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Posted to commits@taverna.apache.org by st...@apache.org on 2015/02/17 21:44:35 UTC
[15/16] incubator-taverna-plugin-bioinformatics git commit:
temporarily empty repository
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
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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
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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
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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;
- }
-
-}