A template example workflow using U-Compare text mining system inside

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import org.dom4j.Document;import org.dom4j.Node;import org.dom4j.io.SAXReader;SAXReader reader = new SAXReader(false);reader.setIncludeInternalDTDDeclarations(false);reader.setIncludeExternalDTDDeclarations(false);Document document = reader.read(new StringReader(xmltext));List nodelist = document.selectNodes(xpath);// Process the elements in the nodelistArrayList outputList = new ArrayList();ArrayList outputXmlList = new ArrayList();String val = null;String xmlVal = null;for (Iterator iter = nodelist.iterator(); iter.hasNext();) {	Node element = (Node) iter.next();	xmlVal = element.asXML();	val = element.getStringValue();	if (val != null && !val.equals("")) {		outputList.add(val);		outputXmlList.add(xmlVal);	}}List nodelist=outputList;List nodelistAsXML=outputXmlList;

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flatten(inputs, outputs, depth) {	for (i = inputs.iterator(); i.hasNext();) {	    element = i.next();		if (element instanceof Collection && depth > 0) {			flatten(element, outputs, depth - 1);		} else {			outputs.add(element);		}	}}outputlist = new ArrayList();flatten(inputlist, outputlist, 1);

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//if (command == void || command.equals("")) {//	throw new RuntimeException("The 'command' port cannot be null.");//}// default -Xms valueif (initialMemory == void || ! initialMemory.matches("\\d+[kmg]")) {  initialMemory = "500m";}// default -Xmx valueif (maximumMemory == void || ! maximumMemory.matches("\\d+[kmg]")) {  maximumMemory = "800m";}//Process bsh.shared.ucompare = null;Runtime rt = Runtime.getRuntime();Properties props = System.getProperties();String javaHome = props.getProperty("java.home");// create .U-Compare/taverna if not existString ucompareHome = System.getProperty("user.home") + "/.U-Compare/taverna/";File ucompareHomeDir = new File(ucompareHome);if ( !ucompareHomeDir.exists() ) ucompareHomeDir.mkdirs();// fetch UCLoader.class if not yetFile ucloader = new File(ucompareHomeDir, "UCLoader.class");if ( ! ucloader.exists() ) {    int BUFFER_SIZE = 64 * 1024;    byte[] buffer = new byte[BUFFER_SIZE];    FileOutputStream writer = null;    InputStream reader = null;    URL url = new URL("http://u-compare.org/downloads/UCLoader.class");    try {      HttpURLConnection conn = (HttpURLConnection) url.openConnection();      conn.setRequestMethod("GET");      int status = conn.getResponseCode();      if (status == 200) {//        System.out.println("Fetching " + url);        writer = new FileOutputStream(ucloader);        reader = conn.getInputStream();        int bytes;        while (-1 != (bytes = reader.read(buffer, 0, BUFFER_SIZE)))          writer.write(buffer, 0, bytes);      } else if (status != 304) {        System.err.println("Error downloading " + url + ": " + status + " " + conn.getResponseMessage());//        System.exit(1);	return;      }    } catch (IOException x) {      System.err.println("Error saving " + url + ": " + x.getMessage());      return;    }}// execute U-Compareif ((args == void) || (args == null)) {	args = new ArrayList();}if ((vmargs == void) || (vmargs == null)) {	vmargs = new ArrayList();}ArrayList argsList = new ArrayList();argsList.add(javaHome + "/bin/java");argsList.add("-Xms" + initialMemory);argsList.add("-Xmx" + maximumMemory);argsList.add("-cp");argsList.add(ucompareHomeDir.getAbsolutePath());argsList.addAll(vmargs);argsList.add("-Djavaws.workflow.path=\"" + workflowPath + "\"");//argsList.add("-Djavaws.workflow.path=\"c:/workspace/UIMA/downloads/StdinProteinTagging-CPE.xml\"");argsList.add("UCLoader");argsList.add("--jnlp");argsList.add("http://u-compare.org/lib/u-compare-runworkflow.jnlp");argsList.addAll(args);try {  if (bsh.shared.ucompare == void || bsh.shared.ucompare == null) {    bsh.shared.ucompare = rt.exec(argsList.toArray(new String[0]));// consume stderr//new Thread(){//  public void run() {	BufferedReader reader = new BufferedReader(new InputStreamReader(     		bsh.shared.ucompare.getErrorStream()));	String line;	while ((line = reader.readLine()) != null) {		System.err.println("STDERR: " + line);		if ( line.startsWith("workflow initialization completed.") ) break;	}//  }//}.start();  } else {    try {      bsh.shared.ucompare.exitValue();      bsh.shared.ucompare = rt.exec(argsList.toArray(new String[0]));	BufferedReader reader = new BufferedReader(new InputStreamReader(     		bsh.shared.ucompare.getErrorStream()));	String line;	while ((line = reader.readLine()) != null) {		System.err.println("STDERR: " + line);		if ( line.startsWith("workflow initialization completed.") ) break;	}   } catch (IllegalThreadStateException ise) {      // not yet terminated        }  }} catch (IOException x) {//      System.err.println("Error saving " + url + ": " + x.getMessage());      return;}// Get the input stream and read from itBufferedWriter writer = new BufferedWriter(new OutputStreamWriter(    bsh.shared.ucompare.getOutputStream()));writer.write(inputText.length() + "\n");writer.write(inputText);writer.write("\n");// no input annotation, empty new linewriter.write("\n");writer.flush();BufferedReader reader = new BufferedReader(new InputStreamReader(     bsh.shared.ucompare.getInputStream()));		System.err.println(inputText.length());StringBuffer sb = new StringBuffer();String line;while ((line = reader.readLine()) != null) {System.out.println(line);	sb.append(line+"\n");if (line.equals("")) break;}//in.close();result = sb.toString();//result = "success?";

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flatten(inputs, outputs, depth) {	for (i = inputs.iterator(); i.hasNext();) {	    element = i.next();		if (element instanceof Collection && depth > 0) {			flatten(element, outputs, depth - 1);		} else {			outputs.add(element);		}	}}outputlist = new ArrayList();flatten(inputlist, outputlist, 1);

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flatten(inputs, outputs, depth) {	for (i = inputs.iterator(); i.hasNext();) {	    element = i.next();		if (element instanceof Collection && depth > 0) {			flatten(element, outputs, depth - 1);		} else {			outputs.add(element);		}	}}outputlist = new ArrayList();flatten(inputlist, outputlist, 1);

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String seperatorString = "\n";if (seperator != void) {	seperatorString = seperator;}StringBuffer sb = new StringBuffer();for (Iterator i = stringlist.iterator(); i.hasNext();) {	String item = (String) i.next();	sb.append(item);	if (i.hasNext()) {		sb.append(seperatorString);	}}concatenated = sb.toString();

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String seperatorString = "\n";if (seperator != void) {	seperatorString = seperator;}StringBuffer sb = new StringBuffer();for (Iterator i = stringlist.iterator(); i.hasNext();) {	String item = (String) i.next();	sb.append(item);	if (i.hasNext()) {		sb.append(seperatorString);	}}concatenated = sb.toString();