svn commit: r1580902 - /ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/ExtractDurationsUsingContainsRelation.java

[dl...@apache.org]

Author: dligach
Date: Mon Mar 24 16:26:58 2014
New Revision: 1580902

URL: http://svn.apache.org/r1580902
Log:
first version of class to extract event durations using CONTAINS relation

Added:
    ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/ExtractDurationsUsingContainsRelation.java   (with props)

Added: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/ExtractDurationsUsingContainsRelation.java
URL: http://svn.apache.org/viewvc/ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/ExtractDurationsUsingContainsRelation.java?rev=1580902&view=auto
==============================================================================
--- ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/ExtractDurationsUsingContainsRelation.java (added)
+++ ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/ExtractDurationsUsingContainsRelation.java Mon Mar 24 16:26:58 2014
@@ -0,0 +1,156 @@
+/**
+ * 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.temporal.data.analysis;
+
+import java.io.File;
+import java.util.ArrayList;
+import java.util.Arrays;
+import java.util.List;
+
+import org.apache.ctakes.relationextractor.eval.XMIReader;
+import org.apache.ctakes.temporal.ae.feature.duration.Utils;
+import org.apache.ctakes.typesystem.type.relation.BinaryTextRelation;
+import org.apache.ctakes.typesystem.type.relation.RelationArgument;
+import org.apache.ctakes.typesystem.type.textsem.EventMention;
+import org.apache.ctakes.typesystem.type.textsem.TimeMention;
+import org.apache.uima.analysis_engine.AnalysisEngine;
+import org.apache.uima.analysis_engine.AnalysisEngineProcessException;
+import org.apache.uima.cas.CASException;
+import org.apache.uima.collection.CollectionReader;
+import org.apache.uima.jcas.JCas;
+import org.threeten.bp.temporal.TemporalUnit;
+import org.uimafit.component.JCasAnnotator_ImplBase;
+import org.uimafit.descriptor.ConfigurationParameter;
+import org.uimafit.factory.AnalysisEngineFactory;
+import org.uimafit.factory.CollectionReaderFactory;
+import org.uimafit.pipeline.SimplePipeline;
+import org.uimafit.util.JCasUtil;
+
+import scala.collection.immutable.Set;
+
+import com.google.common.collect.Lists;
+import com.lexicalscope.jewel.cli.CliFactory;
+import com.lexicalscope.jewel.cli.Option;
+
+/**
+ * @author dmitriy dligach
+ */
+public class ExtractDurationsUsingContainsRelation {
+
+  static interface Options {
+
+    @Option(
+        description = "specify the path to the directory containing the xmi files")
+    public File getInputDirectory();
+
+    @Option(
+        description = "specify the path to the output file")
+    public File getEventOutputFile();
+  }
+
+  public static void main(String[] args) throws Exception {
+
+    Options options = CliFactory.parseArguments(Options.class, args);
+
+    List<File> files = Arrays.asList(options.getInputDirectory().listFiles());
+    CollectionReader collectionReader = getCollectionReader(files);
+
+    AnalysisEngine annotationConsumer = AnalysisEngineFactory.createPrimitive(
+        ProcessRelations.class,
+        "EventOutputFile",
+        options.getEventOutputFile());
+
+    SimplePipeline.runPipeline(collectionReader, annotationConsumer);
+  }
+
+  /**
+   *
+   */
+  public static class ProcessRelations extends JCasAnnotator_ImplBase {
+
+    @ConfigurationParameter(
+        name = "EventOutputFile",
+        mandatory = true,
+        description = "path to the output file that will store the events")
+    private String eventOutputFile;
+
+    @Override
+    public void process(JCas jCas) throws AnalysisEngineProcessException {
+
+      JCas goldView;
+      try {
+        goldView = jCas.getView("GoldView");
+      } catch (CASException e) {
+        throw new AnalysisEngineProcessException(e);
+      }
+
+      JCas systemView;
+      try {
+        systemView = jCas.getView("_InitialView");
+      } catch (CASException e) {
+        throw new AnalysisEngineProcessException(e);
+      }
+
+      for(BinaryTextRelation relation : Lists.newArrayList(JCasUtil.select(goldView, BinaryTextRelation.class))) { 
+        if(! relation.getCategory().equals("CONTAINS")) {
+          continue;
+        }
+        
+        RelationArgument arg1 = relation.getArg1();                                                                             
+        RelationArgument arg2 = relation.getArg2(); 
+
+        String eventText;
+        String timeText;
+        if(arg1.getArgument() instanceof TimeMention && arg2.getArgument() instanceof EventMention) {
+          timeText = arg1.getArgument().getCoveredText().toLowerCase(); 
+          eventText = arg2.getArgument().getCoveredText().toLowerCase();  
+        } else if(arg1.getArgument() instanceof EventMention && arg2.getArgument() instanceof TimeMention) {
+          eventText = arg1.getArgument().getCoveredText().toLowerCase(); 
+          timeText = arg2.getArgument().getCoveredText().toLowerCase();  
+        } else {
+          // this is not a event-time relation
+          continue;
+        }    
+
+        Set<TemporalUnit> units = Utils.normalize(timeText);
+        
+        System.out.println(relation.getCategory() + " / " + timeText + " / " + eventText);
+      }
+    }
+  }
+
+  public static CollectionReader getCollectionReader(List<File> inputFiles) throws Exception {
+
+    List<String> fileNames = new ArrayList<String>();
+    for(File file : inputFiles) {
+      if(! (file.isHidden())) {
+        fileNames.add(file.getPath());
+      }
+    }
+
+    String[] paths = new String[fileNames.size()];
+    fileNames.toArray(paths);
+
+    return CollectionReaderFactory.createCollectionReader(
+        XMIReader.class,
+        XMIReader.PARAM_FILES,
+        paths);
+  }
+}
+

Propchange: ctakes/trunk/ctakes-temporal/src/main/java/org/apache/ctakes/temporal/data/analysis/ExtractDurationsUsingContainsRelation.java
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