http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/RetrieveWsdlThread.java ---------------------------------------------------------------------- diff --git a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/RetrieveWsdlThread.java b/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/RetrieveWsdlThread.java deleted file mode 100644 index a7b873c..0000000 --- a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/RetrieveWsdlThread.java +++ /dev/null @@ -1,57 +0,0 @@ -/******************************************************************************* - * This file is a component of the Taverna project, and is licensed under the - * GNU LGPL. Copyright Edward Kawas, The BioMoby Project - ******************************************************************************/ -/* - * This file is a component of the Taverna project, - * and is licensed under the GNU LGPL. - * Copyright Edward Kawas, The BioMoby Project - */ - -package net.sf.taverna.t2.activities.biomoby; - -import org.biomoby.shared.MobyService; -import org.biomoby.shared.Central; - -/** - * This class is used to create a threaded call to the Biomoby registry that - * retrieves WSDL for services. This is done, because the Biomoby API assumes - * that before calling a service the WSDL is retrieved. - * - * @author Eddie Kawas - * - */ -public class RetrieveWsdlThread extends Thread { - // the service to get wsdl document - MobyService service = null; - - // the registry that we will get the document from - Central worker = null; - - /** - * Constructor - * - * @param worker - * the Central registry that we query for wsdl - * @param service - * the service that we want wsdl for - */ - RetrieveWsdlThread(Central worker, MobyService service) { - super("BioMOBY RetrieveWsdlThread"); - this.service = service; - this.worker = worker; - setDaemon(true); - } - - /* - * (non-Javadoc) - * @see java.lang.Thread#run() - */ - public void run() { - try { - worker.getServiceWSDL(service.getName(), service.getAuthority()); - } catch (Exception e) { - - } - } -}
http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/XMLUtilities.java ---------------------------------------------------------------------- diff --git a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/XMLUtilities.java b/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/XMLUtilities.java deleted file mode 100644 index d791329..0000000 --- a/taverna-biomoby-activity/src/main/java/net/sf/taverna/t2/activities/biomoby/XMLUtilities.java +++ /dev/null @@ -1,1927 +0,0 @@ -/* - * This file is a component of the Taverna project, - * and is licensed under the GNU LGPL. - * Copyright Edward Kawas, The BioMoby Project - */ -package net.sf.taverna.t2.activities.biomoby; - -import java.io.IOException; -import java.io.StringReader; -import java.util.ArrayList; -import java.util.Iterator; -import java.util.List; -import java.util.Vector; - -import org.biomoby.shared.MobyException; -import org.biomoby.shared.Utils; -import org.jdom.Document; -import org.jdom.Element; -import org.jdom.JDOMException; -import org.jdom.Namespace; -import org.jdom.input.SAXBuilder; -import org.jdom.output.Format; -import org.jdom.output.XMLOutputter; - -/** - * - * @author Eddie Kawas - * - */ -@SuppressWarnings("unchecked") -public class XMLUtilities { - - // private variables - // machine independent new line character - public final static String newline = System.getProperty("line.separator"); - - // class variable to keep persistant queryIDs - private static int queryCount = 0; - - // the moby namespaces - public final static Namespace MOBY_NS = Namespace.getNamespace("moby", - "http://www.biomoby.org/moby";); - - /** - * - * @param message - * the structurally valid BioMoby message as a String - * @return true if the message contains multiple invocations, false - * otherwise. - * @throws MobyException - * if the message is null - */ - public static boolean isMultipleInvocationMessage(String message) - throws MobyException { - if (message == null) - throw new MobyException( - newline - + "null 'xml' found where it was not expected in isMultipleInvocationMessage(String message)."); - Element documentElement = getDOMDocument(message).getRootElement(); - return isMultipleInvocationMessage(documentElement); - } - - /** - * - * @param message - * the structurally valid BioMoby message as an Element - * @return true if the message contains multiple invocations, false - * otherwise. - * @throws MobyException - * if the message is null - */ - public static boolean isMultipleInvocationMessage(Element message) - throws MobyException { - if (message == null) - throw new MobyException( - newline - + "null 'xml' found where it was not expected in isMultipleInvocationMessage(Element message)."); - Element e = (Element) message.clone(); - List list = new ArrayList(); - listChildren(e, "mobyData", list); - if (list != null) - if (list.size() > 1) - return true; - return false; - } - - /** - * - * @param element - * the element to extract the list of simples from. This method - * assumes that you are passing in a single invokation and that - * you wish to extract the Simples not contained in any - * collections. This method also maintains any past queryIDs. - * @return an array of elements that are fully 'wrapped' simples. - * @throws MobyException - * if the Element isnt structurally valid in terms of Moby - * message structure - */ - public static Element[] getListOfSimples(Element element) - throws MobyException { - Element temp = (Element) element.clone(); - Element e = (Element) element.clone(); - String queryID = ""; - - if (isMultipleInvocationMessage(element)) - return new Element[] {}; - - Element serviceNotes = getServiceNotes(e); - - // if the current elements name isnt MOBY, see if its direct child is - if (!e.getName().equals("MOBY")) { - if (e.getChild("MOBY") != null) - temp = e.getChild("MOBY"); - else if (e.getChild("MOBY", MOBY_NS) != null) - temp = e.getChild("MOBY", MOBY_NS); - else - throw new MobyException(newline - + "Expected 'MOBY' as the local name for the element " - + newline + "and instead received '" + e.getName() - + "' (getListOfSimples(Element element)."); - } - // parse the mobyContent node - if (temp.getChild("mobyContent") != null) - temp = temp.getChild("mobyContent"); - else if (temp.getChild("mobyContent", MOBY_NS) != null) - temp = temp.getChild("mobyContent", MOBY_NS); - else - throw new MobyException( - newline - + "Expected 'mobyContent' as the local name for the next child element but it " - + newline - + "wasn't there. I even tried a qualified name (getListOfSimples(Element element)."); - - // parse the mobyData node - if (temp.getChild("mobyData") != null) { - temp = temp.getChild("mobyData"); - } else if (temp.getChild("mobyData", MOBY_NS) != null) { - temp = temp.getChild("mobyData", MOBY_NS); - } else { - throw new MobyException( - newline - + "Expected 'mobyData' as the local name for the next child element but it " - + newline - + "wasn't there. I even tried a qualified name (getListOfSimples(Element element)."); - } - - // temp == mobyData now we need to get the queryID and save it - if (temp.getAttribute("queryID") != null) { - queryID = temp.getAttribute("queryID").getValue(); - } else if (temp.getAttribute("queryID", MOBY_NS) != null) { - queryID = temp.getAttribute("queryID", MOBY_NS).getValue(); - } else { - // create a new one -> shouldnt happen very often - queryID = "a" + queryCount++; - } - - // now we iterate through all of the direct children called Simple, wrap - // them individually and set the queryID = queryID - List list = temp.getChildren("Simple", MOBY_NS); - if (list.isEmpty()) { - list = temp.getChildren("Simple"); - if (list.isEmpty()) { - return new Element[] {}; - } - } - // non empty list - Element[] elements = new Element[list.size()]; - int index = 0; - for (Iterator it = list.iterator(); it.hasNext();) { - Element next = (Element) it.next(); - elements[index++] = createMobyDataElementWrapper(next, queryID, - serviceNotes); - } - return elements; - } - - /** - * - * @param message - * the String of xml to extract the list of simples from. This - * method assumes that you are passing in a single invokation and - * that you wish to extract the Simples not contained in any - * collections. This method also maintains any past queryIDs. - * @return an array of Strings that represent fully 'wrapped' simples. - * @throws MobyException - * if the String doesnt contain a structurally valid Moby - * message structure or if an unexpected error occurs - */ - public static String[] getListOfSimples(String message) - throws MobyException { - Element element = getDOMDocument(message).getRootElement(); - Element[] elements = getListOfSimples(element); - String[] strings = new String[elements.length]; - XMLOutputter outputter = new XMLOutputter(Format.getPrettyFormat() - .setOmitDeclaration(false)); - for (int count = 0; count < elements.length; count++) { - try { - strings[count] = outputter.outputString(elements[count]); - } catch (Exception e) { - throw new MobyException(newline - + "Unexpected error occured while creating String[]:" - + newline + Utils.format(e.getLocalizedMessage(), 3)); - } - } - return strings; - } - - /** - * - * @param message - * the String to extract the list of collections from and assumes - * that you are passing in a single invocation message. - * @return an array of Strings representing all of the fully 'wrapped' - * collections in the message. - * @throws MobyException - * if the the element contains an invalid BioMOBY message - */ - public static String[] getListOfCollections(String message) - throws MobyException { - Element element = getDOMDocument(message).getRootElement(); - Element[] elements = getListOfCollections(element); - String[] strings = new String[elements.length]; - XMLOutputter outputter = new XMLOutputter(Format.getPrettyFormat() - .setOmitDeclaration(false)); - for (int count = 0; count < elements.length; count++) { - try { - strings[count] = outputter.outputString(elements[count]); - } catch (Exception e) { - throw new MobyException(newline - + "Unexpected error occured while creating String[]:" - + newline + Utils.format(e.getLocalizedMessage(), 3)); - } - } - return strings; - } - - /** - * - * @param element - * the element to extract the list of collections from and - * assumes that you are passing in a single invocation message. - * @return an array of Elements representing all of the fully 'wrapped' - * collections in the message - * @throws MobyException - * if the element contains an invalid BioMOBY message - */ - public static Element[] getListOfCollections(Element element) - throws MobyException { - Element temp = (Element) element.clone(); - Element e = (Element) element.clone(); - String queryID = ""; - - if (isMultipleInvocationMessage(e)) - return new Element[] {}; - - Element serviceNotes = getServiceNotes(e); - - // if the current elements name isnt MOBY, see if its direct child is - if (!e.getName().equals("MOBY")) { - if (e.getChild("MOBY") != null) - temp = e.getChild("MOBY"); - else if (e.getChild("MOBY", MOBY_NS) != null) - temp = e.getChild("MOBY", MOBY_NS); - else - throw new MobyException(newline - + "Expected 'MOBY' as the local name for the element " - + newline + "and instead received '" + e.getName() - + "' (getListOfCollections(Element element)."); - } - // parse the mobyContent node - if (temp.getChild("mobyContent") != null) - temp = temp.getChild("mobyContent"); - else if (temp.getChild("mobyContent", MOBY_NS) != null) - temp = temp.getChild("mobyContent", MOBY_NS); - else - throw new MobyException( - newline - + "Expected 'mobyContent' as the local name for the next child element but it " - + newline - + "wasn't there. I even tried a qualified name (getListOfCollections(Element element)."); - - // parse the mobyData node - if (temp.getChild("mobyData") != null) { - temp = temp.getChild("mobyData"); - } else if (temp.getChild("mobyData", MOBY_NS) != null) { - temp = temp.getChild("mobyData", MOBY_NS); - } else { - throw new MobyException( - newline - + "Expected 'mobyData' as the local name for the next child element but it " - + newline - + "wasn't there. I even tried a qualified name (getListOfCollections(Element element)."); - } - - // temp == mobyData now we need to get the queryID and save it - if (temp.getAttribute("queryID") != null) { - queryID = temp.getAttribute("queryID").getValue(); - } else if (temp.getAttribute("queryID", MOBY_NS) != null) { - queryID = temp.getAttribute("queryID", MOBY_NS).getValue(); - } else { - // create a new one -> shouldnt happen very often - queryID = "a" + queryCount++; - } - - // now we iterate through all of the direct children called Simple, wrap - // them individually and set the queryID = queryID - List list = temp.getChildren("Collection", MOBY_NS); - if (list.isEmpty()) { - list = temp.getChildren("Collection"); - if (list.isEmpty()) { - return new Element[] {}; - } - } - // non empty list - Element[] elements = new Element[list.size()]; - int index = 0; - for (Iterator it = list.iterator(); it.hasNext();) { - Element next = (Element) it.next(); - elements[index++] = createMobyDataElementWrapper(next, queryID, - serviceNotes); - } - return elements; - } - - /** - * This method assumes a single invocation was passed to it - * <p> - * - * @param name - * the article name of the simple that you are looking for - * @param xml - * the xml that you want to query - * @return a String object that represent the simple found. - * @throws MobyException - * if no simple was found given the article name and/or data - * type or if the xml was not valid moby xml or if an unexpected - * error occurs. - */ - public static String getSimple(String name, String xml) - throws MobyException { - Element element = getDOMDocument(xml).getRootElement(); - XMLOutputter outputter = new XMLOutputter(Format.getPrettyFormat() - .setOmitDeclaration(false)); - Element simples = getSimple(name, element); - if (simples != null) { - try { - return outputter.outputString(simples); - } catch (Exception e) { - throw new MobyException(newline - + "Unexpected error occured while creating String[]:" - + newline + Utils.format(e.getLocalizedMessage(), 3)); - } - } - throw new MobyException(newline + "The simple named '" + name - + "' was not found in the xml:" + newline + xml + newline); - } - - /** - * This method assumes a single invocation was passed to it - * <p> - * - * @param name - * the article name of the simple that you are looking for - * @param element - * the Element that you want to query - * @return an Element that represents the simple found. - * @throws MobyException - * if no simple was found given the article name and/or data - * type or if the xml was not valid moby xml or if an unexpected - * error occurs. - */ - public static Element getSimple(String name, Element element) - throws MobyException { - Element el = (Element) element.clone(); - Element[] elements = getListOfSimples(el); - // try matching based on type(less impt) and/or article name (more impt) - for (int i = 0; i < elements.length; i++) { - // PRE: elements[i] is a fully wrapped element - Element e = elements[i]; - if (e.getChild("mobyContent") != null) { - e = e.getChild("mobyContent"); - } else if (e.getChild("mobyContent", MOBY_NS) != null) { - e = e.getChild("mobyContent", MOBY_NS); - } else { - throw new MobyException( - newline - + "Expected 'mobyContent' as the local name for the next child element but it " - + newline - + "wasn't there. I even tried a qualified name (getSimple(String name, " - + "Element element)."); - } - if (e.getChild("mobyData") != null) { - e = e.getChild("mobyData"); - } else if (e.getChild("mobyData", MOBY_NS) != null) { - e = e.getChild("mobyData", MOBY_NS); - } else { - throw new MobyException( - newline - + "Expected 'mobyData' as the local name for the next child element but it " - + newline - + "wasn't there. I even tried a qualified name (getSimple(String name," - + " Element element)."); - } - if (e.getChild("Simple") != null) { - e = e.getChild("Simple"); - } else if (e.getChild("Simple", MOBY_NS) != null) { - e = e.getChild("Simple", MOBY_NS); - } else { - throw new MobyException( - newline - + "Expected 'Simple' as the local name for the next child element but it " - + newline - + "wasn't there. I even tried a qualified name (getSimple(String name," - + " Element element)."); - } - // e == Simple -> check its name as long as name != "" - if (!name.equals("")) - if (e.getAttributeValue("articleName") != null) { - String value = e.getAttributeValue("articleName"); - if (value.equals(name)) { - return e; - } - } else if (e.getAttributeValue("articleName", MOBY_NS) != null) { - String value = e.getAttributeValue("articleName", MOBY_NS); - if (value.equals(name)) { - return e; - } - } - - } - throw new MobyException(newline - + "The simple named '" - + name - + "' was not found in the xml:" - + newline - + (new XMLOutputter(Format.getPrettyFormat() - .setOmitDeclaration(false))).outputString(element) - + newline); - } - - /** - * - * @param xml - * a string of xml containing a single invocation message to - * extract the queryID from - * @return the queryID contained in the xml or a generated one if one doesnt - * exist - * @throws MobyException - * if the String of xml is invalid or if the message is a - * multiple invocation message - */ - public static String getQueryID(String xml) throws MobyException { - return getQueryID(getDOMDocument(xml).getRootElement()); - } - - /** - * - * @param xml - * a single invocation message to extract the queryID from - * @return the queryID contained in the xml or a generated one if one doesnt - * exist - * @throws if - * the message is a multiple invocation message - */ - public static String getQueryID(Element xml) throws MobyException { - Element temp = (Element) xml.clone(); - Element e = (Element) xml.clone(); - - if (isMultipleInvocationMessage(e)) - throw new MobyException( - "Unable to retrieve the queryID from the BioMOBY message because a message with greater than one IDs exists."); - - if (!e.getName().equals("MOBY")) { - if (e.getChild("MOBY") != null) - temp = e.getChild("MOBY"); - else if (e.getChild("MOBY", MOBY_NS) != null) - temp = e.getChild("MOBY", MOBY_NS); - } - // parse the mobyContent node - if (temp.getChild("mobyContent") != null) - temp = temp.getChild("mobyContent"); - else if (temp.getChild("mobyContent", MOBY_NS) != null) - temp = temp.getChild("mobyContent", MOBY_NS); - - // parse the mobyData node - if (temp.getChild("mobyData") != null) { - temp = temp.getChild("mobyData"); - } else if (temp.getChild("mobyData", MOBY_NS) != null) { - temp = temp.getChild("mobyData", MOBY_NS); - } - - // temp == mobyData now we need to get the queryID and save it - if (temp.getAttribute("queryID") != null) { - return temp.getAttribute("queryID").getValue(); - } else if (temp.getAttribute("queryID", MOBY_NS) != null) { - return temp.getAttribute("queryID", MOBY_NS).getValue(); - } else { - // create a new one -> shouldnt happen very often - return "a" + queryCount++; - } - } - - /** - * - * @param xml - * a string of xml containing a single invocation message to - * extract the queryID from - * @return the element passed in to the method with the queryID set if the - * message was valid. - * @throws MobyException - * if the String of xml is syntatically invalid or if the - * message is a multiple invocation message - */ - public static String setQueryID(String xml, String id) throws MobyException { - return new XMLOutputter(Format.getPrettyFormat().setOmitDeclaration( - false)).outputString(setQueryID(getDOMDocument(xml) - .getRootElement(), id)); - } - - /** - * - * @param xml - * a single invocation message to extract the queryID from - * @return the element passed in to the method with the queryID set if the - * message was valid. - * @throws MobyException - * if the message is a multiple invocation message - */ - public static Element setQueryID(Element xml, String id) - throws MobyException { - Element e = (Element) xml.clone(); - Element temp = e; - if (isMultipleInvocationMessage(e)) - throw new MobyException( - "Unable to set the queryID, because there are more than one queryID to set!"); - if (!e.getName().equals("MOBY")) { - if (e.getChild("MOBY") != null) - temp = e.getChild("MOBY"); - else if (e.getChild("MOBY", MOBY_NS) != null) - temp = e.getChild("MOBY", MOBY_NS); - } - // parse the mobyContent node - if (temp.getChild("mobyContent") != null) - temp = temp.getChild("mobyContent"); - else if (temp.getChild("mobyContent", MOBY_NS) != null) - temp = temp.getChild("mobyContent", MOBY_NS); - - // parse the mobyData node - if (temp.getChild("mobyData") != null) { - temp = temp.getChild("mobyData"); - } else if (temp.getChild("mobyData", MOBY_NS) != null) { - temp = temp.getChild("mobyData", MOBY_NS); - } - - temp.removeAttribute("queryID"); - temp.removeAttribute("queryID", MOBY_NS); - temp.setAttribute("queryID", (id == null || id == "" ? "a" - + queryCount++ : id), MOBY_NS); - return e; - } - - /** - * - * @param name - * the articlename of the simple that you wish to extract - * @param xml - * the xml message - * @return the wrapped simple if it exists - * @throws MobyException - * if the message is a multiple invocation message or if the xml - * is syntatically invalid. - */ - public static String getWrappedSimple(String name, String xml) - throws MobyException { - Element element = getWrappedSimple(name, getDOMDocument(xml) - .getRootElement()); - XMLOutputter outputter = new XMLOutputter(Format.getPrettyFormat() - .setOmitDeclaration(false)); - return outputter.outputString(element); - } - - /** - * - * @param name - * the articlename of the simple that you wish to extract - * @param xml - * the xml message - * @return the wrapped simple if it exists - * @throws MobyException - * if the message is a multiple invocation message. - */ - public static Element getWrappedSimple(String name, Element element) - throws MobyException { - Element e = (Element) element.clone(); - String queryID = getQueryID(e); - Element serviceNotes = getServiceNotes(e); - Element simple = getSimple(name, e); - return createMobyDataElementWrapper(simple, queryID, serviceNotes); - } - - /** - * - * @param name - * the name of the collection to extract - * @param element - * the element to extract the collection from - * @return the collection if found - * @throws MobyException - * if the message is invalid - */ - public static Element getCollection(String name, Element element) - throws MobyException { - Element el = (Element) element.clone(); - Element[] elements = getListOfCollections(el); - for (int i = 0; i < elements.length; i++) { - // PRE: elements[i] is a fully wrapped element - Element e = elements[i]; - if (e.getChild("mobyContent") != null) { - e = e.getChild("mobyContent"); - } else if (e.getChild("mobyContent", MOBY_NS) != null) { - e = e.getChild("mobyContent", MOBY_NS); - } else { - throw new MobyException( - newline - + "Expected 'mobyContent' as the local name for the next child element but it " - + newline - + "wasn't there. I even tried a qualified name (getCollection(String name, " - + "Element element)."); - } - if (e.getChild("mobyData") != null) { - e = e.getChild("mobyData"); - } else if (e.getChild("mobyData", MOBY_NS) != null) { - e = e.getChild("mobyData", MOBY_NS); - } else { - throw new MobyException( - newline - + "Expected 'mobyData' as the local name for the next child element but it " - + newline - + "wasn't there. I even tried a qualified name (getCollection(String name," - + " Element element)."); - } - if (e.getChild("Collection") != null) { - e = e.getChild("Collection"); - } else if (e.getChild("Collection", MOBY_NS) != null) { - e = e.getChild("Collection", MOBY_NS); - } else { - // TODO should i throw exception or continue? - throw new MobyException( - newline - + "Expected 'Collection' as the local name for the next child element but it " - + newline - + "wasn't there. I even tried a qualified name (getCollection(String name," - + " Element element)."); - } - // e == collection -> check its name - if (e.getAttributeValue("articleName") != null) { - String value = e.getAttributeValue("articleName"); - if (value.equals(name)) { - return e; - } - } else if (e.getAttributeValue("articleName", MOBY_NS) != null) { - String value = e.getAttributeValue("articleName", MOBY_NS); - if (value.equals(name)) { - return e; - } - } - if (elements.length == 1) { - if (e.getAttributeValue("articleName") != null) { - String value = e.getAttributeValue("articleName"); - if (value.equals("")) { - // rename it to make it compatible with moby - e.setAttribute("articleName", name, MOBY_NS); - return e; - } - } else if (e.getAttributeValue("articleName", MOBY_NS) != null) { - String value = e.getAttributeValue("articleName", MOBY_NS); - if (value.equals("")) { - // rename it to make it compatible with moby - e.setAttribute("articleName", name, MOBY_NS); - return e; - } - } - } - // name didnt match, so too bad ;-) - } - throw new MobyException( - newline - + "The Collection named '" - + name - + "' was not found in the xml:" - + newline - + (new XMLOutputter(Format.getPrettyFormat() - .setOmitDeclaration(false))) - .outputString(element) - + newline - + "Note: A collection of that may exist, but may be contained in a multiple invocation message."); - } - - /** - * - * @param name - * @param xml - * @return - * @throws MobyException - */ - public static String getCollection(String name, String xml) - throws MobyException { - Element element = getDOMDocument(xml).getRootElement(); - XMLOutputter outputter = new XMLOutputter(Format.getPrettyFormat() - .setOmitDeclaration(false)); - Element collection = getCollection(name, element); - if (collection != null) - return outputter.outputString(collection); - return null; - } - - /** - * - * @param name - * @param element - * @return - * @throws MobyException - */ - public static Element getWrappedCollection(String name, Element element) - throws MobyException { - Element e = (Element) element.clone(); - String queryID = getQueryID(e); - Element collection = getCollection(name, e); - Element serviceNotes = getServiceNotes(e); - return createMobyDataElementWrapper(collection, queryID, serviceNotes); - } - - /** - * - * @param name - * @param xml - * @return - * @throws MobyException - */ - public static String getWrappedCollection(String name, String xml) - throws MobyException { - Element element = getWrappedCollection(name, getDOMDocument(xml) - .getRootElement()); - XMLOutputter outputter = new XMLOutputter(Format.getPrettyFormat() - .setOmitDeclaration(false)); - return outputter.outputString(element); - } - - /** - * - * @param name - * the name of the collection to extract the simples from. - * @param xml - * the XML to extract from - * @return an array of String objects that represent the simples - * @throws MobyException - */ - public static String[] getSimplesFromCollection(String name, String xml) - throws MobyException { - Element[] elements = getSimplesFromCollection(name, getDOMDocument(xml) - .getRootElement()); - String[] strings = new String[elements.length]; - XMLOutputter output = new XMLOutputter(Format.getPrettyFormat() - .setOmitDeclaration(false)); - for (int i = 0; i < elements.length; i++) { - try { - strings[i] = output.outputString(elements[i]); - } catch (Exception e) { - throw new MobyException(newline - + "Unknown error occured while creating String[]." - + newline + Utils.format(e.getLocalizedMessage(), 3)); - } - } - return strings; - } - - /** - * - * @param name - * the name of the collection to extract the simples from. - * @param element - * the Element to extract from - * @return an array of Elements objects that represent the simples - * @throws MobyException - */ - public static Element[] getSimplesFromCollection(String name, - Element element) throws MobyException { - Element e = (Element) element.clone(); - // exception thrown if not found - Element collection = getCollection(name, e); - - List list = collection.getChildren("Simple"); - if (list.isEmpty()) - list = collection.getChildren("Simple", MOBY_NS); - if (list.isEmpty()) - return new Element[] {}; - Vector vector = new Vector(); - for (Iterator it = list.iterator(); it.hasNext();) { - Object o = it.next(); - if (o instanceof Element) { - ((Element) o).setAttribute("articleName", name, MOBY_NS); - if (((Element) o).getChildren().size() > 0) - vector.add(o); - } - - } - Element[] elements = new Element[vector.size()]; - vector.copyInto(elements); - return elements; - } - - /** - * - * @param name - * the name of the simples that you would like to extract. The - * name can be collection name as well. This method extracts - * simples from all invocation messages. - * @param xml - * the xml to extract the simples from - * @return a String[] of Simples that you are looking for, taken from - * collections with your search name as well as simple elements with - * the search name - * @throws MobyException - * if there is a problem with the BioMOBY message - */ - public static String[] getAllSimplesByArticleName(String name, String xml) - throws MobyException { - Element[] elements = getAllSimplesByArticleName(name, getDOMDocument( - xml).getRootElement()); - String[] strings = new String[elements.length]; - XMLOutputter output = new XMLOutputter(Format.getPrettyFormat() - .setOmitDeclaration(false)); - for (int i = 0; i < elements.length; i++) { - try { - strings[i] = output.outputString(elements[i]); - } catch (Exception e) { - throw new MobyException(newline - + "Unknown error occured while creating String[]." - + newline + Utils.format(e.getLocalizedMessage(), 3)); - } - } - return strings; - } - - /** - * - * @param name - * the name of the simples that you would like to extract. The - * name can be collection name as well. This method extracts - * simples from all invocation messages. - * @param element - * the xml to extract the simples from - * @return a String[] of Simples that you are looking for, taken from - * collections with your search name as well as simple elements with - * the search name - * @throws MobyException - * if there is a problem with the BioMOBY message - */ - public static Element[] getAllSimplesByArticleName(String name, - Element element) throws MobyException { - Element e = (Element) element.clone(); - Element[] invocations = getSingleInvokationsFromMultipleInvokations(e); - Vector vector = new Vector(); - for (int i = 0; i < invocations.length; i++) { - Element collection = null; - try { - collection = getCollection(name, invocations[i]); - } catch (MobyException me) { - - } - if (collection != null) { - List list = collection.getChildren("Simple"); - if (list.isEmpty()) - list = collection.getChildren("Simple", MOBY_NS); - if (list.isEmpty()) - return new Element[] {}; - for (Iterator it = list.iterator(); it.hasNext();) { - Object o = it.next(); - if (o instanceof Element) { - ((Element) o) - .setAttribute("articleName", name, MOBY_NS); - } - vector.add(o); - } - } - collection = null; - - Element[] potentialSimples = getListOfSimples(invocations[i]); - for (int j = 0; j < potentialSimples.length; j++) { - Element mobyData = extractMobyData(potentialSimples[j]); - Element simple = mobyData.getChild("Simple"); - if (simple == null) - simple = mobyData.getChild("Simple", MOBY_NS); - if (simple != null) { - if (simple.getAttribute("articleName") != null) { - if (simple.getAttribute("articleName").getValue() - .equals(name)) - vector.add(simple); - } else if (simple.getAttribute("articleName", MOBY_NS) != null) { - if (simple.getAttribute("articleName", MOBY_NS) - .getValue().equals(name)) - vector.add(simple); - } - } - - } - } - - Element[] elements = new Element[vector.size()]; - vector.copyInto(elements); - return elements; - } - - /** - * - * @param xml - * the XML to extract from - * @return an array of String objects that represent the simples - * @throws MobyException - */ - public static String[] getSimplesFromCollection(String xml) - throws MobyException { - Element[] elements = getSimplesFromCollection(getDOMDocument(xml) - .getRootElement()); - String[] strings = new String[elements.length]; - XMLOutputter output = new XMLOutputter(Format.getPrettyFormat() - .setOmitDeclaration(false)); - for (int i = 0; i < elements.length; i++) { - try { - strings[i] = output.outputString(elements[i]); - } catch (Exception e) { - throw new MobyException(newline - + "Unknown error occured while creating String[]." - + newline + Utils.format(e.getLocalizedMessage(), 3)); - } - } - return strings; - } - - /** - * - * @param name - * the name of the collection to extract the simples from. - * @param element - * the Element to extract from - * @return an array of Elements objects that represent the 'unwrapped' - * simples - * @throws MobyException - */ - public static Element[] getSimplesFromCollection(Element element) - throws MobyException { - Element e = (Element) element.clone(); - Element mobyData = extractMobyData(e); - - Element collection = mobyData.getChild("Collection"); - if (collection == null) - collection = mobyData.getChild("Collection", MOBY_NS); - - List list = collection.getChildren("Simple"); - if (list.isEmpty()) - list = collection.getChildren("Simple", MOBY_NS); - if (list.isEmpty()) - return new Element[] {}; - Vector vector = new Vector(); - for (Iterator it = list.iterator(); it.hasNext();) { - vector.add(it.next()); - } - Element[] elements = new Element[vector.size()]; - vector.copyInto(elements); - return elements; - } - - /** - * - * @param name - * the name of the collection to extract the simples from. - * @param xml - * the XML to extract from - * @return an array of String objects that represent the simples, with the - * name of the collection - * @throws MobyException - * if the collection doesnt exist or the xml is invalid - */ - public static String[] getWrappedSimplesFromCollection(String name, - String xml) throws MobyException { - Element[] elements = getWrappedSimplesFromCollection(name, - getDOMDocument(xml).getRootElement()); - String[] strings = new String[elements.length]; - XMLOutputter output = new XMLOutputter(Format.getPrettyFormat() - .setOmitDeclaration(false)); - for (int i = 0; i < elements.length; i++) { - try { - strings[i] = output.outputString(elements[i]); - } catch (Exception e) { - throw new MobyException(newline - + "Unknown error occured while creating String[]." - + newline + Utils.format(e.getLocalizedMessage(), 3)); - } - } - return strings; - } - - /** - * - * @param name - * the name of the collection to extract the simples from. - * @param element - * the Element to extract from - * @return an array of Elements objects that represent the simples, with the - * name of the collection - * @throws MobyException - * MobyException if the collection doesnt exist or the xml is - * invalid - */ - public static Element[] getWrappedSimplesFromCollection(String name, - Element element) throws MobyException { - Element el = (Element) element.clone(); - String queryID = getQueryID(el); - Element collection = getCollection(name, el); - Element serviceNotes = getServiceNotes(el); - List list = collection.getChildren("Simple"); - if (list.isEmpty()) - list = collection.getChildren("Simple", MOBY_NS); - if (list.isEmpty()) - return new Element[] {}; - Vector vector = new Vector(); - for (Iterator it = list.iterator(); it.hasNext();) { - Element e = (Element) it.next(); - e.setAttribute("articleName", name, MOBY_NS); - e = createMobyDataElementWrapper(e, queryID + "_split" - + queryCount++, serviceNotes); - vector.add(e); - } - Element[] elements = new Element[vector.size()]; - vector.copyInto(elements); - return elements; - } - - /** - * - * @param xml - * the message to extract the invocation messages from - * @return an array of String objects each representing a distinct BioMOBY - * invocation message. - * @throws MobyException - * if the moby message is invalid or if the xml is syntatically - * invalid. - */ - public static String[] getSingleInvokationsFromMultipleInvokations( - String xml) throws MobyException { - Element[] elements = getSingleInvokationsFromMultipleInvokations(getDOMDocument( - xml).getRootElement()); - String[] strings = new String[elements.length]; - XMLOutputter output = new XMLOutputter(Format.getPrettyFormat() - .setOmitDeclaration(false)); - - for (int i = 0; i < elements.length; i++) { - strings[i] = output.outputString(new Document(elements[i])); - } - return strings; - } - - /** - * - * @param element - * the message to extract the invocation messages from - * @return an array of Element objects each representing a distinct - * invocation message. - * @throws MobyException - * if the moby message is invalid. - */ - public static Element[] getSingleInvokationsFromMultipleInvokations( - Element element) throws MobyException { - Element e = (Element) element.clone(); - Element serviceNotes = getServiceNotes(e); - if (e.getChild("MOBY") != null) { - e = e.getChild("MOBY"); - } else if (e.getChild("MOBY", MOBY_NS) != null) { - e = e.getChild("MOBY", MOBY_NS); - } - - if (e.getChild("mobyContent") != null) { - e = e.getChild("mobyContent"); - } else if (e.getChild("mobyContent", MOBY_NS) != null) { - e = e.getChild("mobyContent", MOBY_NS); - } else { - throw new MobyException( - newline - + "Expected a child element called 'mobyContent' and did not receive it in:" - + newline - + new XMLOutputter(Format.getPrettyFormat() - .setOmitDeclaration(false)).outputString(e)); - } - List invocations = e.getChildren("mobyData"); - if (invocations.isEmpty()) - invocations = e.getChildren("mobyData", MOBY_NS); - Element[] elements = new Element[] {}; - ArrayList theData = new ArrayList(); - for (Iterator it = invocations.iterator(); it.hasNext();) { - Element MOBY = new Element("MOBY", MOBY_NS); - Element mobyContent = new Element("mobyContent", MOBY_NS); - if (serviceNotes != null) - mobyContent.addContent(serviceNotes.detach()); - Element mobyData = new Element("mobyData", MOBY_NS); - Element next = (Element) it.next(); - String queryID = next.getAttributeValue("queryID", MOBY_NS); - if (queryID == null) - queryID = next.getAttributeValue("queryID"); - - mobyData.setAttribute("queryID", (queryID == null ? "a"+queryCount++ : queryID), MOBY_NS); - mobyData.addContent(next.cloneContent()); - MOBY.addContent(mobyContent); - mobyContent.addContent(mobyData); - if (next.getChildren().size() > 0) - theData.add(MOBY); - } - elements = new Element[theData.size()]; - elements = (Element[]) theData.toArray(elements); - return elements; - } - - /** - * - * @param document - * the string to create a DOM document from - * @return a Document object that represents the string of XML. - * @throws MobyException - * if the xml is invalid syntatically. - */ - public static Document getDOMDocument(String document) throws MobyException { - if (document == null) - throw new MobyException(newline - + "null found where an XML document was expected."); - SAXBuilder builder = new SAXBuilder(); - // Create the document - Document doc = null; - try { - doc = builder.build(new StringReader(document)); - } catch (JDOMException e) { - throw new MobyException(newline + "Error parsing XML:->" + newline - + document + newline - + Utils.format(e.getLocalizedMessage(), 3) + "."); - } catch (IOException e) { - throw new MobyException(newline + "Error parsing XML:->" + newline - + Utils.format(e.getLocalizedMessage(), 3) + "."); - } catch (Exception e) { - throw new MobyException(newline + "Error parsing XML:->" + newline - + Utils.format(e.getLocalizedMessage(), 3) + "."); - } - return doc; - } - - /** - * - * @param elements - * the fully wrapped moby simples and/or collections to wrap an - * input message around - * @param queryID - * the queryID for this input - * @return a fully wrapped message with an appropriate queryID and elements - * added to it - * @throws MobyException - * if an element is invalid or if the XML is syntatically - * invalid. - */ - public static String createServiceInput(String[] elements, String queryID) - throws MobyException { - Element[] element = new Element[elements.length]; - for (int i = 0; i < elements.length; i++) { - element[i] = getDOMDocument(elements[i]).getRootElement(); - } - XMLOutputter output = new XMLOutputter(Format.getPrettyFormat() - .setOmitDeclaration(false)); - return output.outputString(createServiceInput(element, queryID)); - } - - /** - * - * @param elements - * the fully wrapped moby simples and/or collections to wrap an - * input message around - * @param queryID - * the queryID for this input - * @return a fully wrapped message with an appropriate queryID and elements - * added to it - * @throws MobyException - * if an element is invalid. - */ - public static Element createServiceInput(Element[] elements, String queryID) - throws MobyException { - // create the main elements - Element MOBY = new Element("MOBY", MOBY_NS); - Element mobyContent = new Element("mobyContent", MOBY_NS); - Element mobyData = new Element("mobyData", MOBY_NS); - mobyData.setAttribute("queryID", (queryID == null ? "" : queryID), - MOBY_NS); - - // add the content - MOBY.addContent(mobyContent); - mobyContent.addContent(mobyData); - - // iterate through elements adding the content of mobyData - for (int i = 0; i < elements.length; i++) { - Element e = (Element) elements[i].clone(); - e = extractMobyData(e); - mobyData.addContent(e.cloneContent()); - } - - return MOBY; - } - - /** - * @param element - * the element that contains the moby message that you would like - * to extract the mobyData block from (assumes single invocation, - * but returns the first mobyData block in a multiple invocation - * message). - * @return the mobyData element block. - * @throws MobyException - * if the moby message is invalid - */ - public static Element extractMobyData(Element element) throws MobyException { - Element e = (Element) element.clone(); - if (e.getChild("MOBY") != null) { - e = e.getChild("MOBY"); - } else if (e.getChild("MOBY", MOBY_NS) != null) { - e = e.getChild("MOBY", MOBY_NS); - } - - if (e.getChild("mobyContent") != null) { - e = e.getChild("mobyContent"); - } else if (e.getChild("mobyContent", MOBY_NS) != null) { - e = e.getChild("mobyContent", MOBY_NS); - } else { - throw new MobyException( - newline - + "Expected the child element 'mobyContent' and did not receive it in:" - + newline - + new XMLOutputter(Format.getPrettyFormat() - .setOmitDeclaration(false)).outputString(e)); - } - - if (e.getChild("mobyData") != null) { - e = e.getChild("mobyData"); - } else if (e.getChild("mobyData", MOBY_NS) != null) { - e = e.getChild("mobyData", MOBY_NS); - } else { - throw new MobyException( - newline - + "Expected the child element 'mobyData' and did not receive it in:" - + newline - + new XMLOutputter(Format.getPrettyFormat() - .setOmitDeclaration(false)).outputString(e)); - } - return e; - } - - /** - * - * @param newName - * the new name for this fully wrapped BioMOBY collection - * @param element - * the fully wrapped BioMOBY collection - * @return @return an element 'Collection' representing the renamed collection - * @throws MobyException - * if the message is invalid - */ - public static Element renameCollection(String newName, Element element) - throws MobyException { - Element e = (Element) element.clone(); - Element mobyData = extractMobyData(e); - Element coll = mobyData.getChild("Collection"); - if (coll == null) - coll = mobyData.getChild("Collection", MOBY_NS); - if (coll == null) - return e; - coll.removeAttribute("articleName"); - coll.removeAttribute("articleName", MOBY_NS); - coll.setAttribute("articleName", newName, MOBY_NS); - return coll; - } - - /** - * - * @param newName - * the new name for this fully wrapped BioMOBY collection - * @param xml - * the fully wrapped BioMOBY collection - * @return an element 'Collection' representing the renamed collection - * @throws MobyException - * if the BioMOBY message is invalid or the xml is syntatically - * invalid. - */ - public static String renameCollection(String newName, String xml) - throws MobyException { - return new XMLOutputter(Format.getPrettyFormat().setOmitDeclaration( - false)).outputString(renameCollection(newName, getDOMDocument( - xml).getRootElement())); - } - - /** - * - * @param oldName - * @param newName - * @param type - * @param xml - * @return - * @throws MobyException - */ - public static String renameSimple(String newName, String type, String xml) - throws MobyException { - return new XMLOutputter(Format.getPrettyFormat().setOmitDeclaration( - false)).outputString(renameSimple(newName, type, - getDOMDocument(xml).getRootElement())); - } - - /** - * - * @param oldName - * @param newName - * @param type - * @param element - * @return - * @throws MobyException - */ - public static Element renameSimple(String newName, String type, - Element element) throws MobyException { - Element e = (Element) element.clone(); - Element mobyData = extractMobyData(e); - String queryID = getQueryID(e); - Element serviceNotes = getServiceNotes(e); - Element simple = mobyData.getChild("Simple"); - if (simple == null) - simple = mobyData.getChild("Simple", MOBY_NS); - if (simple == null) { - return e; - } - simple.removeAttribute("articleName"); - simple.removeAttribute("articleName", MOBY_NS); - simple.setAttribute("articleName", newName, MOBY_NS); - return createMobyDataElementWrapper(simple, queryID, serviceNotes); - } - - /** - * - * @return - * @throws MobyException - */ - public static Document createDomDocument() throws MobyException { - Document d = new Document(); - d.setBaseURI(MOBY_NS.getURI()); - return d; - } - - /** - * - * @param element - * @param queryID - * @param serviceNotes - * @return - * @throws MobyException - */ - public static Element createMobyDataElementWrapper(Element element, - String queryID, Element serviceNotes) throws MobyException { - Element e = (Element) element.clone(); - Element MOBY = new Element("MOBY", MOBY_NS); - Element mobyContent = new Element("mobyContent", MOBY_NS); - Element mobyData = new Element("mobyData", MOBY_NS); - mobyData.setAttribute("queryID", queryID, MOBY_NS); - MOBY.addContent(mobyContent); - mobyContent.addContent(mobyData); - // add the serviceNotes if they exist - if (serviceNotes != null) - mobyContent.addContent(serviceNotes.detach()); - - if (e != null) { - if (e.getName().equals("Simple")) { - Element simple = new Element("Simple", MOBY_NS); - simple.setAttribute("articleName", (e - .getAttributeValue("articleName") == null ? e - .getAttributeValue("articleName", MOBY_NS, "") : e - .getAttributeValue("articleName", "")), MOBY_NS); - simple.addContent(e.cloneContent()); - if (simple.getChildren().size() > 0) - mobyData.addContent(simple.detach()); - } else if (e.getName().equals("Collection")) { - Element collection = new Element("Collection", MOBY_NS); - collection.setAttribute("articleName", (e - .getAttributeValue("articleName") == null ? e - .getAttributeValue("articleName", MOBY_NS, "") : e - .getAttributeValue("articleName", "")), MOBY_NS); - collection.addContent(e.cloneContent()); - if (collection.getChildren().size() > 0) - mobyData.addContent(collection.detach()); - } - } - - return MOBY; - } - - public static Element createMobyDataWrapper(String queryID, - Element serviceNotes) throws MobyException { - - Element e = null; - - if (serviceNotes != null) - e = (Element) serviceNotes.clone(); - - Element MOBY = new Element("MOBY", MOBY_NS); - Element mobyContent = new Element("mobyContent", MOBY_NS); - if (e != null) - mobyContent.addContent(e.detach()); - Element mobyData = new Element("mobyData", MOBY_NS); - mobyData.setAttribute("queryID", queryID, MOBY_NS); - MOBY.addContent(mobyContent); - mobyContent.addContent(mobyData); - return MOBY; - } - - /** - * - * @param xml - * @return - * @throws MobyException - */ - public static String createMobyDataElementWrapper(String xml) - throws MobyException { - return createMobyDataElementWrapper(xml, "a" + queryCount++); - } - - /** - * - * @param element - * @return - * @throws MobyException - */ - public static Element createMobyDataElementWrapper(Element element) - throws MobyException { - Element serviceNotes = getServiceNotes((Element) element.clone()); - return createMobyDataElementWrapper(element, "a" + queryCount++, - serviceNotes); - } - - /** - * - * @param xml - * @param queryID - * @return - * @throws MobyException - */ - public static String createMobyDataElementWrapper(String xml, String queryID) - throws MobyException { - if (xml == null) - return null; - Element serviceNotes = getServiceNotes(getDOMDocument(xml) - .getRootElement()); - Element element = createMobyDataElementWrapper(getDOMDocument(xml) - .getRootElement(), queryID, serviceNotes); - XMLOutputter outputter = new XMLOutputter(Format.getPrettyFormat() - .setOmitDeclaration(false)); - return (element == null ? null : outputter.outputString(element)); - } - - public static String createMobyDataElementWrapper(String xml, - String queryID, Element serviceNotes) throws MobyException { - if (xml == null) - return null; - Element element = createMobyDataElementWrapper(getDOMDocument(xml) - .getRootElement(), queryID, serviceNotes); - XMLOutputter outputter = new XMLOutputter(Format.getPrettyFormat() - .setOmitDeclaration(false)); - return (element == null ? null : outputter.outputString(element)); - } - - /** - * - * @param elements - * @return - * @throws MobyException - */ - public static Element createMultipleInvokations(Element[] elements) - throws MobyException { - Element MOBY = new Element("MOBY", MOBY_NS); - Element mobyContent = new Element("mobyContent", MOBY_NS); - Element serviceNotes = null; - for (int i = 0; i < elements.length; i++) { - if (serviceNotes == null) { - serviceNotes = getServiceNotes((Element) elements[i].clone()); - if (serviceNotes != null) - mobyContent.addContent(serviceNotes.detach()); - } - Element mobyData = new Element("mobyData", MOBY_NS); - Element md = extractMobyData((Element) elements[i].clone()); - String queryID = getQueryID((Element) elements[i].clone()); - mobyData.setAttribute("queryID", queryID, MOBY_NS); - mobyData.addContent(md.cloneContent()); - mobyContent.addContent(mobyData); - } - MOBY.addContent(mobyContent); - - return MOBY; - } - - /** - * - * @param xmls - * @return - * @throws MobyException - */ - public static String createMultipleInvokations(String[] xmls) - throws MobyException { - Element[] elements = new Element[xmls.length]; - for (int i = 0; i < elements.length; i++) { - elements[i] = getDOMDocument(xmls[i]).getRootElement(); - } - XMLOutputter output = new XMLOutputter(Format.getPrettyFormat() - .setOmitDeclaration(false)); - return output.outputString(createMultipleInvokations(elements)); - } - - /** - * - * @param xml - * a string of xml - * @return true if the xml contains a full moby message (assumes single - * invocation, but will return the first mobyData block from a - * multiple invocation message). - */ - public static boolean isWrapped(Element element) { - try { - extractMobyData((Element) element.clone()); - return true; - } catch (MobyException e) { - return false; - } - } - - /** - * - * @param xml - * a string of xml - * @return true if the xml contains a full moby message (assumes single - * invocation, but will return the first mobyData block from a - * multiple invocation message). - * @throws MobyException - * if the xml is syntatically invalid - */ - public static boolean isWrapped(String xml) throws MobyException { - Element element = getDOMDocument(xml).getRootElement(); - return isWrapped(element); - } - - /** - * - * @param element - * an Element containing a single invocation - * @return true if the element contains a moby collection, false otherwise. - * @throws MobyException - * if xml is invalid - */ - public static boolean isCollection(Element element) throws MobyException { - try { - return getListOfCollections((Element) element.clone()).length > 0; - - } catch (MobyException e) { - return false; - } - } - - /** - * - * @param xml - * a string of xml containing a single invocation - * @return true if the xml contains a moby collection, false otherwise. - * @throws MobyException - * if xml is invalid - */ - public static boolean isCollection(String xml) throws MobyException { - Element element = getDOMDocument(xml).getRootElement(); - return isCollection(element); - } - - /** - * - * @param xml - * a string of xml to check for emptiness - * @return true if the element is empty, false otherwise. - */ - public static boolean isEmpty(String xml) { - try { - return isEmpty(getDOMDocument(xml).getRootElement()); - } catch (MobyException e) { - return true; - } - } - - /** - * - * @param xml - * an element to check for emptiness - * @return true if the element is empty, false otherwise. - */ - public static boolean isEmpty(Element xml) { - try { - Element e = extractMobyData((Element) xml.clone()); - if (e.getChild("Collection") != null) - return false; - if (e.getChild("Collection", MOBY_NS) != null) - return false; - if (e.getChild("Simple") != null) - return false; - if (e.getChild("Simple", MOBY_NS) != null) - return false; - } catch (MobyException e) { - } - return true; - - } - - /** - * - * @param theList - * a list of Elements that represent collections (wrapped in a - * MobyData tag - * @param name - * the name to set for the collection - * @return a list containing a single wrapped collection Element that contains all - * of the simples in the collections in theList - * @throws MobyException - * - */ - public static List mergeCollections(List theList, String name) - throws MobyException { - if (theList == null) - return new ArrayList(); - Element mainCollection = new Element("Collection", MOBY_NS); - mainCollection.setAttribute("articleName", name, MOBY_NS); - String queryID = ""; - for (Iterator iter = theList.iterator(); iter.hasNext();) { - Element mobyData = (Element) iter.next(); - queryID = getQueryID(mobyData); - Element collection = mobyData.getChild("Collection"); - if (collection == null) - collection = mobyData.getChild("Collection", MOBY_NS); - if (collection == null) - continue; - mainCollection.addContent(collection.cloneContent()); - } - theList = new ArrayList(); - theList - .add((createMobyDataElementWrapper(mainCollection, queryID, - null))); - return theList; - } - - /** - * - * @param element - * a full moby message (root element called MOBY) and may be - * prefixed - * @return the serviceNotes element if it exists, null otherwise. - */ - public static Element getServiceNotes(Element element) { - Element serviceNotes = null; - Element e = (Element) element.clone(); - Element mobyContent = e.getChild("mobyContent"); - if (mobyContent == null) - mobyContent = e.getChild("mobyContent", MOBY_NS); - - // should throw exception? - if (mobyContent == null) - return serviceNotes; - - serviceNotes = mobyContent.getChild("serviceNotes"); - if (serviceNotes == null) - serviceNotes = mobyContent.getChild("serviceNotes", MOBY_NS); - // note: servicenotes may be null - return serviceNotes; - } - - /** - * - * @param xml - * a full moby message (root element called MOBY) and may be - * prefixed - * @return the serviceNotes element as a string if it exists, null - * otherwise. - */ - public static String getServiceNotes(String xml) { - try { - Element e = getServiceNotes(getDOMDocument(xml).getRootElement()); - if (e == null) - return null; - XMLOutputter out = new XMLOutputter(Format.getPrettyFormat() - .setOmitDeclaration(false)); - return out.outputString(e); - } catch (MobyException ex) { - return null; - } - } - - /** - * - * @param xml - * a full moby message (root element called MOBY) and may be - * prefixed - * @return the serviceNotes element if it exists, null otherwise. - */ - public static Element getServiceNotesAsElement(String xml) { - try { - Element e = getServiceNotes(getDOMDocument(xml).getRootElement()); - return e; - } catch (MobyException ex) { - return null; - } - } - - /** - * - * @param element - * the xml element - * @param articleName - * the name of the child to extract - * @return an element that represents the direct child or null if it wasnt - * found. - */ - public static Element getDirectChildByArticleName(Element element, - String articleName) { - Element e = (Element) element.clone(); - List list = e.getChildren(); - for (Iterator iter = list.iterator(); iter.hasNext();) { - Object object = iter.next(); - if (object instanceof Element) { - Element child = (Element) object; - if (child.getAttributeValue("articleName") != null) { - if (child.getAttributeValue("articleName").equals( - articleName)) - return child; - } else if (child.getAttributeValue("articleName", MOBY_NS) != null) { - if (child.getAttributeValue("articleName", MOBY_NS).equals( - articleName)) { - return child; - } - } - } - - } - return null; - - } - - /** - * - * @param xml - * the string of xml - * @param articleName - * the name of the child to extract - * @return an xml string that represents the direct child or null if it - * wasnt found. - */ - public static String getDirectChildByArticleName(String xml, - String articleName) { - try { - Element e = getDirectChildByArticleName(getDOMDocument(xml) - .getRootElement(), articleName); - if (e == null) - return null; - XMLOutputter out = new XMLOutputter(Format.getPrettyFormat() - .setOmitDeclaration(false)); - return out.outputString(e); - } catch (MobyException me) { - return null; - } - } - - /** - * - * @param xml - * the xml message to test whether or not there is stuff in the - * mobyData portion of a message. - * @return true if there is data, false otherwise. - */ - public static boolean isThereData(Element xml) { - Element e = null; - e = (Element) xml.clone(); - try { - e = extractMobyData(e); - if (e.getChildren().size() > 0) { - // make sure we dont have empty collections or simples - if (e.getChild("Collection") != null) { - return e.getChild("Collection").getChildren().size() > 0; - } - if (e.getChild("Collection", MOBY_NS) != null) { - return e.getChild("Collection", MOBY_NS).getChildren() - .size() > 0; - } - if (e.getChild("Simple") != null) { - return e.getChild("Simple").getChildren().size() > 0; - } - if (e.getChild("Simple", MOBY_NS) != null) { - return e.getChild("Simple", MOBY_NS).getChildren().size() > 0; - } - return false; - } - } catch (MobyException e1) { - return false; - } - return false; - } - - /** - * - * @param xml - * the xml message to test whether or not there is stuff in the - * mobyData portion of a message. - * @return true if there is data, false otherwise. - */ - public static boolean isThereData(String xml) { - try { - return isThereData(getDOMDocument(xml).getRootElement()); - } catch (Exception e) { - return false; - } - } - - public static void main(String[] args) throws MobyException { - String msg = "<moby:MOBY xmlns:moby=\"http://www.biomoby.org/moby\";>\r\n" - + " <moby:mobyContent>\r\n" - + " <moby:mobyData moby:queryID=\"a2_+_s65_+_s165_+_s1290_a2_+_s65_+_s165_+_s1290_+_s1408_a0_+_s3_+_s1409\">\r\n" - + " <moby:Collection moby:articleName=\"alleles\">\r\n" - + " <moby:Simple>\r\n" - + " <Object xmlns=\"http://www.biomoby.org/moby\"; namespace=\"DragonDB_Allele\" id=\"def-101\" />\r\n" - + " </moby:Simple>\r\n" - + " <moby:Simple>\r\n" - + " <Object xmlns=\"http://www.biomoby.org/moby\"; namespace=\"DragonDB_Allele\" id=\"def-chl\" />\r\n" - + " </moby:Simple>\r\n" - + " <moby:Simple>\r\n" - + " <Object xmlns=\"http://www.biomoby.org/moby\"; namespace=\"DragonDB_Allele\" id=\"def-gli\" />\r\n" - + " </moby:Simple>\r\n" - + " <moby:Simple>\r\n" - + " <Object xmlns=\"http://www.biomoby.org/moby\"; namespace=\"DragonDB_Allele\" id=\"def-nic\" />\r\n" - + " </moby:Simple>\r\n" - + " <moby:Simple>\r\n" - + " <Object xmlns=\"http://www.biomoby.org/moby\"; namespace=\"DragonDB_Allele\" id=\"def-23\" />\r\n" - + " </moby:Simple>\r\n" - + " </moby:Collection>\r\n" - + " </moby:mobyData>\r\n" - + " </moby:mobyContent>\r\n" - + "</moby:MOBY>"; - Element inputElement = getDOMDocument(msg).getRootElement(); - String queryID = XMLUtilities.getQueryID(inputElement); - Element[] simples = XMLUtilities.getSimplesFromCollection(inputElement); - - ArrayList list = new ArrayList(); - for (int j = 0; j < simples.length; j++) { - Element wrappedSimple = XMLUtilities - .createMobyDataElementWrapper(simples[j]); - wrappedSimple = XMLUtilities.renameSimple("Allele", "Object", - wrappedSimple); - wrappedSimple = XMLUtilities.setQueryID(wrappedSimple, queryID - + "_+_" + XMLUtilities.getQueryID(wrappedSimple)); - list.add(XMLUtilities.extractMobyData(wrappedSimple)); - } - } - - /* - * - * @param current the Element that you would like to search @param name the - * name of the element that you would like to find @param list the list to - * put the elements that are found in @return a list containing the elements - * that are named name - */ - private static List listChildren(Element current, String name, List list) { - if (list == null) - list = new ArrayList(); - if (current.getName().equals(name)) - list.add(current); - List children = current.getChildren(); - Iterator iterator = children.iterator(); - while (iterator.hasNext()) { - Element child = (Element) iterator.next(); - if (child instanceof Element) - listChildren(child, name, list); - } - return list; - } - - /** - * - * @param collectionName - * the name you would like the collection to be called - * @param simples2makeCollection - * the list of Elements to merge into a collection - * @return null if a collection wasnt made, otherwise a fully wrapped - * collection is returned. - * @throws MobyException - */ - public static Element createCollectionFromListOfSimples( - String collectionName, List<Element> simples2makeCollection) - throws MobyException { - if (simples2makeCollection.size() > 0) { - // create a collection from the list of - // simples - Element mimCollection = new Element("Collection", - XMLUtilities.MOBY_NS); - for (Element simple : simples2makeCollection) { - Element theSimple = XMLUtilities.extractMobyData(simple); - if (theSimple.getChild("Simple") != null) - theSimple = theSimple.getChild("Simple"); - else if (theSimple.getChild("Simple", XMLUtilities.MOBY_NS) != null) - theSimple = theSimple.getChild("Simple", - XMLUtilities.MOBY_NS); - mimCollection.addContent(theSimple.detach()); - } - String mimQueryID = "merged_" + queryCount++; - - mimCollection = XMLUtilities.createMobyDataElementWrapper( - mimCollection, mimQueryID, null); - mimCollection = XMLUtilities.renameCollection(collectionName, - mimCollection); - mimCollection = XMLUtilities.createMobyDataElementWrapper( - mimCollection, mimQueryID, null); - return mimCollection; - } - return null; - } -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity/src/main/resources/META-INF/services/net.sf.taverna.t2.workflowmodel.health.HealthChecker ---------------------------------------------------------------------- diff --git a/taverna-biomoby-activity/src/main/resources/META-INF/services/net.sf.taverna.t2.workflowmodel.health.HealthChecker b/taverna-biomoby-activity/src/main/resources/META-INF/services/net.sf.taverna.t2.workflowmodel.health.HealthChecker deleted file mode 100644 index 7d50ca3..0000000 --- a/taverna-biomoby-activity/src/main/resources/META-INF/services/net.sf.taverna.t2.workflowmodel.health.HealthChecker +++ /dev/null @@ -1,3 +0,0 @@ -net.sf.taverna.t2.activities.biomoby.BiomobyActivityHealthChecker -net.sf.taverna.t2.activities.biomoby.BiomobyObjectActivityHealthChecker -net.sf.taverna.t2.activities.biomoby.MobyParseDatatypeActivityHealthChecker \ No newline at end of file http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity/src/main/resources/META-INF/spring/biomoby-activity-context-osgi.xml ---------------------------------------------------------------------- diff --git a/taverna-biomoby-activity/src/main/resources/META-INF/spring/biomoby-activity-context-osgi.xml b/taverna-biomoby-activity/src/main/resources/META-INF/spring/biomoby-activity-context-osgi.xml deleted file mode 100644 index 449a31e..0000000 --- a/taverna-biomoby-activity/src/main/resources/META-INF/spring/biomoby-activity-context-osgi.xml +++ /dev/null @@ -1,17 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<beans:beans xmlns="http://www.springframework.org/schema/osgi"; xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"; - xmlns:beans="http://www.springframework.org/schema/beans"; - xsi:schemaLocation="http://www.springframework.org/schema/beans - http://www.springframework.org/schema/beans/spring-beans.xsd - http://www.springframework.org/schema/osgi - http://www.springframework.org/schema/osgi/spring-osgi.xsd";> - - <service ref="biomobyActivityHealthChecker" interface="net.sf.taverna.t2.workflowmodel.health.HealthChecker" /> - <service ref="biomobyObjectActivityHealthChecker" interface="net.sf.taverna.t2.workflowmodel.health.HealthChecker" /> - <service ref="mobyParseDatatypeActivityHealthChecker" interface="net.sf.taverna.t2.workflowmodel.health.HealthChecker" /> - - <service ref="biomobyActivityFactory" interface="net.sf.taverna.t2.workflowmodel.processor.activity.ActivityFactory" /> - <service ref="biomobyObjectActivityFactory" interface="net.sf.taverna.t2.workflowmodel.processor.activity.ActivityFactory" /> - <service ref="mobyParseDatatypeActivityFactory" interface="net.sf.taverna.t2.workflowmodel.processor.activity.ActivityFactory" /> - -</beans:beans> http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity/src/main/resources/META-INF/spring/biomoby-activity-context.xml ---------------------------------------------------------------------- diff --git a/taverna-biomoby-activity/src/main/resources/META-INF/spring/biomoby-activity-context.xml b/taverna-biomoby-activity/src/main/resources/META-INF/spring/biomoby-activity-context.xml deleted file mode 100644 index 3fbeaaf..0000000 --- a/taverna-biomoby-activity/src/main/resources/META-INF/spring/biomoby-activity-context.xml +++ /dev/null @@ -1,14 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<beans xmlns="http://www.springframework.org/schema/beans"; xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"; - xsi:schemaLocation="http://www.springframework.org/schema/beans - http://www.springframework.org/schema/beans/spring-beans.xsd";> - - <bean id="biomobyActivityHealthChecker" class="net.sf.taverna.t2.activities.biomoby.BiomobyActivityHealthChecker" /> - <bean id="biomobyObjectActivityHealthChecker" class="net.sf.taverna.t2.activities.biomoby.BiomobyObjectActivityHealthChecker" /> - <bean id="mobyParseDatatypeActivityHealthChecker" class="net.sf.taverna.t2.activities.biomoby.MobyParseDatatypeActivityHealthChecker" /> - - <bean id="biomobyActivityFactory" class="net.sf.taverna.t2.activities.biomoby.BiomobyActivityFactory" /> - <bean id="biomobyObjectActivityFactory" class="net.sf.taverna.t2.activities.biomoby.BiomobyObjectActivityFactory" /> - <bean id="mobyParseDatatypeActivityFactory" class="net.sf.taverna.t2.activities.biomoby.MobyParseDatatypeActivityFactory" /> - -</beans> http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity/src/test/java/net/sf/taverna/t2/activities/biomoby/BiomobyActivityHealthCheckerTest.java ---------------------------------------------------------------------- diff --git a/taverna-biomoby-activity/src/test/java/net/sf/taverna/t2/activities/biomoby/BiomobyActivityHealthCheckerTest.java b/taverna-biomoby-activity/src/test/java/net/sf/taverna/t2/activities/biomoby/BiomobyActivityHealthCheckerTest.java deleted file mode 100644 index 504fdc6..0000000 --- a/taverna-biomoby-activity/src/test/java/net/sf/taverna/t2/activities/biomoby/BiomobyActivityHealthCheckerTest.java +++ /dev/null @@ -1,45 +0,0 @@ -/******************************************************************************* - * This file is a component of the Taverna project, and is licensed under the - * GNU LGPL. Copyright Edward Kawas, The BioMoby Project - ******************************************************************************/ -package net.sf.taverna.t2.activities.biomoby; - -import static org.junit.Assert.assertFalse; -import static org.junit.Assert.assertTrue; -import net.sf.taverna.t2.workflowmodel.processor.activity.AbstractActivity; -import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityConfigurationException; - -import org.junit.Before; -import org.junit.Test; - -/** - * Unit tests for BiomobyActivityHealthChecker. - * - */ -public class BiomobyActivityHealthCheckerTest { - - private BiomobyActivity activity; - - private BiomobyActivityHealthChecker activityHealthChecker; - - @Before - public void setUp() throws Exception { - activity = new BiomobyActivity(); - activityHealthChecker = new BiomobyActivityHealthChecker(); - } - - @Test - public void testCanHandle() { - assertFalse(activityHealthChecker.canVisit(null)); - assertFalse(activityHealthChecker.canVisit(new Object())); - assertFalse(activityHealthChecker.canVisit(new AbstractActivity<Object>() { - public void configure(Object conf) throws ActivityConfigurationException { - } - public Object getConfiguration() { - return null; - } - })); - assertTrue(activityHealthChecker.canVisit(activity)); - } - -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity/src/test/java/net/sf/taverna/t2/activities/biomoby/BiomobyObjectActivityHealthCheckerTest.java ---------------------------------------------------------------------- diff --git a/taverna-biomoby-activity/src/test/java/net/sf/taverna/t2/activities/biomoby/BiomobyObjectActivityHealthCheckerTest.java b/taverna-biomoby-activity/src/test/java/net/sf/taverna/t2/activities/biomoby/BiomobyObjectActivityHealthCheckerTest.java deleted file mode 100644 index 403d744..0000000 --- a/taverna-biomoby-activity/src/test/java/net/sf/taverna/t2/activities/biomoby/BiomobyObjectActivityHealthCheckerTest.java +++ /dev/null @@ -1,45 +0,0 @@ -/******************************************************************************* - * This file is a component of the Taverna project, and is licensed under the - * GNU LGPL. Copyright Edward Kawas, The BioMoby Project - ******************************************************************************/ -package net.sf.taverna.t2.activities.biomoby; - -import static org.junit.Assert.assertFalse; -import static org.junit.Assert.assertTrue; -import net.sf.taverna.t2.workflowmodel.processor.activity.AbstractActivity; -import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityConfigurationException; - -import org.junit.Before; -import org.junit.Test; - -/** - * Unit tests for BiomobyActivityHealthChecker. - * - */ -public class BiomobyObjectActivityHealthCheckerTest { - - private BiomobyActivity activity; - - private BiomobyActivityHealthChecker activityHealthChecker; - - @Before - public void setUp() throws Exception { - activity = new BiomobyActivity(); - activityHealthChecker = new BiomobyActivityHealthChecker(); - } - - @Test - public void testCanHandle() { - assertFalse(activityHealthChecker.canVisit(null)); - assertFalse(activityHealthChecker.canVisit(new Object())); - assertFalse(activityHealthChecker.canVisit(new AbstractActivity<Object>() { - public void configure(Object conf) throws ActivityConfigurationException { - } - public Object getConfiguration() { - return null; - } - })); - assertTrue(activityHealthChecker.canVisit(activity)); - } - -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-biomoby-activity/src/test/java/net/sf/taverna/t2/activities/biomoby/MobyParseDatatypeActivityHealthCheckerTest.java ---------------------------------------------------------------------- diff --git a/taverna-biomoby-activity/src/test/java/net/sf/taverna/t2/activities/biomoby/MobyParseDatatypeActivityHealthCheckerTest.java b/taverna-biomoby-activity/src/test/java/net/sf/taverna/t2/activities/biomoby/MobyParseDatatypeActivityHealthCheckerTest.java deleted file mode 100644 index 30c8a1d..0000000 --- a/taverna-biomoby-activity/src/test/java/net/sf/taverna/t2/activities/biomoby/MobyParseDatatypeActivityHealthCheckerTest.java +++ /dev/null @@ -1,45 +0,0 @@ -/******************************************************************************* - * This file is a component of the Taverna project, and is licensed under the - * GNU LGPL. Copyright Edward Kawas, The BioMoby Project - ******************************************************************************/ -package net.sf.taverna.t2.activities.biomoby; - -import static org.junit.Assert.assertFalse; -import static org.junit.Assert.assertTrue; -import net.sf.taverna.t2.workflowmodel.processor.activity.AbstractActivity; -import net.sf.taverna.t2.workflowmodel.processor.activity.ActivityConfigurationException; - -import org.junit.Before; -import org.junit.Test; - -/** - * Unit tests for BiomobyActivityHealthChecker. - * - */ -public class MobyParseDatatypeActivityHealthCheckerTest { - - private BiomobyActivity activity; - - private BiomobyActivityHealthChecker activityHealthChecker; - - @Before - public void setUp() throws Exception { - activity = new BiomobyActivity(); - activityHealthChecker = new BiomobyActivityHealthChecker(); - } - - @Test - public void testCanHandle() { - assertFalse(activityHealthChecker.canVisit(null)); - assertFalse(activityHealthChecker.canVisit(new Object())); - assertFalse(activityHealthChecker.canVisit(new AbstractActivity<Object>() { - public void configure(Object conf) throws ActivityConfigurationException { - } - public Object getConfiguration() { - return null; - } - })); - assertTrue(activityHealthChecker.canVisit(activity)); - } - -} http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-ncbi-activity-ui/pom.xml ---------------------------------------------------------------------- diff --git a/taverna-ncbi-activity-ui/pom.xml b/taverna-ncbi-activity-ui/pom.xml deleted file mode 100644 index 0a8a983..0000000 --- a/taverna-ncbi-activity-ui/pom.xml +++ /dev/null @@ -1,49 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<project xmlns="http://maven.apache.org/POM/4.0.0"; xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"; xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd";> - <modelVersion>4.0.0</modelVersion> - <parent> - <groupId>net.sf.taverna</groupId> - <artifactId>taverna-parent</artifactId> - <version>3.0.1-SNAPSHOT</version> - </parent> - <groupId>net.sf.taverna.t2.ui-activities</groupId> - <artifactId>ncbi-activity-ui</artifactId> - <name>Taverna 2 NCBI web service Activity UI</name> - <dependencies> - <dependency> - <groupId>junit</groupId> - <artifactId>junit</artifactId> - <version>${junit.version}</version> - <scope>test</scope> - </dependency> - <dependency> - <groupId>net.sf.taverna.t2.activities</groupId> - <artifactId>wsdl-activity</artifactId> - <version>${t2.activities.version}</version> - </dependency> - - <!-- testing dependencies --> - </dependencies> - <repositories> - <repository> - <releases /> - <snapshots> - <enabled>false</enabled> - </snapshots> - <id>mygrid-repository</id> - <name>myGrid Repository</name> - <url>http://www.mygrid.org.uk/maven/repository</url> - </repository> - <repository> - <releases> - <enabled>false</enabled> - </releases> - <snapshots /> - <id>mygrid-snapshot-repository</id> - <name>myGrid Snapshot Repository</name> - <url>http://www.mygrid.org.uk/maven/snapshot-repository</url> - </repository> - </repositories> - -</project> - http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-ncbi-activity-ui/src/main/resources/META-INF/spring/ncbi-activity-ui-context-osgi.xml ---------------------------------------------------------------------- diff --git a/taverna-ncbi-activity-ui/src/main/resources/META-INF/spring/ncbi-activity-ui-context-osgi.xml b/taverna-ncbi-activity-ui/src/main/resources/META-INF/spring/ncbi-activity-ui-context-osgi.xml deleted file mode 100644 index 1c13381..0000000 --- a/taverna-ncbi-activity-ui/src/main/resources/META-INF/spring/ncbi-activity-ui-context-osgi.xml +++ /dev/null @@ -1,9 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<beans:beans xmlns="http://www.springframework.org/schema/osgi"; xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"; - xmlns:beans="http://www.springframework.org/schema/beans"; - xsi:schemaLocation="http://www.springframework.org/schema/beans - http://www.springframework.org/schema/beans/spring-beans.xsd - http://www.springframework.org/schema/osgi - http://www.springframework.org/schema/osgi/spring-osgi.xsd";> - -</beans:beans> http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-ncbi-activity-ui/src/main/resources/META-INF/spring/ncbi-activity-ui-context.xml ---------------------------------------------------------------------- diff --git a/taverna-ncbi-activity-ui/src/main/resources/META-INF/spring/ncbi-activity-ui-context.xml b/taverna-ncbi-activity-ui/src/main/resources/META-INF/spring/ncbi-activity-ui-context.xml deleted file mode 100644 index 861c878..0000000 --- a/taverna-ncbi-activity-ui/src/main/resources/META-INF/spring/ncbi-activity-ui-context.xml +++ /dev/null @@ -1,6 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<beans xmlns="http://www.springframework.org/schema/beans"; xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"; - xsi:schemaLocation="http://www.springframework.org/schema/beans - http://www.springframework.org/schema/beans/spring-beans.xsd";> - -</beans> http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-ncbi-activity-ui/src/main/resources/ncbi_services ---------------------------------------------------------------------- diff --git a/taverna-ncbi-activity-ui/src/main/resources/ncbi_services b/taverna-ncbi-activity-ui/src/main/resources/ncbi_services deleted file mode 100644 index e69de29..0000000 http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-ncbi-activity-ui/src/main/resources/wsdl.png ---------------------------------------------------------------------- diff --git a/taverna-ncbi-activity-ui/src/main/resources/wsdl.png b/taverna-ncbi-activity-ui/src/main/resources/wsdl.png deleted file mode 100644 index f9fdae8..0000000 Binary files a/taverna-ncbi-activity-ui/src/main/resources/wsdl.png and /dev/null differ http://git-wip-us.apache.org/repos/asf/incubator-taverna-plugin-bioinformatics/blob/e13e3b74/taverna-soaplab-activity-ui/pom.xml ---------------------------------------------------------------------- diff --git a/taverna-soaplab-activity-ui/pom.xml b/taverna-soaplab-activity-ui/pom.xml deleted file mode 100644 index 737a13d..0000000 --- a/taverna-soaplab-activity-ui/pom.xml +++ /dev/null @@ -1,103 +0,0 @@ -<?xml version="1.0" encoding="UTF-8"?> -<project xmlns="http://maven.apache.org/POM/4.0.0"; xmlns:xsi="http://www.w3.org/2001/XMLSchema-instance"; xsi:schemaLocation="http://maven.apache.org/POM/4.0.0 http://maven.apache.org/maven-v4_0_0.xsd";> - <modelVersion>4.0.0</modelVersion> - <parent> - <groupId>net.sf.taverna</groupId> - <artifactId>taverna-parent</artifactId> - <version>3.0.1-SNAPSHOT</version> - </parent> - <groupId>net.sf.taverna.t2.ui-activities</groupId> - <artifactId>soaplab-activity-ui</artifactId> - <version>2.0-SNAPSHOT</version> - <packaging>bundle</packaging> - <name>Taverna 2 Soaplab Activity UI</name> - <dependencies> - <dependency> - <groupId>net.sf.taverna.t2.activities</groupId> - <artifactId>soaplab-activity</artifactId> - <version>${t2.activities.version}</version> - </dependency> - <dependency> - <groupId>net.sf.taverna.t2.ui-api</groupId> - <artifactId>activity-icons-api</artifactId> - <version>${t2.ui.api.version}</version> - </dependency> - <dependency> - <groupId>net.sf.taverna.t2.ui-api</groupId> - <artifactId>activity-palette-api</artifactId> - <version>${t2.ui.api.version}</version> - </dependency> - <dependency> - <groupId>net.sf.taverna.t2.ui-api</groupId> - <artifactId>contextual-views-api</artifactId> - <version>${t2.ui.api.version}</version> - </dependency> - <dependency> - <groupId>net.sf.taverna.t2.ui-api</groupId> - <artifactId>activity-tools</artifactId> - <version>${t2.ui.api.version}</version> - </dependency> - <dependency> - <groupId>net.sf.taverna.t2.ui-api</groupId> - <artifactId>edits-api</artifactId> - <version>${t2.ui.api.version}</version> - </dependency> - <dependency> - <groupId>net.sf.taverna.t2.ui-api</groupId> - <artifactId>file-api</artifactId> - <version>${t2.ui.api.version}</version> - </dependency> - <dependency> - <groupId>net.sf.taverna.t2.ui-api</groupId> - <artifactId>menu-api</artifactId> - <version>${t2.ui.api.version}</version> - </dependency> - - <dependency> - <groupId>org.apache.axis</groupId> - <artifactId>com.springsource.org.apache.axis</artifactId> - <version>${axis.version}</version> - </dependency> - <dependency> - <groupId>javax.xml.rpc</groupId> - <artifactId>com.springsource.javax.xml.rpc</artifactId> - <version>${xml.rpc.version}</version> - </dependency> - - <dependency> - <groupId>junit</groupId> - <artifactId>junit</artifactId> - <version>${junit.version}</version> - <scope>test</scope> - </dependency> - </dependencies> - <repositories> - <repository> - <releases /> - <snapshots> - <enabled>false</enabled> - </snapshots> - <id>mygrid-repository</id> - <name>myGrid Repository</name> - <url>http://www.mygrid.org.uk/maven/repository - </url> - </repository> - <repository> - <releases> - <enabled>false</enabled> - </releases> - <snapshots /> - <id>mygrid-snapshot-repository</id> - <name>myGrid Snapshot Repository</name> - <url>http://www.mygrid.org.uk/maven/snapshot-repository</url> - </repository> - </repositories> - <scm> - <connection>scm:git:https://github.com/taverna/taverna-soaplab-activity-ui.git</connection> - <developerConnection>scm:git:ssh://g...@github.com/taverna/taverna-soaplab-activity-ui.git</developerConnection> - <url>https://github.com/taverna/taverna-soaplab-activity-ui/</url> - <tag>HEAD</tag> - </scm> - -</project> -
