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From dlig...@apache.org
Subject svn commit: r1489548 - /ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/SelectiveRelationAnnotationViewer.java
Date Tue, 04 Jun 2013 18:31:34 GMT
Author: dligach
Date: Tue Jun  4 18:31:21 2013
New Revision: 1489548

URL: http://svn.apache.org/r1489548
Log:
display the relations whose arg1 is defined in a separate file

Added:
    ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/SelectiveRelationAnnotationViewer.java

Added: ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/SelectiveRelationAnnotationViewer.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/SelectiveRelationAnnotationViewer.java?rev=1489548&view=auto
==============================================================================
--- ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/SelectiveRelationAnnotationViewer.java
(added)
+++ ctakes/trunk/ctakes-relation-extractor/src/main/java/org/apache/ctakes/relationextractor/pipelines/SelectiveRelationAnnotationViewer.java
Tue Jun  4 18:31:21 2013
@@ -0,0 +1,220 @@
+/**
+ * Licensed to the Apache Software Foundation (ASF) under one
+ * or more contributor license agreements.  See the NOTICE file
+ * distributed with this work for additional information
+ * regarding copyright ownership.  The ASF licenses this file
+ * to you 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.apache.ctakes.relationextractor.pipelines;
+
+import java.io.File;
+import java.io.FileNotFoundException;
+import java.util.Arrays;
+import java.util.HashSet;
+import java.util.List;
+import java.util.Scanner;
+import java.util.Set;
+
+import org.apache.ctakes.relationextractor.eval.XMIReader;
+import org.apache.ctakes.typesystem.type.refsem.OntologyConcept;
+import org.apache.ctakes.typesystem.type.refsem.UmlsConcept;
+import org.apache.ctakes.typesystem.type.relation.BinaryTextRelation;
+import org.apache.ctakes.typesystem.type.textsem.IdentifiedAnnotation;
+import org.apache.ctakes.typesystem.type.textspan.Sentence;
+import org.apache.uima.UimaContext;
+import org.apache.uima.analysis_engine.AnalysisEngine;
+import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.cas.CAS;
+import org.apache.uima.cas.CASException;
+import org.apache.uima.cas.FeatureStructure;
+import org.apache.uima.collection.CollectionReader;
+import org.apache.uima.jcas.JCas;
+import org.apache.uima.jcas.cas.FSArray;
+import org.apache.uima.resource.ResourceInitializationException;
+import org.cleartk.util.Options_ImplBase;
+import org.kohsuke.args4j.Option;
+import org.uimafit.component.JCasAnnotator_ImplBase;
+import org.uimafit.factory.AnalysisEngineFactory;
+import org.uimafit.factory.CollectionReaderFactory;
+import org.uimafit.pipeline.SimplePipeline;
+import org.uimafit.util.JCasUtil;
+
+/**
+ * View relation instances in xmi files. Only display the relations
+ * whose arg1s are specified in a dictionary of CUIs.
+ * 
+ * @author dmitriy dligach
+ */
+public class SelectiveRelationAnnotationViewer {
+
+  public static class Options extends Options_ImplBase {
+
+    @Option(
+        name = "--input-dir",
+        usage = "specify the path to the directory containing the clinical notes to be processed",
+        required = true)
+    public File inputDirectory;
+  }
+  
+	public static void main(String[] args) throws Exception {
+		
+		Options options = new Options();
+		options.parseOptions(args);
+
+		List<File> trainFiles = Arrays.asList(options.inputDirectory.listFiles());
+    CollectionReader collectionReader = getCollectionReader(trainFiles);
+		
+    AnalysisEngine relationExtractorPrinter = AnalysisEngineFactory.createPrimitive(
+    		RelationExtractorPrinter.class);
+    		
+		SimplePipeline.runPipeline(collectionReader, relationExtractorPrinter);
+	}
+  
+	/*
+	 * Displays the relations whose arg1 is specified in a dictionary file.
+	 */
+  public static class RelationExtractorPrinter extends JCasAnnotator_ImplBase {
+    
+    // file containing one cui per line
+    private String dictionaryPath = "cuis.txt";
+    private Set<String> cuiDictionary;
+    
+    @Override
+    public void initialize(UimaContext aContext) throws ResourceInitializationException {
+      super.initialize(aContext);      
+      cuiDictionary = getCustomizedDictionary(dictionaryPath);
+    }
+
+    @Override
+    public void process(JCas jCas) throws AnalysisEngineProcessException {
+
+      JCas systemView;
+      try {
+        systemView = jCas.getView(CAS.NAME_DEFAULT_SOFA);
+      } catch (CASException e) {
+        throw new AnalysisEngineProcessException(e);
+      }   
+      
+      for(BinaryTextRelation binaryTextRelation : JCasUtil.select(systemView, BinaryTextRelation.class))
{
+        IdentifiedAnnotation entity1; // entity whose role is "Argument"
+        IdentifiedAnnotation entity2; // entity whose role is "Related_to"
+        
+        if(binaryTextRelation.getArg1().getRole().equals("Argument")) {
+          entity1 = (IdentifiedAnnotation) binaryTextRelation.getArg1().getArgument();
+          entity2 = (IdentifiedAnnotation) binaryTextRelation.getArg2().getArgument();
+        } else {
+          entity1 = (IdentifiedAnnotation) binaryTextRelation.getArg2().getArgument();
+          entity2 = (IdentifiedAnnotation) binaryTextRelation.getArg1().getArgument();
+        }
+        
+        String category = binaryTextRelation.getCategory();
+        String arg1 = entity1.getCoveredText().toLowerCase();
+        String arg2 = entity2.getCoveredText().toLowerCase();
+        int type1 = entity1.getTypeID();
+        int type2 = entity2.getTypeID();
+        
+        // first argument has to be an anatomical site
+        if(type1 != 6) {
+          continue;
+        }
+        // skip location_of(anatomical site, anatomical site)
+        if(type1 == 6 && type2 == 6) {
+          continue; 
+        }
+        // "to" is not a valid disease/disorder
+        if(type2 == 3 && arg2.equals("to")) {
+          continue;
+        }
+
+        // print relations as long as arg1 exists in the dictionary
+        Set<String> codes = getOntologyConceptCodes(entity1);
+        codes.retainAll(cuiDictionary);
+        if(codes.size() > 0) {
+          // print relation and its arguments: location_of(colon/6, colon cancer/2)
+          System.out.format("%s(%s/%d, %s/%d)\n", category, arg1, type1, arg2, type2);
+          List<Sentence> sentences = JCasUtil.selectCovering(systemView, Sentence.class,
entity1.getBegin(), entity1.getEnd());
+          System.out.println(sentences.get(0).getCoveredText());
+          System.out.println();
+        }
+      }
+    }
+  }
+  
+  private static CollectionReader getCollectionReader(List<File> items) throws Exception
{
+
+    // convert the List<File> to a String[]
+    String[] paths = new String[items.size()];
+    for (int i = 0; i < paths.length; ++i) {
+      paths[i] = items.get(i).getPath();
+    }
+    
+    // return a reader that will load each of the XMI files
+    return CollectionReaderFactory.createCollectionReader(
+        XMIReader.class,
+        XMIReader.PARAM_FILES,
+        paths);
+  }
+  
+  /**
+   * Get the CUIs, RxNorm codes specified for this entity.
+   */
+  public static HashSet<String> getOntologyConceptCodes(IdentifiedAnnotation identifiedAnnotation)
{
+    
+    HashSet<String> codes = new HashSet<String>();
+    
+    FSArray fsArray = identifiedAnnotation.getOntologyConceptArr();
+    if(fsArray == null) {
+      return codes;
+    }
+    
+    for(FeatureStructure featureStructure : fsArray.toArray()) {
+      OntologyConcept ontologyConcept = (OntologyConcept) featureStructure;
+      
+      if(ontologyConcept instanceof UmlsConcept) {
+        UmlsConcept umlsConcept = (UmlsConcept) ontologyConcept;
+        String code = umlsConcept.getCui();
+        codes.add(code);
+      } else { // SNOMED or RxNorm
+        String code = ontologyConcept.getCodingScheme() + ontologyConcept.getCode();
+        codes.add(code);
+      }
+    }
+    
+    return codes;
+  }
+  
+  /**
+   * Read comma separate file containing target CUIs.
+   */
+  public static Set<String> getCustomizedDictionary(String path) {
+    
+    Set<String> cuis = new HashSet<String>();
+    
+    File file = new File(path);
+    Scanner scan = null;
+    try {
+      scan = new Scanner(file);
+    } catch (FileNotFoundException e) {
+      System.err.println("couldn't open file: " + path);
+      return cuis;
+    }
+    
+    while(scan.hasNextLine()) {
+      String line = scan.nextLine();
+      cuis.add(line);
+    }
+    
+    return cuis;
+  }
+}



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