev/null
@@ -1,198 +0,0 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: Attribute.java,v $
- * Revision $Revision: 1.2 $
- * Release status $State: Exp $
- * Last modified on $Date: 2008/03/04 16:43:40 $
- * by $Author: davidwithers $
- * Created on 26-Apr-2006
- *****************************************************************/
-package org.biomart.martservice.query;
-
-/**
- * Class for creating attribute elements of mart queries.
- *
- * @author David Withers
- */
-public class Attribute {
- private String name;
-
- private String attributes;
-
- private int attributesCount;
-
- private Dataset containingDataset;
-
- /**
- * Constructs an instance of an <code>Attribute</code> with the specified name.
- *
- * @param name
- * the name of the <code>Attribute</code>; must not be <code>null</code>
- */
- public Attribute(String name) {
- if (name == null) {
- throw new IllegalArgumentException("Parameter 'name' must not be null");
- }
- this.name = name;
- }
-
- /**
- * Constructs an instance of an <code>Attribute</code> which is a copy of
- * another <code>Attribute</code>.
- *
- * @param attribute
- * the <code>Attribute</code> to copy; must not be <code>null</code>
- */
- public Attribute(Attribute attribute) {
- if (attribute == null) {
- throw new IllegalArgumentException("Parameter 'attribute' must not be null");
- }
- setName(attribute.getName());
- setAttributes(attribute.getAttributes());
- }
-
- /**
- * Returns the name of the Attribute.
- *
- * @return the name of the Attribute
- */
- public String getName() {
- return name;
- }
-
- /**
- * Sets the name of the Attribute.
- *
- * @param name
- * the name of the Attribute; must not be <code>null</code>
- */
- public void setName(String name) {
- if (name == null) {
- throw new IllegalArgumentException("Parameter 'name' must not be null");
- }
- this.name = name;
- }
-
- /**
- * Returns the qualified name of this <code>Attribute</code>.
- *
- * The qualified name is <code>containingDatasetName.attributeName</code>
- * or just <code>attributeName</code> if the <code>Attribute</code> is
- * not in a <code>Dataset</code>.
- *
- * @return the qualified name of this <code>Attribute</code>
- */
- public String getQualifiedName() {
- if (containingDataset == null) {
- return name;
- } else {
- return containingDataset.getName() + "." + getName();
- }
- }
-
- /**
- * Returns the component attributes as a comma separated list.
- *
- * @return the attributes as a comma separated list or null if there are no component attributes
- */
- public String getAttributes() {
- return attributes;
- }
-
- /**
- * Sets the attributes.
- *
- * @param attributes the new attributes
- */
- public void setAttributes(String attributes) {
- this.attributes = attributes;
- if (attributes == null) {
- attributesCount = 0;
- } else {
- attributesCount = attributes.split(",").length;
- }
- }
-
- /**
- * Returns the number of component attributes.
- *
- * @return the number of component attributes
- */
- public int getAttributesCount() {
- return attributesCount;
- }
-
- /**
- * Returns the Dataset containing this Attribute or null if it is not in a
- * Dataset.
- *
- * @return the Dataset containing this Attribute or null if it is not in a
- * Dataset
- */
- public Dataset getContainingDataset() {
- return containingDataset;
- }
-
- /**
- * Sets the containing Dataset.
- *
- * @param dataset
- * the containing Dataset
- */
- void setContainingDataset(Dataset dataset) {
- this.containingDataset = dataset;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see java.lang.Object#equals(java.lang.Object)
- */
- public boolean equals(Object obj) {
- boolean result = false;
- if (obj != null) {
- Attribute attribute = (Attribute) obj;
- String qualifiedName = getQualifiedName();
- if (qualifiedName == null) {
- result = attribute.getQualifiedName() == null;
- } else {
- result = qualifiedName.equals(attribute.getQualifiedName());
- }
- }
- return result;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see java.lang.Object#hashCode()
- */
- public int hashCode() {
- return getQualifiedName().hashCode();
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Dataset.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Dataset.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Dataset.java
deleted file mode 100644
index 20ea68f..0000000
--- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Dataset.java
+++ /dev/null
@@ -1,309 +0,0 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: Dataset.java,v $
- * Revision $Revision: 1.2 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/10/03 15:57:30 $
- * by $Author: davidwithers $
- * Created on 21-Apr-2006
- *****************************************************************/
-package org.biomart.martservice.query;
-
-import java.util.ArrayList;
-import java.util.List;
-
-/**
- * Class for creating dataset elements of mart queries.
- *
- * @author David Withers
- */
-public class Dataset {
- private String name;
-
- private List<Attribute> attributes = new ArrayList<Attribute>();
-
- private List<Filter> filters = new ArrayList<Filter>();
-
- private Query containingQuery;
-
- /**
- * Constructs an instance of a <code>Dataset</code> with the specified
- * name.
- *
- * @param name
- * the name of the <code>Dataset</code>
- */
- public Dataset(String name) {
- setName(name);
- }
-
- /**
- * Constructs an instance of a <code>Dataset</code> which is a deep copy
- * of another <code>Dataset</code>.
- *
- * @param dataset
- * the <code>Dataset</code> to copy
- */
- public Dataset(Dataset dataset) {
- setName(dataset.getName());
- for (Attribute attribute : dataset.getAttributes()) {
- addAttribute(new Attribute(attribute));
- }
- for (Filter filter : dataset.getFilters()) {
- addFilter(new Filter(filter));
- }
- }
-
- /**
- * Returns the name of the Dataset.
- *
- * @return the name of the Dataset.
- */
- public String getName() {
- return name;
- }
-
- /**
- * Set the name of the Dataset.
- *
- * @param name
- * the new name for this Dataset.
- */
- public void setName(String name) {
- this.name = name;
- }
-
- /**
- * Returns a List of the Attributes in this dataset.
- *
- * @return a List of the Attributes in this dataset
- */
- public List<Attribute> getAttributes() {
- return new ArrayList<Attribute>(attributes);
- }
-
- /**
- * Adds an Attribute to the dataset. The attribute's containing dataset will
- * be set to this dataset. If this dataset is in a query an attribute added
- * event will be fired.
- *
- * @param attribute
- * the Attribute to add
- * @return true if the Attribute is not already in the dataset
- */
- public boolean addAttribute(Attribute attribute) {
- if (!attributes.contains(attribute)) {
- attributes.add(attribute);
- attribute.setContainingDataset(this);
- if (containingQuery != null) {
- containingQuery.fireAttributeAdded(attribute, this);
- }
- return true;
- } else {
- return false;
- }
- }
-
- /**
- * Adds an array of Attributes to the dataset.
- *
- * @param attributeArray
- * the array of Attributes to add
- */
- public void addAttributes(Attribute[] attributeArray) {
- for (int i = 0; i < attributeArray.length; i++) {
- addAttribute(attributeArray[i]);
- }
- }
-
- /**
- * Returns true if attribute is in the dataset.
- *
- * @param attribute
- * @return true if attribute is in the dataset.
- */
- public boolean hasAttribute(Attribute attribute) {
- return attributes.contains(attribute);
- }
-
- /**
- * Returns true if the dataset contains any Attributes.
- *
- * @return true if the dataset contains any Attributes
- */
- public boolean hasAttributes() {
- return attributes.size() > 0;
- }
-
- /**
- * Removes an Attribute from the dataset.
- *
- * If the attribute is contained in this dataset:
- * <ul>
- * <li>The attribute's containing dataset will be set to null.
- * <li>If this dataset is in a query an attribute removed event will be fired.
- *
- * @param attribute
- * the attribute to remove
- * @return true if the attribute is removed
- */
- public boolean removeAttribute(Attribute attribute) {
- if (attributes.remove(attribute)) {
- attribute.setContainingDataset(null);
- if (containingQuery != null) {
- containingQuery.fireAttributeRemoved(attribute, this);
- }
- return true;
- } else {
- return false;
- }
- }
-
- /**
- * Removes all the Attributes from this dataset.
- */
- public void removeAllAttributes() {
- for (Attribute attribute : getAttributes()) {
- removeAttribute(attribute);
- }
- }
-
- /**
- * Returns a List of the Filters in this dataset.
- *
- * @return a List of the Filters in this dataset
- */
- public List<Filter> getFilters() {
- return new ArrayList<Filter>(filters);
- }
-
- /**
- * Adds a Filter to the dataset. The filter's containing dataset will be set
- * to this dataset. If this dataset is in a query a filter added event will
- * be fired.
- *
- * @param filter
- * the Filter to add
- * @return true if the Filter is not already in the dataset
- */
- public boolean addFilter(Filter filter) {
- if (!filters.contains(filter)) {
- filters.add(filter);
- filter.setContainingDataset(this);
- if (containingQuery != null) {
- containingQuery.fireFilterAdded(filter, this);
- }
- return true;
- } else {
- return false;
- }
- }
-
- /**
- * Adds an array of Filters to the dataset.
- *
- * @param filterArray
- * the array of Filters to add
- */
- public void addFilters(Filter[] filterArray) {
- for (int i = 0; i < filterArray.length; i++) {
- addFilter(filterArray[i]);
- }
- }
-
- /**
- * Returns true if filter is in the dataset.
- *
- * @param filter
- * @return true if filter is in the dataset
- */
- public boolean hasFilter(Filter filter) {
- return filters.contains(filter);
- }
-
- /**
- * Returns true if the dataset contains any filters.
- *
- * @return true if the dataset contains any filters
- */
- public boolean hasFilters() {
- return filters.size() > 0;
- }
-
- /**
- * Removes an Filter from the dataset.
- *
- * If the filter is contained in this dataset:
- * <ul>
- * <li>The filter's containing dataset will be set to null.
- * <li>If this dataset is in a query an attribute removed event will be fired.
- *
- * @param filter
- * the filter to remove
- * @return true if the filter is removed
- */
- public boolean removeFilter(Filter filter) {
- if (filters.remove(filter)) {
- filter.setContainingDataset(null);
- if (containingQuery != null) {
- containingQuery.fireFilterRemoved(filter, this);
- }
- return true;
- } else {
- return false;
- }
- }
-
- /**
- * Removes all the filters from the dataset.
- */
- public void removeAllFilters() {
- for (Filter filter : getFilters()) {
- removeFilter(filter);
- }
- }
-
- /**
- * Returns the containingQuery.
- *
- * @return the containingQuery.
- */
- public Query getContainingQuery() {
- return containingQuery;
- }
-
- /**
- * Sets the containingQuery.
- *
- * @param containingQuery
- * the containingQuery to set.
- */
- void setContainingQuery(Query containingQuery) {
- this.containingQuery = containingQuery;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Filter.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Filter.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Filter.java
deleted file mode 100644
index 1c088d0..0000000
--- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Filter.java
+++ /dev/null
@@ -1,243 +0,0 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: Filter.java,v $
- * Revision $Revision: 1.1 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/01/31 14:12:09 $
- * by $Author: davidwithers $
- * Created on 26-Apr-2006
- *****************************************************************/
-package org.biomart.martservice.query;
-
-/**
- * Class for creating filter elements of mart queries.
- *
- * @author David Withers
- */
-public class Filter {
- private String name;
-
- private String value;
-
- private boolean booleanFilter;
-
- private boolean listFilter;
-
- private Dataset containingDataset;
-
- /**
- * Constructs an instance of a <code>Filter</code> with the specified name.
- *
- * @param name
- * the name of the <code>Filter</code>; must not be <code>null</code>
- */
- public Filter(String name) {
- this(name, null);
- }
-
- /**
- * Constructs a instance of a <code>Filter</code> with the specified name
- * and value.
- *
- * @param name
- * the name of the <code>Filter</code>; must not be <code>null</code>
- * @param value
- * the value of the <code>Filter</code>
- */
- public Filter(String name, String value) {
- this(name, value, false);
- }
-
- /**
- * Constructs a instance of a <code>Filter</code> with the specified name
- * and value, and sets a flag to indicate if this is a boolean
- * <code>Filter</code>.
- *
- * @param name
- * the name of the <code>Filter</code>; must not be <code>null</code>
- * @param value
- * the value of the <code>Filter</code>
- * @param booleanFilter
- */
- public Filter(String name, String value, boolean booleanFilter) {
- if (name == null) {
- throw new IllegalArgumentException("Parameter 'name' must not be null");
- }
- this.name = name;
- this.value = value;
- this.booleanFilter = booleanFilter;
- }
-
- /**
- * Constructs an instance of a <code>Filter</code> which is a copy of
- * another <code>Filter</code>.
- *
- * @param filter
- * the <code>Filter</code> to copy; must not be <code>null</code>
- */
- public Filter(Filter filter) {
- if (filter == null) {
- throw new IllegalArgumentException("Parameter 'filter' must not be null");
- }
- this.name = filter.name;
- this.value = filter.value;
- this.booleanFilter = filter.booleanFilter;
- }
-
- /**
- * Returns the name of the Filter.
- *
- * @return the name of the Filter
- */
- public String getName() {
- return name;
- }
-
- /**
- * Sets the name of the Filter.
- *
- * @param name
- * the name of the Filter; must not be <code>null</code>
- */
- public void setName(String name) {
- if (name == null) {
- throw new IllegalArgumentException("Parameter 'name' must not be null");
- }
- this.name = name;
- }
-
- /**
- * Returns the qualified name of this <code>Filter</code>.
- *
- * The qualified name is <code>containingDatasetName.filterName</code> or
- * just <code>attributeName</code> if the <code>Filter</code> is not in
- * a <code>Dataset</code>.
- *
- * @return the qualified name of this <code>Filter</code>.
- */
- public String getQualifiedName() {
- if (containingDataset == null) {
- return name;
- } else {
- return containingDataset.getName() + "." + getName();
- }
- }
-
- /**
- * Returns the <code>Dataset</code> containing this <code>Filter</code>
- * or null if it is not in a <code>Dataset</code>.
- *
- * @return the <code>Dataset</code> containing this <code>Filter</code>
- * or null if it is not in a <code>Dataset</code>
- */
- public Dataset getContainingDataset() {
- return containingDataset;
- }
-
- /**
- * Sets the containing <code>Dataset</code>.
- *
- * @param dataset
- * the containing <code>Dataset</code>
- */
- void setContainingDataset(Dataset dataset) {
- this.containingDataset = dataset;
- }
-
- /**
- * Returns the value.
- *
- * @return the value.
- */
- public String getValue() {
- return value;
- }
-
- /**
- * Sets the value.
- *
- * @param value
- * the value to set.
- */
- public void setValue(String value) {
- boolean valueChanged = false;
- if (this.value == null) {
- if (value != null) {
- this.value = value;
- valueChanged = true;
- }
- } else if (!this.value.equals(value)) {
- this.value = value;
- valueChanged = true;
- }
- if (valueChanged) {
- if (containingDataset != null) {
- if (containingDataset.getContainingQuery() != null) {
- containingDataset.getContainingQuery().fireFilterChanged(
- this, containingDataset);
- }
- }
- }
- }
-
- /**
- * Returns <code>true</code> if this is a boolean filter.
- *
- * @return <code>true</code> if this is a boolean filter.
- */
- public boolean isBoolean() {
- return booleanFilter;
- }
-
- /**
- * Sets the booleanFilter flag.
- *
- * @param booleanFilter
- */
- public void setBoolean(boolean booleanFilter) {
- this.booleanFilter = booleanFilter;
- }
-
- /**
- * Returns <code>true</code> if this is a list filter.
- *
- * @return <code>true</code> if this is a list filter.
- */
- public boolean isList() {
- return listFilter;
- }
-
- /**
- * Sets the listFilter flag.
- *
- * @param listFilter
- */
- public void setList(boolean listFilter) {
- this.listFilter = listFilter;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Link.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Link.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Link.java
deleted file mode 100644
index 721428c..0000000
--- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Link.java
+++ /dev/null
@@ -1,181 +0,0 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: Link.java,v $
- * Revision $Revision: 1.1 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/01/31 14:12:09 $
- * by $Author: davidwithers $
- * Created on 26-Apr-2006
- *****************************************************************/
-package org.biomart.martservice.query;
-
-/**
- * Class for creating link elements of mart queries.
- *
- * @author David Withers
- */
-public class Link {
- private String source;
-
- private String target;
-
- private String defaultLink;
-
- private Query containingQuery;
-
- /**
- * Constructs an instance of a <code>Link</code>.
- *
- * @param source
- * the source dataset of the <code>Link</code>
- * @param target
- * the target dataset of the <code>Link</code>
- * @param defaultLink
- * the ID the links the datasets
- */
- public Link(String source, String target, String defaultLink) {
- this.source = source;
- this.target = target;
- this.defaultLink = defaultLink;
- }
-
- /**
- * Constructs an instance of a <code>Link</code> which is a copy of
- * another <code>Link</code>.
- *
- * @param filter
- * the <code>Link</code> to copy
- */
- public Link(Link link) {
- this.source = link.source;
- this.target = link.target;
- this.defaultLink = link.defaultLink;
- }
-
- /**
- * Returns the defaultLink.
- *
- * @return the defaultLink.
- */
- public String getDefaultLink() {
- return defaultLink;
- }
-
- /**
- * @param defaultLink
- * the defaultLink to set.
- */
- public void setDefaultLink(String defaultLink) {
- this.defaultLink = defaultLink;
- }
-
- /**
- * Returns the source dataset.
- *
- * @return the source dataset.
- */
- public String getSource() {
- return source;
- }
-
- /**
- * Sets the source dataset.
- *
- * @param source
- * the source dataset to set.
- */
- public void setSource(String source) {
- this.source = source;
- }
-
- /**
- * Returns the target dataset.
- *
- * @return the target dataset.
- */
- public String getTarget() {
- return target;
- }
-
- /**
- * Sets the target dataset.
- *
- * @param target
- * the target dataset to set.
- */
- public void setTarget(String target) {
- this.target = target;
- }
-
- /**
- * Returns the containingQuery.
- *
- * @return the containingQuery.
- */
- public Query getContainingQuery() {
- return containingQuery;
- }
-
- /**
- * Sets the containingQuery.
- *
- * @param containingQuery
- * the containingQuery to set.
- */
- void setContainingQuery(Query containingQuery) {
- this.containingQuery = containingQuery;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see java.lang.Object#equals(java.lang.Object)
- */
- public boolean equals(Object obj) {
- boolean result = false;
- if (obj != null) {
- Link link = (Link) obj;
- result = ((source == null && link.source == null) || source
- .equals(link.source))
- && ((target == null && link.target == null) || target
- .equals(link.target))
- && ((defaultLink == null && link.defaultLink == null) || defaultLink
- .equals(link.defaultLink));
- }
- return result;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see java.lang.Object#hashCode()
- */
- public int hashCode() {
- return source.hashCode() + target.hashCode() + defaultLink.hashCode();
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Query.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Query.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Query.java
deleted file mode 100644
index c7c9f20..0000000
--- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/Query.java
+++ /dev/null
@@ -1,555 +0,0 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: Query.java,v $
- * Revision $Revision: 1.4 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/10/03 15:57:30 $
- * by $Author: davidwithers $
- * Created on 03-Apr-2006
- *****************************************************************/
-package org.biomart.martservice.query;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.HashSet;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import org.biomart.martservice.MartServiceException;
-
-/**
- * Class for creating mart queries.
- *
- * @author David Withers
- */
-public class Query {
- private String virtualSchemaName;
-
- private int count;
-
- private int uniqueRows;
-
- private String softwareVersion;
-
- private String formatter;
-
- private String requestId;
-
- private List<Dataset> datasets = new ArrayList<Dataset>();
-
- private Map<String, Dataset> datasetMap = new HashMap<String, Dataset>();
-
- private Set<Link> links = new HashSet<Link>();
-
- private Map<String, Link> linkSourceMap = new HashMap<String, Link>();
-
- private List<QueryListener> listeners = new ArrayList<QueryListener>();
-
- /**
- * Constructs an instance of a <code>Query</code> with the specified
- * <code>virtualSchemaName</code> and a <code>count</code> of 0.
- *
- * @param virtualSchemaName
- */
- public Query(String virtualSchemaName) {
- this(virtualSchemaName, 0);
- }
-
- /**
- * Constructs an instance of a <code>Query</code> with the specified
- * <code>virtualSchemaName</code> and <code>count</code>.
- *
- * @param virtualSchemaName
- * @param count
- */
- public Query(String virtualSchemaName, int count) {
- setVirtualSchemaName(virtualSchemaName);
- setCount(count);
- }
-
- /**
- * Constructs an instance of a <code>Query</code> with the specified
- * <code>virtualSchemaName</code>, <code>softwareVersion</code> and
- * <code>requestId</code>.
- *
- * @param virtualSchemaName
- * @param softwareVersion
- * @param requestId
- */
- public Query(String virtualSchemaName, String softwareVersion,
- String requestId) {
- this(virtualSchemaName, 0, softwareVersion, requestId);
- }
-
- /**
- * Constructs an instance of a <code>Query</code> with the specified
- * <code>virtualSchemaName</code>, <code>count</code> and
- * <code>softwareVersion</code>.
- *
- * @param virtualSchemaName
- * @param count
- * @param softwareVersion
- */
- public Query(String virtualSchemaName, int count, String softwareVersion) {
- this(virtualSchemaName, count, softwareVersion, null);
- }
-
- /**
- * Constructs an instance of a <code>Query</code> with the specified
- * <code>virtualSchemaName</code>, <code>count</code>,
- * <code>softwareVersion</code> and <code>requestId</code>.
- *
- * @param virtualSchemaName
- * @param count
- * @param softwareVersion
- * @param requestId
- */
- public Query(String virtualSchemaName, int count, String softwareVersion,
- String requestId) {
- setVirtualSchemaName(virtualSchemaName);
- setCount(count);
- setSoftwareVersion(softwareVersion);
- setRequestId(requestId);
- }
-
- /**
- * Constructs an instance of a <code>Query</code> which is a deep copy of
- * another <code>Query</code>.
- *
- * @param query
- * the <code>Query</code> to copy
- * @throws MartServiceException
- */
- public Query(Query query) {
- setVirtualSchemaName(query.virtualSchemaName);
- setCount(query.count);
- setUniqueRows(query.uniqueRows);
- setSoftwareVersion(query.softwareVersion);
- setFormatter(query.formatter);
- setRequestId(query.requestId);
- for (Dataset dataset : query.getDatasets()) {
- addDataset(new Dataset(dataset));
- }
- for (Link link : query.getLinks()) {
- addLink(new Link(link));
- }
- }
-
- /**
- * Returns the virtualSchema.
- *
- * @return the virtualSchema.
- */
- public String getVirtualSchemaName() {
- return virtualSchemaName;
- }
-
- /**
- * Sets the virtualSchema.
- *
- * @param virtualSchemaName
- * the virtualSchema to set.
- */
- public void setVirtualSchemaName(String virtualSchemaName) {
- this.virtualSchemaName = virtualSchemaName;
- }
-
- /**
- * Returns the count.
- *
- * @return the count.
- */
- public int getCount() {
- return count;
- }
-
- /**
- * Sets the count.
- *
- * @param count
- * the count to set.
- */
- public void setCount(int count) {
- this.count = count;
- }
-
- /**
- * Returns the uniqueRows query attribute
- *
- * @return the uniqueRows query attribute
- */
- public int getUniqueRows() {
- return uniqueRows;
- }
-
- /**
- * Sets the uniqueRows query attribute.
- *
- * Valid values are 0 or 1.
- *
- * @param uniqueRows value for the uniqueRows query attribute
- */
- public void setUniqueRows(int uniqueRows) {
- this.uniqueRows = uniqueRows;
- }
-
- /**
- * Returns the softwareVersion.
- *
- * @return the softwareVersion
- */
- public String getSoftwareVersion() {
- return softwareVersion;
- }
-
- /**
- * Sets the softwareVersion.
- *
- * @param softwareVersion
- * the new softwareVersion
- */
- public void setSoftwareVersion(String softwareVersion) {
- this.softwareVersion = softwareVersion;
- }
-
- /**
- * Returns the formatter.
- *
- * @return the formatter
- */
- public String getFormatter() {
- return formatter;
- }
-
- /**
- * Sets the formatter.
- *
- * @param formatter the new formatter
- */
- public void setFormatter(String formatter) {
- if (this.formatter == null) {
- if (formatter != null) {
- this.formatter = formatter;
- fireFormatterAdded(formatter);
- }
- } else if (!this.formatter.equals(formatter)) {
- if (formatter == null) {
- String removedFormatter = this.formatter;
- this.formatter = formatter;
- fireFormatterRemoved(removedFormatter);
- } else {
- this.formatter = formatter;
- fireFormatterChanged(formatter);
- }
- }
- }
-
- /**
- * Returns the requestId.
- *
- * @return the requestId
- */
- public String getRequestId() {
- return requestId;
- }
-
- /**
- * Sets the requestId.
- *
- * @param requestId
- * the new requestId
- */
- public void setRequestId(String requestId) {
- this.requestId = requestId;
- }
-
- /**
- * Adds a Dataset to the Query.
- *
- * The Dataset is added at the end of the list of Datasets.
- *
- * @param dataset
- * the Dataset to add
- */
- public void addDataset(Dataset dataset) {
- addDataset(datasets.size(), dataset);
- }
-
- /**
- * Adds a Dataset to the Query at the specified position.
- *
- * @param index
- * the position to add the Dataset
- * @param dataset
- * the Dataset to add
- */
- public void addDataset(int index, Dataset dataset) {
- datasets.add(index, dataset);
- datasetMap.put(dataset.getName(), dataset);
- if (dataset.getContainingQuery() != null) {
- dataset.getContainingQuery().removeDataset(dataset);
- }
- dataset.setContainingQuery(this);
- }
-
- /**
- * Removes a Dataset from the Query.
- *
- * @param dataset
- * the Dataset to remove
- */
- public void removeDataset(Dataset dataset) {
- datasets.remove(dataset);
- datasetMap.remove(dataset.getName());
- dataset.setContainingQuery(null);
- }
-
- /**
- * Removes all the Datasets from the Query.
- */
- public void removeAllDatasets() {
- for (Dataset dataset : datasets) {
- dataset.setContainingQuery(null);
- }
- datasets.clear();
- datasetMap.clear();
- }
-
- /**
- * Returns the Datasets that this Query contains.
- *
- * @return the Datasets that this Query contains.
- */
- public List<Dataset> getDatasets() {
- return new ArrayList<Dataset>(datasets);
- }
-
- /**
- * Returns a Dataset with the given datasetName. If the Query has no Dataset
- * with the given datasetName null is returned.
- *
- * @param datasetName
- * @return a Dataset with the given datasetName
- */
- public Dataset getDataset(String datasetName) {
- return (Dataset) datasetMap.get(datasetName);
- }
-
- /**
- * Returns true if this Query contains a Dataset with the name
- * <code>datasetName</code>.
- *
- * @param datasetName
- * @return true if this Query contains a Dataset with the name
- * <code>datasetName</code>.
- */
- public boolean containsDataset(String datasetName) {
- return datasetMap.containsKey(datasetName);
- }
-
- /**
- * Adds a Link to the Query.
- *
- * @param link
- * the Link to add
- */
- public void addLink(Link link) {
- links.add(link);
- linkSourceMap.put(link.getSource(), link);
- if (link.getContainingQuery() != null) {
- link.getContainingQuery().removeLink(link);
- }
- link.setContainingQuery(this);
- }
-
- /**
- * Removes a link from the Query
- *
- * @param link
- * the Link to remove
- */
- public void removeLink(Link link) {
- links.remove(link);
- linkSourceMap.remove(link.getSource());
- link.setContainingQuery(null);
- }
-
- /**
- * Returns the Links that this Query contains.
- *
- * @return the Links that this Query contains.
- */
- public Set<Link> getLinks() {
- return new HashSet<Link>(links);
- }
-
- /**
- * Returns a Link with the given source. If the Query has no Link with the
- * given source null is returned.
- *
- * @param source
- * the source of the link
- * @return a Link with the given source
- */
- public Link getLink(String source) {
- return (Link) linkSourceMap.get(source);
- }
-
- /**
- * Returns true if this Query contains a Link with the same source.
- *
- * @param source
- * the source of the link
- * @return true if this Query contains a Link with the same source.
- */
- public boolean containsLink(String source) {
- return linkSourceMap.containsKey(source);
- }
-
- /**
- * Returns a List of Links with the given target. If the Query has no Link
- * with the given target an empty List is returned.
- *
- * @param target
- * the target of the link
- * @return a Link with the given target
- */
- public Set<Link> getLinks(String target) {
- Set<Link> result = new HashSet<Link>();
- Set<Link> links = getLinks();
- for (Link link: links) {
- if (link.getTarget().equals(target)) {
- result.add(link);
- }
- }
- return result;
- }
-
- /**
- * Returns all the Attributes from all the Datasets in this Query.
- *
- * @return all the Attributes from all the Datasets in this Query.
- */
- public List<Attribute> getAttributes() {
- List<Attribute> attributes = new ArrayList<Attribute>();
- for (Dataset dataset : datasets) {
- attributes.addAll(dataset.getAttributes());
- }
- return attributes;
- }
-
- /**
- * Returns all the Filters from all the Datasets in this Query.
- *
- * @return all the Filters from all the Datasets in this Query.
- */
- public List<Filter> getFilters() {
- List<Filter> filters = new ArrayList<Filter>();
- for (Dataset dataset : datasets) {
- filters.addAll(dataset.getFilters());
- }
- return filters;
- }
-
- /**
- * Adds the specified query listener to receive query events. If
- * <code>listener</code> is null, no exception is thrown and no action is
- * performed.
- *
- * @param listener
- * the query listener
- */
- public void addQueryListener(QueryListener listener) {
- if (listener != null) {
- listeners.add(listener);
- }
- }
-
- /**
- * Removes the specified query listener so that it no longer receives query
- * events. This method performs no function, nor does it throw an exception,
- * if <code>listener</code> was not previously added to this component. If
- * <code>listener</code> is null, no exception is thrown and no action is
- * performed.
- *
- * @param listener
- * the query listener
- */
- public void removeQueryListener(QueryListener listener) {
- listeners.remove(listener);
- }
-
- void fireAttributeAdded(Attribute attribute, Dataset dataset) {
- for (QueryListener listener : listeners) {
- listener.attributeAdded(attribute, dataset);
- }
- }
-
- void fireAttributeRemoved(Attribute attribute, Dataset dataset) {
- for (QueryListener listener : listeners) {
- listener.attributeRemoved(attribute, dataset);
- }
- }
-
- void fireFilterAdded(Filter filter, Dataset dataset) {
- for (QueryListener listener : listeners) {
- listener.filterAdded(filter, dataset);
- }
- }
-
- void fireFilterRemoved(Filter filter, Dataset dataset) {
- for (QueryListener listener : listeners) {
- listener.filterRemoved(filter, dataset);
- }
- }
-
- void fireFilterChanged(Filter filter, Dataset dataset) {
- for (QueryListener listener : listeners) {
- listener.filterChanged(filter, dataset);
- }
- }
-
- void fireFormatterAdded(String formatter) {
- for (QueryListener listener : listeners) {
- listener.formatterAdded(formatter);
- }
- }
-
- void fireFormatterRemoved(String formatter) {
- for (QueryListener listener : listeners) {
- listener.formatterRemoved(formatter);
- }
- }
-
- void fireFormatterChanged(String formatter) {
- for (QueryListener listener : listeners) {
- listener.formatterChanged(formatter);
- }
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/QueryListener.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/QueryListener.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/QueryListener.java
deleted file mode 100644
index 9f10f45..0000000
--- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/QueryListener.java
+++ /dev/null
@@ -1,108 +0,0 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: QueryListener.java,v $
- * Revision $Revision: 1.2 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/10/03 15:57:30 $
- * by $Author: davidwithers $
- * Created on 03-Apr-2006
- *****************************************************************/
-package org.biomart.martservice.query;
-
-/**
- * The listener interface for receiving Query events.
- *
- * @author David Withers
- */
-public interface QueryListener {
-
- /**
- * Invoked when an <code>Attribute</code> is added to a <code>Query</code>.
- *
- * @param attribute
- * the <code>Attribute</code> added.
- */
- public void attributeAdded(Attribute attribute, Dataset dataset);
-
- /**
- * Invoked when an <code>Attribute</code> is removed from a
- * <code>Query</code>.
- *
- * @param attribute
- * the <code>Attribute</code> removed.
- */
- public void attributeRemoved(Attribute attribute, Dataset dataset);
-
- /**
- * Invoked when a <code>Filter</code> is added to a <code>Query</code>.
- *
- * @param filter
- * the <code>Filter</code> added.
- */
- public void filterAdded(Filter filter, Dataset dataset);
-
- /**
- * Invoked when a <code>Filter</code> is removed from a <code>Query</code>.
- *
- * @param filter
- * the <code>Filter</code> removed.
- */
- public void filterRemoved(Filter filter, Dataset dataset);
-
- /**
- * Invoked when the value of a <code>Filter</code> is changed.
- *
- * @param filter
- * the <code>Filter</code> whose value has changed.
- */
- public void filterChanged(Filter filter, Dataset dataset);
-
- /**
- * Invoked when a formatter is added to a <code>Query</code>.
- *
- * @param formatter
- * the formatter added.
- */
- public void formatterAdded(String formatter);
-
- /**
- * Invoked when a formatter is removed from a <code>Query</code>.
- *
- * @param formatter
- * the formatter removed.
- */
- public void formatterRemoved(String formatter);
-
- /**
- * Invoked when the value of the formatter is changed.
- *
- * @param filter
- * the new value of the formatter.
- */
- public void formatterChanged(String formatter);
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/QueryXMLHandler.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/QueryXMLHandler.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/QueryXMLHandler.java
deleted file mode 100644
index 13c7791..0000000
--- a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/query/QueryXMLHandler.java
+++ /dev/null
@@ -1,332 +0,0 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: QueryXMLHandler.java,v $
- * Revision $Revision: 1.6 $
- * Release status $State: Exp $
- * Last modified on $Date: 2008/03/04 16:45:18 $
- * by $Author: davidwithers $
- * Created on 28-Apr-2006
- *****************************************************************/
-package org.biomart.martservice.query;
-
-import java.util.List;
-
-import org.jdom.Element;
-import org.jdom.Namespace;
-
-/**
- * Utility class for serializing <code>Query</code> classes to XML.
- *
- * @author David Withers
- */
-public class QueryXMLHandler {
- public static final String QUERY_ELEMENT = "Query";
-
- public static final String DATASET_ELEMENT = "Dataset";
-
- public static final String ATTRIBUTE_ELEMENT = "Attribute";
-
- public static final String FILTER_ELEMENT = "Filter";
-
- public static final String LINK_ELEMENT = "Links";
-
- public static final String ATTRIBUTES_ATTRIBUTE = "attributes";
-
- public static final String NAME_ATTRIBUTE = "name";
-
- public static final String COUNT_ATTRIBUTE = "count";
-
- public static final String UNIQUE_ROWS_ATTRIBUTE = "uniqueRows";
-
- public static final String VERSION_ATTRIBUTE = "softwareVersion";
-
- public static final String FORMATTER_ATTRIBUTE = "formatter";
-
- public static final String HEADER_ATTRIBUTE = "header";
-
- public static final String REQUEST_ID_ATTRIBUTE = "requestId";
-
- public static final String SCHEMA_ATTRIBUTE = "virtualSchemaName";
-
- /**
- * Converts a <code>Query</code> to an XML element.
- *
- * @param query
- * the <code>Query</code> to serialize
- * @param namespace
- * the <code>Namespace</code> to use when constructing the
- * <code>Element</code>
- * @return an XML serialization of the <code>Query</code>
- */
- public static Element queryToElement(Query query, Namespace namespace) {
- Element queryElement = new Element(QUERY_ELEMENT, namespace);
- String virtualSchemaName = query.getVirtualSchemaName();
- if (virtualSchemaName == null) {
- queryElement.setAttribute(SCHEMA_ATTRIBUTE, "default");
- } else {
- queryElement.setAttribute(SCHEMA_ATTRIBUTE, virtualSchemaName);
- }
- queryElement.setAttribute(COUNT_ATTRIBUTE, String.valueOf(query.getCount()));
- queryElement.setAttribute(UNIQUE_ROWS_ATTRIBUTE, String.valueOf(query.getUniqueRows()));
- String softwareVersion = query.getSoftwareVersion();
- if (softwareVersion != null) {
- queryElement.setAttribute(VERSION_ATTRIBUTE, softwareVersion);
- }
- String formatter = query.getFormatter();
- if (formatter != null) {
- queryElement.setAttribute(FORMATTER_ATTRIBUTE, formatter);
- queryElement.setAttribute(HEADER_ATTRIBUTE, "1");
- }
- String requestId = query.getRequestId();
- if (requestId != null) {
- queryElement.setAttribute(REQUEST_ID_ATTRIBUTE, requestId);
- }
- for (Dataset dataset : query.getDatasets()) {
- queryElement.addContent(datasetToElement(dataset, namespace));
- }
- for (Link link : query.getLinks()) {
- queryElement.addContent(linkToElement(link, namespace));
- }
-
- return queryElement;
- }
-
- /**
- * Converts a <code>Dataset</code> to an XML element.
- *
- * @param dataset
- * the <code>Dataset</code> to serialize
- * @param namespace
- * the <code>Namespace</code> to use when constructing the
- * <code>Element</code>
- * @return an XML serialization of the <code>Dataset</code>
- */
- public static Element datasetToElement(Dataset dataset, Namespace namespace) {
- Element datasetElement = new Element(DATASET_ELEMENT, namespace);
- datasetElement.setAttribute(NAME_ATTRIBUTE, dataset.getName());
-
- for (Attribute attribute : dataset.getAttributes()) {
- datasetElement.addContent(attributeToElement(attribute, namespace));
- }
-
- for (Filter filter : dataset.getFilters()) {
- datasetElement.addContent(filterToElement(filter, namespace));
- }
-
- return datasetElement;
- }
-
- /**
- * Converts a <code>Link</code> to an XML element.
- *
- * @param link
- * the <code>Link</code> to serialize
- * @param namespace
- * the <code>Namespace</code> to use when constructing the
- * <code>Element</code>
- * @return an XML serialization of the <code>Link</code>
- */
- public static Element linkToElement(Link link, Namespace namespace) {
- Element linkElement = new Element(LINK_ELEMENT, namespace);
- linkElement.setAttribute("source", link.getSource());
- linkElement.setAttribute("target", link.getTarget());
- linkElement.setAttribute("defaultLink", link.getDefaultLink());
- return linkElement;
- }
-
- /**
- * Converts an <code>Attribute</code> to an XML element.
- *
- * @param attribute
- * the <code>Attribute</code> to serialize
- * @param namespace
- * the <code>Namespace</code> to use when constructing the
- * <code>Element</code>
- * @return an XML serialization of the <code>Attribute</code>
- */
- public static Element attributeToElement(Attribute attribute,
- Namespace namespace) {
- Element attributeElement = new Element(ATTRIBUTE_ELEMENT, namespace);
- attributeElement.setAttribute(NAME_ATTRIBUTE, attribute.getName());
- String attributes = attribute.getAttributes();
- if (attributes != null) {
- attributeElement.setAttribute(ATTRIBUTES_ATTRIBUTE, attributes);
- }
- return attributeElement;
- }
-
- /**
- * Converts a <code>Filter</code> to an XML element.
- *
- * @param filter
- * the <code>Filter</code> to serialize
- * @param namespace
- * the <code>Namespace</code> to use when constructing the
- * <code>Element</code>
- * @return an XML serialization of the <code>Filter</code>
- */
- public static Element filterToElement(Filter filter, Namespace namespace) {
- Element filterElement = new Element(FILTER_ELEMENT, namespace);
- filterElement.setAttribute(NAME_ATTRIBUTE, filter.getName());
- String value = filter.getValue();
- if (filter.isBoolean()) {
- if ("excluded".equalsIgnoreCase(value)) {
- filterElement.setAttribute("excluded", "1");
- } else {
- filterElement.setAttribute("excluded", "0");
- }
- } else {
- if (value == null) {
- filterElement.setAttribute("value", "");
- } else {
- filterElement.setAttribute("value", value);
- }
- }
- if (filter.isList()) {
- filterElement.setAttribute("list", "true");
- }
- return filterElement;
- }
-
- /**
- * Creates a <code>Query</code> from an XML element.
- *
- * @param element
- * the <code>Element</code> to deserialize
- * @param namespace
- * the <code>Namespace</code> containing the
- * <code>Element</code>
- * @return a deserialized <code>Query</code>
- */
- public static Query elementToQuery(Element element, Namespace namespace) {
- String virtualSchema = element.getAttributeValue(SCHEMA_ATTRIBUTE);
- int count = Integer.parseInt(element.getAttributeValue(COUNT_ATTRIBUTE));
- String version = element.getAttributeValue(VERSION_ATTRIBUTE);
- String formatter = element.getAttributeValue(FORMATTER_ATTRIBUTE);
- String requestId = element.getAttributeValue(REQUEST_ID_ATTRIBUTE);
- Query query = new Query(virtualSchema, count, version, requestId);
- query.setFormatter(formatter);
- String uniqueRows = element.getAttributeValue(UNIQUE_ROWS_ATTRIBUTE);
- if (uniqueRows != null) {
- query.setUniqueRows(Integer.parseInt(uniqueRows));
- }
- List<Element> datasets = element.getChildren(DATASET_ELEMENT, namespace);
- for (Element datasetElement : datasets) {
- query.addDataset(elementToDataset(datasetElement, namespace));
- }
- List<Element> links = element.getChildren(LINK_ELEMENT, namespace);
- for (Element linkElement : links) {
- query.addLink(elementToLink(linkElement));
- }
- return query;
- }
-
- /**
- * Creates a <code>Dataset</code> from an XML element.
- *
- * @param element
- * the <code>Element</code> to deserialize
- * @param namespace
- * the <code>Namespace</code> containing the
- * <code>Element</code>
- * @return a deserialized <code>Dataset</code>
- */
- public static Dataset elementToDataset(Element element, Namespace namespace) {
- Dataset dataset = new Dataset(element.getAttributeValue(NAME_ATTRIBUTE));
-
- List<Element> attributes = element.getChildren(ATTRIBUTE_ELEMENT, namespace);
- for (Element attributeElement : attributes) {
- dataset.addAttribute(elementToAttribute(attributeElement));
- }
-
- List<Element> filters = element.getChildren(FILTER_ELEMENT, namespace);
- for (Element filterElement : filters) {
- dataset.addFilter(elementToFilter(filterElement));
- }
- return dataset;
- }
-
- /**
- * Creates a <code>Filter</code> from an XML element.
- *
- * @param element
- * the <code>Element</code> to deserialize
- * @return a deserialized <code>Filter</code>
- */
- public static Filter elementToFilter(Element element) {
- Filter filter;
- String filterName = element.getAttributeValue(NAME_ATTRIBUTE);
- String filterValue = element.getAttributeValue("value");
- if (filterValue != null) {
- filter = new Filter(filterName, filterValue);
- } else {
- filterValue = element.getAttributeValue("excluded");
- if ("1".equals(filterValue)) {
- filter = new Filter(filterName, "excluded", true);
- } else {
- filter = new Filter(filterName, "only", true);
- }
- }
- String listValue = element.getAttributeValue("list");
- if ("true".equals(listValue)) {
- filter.setList(true);
- }
- return filter;
- }
-
- /**
- * Creates an <code>Attribute</code> from an XML element.
- *
- * @param element
- * the <code>Element</code> to deserialize
- * @return a deserialized <code>Attribute</code>
- */
- public static Attribute elementToAttribute(Element element) {
- String attributeName = element.getAttributeValue(NAME_ATTRIBUTE);
- Attribute attribute = new Attribute(attributeName);
- String attributes = element.getAttributeValue(ATTRIBUTES_ATTRIBUTE);
- if (attributes != null) {
- attribute.setAttributes(attributes);
- }
- return attribute;
- }
-
- /**
- * Creates an <code>Link</code> from an XML element.
- *
- * @param element
- * the <code>Element</code> to deserialize
- * @return a deserialized <code>Link</code>
- * @deprecated MartJ 0.5 won't require links to be specified
- */
- public static Link elementToLink(Element element) {
- return new Link(element.getAttributeValue("source"), element
- .getAttributeValue("target"), element
- .getAttributeValue("defaultLink"));
- }
-
-}
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diff --git a/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/MartServiceQueryConfigUIFactory.java b/taverna-biomart-martservice/src/main/java/org/biomart/martservice/config/ui/MartServiceQueryConfigUIFactory.java
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-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: MartServiceQueryConfigUIFactory.java,v $
- * Revision $Revision: 1.6 $
- * Release status $State: Exp $
- * Last modified on $Date: 2008/03/04 16:46:53 $
- * by $Author: davidwithers $
- * Created on 21-Jun-2007
- *****************************************************************/
-package org.biomart.martservice.config.ui;
-
-import java.awt.BorderLayout;
-import java.awt.Color;
-import java.awt.Component;
-import java.awt.Container;
-import java.awt.Dimension;
-import java.awt.Font;
-import java.awt.Graphics;
-import java.awt.GridBagConstraints;
-import java.awt.GridBagLayout;
-import java.awt.GridLayout;
-import java.awt.Insets;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.ItemEvent;
-import java.awt.event.ItemListener;
-import java.io.BufferedReader;
-import java.io.File;
-import java.io.FileReader;
-import java.io.IOException;
-import java.util.ArrayList;
-import java.util.Arrays;
-import java.util.Collection;
-import java.util.Collections;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-import java.util.Set;
-
-import javax.swing.AbstractButton;
-import javax.swing.AbstractListModel;
-import javax.swing.Box;
-import javax.swing.BoxLayout;
-import javax.swing.ButtonGroup;
-import javax.swing.DefaultComboBoxModel;
-import javax.swing.DefaultListCellRenderer;
-import javax.swing.JButton;
-import javax.swing.JCheckBox;
-import javax.swing.JComboBox;
-import javax.swing.JComponent;
-import javax.swing.JFileChooser;
-import javax.swing.JLabel;
-import javax.swing.JList;
-import javax.swing.JOptionPane;
-import javax.swing.JPanel;
-import javax.swing.JProgressBar;
-import javax.swing.JRadioButton;
-import javax.swing.JScrollPane;
-import javax.swing.JSplitPane;
-import javax.swing.JTextArea;
-import javax.swing.JTextField;
-import javax.swing.ListModel;
-import javax.swing.SwingConstants;
-import javax.swing.border.AbstractBorder;
-import javax.swing.border.CompoundBorder;
-import javax.swing.border.EmptyBorder;
-import javax.swing.border.LineBorder;
-import javax.swing.event.DocumentEvent;
-import javax.swing.event.DocumentListener;
-
-import org.apache.log4j.Logger;
-import org.biomart.martservice.DatasetLink;
-import org.biomart.martservice.MartDataset;
-import org.biomart.martservice.MartQuery;
-import org.biomart.martservice.MartService;
-import org.biomart.martservice.MartServiceException;
-import org.biomart.martservice.config.QueryConfigController;
-import org.biomart.martservice.config.QueryConfigUtils;
-import org.biomart.martservice.config.event.QueryComponentAdapter;
-import org.biomart.martservice.config.event.QueryComponentEvent;
-import org.biomart.martservice.query.Attribute;
-import org.biomart.martservice.query.Dataset;
-import org.biomart.martservice.query.Filter;
-import org.biomart.martservice.query.Query;
-import org.biomart.martservice.query.QueryListener;
-import org.ensembl.mart.lib.config.AttributeCollection;
-import org.ensembl.mart.lib.config.AttributeDescription;
-import org.ensembl.mart.lib.config.AttributeGroup;
-import org.ensembl.mart.lib.config.AttributeList;
-import org.ensembl.mart.lib.config.AttributePage;
-import org.ensembl.mart.lib.config.BaseNamedConfigurationObject;
-import org.ensembl.mart.lib.config.DatasetConfig;
-import org.ensembl.mart.lib.config.FilterCollection;
-import org.ensembl.mart.lib.config.FilterDescription;
-import org.ensembl.mart.lib.config.FilterGroup;
-import org.ensembl.mart.lib.config.FilterPage;
-import org.ensembl.mart.lib.config.Option;
-import org.ensembl.mart.lib.config.PushAction;
-
-/**
- * Implementation of the <code>QueryConfigUIFactory</code> interface that
- * creates a UI which looks like the Biomart web interface.
- *
- * @author David Withers
- */
-public class MartServiceQueryConfigUIFactory implements QueryConfigUIFactory {
-
- private static Logger logger = Logger
- .getLogger(MartServiceQueryConfigUIFactory.class);
-
- private String version;
-
- private Color borderColor = new Color(202, 207, 213);
-
- private Color backgroundColor = Color.WHITE;
-
- private Color componentBackgroundColor = Color.WHITE;
-
- private MartService martService;
-
- private QueryConfigController controller;
-
- private MartDataset martDataset;
-
- private DatasetConfig datasetConfig;
-
- private Map<String, Component> filterNameToComponentMap = new HashMap<String, Component>();
-
- private Map<String, List<Component>> attributeNameToComponentMap = new HashMap<String, List<Component>>();
-
- private Map<String, String> filterToDisplayName = new HashMap<String, String>();
-
- private Map<String, String> attributeToDisplayName = new HashMap<String, String>();
-
- private Map<String, Component> attributePageNameToComponent = new HashMap<String, Component>();
-
- private Map<String, JRadioButton> attributePageNameToButton = new HashMap<String, JRadioButton>();
-
- private boolean settingAttributeState = false;
-
- private List<Component> componentRegister = new ArrayList<Component>();
-
- private int datasetNumber;
-
- public MartServiceQueryConfigUIFactory(MartService martService,
- QueryConfigController controller, MartDataset martDataset)
- throws MartServiceException {
- this(martService, controller, martDataset, 1);
- }
-
- public MartServiceQueryConfigUIFactory(MartService martService,
- QueryConfigController controller, MartDataset martDataset,
- int datasetNumber) throws MartServiceException {
- this.martService = martService;
- this.controller = controller;
- this.martDataset = martDataset;
- this.datasetNumber = datasetNumber;
- version = getConfigStyle();
- }
-
- private String getConfigStyle() {
- String configStyle = "0.5";
- String version = controller.getMartQuery().getQuery()
- .getSoftwareVersion();
- if (version == null || "0.4".equals(version)) {
- configStyle = "0.4";
- }
- return configStyle;
- }
-
- /**
- * Returns the martDataset.
- *
- * @return the martDataset.
- */
- public MartDataset getMartDataset() {
- return martDataset;
- }
-
- /**
- * Returns the query configuration for the dataset.
- *
- * @return the query configuration for the dataset
- * @throws MartServiceException
- * if the MartService returns an error or is unavailable
- */
- public DatasetConfig getDatasetConfig() throws MartServiceException {
- if (datasetConfig == null) {
- datasetConfig = martService.getDatasetConfig(martDataset);
- }
- return datasetConfig;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryConfigUIFactory#getDatasetConfigUI(org.ensembl.mart.lib.config.DatasetConfig)
- */
- public Component getDatasetConfigUI() throws MartServiceException {
- JPanel panel = new JPanel(new BorderLayout());
-
- final SummaryPanel summaryPanel = new SummaryPanel();
-
- final JButton countButton = new JButton("Count");
- countButton.setFont(countButton.getFont().deriveFont(Font.BOLD));
- countButton.setOpaque(false);
- countButton.addActionListener(new ActionListener() {
-
- public void actionPerformed(ActionEvent e) {
- countButton.setEnabled(false);
- countButton.setText("Counting...");
- new Thread("BiomartDatasetCount") {
- public void run() {
- try {
- MartQuery martQuery = controller.getMartQuery();
- Query query = martQuery.getQuery();
- String datasetName = martQuery.getMartDataset()
- .getName();
-
- JLabel label1 = summaryPanel
- .getDataset1CountLabel();
- setSummaryCount(query, datasetName, label1);
-
- Set<String> linkedDatasets = martQuery.getLinkedDatasets();
- if (linkedDatasets.size() == 1) {
- String linkedDatasetName = linkedDatasets
- .iterator().next();
- JLabel label2 = summaryPanel
- .getDataset2CountLabel();
- setSummaryCount(query, linkedDatasetName,
- label2);
- }
-
- } catch (MartServiceException e) {
- }
- countButton.setText("Count");
- countButton.setEnabled(true);
- }
- }.start();
- }
-
- });
-
- final JCheckBox uniqueCheckBox = new JCheckBox("Unique results only");
- uniqueCheckBox.setBackground(Color.BLACK);
- uniqueCheckBox.setForeground(Color.WHITE);
- uniqueCheckBox.setSelected(controller.getMartQuery().getQuery()
- .getUniqueRows() == 1);
-
- uniqueCheckBox.addItemListener(new ItemListener() {
- public void itemStateChanged(ItemEvent e) {
- if (e.getStateChange() == ItemEvent.SELECTED) {
- controller.getMartQuery().getQuery().setUniqueRows(1);
- } else if (e.getStateChange() == ItemEvent.DESELECTED) {
- controller.getMartQuery().getQuery().setUniqueRows(0);
- }
- }
- });
-
- JPanel buttonPanel = new JPanel(new BorderLayout());
- buttonPanel.setBackground(Color.BLACK);
- buttonPanel.setBorder(new EmptyBorder(5, 5, 5, 5));
- buttonPanel.add(countButton, BorderLayout.WEST);
- buttonPanel.add(uniqueCheckBox, BorderLayout.EAST);
- panel.add(buttonPanel, BorderLayout.NORTH);
-
- JLabel label = new JLabel("biomart version 0.6");
- label.setBackground(Color.BLACK);
- label.setForeground(Color.WHITE);
- label.setOpaque(true);
- label.setBorder(new EmptyBorder(5, 5, 5, 5));
- panel.add(label, BorderLayout.SOUTH);
-
- JSplitPane splitPanel = new JSplitPane(JSplitPane.HORIZONTAL_SPLIT,
- true);
- splitPanel.setBackground(backgroundColor);
- splitPanel.setBorder(new EmptyBorder(10, 0, 10, 0));
- splitPanel.setDividerLocation(250);
-
- panel.add(splitPanel, BorderLayout.CENTER);
-
- JScrollPane scrollPane1 = new JScrollPane(summaryPanel);
- scrollPane1.getVerticalScrollBar().setUnitIncrement(10);
- scrollPane1.setBorder(new LineBorder(Color.BLACK, 1));
-
- splitPanel.setLeftComponent(scrollPane1);
-
- final JComponent inputPanel = createVerticalBox(backgroundColor);
- inputPanel.setBorder(new EmptyBorder(10, 5, 10, 5));
-
- JScrollPane scrollPane = new JScrollPane(inputPanel);
- scrollPane.getVerticalScrollBar().setUnitIncrement(10);
- scrollPane.setBorder(new LineBorder(Color.BLACK, 1));
-
- splitPanel.setRightComponent(scrollPane);
-
- final JComponent datasetPanel = new DatasetPanel();
- inputPanel.add(datasetPanel);
-
-// final Component linkComponent = new DatasetLinkComponent(inputPanel,
-// summaryPanel);
-// componentRegister.add(linkComponent);
-
- final JComponent attributePanel = createVerticalBox(backgroundColor);
- attributePanel.setBorder(new EmptyBorder(10, 5, 10, 5));
-
- final JComponent filterPanel = createVerticalBox(backgroundColor);
- filterPanel.setBorder(new EmptyBorder(10, 5, 10, 5));
-
- summaryPanel.getDataset1Button().addActionListener(
- new ActionListener() {
- public void actionPerformed(ActionEvent e) {
- inputPanel.removeAll();
- inputPanel.add(datasetPanel);
- inputPanel.revalidate();
- inputPanel.repaint();
- }
- });
-
-// summaryPanel.getDataset2Button().addActionListener(
-// new ActionListener() {
-// public void actionPerformed(ActionEvent e) {
-// inputPanel.removeAll();
-// inputPanel.add(linkComponent);
-// inputPanel.revalidate();
-// inputPanel.repaint();
-// }
-// });
-
- generateConfiguration(this, summaryPanel, inputPanel, attributePanel,
- filterPanel);
-
- summaryPanel.getFilters1Button().addActionListener(
- new ActionListener() {
- public void actionPerformed(ActionEvent e) {
- inputPanel.removeAll();
- inputPanel.add(filterPanel);
- inputPanel.revalidate();
- inputPanel.repaint();
- }
- });
-
- summaryPanel.getAttributes1Button().addActionListener(
- new ActionListener() {
- public void actionPerformed(ActionEvent e) {
- inputPanel.removeAll();
- inputPanel.add(attributePanel);
- inputPanel.revalidate();
- inputPanel.repaint();
- }
- });
-
- return panel;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryConfigUIFactory#getAttributePagesUI(org.ensembl.mart.lib.config.AttributePage[])
- */
- public Component getAttributePagesUI(AttributePage[] attributePages,
- Object data) throws MartServiceException {
- final JComponent box = createVerticalBox(backgroundColor);
-
- final JComboBox formatList = new JComboBox();
- formatList.setBackground(backgroundColor);
-
- if (datasetNumber == 1) {
- formatList.addItemListener(new ItemListener() {
- public void itemStateChanged(ItemEvent e) {
- if (e.getStateChange() == ItemEvent.SELECTED) {
- controller.getMartQuery().getQuery().setFormatter(
- (String) e.getItem());
- }
- }
- });
-
- ButtonGroup outputButtons = new ButtonGroup();
- JRadioButton multipleOutput = new JRadioButton(
- "Multiple outputs (one per attribute)");
- multipleOutput.setBackground(backgroundColor);
- JRadioButton singleOutput = new JRadioButton(
- "Single output formatted as");
- singleOutput.setBackground(backgroundColor);
- outputButtons.add(multipleOutput);
- outputButtons.add(singleOutput);
- if (controller.getMartQuery().getQuery().getFormatter() == null) {
- multipleOutput.setSelected(true);
- formatList.setEnabled(false);
- } else {
- singleOutput.setSelected(true);
- formatList.setEnabled(true);
- }
-
- singleOutput.addItemListener(new ItemListener() {
- public void itemStateChanged(ItemEvent e) {
- if (e.getStateChange() == ItemEvent.SELECTED) {
- controller.getMartQuery().getQuery().setFormatter(
- (String) formatList.getSelectedItem());
- formatList.setEnabled(true);
- } else if (e.getStateChange() == ItemEvent.DESELECTED) {
- controller.getMartQuery().getQuery().setFormatter(null);
- formatList.setEnabled(false);
- }
- }
- });
-
- JPanel multipleOutputBox = new JPanel(new MinimalLayout());
- multipleOutputBox.setBackground(componentBackgroundColor);
- multipleOutputBox.add(multipleOutput);
-
- JComponent formatBox = createHorizontalBox(backgroundColor);
- formatBox.add(singleOutput);
- formatBox.add(Box.createHorizontalStrut(10));
- formatBox.add(formatList);
- formatBox.add(Box.createHorizontalGlue());
-
- JComponent outputBox = createVerticalBox(backgroundColor);
- outputBox.setBorder(new CompoundBorder(new LineBorder(borderColor,
- 1), new EmptyBorder(10, 10, 10, 10)));
- outputBox.add(multipleOutputBox);
- outputBox.add(formatBox);
-
- box.add(Box.createVerticalStrut(2));
- box.add(outputBox);
-
- }
-
- if (attributePages.length > 1) {
- ButtonGroup buttonGroup = new ButtonGroup();
- final Map<String, Component> componentMap = new HashMap<String, Component>();
- final Map<String, List<String>> formatMap = new HashMap<String, List<String>>();
-
- final JComponent buttonBox = new JPanel(new GridLayout(0, 2));
- buttonBox.setBorder(new CompoundBorder(new LineBorder(borderColor,
- 1), new EmptyBorder(10, 10, 10, 10)));
- buttonBox.setBackground(backgroundColor);
- box.add(buttonBox, 0);
-
- final JComponent pagePanel = new JPanel(new BorderLayout());
- pagePanel.setBackground(backgroundColor);
- box.add(pagePanel);
-
- ItemListener listener = new ItemListener() {
- Component lastSelectedComponent;
-
- JRadioButton lastSelectedButton;
-
- public void itemStateChanged(ItemEvent e) {
- JRadioButton button = (JRadioButton) e.getItem();
- if (button != null) {
- Component selectedComponent = componentMap.get(button
- .getActionCommand());
- if (e.getStateChange() == ItemEvent.SELECTED) {
- boolean switchPage = true;
- if (lastSelectedComponent != null) {
- Map<String, AttributeComponent> selected = new HashMap<String, AttributeComponent>();
- // find all attributes on the last page that
- // were selected
- List<AttributeComponent> oldChildren = getAttributeComponents(lastSelectedComponent);
- for (AttributeComponent attributeComponent : oldChildren) {
- if (attributeComponent.isSelected()) {
- selected.put(attributeComponent
- .getQualifiedName(),
- attributeComponent);
- }
- }
- // remove attributes that are already selected
- // on
- // the new page
- List<AttributeComponent> newChildren = getAttributeComponents(selectedComponent);
- for (AttributeComponent attributeComponent : newChildren) {
- if (attributeComponent.isSelected()) {
- selected.remove(attributeComponent
- .getQualifiedName());
- }
- }
- Collection<AttributeComponent> stillSelected = selected
- .values();
- if (stillSelected.size() > 0) {
- List<String> attributeNames = new ArrayList<String>();
- for (AttributeComponent component : stillSelected) {
- attributeNames.add(component
- .getButton().getText());
- }
- List<Object> message = new ArrayList<Object>();
- message
- .add("The "
- + button.getText()
- + " page does not contain the following attributes:");
- JList jList = new JList(attributeNames
- .toArray());
- jList.setBorder(LineBorder
- .createGrayLineBorder());
- message.add(jList);
- message
- .add("These attributes will be removed. Do you wish to continue?");
- switchPage = JOptionPane.showConfirmDialog(
- buttonBox, message.toArray(),
- "Confirm page change",
- JOptionPane.YES_NO_OPTION) == JOptionPane.YES_OPTION;
- }
- if (switchPage) {
- // deselect any attributes on the old page
- // that are not on the new page
- for (AttributeComponent attributeComponent : stillSelected) {
- attributeComponent.setSelected(false);
- }
- }
- }
- if (switchPage) {
- pagePanel.add(selectedComponent,
- BorderLayout.NORTH);
- if (datasetNumber == 1) {
- List<String> formats = formatMap.get(button
- .getActionCommand());
- formatList
- .setModel(new DefaultComboBoxModel(
- formats.toArray()));
- String formatter = controller
- .getMartQuery().getQuery()
- .getFormatter();
- if (formatter != null) {
- formatList.getModel().setSelectedItem(
- null);
- if (formats.contains(formatter)) {
- formatList.getModel()
- .setSelectedItem(formatter);
- } else if (formats.size() > 0) {
- formatList.getModel()
- .setSelectedItem(
- formats.get(0));
- }
- }
- }
- } else {
- lastSelectedButton.setSelected(true);
- }
- box.revalidate();
- box.repaint();
- } else if (e.getStateChange() == ItemEvent.DESELECTED) {
- pagePanel.removeAll();
- lastSelectedComponent = selectedComponent;
- lastSelectedButton = button;
- }
- }
- }
-
- };
-
- for (int i = 0; i < attributePages.length; i++) {
- if (QueryConfigUtils.display(attributePages[i])) {
- Component component = getAttributePageUI(attributePages[i],
- data);
- JRadioButton button = new JRadioButton(attributePages[i]
- .getDisplayName());
- String description = attributePages[i].getDescription();
- if (description != null) {
- button.setToolTipText(description);
- }
- button.setBackground(backgroundColor);
- button.setFont(button.getFont().deriveFont(Font.BOLD));
- button
- .setActionCommand(attributePages[i]
- .getInternalName());
- button.addItemListener(listener);
- buttonGroup.add(button);
- buttonBox.add(button);
- componentMap.put(attributePages[i].getInternalName(),
- component);
- formatMap.put(attributePages[i].getInternalName(), getFormatList(attributePages[i]));
- attributePageNameToComponent.put(attributePages[i]
- .getInternalName(), component);
- attributePageNameToButton.put(attributePages[i]
- .getInternalName(), button);
- }
- }
-
- } else if (attributePages.length == 1) {
- if (datasetNumber == 1) {
- List<String> formats = Arrays.asList(attributePages[0]
- .getOutFormats().toUpperCase().split(","));
- formatList
- .setModel(new DefaultComboBoxModel(formats.toArray()));
- String formatter = controller.getMartQuery().getQuery()
- .getFormatter();
- if (formatter != null) {
- formatList.getModel().setSelectedItem(null);
- if (formats.contains(formatter)) {
- formatList.getModel().setSelectedItem(formatter);
- } else if (formats.size() > 0) {
- formatList.getModel().setSelectedItem(formats.get(0));
- }
- }
- }
- box.add(getAttributePageUI(attributePages[0], data));
-
- } else {
- box.add(new JLabel("No attributes available"));
- }
-
- JPanel northPanel = new JPanel(new BorderLayout());
- northPanel.setBackground(backgroundColor);
- northPanel.add(box, BorderLayout.NORTH);
-
- return northPanel;
-
- // return box;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryConfigUIFactory#getAttributePageUI(org.ensembl.mart.lib.config.AttributePage)
- */
- public Component getAttributePageUI(AttributePage attributePage, Object data)
- throws MartServiceException {
- JComponent box = createVerticalBox(backgroundColor);
-
- AttributeGroup[] attributeGroups = (AttributeGroup[]) attributePage
- .getAttributeGroups().toArray(new AttributeGroup[0]);
-
- box.add(getAttributeGroupsUI(attributeGroups, data));
-
- return box;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryConfigUIFactory#getAttributeGroupsUI(org.ensembl.mart.lib.config.AttributeGroup[])
- */
- public Component getAttributeGroupsUI(AttributeGroup[] attributeGroups,
- Object data) throws MartServiceException {
- JComponent box = createVerticalBox(backgroundColor);
-
- for (int i = 0; i < attributeGroups.length; i++) {
- if (QueryConfigUtils.display(attributeGroups[i])) {
- box.add(Box.createVerticalStrut(2));
- box.add(getAttributeGroupUI(attributeGroups[i], data));
- }
- }
-
- return box;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryConfigUIFactory#getAttributeGroupUI(org.ensembl.mart.lib.config.AttributeGroup)
- */
- public Component getAttributeGroupUI(AttributeGroup attributeGroup,
- Object data) throws MartServiceException {
- JLabel title = new JLabel(attributeGroup.getDisplayName());
- title.setFont(title.getFont().deriveFont(Font.PLAIN));
-
- String description = attributeGroup.getDescription();
- if (description != null) {
- title.setToolTipText(description);
- }
- ExpandableBox box = new ExpandableBox(title, componentBackgroundColor,
- borderColor, new Insets(10, 10, 10, 10));
-
- AttributeCollection[] attributeCollections = attributeGroup
- .getAttributeCollections();
- box.add(getAttributeCollectionsUI(attributeCollections, data));
-
- box.setExpanded(false);
-
- return box;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryConfigUIFactory#getAttributeCollectionsUI(org.ensembl.mart.lib.config.AttributeCollection[])
- */
- public Component getAttributeCollectionsUI(
- AttributeCollection[] attributeCollections, Object data)
- throws MartServiceException {
- JComponent box = createVerticalBox(componentBackgroundColor);
-
- for (int i = 0; i < attributeCollections.length; i++) {
- if (QueryConfigUtils.display(attributeCollections[i])) {
- box.add(Box.createVerticalStrut(10));
- box
- .add(getAttributeCollectionUI(attributeCollections[i],
- data));
- }
- }
-
- return box;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryConfigUIFactory#getAttributeCollectionUI(org.ensembl.mart.lib.config.AttributeCollection)
- */
- public Component getAttributeCollectionUI(
- AttributeCollection attributeCollection, Object data)
- throws MartServiceException {
- JComponent box = null;
-
- AttributeDescription[] attributeDescriptions = (AttributeDescription[]) attributeCollection
- .getAttributeDescriptions()
- .toArray(new AttributeDescription[0]);
-
- AttributeList[] attributeLists = (AttributeList[]) attributeCollection
- .getAttributeLists().toArray(new AttributeList[0]);
-
- JLabel sequenceLabel = null;
- if ("seq_scope_type".equals(attributeCollection.getInternalName())) {
- sequenceLabel = new JLabel(MartServiceIcons
- .getIcon("gene_schematic"));
- box = createBox(sequenceLabel, false);
- } else if (attributeDescriptions.length > 1
- || attributeLists.length > 1) {
- // more than one attribute so create a box with the collection name
- // as a header
- JLabel title = new JLabel(attributeCollection.getDisplayName());
- title.setFont(title.getFont().deriveFont(Font.BOLD));
- String description = attributeCollection.getDescription();
- if (description != null) {
- title.setToolTipText(description);
- }
- box = createBox(title, false);
- } else {
- box = createBox(null, false);
- }
-
- int maxSelect = attributeCollection.getMaxSelect();
- if (maxSelect == 1) {
- if (attributeDescriptions.length > 0) {
- box.add(getAttributeDescriptionsUI(attributeDescriptions,
- new Object[] { SINGLE_SELECTION, sequenceLabel }));
- } else {
- box.add(getAttributeListsUI(attributeLists, new Object[] {
- SINGLE_SELECTION, sequenceLabel }));
- }
- } else {
- if (attributeDescriptions.length > 0) {
- box.add(getAttributeDescriptionsUI(attributeDescriptions,
- new Object[] { MULTIPLE_SELECTION, sequenceLabel }));
- } else {
- box.add(getAttributeListsUI(attributeLists, new Object[] {
- MULTIPLE_SELECTION, sequenceLabel }));
- }
- }
-
- return box;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryConfigUIFactory#getAttributeDescriptionsUI(org.ensembl.mart.lib.config.AttributeDescription[],
- * int)
- */
- public Component getAttributeDescriptionsUI(
- AttributeDescription[] attributeDescriptions, Object data)
- throws MartServiceException {
- Object[] dataArray = (Object[]) data;
- JComponent box = new JPanel(new GridLayout(1, 2));
- box.setBackground(componentBackgroundColor);
- JComponent box1 = createVerticalBox(componentBackgroundColor);
- JComponent box2 = createVerticalBox(componentBackgroundColor);
- box.add(box1);
- box.add(box2);
-
- // button group used if the attribute collection is SINGLE_SELECTION
- ButtonGroup buttonGroup = new ButtonGroup();
- JRadioButton off = new JRadioButton("OFF");
- buttonGroup.add(off);
-
- JComponent currentBox = box1;
-
- for (int i = 0; i < attributeDescriptions.length; i++) {
- if (QueryConfigUtils.display(attributeDescriptions[i])) {
- Component component = getAttributeDescriptionUI(
- attributeDescriptions[i],
- dataArray[0] == SINGLE_SELECTION ? new Object[] { off,
- dataArray[1] } : new Object[] { null,
- dataArray[1] });
- if (component != null) {
- currentBox.add(component);
- if (dataArray[0] == SINGLE_SELECTION
- && component instanceof AttributeComponent) {
- AttributeComponent attributeComponent = (AttributeComponent) component;
- buttonGroup.add(attributeComponent.getButton());
- }
- if (QueryConfigUtils.isFilterReference(
- attributeDescriptions[i], version)) {
- FilterDescription filterDescription = QueryConfigUtils
- .getReferencedFilterDescription(
- attributeDescriptions[i], version);
- Component filterComponent = getFilterDescriptionUI(
- filterDescription, data);
- if (filterComponent instanceof QueryComponent
- && component instanceof AttributeComponent) {
- AttributeComponent attributeComponent = (AttributeComponent) component;
- ((QueryComponent) filterComponent)
- .setSelectorButton(attributeComponent
- .getButton());
- }
- componentRegister.add(filterComponent);
- box2.add(filterComponent);
- currentBox = box2;
- }
- if (currentBox == box1) {
- currentBox = box2;
- } else {
- currentBox = box1;
- }
- }
- }
- }
- currentBox.add(Box.createVerticalGlue());
- return box;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryConfigUIFactory#getAttributeDescriptionUI(org.ensembl.mart.lib.config.AttributeDescription,
- * int)
- */
- public Component getAttributeDescriptionUI(
- AttributeDescription attributeDescription, Object data)
- throws MartServiceException {
- Object[] dataArray = (Object[]) data;
- MartDataset dataset = martDataset;
- AttributeDescription displayedAttribute;
- if (QueryConfigUtils.isReference(attributeDescription, version)) {
- dataset = QueryConfigUtils.getReferencedDataset(martService,
- martDataset, attributeDescription, version);
- if (dataset == null) {
- return null;
- }
- if (QueryConfigUtils.isFilterReference(attributeDescription,
- version)) {
- FilterDescription filter = QueryConfigUtils
- .getReferencedFilterDescription(martService, dataset,
- attributeDescription, version);
- if (filter == null) {
- return null;
- }
- displayedAttribute = attributeDescription;
- displayedAttribute.setDisplayName(filter.getDisplayName());
- filterToDisplayName.put(filter.getInternalName(), filter
- .getDisplayName());
- } else {
- displayedAttribute = QueryConfigUtils
- .getReferencedAttributeDescription(martService,
- dataset, attributeDescription, version);
- if (displayedAttribute == null) {
- // if the reference can't be resolved the the attribute just
- // doesn't get displayed
- return null;
- }
- }
- } else {
- displayedAttribute = attributeDescription;
- }
-
- final AttributeComponent component = new AttributeComponent(
- displayedAttribute, martDataset, dataArray[0]);
- component.setPointerDataset(attributeDescription
- .getAttribute("pointerDataset"));
- if (!QueryConfigUtils.isFilterReference(attributeDescription, version)) {
- if (!attributeNameToComponentMap.containsKey(component
- .getQualifiedName())) {
- attributeNameToComponentMap.put(component.getQualifiedName(),
- new ArrayList<Component>());
- }
- attributeNameToComponentMap.get(component
- .getQualifiedName()).add(component);
- componentRegister.add(component);
- // nasty hard coded rules that aren't in the configs
- // component.addQueryComponentListener(new QueryComponentAdapter() {
- // public void attributeAdded(QueryComponentEvent event) {
- // String name = component.getName();
- // String dataset = component.getDataset().getName();
- // if (name.equals("coding_gene_flank")
- // || name.equals("coding_transcript_flank")
- // || name.equals("transcript_flank")
- // || name.equals("gene_flank")) {
- // QueryComponent filterComponent = (QueryComponent)
- // filterNameToComponentMap
- // .get("upstream_flank");
- // if (filterComponent != null) {
- // filterComponent.setSelected(true);
- // }
- // filterComponent = (QueryComponent) filterNameToComponentMap
- // .get("downstream_flank");
- // if (filterComponent != null) {
- // filterComponent.setSelected(true);
- // }
- // }
- // }
- //
- // });
- }
- if (dataArray[1] instanceof JLabel) {
- final JLabel sequenceLabel = (JLabel) dataArray[1];
- component.addQueryComponentListener(new QueryComponentAdapter() {
- public void attributeAdded(QueryComponentEvent event) {
- String name = component.getName();
- if ("3utr".equals(name)) {
- sequenceLabel.setIcon(MartServiceIcons
- .getIcon("gene_schematic_3utr"));
- } else if ("5utr".equals(name)) {
- sequenceLabel.setIcon(MartServiceIcons
- .getIcon("gene_schematic_5utr"));
- } else if ("cdna".equals(name)) {
- sequenceLabel.setIcon(MartServiceIcons
- .getIcon("gene_schematic_cdna"));
- } else if ("coding_gene_flank".equals(name)) {
- sequenceLabel.setIcon(MartServiceIcons
- .getIcon("gene_schematic_coding_gene_flank"));
- } else if ("coding_transcript_flank".equals(name)) {
- sequenceLabel
- .setIcon(MartServiceIcons
- .getIcon("gene_schematic_coding_transcript_flank"));
- } else if ("coding".equals(name)) {
- sequenceLabel.setIcon(MartServiceIcons
- .getIcon("gene_schematic_coding"));
- } else if ("gene_exon_intron".equals(name)) {
- sequenceLabel.setIcon(MartServiceIcons
- .getIcon("gene_schematic_gene_exon_intron"));
- } else if ("gene_exon".equals(name)) {
- sequenceLabel.setIcon(MartServiceIcons
- .getIcon("gene_schematic_gene_exon"));
- } else if ("gene_flank".equals(name)) {
- sequenceLabel.setIcon(MartServiceIcons
- .getIcon("gene_schematic_gene_flank"));
- } else if ("peptide".equals(name)) {
- sequenceLabel.setIcon(MartServiceIcons
- .getIcon("gene_schematic_peptide"));
- } else if ("transcript_exon_intron".equals(name)) {
- sequenceLabel
- .setIcon(MartServiceIcons
- .getIcon("gene_schematic_transcript_exon_intron"));
- } else if ("transcript_exon".equals(name)) {
- sequenceLabel.setIcon(MartServiceIcons
- .getIcon("gene_schematic_transcript_exon"));
- } else if ("transcript_flank".equals(name)) {
- sequenceLabel.setIcon(MartServiceIcons
- .getIcon("gene_schematic_transcript_flank"));
- }
- }
-
- });
- }
- return component;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryConfigUIFactory#getAttributeListsUI(org.ensembl.mart.lib.config.AttributeList[],
- * int)
- */
- public Component getAttributeListsUI(AttributeList[] attributeLists,
- Object data) throws MartServiceException {
- Object[] dataArray = (Object[]) data;
- JComponent box = new JPanel(new GridLayout(1, 2));
- box.setBackground(componentBackgroundColor);
- JComponent box1 = createVerticalBox(componentBackgroundColor);
- JComponent box2 = createVerticalBox(componentBackgroundColor);
- box.add(box1);
- box.add(box2);
-
- // button group used if the attribute collection is SINGLE_SELECTION
- ButtonGroup buttonGroup = new ButtonGroup();
- JRadioButton off = new JRadioButton("OFF");
- buttonGroup.add(off);
-
- JComponent currentBox = box1;
-
- for (int i = 0; i < attributeLists.length; i++) {
- if (QueryConfigUtils.display(attributeLists[i])) {
- Component component = getAttributeListUI(attributeLists[i],
- dataArray[0] == SINGLE_SELECTION ? new Object[] { off,
- dataArray[1] } : new Object[] { null,
- dataArray[1] });
- if (component != null) {
- currentBox.add(component);
- if (dataArray[0] == SINGLE_SELECTION
- && component instanceof AttributeComponent) {
- AttributeComponent attributeComponent = (AttributeComponent) component;
- buttonGroup.add(attributeComponent.getButton());
- }
- if (currentBox == box1) {
- currentBox = box2;
- } else {
- currentBox = box1;
- }
- }
- }
- }
- currentBox.add(Box.createVerticalGlue());
- return box;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryConfigUIFactory#getAttributeListUI(org.ensembl.mart.lib.config.AttributeList,
- * int)
- */
- public Component getAttributeListUI(AttributeList attributeList, Object data)
- throws MartServiceException {
- Object[] dataArray = (Object[]) data;
-
- AttributeComponent component = new AttributeComponent(attributeList,
- martDataset, dataArray[0]);
-
- if (!attributeNameToComponentMap.containsKey(component
- .getQualifiedName())) {
- attributeNameToComponentMap.put(component.getQualifiedName(),
- new ArrayList<Component>());
- }
- attributeNameToComponentMap.get(component.getQualifiedName())
- .add(component);
- componentRegister.add(component);
- /*
- * if (dataArray[1] instanceof JLabel) { final JLabel sequenceLabel =
- * (JLabel) dataArray[1]; component.addQueryComponentListener(new
- * QueryComponentAdapter() { public void
- * attributeAdded(QueryComponentEvent event) { String name =
- * component.getName(); if ("3utr".equals(name)) {
- * sequenceLabel.setIcon(MartServiceIcons
- * .getIcon("gene_schematic_3utr")); } else if ("5utr".equals(name)) {
- * sequenceLabel.setIcon(MartServiceIcons
- * .getIcon("gene_schematic_5utr")); } else if ("cdna".equals(name)) {
- * sequenceLabel.setIcon(MartServiceIcons
- * .getIcon("gene_schematic_cdna")); } else if
- * ("coding_gene_flank".equals(name)) {
- * sequenceLabel.setIcon(MartServiceIcons
- * .getIcon("gene_schematic_coding_gene_flank")); } else if
- * ("coding_transcript_flank".equals(name)) { sequenceLabel
- * .setIcon(MartServiceIcons
- * .getIcon("gene_schematic_coding_transcript_flank")); } else if
- * ("coding".equals(name)) { sequenceLabel.setIcon(MartServiceIcons
- * .getIcon("gene_schematic_coding")); } else if
- * ("gene_exon_intron".equals(name)) {
- * sequenceLabel.setIcon(MartServiceIcons
- * .getIcon("gene_schematic_gene_exon_intron")); } else if
- * ("gene_exon".equals(name)) { sequenceLabel.setIcon(MartServiceIcons
- * .getIcon("gene_schematic_gene_exon")); } else if
- * ("gene_flank".equals(name)) { sequenceLabel.setIcon(MartServiceIcons
- * .getIcon("gene_schematic_gene_flank")); } else if
- * ("peptide".equals(name)) { sequenceLabel.setIcon(MartServiceIcons
- * .getIcon("gene_schematic_peptide")); } else if
- * ("transcript_exon_intron".equals(name)) { sequenceLabel
- * .setIcon(MartServiceIcons
- * .getIcon("gene_schematic_transcript_exon_intron")); } else if
- * ("transcript_exon".equals(name)) {
- * sequenceLabel.setIcon(MartServiceIcons
- * .getIcon("gene_schematic_transcript_exon")); } else if
- * ("transcript_flank".equals(name)) {
- * sequenceLabel.setIcon(MartServiceIcons
- * .getIcon("gene_schematic_transcript_flank")); } }
- *
- * }); }
- */
- return component;
-
- }
-
- /*
- * (non-Javadoc)
- *
- * @see org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryConfigUIFactory#getFilterPagesUI(org.ensembl.mart.lib.config.FilterPage[])
- */
- public Component getFilterPagesUI(FilterPage[] filterPages, Object data)
- throws MartServiceException {
- final JComponent box = createVerticalBox(backgroundColor);
-
- for (int i = 0; i < filterPages.length; i++) {
- if (QueryConfigUtils.display(filterPages[i])) {
- box.add(getFilterPageUI(filterPages[i], data));
- }
- }
-
- JPanel panel = new JPanel(new BorderLayout());
- panel.setBackground(backgroundColor);
- panel.add(box, BorderLayout.NORTH);
-
- return panel;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryConfigUIFactory#getFilterPageUI(org.ensembl.mart.lib.config.FilterPage)
- */
- public Component getFilterPageUI(FilterPage filterPage, Object data)
- throws MartServiceException {
- JComponent box = createVerticalBox(backgroundColor);
-
- FilterGroup[] filterGroups = (FilterGroup[]) filterPage
- .getFilterGroups().toArray(new FilterGroup[0]);
- box.add(getFilterGroupsUI(filterGroups, data));
-
- return box;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryConfigUIFactory#getFilterGroupsUI(org.ensembl.mart.lib.config.FilterGroup[])
- */
- public Component getFilterGroupsUI(FilterGroup[] filterGroups, Object data)
- throws MartServiceException {
- JComponent box = createVerticalBox(backgroundColor);
-
- for (int i = 0; i < filterGroups.length; i++) {
- if (QueryConfigUtils.display(filterGroups[i])) {
- box.add(Box.createVerticalStrut(2));
- box.add(getFilterGroupUI(filterGroups[i], data));
- }
- }
-
- return box;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryConfigUIFactory#getFilterGroupUI(org.ensembl.mart.lib.config.FilterGroup)
- */
- public Component getFilterGroupUI(FilterGroup filterGroup, Object data)
- throws MartServiceException {
- JLabel title = new JLabel(filterGroup.getDisplayName());
- title.setFont(title.getFont().deriveFont(Font.PLAIN));
- String description = filterGroup.getDescription();
- if (description != null) {
- title.setToolTipText(description);
- }
- ExpandableBox box = new ExpandableBox(title, componentBackgroundColor,
- borderColor, new Insets(10, 10, 10, 10));
-
- FilterCollection[] filterCollections = filterGroup
- .getFilterCollections();
- box.add(getFilterCollectionsUI(filterCollections, data));
-
- box.setExpanded(false);
-
- return box;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryConfigUIFactory#getFilterCollectionsUI(org.ensembl.mart.lib.config.FilterCollection[])
- */
- public Component getFilterCollectionsUI(
- FilterCollection[] filterCollections, Object data)
- throws MartServiceException {
- JComponent box = createVerticalBox(componentBackgroundColor);
-
- for (int i = 0; i < filterCollections.length; i++) {
- if (QueryConfigUtils.display(filterCollections[i])) {
- Component component = getFilterCollectionUI(
- filterCollections[i], data);
- if (component != null) {
- box.add(Box.createVerticalStrut(10));
- box.add(component);
- }
- }
- }
-
- return box;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryConfigUIFactory#getFilterCollectionUI(org.ensembl.mart.lib.config.FilterCollection)
- */
- public Component getFilterCollectionUI(FilterCollection filterCollection,
- Object data) throws MartServiceException {
- JComponent box = null;
-
- String displayName = filterCollection.getDisplayName();
- if (displayName == null) {
- displayName = filterCollection.getInternalName();
- }
- AbstractButton selectorButton = new JCheckBox(QueryConfigUtils
- .splitSentence(displayName));
- selectorButton.setFont(selectorButton.getFont().deriveFont(Font.PLAIN));
- selectorButton.setBackground(componentBackgroundColor);
- String description = filterCollection.getDescription();
- if (description != null) {
- selectorButton.setToolTipText(description);
- }
-
- FilterDescription[] filterDescriptions = (FilterDescription[]) filterCollection
- .getFilterDescriptions().toArray(new FilterDescription[0]);
-
- if (filterDescriptions.length == 1) {
- if (QueryConfigUtils.display(filterDescriptions[0])) {
- Component filterComponent = getFilterDescriptionUI(
- filterDescriptions[0], data);
- if (filterComponent != null) {
- filterToDisplayName.put(
- filterDescriptions[0].getInternalName(), displayName);
- if (QueryConfigUtils
- .isReference(filterDescriptions[0], version)) {
- MartDataset dataset = QueryConfigUtils
- .getReferencedDataset(martService, martDataset,
- filterDescriptions[0], version);
- FilterDescription referencedFilter = QueryConfigUtils
- .getReferencedFilterDescription(martService,
- dataset, filterDescriptions[0], version);
- filterToDisplayName.put(referencedFilter.getInternalName(),
- displayName);
- }
-
- box = createBox(null, false);
- JComponent grid = new JPanel(new GridLayout(1, 2));
- grid.setBackground(componentBackgroundColor);
- JPanel buttonPanel = new JPanel(new MinimalLayout());
- buttonPanel.setBackground(componentBackgroundColor);
- buttonPanel.add(selectorButton);
- grid.add(buttonPanel);
- if (filterComponent instanceof QueryComponent) {
- ((QueryComponent) filterComponent)
- .setSelectorButton(selectorButton);
- }
- grid.add(filterComponent);
- box.add(grid);
- }
- }
- } else {
- Component component = getFilterDescriptionsUI(filterDescriptions,
- selectorButton);
- if (component != null) {
- box = createBox(selectorButton, false);
- box.add(component);
- }
- }
-
- return box;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryConfigUIFactory#getFilterDescriptionsUI(org.ensembl.mart.lib.config.FilterDescription[],
- * int)
- */
- public Component getFilterDescriptionsUI(
- FilterDescription[] filterDescriptions, Object data)
- throws MartServiceException {
- List<Component> components = new ArrayList<Component>();
- for (int i = 0; i < filterDescriptions.length; i++) {
- if (QueryConfigUtils.display(filterDescriptions[i])) {
- Component component = getFilterDescriptionUI(
- filterDescriptions[i], data);
- if (component != null) {
- if (component instanceof QueryComponent
- && data instanceof AbstractButton) {
- ((QueryComponent) component)
- .setSelectorButton((AbstractButton) data);
- }
-
- String displayName = filterDescriptions[i].getDisplayName();
- if (displayName == null) {
- logger.info("Cant find a display name for filter '"
- + filterDescriptions[i].getInternalName() + "'");
- displayName = filterDescriptions[i].getInternalName();
- }
- filterToDisplayName.put(
- filterDescriptions[i].getInternalName(), displayName);
- JLabel displayLabel = new JLabel(QueryConfigUtils
- .splitSentence(displayName));
- displayLabel.setFont(displayLabel.getFont().deriveFont(
- Font.PLAIN));
- String description = filterDescriptions[i].getDescription();
- if (description != null) {
- displayLabel.setToolTipText(description);
- }
- displayLabel.setBackground(componentBackgroundColor);
- displayLabel.setBorder(new EmptyBorder(0, 22, 0, 0));
-
- components.add(displayLabel);
- components.add(component);
- }
- }
- }
-
- if (components.size() > 0) {
- JComponent box = new JPanel(
- new GridLayout(components.size() / 2, 2));
- box.setBackground(componentBackgroundColor);
- for (Component component : components) {
- box.add(component);
- }
- return box;
- } else {
- return null;
- }
- }
-
- /*
- * (non-Javadoc)
- *
- * @see org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryConfigUIFactory#getFilterDescriptionUI(org.ensembl.mart.lib.config.FilterDescription,
- * int)
- */
- public Component getFilterDescriptionUI(
- FilterDescription filterDescription, Object data)
- throws MartServiceException {
- QueryComponent component;
-
- String pointerDataset = filterDescription
- .getAttribute("pointerDataset");
- MartDataset dataset = martDataset;
- FilterDescription displayedFilter;
- if (QueryConfigUtils.isReference(filterDescription, version)) {
- dataset = QueryConfigUtils.getReferencedDataset(martService,
- martDataset, filterDescription, version);
- if (dataset == null) {
- return null;
- }
- displayedFilter = QueryConfigUtils.getReferencedFilterDescription(
- martService, dataset, filterDescription, version);
- if (displayedFilter == null){
- return null;
- }
- filterDescription.setDisplayName(displayedFilter.getDisplayName());
- } else {
- displayedFilter = filterDescription;
- }
- assert dataset != null;
-
- String type = displayedFilter.getType();
- if (type == null) {
- type = "text";// default filter type
- }
-
- if (type.equals("boolean") || type.equals("boolean_num")) {
- component = new BooleanFilterComponent(displayedFilter, martDataset);
- component.setPointerDataset(pointerDataset);
- componentRegister.add(component);
- } else if (type.endsWith("list") || type.endsWith("basic_filter")
- || QueryConfigUtils.isList(displayedFilter)) {
- if (type.equals("boolean_list")
- || QueryConfigUtils.isBooleanList(displayedFilter)) {
- Option[] options = displayedFilter.getOptions();
- List filters = new ArrayList();
- for (int i = 0; i < options.length; i++) {
- FilterDescription booleanFilterDescription = new FilterDescription(
- options[i]);
- QueryComponent queryComponent = new BooleanFilterComponent(
- booleanFilterDescription, martDataset);
- queryComponent.setPointerDataset(pointerDataset);
- filters.add(queryComponent);
- componentRegister.add(queryComponent);
- }
- component = new BooleanListFilterComponent(displayedFilter,
- martDataset, filters);
- component.setPointerDataset(pointerDataset);
- } else if (type.equals("id_list")
- || QueryConfigUtils.isIdList(displayedFilter)) {
- Option[] options = displayedFilter.getOptions();
- List<TextFilterComponent> filters = new ArrayList<TextFilterComponent>();
- for (int i = 0; i < options.length; i++) {
- FilterDescription idFilterDescription = new FilterDescription(
- options[i]);
- idFilterDescription.setType("id_list");
- TextFilterComponent queryComponent = new TextFilterComponent(
- idFilterDescription, martDataset);
- queryComponent.setPointerDataset(pointerDataset);
- filters.add(queryComponent);
- componentRegister.add(queryComponent);
- }
- component = new IdListFilterComponent(displayedFilter,
- martDataset, filters);
- component.setPointerDataset(pointerDataset);
- } else if (QueryConfigUtils.isNestedList(displayedFilter)) {
- TextFilterComponent filterComponent = new TextFilterComponent(
- displayedFilter, martDataset);
- filterComponent.setPointerDataset(pointerDataset);
- filterComponent.add(QueryConfigUtils.getOptionButton(
- displayedFilter, filterComponent));
- component = filterComponent;
- componentRegister.add(component);
- } else {
- ListFilterComponent filterComponent = new ListFilterComponent(
- getDatasetConfig().getDataset(), displayedFilter,
- martDataset, filterNameToComponentMap);
- filterComponent.setPointerDataset(pointerDataset);
- // map the component to a local dataset name as the 'ref' of a
- // pushaction may be a local reference
- filterNameToComponentMap.put(getDatasetConfig().getDataset()
- + "." + displayedFilter.getInternalName(),
- filterComponent);
- // if the filter is a reference then also map the component to
- // its referenced dataset name as the 'ref' of a pushaction may
- // be a non-local reference
- if (QueryConfigUtils.isReference(filterDescription, version)) {
- filterNameToComponentMap.put(filterDescription
- .getInternalName(), filterComponent);
- }
- component = filterComponent;
- componentRegister.add(component);
- }
- } else {
- String multipleValues = displayedFilter.getMultipleValues();
- if ("1".equals(multipleValues)) {
- component = new MultipleTextFilterComponent(displayedFilter, martDataset);
- } else {
- component = new TextFilterComponent(displayedFilter, martDataset);
- }
- component.setPointerDataset(pointerDataset);
- componentRegister.add(component);
- // mapping for hard coded rules
- filterNameToComponentMap.put(filterDescription.getInternalName(),
- component);
- }
-
- return component;
- }
-
- private void registerComponents() {
- for (Iterator iter = componentRegister.iterator(); iter.hasNext();) {
- QueryComponent component = (QueryComponent) iter.next();
- controller.register(component);
- }
- }
-
- private void deregisterComponents() {
- for (Iterator iter = componentRegister.iterator(); iter.hasNext();) {
- QueryComponent component = (QueryComponent) iter.next();
- controller.deregister(component);
- }
- }
-
- /**
- *
- * @param inputPanel
- * @param attributePanel
- * @param filterPanel
- */
- private void generateConfiguration(
- final MartServiceQueryConfigUIFactory factory,
- final SummaryPanel summaryPanel, final JComponent inputPanel,
- final JComponent attributePanel, final JComponent filterPanel) {
- final JProgressBar filterProgressBar = new JProgressBar();
- filterProgressBar.setIndeterminate(true);
- filterProgressBar.setStringPainted(true);
- filterProgressBar.setString("Fetching filter configuration");
- filterPanel.add(filterProgressBar);
-
- final JProgressBar attributeProgressBar = new JProgressBar();
- attributeProgressBar.setIndeterminate(true);
- attributeProgressBar.setStringPainted(true);
- attributeProgressBar.setString("Fetching attribute configuration");
- attributePanel.add(attributeProgressBar);
-
- new Thread("DatasetConfigUI") {
- public void run() {
- try {
-
- FilterPage[] filterPages = factory.getDatasetConfig()
- .getFilterPages();
- AttributePage[] attributePages = factory.getDatasetConfig()
- .getAttributePages();
-
- final Component filterPagesComponent = factory
- .getFilterPagesUI(filterPages, null);
- final Component attributePagesComponent = factory
- .getAttributePagesUI(attributePages, null);
-
- filterPanel.remove(filterProgressBar);
- filterPanel.add(filterPagesComponent);
-
- attributePanel.remove(attributeProgressBar);
- attributePanel.add(attributePagesComponent);
-
- factory.registerComponents();
-
- factory.selectAttributePage(attributePages);
-
- } catch (MartServiceException e) {
- logger.error("Error while fetching dataset configuration", e);
- JTextArea textArea = new JTextArea();
- textArea
- .append("Error while fetching dataset configuration\n\n");
- textArea.append(e.getMessage());
- inputPanel.removeAll();
- inputPanel.add(textArea);
- } catch (Exception e) {
- logger.error("Error while generating the Query Editor", e);
- JTextArea textArea = new JTextArea();
- textArea
- .append("Error while generating the Query Editor\n\n");
- textArea.append(e.toString());
- inputPanel.removeAll();
- inputPanel.add(textArea);
- } finally {
- inputPanel.revalidate();
- inputPanel.repaint();
- summaryPanel.updateDatasets();
- }
- }
- }.start();
- }
-
- private List<AttributeComponent> getAttributeComponents(Component component) {
- List<AttributeComponent> attributeComponents = new ArrayList<AttributeComponent>();
- if (component instanceof AttributeComponent) {
- attributeComponents.add((AttributeComponent) component);
- } else if (component instanceof ExpandableBox) {
- Component[] children = ((ExpandableBox) component).getComponents();
- for (int i = 0; i < children.length; i++) {
- attributeComponents.addAll(getAttributeComponents(children[i]));
- }
- } else if (component instanceof Container) {
- Component[] children = ((Container) component).getComponents();
- for (int i = 0; i < children.length; i++) {
- attributeComponents.addAll(getAttributeComponents(children[i]));
- }
- }
- return attributeComponents;
- }
-
- private List<AttributeComponent> getSelectedAttributeComponents(
- Component component) {
- List<AttributeComponent> attributeComponents = new ArrayList<AttributeComponent>();
- if (component instanceof AttributeComponent) {
- if (((AttributeComponent) component).isSelected()) {
- attributeComponents.add((AttributeComponent) component);
- }
- } else if (component instanceof ExpandableBox) {
- Component[] children = ((ExpandableBox) component).getComponents();
- for (int i = 0; i < children.length; i++) {
- attributeComponents
- .addAll(getSelectedAttributeComponents(children[i]));
- }
- } else if (component instanceof Container) {
- Component[] children = ((Container) component).getComponents();
- for (int i = 0; i < children.length; i++) {
- attributeComponents
- .addAll(getSelectedAttributeComponents(children[i]));
- }
- }
- return attributeComponents;
- }
-
- private void selectAttributePage(AttributePage[] attributePages) {
- int selectedAttributes = -1;
- JRadioButton selectedButton = null;
- Component selectedComponent = null;
-
- for (int i = 0; i < attributePages.length; i++) {
- if (QueryConfigUtils.display(attributePages[i])) {
- Component component = attributePageNameToComponent
- .get(attributePages[i].getInternalName());
- JRadioButton button = attributePageNameToButton
- .get(attributePages[i].getInternalName());
- if (component != null && button != null) {
- int attributeCount = getSelectedAttributeComponents(
- component).size();
- if (attributeCount > selectedAttributes) {
- selectedAttributes = attributeCount;
- selectedButton = button;
- selectedComponent = component;
- }
- }
- }
- if (selectedButton != null && selectedComponent != null) {
- selectedButton.setSelected(true);
- }
- }
- }
-
- private List<String> getFormatList(AttributePage attributePage) {
- List<String> formatList = new ArrayList<String>();
- for (String format : attributePage.getOutFormats()
- .toUpperCase().split(",")) {
- if (!"".equals(format)) {
- formatList.add(format);
- }
- }
- return formatList;
- }
-
- private JComponent createHorizontalBox(Color background) {
- // using a JPanel instead of a Box as a workaround for bug 4907674
- JPanel box = new JPanel();
- box.setLayout(new BoxLayout(box, BoxLayout.X_AXIS));
- box.setBackground(background);
- return box;
- }
-
- private JComponent createVerticalBox(Color background) {
- // using a JPanel instead of a Box as a workaround for bug 4907674
- JPanel box = new JPanel();
- box.setLayout(new BoxLayout(box, BoxLayout.Y_AXIS));
- box.setBackground(background);
- return box;
- }
-
- private JComponent createBox(Component titleComponent, boolean fullBorder) {
- JComponent box = createVerticalBox(componentBackgroundColor);
- box.add(Box.createHorizontalStrut(400));
- if (fullBorder) {
- box.setBorder(new CompoundBorder(new LineBorder(borderColor, 1),
- new EmptyBorder(10, 10, 10, 10)));
- } else {
- box.setBorder(new CompoundBorder(new SideBorder06(
- SwingConstants.TOP, borderColor), new EmptyBorder(5, 10, 0,
- 10)));
- }
- if (titleComponent != null) {
- JComponent labelBox = createHorizontalBox(componentBackgroundColor);
- labelBox.add(titleComponent);
- labelBox.add(Box.createHorizontalGlue());
- box.add(labelBox);
- }
- return box;
- }
-
- private void setSummaryCount(Query query, String datasetName, JLabel label)
- throws MartServiceException {
- if ("".equals(label.getText())) {
- String count = null;
- String total = null;
- Query countQuery = new Query(query);
- countQuery.removeAllDatasets();
- countQuery.addDataset(new Dataset(datasetName));
- countQuery.setCount(1);
- countQuery.setFormatter(null);
-
- Object[] results = martService.executeQuery(countQuery);
- if (results.length == 1) {
- if (results[0] instanceof List) {
- List result = (List) results[0];
- if (result.size() >= 1) {
- total = (String) result.get(0);
- // test for biomart's 'let add a random blank line'
- // thing
- if ("".equals(total) && result.size() > 1) {
- total = (String) result.get(1);
- }
- try {
- Integer.parseInt(total);
- } catch (NumberFormatException e) {
- total = "?";
- }
- }
- }
- }
- Dataset dataset = query.getDataset(datasetName);
- if (dataset != null && dataset.getFilters().size() > 0) {
- Dataset countDataset = new Dataset(dataset);
- countQuery.removeAllDatasets();
- countQuery.addDataset(countDataset);
- results = martService.executeQuery(countQuery);
- if (results.length == 1) {
- if (results[0] instanceof List) {
- List result = (List) results[0];
- if (result.size() >= 1) {
- count = (String) result.get(0);
- // test for biomart's 'let add a random blank
- // line' thing
- if ("".equals(count) && result.size() > 1) {
- count = (String) result.get(1);
- }
- try {
- Integer.parseInt(count);
- } catch (NumberFormatException e) {
- count = "";
- }
- }
- }
- }
- } else {
- count = total;
- }
-
- if (count != null && total != null) {
- if (count.equals("")) {
- label.setText("0 / " + total + " Genes");
- } else {
- label.setText(count + " / " + total + " Genes");
- }
- }
-
- }
- }
-
- class TextFilterComponent extends QueryComponent {
- private static final long serialVersionUID = 1L;
-
- private JTextField textField;
-
- public TextFilterComponent(FilterDescription filterDescription,
- MartDataset dataset) {
- setConfigObject(filterDescription);
- setDataset(dataset);
- setName(filterDescription.getInternalName());
- setLayout(new MinimalLayout(MinimalLayout.HORIZONTAL));
- setBackground(componentBackgroundColor);
-
- textField = new JTextField();
- textField.setBackground(componentBackgroundColor);
- textField.setPreferredSize(new Dimension(200, textField
- .getPreferredSize().height + 4));
-
- textField.getDocument().addDocumentListener(new DocumentListener() {
- public void changedUpdate(DocumentEvent e) {
- }
-
- public void insertUpdate(DocumentEvent e) {
- fireFilterChanged(new QueryComponentEvent(this, getName(),
- getDataset(), textField.getText()));
- }
-
- public void removeUpdate(DocumentEvent e) {
- fireFilterChanged(new QueryComponentEvent(this, getName(),
- getDataset(), textField.getText()));
- }
- });
-
- add(textField);
- }
-
- /*
- * (non-Javadoc)
- *
- * @see org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponent#getType()
- */
- public int getType() {
- return FILTER;
- }
-
- public void setValue(String value) {
- textField.setText(value);
- }
-
- public String getValue() {
- return textField.getText();
- }
-
- }
-
- class MultipleTextFilterComponent extends QueryComponent {
- private static final long serialVersionUID = 1L;
-
- private JTextArea textArea;
-
- public MultipleTextFilterComponent(FilterDescription filterDescription,
- MartDataset dataset) {
- setConfigObject(filterDescription);
- setDataset(dataset);
- setName(filterDescription.getInternalName());
- setLayout(new MinimalLayout(MinimalLayout.HORIZONTAL));
- setBackground(componentBackgroundColor);
-
- textArea = new JTextArea();
- textArea.getDocument().addDocumentListener(new DocumentListener() {
- public void changedUpdate(DocumentEvent e) {
- }
-
- public void insertUpdate(DocumentEvent e) {
- fireFilterChanged(new QueryComponentEvent(this, getName(),
- getDataset(), getValue()));
- }
-
- public void removeUpdate(DocumentEvent e) {
- fireFilterChanged(new QueryComponentEvent(this, getName(),
- getDataset(), getValue()));
- }
- });
-
- final JFileChooser chooser = new JFileChooser();
- JButton chooserButton = new JButton("Browse...");
- chooserButton.setBackground(componentBackgroundColor);
- chooserButton.setFont(chooserButton.getFont()
- .deriveFont(Font.PLAIN));
- chooserButton.addActionListener(new ActionListener() {
- public void actionPerformed(ActionEvent e) {
- int returnVal = chooser
- .showOpenDialog(MultipleTextFilterComponent.this);
- if (returnVal == JFileChooser.APPROVE_OPTION) {
- File file = chooser.getSelectedFile();
- if (file != null && file.exists() && file.canRead()
- && !file.isDirectory()) {
- StringBuffer buffer = new StringBuffer();
- BufferedReader in = null;
- try {
- in = new BufferedReader(new FileReader(file));
- String line = in.readLine();
- while (line != null) {
- buffer.append(line);
- buffer.append(QueryConfigUtils.LINE_END);
- line = in.readLine();
- }
- } catch (IOException e1) {
- // no action
- } finally {
- if (in != null) {
- try {
- in.close();
- } catch (IOException e1) {
- // give up
- }
- }
- }
- setValue(buffer.toString());
- }
- }
- }
- });
-
- JPanel buttonPanel = new JPanel(new BorderLayout());
- buttonPanel.setBackground(componentBackgroundColor);
- buttonPanel.add(chooserButton, BorderLayout.WEST);
-
- JScrollPane textScrollPane = new JScrollPane(textArea);
- textScrollPane.setBackground(componentBackgroundColor);
- textScrollPane.setPreferredSize(new Dimension(200, 80));
-
- add(textScrollPane, BorderLayout.CENTER);
- add(buttonPanel, BorderLayout.SOUTH);
- }
-
- /*
- * (non-Javadoc)
- *
- * @see org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponent#getType()
- */
- public int getType() {
- return FILTER;
- }
-
- public void setValue(String value) {
- textArea.setText(QueryConfigUtils.csvToValuePerLine(value));
- }
-
- public String getValue() {
- return QueryConfigUtils.valuePerLineToCsv(textArea.getText());
- }
-
- }
-
- class ListFilterComponent extends QueryComponent {
- private static final long serialVersionUID = 1L;
-
- private DefaultComboBoxModel comboBoxModel = new DefaultComboBoxModel();
-
- private JComboBox comboBox;
-
- private JTextField textField;
-
- private Map optionMap = new HashMap();
-
- private List optionList = new ArrayList();
-
- private String dataset;
-
- private Map componentMap;
-
- private String type;
-
- public ListFilterComponent(String refDataset,
- FilterDescription filterDescription, MartDataset dataset,
- Map componentMap) {
- this.dataset = refDataset;
- this.componentMap = componentMap;
- setConfigObject(filterDescription);
- setDataset(dataset);
- setName(filterDescription.getInternalName());
- setLayout(new BorderLayout());
- setBackground(componentBackgroundColor);
-
- Option[] options = filterDescription.getOptions();
- // if there are no options but there is a default value then use the
- // default value as an option
- if (options.length == 0) {
- String defaultValue = filterDescription.getDefaultValue();
- if (defaultValue != null) {
- Option newOption = new Option();
- newOption.setInternalName(defaultValue);
- newOption.setDisplayName(defaultValue);
- newOption.setValue(defaultValue);
- newOption.setSelectable("true");
- options = new Option[] { newOption };
- }
- }
-
- textField = new JTextField();
- textField.setBackground(componentBackgroundColor);
- textField.setPreferredSize(new Dimension(200, textField
- .getPreferredSize().height + 4));
-
- textField.getDocument().addDocumentListener(new DocumentListener() {
- public void changedUpdate(DocumentEvent e) {
- fireFilterChanged(new QueryComponentEvent(this, getName(),
- getDataset(), textField.getText()));
- }
-
- public void insertUpdate(DocumentEvent e) {
- fireFilterChanged(new QueryComponentEvent(this, getName(),
- getDataset(), textField.getText()));
- }
-
- public void removeUpdate(DocumentEvent e) {
- fireFilterChanged(new QueryComponentEvent(this, getName(),
- getDataset(), textField.getText()));
- }
- });
-
- comboBox = new JComboBox();
- comboBox.setFont(comboBox.getFont().deriveFont(Font.PLAIN));
- comboBox.setBackground(componentBackgroundColor);
- comboBox.setModel(comboBoxModel);
-
- if (options.length == 0) {
- add(textField, BorderLayout.WEST);
- type = "text";
- } else {
- add(comboBox, BorderLayout.WEST);
- type = "list";
- }
-
- setOptions(options);
- // comboBox.setSelectedIndex(-1);
-
- comboBox.addItemListener(new ItemListener() {
-
- public void itemStateChanged(ItemEvent e) {
- if (e.getStateChange() == ItemEvent.SELECTED) {
- Option option = (Option) optionList.get(comboBox
- .getSelectedIndex());
- optionSelected(option);
- ListFilterComponent.super.setValue(option.getValue());
- fireFilterChanged(new QueryComponentEvent(this,
- getName(), getDataset(), option.getValue()));
- } else if (e.getStateChange() == ItemEvent.DESELECTED) {
- Option option = (Option) optionMap.get(getValue());
- if (option != null) {
- optionDeselected(option);
- }
- fireFilterChanged(new QueryComponentEvent(this,
- getName(), getDataset(), ""));
- }
- }
-
- });
-
- }
-
- public void setOptions(Option[] options) {
- clearOptions();
- for (int i = 0; i < options.length; i++) {
- if (options[i].getHidden() == null
- || !options[i].getHidden().equals("true")) {
- optionMap.put(options[i].getValue(), options[i]);
- optionList.add(options[i]);
- String displayName = options[i].getDisplayName();
- if (displayName != null) {
- comboBoxModel.addElement(QueryConfigUtils
- .truncateName(displayName));
- }
- }
- }
- if (optionList.size() > 0) {
- if ("text".equals(type)) {
- removeAll();
- add(comboBox, BorderLayout.WEST);
- type = "list";
- revalidate();
- repaint();
- }
- setValue(((Option) optionList.get(0)).getValue());
- } else {
- if ("list".equals(type)) {
- removeAll();
- add(textField, BorderLayout.WEST);
- type = "text";
- revalidate();
- repaint();
- }
- }
- }
-
- private void clearOptions() {
- comboBox.setSelectedIndex(-1);
- comboBoxModel.removeAllElements();
- optionMap.clear();
- optionList.clear();
- }
-
- public void setValue(String value) {
- if ("list".equals(type)) {
- if (value == null) {
- if (getValue() != null) {
- optionDeselected((Option) optionMap.get(getValue()));
- comboBox.setSelectedIndex(-1);
- }
- } else {
- if (getValue() != null) {
- Option option = (Option) optionMap.get(getValue());
- if (option != null) {
- optionDeselected(option);
- }
- }
- Option option = (Option) optionMap.get(value);
- if (option != null) {
- optionSelected(option);
- }
- int index = optionList.indexOf(option);
- comboBox.setSelectedIndex(index);
- }
- } else if ("text".equals(type)) {
- textField.setText(value);
- }
- super.setValue(value);
- }
-
- private void optionSelected(Option option) {
- if (option == null) {
- logger.info("null option for " + getName());
- } else {
- PushAction[] pushActions = option.getPushActions();
- for (int i = 0; i < pushActions.length; i++) {
- QueryComponent queryComponent = getReferencedComponent(pushActions[i]);
- if (queryComponent instanceof ListFilterComponent) {
- ListFilterComponent filterComponent = (ListFilterComponent) queryComponent;
- if (filterComponent != null) {
- filterComponent.setOptions(pushActions[i]
- .getOptions());
- }
- }
- }
- }
- }
-
- private void optionDeselected(Option option) {
- PushAction[] pushActions = option.getPushActions();
- for (int i = 0; i < pushActions.length; i++) {
- QueryComponent queryComponent = getReferencedComponent(pushActions[i]);
- if (queryComponent instanceof ListFilterComponent) {
- ListFilterComponent filterComponent = (ListFilterComponent) queryComponent;
- if (filterComponent != null) {
- filterComponent.clearOptions();
- }
- }
- }
- }
-
- private QueryComponent getReferencedComponent(PushAction pushAction) {
- String ref = pushAction.getRef();
- if (ref.indexOf('.') == -1) {
- return (QueryComponent) componentMap.get(dataset + "." + ref);
- } else {
- return (QueryComponent) componentMap.get(ref);
- }
- }
-
- /*
- * (non-Javadoc)
- *
- * @see org.embl.ebi.escience.scuflworkers.biomartservice.config.QueryComponent#getType()
- */
- public int getType() {
- return FILTER;
- }
- }
-
- class IdListFilterComponent extends QueryComponent {
- private static final long serialVersionUID = 1L;
-
- private DefaultComboBoxModel comboBoxModel = new DefaultComboBoxModel();
-
- private JComboBox comboBox;
-
- private JTextArea textArea;
-
- private Map<String, QueryComponent> componentMap = new HashMap<String, QueryComponent>();
-
- private List<String> filterList = new ArrayList<String>();
-
- private int currentIndex;
-
- private boolean valueChanging;
-
- public IdListFilterComponent(FilterDescription description,
- MartDataset dataset, List<TextFilterComponent> filterComponentList) {
- setLayout(new MinimalLayout(MinimalLayout.VERTICAL));
- setBackground(componentBackgroundColor);
-
- comboBox = new JComboBox();
- comboBox.setFont(comboBox.getFont().deriveFont(Font.PLAIN));
- comboBox.setBackground(componentBackgroundColor);
- comboBox.setModel(comboBoxModel);
-
- for (TextFilterComponent filterComponent : filterComponentList) {
- BaseNamedConfigurationObject filterDescription = filterComponent
- .getConfigObject();
- componentMap.put(filterDescription.getInternalName(),
- filterComponent);
- filterList.add(filterDescription.getInternalName());
- comboBoxModel.addElement(filterDescription.getDisplayName());
- filterToDisplayName.put(filterDescription.getInternalName(),
- filterDescription.getDisplayName());
- filterComponent
- .addQueryComponentListener(new QueryComponentAdapter() {
- public void filterAdded(QueryComponentEvent event) {
- if (!valueChanging) {
- valueChanging = true;
- comboBox.setSelectedIndex(filterList
- .indexOf(event.getName()));
- selectorButton.setSelected(true);
- valueChanging = false;
- }
- }
-
- public void filterRemoved(QueryComponentEvent event) {
- if (!valueChanging) {
- valueChanging = true;
- selectorButton.setSelected(false);
- valueChanging = false;
- }
- }
-
- public void filterChanged(QueryComponentEvent event) {
- if (!valueChanging) {
- valueChanging = true;
- textArea
- .setText(QueryConfigUtils
- .csvToValuePerLine(event
- .getValue()));
- valueChanging = false;
- }
- }
- });
- filterComponent.setSelectorButton(new JCheckBox());
- }
-
- comboBox.addItemListener(new ItemListener() {
- public void itemStateChanged(ItemEvent e) {
- int selectedIndex = comboBox.getSelectedIndex();
- if (selectorButton.isSelected()) {
- if (e.getStateChange() == ItemEvent.SELECTED) {
- if (!valueChanging) {
- valueChanging = true;
- QueryComponent queryComponent = componentMap
- .get(filterList.get(selectedIndex));
- queryComponent.setValue(QueryConfigUtils
- .valuePerLineToCsv(textArea.getText()));
- queryComponent.setSelected(true);
- valueChanging = false;
- }
- } else if (e.getStateChange() == ItemEvent.DESELECTED) {
- if (!valueChanging) {
- valueChanging = true;
- componentMap.get(filterList
- .get(currentIndex)).setSelected(false);
- valueChanging = false;
- }
- }
- }
- currentIndex = selectedIndex;
- }
- });
-
- textArea = new JTextArea();
- textArea.getDocument().addDocumentListener(new DocumentListener() {
- public void changedUpdate(DocumentEvent e) {
- }
-
- public void insertUpdate(DocumentEvent e) {
- updateValue();
- }
-
- public void removeUpdate(DocumentEvent e) {
- updateValue();
- }
-
- private void updateValue() {
- if (!valueChanging) {
- valueChanging = true;
- int selectedIndex = comboBox.getSelectedIndex();
- String value = QueryConfigUtils
- .valuePerLineToCsv(textArea.getText());
- componentMap.get(filterList
- .get(selectedIndex)).setValue(value);
- valueChanging = false;
- }
- }
- });
-
- final JFileChooser chooser = new JFileChooser();
- JButton chooserButton = new JButton("Browse...");
- chooserButton.setBackground(componentBackgroundColor);
- chooserButton.setFont(chooserButton.getFont()
- .deriveFont(Font.PLAIN));
- chooserButton.addActionListener(new ActionListener() {
- public void actionPerformed(ActionEvent e) {
- int returnVal = chooser
- .showOpenDialog(IdListFilterComponent.this);
- if (returnVal == JFileChooser.APPROVE_OPTION) {
- File file = chooser.getSelectedFile();
- if (file != null && file.exists() && file.canRead()
- && !file.isDirectory()) {
- StringBuffer buffer = new StringBuffer();
- BufferedReader in = null;
- try {
- in = new BufferedReader(new FileReader(file));
- String line = in.readLine();
- while (line != null) {
- buffer.append(line);
- buffer.append(QueryConfigUtils.LINE_END);
- line = in.readLine();
- }
- } catch (IOException e1) {
- // no action
- } finally {
- if (in != null) {
- try {
- in.close();
- } catch (IOException e1) {
- // give up
- }
- }
- }
- textArea.setText(buffer.toString());
- }
- }
- }
- });
-
- JPanel buttonPanel = new JPanel(new BorderLayout());
- buttonPanel.setBackground(componentBackgroundColor);
- buttonPanel.add(chooserButton, BorderLayout.WEST);
-
- JScrollPane textScrollPane = new JScrollPane(textArea);
- textScrollPane.setBackground(componentBackgroundColor);
- textScrollPane.setPreferredSize(new Dimension(200, 80));
-
- add(comboBox, BorderLayout.NORTH);
- add(textScrollPane, BorderLayout.CENTER);
- add(buttonPanel, BorderLayout.SOUTH);
-
- }
-
- public void setSelectorButton(AbstractButton button) {
- selectorButton = button;
- button.addItemListener(new ItemListener() {
- public void itemStateChanged(ItemEvent e) {
- int selectedIndex = comboBox.getSelectedIndex();
- if (e.getStateChange() == ItemEvent.SELECTED) {
- if (!valueChanging) {
- valueChanging = true;
- QueryComponent queryComponent = componentMap
- .get(filterList.get(selectedIndex));
- queryComponent.setValue(QueryConfigUtils
- .valuePerLineToCsv(textArea.getText()));
- queryComponent.setSelected(true);
- valueChanging = false;
- }
- } else if (e.getStateChange() == ItemEvent.DESELECTED) {
- if (!valueChanging) {
- valueChanging = true;
- componentMap.get(filterList
- .get(selectedIndex)).setSelected(false);
- valueChanging = false;
- }
- }
- }
- });
-
- }
-
- public int getType() {
- return FILTER;
- }
-
- }
-
- class BooleanListFilterComponent extends QueryComponent {
- private static final long serialVersionUID = 1L;
-
- private DefaultComboBoxModel comboBoxModel = new DefaultComboBoxModel();
-
- private JComboBox comboBox;
-
- private BooleanFilterComponent booleanFilterComponent;
-
- private Map componentMap = new HashMap();
-
- private List<String> filterList = new ArrayList<String>();
-
- private int currentIndex;
-
- public BooleanListFilterComponent(FilterDescription description,
- MartDataset dataset, List filterComponentList) {
- setLayout(new MinimalLayout(MinimalLayout.HORIZONTAL));
- setBackground(componentBackgroundColor);
-
- comboBox = new JComboBox();
- comboBox.setFont(comboBox.getFont().deriveFont(Font.PLAIN));
- comboBox.setBackground(componentBackgroundColor);
- comboBox.setModel(comboBoxModel);
-
- for (Iterator iter = filterComponentList.iterator(); iter.hasNext();) {
- BooleanFilterComponent filterComponent = (BooleanFilterComponent) iter
- .next();
- BaseNamedConfigurationObject filterDescription = filterComponent
- .getConfigObject();
- componentMap.put(filterDescription.getInternalName(),
- filterComponent);
- filterList.add(filterDescription.getInternalName());
- comboBoxModel.addElement(filterDescription.getDisplayName());
- filterToDisplayName.put(filterDescription.getInternalName(),
- filterDescription.getDisplayName());
- filterComponent
- .addQueryComponentListener(new QueryComponentAdapter() {
- public void filterAdded(QueryComponentEvent event) {
- comboBox.setSelectedIndex(filterList
- .indexOf(event.getName()));
- selectorButton.setSelected(true);
- }
-
- public void filterChanged(QueryComponentEvent event) {
- booleanFilterComponent.setValue(event
- .getValue());
- }
- });
- filterComponent.setSelectorButton(new JCheckBox());
- }
-
- comboBox.addItemListener(new ItemListener() {
- public void itemStateChanged(ItemEvent e) {
- int selectedIndex = comboBox.getSelectedIndex();
- if (selectorButton.isSelected()) {
- if (e.getStateChange() == ItemEvent.SELECTED) {
- QueryComponent queryComponent = (QueryComponent) componentMap
- .get(filterList.get(selectedIndex));
- queryComponent.setValue(booleanFilterComponent
- .getValue());
- queryComponent.setSelected(true);
- } else if (e.getStateChange() == ItemEvent.DESELECTED) {
- ((QueryComponent) componentMap.get(filterList
- .get(currentIndex))).setSelected(false);
- }
- }
- currentIndex = selectedIndex;
- }
- });
-
- booleanFilterComponent = new BooleanFilterComponent(
- new FilterDescription(), dataset);
- booleanFilterComponent
- .addQueryComponentListener(new QueryComponentAdapter() {
- public void filterChanged(QueryComponentEvent event) {
- int selectedIndex = comboBox.getSelectedIndex();
- ((QueryComponent) componentMap.get(filterList
- .get(selectedIndex))).setValue(event
- .getValue());
- }
- });
-
- JPanel comboBoxPanel = new JPanel(new MinimalLayout());
- comboBoxPanel.setBackground(componentBackgroundColor);
- comboBoxPanel.setBorder(new EmptyBorder(5, 5, 0, 0));
- add(comboBox);
- add(booleanFilterComponent);
- }
-
- public void setSelectorButton(AbstractButton button) {
- selectorButton = button;
- button.addItemListener(new ItemListener() {
- public void itemStateChanged(ItemEvent e) {
- int selectedIndex = comboBox.getSelectedIndex();
- if (e.getStateChange() == ItemEvent.SELECTED) {
- QueryComponent queryComponent = (QueryComponent) componentMap
- .get(filterList.get(selectedIndex));
- queryComponent.setValue(booleanFilterComponent
- .getValue());
- queryComponent.setSelected(true);
- } else if (e.getStateChange() == ItemEvent.DESELECTED) {
- ((QueryComponent) componentMap.get(filterList
- .get(selectedIndex))).setSelected(false);
- }
- }
- });
- }
-
- public int getType() {
- return FILTER;
- }
-
- }
-
- class BooleanFilterComponent extends QueryComponent {
- private static final long serialVersionUID = 1L;
-
- private static final String ONLY = "only";
-
- private static final String EXCLUDED = "excluded";
-
- private ButtonGroup buttonGroup = new ButtonGroup();
-
- private JRadioButton only;
-
- private JRadioButton excluded;
-
- public BooleanFilterComponent(FilterDescription filterDescription,
- MartDataset dataset) {
- setConfigObject(filterDescription);
- setDataset(dataset);
- setName(filterDescription.getInternalName());
- setBackground(componentBackgroundColor);
-
- setLayout(new BoxLayout(this, BoxLayout.Y_AXIS));
- setBackground(componentBackgroundColor);
-
- only = new JRadioButton("Only");
- only.setFont(only.getFont().deriveFont(Font.PLAIN));
- only.setBackground(componentBackgroundColor);
- only.addItemListener(new ItemListener() {
- public void itemStateChanged(ItemEvent e) {
- if (e.getStateChange() == ItemEvent.SELECTED) {
- fireFilterChanged(new QueryComponentEvent(this,
- getName(), getDataset(), ONLY));
- }
- }
- });
- buttonGroup.add(only);
- add(only);
-
- excluded = new JRadioButton("Excluded");
- excluded.setFont(excluded.getFont().deriveFont(Font.PLAIN));
- excluded.setBackground(componentBackgroundColor);
- excluded.addItemListener(new ItemListener() {
- public void itemStateChanged(ItemEvent e) {
- if (e.getStateChange() == ItemEvent.SELECTED) {
- fireFilterChanged(new QueryComponentEvent(this,
- getName(), getDataset(), EXCLUDED));
- }
- }
- });
- buttonGroup.add(excluded);
- add(excluded);
-
- setValue(filterDescription.getQualifier());
- }
-
- public int getType() {
- return FILTER;
- }
-
- public String getValue() {
- if (excluded.isSelected()) {
- return EXCLUDED;
- } else {
- return ONLY;
- }
- }
-
- public void setValue(String value) {
- if (EXCLUDED.equals(value)) {
- excluded.setSelected(true);
- } else {
- only.setSelected(true);
- }
- }
-
- }
-
- class AttributeComponent extends QueryComponent {
- private static final long serialVersionUID = 1L;
-
- private AbstractButton button;
-
- private AbstractButton offButton;
-
- public AttributeComponent(
- BaseNamedConfigurationObject attributeDescription,
- MartDataset dataset, Object offButton) {
- this.offButton = (AbstractButton) offButton;
- setConfigObject(attributeDescription);
- setDataset(dataset);
- setName(attributeDescription.getInternalName());
- if (attributeDescription instanceof AttributeList) {
- setValue(((AttributeList) attributeDescription).getAttributes());
- }
- setLayout(new BorderLayout());
- setBackground(componentBackgroundColor);
- // if there's no display name the attribute isn't displayed
- String displayName = attributeDescription.getDisplayName();
- if (displayName != null) {
- attributeToDisplayName.put(attributeDescription
- .getInternalName(), displayName);
- if (offButton != null) {
- button = new JRadioButton(QueryConfigUtils
- .splitSentence(displayName));
- } else {
- button = new JCheckBox(QueryConfigUtils
- .splitSentence(displayName));
- }
- button.setFont(button.getFont().deriveFont(Font.PLAIN));
- button.setBackground(componentBackgroundColor);
- setSelectorButton(button);
-
- String description = attributeDescription.getDescription();
- if (description != null) {
- button.setToolTipText(description);
- }
-
- add(button, BorderLayout.WEST);
-
- button.addItemListener(new ItemListener() {
- public void itemStateChanged(ItemEvent e) {
- if (!settingAttributeState) {
- settingAttributeState = true;
- List attributes = (List) attributeNameToComponentMap
- .get(getQualifiedName());
- if (attributes != null) {
- for (Iterator iter = attributes.iterator(); iter
- .hasNext();) {
- AttributeComponent attribute = (AttributeComponent) iter
- .next();
- if (attribute != AttributeComponent.this) {
- if (e.getStateChange() == ItemEvent.SELECTED) {
- attribute.setSelected(true);
- } else if (e.getStateChange() == ItemEvent.DESELECTED) {
- attribute.setSelected(false);
- }
- }
- }
- }
- settingAttributeState = false;
- }
- }
- });
- }
- }
-
- public int getType() {
- return ATTRIBUTE;
- }
-
- public void setSelected(boolean selected) {
- if (offButton != null) {
- if (selected) {
- button.setSelected(true);
- } else {
- offButton.setSelected(true);
- }
-
<TRUNCATED>
[05/16] incubator-taverna-plugin-bioinformatics git commit:
temporarily empty repository
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyActivity.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyActivity.java b/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyActivity.java
deleted file mode 100644
index e61406b..0000000
--- a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyActivity.java
+++ /dev/null
@@ -1,1319 +0,0 @@
-/*******************************************************************************
- * This file is a component of the Taverna project, and is licensed under the
- * GNU LGPL. Copyright Edward Kawas, The BioMoby Project
- ******************************************************************************/
-package net.sf.taverna.t2.activities.biomoby;
-
-import java.net.MalformedURLException;
-import java.net.URL;
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.Iterator;
-import java.util.List;
-import java.util.Map;
-import java.util.Map.Entry;
-import java.util.Vector;
-
-import net.sf.taverna.t2.annotation.annotationbeans.MimeType;
-import net.sf.taverna.t2.reference.ExternalReferenceSPI;
-import net.sf.taverna.t2.reference.ReferenceContext;
-import net.sf.taverna.t2.reference.ReferenceService;
-import net.sf.taverna.t2.reference.ReferenceServiceException;
-import net.sf.taverna.t2.reference.T2Reference;
-import net.sf.taverna.t2.workflowmodel.EditException;
-import net.sf.taverna.t2.workflowmodel.OutputPort;
-import net.sf.taverna.t2.workflowmodel.processor.activity.AbstractAsynchronousActivity;
-import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityConfigurationException;
-import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityInputPort;
-import net.sf.taverna.t2.workflowmodel.processor.activity.AsynchronousActivityCallback;
-
-import org.apache.log4j.Logger;
-import org.biomoby.client.CentralImpl;
-import org.biomoby.service.dashboard.data.ParametersTable;
-import org.biomoby.shared.Central;
-import org.biomoby.shared.MobyData;
-import org.biomoby.shared.MobyException;
-import org.biomoby.shared.MobyPrimaryDataSet;
-import org.biomoby.shared.MobyPrimaryDataSimple;
-import org.biomoby.shared.MobySecondaryData;
-import org.biomoby.shared.MobyService;
-import org.biomoby.shared.Utils;
-import org.jdom.Element;
-import org.jdom.output.Format;
-import org.jdom.output.XMLOutputter;
-
-/**
- * An Activity based on the Biomoby compliant web services. This activity
- * implementation will contact Biomoby registry in order to find the list of
- * extant ports at creation time.
- *
- * Copied from org.biomoby.client.taverna.plugin.BiomobyProcessor and
- * org.biomoby.client.taverna.plugin.BiomobyTask and converted to a Taverna 2
- * Activity.
- *
- * @author Martin Senger
- * @author Edward Kawas
- * @author Jose Maria Fernandez, INB
- * @author David Withers
- */
-public class BiomobyActivity extends
- AbstractAsynchronousActivity<BiomobyActivityConfigurationBean> {
-
- public static final String URI = "http://ns.taverna.org.uk/2010/activity/biomoby/service";
-
- private static Logger logger = Logger.getLogger(BiomobyActivity.class);
-
- protected BiomobyActivityConfigurationBean configurationBean = new BiomobyActivityConfigurationBean();
-
- private URL endpoint;
-
- private Central worker = null;
-
- private MobyService mobyService = null;
-
- private boolean containSecondary = false;
-
- private ParametersTable parameterTable = null;
-
-
-
- private boolean doInit = true;
-
- @Override
- public void configure(BiomobyActivityConfigurationBean configurationBean)
- throws ActivityConfigurationException {
- this.configurationBean = configurationBean;
- if (doInit) {
- init();
- generatePorts();
- configureSecondaries();
- doInit = false;
- } else {
- configureSecondaries();
- }
- }
-
- @Override
- public BiomobyActivityConfigurationBean getConfiguration() {
- return configurationBean;
- }
-
- @Override
- public void executeAsynch(final Map<String, T2Reference> inputMap,
- final AsynchronousActivityCallback callback) {
- callback.requestRun(new Runnable() {
- @SuppressWarnings("unchecked")
- public void run() {
- ReferenceService referenceService = callback.getContext()
- .getReferenceService();
-
- Map<String, T2Reference> outputMap = new HashMap<String, T2Reference>();
-
- if (logger.isDebugEnabled()) {
- logger.debug("Service " + mobyService.getUniqueName());
- for (Iterator it = inputMap.keySet().iterator(); it
- .hasNext();) {
- String key = (String) it.next();
- try {
- Object input = referenceService.renderIdentifier(
- inputMap.get(key), String.class, callback
- .getContext());
- if (input instanceof String) {
- logger.debug("key " + key + "has value of\n"
- + input);
- continue;
- } else if (input instanceof List) {
- List list = (List) input;
- for (Iterator it2 = list.iterator(); it2
- .hasNext();) {
- logger.debug("List key " + key
- + "has value of\n" + it2.next());
- }
- }
- } catch (ReferenceServiceException e) {
- logger.debug(
- "Error resolving data for port " + key, e);
- }
- }
- logger.debug("Printing of ports complete.");
- }
- // invoke services with no defined input (as per BioMOBY API)
- if (mobyService.getPrimaryInputs().length == 0) {
- try {
- String methodName = configurationBean.getServiceName();
- String serviceEndpoint = endpoint.toExternalForm();
- String serviceInput = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>"
- + "<moby:MOBY xmlns:moby=\"http://www.biomoby.org/moby\">"
- + " <moby:mobyContent>"
- + " <moby:mobyData moby:queryID=\"sip_1_\" />"
- + " </moby:mobyContent>" + "</moby:MOBY>";
- String[] invocations = new String[] { serviceInput };
- // add secondaries
- if (containSecondary) {
- @SuppressWarnings("unused")
- ParametersTable pt = getParameterTable();
- Element[] parameters = null;
- parameters = getParameterTable().toXML();
- serviceInput = "<?xml version=\"1.0\" encoding=\"UTF-8\"?>"
- + "<moby:MOBY xmlns:moby=\"http://www.biomoby.org/moby\">"
- + " <moby:mobyContent>"
- + " <moby:mobyData moby:queryID=\"sip_1_\">";
- XMLOutputter out = new XMLOutputter(Format
- .getCompactFormat());
- Format format = out.getFormat();
- format.setOmitDeclaration(true);
- out.setFormat(format);
- for (int i = 0; i < parameters.length; i++) {
- serviceInput += out.outputString(parameters[i]);
- }
- serviceInput += " </moby:mobyData>"
- + " </moby:mobyContent>" + "</moby:MOBY>";
- format = Format.getPrettyFormat();
- format.setOmitDeclaration(false);
- format.setIndent(" ");
- serviceInput = new XMLOutputter(format)
- .outputString(XMLUtilities
- .getDOMDocument(serviceInput));
- invocations = new String[] { serviceInput };
- }
-
- // execute the service that takes no Biomoby datatypes
- // as input
- for (int inCount = 0; inCount < invocations.length; inCount++) {
- if (logger.isDebugEnabled())
- logger.debug("input(" + inCount + "):\n"
- + invocations[inCount]);
- // execute a 'moby' service
- invocations[inCount] = executeService(
- serviceEndpoint, methodName,
- invocations[inCount]);
- if (logger.isDebugEnabled())
- logger.debug("output(" + inCount + "):\n"
- + invocations[inCount]);
- }
- String outputXML = XMLUtilities
- .createMultipleInvokations(invocations);
- // create the other ports
- processOutputPorts(outputXML, outputMap,
- referenceService, callback.getContext());
-
- callback.receiveResult(outputMap, new int[0]);
- return;
- } catch (ReferenceServiceException e) {
- callback.fail("Error accessing input/output data", e);
- } catch (MobyException ex) {
- // a MobyException should be already reasonably
- // formatted
- logger
- .error(
- "Error invoking biomoby service for biomoby. A MobyException caught",
- ex);
- callback.fail(
- "Service failed due to problem invoking remote biomoby service.\n"
- + ex.getMessage(), ex);
-
- } catch (Exception ex) {
- logger.error(
- "Error invoking biomoby service for biomoby",
- ex);
- callback
- .fail(
- "Task failed due to problem invoking biomoby service (see details in log)",
- ex);
- }
- }
-
- {
- // now try other named ports
- try {
- String inputXML = null;
- Element root = new Element("MOBY", XMLUtilities.MOBY_NS);
- Element content = new Element("mobyContent",
- XMLUtilities.MOBY_NS);
- root.addContent(content);
- int totalMobyDatas = 0;
- Vector mobyDatas = new Vector(); // list of mobyData
- // element
- for (ActivityInputPort myInput : getInputPorts()) {
- if (myInput.getName().equalsIgnoreCase("input")) {
- continue;
- }
- // the port name
- String portName = myInput.getName();
- // the article name
- String articleName = "";
- String type = portName;
- if (portName.indexOf("(") >= 0
- && portName.indexOf(")") > 0) {
- articleName = portName.substring(portName
- .indexOf("(") + 1, portName
- .indexOf(")"));
-
- if (articleName.indexOf("'") >= 0
- && articleName.lastIndexOf("'") > 0)
- articleName = articleName.substring(
- articleName.indexOf("'") + 1,
- articleName.lastIndexOf("'"));
-
- type = portName.substring(0, portName
- .indexOf("("));
- }
-
- // String inputType = myInput.getSyntacticType();
- Object input = referenceService.renderIdentifier(
- inputMap.get(portName), myInput
- .getTranslatedElementClass(),
- callback.getContext());
- if (myInput.getDepth() == 0) {
- inputXML = (String) input;
- Element inputElement = null;
- try {
- inputElement = XMLUtilities.getDOMDocument(
- inputXML).getRootElement();
-
- } catch (MobyException e) {
- callback
- .fail(XMLUtilities.newline
- + "There was an error parsing the input XML:"
- + XMLUtilities.newline
- + Utils.format(inputXML, 3)
- + XMLUtilities.newline
- + e.getLocalizedMessage());
- return;
- }
- // determine whether we have a multiple
- // invocation message
- if (XMLUtilities
- .isMultipleInvocationMessage(inputElement)) {
- // multiple invocations
- Element[] invocations = XMLUtilities
- .getSingleInvokationsFromMultipleInvokations(inputElement);
- ArrayList list = new ArrayList();
- for (int j = 0; j < invocations.length; j++) {
- Element[] elements = XMLUtilities
- .getListOfCollections(invocations[j]);
- if (elements.length == 0) {
- // single simple
- inputElement = XMLUtilities
- .renameSimple(articleName,
- type,
- invocations[j]);
- Element md = XMLUtilities
- .extractMobyData(inputElement);
- list.add(md);
- } else {
- // collection of simples => create
- // multiple
- // invocation message
- String queryID = XMLUtilities
- .getQueryID(invocations[j]);
- Element[] simples = XMLUtilities
- .getSimplesFromCollection(invocations[j]);
- for (int k = 0; k < simples.length; k++) {
- Element wrappedSimple = XMLUtilities
- .createMobyDataElementWrapper(simples[k]);
- wrappedSimple = XMLUtilities
- .renameSimple(
- articleName,
- type,
- wrappedSimple);
- wrappedSimple = XMLUtilities
- .setQueryID(
- wrappedSimple,
- queryID );
- list
- .add(XMLUtilities
- .extractMobyData(wrappedSimple));
- }
- }
- }
- if (list.isEmpty())
- continue;
- if (totalMobyDatas < 1)
- totalMobyDatas = 1;
- totalMobyDatas *= list.size();
- mobyDatas.add(list);
- } else {
- // single invocation
- // is this a collection
- Element[] elements = XMLUtilities
- .getListOfCollections(inputElement);
- if (elements.length == 0) {
- // single simple
- inputElement = XMLUtilities
- .renameSimple(articleName,
- type, inputElement);
- ArrayList list = new ArrayList();
- Element md = XMLUtilities
- .extractMobyData(inputElement);
- list.add(md);
- mobyDatas.add(list);
- if (totalMobyDatas < 1)
- totalMobyDatas = 1;
- } else {
- // collection of simples => create
- // multiple
- // invocation message
- String queryID = XMLUtilities
- .getQueryID(inputElement);
- Element[] simples = XMLUtilities
- .getSimplesFromCollection(inputElement);
-
- ArrayList list = new ArrayList();
- for (int j = 0; j < simples.length; j++) {
- Element wrappedSimple = XMLUtilities
- .createMobyDataElementWrapper(simples[j]);
- wrappedSimple = XMLUtilities
- .renameSimple(articleName,
- type, wrappedSimple);
- wrappedSimple = XMLUtilities
- .setQueryID(wrappedSimple,
- queryID );
- list
- .add(XMLUtilities
- .extractMobyData(wrappedSimple));
- }
- if (list.isEmpty())
- continue;
- mobyDatas.add(list);
- if (totalMobyDatas < 1)
- totalMobyDatas = 1 * list.size();
- else {
- totalMobyDatas *= list.size();
- }
- }
-
- }
- } else {
- // we have a collection!
- // inputThing is a list of Strings
- List list = (List) input;
- /*
- * need this map in cases where simples are
- * passed into a service that wants a
- * collection. each simple is then added into
- * the same collection
- */
- Map collectionMap = new HashMap();
- for (Iterator it = list.iterator(); it
- .hasNext();) {
- Element inputElement = null;
- String next = (String) it.next();
- try {
- inputElement = XMLUtilities
- .getDOMDocument(next)
- .getRootElement();
-
- } catch (MobyException e) {
- callback
- .fail(XMLUtilities.newline
- + "There was an error parsing the input XML:"
- + XMLUtilities.newline
- + Utils.format(
- inputXML, 3)
- + XMLUtilities.newline
- + e
- .getLocalizedMessage());
- return;
- }
- // determine whether we have a multiple
- // invocation message
- if (XMLUtilities
- .isMultipleInvocationMessage(inputElement)) {
- // multiple invocations (update
- // totalMobyDatas)
- Element[] invocations = XMLUtilities
- .getSingleInvokationsFromMultipleInvokations(inputElement);
- ArrayList mdList = new ArrayList();
- // this is here for mim messages of
- // simples
- Element mimCollection = null;
- String mimQueryID = "";
- for (int j = 0; j < invocations.length; j++) {
- Element[] elements = XMLUtilities
- .getListOfCollections(invocations[j]);
- mimQueryID = XMLUtilities
- .getQueryID(invocations[j]);
- if (elements.length == 0) {
- if (mimCollection == null)
- mimCollection = new Element(
- "Collection",
- XMLUtilities.MOBY_NS);
-
- Element theSimple = XMLUtilities
- .extractMobyData(invocations[j]);
- if (theSimple
- .getChild("Simple") != null)
- theSimple = theSimple
- .getChild("Simple");
- else if (theSimple.getChild(
- "Simple",
- XMLUtilities.MOBY_NS) != null)
- theSimple = theSimple
- .getChild(
- "Simple",
- XMLUtilities.MOBY_NS);
- mimCollection
- .addContent(theSimple
- .detach());
- } else {
- // collection passed in (always
- // 1 passed in)
- Element collection = invocations[j];
- collection = XMLUtilities
- .renameCollection(
- articleName,
- collection);
- collection = XMLUtilities
- .createMobyDataElementWrapper(
- collection,
- XMLUtilities
- .getQueryID(invocations[j]),
- null);
- mdList
- .add(XMLUtilities
- .extractMobyData(collection));
- }
- }
- if (mimCollection != null) {
- mimCollection = XMLUtilities
- .createMobyDataElementWrapper(
- mimCollection,
- mimQueryID, null);
- mimCollection = XMLUtilities
- .renameCollection(
- articleName,
- mimCollection);
- mimCollection = XMLUtilities
- .createMobyDataElementWrapper(
- mimCollection,
- mimQueryID, null);
- mdList
- .add(XMLUtilities
- .extractMobyData(mimCollection));
- }
-
- if (mdList.isEmpty())
- continue;
-
- mobyDatas.add(mdList);
- if (totalMobyDatas < 1)
- totalMobyDatas = 1;
- totalMobyDatas *= mdList.size();
- } else {
- // single invocation
- Element[] elements = XMLUtilities
- .getListOfCollections(inputElement);
- if (elements.length == 0) {
- // simple was passed in so wrap it
- Element collection = new Element(
- "Collection",
- XMLUtilities.MOBY_NS);
- collection.addContent(XMLUtilities
- .extractMobyData(
- inputElement)
- .cloneContent());
- collection = XMLUtilities
- .createMobyDataElementWrapper(
- collection,
- XMLUtilities
- .getQueryID(inputElement),
- null);
- collection = XMLUtilities
- .renameCollection(
- articleName,
- collection);
- collection = XMLUtilities
- .createMobyDataElementWrapper(
- collection,
- XMLUtilities
- .getQueryID(inputElement),
- null);
- if (collectionMap
- .containsKey(articleName)) {
- // add the simple to a
- // pre-existing
- // collection
- ArrayList mdList = (ArrayList) collectionMap
- .remove(articleName);
- mdList
- .add(XMLUtilities
- .extractMobyData(collection));
- collectionMap.put(articleName,
- mdList);
- } else {
- // new collection - add element
- // and
- // increment count
- ArrayList mdList = new ArrayList();
- mdList
- .add(XMLUtilities
- .extractMobyData(collection));
- collectionMap.put(articleName,
- mdList);
- // totalMobyDatas++;
- if (totalMobyDatas < 1)
- totalMobyDatas = 1;
- }
- } else {
- // we have a collection
- Element collection = inputElement;
- collection = XMLUtilities
- .renameCollection(
- articleName,
- collection);
- ArrayList mdList = new ArrayList();
- collection = XMLUtilities
- .createMobyDataElementWrapper(
- collection,
- XMLUtilities
- .getQueryID(inputElement),
- null);
- mdList
- .add(XMLUtilities
- .extractMobyData(collection));
- mobyDatas.add(mdList);
- if (totalMobyDatas < 1)
- totalMobyDatas = 1;
-
- }
- } // end if SIM
- } // end iteration over inputThing list
- Iterator collectionIterator = collectionMap
- .keySet().iterator();
- while (collectionIterator.hasNext()) {
- String key = (String) collectionIterator
- .next();
- List theList = (List) collectionMap
- .get(key);
- theList = XMLUtilities.mergeCollections(
- theList, key);
- List unwrappedList = new ArrayList();
- for (Iterator it = theList.iterator(); it
- .hasNext();) {
- Element e = (Element) it.next();
- if (XMLUtilities.isWrapped(e))
- unwrappedList.add(XMLUtilities
- .extractMobyData(e));
- else
- unwrappedList.add(e);
- }
- mobyDatas.add(unwrappedList);
- }
- }
- }
-
- if (logger.isDebugEnabled()) {
- logger.debug("Before MobyData aggregation");
- for (Iterator itr = mobyDatas.iterator(); itr
- .hasNext();) {
- List eList = (List) itr.next();
- for (int x = 0; x < eList.size(); x++) {
- logger.debug(new XMLOutputter(Format
- .getPrettyFormat())
- .outputString((Element) eList
- .get(x)));
- }
- }
- logger.debug("******* End ******");
- }
- /*
- * ports have been processed -> vector contains a list
- * of all the different types of inputs with their
- * article names set correctly. The elements are from
- * mobyData down. Moreover, there are totalMobyData
- * number of invocations in the output moby message
- */
- if (logger.isDebugEnabled()) {
- logger.debug("TotalMobyDatas: " + totalMobyDatas);
- }
- Element[] mds = new Element[totalMobyDatas];
- // initialize the mobydata blocks
- for (int x = 0; x < mds.length; x++) {
- mds[x] = new Element("mobyData",
- XMLUtilities.MOBY_NS);
- String queryID = "_";
- // add the content
- for (Iterator iter = mobyDatas.iterator(); iter
- .hasNext();) {
- ArrayList list = (ArrayList) iter.next();
- int index = x % list.size();
- Element next = ((Element) list.get(index));
- logger.debug(new XMLOutputter(Format
- .getPrettyFormat()).outputString(next));
- // queryID += "_" +
- // XMLUtilities.getQueryID(next);
- queryID = XMLUtilities.getQueryID(next);
- mds[x].addContent(next.cloneContent());
-
- }
- // remove the first _
- // if (queryID != null && queryID.length() > 1)
- // queryID = queryID.substring(1);
- mds[x].setAttribute("queryID", queryID,
- XMLUtilities.MOBY_NS);
- // if secondarys exist add them here
- if (containSecondary) {
- @SuppressWarnings("unused")
- ParametersTable pt = parameterTable;
- Element[] parameters = null;
- parameters = parameterTable.toXML();
- for (int i = 0; i < parameters.length; i++) {
- mds[x].addContent((parameters[i]).detach());
- }
- }
- content.addContent(mds[x].detach());
- }
-
- if (logger.isDebugEnabled()) {
- logger.debug("After MobyData aggregation");
- logger.debug(new XMLOutputter(Format
- .getPrettyFormat()).outputString(root));
- logger.debug("******* End ******");
- }
- // do the task and populate outputXML
-
- String methodName = configurationBean.getServiceName();
- String serviceEndpoint = endpoint.toExternalForm();
-
- String serviceInput = new XMLOutputter(Format
- .getPrettyFormat()).outputString(root);
- String[] invocations = XMLUtilities
- .getSingleInvokationsFromMultipleInvokations(serviceInput);
- // logger.debug(serviceInput);
- // going to iterate over all invocations so that
- // messages with
- // many mobyData blocks dont timeout.
- logger.debug("Total invocations " + invocations.length);
- if (invocations.length > 0)
- logger.debug("invocation 00");
- for (int inCount = 0; inCount < invocations.length; inCount++) {
- if (logger.isDebugEnabled())
- logger.info("input(" + inCount + "):\n"
- + invocations[inCount]);
- if (!XMLUtilities.isEmpty(invocations[inCount]))
- invocations[inCount] = executeService(
- serviceEndpoint, methodName,
- invocations[inCount]);
- if (logger.isDebugEnabled())
- logger.info("output(" + inCount + "):\n"
- + invocations[inCount]);
- }
-
- String outputXML = XMLUtilities
- .createMultipleInvokations(invocations);
- // create the other ports
- processOutputPorts(outputXML, outputMap,
- referenceService, callback.getContext());
-
- callback.receiveResult(outputMap, new int[0]);
-
- } catch (ReferenceServiceException e) {
- callback.fail("Error accessing input/output data", e);
- } catch (MobyException ex) {
- // a MobyException should be already reasonably
- // formatted
- logger
- .error(
- "Error invoking biomoby service for biomoby. A MobyException caught",
- ex);
- callback.fail(
- "Service failed due to exception invoking remote biomoby service.\n"
- + ex.getMessage(), ex);
-
- } catch (Exception ex) {
- // details of other exceptions will appear only in a log
-// ex.();
- logger.error(
- "Error invoking biomoby service for biomoby",
- ex);
- callback
- .fail(
- "Task failed due to problem invoking biomoby service (see details in log)",
- ex);
- }
-
- }
- }
-
- });
-
- }
-
- private void init() throws ActivityConfigurationException {
- // Find the service endpoint (by calling Moby registry)
- try {
- if (mobyService == null) {
- worker = new CentralImpl(configurationBean.getMobyEndpoint());
-
- MobyService pattern = new MobyService(configurationBean
- .getServiceName());
- pattern.setAuthority(configurationBean.getAuthorityName());
- pattern.setCategory("");
- MobyService[] services = worker.findService(pattern);
- if (services == null || services.length == 0)
- throw new ActivityConfigurationException(
- formatError("I cannot find the service."));
- mobyService = services[0];
- }
- String serviceEndpoint = mobyService.getURL();
- if (serviceEndpoint == null || serviceEndpoint.equals(""))
- throw new ActivityConfigurationException(
- formatError("Service has an empty endpoint."));
- try {
- endpoint = new URL(serviceEndpoint);
- } catch (MalformedURLException e2) {
- throw new ActivityConfigurationException(
- formatError("Service has malformed endpoint: '"
- + serviceEndpoint + "'."));
- }
-
- } catch (Exception e) {
- if (e instanceof ActivityConfigurationException) {
- throw (ActivityConfigurationException) e;
- }
- throw new ActivityConfigurationException(formatError(e.toString()));
- }
- // here we make sure that we have downloaded the ontology for the
- // registry that we got this service from
- try {
- new GetOntologyThread(worker.getRegistryEndpoint()).start();
- } catch (Exception e) {
- /* don't care if an exception occurs here ... */
- }
-
- }
-
- /**
- * Use the endpoint data to create new ports and attach them to the
- * processor.
- */
- private void generatePorts() {
-
- // inputs TODO - find a better way to deal with collections
- MobyData[] serviceInputs = this.mobyService.getPrimaryInputs();
- int inputDepth = 0;
- for (int x = 0; x < serviceInputs.length; x++) {
- if (serviceInputs[x] instanceof MobyPrimaryDataSimple) {
- MobyPrimaryDataSimple simple = (MobyPrimaryDataSimple) serviceInputs[x];
-
- // retrieve the simple article name
- String simpleName = simple.getName();
- if (simpleName.equals("")) {
- simpleName = "_ANON_";
- }
- simpleName = "(" + simpleName + ")";
-
- String portName = simple.getDataType().getName() + simpleName;
- addInput(portName, inputDepth, true,
- new ArrayList<Class<? extends ExternalReferenceSPI>>(),
- String.class);
- } else {
- // collection of items
- inputDepth = 1;
- MobyPrimaryDataSet collection = (MobyPrimaryDataSet) serviceInputs[x];
- String collectionName = collection.getName();
- if (collectionName.equals(""))
- collectionName = "MobyCollection";
- MobyPrimaryDataSimple[] simples = collection.getElements();
- for (int y = 0; y < simples.length; y++) {
- // collection port
- String portName = simples[y].getDataType().getName()
- + "(Collection - '" + collectionName + "')";
- addInput(
- portName,
- inputDepth,
- true,
- new ArrayList<Class<? extends ExternalReferenceSPI>>(),
- String.class);
-
- }
- }
- }
- /*addInput("input", inputDepth, true,
- new ArrayList<Class<? extends ExternalReferenceSPI>>(),
- String.class);*/
-
- MobyData[] secondaries = this.mobyService.getSecondaryInputs();
-
- if (secondaries.length > 0) {
- MobySecondaryData[] msd = new MobySecondaryData[secondaries.length];
- for (int i = 0; i < secondaries.length; i++) {
- msd[i] = (MobySecondaryData) secondaries[i];
- }
- containSecondary = true;
- this.parameterTable = new org.biomoby.service.dashboard.data.ParametersTable(
- msd);
- updateConfigBeanSecondaries();
- }
-
- // outputs
- MobyData[] serviceOutputs = this.mobyService.getPrimaryOutputs();
- int outputDepth = 0;
- for (int x = 0; x < serviceOutputs.length; x++) {
- if (serviceOutputs[x] instanceof MobyPrimaryDataSimple) {
- MobyPrimaryDataSimple simple = (MobyPrimaryDataSimple) serviceOutputs[x];
-
- // retrieve the simple article name
- String simpleName = simple.getName();
- if (simpleName.equals("")) {
- simpleName = "_ANON_";
- }
- simpleName = "(" + simpleName + ")";
-
- String outputName = simple.getDataType().getName() + simpleName;
- addOutput(outputName, outputDepth, "text/xml");
- } else {
- outputDepth = 1;
- // collection of items
- MobyPrimaryDataSet collection = (MobyPrimaryDataSet) serviceOutputs[x];
- String collectionName = collection.getName();
- if (collectionName.equals(""))
- collectionName = "MobyCollection";
- MobyPrimaryDataSimple[] simples = collection.getElements();
- for (int y = 0; y < simples.length; y++) {
- String outputName = simples[y].getDataType().getName()
- + "(Collection - '" + collectionName + "')";
- addOutput(outputName, outputDepth, "text/xml");
-
- outputName = simples[y].getDataType().getName()
- + "(Collection - '" + collectionName
- + "' As Simples)";
- addOutput(outputName, outputDepth, "text/xml");
- }
- }
- }
-
-// addOutput("output", outputDepth, "text/xml");
-
- }
-
- /**
- * Updates config bean secondaries for those that aren't already defined so
- * this only records new ones, but doesn't overwrite existing ones.
- */
- private void updateConfigBeanSecondaries() {
- ParametersTable table = getParameterTable();
- int rows = table.getModel().getRowCount();
- Map<String, String> secondaries = getConfiguration().getSecondaries();
- for (int i = 0; i < rows; i++) {
- String key = (String) table.getModel().getValueAt(i, 0);
- String value = table.getModel().getValueAt(i, 1).toString();
- if (!secondaries.containsKey(key)) {
- secondaries.put(key, value);
- }
- }
-
- }
-
- public ParametersTable getParameterTable() {
- return parameterTable;
- }
-
- public boolean containsSecondaries() {
- return containSecondary;
- }
-
- public MobyService getMobyService() {
- return mobyService;
- }
-
- @SuppressWarnings("unchecked")
- private void processOutputPorts(String outputXML, Map outputMap,
- ReferenceService referenceService, ReferenceContext context)
- throws MobyException, ReferenceServiceException {
- boolean isMIM = XMLUtilities.isMultipleInvocationMessage(outputXML);
- for (OutputPort outputPort : getOutputPorts()) {
- String name = outputPort.getName();
- if (!name.equalsIgnoreCase("output")) {
- if (outputPort.getDepth() == 1) {
- // collection - list of strings
- String articleName = "";
- if (name.indexOf("MobyCollection") > 0) {
- // un-named collection -> ignore it as it is illegal
- // in the api
- // TODO could throw exception
-
- List innerList = new ArrayList();
- outputMap.put(name, referenceService
- .register(innerList, outputPort.getDepth(),
- true, context));
- continue;
- } else {
- articleName = name.substring(name.indexOf("'") + 1,
- name.lastIndexOf("'"));
- if (name.indexOf("' As Simples)") > 0) {
- // list of simples wanted
- if (isMIM) {
- String[] invocations = XMLUtilities
- .getSingleInvokationsFromMultipleInvokations(outputXML);
-
- List innerList = new ArrayList();
- Element serviceNotesElement = XMLUtilities
- .getServiceNotesAsElement(outputXML);
- for (int i = 0; i < invocations.length; i++) {
- try {
- String collection = XMLUtilities
- .getWrappedCollection(
- articleName,
- invocations[i]);
- String[] simples = XMLUtilities
- .getSimplesFromCollection(
- articleName, collection);
- for (int j = 0; j < simples.length; j++) {
- innerList
- .add(XMLUtilities
- .createMobyDataElementWrapper(
- simples[j],
- XMLUtilities
- .getQueryID(collection)
- /*
- * + "_+_s"
- * +
- * qCounter
- * ++
- */,
- serviceNotesElement));
- }
- } catch (MobyException e) {
- // collection didnt exist, so put an
- // empty
- // mobyData
- // TODO keep the original wrapper
- /*
- * String qID =
- * XMLUtilities.getQueryID(invocations
- * [i]); Element empty =
- * XMLUtilities.createMobyDataWrapper
- * (qID,
- * XMLUtilities.getServiceNotesAsElement
- * (outputXML)); XMLOutputter output =
- * new XMLOutputter(Format
- * .getPrettyFormat());
- * innerList.add(output
- * .outputString(empty));
- */
- }
- }
- outputMap.put(name, referenceService.register(
- innerList, outputPort.getDepth(), true,
- context));
- } else {
- // process the single invocation and put string
- // into
- // a
- // list
- try {
-
- List innerList = new ArrayList();
- String collection = XMLUtilities
- .getWrappedCollection(articleName,
- outputXML);
-
- String[] simples = XMLUtilities
- .getSimplesFromCollection(
- articleName, collection);
- Element serviceNotesElement = XMLUtilities
- .getServiceNotesAsElement(outputXML);
- for (int i = 0; i < simples.length; i++) {
- innerList
- .add(XMLUtilities
- .createMobyDataElementWrapper(
- simples[i],
- XMLUtilities
- .getQueryID(collection),
- serviceNotesElement));
- }
-
- outputMap
- .put(
- name,
- referenceService
- .register(
- innerList,
- outputPort
- .getDepth(),
- true,
- context));
- } catch (MobyException e) {
- List innerList = new ArrayList();
- outputMap
- .put(
- name,
- referenceService
- .register(
- innerList,
- outputPort
- .getDepth(),
- true,
- context));
- }
- }
- } else {
- if (isMIM) {
- // process each invocation and then merge them
- // into
- // a
- // single string
- String[] invocations = XMLUtilities
- .getSingleInvokationsFromMultipleInvokations(outputXML);
-
- List innerList = new ArrayList();
- for (int i = 0; i < invocations.length; i++) {
- try {
- String collection = XMLUtilities
- .getWrappedCollection(
- articleName,
- invocations[i]);
- innerList.add(collection);
- } catch (MobyException e) {
-
- }
- }
-
- outputMap.put(name, referenceService.register(
- innerList, outputPort.getDepth(), true,
- context));
- } else {
-
- try {
-
- List innerList = new ArrayList();
- String collection = XMLUtilities
- .getWrappedCollection(articleName,
- outputXML);
- innerList.add(collection);
- outputMap
- .put(
- name,
- referenceService
- .register(
- innerList,
- outputPort
- .getDepth(),
- true,
- context));
- } catch (MobyException e) {
- List innerList = new ArrayList();
- outputMap
- .put(
- name,
- referenceService
- .register(
- innerList,
- outputPort
- .getDepth(),
- true,
- context));
- }
- }
- }
- }
- } else {
- // simple - single string
- if (name.indexOf("_ANON_") > 0) {
- // un-named simple -> ignore it as it is illegal in the
- // api
- // TODO could throw exception
-
- String empty = new XMLOutputter()
- .outputString(XMLUtilities
- .createMobyDataWrapper(
- XMLUtilities
- .getQueryID(outputXML),
- XMLUtilities
- .getServiceNotesAsElement(outputXML)));
- List innerList = new ArrayList();
- innerList.add(empty);
- outputMap.put(name, referenceService.register(empty,
- outputPort.getDepth(), true, context));
- // FIXME outputMap.put(name, new
- // DataThing((Object)null));
- continue;
- } else {
- // TODO what if you make mim messages a single string
- // and then simples always output 'text/xml'?
- String articleName = name.substring(
- name.indexOf("(") + 1, name.indexOf(")"));
- if (isMIM) {
-
- String[] invocations = XMLUtilities
- .getSingleInvokationsFromMultipleInvokations(outputXML);
-
- ArrayList innerList = new ArrayList();
-
- for (int i = 0; i < invocations.length; i++) {
- try {
- String simple = XMLUtilities
- .getWrappedSimple(articleName,
- invocations[i]);
- innerList.add(simple);
- } catch (MobyException e) {
- // simple didnt exist, so put an empty
- // mobyData
- // TODO keep the original wrapper
- String qID = XMLUtilities
- .getQueryID(invocations[i]);
-
- Element empty = XMLUtilities
- .createMobyDataWrapper(
- qID,
- XMLUtilities
- .getServiceNotesAsElement(outputXML));
- XMLOutputter output = new XMLOutputter(
- Format.getPrettyFormat());
- // invocations[i] =
- // output.outputString(empty);
- innerList.add(output.outputString(empty));
- // FIXME outputMap.put(name, new
- // DataThing(""));
- }
- }
- String[] s = new String[innerList.size()];
- s = (String[]) innerList.toArray(s);
- try {
- outputMap.put(name, referenceService.register(
- XMLUtilities
- .createMultipleInvokations(s),
- outputPort.getDepth(), true, context));
- } catch (MobyException e) {
- logger
- .error("Error creating output for service: "
- + "."
- + System
- .getProperty("line.separator")
- + e.getMessage());
- outputMap.put(name, referenceService.register(
- "", outputPort.getDepth(), true,
- context));
- }
- } else {
- // process the single invocation and put into a
- // string
- try {
- String simple = XMLUtilities.getWrappedSimple(
- articleName, outputXML);
- ArrayList innerList = new ArrayList();
- innerList.add(simple);
- outputMap.put(name, referenceService.register(
- simple, outputPort.getDepth(), true,
- context));
- } catch (MobyException e) {
- // simple didnt exist, so put an empty mobyData
- // TODO keep the original wrapper
- String qID = XMLUtilities.getQueryID(outputXML);
- Element empty = XMLUtilities
- .createMobyDataWrapper(
- qID,
- XMLUtilities
- .getServiceNotesAsElement(outputXML));
- XMLOutputter output = new XMLOutputter(Format
- .getPrettyFormat());
- ArrayList innerList = new ArrayList();
- innerList.add(output.outputString(empty));
- outputMap.put(name, referenceService.register(
- output.outputString(empty), outputPort
- .getDepth(), true, context));
- // FIXME outputMap.put(name, new DataThing(""));
-
- }
- }
- }
- }
- }
- }
- }
-
- protected String formatError(String msg) {
- // Removed references to the authority, some errors
- // were causing it to be null which in turn threw
- // a NPE from here, breaking Taverna's error handlers
- return ("Problems with service '" + configurationBean.getServiceName()
- + "' provided by authority '"
- + configurationBean.getAuthorityName()
- + "'\nfrom Moby registry at "
- + configurationBean.getMobyEndpoint() + ":\n\n" + msg);
- }
-
- protected ActivityInputPort getInputPort(String name) {
- for (ActivityInputPort port : getInputPorts()) {
- if (port.getName().equals(name)) {
- return port;
- }
- }
- return null;
- }
-
- protected OutputPort getOutputPort(String name) {
- for (OutputPort port : getOutputPorts()) {
- if (port.getName().equals(name)) {
- return port;
- }
- }
- return null;
- }
-
- protected void addOutput(String portName, int portDepth, String type) {
- OutputPort port = edits.createActivityOutputPort(
- portName, portDepth, portDepth);
- MimeType mimeType = new MimeType();
- mimeType.setText(type);
- try {
- edits.getAddAnnotationChainEdit(port, mimeType)
- .doEdit();
- } catch (EditException e) {
- logger.debug("Error adding MimeType annotation to port", e);
- }
- outputPorts.add(port);
- }
-
- private void configureSecondaries() {
- if (configurationBean.getSecondaries().size() > 0
- && containsSecondaries()) {
- MobyData[] datas = getMobyService().getSecondaryInputs();
- for (Entry<String, String> entry : configurationBean
- .getSecondaries().entrySet()) {
- String name = entry.getKey();
- String value = entry.getValue();
- for (int i = 0; i < datas.length; i++) {
- if (datas[i].getName().equals(name)) {
- ((MobySecondaryData) datas[i]).setDefaultValue(value);
- break;
- }
- }
- }
- MobySecondaryData[] msd = new MobySecondaryData[datas.length];
- for (int i = 0; i < datas.length; i++) {
- msd[i] = (MobySecondaryData) datas[i];
- }
- setParameterTable(new ParametersTable(msd));
- }
- }
-
- private void setParameterTable(ParametersTable table) {
- parameterTable = table;
- }
-
- private String executeService(String url, String serviceName, String xml)
- throws MobyException {
- // here we get the wsdl before calling the service, as the biomoby api assumes ...
- try {
- new RetrieveWsdlThread(worker, mobyService).start();
- } catch (Exception e) {
- /* don't care if an exception occurs here ... */
- logger.info("Problem getting the biomoby wsdl for " + mobyService.getUniqueName() + ".\n" + e.getLocalizedMessage());
- }
- String serviceCategory = mobyService.getCategory();
- if (serviceCategory.equalsIgnoreCase(MobyService.CATEGORY_MOBY)) {
- return ExecuteMobyService.executeMobyService(url, serviceName, xml);
- } else if (serviceCategory.equalsIgnoreCase("cgi")) {
- return ExecuteCgiService.executeCgiService(url, xml);
- } else if (serviceCategory.equalsIgnoreCase(MobyService.CATEGORY_MOBY_ASYNC)) {
- return ExecuteAsyncMobyService.executeMobyAsyncService(url, serviceName, xml);
- } else if (serviceCategory.equalsIgnoreCase("cgi-async")) {
- return ExecuteAsyncCgiService.executeMobyCgiAsyncService(url, serviceName, xml);
- }
- // TODO should we throw an exception here?
- return "";
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyActivityConfigurationBean.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyActivityConfigurationBean.java b/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyActivityConfigurationBean.java
deleted file mode 100644
index 03abb6e..0000000
--- a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyActivityConfigurationBean.java
+++ /dev/null
@@ -1,142 +0,0 @@
-/*******************************************************************************
- * This file is a component of the Taverna project, and is licensed under the
- * GNU LGPL. Copyright Edward Kawas, The BioMoby Project
- ******************************************************************************/
-package net.sf.taverna.t2.activities.biomoby;
-
-import java.util.HashMap;
-import java.util.Map;
-import java.util.Set;
-
-import net.sf.taverna.t2.workflowmodel.processor.config.ConfigurationBean;
-import net.sf.taverna.t2.workflowmodel.processor.config.ConfigurationProperty;
-
-/**
- * A configuration bean specific to the Biomoby activity.
- *
- * @author David Withers
- */
-@ConfigurationBean(uri = BiomobyActivity.URI + "#Config")
-public class BiomobyActivityConfigurationBean {
-
- private String mobyEndpoint="";
-
- private String serviceName="";
-
- private String authorityName="";
-
- @Deprecated
- private String category = "";
- @Deprecated
- private String serviceType = "";
-
- private Map<String,String> secondaries=new HashMap<String,String>();
-
- /**
- * Returns the mobyEndpoint.
- *
- * @return the mobyEndpoint
- */
- public String getMobyEndpoint() {
- return mobyEndpoint;
- }
-
- /**
- * Sets the mobyEndpoint.
- *
- * @param mobyEndpoint the new mobyEndpoint
- */
- @ConfigurationProperty(name = "mobyEndpoint", label = "Moby Endpoint")
- public void setMobyEndpoint(String mobyEndpoint) {
- this.mobyEndpoint = mobyEndpoint;
- }
-
- /**
- * Returns the serviceName.
- *
- * @return the serviceName
- */
- public String getServiceName() {
- return serviceName;
- }
-
- /**
- * Sets the serviceName.
- *
- * @param serviceName the new serviceName
- */
- @ConfigurationProperty(name = "serviceName", label = "Service Name")
- public void setServiceName(String serviceName) {
- this.serviceName = serviceName;
- }
-
- /**
- * Returns the authorityName.
- *
- * @return the authorityName
- */
- public String getAuthorityName() {
- return authorityName;
- }
-
- /**
- * Sets the authorityName.
- *
- * @param authorityName the new authorityName
- */
- @ConfigurationProperty(name = "authorityName", label = "Authority Name")
- public void setAuthorityName(String authorityName) {
- this.authorityName = authorityName;
- }
-
- /**
- * Returns the secondaries
- *
- * @return secondaries as a HashMap
- */
- public Map<String,String> getSecondaries() {
- return secondaries;
- }
-
- /**
- *
- * @param secondaries
- */
- public void setSecondaries(Map<String,String> secondaries) {
- this.secondaries=secondaries;
- }
-
- @ConfigurationProperty(name = "secondaries", label = "Secondaries", required=false)
- public void setSecondaries(Set<Secondary> secondaries) {
- Map<String,String> secondariesMap = new HashMap<String,String>();
- for (Secondary secondary : secondaries) {
- secondariesMap.put(secondary.getKey(), secondary.getValue());
- }
- this.secondaries=secondariesMap;
- }
-
- @ConfigurationBean(uri = BiomobyActivity.URI + "#Secondary")
- public static class Secondary {
- private String key, value;
-
- public String getKey() {
- return key;
- }
-
- @ConfigurationProperty(name = "key", label = "Key")
- public void setKey(String key) {
- this.key = key;
- }
-
- public String getValue() {
- return value;
- }
-
- @ConfigurationProperty(name = "value", label = "Value")
- public void setValue(String value) {
- this.value = value;
- }
-
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyActivityFactory.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyActivityFactory.java b/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyActivityFactory.java
deleted file mode 100644
index 9a7bdf0..0000000
--- a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyActivityFactory.java
+++ /dev/null
@@ -1,49 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2011 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.biomoby;
-
-import java.net.URI;
-
-import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityFactory;
-
-/**
- * An {@link ActivityFactory} for creating <code>BiomobyActivity</code>.
- *
- * @author David Withers
- */
-public class BiomobyActivityFactory implements ActivityFactory {
-
- @Override
- public BiomobyActivity createActivity() {
- return new BiomobyActivity();
- }
-
- @Override
- public URI getActivityURI() {
- return URI.create(BiomobyActivity.URI);
- }
-
- @Override
- public Object createActivityConfiguration() {
- return new BiomobyActivityConfigurationBean();
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyActivityHealthChecker.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyActivityHealthChecker.java b/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyActivityHealthChecker.java
deleted file mode 100644
index aec3d1a..0000000
--- a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyActivityHealthChecker.java
+++ /dev/null
@@ -1,45 +0,0 @@
-/*******************************************************************************
- * This file is a component of the Taverna project, and is licensed under the
- * GNU LGPL. Copyright Edward Kawas, The BioMoby Project
- ******************************************************************************/
-package net.sf.taverna.t2.activities.biomoby;
-
-import java.util.List;
-
-import net.sf.taverna.t2.workflowmodel.processor.activity.Activity;
-import net.sf.taverna.t2.visit.VisitReport;
-
-import net.sf.taverna.t2.workflowmodel.health.RemoteHealthChecker;
-import net.sf.taverna.t2.workflowmodel.processor.activity.DisabledActivity;
-
-/**
- * A health checker for the Biomoby activity.
- *
- * @author David Withers
- */
-public class BiomobyActivityHealthChecker extends RemoteHealthChecker {
-
- public boolean canVisit(Object subject) {
- if (subject == null) {
- return false;
- }
- if (subject instanceof BiomobyActivity) {
- return true;
- }
- if (subject instanceof DisabledActivity) {
- return (((DisabledActivity) subject).getActivity() instanceof BiomobyActivity);
- }
- return false;
- }
-
- public VisitReport visit(Object o, List<Object> ancestors) {
- Activity activity = (Activity) o;
- BiomobyActivityConfigurationBean configuration = null;
- if (activity instanceof BiomobyActivity) {
- configuration = (BiomobyActivityConfigurationBean) activity.getConfiguration();
- } else if (activity instanceof DisabledActivity) {
- configuration = (BiomobyActivityConfigurationBean) ((DisabledActivity) activity).getActivityConfiguration();
- }
- return contactEndpoint(activity, configuration.getMobyEndpoint());
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyCache.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyCache.java b/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyCache.java
deleted file mode 100644
index 288e654..0000000
--- a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyCache.java
+++ /dev/null
@@ -1,78 +0,0 @@
-/*******************************************************************************
- * This file is a component of the Taverna project, and is licensed under the
- * GNU LGPL. Copyright Edward Kawas, The BioMoby Project
- ******************************************************************************/
-
-package net.sf.taverna.t2.activities.biomoby;
-
-import java.util.HashMap;
-import java.util.Map;
-
-import org.apache.log4j.Logger;
-import org.biomoby.client.CentralDigestCachedImpl;
-import org.biomoby.client.CentralImpl;
-import org.biomoby.registry.meta.Registry;
-import org.biomoby.shared.Central;
-import org.biomoby.shared.MobyDataType;
-import org.biomoby.shared.MobyException;
-import org.biomoby.shared.MobyNamespace;
-
-/**
- * A utility class that handles triggering JMoby to cache for a given {@link Registry} for a given registry
- *
- * @author Stuart Owen
- * @author Eddie Kawas
- */
-
-public class BiomobyCache {
-
- private static Logger logger = Logger.getLogger(BiomobyCache.class);
-
- private static Map<String,Object> cached = new HashMap<String, Object>();
-
- /**
- * If necessary caches the Ontology and namespace information.
- * This call immediately returns if the cache has been previously called for this endpoint
- *
- * @param reg - the Registry instance
- *
- */
- public static synchronized void cacheForRegistry(Registry reg) {
- if (cached.get(reg.getEndpoint()) == null) {
- logger.info("Caching started for Biomoby registry"
- + reg.getEndpoint());
-
- Central c;
- try {
- c = CentralImpl.getDefaultCentral(reg);
- if (c instanceof CentralDigestCachedImpl)
- ((CentralDigestCachedImpl) c)
- .updateCache(CentralDigestCachedImpl.CACHE_PART_DATATYPES);
- MobyDataType.getDataType("Object", reg);
- MobyNamespace.getNamespace("foo", reg);
-
- cached.put(reg.getEndpoint(), new Boolean(true));
- logger.info("Caching complete for Biomoby registry"
- + reg.getEndpoint());
-
- } catch (MobyException e) {
- logger.error("Error whilst caching for Biomoby registry",e);
- }
-
- }
- }
-
- /**
- * If necessary caches the Ontology and namespace information.
- * This call immediately returns if the cache has been previously called for this endpoint url.
- *
- * @param endpointUrl - the Registry endpoint Url
- *
- */
- public static synchronized void cacheForRegistryEndpoint(String endpointUrl) {
- Registry registry = new Registry(endpointUrl, endpointUrl,
- "http://domain.com/MOBY/Central");
- cacheForRegistry(registry);
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyObjectActivity.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyObjectActivity.java b/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyObjectActivity.java
deleted file mode 100644
index 41e8c4f..0000000
--- a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyObjectActivity.java
+++ /dev/null
@@ -1,545 +0,0 @@
-/*******************************************************************************
- * This file is a component of the Taverna project, and is licensed under the
- * GNU LGPL. Copyright Edward Kawas, The BioMoby Project
- ******************************************************************************/
-package net.sf.taverna.t2.activities.biomoby;
-
-import java.util.ArrayList;
-import java.util.HashMap;
-import java.util.Map;
-
-import net.sf.taverna.t2.annotation.annotationbeans.MimeType;
-import net.sf.taverna.t2.reference.ExternalReferenceSPI;
-import net.sf.taverna.t2.reference.ReferenceService;
-import net.sf.taverna.t2.reference.T2Reference;
-import net.sf.taverna.t2.workflowmodel.EditException;
-import net.sf.taverna.t2.workflowmodel.OutputPort;
-import net.sf.taverna.t2.workflowmodel.processor.activity.AbstractAsynchronousActivity;
-import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityConfigurationException;
-import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityInputPort;
-import net.sf.taverna.t2.workflowmodel.processor.activity.AsynchronousActivityCallback;
-
-import org.apache.log4j.Logger;
-import org.biomoby.client.CentralImpl;
-import org.biomoby.registry.meta.Registry;
-import org.biomoby.shared.Central;
-import org.biomoby.shared.MobyDataType;
-import org.biomoby.shared.MobyException;
-import org.biomoby.shared.MobyNamespace;
-import org.biomoby.shared.MobyRelationship;
-import org.biomoby.shared.NoSuccessException;
-import org.biomoby.shared.data.MobyDataBoolean;
-import org.biomoby.shared.data.MobyDataComposite;
-import org.biomoby.shared.data.MobyDataDateTime;
-import org.biomoby.shared.data.MobyDataFloat;
-import org.biomoby.shared.data.MobyDataInstance;
-import org.biomoby.shared.data.MobyDataInt;
-import org.biomoby.shared.data.MobyDataString;
-import org.jdom.Element;
-
-/**
- * An Activity providing Biomoby Object functionality.
- *
- * Copied from org.biomoby.client.taverna.plugin.BiomobyObjectProcessor and
- * org.biomoby.client.taverna.plugin.BiomobyObjectTask and converted to a Taverna 2
- * Activity.
- *
- * @author Edward Kawas
- * @author David Withers
- */
-public class BiomobyObjectActivity extends AbstractAsynchronousActivity<BiomobyObjectActivityConfigurationBean> {
-
- public static final String URI = "http://ns.taverna.org.uk/2010/activity/biomoby/object";
-
- private static Logger logger = Logger.getLogger(BiomobyObjectActivity.class);
-
- private BiomobyObjectActivityConfigurationBean configurationBean = new BiomobyObjectActivityConfigurationBean();
-
- private Central worker = null;
-
- private MobyDataType mobyObject = null;
-
- @Override
- public void configure(BiomobyObjectActivityConfigurationBean configurationBean) throws ActivityConfigurationException {
- this.configurationBean = configurationBean;
- init();
- generatePorts();
- }
-
- @Override
- public void executeAsynch(final Map<String, T2Reference> data,
- final AsynchronousActivityCallback callback) {
- callback.requestRun(new Runnable() {
-
- public void run() {
- ReferenceService referenceService = callback.getContext().getReferenceService();
-
- Map<String, T2Reference> outputMap = new HashMap<String, T2Reference>();
-
- // initialize the namespace and id fields
- String namespace = "";
- String id = "";
- String article = "";
- boolean isPrimitiveType = getInputPort("value")!=null;
- String objectName = configurationBean.getServiceName();
- // would like to use the MobyObjectClass to generate a skeleton
-
- String registryEndpoint = worker.getRegistryEndpoint();
- Registry mRegistry = new Registry(registryEndpoint,registryEndpoint,"http://domain.com/MOBY/Central");
-
- BiomobyCache.cacheForRegistry(mRegistry);
-
- if (isPrimitiveType) {
- try {
-
- T2Reference inputId;
- try {
- inputId = data.get("namespace");
- namespace = (String) referenceService.renderIdentifier(inputId, String.class, callback.getContext());
- } catch (Exception e) {
- }
-
- try {
- inputId = data.get("id");
- id = (String) referenceService.renderIdentifier(inputId, String.class, callback.getContext());
- } catch (Exception e) {
- }
-
- try {
- inputId = data.get("article name");
- article = (String) referenceService.renderIdentifier(inputId, String.class, callback.getContext());
- } catch (Exception e) {
- }
-
- inputId = data.get("value");
- String value = null;
- try {
- value = (String) referenceService.renderIdentifier(inputId, String.class, callback.getContext());
- }
- catch(NullPointerException e) {
- //means the value hasn't been set and is handled below
- }
-
- if (objectName.equals("String")) {
- if (value == null) {
- value = "";
- }
- MobyDataString d = new MobyDataString(value,mRegistry);
- d.setId(id);
- MobyNamespace mNamespace = MobyNamespace.getNamespace(namespace,mRegistry);
- if (mNamespace != null)
- d.setPrimaryNamespace(MobyNamespace.getNamespace(namespace,mRegistry));
- d.setXmlMode(MobyDataInstance.SERVICE_XML_MODE);
- outputMap.put("mobyData", referenceService.register(XMLUtilities.createMobyDataElementWrapper(
- "<Simple articleName=\""+article+"\">" + d.toXML() +"</Simple>" ), 0, true, callback.getContext()));
- } else if (objectName.equals("Float")) {
- if (value == null || value.trim().equals("")) {
- MobyDataComposite d = new MobyDataComposite(
- MobyDataType.getDataType("Float", mRegistry));
- d.setId(id);
- MobyNamespace mNamespace = MobyNamespace.getNamespace(namespace,mRegistry);
- if (mNamespace != null)
- d.setPrimaryNamespace(MobyNamespace.getNamespace(namespace,mRegistry));
- d.setXmlMode(MobyDataInstance.SERVICE_XML_MODE);
- outputMap.put("mobyData", referenceService.register(XMLUtilities.createMobyDataElementWrapper(
- "<Simple articleName=\""+article+"\">" + d.toXML() +"</Simple>" ), 0, true, callback.getContext()));
- } else {
- MobyDataFloat d = new MobyDataFloat(value,mRegistry);
- d.setId(id);
- MobyNamespace mNamespace = MobyNamespace.getNamespace(namespace,mRegistry);
- if (mNamespace != null)
- d.setPrimaryNamespace(MobyNamespace.getNamespace(namespace,mRegistry));
- d.setXmlMode(MobyDataInstance.SERVICE_XML_MODE);
- outputMap.put("mobyData", referenceService.register(XMLUtilities.createMobyDataElementWrapper(
- "<Simple articleName=\""+article+"\">" + d.toXML() +"</Simple>" ), 0, true, callback.getContext()));
- }
- } else if (objectName.equals("Integer")) {
-
- try {
- int val = 0;
- val = Integer.parseInt(value);
- MobyDataInt d = new MobyDataInt(val,mRegistry);
- d.setId(id);
- MobyNamespace mNamespace = MobyNamespace.getNamespace(namespace,mRegistry);
- if (mNamespace != null)
- d.setPrimaryNamespace(MobyNamespace.getNamespace(namespace,mRegistry));
- d.setXmlMode(MobyDataInstance.SERVICE_XML_MODE);
- outputMap.put("mobyData", referenceService.register(XMLUtilities.createMobyDataElementWrapper(
- "<Simple articleName=\""+article+"\">" + d.toXML() +"</Simple>" ), 0, true, callback.getContext()));
- } catch (Exception e) {
- MobyDataComposite d = new MobyDataComposite(
- MobyDataType.getDataType("Integer", mRegistry));
- d.setId(id);
- MobyNamespace mNamespace = MobyNamespace.getNamespace(namespace,mRegistry);
- if (mNamespace != null)
- d.setPrimaryNamespace(MobyNamespace.getNamespace(namespace,mRegistry));
- d.setXmlMode(MobyDataInstance.SERVICE_XML_MODE);
- outputMap.put("mobyData", referenceService.register(XMLUtilities.createMobyDataElementWrapper(
- "<Simple articleName=\""+article+"\">" + d.toXML() +"</Simple>" ), 0, true, callback.getContext()));
- }
- }else if (objectName.equals("Boolean")) {
- if (value == null || value.trim().equals("")) {
- MobyDataComposite d = new MobyDataComposite(MobyDataType.getDataType("Boolean", mRegistry));
- d.setId(id);
- MobyNamespace mNamespace = MobyNamespace.getNamespace(namespace,mRegistry);
- if (mNamespace != null)
- d.setPrimaryNamespace(MobyNamespace.getNamespace(namespace,mRegistry));
- d.setXmlMode(MobyDataInstance.SERVICE_XML_MODE);
- outputMap.put("mobyData", referenceService.register(XMLUtilities.createMobyDataElementWrapper(
- "<Simple articleName=\""+article+"\">" + d.toXML() +"</Simple>" ), 0, true, callback.getContext()));
- } else {
- MobyDataBoolean d = new MobyDataBoolean(value,mRegistry);
- d.setId(id);
- MobyNamespace mNamespace = MobyNamespace.getNamespace(namespace,mRegistry);
- if (mNamespace != null)
- d.setPrimaryNamespace(MobyNamespace.getNamespace(namespace,mRegistry));
- d.setXmlMode(MobyDataInstance.SERVICE_XML_MODE);
- outputMap.put("mobyData", referenceService.register(XMLUtilities.createMobyDataElementWrapper(
- "<Simple articleName=\""+article+"\">" + d.toXML() +"</Simple>" ), 0, true, callback.getContext()));
- }
- } else if (objectName.equals("DateTime")) {
- if (value == null || value.trim().equals("")) {
- MobyDataComposite d = new MobyDataComposite(MobyDataType.getDataType("DateTime", mRegistry));
- d.setId(id);
- MobyNamespace mNamespace = MobyNamespace.getNamespace(namespace,mRegistry);
- if (mNamespace != null)
- d.setPrimaryNamespace(MobyNamespace.getNamespace(namespace,mRegistry));
- d.setXmlMode(MobyDataInstance.SERVICE_XML_MODE);
- outputMap.put("mobyData", referenceService.register(XMLUtilities.createMobyDataElementWrapper(
- "<Simple articleName=\""+article+"\">" + d.toXML() +"</Simple>" ), 0, true, callback.getContext()));
- } else {
- MobyDataDateTime d = new MobyDataDateTime("", value,mRegistry);
- d.setId(id);
- MobyNamespace mNamespace = MobyNamespace.getNamespace(namespace,mRegistry);
- if (mNamespace != null)
- d.setPrimaryNamespace(MobyNamespace.getNamespace(namespace,mRegistry));
- d.setXmlMode(MobyDataInstance.SERVICE_XML_MODE);
- outputMap.put("mobyData", referenceService.register(XMLUtilities.createMobyDataElementWrapper(
- "<Simple articleName=\""+article+"\">" + d.toXML() +"</Simple>" ), 0, true, callback.getContext()));
- }
- }
- callback.receiveResult(outputMap, new int[0]);
- } catch (Exception ex) {
- // details of other exceptions will appear only in a log
- logger.error("Error creating biomoby object for biomoby", ex);
- callback.fail("Service failed due to problem creating biomoby object (see details in log)", ex);
- }
- } else {
- // Situation where simples are feeding into this non primitive type
- try {
- T2Reference inputId;
- try {
- inputId = data.get("namespace");
- namespace = (String) referenceService.renderIdentifier(inputId, String.class, callback.getContext());
- } catch (Exception e) {
- }
-
- try {
- inputId = data.get("id");
- id = (String) referenceService.renderIdentifier(inputId, String.class, callback.getContext());
- } catch (Exception e) {
- }
-
- try {
- inputId = data.get("article name");
- article = (String) referenceService.renderIdentifier(inputId, String.class, callback.getContext());
- } catch (Exception e) {
- }
-
- //Element mobyObjectElement = mo.createObject(objectName,namespace, id, article);
-
- MobyDataComposite composite = new MobyDataComposite(MobyDataType.getDataType(objectName, mRegistry));
- composite.setId(id);
- MobyNamespace mNamespace = MobyNamespace.getNamespace(namespace,mRegistry);
- if (mNamespace != null)
- composite.setPrimaryNamespace(MobyNamespace.getNamespace(namespace,mRegistry));
- composite.setXmlMode(MobyDataInstance.SERVICE_XML_MODE);
-
- // Element mobyObjectElement = XMLUtilities.getDOMDocument(XMLUtilities.createMobyDataElementWrapper( "<Simple articleName=\""+article+"\">" + composite.toXML() +"</Simple>" )).detachRootElement();
- Element mobyObjectElement = XMLUtilities.getDOMDocument(( composite.toXML() )).detachRootElement();
-
- // using the inputs, iterate through and fill in data
- for (ActivityInputPort inputPort : getInputPorts()) {
- String portName = inputPort.getName();
- if (!(portName.equalsIgnoreCase("namespace")
- || portName.equalsIgnoreCase("id") || portName
- .equalsIgnoreCase("article name"))) {
- String type = portName.substring(0, portName
- .indexOf("("));
- String articleName = portName.substring(
- type.length() + 1, portName.length() - 1);
- inputId = null;
- try {
- inputId = data.get(portName);
- } catch (Exception e) {
-
- }
- if (inputId != null) {
- String value = (String) referenceService.renderIdentifier(inputId, inputPort.getTranslatedElementClass(), callback.getContext());
- Element valueElement = (XMLUtilities.getDOMDocument(value)).getRootElement();
- if (valueElement.getChild("mobyContent",XMLUtilities.MOBY_NS) != null) {
- valueElement = valueElement.getChild("mobyContent",XMLUtilities.MOBY_NS);
- } else {
- valueElement = valueElement.getChild("mobyContent");
- }
- if (valueElement.getChild("mobyData",XMLUtilities.MOBY_NS) != null ) {
- valueElement = valueElement.getChild("mobyData",XMLUtilities.MOBY_NS);
- } else {
- valueElement = valueElement.getChild("mobyData");
- }
- if (valueElement.getChild("Simple",XMLUtilities.MOBY_NS) != null ) {
- valueElement = valueElement.getChild("Simple",XMLUtilities.MOBY_NS);
- } else {
- valueElement = valueElement.getChild("Simple");
- }
- if (valueElement.getChild(type,XMLUtilities.MOBY_NS) != null ) {
- valueElement = valueElement.getChild(type,XMLUtilities.MOBY_NS);
- } else {
- valueElement = valueElement.getChild(type);
- }
- // Element _child = mo.getObject(mobyObjectElement,type, articleName);
-
- valueElement.removeAttribute("articleName");
- valueElement.removeAttribute("articleName", XMLUtilities.MOBY_NS);
- valueElement.setAttribute("articleName", articleName, XMLUtilities.MOBY_NS);
-// Element _newChild = mo.createObject(type, _ns, _id,
-// articleName);
-// _newChild.setText(valueElement
-// .getText());
-// _newChild.addContent(_child.cloneContent());
- // import and replace the node
- // mobyObjectElement.removeContent(_child);
- mobyObjectElement.addContent(valueElement.detach());
- }
- }
- }
- Element simple = new Element("Simple", XMLUtilities.MOBY_NS);
- simple.setAttribute("articleName", article, XMLUtilities.MOBY_NS);
- simple.addContent(mobyObjectElement);
-
- org.jdom.output.XMLOutputter outputter = new org.jdom.output.XMLOutputter(org.jdom.output.Format.getPrettyFormat());
- String mobyDataString = outputter.outputString(XMLUtilities.createMobyDataElementWrapper(simple));
- outputMap.put("mobyData", referenceService.register(mobyDataString, 0, true, callback.getContext()));
-
- callback.receiveResult(outputMap, new int[0]);
- } catch (Exception ex) {
- // details of other exceptions will appear only in a log
- logger.error("Error creating biomoby object for biomoby", ex);
- callback.fail("Service failed due to problem creating biomoby object (see details in log)", ex);
- }
- }
- }
- });
-
- }
-
- @Override
- public BiomobyObjectActivityConfigurationBean getConfiguration() {
- return configurationBean;
- }
-
- private void init() throws ActivityConfigurationException {
- // Find the service endpoint (by calling Moby registry)
- try {
- if (mobyObject == null) {
- worker = new CentralImpl(configurationBean.getMobyEndpoint());
- mobyObject = worker.getDataType(configurationBean.getServiceName());
- }
-
- } catch (Exception e) {
- if (e instanceof ActivityConfigurationException) {
- throw (ActivityConfigurationException) e;
- }
- throw new ActivityConfigurationException(formatError(e.toString()));
- }
- // here we make sure that we have downloaded the ontology for the
- // registry that we got this service from
- try {
- new GetOntologyThread(worker.getRegistryEndpoint()).start();
- } catch (Exception e) {
- /* don't care if an exception occurs here ... */
- }
- }
-
- private void generatePorts() {
- removeInputs();
- removeOutputs();
-
- //inputs
- addInput("namespace", 0, true,
- new ArrayList<Class<? extends ExternalReferenceSPI>>(),
- String.class);
-
- addInput("id", 0, true,
- new ArrayList<Class<? extends ExternalReferenceSPI>>(),
- String.class);
-
- addInput("article name", 0, true,
- new ArrayList<Class<? extends ExternalReferenceSPI>>(),
- String.class);
-
- try {
- String serviceName = configurationBean.getServiceName();
- MobyDataType datatype = worker.getDataType(serviceName);
- MobyRelationship[] relations = datatype.getChildren();
- processRelationships(relations);
- String parent = "Object";
- try {
- parent = datatype.getParentNames()[0];
- if (parent.indexOf(":") > 0) {
- parent = parent.substring(parent.lastIndexOf(":") + 1);
- }
- } catch (ArrayIndexOutOfBoundsException e) {
- // parent is then by default object
- }
- if (parent.equalsIgnoreCase("String")
- || parent.equalsIgnoreCase("Integer")
- || parent.equalsIgnoreCase("float")
- || parent.equalsIgnoreCase("DateTime")
- || parent.equalsIgnoreCase("Boolean")
- || serviceName.equalsIgnoreCase("String")
- || serviceName.equalsIgnoreCase("Boolean")
- || serviceName.equalsIgnoreCase("Integer")
- || serviceName.equalsIgnoreCase("float")
- || serviceName.equalsIgnoreCase("DateTime")) {
- addInput("value", 0, true,
- new ArrayList<Class<? extends ExternalReferenceSPI>>(),
- String.class);
- } else {
- if (!parent.equalsIgnoreCase("Object"))
- extractParentContainerRelationships(parent);
- }
- } catch (MobyException e) {
- } catch (NoSuccessException e) {
- }
-
- //outputs
- addOutput("mobyData", 0, "text/xml");
- }
-
- private void extractParentContainerRelationships(String string) {
- try {
- MobyDataType datatype = worker.getDataType(string);
- // need to propagate the isa up to Object to get all of the has/hasa
- MobyRelationship[] relations = datatype.getChildren();
- processRelationships(relations);
- String parent = "Object";
- try {
- parent = datatype.getParentNames()[0];
- if (parent.indexOf(":") > 0) {
- parent = parent.substring(parent.lastIndexOf(":") + 1);
- }
- } catch (ArrayIndexOutOfBoundsException e) {
- // parent is then by default object
- }
- String serviceName = configurationBean.getServiceName();
- if (parent.equalsIgnoreCase("String")
- || parent.equalsIgnoreCase("Integer")
- || parent.equalsIgnoreCase("float")
- || serviceName.equalsIgnoreCase("String")
- || parent.equalsIgnoreCase("Boolean")
- || serviceName.equalsIgnoreCase("Boolean")
- || serviceName.equalsIgnoreCase("Integer")
- || serviceName.equalsIgnoreCase("float")) {
- addInput("value", 0, true,
- new ArrayList<Class<? extends ExternalReferenceSPI>>(),
- String.class);
- } else {
- if (!parent.equalsIgnoreCase("Object"))
- extractParentContainerRelationships(parent);
- }
- } catch (MobyException e) {
- } catch (NoSuccessException e) {
- }
- }
-
- private void processRelationships(MobyRelationship[] relations) {
- for (int x = 0; x < relations.length; x++) {
- MobyRelationship relationship = relations[x];
-
- // strip urn:lsid:...
- String name = relationship.getDataTypeName();
- if (name.indexOf(":") > 0) {
- name = name.substring(name.lastIndexOf(":") + 1);
- }
- // port name == DataType(articleName)
- name = name + "(" + relationship.getName() + ")";
- switch (relationship.getRelationshipType()) {
- case (Central.iHAS): {
- // TODO - not really supported
- addInput(name, 0, true,
- new ArrayList<Class<? extends ExternalReferenceSPI>>(),
- String.class);
- break;
- }
- case (Central.iHASA): {
- addInput(name, 0, true,
- new ArrayList<Class<? extends ExternalReferenceSPI>>(),
- String.class);
- break;
- }
- default:
- break;
- }
- }
- }
-
-
- protected String formatError(String msg) {
- // Removed references to the authority, some errors
- // were causing it to be null which in turn threw
- // a NPE from here, breaking Taverna's error handlers
- return ("Problems with service '" + configurationBean.getServiceName()
- + "' provided by authority '"
- + configurationBean.getAuthorityName()
- + "'\nfrom Moby registry at "
- + configurationBean.getMobyEndpoint() + ":\n\n" + msg);
- }
-
- protected ActivityInputPort getInputPort(String name) {
- for (ActivityInputPort port : getInputPorts()) {
- if (port.getName().equals(name)) {
- return port;
- }
- }
- return null;
- }
-
- protected OutputPort getOutputPort(String name) {
- for (OutputPort port : getOutputPorts()) {
- if (port.getName().equals(name)) {
- return port;
- }
- }
- return null;
- }
-
- protected void addOutput(String portName, int portDepth, String type) {
- OutputPort port = edits.createActivityOutputPort(
- portName, portDepth, portDepth);
- MimeType mimeType = new MimeType();
- mimeType.setText(type);
- try {
- edits.getAddAnnotationChainEdit(port, mimeType).doEdit();
- } catch (EditException e) {
- logger.debug("Error adding MimeType annotation to port", e);
- }
- outputPorts.add(port);
- }
-
- public Central getCentral() {
- if (worker != null)
- return worker;
- else
- try {
- return new CentralImpl(getConfiguration().getMobyEndpoint());
- } catch (MobyException e) {
- return null;
- }
- }
-
- public MobyDataType getMobyObject() {
- return mobyObject;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyObjectActivityConfigurationBean.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyObjectActivityConfigurationBean.java b/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyObjectActivityConfigurationBean.java
deleted file mode 100644
index ab26b32..0000000
--- a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyObjectActivityConfigurationBean.java
+++ /dev/null
@@ -1,81 +0,0 @@
-/*******************************************************************************
- * This file is a component of the Taverna project, and is licensed under the
- * GNU LGPL. Copyright Edward Kawas, The BioMoby Project
- ******************************************************************************/
-package net.sf.taverna.t2.activities.biomoby;
-
-import net.sf.taverna.t2.workflowmodel.processor.config.ConfigurationBean;
-import net.sf.taverna.t2.workflowmodel.processor.config.ConfigurationProperty;
-
-/**
- * A configuration bean specific to the Biomoby Object activity.
- *
- * @author David Withers
- */
-@ConfigurationBean(uri = BiomobyObjectActivity.URI + "#Config")
-public class BiomobyObjectActivityConfigurationBean {
-
- private String mobyEndpoint="";
-
- private String serviceName="";
-
- private String authorityName="";
-
- /**
- * Returns the mobyEndpoint.
- *
- * @return the mobyEndpoint
- */
- public String getMobyEndpoint() {
- return mobyEndpoint;
- }
-
- /**
- * Sets the mobyEndpoint.
- *
- * @param mobyEndpoint the new mobyEndpoint
- */
- @ConfigurationProperty(name = "mobyEndpoint", label = "Moby Endpoint", description = "")
- public void setMobyEndpoint(String mobyEndpoint) {
- this.mobyEndpoint = mobyEndpoint;
- }
-
- /**
- * Returns the serviceName.
- *
- * @return the serviceName
- */
- public String getServiceName() {
- return serviceName;
- }
-
- /**
- * Sets the serviceName.
- *
- * @param serviceName the new serviceName
- */
- @ConfigurationProperty(name = "serviceName", label = "Service Name", description = "")
- public void setServiceName(String serviceName) {
- this.serviceName = serviceName;
- }
-
- /**
- * Returns the authorityName.
- *
- * @return the authorityName
- */
- public String getAuthorityName() {
- return authorityName;
- }
-
- /**
- * Sets the authorityName.
- *
- * @param authorityName the new authorityName
- */
- @ConfigurationProperty(name = "authorityName", label = "Authority Name", description = "")
- public void setAuthorityName(String authorityName) {
- this.authorityName = authorityName;
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyObjectActivityFactory.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyObjectActivityFactory.java b/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyObjectActivityFactory.java
deleted file mode 100644
index 955b808..0000000
--- a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/BiomobyObjectActivityFactory.java
+++ /dev/null
@@ -1,49 +0,0 @@
-/*******************************************************************************
- * Copyright (C) 2011 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- ******************************************************************************/
-package net.sf.taverna.t2.activities.biomoby;
-
-import java.net.URI;
-
-import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityFactory;
-
-/**
- * An {@link ActivityFactory} for creating <code>BiomobyObjectActivity</code>.
- *
- * @author David Withers
- */
-public class BiomobyObjectActivityFactory implements ActivityFactory {
-
- @Override
- public BiomobyObjectActivity createActivity() {
- return new BiomobyObjectActivity();
- }
-
- @Override
- public URI getActivityURI() {
- return URI.create(BiomobyObjectActivity.URI);
- }
-
- @Override
- public Object createActivityConfiguration() {
- return new BiomobyObjectActivityConfigurationBean();
- }
-
-}
[09/16] incubator-taverna-plugin-bioinformatics git commit:
temporarily empty repository
Posted by st...@apache.org.
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomart-martservice/src/test/java/org/biomart/martservice/query/QueryTest.java
----------------------------------------------------------------------
diff --git a/taverna-biomart-martservice/src/test/java/org/biomart/martservice/query/QueryTest.java b/taverna-biomart-martservice/src/test/java/org/biomart/martservice/query/QueryTest.java
deleted file mode 100644
index b2b93cc..0000000
--- a/taverna-biomart-martservice/src/test/java/org/biomart/martservice/query/QueryTest.java
+++ /dev/null
@@ -1,303 +0,0 @@
-/*
- * Copyright (C) 2003 The University of Manchester
- *
- * Modifications to the initial code base are copyright of their
- * respective authors, or their employers as appropriate. Authorship
- * of the modifications may be determined from the ChangeLog placed at
- * the end of this file.
- *
- * This program is free software; you can redistribute it and/or
- * modify it under the terms of the GNU Lesser General Public License
- * as published by the Free Software Foundation; either version 2.1 of
- * the License, or (at your option) any later version.
- *
- * This program is distributed in the hope that it will be useful, but
- * WITHOUT ANY WARRANTY; without even the implied warranty of
- * MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
- * Lesser General Public License for more details.
- *
- * You should have received a copy of the GNU Lesser General Public
- * License along with this program; if not, write to the Free Software
- * Foundation, Inc., 59 Temple Place, Suite 330, Boston, MA 02111-1307
- * USA.
- *
- ****************************************************************
- * Source code information
- * -----------------------
- * Filename $RCSfile: QueryTest.java,v $
- * Revision $Revision: 1.3 $
- * Release status $State: Exp $
- * Last modified on $Date: 2007/10/01 12:11:30 $
- * by $Author: davidwithers $
- * Created on 03-May-2006
- *****************************************************************/
-package org.biomart.martservice.query;
-
-import junit.framework.TestCase;
-
-/**
- *
- * @author David Withers
- */
-public class QueryTest extends TestCase {
- private String attributeName;
-
- private Attribute attribute;
-
- private String filterName;
-
- private String filterValue;
-
- private Filter filter;
-
- private Link link;
-
- private String datasetName;
-
- private Dataset dataset;
-
- private String virtualSchemaName;
-
- private String softwareVersion;
-
- private String formatter;
-
- private Query query;
-
- /*
- * @see TestCase#setUp()
- */
- protected void setUp() throws Exception {
- super.setUp();
- attributeName = "attribute name";
- attribute = new Attribute(attributeName);
-
- filterName = "filter name";
- filterValue = "filter value";
- filter = new Filter(filterName, filterValue);
-
- link = new Link("source", "target", "id");
-
- datasetName = "dataset name";
- dataset = new Dataset(datasetName);
-
- dataset.addAttribute(attribute);
- dataset.addFilter(filter);
-
- virtualSchemaName = "default";
-
- softwareVersion = "software version";
-
- formatter = "page formatter";
-
- query = new Query(virtualSchemaName);
- }
-
- /*
- * Test method for 'org.biomart.martservice.query.Query.Query(String)'
- */
- public final void testQueryString() {
- Query query = new Query(virtualSchemaName);
- assertEquals("virtualSchemaName should be '" + virtualSchemaName + "'",
- query.getVirtualSchemaName(), virtualSchemaName);
- assertEquals("count should be '0'", query.getCount(), 0);
- }
-
- /*
- * Test method for 'org.biomart.martservice.query.Query.Query(String, int)'
- */
- public final void testQueryStringInt() {
- Query query = new Query(virtualSchemaName, 1);
- assertEquals("virtualSchemaName should be '" + virtualSchemaName + "'",
- query.getVirtualSchemaName(), virtualSchemaName);
- assertEquals("count should be '1'", query.getCount(), 1);
- }
-
- /*
- * Test method for 'org.biomart.martservice.query.Query.Query(Query)'
- */
- public final void testQueryQuery() {
- query.addDataset(dataset);
- query.addLink(link);
- query.setCount(1);
- query.setUniqueRows(1);
- query.setSoftwareVersion(softwareVersion);
- query.setFormatter(formatter);
- Query copy = new Query(query);
- assertEquals(copy.getDatasets().size(), 1);
- assertEquals(copy.getAttributes().size(), 1);
- assertEquals(copy.getFilters().size(), 1);
- assertEquals(copy.getLinks().size(), 1);
- assertEquals(copy.getCount(), 1);
- assertEquals(copy.getUniqueRows(), 1);
- assertEquals(copy.getSoftwareVersion(), softwareVersion);
- assertEquals(copy.getFormatter(), formatter);
- }
-
- /*
- * Test method for
- * 'org.biomart.martservice.query.Query.getVirtualSchemaName()'
- */
- public final void testGetVirtualSchemaName() {
- assertEquals("virtualSchemaName should be '" + virtualSchemaName + "'",
- query.getVirtualSchemaName(), virtualSchemaName);
- }
-
- /*
- * Test method for
- * 'org.biomart.martservice.query.Query.setVirtualSchemaName(String)'
- */
- public final void testSetVirtualSchemaName() {
- String newVirtualSchemaName = "new virtual schema name";
- query.setVirtualSchemaName(newVirtualSchemaName);
- assertEquals("virtualSchemaName should be '" + newVirtualSchemaName
- + "'", query.getVirtualSchemaName(), newVirtualSchemaName);
- }
-
- /*
- * Test method for 'org.biomart.martservice.query.Query.getCount()'
- */
- public final void testGetCount() {
- assertEquals("count should be '0'", query.getCount(), 0);
- }
-
- /*
- * Test method for 'org.biomart.martservice.query.Query.setCount(int)'
- */
- public final void testSetCount() {
- query.setCount(1);
- assertEquals("count should be '1'", query.getCount(), 1);
- }
-
- /*
- * Test method for 'org.biomart.martservice.query.Query.getUniqueRows()'
- */
- public final void testGetUniqueRows() {
- assertEquals("uniqueRows should be '0'", query.getUniqueRows(), 0);
- }
-
- /*
- * Test method for 'org.biomart.martservice.query.Query.setUniqueRows(int)'
- */
- public final void testSetUniqueRows() {
- query.setUniqueRows(1);
- assertEquals("uniqueRows should be '1'", query.getUniqueRows(), 1);
- }
-
- /*
- * Test method for 'org.biomart.martservice.query.Query.getSoftwareVersion()'
- */
- public final void testGetSoftwareVersion() {
- assertNull("softwareVersion should be null", query.getSoftwareVersion());
- }
-
- /*
- * Test method for 'org.biomart.martservice.query.Query.setSoftwareVersion(String)'
- */
- public final void testSetSoftwareVersion() {
- String newSoftwareVersion = "new software version";
- query.setSoftwareVersion(newSoftwareVersion);
- assertEquals("softwareVersion should be '" + newSoftwareVersion + "'", query.getSoftwareVersion(), newSoftwareVersion);
- }
-
- /*
- * Test method for 'org.biomart.martservice.query.Query.getFormatter()'
- */
- public final void testGetFormatter() {
- assertNull("formatter should be null", query.getFormatter());
- }
-
- /*
- * Test method for 'org.biomart.martservice.query.Query.setFormatter(String)'
- */
- public final void testSetFormatter() {
- String newFormatter = "new formatter";
- query.setFormatter(newFormatter);
- assertEquals("formatter should be '" + newFormatter + "'", query.getFormatter(), newFormatter);
- }
-
- /*
- * Test method for 'org.biomart.martservice.query.Query.getRequestId()'
- */
- public final void testGetRequestId() {
- assertNull("requestId should be null", query.getRequestId());
- }
-
- /*
- * Test method for 'org.biomart.martservice.query.Query.setnewRequestId(String)'
- */
- public final void testSetRequestId() {
- String newRequestId = "new RequestId";
- query.setRequestId(newRequestId);
- assertEquals("requestId should be '" + newRequestId + "'", query.getRequestId(), newRequestId);
- }
-
- /*
- * Test method for 'org.biomart.martservice.query.Query.addDataset(Dataset)'
- */
- public final void testAddDataset() {
- query.addDataset(dataset);
- assertEquals(query.getDatasets().size(), 1);
- assertSame(query.getDatasets().get(0), dataset);
- }
-
- /*
- * Test method for
- * 'org.biomart.martservice.query.Query.removeDataset(Dataset)'
- */
- public final void testRemoveDataset() {
- query.addDataset(dataset);
- query.removeDataset(dataset);
- assertEquals(query.getDatasets().size(), 0);
- }
-
- /*
- * Test method for 'org.biomart.martservice.query.Query.getDatasets()'
- */
- public final void testGetDatasets() {
- query.addDataset(dataset);
- assertEquals(query.getDatasets().size(), 1);
- assertSame(query.getDatasets().get(0), dataset);
- }
-
- /*
- * Test method for 'org.biomart.martservice.query.Query.getDataset(String)'
- */
- public final void testGetDataset() {
- query.addDataset(dataset);
- assertSame(query.getDataset(dataset.getName()), dataset);
- }
-
- /*
- * Test method for 'org.biomart.martservice.query.Query.getAttributes()'
- */
- public final void testGetAttributes() {
- query.addDataset(dataset);
- assertEquals(query.getAttributes().size(), 1);
- assertSame(query.getAttributes().get(0), attribute);
- }
-
- /*
- * Test method for 'org.biomart.martservice.query.Query.getFilters()'
- */
- public final void testGetFilters() {
- query.addDataset(dataset);
- assertEquals(query.getFilters().size(), 1);
- assertSame(query.getFilters().get(0), filter);
- }
-
- /*
- * Test method for
- * 'org.biomart.martservice.query.Query.addQueryListener(QueryListener)'
- */
- public final void testAddQueryListener() {
- }
-
- /*
- * Test method for
- * 'org.biomart.martservice.query.Query.removeQueryListener(QueryListener)'
- */
- public final void testRemoveQueryListener() {
- }
-
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/pom.xml
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/pom.xml b/taverna-biomoby-activity-ui/pom.xml
deleted file mode 100644
index 8f92c83..0000000
--- a/taverna-biomoby-activity-ui/pom.xml
+++ /dev/null
@@ -1,86 +0,0 @@
-<?xml version="1.0" encoding="UTF-8"?>
-<project xmlns="http://maven.apache.org/POM/4.0.0" xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance" xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd">
- <modelVersion>4.0.0</modelVersion>
- <parent>
- <groupId>net.sf.taverna</groupId>
- <artifactId>taverna-parent</artifactId>
- <version>3.0.1-SNAPSHOT</version>
- </parent>
- <groupId>net.sf.taverna.t2.ui-activities</groupId>
- <artifactId>biomoby-activity-ui</artifactId>
- <version>2.0.1-SNAPSHOT</version>
- <name>Taverna 2 Biomoby Activity UI</name>
- <dependencies>
- <dependency>
- <groupId>net.sf.taverna.t2.ui-api</groupId>
- <artifactId>activity-icons-api</artifactId>
- <version>${t2.ui.api.version}</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.ui-api</groupId>
- <artifactId>activity-palette-api</artifactId>
- <version>${t2.ui.api.version}</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.ui-impl</groupId>
- <artifactId>activity-palette-impl</artifactId>
- <version>${t2.ui.impl.version}</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.activities</groupId>
- <artifactId>biomoby-activity</artifactId>
- <version>${t2.activities.version}</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.ui-impl</groupId>
- <artifactId>contextual-views-impl</artifactId>
- <version>${t2.ui.impl.version}</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.ui-api</groupId>
- <artifactId>contextual-views-api</artifactId>
- <version>${t2.ui.api.version}</version>
- </dependency>
- <dependency>
- <groupId>net.sf.taverna.t2.ui-api</groupId>
- <artifactId>activity-tools</artifactId>
- <version>${t2.ui.api.version}</version>
- </dependency>
-
- <!-- testing dependencies -->
- <dependency>
- <groupId>junit</groupId>
- <artifactId>junit</artifactId>
- <version>${junit.version}</version>
- <scope>test</scope>
- </dependency>
-<!-- <dependency>
- <groupId>net.sf.taverna.t2.ui-impl</groupId>
- <artifactId>activity-palette-impl</artifactId>
- <version>${t2.ui.impl.version}</version>
- <scope>test</scope>
- </dependency> -->
- </dependencies>
- <repositories>
- <repository>
- <releases />
- <snapshots>
- <enabled>false</enabled>
- </snapshots>
- <id>mygrid-repository</id>
- <name>myGrid Repository</name>
- <url>http://www.mygrid.org.uk/maven/repository
- </url>
- </repository>
- <repository>
- <releases>
- <enabled>false</enabled>
- </releases>
- <snapshots />
- <id>mygrid-snapshot-repository</id>
- <name>myGrid Snapshot Repository</name>
- <url>http://www.mygrid.org.uk/maven/snapshot-repository</url>
- </repository>
- </repositories>
-</project>
-
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/AddParserActionHelper.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/AddParserActionHelper.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/AddParserActionHelper.java
deleted file mode 100644
index b03b98c..0000000
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/AddParserActionHelper.java
+++ /dev/null
@@ -1,280 +0,0 @@
-/*
- * This file is a component of the Taverna project, and is licensed under the
- * GNU LGPL. Copyright Edward Kawas, The BioMoby Project
- */
-package net.sf.taverna.t2.activities.biomoby.actions;
-
-import java.awt.BorderLayout;
-import java.awt.Dimension;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.MouseEvent;
-import java.awt.event.MouseListener;
-
-import javax.swing.ImageIcon;
-import javax.swing.JComponent;
-import javax.swing.JLabel;
-import javax.swing.JMenuItem;
-import javax.swing.JPanel;
-import javax.swing.JPopupMenu;
-import javax.swing.JScrollPane;
-import javax.swing.JSeparator;
-import javax.swing.JTree;
-import javax.swing.ToolTipManager;
-import javax.swing.tree.DefaultMutableTreeNode;
-import javax.swing.tree.TreePath;
-import javax.swing.tree.TreeSelectionModel;
-
-import net.sf.taverna.t2.activities.biomoby.BiomobyActivity;
-import net.sf.taverna.t2.activities.biomoby.edits.AddMobyParseDatatypeEdit;
-import net.sf.taverna.t2.workbench.edits.EditManager;
-import net.sf.taverna.t2.workbench.file.FileManager;
-import net.sf.taverna.t2.workflowmodel.Dataflow;
-import net.sf.taverna.t2.workflowmodel.Edit;
-
-import org.apache.log4j.Logger;
-import org.biomoby.shared.MobyData;
-import org.biomoby.shared.MobyNamespace;
-import org.biomoby.shared.MobyPrimaryDataSet;
-import org.biomoby.shared.MobyPrimaryDataSimple;
-
-/**
- * An action to add a parser from within the Workflow editor
- *
- * @author Eddie Kawas
- * @author Stuart Owen - adapted for Taverna 2
- */
-public class AddParserActionHelper {
- private static Logger logger = Logger.getLogger(AddParserActionHelper.class);
-
- private EditManager editManager;
-
- private final FileManager fileManager;
-
- public AddParserActionHelper(EditManager editManager, FileManager fileManager) {
- this.editManager = editManager;
- this.fileManager = fileManager;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see org.embl.ebi.escience.scuflui.processoractions.AbstractProcessorAction#getComponent(org.embl.ebi.escience.scufl.Processor)
- */
- public JComponent getComponent(final BiomobyActivity activity) {
-
-
- // set up the root node
- String serviceName = activity.getMobyService().getName();
- String description = activity.getMobyService().getDescription();
- MobyServiceTreeNode service = new MobyServiceTreeNode(serviceName,
- description);
- DefaultMutableTreeNode rootNode = new DefaultMutableTreeNode(service);
-
- // now add the child nodes containing useful information about the
- // service
- DefaultMutableTreeNode output = new DefaultMutableTreeNode("Parse:");
- rootNode.add(output);
- // process outputs
- MobyData[] outputs = activity.getMobyService().getPrimaryOutputs();
- for (int i = 0; i < outputs.length; i++) {
- if (outputs[i] instanceof MobyPrimaryDataSimple) {
- MobyPrimaryDataSimple simple = (MobyPrimaryDataSimple) outputs[i];
- StringBuffer sb = new StringBuffer(
- "Namespaces used by this object: ");
- MobyNamespace[] namespaces = simple.getNamespaces();
- for (int j = 0; j < namespaces.length; j++) {
- sb.append(namespaces[j].getName() + " ");
- }
- if (namespaces.length == 0)
- sb.append(" ANY ");
- MobyObjectTreeNode mobyObjectTreeNode = new MobyObjectTreeNode(
- simple.getDataType().getName() + "('"
- + simple.getName() + "')", sb.toString());
- mobyObjectTreeNode.setNamespaces(simple.getNamespaces());
- output.insert(new DefaultMutableTreeNode(mobyObjectTreeNode),
- output.getChildCount());
- } else {
- // we have a collection
- MobyPrimaryDataSet collection = (MobyPrimaryDataSet) outputs[i];
- DefaultMutableTreeNode collectionNode = new DefaultMutableTreeNode(
- "Collection('" + collection.getName() + "')");
- output.insert(collectionNode, output.getChildCount());
- MobyPrimaryDataSimple[] simples = collection.getElements();
- for (int j = 0; j < simples.length; j++) {
- MobyPrimaryDataSimple simple = simples[j];
- StringBuffer sb = new StringBuffer(
- "Namespaces used by this object: ");
- MobyNamespace[] namespaces = simple.getNamespaces();
- for (int k = 0; k < namespaces.length; k++) {
- sb.append(namespaces[k].getName() + " ");
- }
- if (namespaces.length == 0)
- sb.append("ANY ");
- MobyObjectTreeNode mobyObjectTreeNode = new MobyObjectTreeNode(
- simple.getDataType().getName() + "('"
- + simple.getName() + "')", sb.toString());
- mobyObjectTreeNode.setNamespaces(simple.getNamespaces());
- collectionNode
- .insert(new DefaultMutableTreeNode(
- mobyObjectTreeNode), collectionNode
- .getChildCount());
- }
-
- }
- }
- if (outputs.length == 0) {
- output.add(new DefaultMutableTreeNode(" None "));
- }
-
- // finally return a tree describing the object
- final JTree tree = new JTree(rootNode);
- tree.setCellRenderer(new BioMobyServiceTreeCustomRenderer());
- ToolTipManager.sharedInstance().registerComponent(tree);
- tree.addMouseListener(new MouseListener() {
- public void mouseClicked(MouseEvent me) {
- }
-
- public void mousePressed(MouseEvent me) {
- mouseReleased(me);
- }
-
- public void mouseReleased(MouseEvent me) {
- if (me.isPopupTrigger()) // right click, show popup menu
- {
- TreePath path = tree.getPathForLocation(me.getX(), me
- .getY());
- if (path == null)
- return;
- if (path.getPathCount() >= 3) {
- if (path.getParentPath().toString().indexOf("Parse:") >= 0
- && path.getLastPathComponent().toString()
- .indexOf(" None ") == -1) {
- DefaultMutableTreeNode node = (DefaultMutableTreeNode) tree
- .getLastSelectedPathComponent();
- if (node == null)
- return;
- final String selectedObject = node.toString();
- if (!selectedObject.equals(path
- .getLastPathComponent().toString()))
- return;
-
- logger.debug("TreePath " + path.toString());
- if (
- // path has a collection in it
- (path.getPathCount() == 4
- && path.getParentPath()
- .getLastPathComponent().toString()
- .startsWith("Collection(") && (path
- .getParentPath().toString())
- .indexOf("Parse:") > 0)
- // or path is just a simple
- || (path.toString().indexOf("Collection(") < 0)) {
-
- final JPopupMenu menu = new JPopupMenu();
-
- final String potentialCollectionString = path
- .getParentPath().getLastPathComponent()
- .toString();
- final boolean isCollection = potentialCollectionString
- .indexOf("Collection('") >= 0;
- JMenuItem item3 = new JMenuItem(
- "Add parser for " + selectedObject
- + " to the workflow");
- item3
- .setIcon(getIcon("/Cut24.gif"));
- item3.addActionListener(new ActionListener() {
-
- public void actionPerformed(ActionEvent ae) {
- // you would like to search for
- // selectedObject
- try {
- try {
- Dataflow currentDataflow = fileManager.getCurrentDataflow();
- Edit<?> edit = new AddMobyParseDatatypeEdit(
- currentDataflow, activity,
- selectedObject,isCollection, potentialCollectionString, editManager.getEdits());
- editManager.doDataflowEdit(
- currentDataflow, edit);
-
- } catch (Exception e) {
- logger.error("", e);
- }
-
- } catch (Exception e) {
- logger.error("", e);
- }
-
- }
- });
-
- menu.add(new JSeparator());
- menu.add(new JLabel("Parse Moby Data ... ",
- JLabel.CENTER));
- menu.add(new JSeparator());
- menu.add(item3);
- menu.show(me.getComponent(), me.getX(), me
- .getY());
- } else {
- logger
- .debug("unexpected situation occured; '"
- + selectedObject
- + "' was the object selected and the path is: "
- + path.toString());
- }
- }
- }
- }
- }
-
- public void mouseEntered(MouseEvent me) {
- }
-
- public void mouseExited(MouseEvent me) {
- }
- });
-
- tree.getSelectionModel().setSelectionMode(
- TreeSelectionModel.SINGLE_TREE_SELECTION);
- JScrollPane jsp = new JScrollPane(tree);
- JPanel thePanel = new JPanel(new BorderLayout());
- thePanel.add(jsp, BorderLayout.CENTER);
- return thePanel;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see org.embl.ebi.escience.scuflui.processoractions.ProcessorActionSPI#getDescription()
- */
- public String getDescription() {
- return "Add BioMOBY Parser ...";
- }
-
- /*
- * (non-Javadoc)
- *
- * @see org.embl.ebi.escience.scuflui.processoractions.ProcessorActionSPI#getIcon()
- */
- public ImageIcon getIcon() {
- return MobyPanel.getIcon("/Cut24.gif");
- }
-
- /**
- * returns the frame size as a dimension for the content pane housing
- * this action
- */
- public Dimension getFrameSize() {
- return new Dimension(450, 450);
- }
-
- /**
- * Return an Icon to represent this action
- *
- * @param loc
- * the location of the image to use as an icon
- */
- private ImageIcon getIcon(String loc) {
- return MobyPanel.getIcon(loc);
- }
-}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BioMobyObjectTreeCustomRenderer.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BioMobyObjectTreeCustomRenderer.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BioMobyObjectTreeCustomRenderer.java
deleted file mode 100644
index 46b4d5a..0000000
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BioMobyObjectTreeCustomRenderer.java
+++ /dev/null
@@ -1,97 +0,0 @@
-/*
- * This file is a component of the Taverna project,
- * and is licensed under the GNU LGPL.
- * Copyright Edward Kawas, The BioMoby Project
- */
-package net.sf.taverna.t2.activities.biomoby.actions;
-
-import java.awt.Color;
-import java.awt.Component;
-
-import javax.swing.JComponent;
-import javax.swing.JTree;
-import javax.swing.tree.DefaultMutableTreeNode;
-import javax.swing.tree.DefaultTreeCellRenderer;
-
-public class BioMobyObjectTreeCustomRenderer extends DefaultTreeCellRenderer {
-
- private static final long serialVersionUID = 1L;
-
- private Color leafForeground = Color.blue;
-
- private Color rootColor = Color.black;
-
- @SuppressWarnings("unused")
- private Color feedsIntoColor = Color.gray;
-
- @SuppressWarnings("unused")
- private Color producedColor = Color.lightGray;
-
- @SuppressWarnings("unused")
- private Color authorityColor = Color.orange;
-
- private Color serviceColor = Color.magenta;
-
- private Color objectColor = Color.green;
-
- public Component getTreeCellRendererComponent(JTree tree, Object value,
- boolean selected, boolean expanded, boolean leaf, int row,
- boolean hasFocus) {
- // Allow the original renderer to set up the label
- Component c = super.getTreeCellRendererComponent(tree, value, selected,
- expanded, leaf, row, hasFocus);
-
- if (value instanceof DefaultMutableTreeNode) {
- DefaultMutableTreeNode node = (DefaultMutableTreeNode) value;
- if (node.getUserObject() instanceof MobyServiceTreeNode) {
- // service node
- c.setForeground(serviceColor);
- ((JComponent) c).setToolTipText(((MobyServiceTreeNode) node
- .getUserObject()).getDescription());
- setIcon(MobyPanel.getIcon("/service.png"));
- } else if (node.getUserObject() instanceof MobyObjectTreeNode) {
- // object node
- c.setForeground(objectColor);
- ((JComponent) c).setToolTipText(((MobyObjectTreeNode) node
- .getUserObject()).getDescription());
- } else if (node.isRoot()) {
- // root node
- setIcon(MobyPanel.getIcon("/moby.png"));
- ((JComponent) c).setToolTipText(" Description of "
- + node.getUserObject());
- c.setForeground(rootColor);
- } else if (node.getUserObject() instanceof String) {
- // check for feeds into and produced by nodes
- String string = (String) node.getUserObject();
- if (string.equalsIgnoreCase("feeds into")) {
- setIcon(MobyPanel.getIcon("/input.png"));
- ((JComponent) c).setToolTipText(null);
- } else if (string.equalsIgnoreCase("produced by")) {
- setIcon(MobyPanel.getIcon("/output.png"));
- ((JComponent) c).setToolTipText(null);
- } else if (string.equalsIgnoreCase("produces")) {
- ((JComponent) c).setToolTipText(null);
- } else {
-
- ((JComponent) c).setToolTipText(null);
-
- if (!leaf) {
- if (string.startsWith("Collection('")) {
- setIcon(MobyPanel.getIcon("/collection.png"));
- } else {
- setIcon(MobyPanel.getIcon("/authority.png"));
- }
- }
- }
-
- } else {
- ((JComponent) c).setToolTipText("nothing node");
- }
- }
- if (selected)
- c.setBackground(Color.lightGray);
- if (leaf)
- c.setForeground(this.leafForeground);
- return c;
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BioMobyServiceTreeCustomRenderer.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BioMobyServiceTreeCustomRenderer.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BioMobyServiceTreeCustomRenderer.java
deleted file mode 100644
index ecce3ca..0000000
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BioMobyServiceTreeCustomRenderer.java
+++ /dev/null
@@ -1,86 +0,0 @@
-/*
- * This file is a component of the Taverna project,
- * and is licensed under the GNU LGPL.
- * Copyright Edward Kawas, The BioMoby Project
- */
-package net.sf.taverna.t2.activities.biomoby.actions;
-
-import java.awt.Color;
-import java.awt.Component;
-
-import javax.swing.JComponent;
-import javax.swing.JTree;
-import javax.swing.tree.DefaultMutableTreeNode;
-import javax.swing.tree.DefaultTreeCellRenderer;
-
-public class BioMobyServiceTreeCustomRenderer extends DefaultTreeCellRenderer {
-
- private static final long serialVersionUID = 1L;
-
- private Color leafForeground = Color.blue;
-
- @SuppressWarnings("unused")
- private Color rootColor = Color.black;
-
- @SuppressWarnings("unused")
- private Color feedsIntoColor = Color.gray;
-
- @SuppressWarnings("unused")
- private Color producedColor = Color.lightGray;
-
- @SuppressWarnings("unused")
- private Color authorityColor = Color.orange;
-
- private Color serviceColor = Color.magenta;
-
- private Color objectColor = Color.green;
-
- public Component getTreeCellRendererComponent(JTree tree, Object value,
- boolean selected, boolean expanded, boolean leaf, int row,
- boolean hasFocus) {
- // Allow the original renderer to set up the label
- Component c = super.getTreeCellRendererComponent(tree, value, selected,
- expanded, leaf, row, hasFocus);
-
- if (value instanceof DefaultMutableTreeNode) {
- DefaultMutableTreeNode node = (DefaultMutableTreeNode) value;
- if (node.getUserObject() instanceof MobyServiceTreeNode) {
- // service node
- c.setForeground(serviceColor);
- ((JComponent) c).setToolTipText(((MobyServiceTreeNode) node
- .getUserObject()).getDescription());
- setIcon(MobyPanel.getIcon("/service.png"));
- } else if (node.getUserObject() instanceof MobyObjectTreeNode) {
- // object node
- c.setForeground(objectColor);
- ((JComponent) c).setToolTipText(((MobyObjectTreeNode) node
- .getUserObject()).getDescription());
- } else if (node.getUserObject() instanceof String) {
- // check for feeds into and produced by nodes
- String string = (String) node.getUserObject();
- if (string.equalsIgnoreCase("inputs")) {
- setIcon(MobyPanel.getIcon("/input.png"));
- ((JComponent) c).setToolTipText(null);
- } else if (string.equalsIgnoreCase("outputs")) {
- setIcon(MobyPanel.getIcon("/output.png"));
- ((JComponent) c).setToolTipText(null);
- } else {
-
- ((JComponent) c).setToolTipText(null);
-
- if (!leaf) {
- if (string.startsWith("Collection('")) {
- setIcon(MobyPanel.getIcon("/collection.png"));
- }
- }
- }
-
- } else {
- ((JComponent) c).setToolTipText("nothing node");
- }
- }
- if (leaf)
- c.setForeground(this.leafForeground);
- return c;
- }
-}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BiomobyActionHelper.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BiomobyActionHelper.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BiomobyActionHelper.java
deleted file mode 100644
index 9579627..0000000
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BiomobyActionHelper.java
+++ /dev/null
@@ -1,852 +0,0 @@
-/*
- * This file is a component of the Taverna project, and is licensed under the
- * GNU LGPL. Copyright Edward Kawas, The BioMoby Project
- */
-package net.sf.taverna.t2.activities.biomoby.actions;
-
-import java.awt.BorderLayout;
-import java.awt.Component;
-import java.awt.Dimension;
-import java.awt.Frame;
-import java.awt.event.ActionEvent;
-import java.awt.event.ActionListener;
-import java.awt.event.MouseEvent;
-import java.awt.event.MouseListener;
-
-import javax.swing.ImageIcon;
-import javax.swing.JComponent;
-import javax.swing.JFrame;
-import javax.swing.JLabel;
-import javax.swing.JMenuItem;
-import javax.swing.JPanel;
-import javax.swing.JPopupMenu;
-import javax.swing.JProgressBar;
-import javax.swing.JScrollPane;
-import javax.swing.JSeparator;
-import javax.swing.JTree;
-import javax.swing.ToolTipManager;
-import javax.swing.tree.DefaultMutableTreeNode;
-import javax.swing.tree.TreePath;
-import javax.swing.tree.TreeSelectionModel;
-
-import net.sf.taverna.t2.activities.biomoby.BiomobyActivity;
-import net.sf.taverna.t2.activities.biomoby.BiomobyObjectActivity;
-import net.sf.taverna.t2.activities.biomoby.BiomobyObjectActivityConfigurationBean;
-import net.sf.taverna.t2.activities.biomoby.edits.AddBiomobyCollectionDataTypeEdit;
-import net.sf.taverna.t2.activities.biomoby.edits.AddBiomobyDataTypeEdit;
-import net.sf.taverna.t2.activities.biomoby.edits.AddMobyParseDatatypeEdit;
-import net.sf.taverna.t2.workbench.edits.EditManager;
-import net.sf.taverna.t2.workbench.file.FileManager;
-import net.sf.taverna.t2.workflowmodel.Dataflow;
-import net.sf.taverna.t2.workflowmodel.Edit;
-import net.sf.taverna.t2.workflowmodel.OutputPort;
-import net.sf.taverna.t2.workflowmodel.utils.Tools;
-
-import org.apache.log4j.Logger;
-import org.biomoby.client.CentralImpl;
-import org.biomoby.shared.Central;
-import org.biomoby.shared.MobyData;
-import org.biomoby.shared.MobyDataType;
-import org.biomoby.shared.MobyException;
-import org.biomoby.shared.MobyNamespace;
-import org.biomoby.shared.MobyPrimaryDataSet;
-import org.biomoby.shared.MobyPrimaryDataSimple;
-import org.biomoby.shared.NoSuccessException;
-
-
-/**
- *
- * @author Eddie An action that for BioMobyProcessors
- * @auther Stuart Owen - helped port to T2 - but with the minimum code changes possible!
- */
-public class BiomobyActionHelper {
-
- private static Logger logger = Logger
- .getLogger(BiomobyActionHelper.class);
-
- JProgressBar progressBar = new JProgressBar();
-
- private EditManager editManager;
-
- private final FileManager fileManager;
-
- public BiomobyActionHelper(EditManager editManager, FileManager fileManager) {
- this.editManager = editManager;
- this.fileManager = fileManager;
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * org.embl.ebi.escience.scuflui.processoractions.AbstractProcessorAction
- * #getComponent(org.embl.ebi.escience.scufl.Processor)
- */
-
- public JComponent getComponent(final BiomobyActivity activity) {
- // variables i need
-
- final String endpoint = activity.getConfiguration().getMobyEndpoint();
- // set up the root node
- String serviceName = activity.getMobyService().getName();
- String description = activity.getMobyService().getDescription();
-
- MobyServiceTreeNode service = new MobyServiceTreeNode(serviceName,
- description);
- DefaultMutableTreeNode rootNode = new DefaultMutableTreeNode(service);
-
- // now add the child nodes containing useful information about the
- // service
- DefaultMutableTreeNode input = new DefaultMutableTreeNode("Inputs");
- DefaultMutableTreeNode output = new DefaultMutableTreeNode("Outputs");
- rootNode.add(input);
- rootNode.add(output);
-
- // process inputs
- MobyData[] inputs = activity.getMobyService().getPrimaryInputs();
- for (int i = 0; i < inputs.length; i++) {
- if (inputs[i] instanceof MobyPrimaryDataSimple) {
- MobyPrimaryDataSimple simple = (MobyPrimaryDataSimple) inputs[i];
- StringBuffer sb = new StringBuffer(
- "Namespaces used by this object: ");
- MobyNamespace[] namespaces = simple.getNamespaces();
- for (int j = 0; j < namespaces.length; j++) {
- sb.append(namespaces[j].getName() + " ");
- }
- if (namespaces.length == 0)
- sb.append(" ANY ");
- MobyObjectTreeNode mobyObjectTreeNode = new MobyObjectTreeNode(
- simple.getDataType().getName() + "('"
- + simple.getName() + "')", sb.toString());
- input.insert(new DefaultMutableTreeNode(mobyObjectTreeNode),
- input.getChildCount());
- } else {
- // we have a collection
- MobyPrimaryDataSet collection = (MobyPrimaryDataSet) inputs[i];
- DefaultMutableTreeNode collectionNode = new DefaultMutableTreeNode(
- "Collection('" + collection.getName() + "')");
- input.insert(collectionNode, input.getChildCount());
- MobyPrimaryDataSimple[] simples = collection.getElements();
- for (int j = 0; j < simples.length; j++) {
- MobyPrimaryDataSimple simple = simples[j];
- StringBuffer sb = new StringBuffer(
- "Namespaces used by this object: ");
- MobyNamespace[] namespaces = simple.getNamespaces();
- for (int k = 0; k < namespaces.length; k++) {
- sb.append(namespaces[k].getName() + " ");
- }
- if (namespaces.length == 0)
- sb.append(" ANY ");
- MobyObjectTreeNode mobyObjectTreeNode = new MobyObjectTreeNode(
- simple.getDataType().getName() + "('"
- + simple.getName() + "')", sb.toString());
- collectionNode
- .insert(new DefaultMutableTreeNode(
- mobyObjectTreeNode), collectionNode
- .getChildCount());
- }
-
- }
- }
- if (inputs.length == 0) {
- input.add(new DefaultMutableTreeNode(" None "));
- }
-
- // process outputs
- MobyData[] outputs = activity.getMobyService().getPrimaryOutputs();
- for (int i = 0; i < outputs.length; i++) {
- if (outputs[i] instanceof MobyPrimaryDataSimple) {
- MobyPrimaryDataSimple simple = (MobyPrimaryDataSimple) outputs[i];
- StringBuffer sb = new StringBuffer(
- "Namespaces used by this object: ");
- MobyNamespace[] namespaces = simple.getNamespaces();
- for (int j = 0; j < namespaces.length; j++) {
- sb.append(namespaces[j].getName() + " ");
- }
- if (namespaces.length == 0)
- sb.append(" ANY ");
- MobyObjectTreeNode mobyObjectTreeNode = new MobyObjectTreeNode(
- simple.getDataType().getName() + "('"
- + simple.getName() + "')", sb.toString());
- mobyObjectTreeNode.setNamespaces(simple.getNamespaces());
- output.insert(new DefaultMutableTreeNode(mobyObjectTreeNode),
- output.getChildCount());
- } else {
- // we have a collection
- MobyPrimaryDataSet collection = (MobyPrimaryDataSet) outputs[i];
- DefaultMutableTreeNode collectionNode = new DefaultMutableTreeNode(
- "Collection('" + collection.getName() + "')");
- output.insert(collectionNode, output.getChildCount());
- MobyPrimaryDataSimple[] simples = collection.getElements();
- for (int j = 0; j < simples.length; j++) {
- MobyPrimaryDataSimple simple = simples[j];
- StringBuffer sb = new StringBuffer(
- "Namespaces used by this object: ");
- MobyNamespace[] namespaces = simple.getNamespaces();
- for (int k = 0; k < namespaces.length; k++) {
- sb.append(namespaces[k].getName() + " ");
- }
- if (namespaces.length == 0)
- sb.append("ANY ");
- MobyObjectTreeNode mobyObjectTreeNode = new MobyObjectTreeNode(
- simple.getDataType().getName() + "('"
- + simple.getName() + "')", sb.toString());
- mobyObjectTreeNode.setNamespaces(simple.getNamespaces());
- collectionNode
- .insert(new DefaultMutableTreeNode(
- mobyObjectTreeNode), collectionNode
- .getChildCount());
- }
-
- }
- }
- if (outputs.length == 0) {
- output.add(new DefaultMutableTreeNode(" None "));
- }
-
- // finally return a tree describing the object
- final JTree tree = new JTree(rootNode);
- tree.setCellRenderer(new BioMobyServiceTreeCustomRenderer());
- ToolTipManager.sharedInstance().registerComponent(tree);
- tree.addMouseListener(new MouseListener() {
- public void mouseClicked(MouseEvent me) {
- }
-
- public void mousePressed(MouseEvent me) {
- mouseReleased(me);
- }
-
- public void mouseReleased(MouseEvent me) {
- if (me.isPopupTrigger()) // right click, show popup menu
- {
- TreePath path = tree.getPathForLocation(me.getX(), me
- .getY());
- if (path == null)
- return;
- if (path.getPathCount() >= 3) {
- if (path.getPathCount() == 4
- && path.getParentPath().getLastPathComponent()
- .toString().startsWith("Collection(")
- && (path.getParentPath().toString())
- .indexOf("Inputs") > 0) {
- // we have a collection input
- DefaultMutableTreeNode node = (DefaultMutableTreeNode) tree
- .getLastSelectedPathComponent();
- final String selectedObject = node.toString();
- // ensure that the last selected item is an object!
- if (!selectedObject.equals(path
- .getLastPathComponent().toString()))
- return;
- String collectionName = "";
- if (path.getParentPath().getLastPathComponent()
- .toString().indexOf("('") > 0
- && path.getParentPath()
- .getLastPathComponent().toString()
- .indexOf("')") > 0) {
- collectionName = path.getParentPath()
- .getLastPathComponent().toString()
- .substring(
- path.getParentPath()
- .getLastPathComponent()
- .toString().indexOf(
- "('") + 2,
- path.getParentPath()
- .getLastPathComponent()
- .toString().indexOf(
- "')"));
- }
- final String theCollectionName = collectionName;
- final JPopupMenu menu = new JPopupMenu();
- // Create and add a menu item for adding to the item
- // to the workflow
- JMenuItem item = new JMenuItem("Add Datatype - "
- + selectedObject + " to the workflow?");
- item
- .setIcon(MobyPanel.getIcon("/Add24.gif"));
- item.addActionListener(new ActionListener() {
- // private boolean added = false;
-
- public void actionPerformed(ActionEvent ae) {
-
- try {
- Dataflow currentDataflow = fileManager.getCurrentDataflow();
- Edit<?> edit = new AddBiomobyCollectionDataTypeEdit(
- currentDataflow, activity,
- selectedObject,
- theCollectionName, editManager.getEdits());
- editManager.doDataflowEdit(
- currentDataflow, edit);
-
- } catch (Exception e) {
- logger.error("", e);
- }
- }
- });
- // Create and add a menu item for service details
- JMenuItem details = new JMenuItem("Find out about "
- + selectedObject);
- details
- .setIcon(MobyPanel.getIcon("/Information24.gif"));
- details.addActionListener(new ActionListener() {
- public void actionPerformed(ActionEvent ae) {
-
- // TODO Create a frame
- Frame frame = MobyPanel.CreateFrame("A BioMoby Object Description");
- JPanel panel = new MobyPanel(
- selectedObject,
- "A BioMoby Object Description", "");
-
- frame.add(panel);
- frame.setSize(getFrameSize());
- frame.pack();
- frame.setVisible(true);
- }
- });
- // add the components to the menu
- menu.add(new JLabel("Add to workflow ... ",
- JLabel.CENTER));
- menu.add(new JSeparator());
- menu.add(item);
- menu.add(new JSeparator());
- menu.add(new JLabel("Datatype Details ... ",
- JLabel.CENTER));
- menu.add(new JSeparator());
- menu.add(details);
- // show the window
- menu.show(me.getComponent(), me.getX(), me.getY());
- } else if (path.getPathCount() == 3
- && path.getParentPath().getLastPathComponent()
- .toString().startsWith("Inputs")
- && !path.getLastPathComponent().toString()
- .startsWith("Collection(")
- && !path.getLastPathComponent().toString()
- .equals(" None ")) {
- // we have a simple input
- DefaultMutableTreeNode node = (DefaultMutableTreeNode) tree
- .getLastSelectedPathComponent();
- if (node == null)
- return;
- final String selectedObject = node.toString();
- // ensure that the last selected item is an object!
- if (!selectedObject.equals(path
- .getLastPathComponent().toString()))
- return;
-
- final JPopupMenu menu = new JPopupMenu();
- // Create and add a menu item for adding to the item
- // to the workflow
- JMenuItem item = new JMenuItem("Add Datatype - "
- + selectedObject + " to the workflow?");
- item
- .setIcon(MobyPanel.getIcon("/Add24.gif"));
- item.addActionListener(new ActionListener() {
- // private boolean added = false;
-
- public void actionPerformed(ActionEvent ae) {
-
- try {
- Dataflow currentDataflow = fileManager.getCurrentDataflow();
- Edit<?> edit = new AddBiomobyDataTypeEdit(
- currentDataflow, activity,
- selectedObject, editManager.getEdits());
- editManager.doDataflowEdit(
- currentDataflow, edit);
-
- } catch (Exception e) {
- logger.error("Could not perform action", e);
- }
- }
- });
-
- // Create and add a menu item for service details
- JMenuItem details = new JMenuItem(
- "Find out about 1 " + selectedObject);
- details
- .setIcon(MobyPanel.getIcon("/Information24.gif"));
- details.addActionListener(new ActionListener() {
- public void actionPerformed(ActionEvent ae) {
- // TODO Create a frame
- Frame frame = MobyPanel.CreateFrame("A BioMoby Object Description");
- JPanel panel = new MobyPanel(
- // TODO create a valid description
- selectedObject,
- "A BioMoby Object Description",
- createDataDescription(
- selectedObject.split("\\(")[0],
- activity.getConfiguration()
- .getMobyEndpoint()));
- frame.add(panel);
- frame.setSize(getFrameSize());
- frame.pack();
- frame.setVisible(true);
- }
-
- private String createDataDescription(
- String dataName, String mobyEndpoint) {
- MobyDataType data;
- try {
- Central central = new CentralImpl(
- mobyEndpoint);
- data = central.getDataType(dataName);
-
- } catch (MobyException e) {
- return "Couldn't retrieve a description on the BioMoby service '"
- + dataName + "'";
- } catch (NoSuccessException e) {
- return "Couldn't retrieve a description on the BioMoby service '"
- + dataName + "'";
- }
- return data.toString();
- }
- });
- // add the components to the menu
- menu.add(new JLabel("Add to workflow ... ",
- JLabel.CENTER));
- menu.add(new JSeparator());
- menu.add(item);
- menu.add(new JSeparator());
- menu.add(new JLabel("Datatype Details ... ",
- JLabel.CENTER));
- menu.add(new JSeparator());
- menu.add(details);
- // show the window
- menu.show(me.getComponent(), me.getX(), me.getY());
-
- } else if (path.getParentPath().toString().indexOf(
- "Outputs") >= 0
- && path.getLastPathComponent().toString()
- .indexOf(" None ") == -1) {
- DefaultMutableTreeNode node = (DefaultMutableTreeNode) tree
- .getLastSelectedPathComponent();
- if (node == null)
- return;
- final String selectedObject = node.toString();
- if (!selectedObject.equals(path
- .getLastPathComponent().toString()))
- return;
-
- if ((path.getPathCount() == 4
- && path.getParentPath()
- .getLastPathComponent().toString()
- .startsWith("Collection(") && (path
- .getParentPath().toString())
- .indexOf("Outputs") > 0)
- || (path.toString().indexOf("Collection(") < 0)) {
- final JPopupMenu menu = new JPopupMenu();
- JMenuItem item = new JMenuItem(
- "Find Services that Consume "
- + selectedObject
- + " - brief search");
- item
- .setIcon(MobyPanel.getIcon("/Information24.gif"));
- final String potentialCollectionString = path
- .getParentPath().getLastPathComponent()
- .toString();
- final boolean isCollection = potentialCollectionString
- .indexOf("Collection('") >= 0;
- final Object selectedMobyObjectTreeNodeHolder = (DefaultMutableTreeNode) tree
- .getLastSelectedPathComponent();
- item.addActionListener(new ActionListener() {
-
- public void actionPerformed(ActionEvent ae) {
- // you would like to search for
- // selectedObject
- new Thread("Finding biomoby services") {
- public void run() {
- try {
- // FIXME: ignored for now -
- // Stuart
- String name = selectedObject;
- if (name.indexOf("(") > 0)
- name = name
- .substring(
- 0,
- name
- .indexOf("("));
- String articlename = "";
- if (isCollection) {
- articlename = potentialCollectionString
- .substring(
- potentialCollectionString
- .indexOf("('") + 2,
- potentialCollectionString
- .lastIndexOf("'"));
- } else {
- articlename = selectedObject
- .substring(
- selectedObject
- .indexOf("'") + 1,
- selectedObject
- .lastIndexOf("'"));
- }
-
- BiomobyObjectActivity boAct = new BiomobyObjectActivity();
- BiomobyObjectActivityConfigurationBean bean = new BiomobyObjectActivityConfigurationBean();
- MobyDataType dataType = new MobyDataType(
- name);
- bean
- .setAuthorityName(dataType
- .getAuthority());
- bean
- .setServiceName(dataType
- .getName());
- bean
- .setMobyEndpoint(endpoint);
- boAct.configure(bean);
-
- OutputPort theServiceport = null;
-
- try {
- if (isCollection)
- theServiceport = Tools
- .getActivityOutputPort(
- activity,
- name
- + "(Collection - '"
- + (articlename
- .equals("") ? "MobyCollection"
- : articlename)
- + "' As Simples)");
-
- else
- theServiceport = Tools
- .getActivityOutputPort(
- activity,
- name
- + "("
- + articlename
- + ")");
- } catch (Exception except) {
- }
- BiomobyObjectActionHelper boa = null;
-
- if (theServiceport == null) {
- boa = new BiomobyObjectActionHelper(
- false, editManager, fileManager);
- } else {
- boa = new BiomobyObjectActionHelper(
- theServiceport,
- false, editManager, fileManager);
- }
-
- if (selectedMobyObjectTreeNodeHolder instanceof DefaultMutableTreeNode
- && ((DefaultMutableTreeNode) selectedMobyObjectTreeNodeHolder)
- .getUserObject() instanceof MobyObjectTreeNode) {
- DefaultMutableTreeNode dmtn = (DefaultMutableTreeNode) selectedMobyObjectTreeNodeHolder;
- MobyObjectTreeNode motn = (MobyObjectTreeNode) dmtn
- .getUserObject();
- boa
- .setNamespaces(motn
- .getNamespaces());
- }
- PopupThread popupthread = new PopupThread(
- boAct, boa);
- progressBar
- .setStringPainted(true);
- progressBar
- .setVisible(true);
- popupthread.start();
-
- while (popupthread
- .isAlive()) {
- Thread.sleep(4000);
- }
-
- progressBar
- .setVisible(false);
- Component c = popupthread
- .getComponent();
- Dimension loc = getFrameLocation();
- Dimension size = getFrameSize();
- JPanel frame = new SimpleActionFrame(
- c,
- "Moby Object Details");
- createFrame(
- frame,
- (int) loc
- .getWidth(),
- (int) loc
- .getHeight(),
- (int) size
- .getWidth(),
- (int) size
- .getHeight());
- } catch (Exception e) {
- }
- }
- }.start();
-
- }
- });
-
- JMenuItem item2 = new JMenuItem(
- "Find Services that Consume "
- + selectedObject
- + " - semantic search");
- item2
- .setIcon(MobyPanel.getIcon("/Search24.gif"));
- item2.addActionListener(new ActionListener() {
- public void actionPerformed(ActionEvent ae) {
- // you would like to search for
- // selectedObject
- new Thread("Finding BioMoby services") {
-
- public void run() {
- try {
- String name = selectedObject;
- if (name.indexOf("(") > 0)
- name = name
- .substring(
- 0,
- name
- .indexOf("("));
- String articlename = "";
- if (isCollection) {
- articlename = potentialCollectionString
- .substring(
- potentialCollectionString
- .indexOf("('") + 2,
- potentialCollectionString
- .lastIndexOf("'"));
- } else {
- articlename = selectedObject
- .substring(
- selectedObject
- .indexOf("'") + 1,
- selectedObject
- .lastIndexOf("'"));
- }
- BiomobyObjectActivity boAct = new BiomobyObjectActivity();
- BiomobyObjectActivityConfigurationBean bean = new BiomobyObjectActivityConfigurationBean();
- MobyDataType dataType = new MobyDataType(
- name);
- bean
- .setAuthorityName(dataType
- .getAuthority());
- bean
- .setServiceName(dataType
- .getName());
- bean
- .setMobyEndpoint(endpoint);
- boAct.configure(bean);
-
- OutputPort theServiceport = null;
-
- try {
-
- if (isCollection)
- theServiceport = Tools
- .getActivityOutputPort(
- activity,
- name
- + "(Collection - '"
- + (articlename
- .equals("") ? "MobyCollection"
- : articlename)
- + "' As Simples)");
-
- else
- theServiceport = Tools
- .getActivityOutputPort(
- activity,
- name
- + "("
- + articlename
- + ")");
- } catch (Exception except) {
- }
- BiomobyObjectActionHelper boa = null;
-
- if (theServiceport == null)
- boa = new BiomobyObjectActionHelper(
- true, editManager, fileManager);
- else
- boa = new BiomobyObjectActionHelper(
- theServiceport,
- true, editManager, fileManager);
- if (selectedMobyObjectTreeNodeHolder instanceof DefaultMutableTreeNode
- && ((DefaultMutableTreeNode) selectedMobyObjectTreeNodeHolder)
- .getUserObject() instanceof MobyObjectTreeNode) {
- DefaultMutableTreeNode dmtn = (DefaultMutableTreeNode) selectedMobyObjectTreeNodeHolder;
- MobyObjectTreeNode motn = (MobyObjectTreeNode) dmtn
- .getUserObject();
- boa
- .setNamespaces(motn
- .getNamespaces());
- }
-
- PopupThread popupthread = new PopupThread(
- boAct, boa);
- progressBar
- .setStringPainted(true);
- progressBar
- .setVisible(true);
- popupthread.start();
-
- while (popupthread
- .isAlive()) {
- Thread.sleep(4000);
- }
-
- progressBar
- .setVisible(false);
- Component c = popupthread
- .getComponent();
- Dimension loc = getFrameLocation();
- Dimension size = getFrameSize();
- JPanel frame = new SimpleActionFrame(
- c,
- "Moby Object Details");
- createFrame(
- frame,
- (int) loc
- .getWidth(),
- (int) loc
- .getHeight(),
- (int) size
- .getWidth(),
- (int) size
- .getHeight());
- } catch (Exception e) {
- }
- }
- }.start();
- }
- });
-
- // string may be needed to extract the
- // collection article name
- // final String potentialCollectionString =
- // path.getParentPath()
- // .getLastPathComponent().toString();
- // final boolean isCollection =
- // potentialCollectionString
- // .indexOf("Collection('") >= 0;
-
- JMenuItem item3 = new JMenuItem(
- "Add parser for " + selectedObject
- + " to the workflow");
- item3
- .setIcon(MobyPanel.getIcon("/Cut24.gif"));
- item3.addActionListener(new ActionListener() {
-
- public void actionPerformed(ActionEvent ae) {
-
- try {
- Dataflow currentDataflow = fileManager.getCurrentDataflow();
- Edit<?> edit = new AddMobyParseDatatypeEdit(
- currentDataflow, activity,
- selectedObject,isCollection, potentialCollectionString, editManager.getEdits());
- editManager.doDataflowEdit(
- currentDataflow, edit);
-
- } catch (Exception e) {
- logger.error("Could not perform action", e);
- }
-
- }
- });
-
- menu.add(new JLabel(
- "Moby Service Discovery ... ",
- JLabel.CENTER));
- menu.add(new JSeparator());
- menu.add(item);
- menu.add(new JSeparator());
- menu.add(item2);
- menu.add(new JLabel("Parse Moby Data ... ",
- JLabel.CENTER));
- menu.add(new JSeparator());
- menu.add(item3);
-
- menu.show(me.getComponent(), me.getX(), me
- .getY());
- }
- }
- }
- }
- }
-
- public void mouseEntered(MouseEvent me) {
- }
-
- public void mouseExited(MouseEvent me) {
- }
- });
-
- tree.getSelectionModel().setSelectionMode(
- TreeSelectionModel.SINGLE_TREE_SELECTION);
- JScrollPane jsp = new JScrollPane(tree);
- JPanel thePanel = new JPanel(new BorderLayout());
- thePanel.add(jsp, BorderLayout.CENTER);
- progressBar = new JProgressBar();
- progressBar.setValue(0);
- progressBar.setString("Finding Services ... ");
- progressBar.setStringPainted(true);
- progressBar.setIndeterminate(true);
- progressBar.setVisible(false);
- thePanel.add(progressBar, BorderLayout.PAGE_END);
- return thePanel;
- }
-
- /*
- * (non-Javadoc)
- *
- * @seeorg.embl.ebi.escience.scuflui.processoractions.ProcessorActionSPI#
- * getDescription()
- */
- public String getDescription() {
- return "Moby Service Details";
- }
-
- /*
- * (non-Javadoc)
- *
- * @see
- * org.embl.ebi.escience.scuflui.processoractions.ProcessorActionSPI#getIcon
- * ()
- */
- public ImageIcon getIcon() {
- return MobyPanel.getIcon("/moby_small.gif");
- }
-
- /**
- * returns the frame size as a dimension for the content pane housing this
- * action
- */
- public Dimension getFrameSize() {
- return new Dimension(450, 450);
- }
-
- /**
- * Return an Icon to represent this action
- *
- * @param loc
- * the location of the image to use as an icon
- */
- public ImageIcon getIcon(String loc) {
- return MobyPanel.getIcon(loc);
- }
-
- /**
- * Where should the frame open?
- */
- public Dimension getFrameLocation() {
- return new Dimension(100, 100);
- }
-
- public void createFrame(JPanel targetComponent,
- int posX, int posY, int sizeX, int sizeY) {
- final JPanel component = targetComponent;
- JFrame newFrame = new JFrame(component.getName());
- newFrame.getContentPane().setLayout(new BorderLayout());
- newFrame.getContentPane().add(
- new JScrollPane((JComponent) targetComponent),
- BorderLayout.CENTER);
- newFrame.setDefaultCloseOperation(JFrame.DISPOSE_ON_CLOSE);
- newFrame.setSize(sizeX, sizeY);
- newFrame.setLocation(posX, posY);
- newFrame.setVisible(true);
- }
-
-}
\ No newline at end of file
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BiomobyActivityConfigurationAction.java
----------------------------------------------------------------------
diff --git a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BiomobyActivityConfigurationAction.java b/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BiomobyActivityConfigurationAction.java
deleted file mode 100644
index f74c76a..0000000
--- a/taverna-biomoby-activity-ui/src/main/java/net/sf/taverna/t2/activities/biomoby/actions/BiomobyActivityConfigurationAction.java
+++ /dev/null
@@ -1,60 +0,0 @@
-/*******************************************************************************
- * This file is a component of the Taverna project, and is licensed under the
- * GNU LGPL. Copyright Edward Kawas, The BioMoby Project
- ******************************************************************************/
-package net.sf.taverna.t2.activities.biomoby.actions;
-
-import java.awt.Frame;
-import java.awt.event.ActionEvent;
-
-import net.sf.taverna.t2.activities.biomoby.BiomobyActivity;
-import net.sf.taverna.t2.activities.biomoby.BiomobyActivityConfigurationBean;
-import net.sf.taverna.t2.activities.biomoby.view.BiomobyConfigView;
-import net.sf.taverna.t2.workbench.activityicons.ActivityIconManager;
-import net.sf.taverna.t2.workbench.edits.EditManager;
-import net.sf.taverna.t2.workbench.file.FileManager;
-import net.sf.taverna.t2.workbench.ui.actions.activity.ActivityConfigurationAction;
-import net.sf.taverna.t2.workbench.ui.views.contextualviews.activity.ActivityConfigurationDialog;
-
-import org.apache.log4j.Logger;
-
-@SuppressWarnings("serial")
-public class BiomobyActivityConfigurationAction extends
- ActivityConfigurationAction<BiomobyActivity, BiomobyActivityConfigurationBean> {
-
- private final Frame owner;
- private static Logger logger = Logger.getLogger(BiomobyActivityConfigurationAction.class);
- private final EditManager editManager;
- private final FileManager fileManager;
-
- public BiomobyActivityConfigurationAction(BiomobyActivity activity, Frame owner,
- EditManager editManager, FileManager fileManager,
- ActivityIconManager activityIconManager) {
- super(activity, activityIconManager);
- this.owner = owner;
- this.editManager = editManager;
- this.fileManager = fileManager;
- }
-
- public void actionPerformed(ActionEvent arg0) {
- ActivityConfigurationDialog<BiomobyActivity, BiomobyActivityConfigurationBean> currentDialog = ActivityConfigurationAction
- .getDialog(getActivity());
- if (currentDialog != null) {
- currentDialog.toFront();
- return;
- }
-
- final BiomobyConfigView biomobyConfigView = new BiomobyConfigView(
- (BiomobyActivity) getActivity());
- final ActivityConfigurationDialog<BiomobyActivity, BiomobyActivityConfigurationBean> dialog = new ActivityConfigurationDialog<BiomobyActivity, BiomobyActivityConfigurationBean>(
- getActivity(), biomobyConfigView, editManager, fileManager);
-
- ActivityConfigurationAction.setDialog(getActivity(), dialog, fileManager);
- }
-
- public boolean isEnabled() {
- BiomobyActivity activity = (BiomobyActivity) getActivity();
- return (activity.getMobyService() != null && activity.containsSecondaries());
- }
-
-}