Update the default standalone writer to Medtator format

src/main/java/org/ohnlp/medtagger/fit/Main.java

@@ -8,7 +8,7 @@
 import org.apache.uima.fit.pipeline.SimplePipeline;
 import org.apache.uima.resource.metadata.ConfigurationParameterSettings;
 import org.ohnlp.medtagger.cr.FileSystemReader;
-import org.ohnlp.medtagger.ie.cc.IETabDelimitedWriter;
+import org.ohnlp.medtagger.ie.cc.MedTatorWriter;
 
 import java.nio.file.Path;
 import java.nio.file.Paths;
@@ -43,8 +43,8 @@ public static void main(String[] args) throws Exception {
 
         AnalysisEngineDescription writer =
                 AnalysisEngineFactory.createEngineDescription(
-                        IETabDelimitedWriter.class,
-                        IETabDelimitedWriter.PARAM_OUTPUTDIR, outputDirPath.toString());
+                        MedTatorWriter.class,
+                       MedTatorWriter.PARAM_OUTPUTDIR, outputDirPath.toString());
 
         SimpleCliPipeline.runPipeline(reader, descMedTaggerTAE, writer);
 

src/main/java/org/ohnlp/medtagger/ie/cc/MedTatorWriter.java

@@ -0,0 +1,176 @@
+/*******************************************************************************
+ * Copyright: (c)  2013  Mayo Foundation for Medical Education and 
+ *  Research (MFMER). All rights reserved. MAYO, MAYO CLINIC, and the
+ *  triple-shield Mayo logo are trademarks and service marks of MFMER.
+ *
+ *  Except as contained in the copyright notice above, or as used to identify 
+ *  MFMER as the author of this software, the trade names, trademarks, service
+ *  marks, or product names of the copyright holder shall not be used in
+ *  advertising, promotion or otherwise in connection with this software without
+ *  prior written authorization of the copyright holder.
+ *   
+ *  Licensed under the Apache License, Version 2.0 (the "License");
+ *  you may not use this file except in compliance with the License.
+ *  You may obtain a copy of the License at
+ *   
+ *  http://www.apache.org/licenses/LICENSE-2.0 
+ *   
+ *  Unless required by applicable law or agreed to in writing, software
+ *  distributed under the License is distributed on an "AS IS" BASIS,
+ *  WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+ *  See the License for the specific language governing permissions and 
+ *  limitations under the License. 
+ *******************************************************************************/
+package org.ohnlp.medtagger.ie.cc;
+
+
+import org.apache.uima.UimaContext;
+import org.apache.uima.analysis_component.JCasAnnotator_ImplBase;
+import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.cas.FSIterator;
+import org.apache.uima.jcas.JCas;
+import org.apache.uima.jcas.JFSIndexRepository;
+import org.apache.uima.jcas.cas.TOP;
+import org.apache.uima.jcas.tcas.Annotation;
+import org.apache.uima.resource.ResourceInitializationException;
+import org.ohnlp.medtagger.type.ConceptMention;
+import org.ohnlp.typesystem.type.structured.Document;
+
+import org.ohnlp.typesystem.type.textspan.Sentence;
+import org.w3c.dom.Element;
+import org.w3c.dom.Node;
+
+import javax.xml.parsers.DocumentBuilder;
+import javax.xml.parsers.DocumentBuilderFactory;
+import javax.xml.parsers.ParserConfigurationException;
+import javax.xml.transform.*;
+import javax.xml.transform.dom.DOMSource;
+import javax.xml.transform.stream.StreamResult;
+import java.io.*;
+
+import java.net.MalformedURLException;
+import java.net.URL;
+
+
+/**
+ * 
+ * Generate XML output format
+ * @author Hongfang Liu
+ *
+ */
+public class MedTatorWriter extends JCasAnnotator_ImplBase {
+
+	public static final String PARAM_OUTPUTDIR = "OutputDir";
+
+	private File mOutputDir;
+
+	private int mDocNum;
+
+    private DocumentBuilderFactory dbf;
+    private DocumentBuilder db;
+
+    /**
+	 * initialize
+	 */
+	public void initialize(UimaContext aContext) throws ResourceInitializationException {
+
+		mDocNum = 0;
+		mOutputDir = new File((String) aContext.getConfigParameterValue(PARAM_OUTPUTDIR));
+		if (!mOutputDir.exists()) {
+			mOutputDir.mkdirs();
+		}
+		dbf = DocumentBuilderFactory.newInstance();
+        try {
+            db = dbf.newDocumentBuilder();
+        } catch (ParserConfigurationException e) {
+            throw new RuntimeException(e);
+        }
+    }
+
+	// print out match and concept mention
+	public void printAnnotationsInline(JCas jcas) throws IOException {
+		JFSIndexRepository indexes = jcas.getJFSIndexRepository();
+	 	FSIterator<TOP> docIterator = indexes.getAllIndexedFS(Document.type);
+	 	 File outFile = null;
+		  File inFile = null;
+
+
+		  if (docIterator.hasNext()) {
+	    	Document docAnn = (Document) docIterator.next();
+	 	    String fileLoc =docAnn.getFileLoc(); 
+	      try {
+	        inFile = new File(new URL(fileLoc).getPath());
+	        String outFileName = inFile.getName();
+	        outFile = new File(mOutputDir, outFileName+".xml");
+	      } catch (MalformedURLException e1) {
+	       }
+	    }
+	    if (outFile == null) {
+	      outFile = new File(mOutputDir, "doc" + mDocNum++);
+	    }
+
+
+
+		String toprint = "";
+		int tagid = 0;
+		// document text
+		String doctext    = jcas.getDocumentText();
+
+        org.w3c.dom.Document doc = db.newDocument();
+		Element rootElement = doc.createElement("MedTagger");
+		doc.appendChild(rootElement);
+		Node cdata = doc.createCDATASection(doctext);
+		Element textElement = (Element) doc.createElement("TEXT");
+		textElement.appendChild(cdata);
+		rootElement.appendChild(textElement);
+		Element tagsElement = (Element) doc.createElement("TAGS");
+
+
+		// get concept mention index
+		FSIterator<? extends Annotation> cmIter = jcas.getAnnotationIndex(ConceptMention.type).iterator();
+
+		while (cmIter.hasNext()) {
+			ConceptMention cm = (ConceptMention) cmIter.next();
+			Element tagElement = doc.createElement("CM");
+			tagElement.setAttribute("spans", cm.getBegin()+"~"+cm.getEnd());
+			tagElement.setAttribute("text", cm.getCoveredText());
+			tagElement.setAttribute("id", "P"+tagid);
+			tagElement.setAttribute("certainty", cm.getCertainty());
+			tagElement.setAttribute("status", cm.getStatus());
+			tagElement.setAttribute("experiencer", cm.getExperiencer());
+			tagElement.setAttribute("semG", cm.getSemGroup());
+			tagElement.setAttribute("normTarget", cm.getNormTarget());
+			tagsElement.appendChild(tagElement);
+			tagid++;
+		}
+		rootElement.appendChild(tagsElement);
+
+	     try{
+			 FileOutputStream output =
+					 new FileOutputStream(outFile);
+			writeXml(doc, output);
+		} catch (TransformerException e) {
+            throw new RuntimeException(e);
+        }
+    }
+
+	private static void writeXml(org.w3c.dom.Document doc,
+								 OutputStream output)
+			throws TransformerException {
+
+		TransformerFactory transformerFactory = TransformerFactory.newInstance();
+		Transformer transformer = transformerFactory.newTransformer();
+		transformer.setOutputProperty(OutputKeys.INDENT, "yes");
+		DOMSource source = new DOMSource((Node) doc);
+		StreamResult result = new StreamResult(output);
+		transformer.transform(source, result);
+	}
+	@Override
+	public void process(JCas jCas) throws AnalysisEngineProcessException {
+        try {
+            printAnnotationsInline(jCas);
+        } catch (IOException e) {
+            throw new RuntimeException(e);
+        }
+    }
+}

src/main/resources/org/ohnlp/medtagger/ie/ccs/MedTatorWriter.xml

@@ -0,0 +1,47 @@
+<?xml version="1.0" encoding="UTF-8"?>
+<casConsumerDescription xmlns="http://uima.apache.org/resourceSpecifier">
+  <frameworkImplementation>org.apache.uima.java</frameworkImplementation>
+  <implementationName>org.ohnlp.medtagger.ie.cc.MedTatorWriter</implementationName>
+  <processingResourceMetaData>
+    <name>org.ohnlp.medtagger.ie.ccs.MedTatorWriter</name>
+    <description>Print out annotation in attribute and value format</description>
+    <version>1.0</version>
+    <vendor/>
+    <configurationParameters>
+      <configurationParameter>
+        <name>OutputDir</name>
+        <type>String</type>
+        <multiValued>false</multiValued>
+        <mandatory>true</mandatory>
+      </configurationParameter>
+    </configurationParameters>
+    <configurationParameterSettings>
+      <nameValuePair>
+        <name>OutputDir</name>
+        <value>
+          <string>data/output/</string>
+        </value>
+      </nameValuePair>
+    </configurationParameterSettings>
+    <typeSystemDescription>
+      <imports>
+           <import name="org.ohnlp.medtagger.ie.types.MedTaggerIETypes"/>
+      </imports>
+    </typeSystemDescription>
+    <typePriorities/>
+    <fsIndexCollection/>
+    <capabilities>
+      <capability>
+        <inputs/>
+        <outputs/>
+        <languagesSupported/>
+      </capability>
+    </capabilities>
+    <operationalProperties>
+      <modifiesCas>false</modifiesCas>
+      <multipleDeploymentAllowed>true</multipleDeploymentAllowed>
+      <outputsNewCASes>false</outputsNewCASes>
+    </operationalProperties>
+  </processingResourceMetaData>
+  <resourceManagerConfiguration/>
+</casConsumerDescription>