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Posted to commits@taverna.apache.org by st...@apache.org on 2015/02/17 21:44:23 UTC
[03/16] incubator-taverna-plugin-bioinformatics git commit:
temporarily empty repository
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/RetrieveWsdlThread.java
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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
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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
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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
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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
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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
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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
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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
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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
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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
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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>
-