/**
* 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.pipelines;
import java.io.File;
import org.apache.ctakes.chunker.ae.Chunker;
import org.apache.ctakes.chunker.ae.DefaultChunkCreator;
import org.apache.ctakes.chunker.ae.adjuster.ChunkAdjuster;
import org.apache.ctakes.clinicalpipeline.ClinicalPipelineFactory;
import org.apache.ctakes.constituency.parser.ae.ConstituencyParser;
import org.apache.ctakes.contexttokenizer.ae.ContextDependentTokenizerAnnotator;
import org.apache.ctakes.core.ae.SentenceDetector;
import org.apache.ctakes.core.ae.SimpleSegmentAnnotator;
import org.apache.ctakes.core.ae.TokenizerAnnotatorPTB;
import org.apache.ctakes.core.resource.FileLocator;
import org.apache.ctakes.core.resource.FileResourceImpl;
import org.apache.ctakes.core.resource.JdbcConnectionResourceImpl;
import org.apache.ctakes.core.resource.LuceneIndexReaderResourceImpl;
import org.apache.ctakes.core.util.DocumentIDAnnotationUtil;
import org.apache.ctakes.dependency.parser.ae.ClearNLPDependencyParserAE;
import org.apache.ctakes.dependency.parser.ae.ClearNLPSemanticRoleLabelerAE;
import org.apache.ctakes.dictionary.lookup.ae.UmlsDictionaryLookupAnnotator;
import org.apache.ctakes.lvg.ae.LvgAnnotator;
import org.apache.ctakes.lvg.resource.LvgCmdApiResourceImpl;
import org.apache.ctakes.postagger.POSTagger;
import org.apache.ctakes.temporal.eval.Evaluation_ImplBase.CopyNPChunksToLookupWindowAnnotations;
import org.apache.ctakes.temporal.eval.Evaluation_ImplBase.RemoveEnclosedLookupWindows;
import org.apache.ctakes.typesystem.type.syntax.BaseToken;
import org.apache.ctakes.typesystem.type.textspan.Segment;
import org.apache.ctakes.typesystem.type.textspan.Sentence;
import org.apache.uima.analysis_engine.AnalysisEngine;
import org.apache.uima.analysis_engine.AnalysisEngineDescription;
import org.apache.uima.jcas.JCas;
import org.apache.uima.resource.ResourceInitializationException;
import org.uimafit.component.xwriter.XWriter;
import org.uimafit.component.xwriter.XWriterFileNamer;
import org.uimafit.factory.AggregateBuilder;
import org.uimafit.factory.AnalysisEngineFactory;
import org.uimafit.factory.ExternalResourceFactory;
import org.uimafit.factory.TypePrioritiesFactory;
import org.uimafit.factory.TypeSystemDescriptionFactory;
import com.lexicalscope.jewel.cli.Option;
public abstract class TemporalExtractionPipeline_ImplBase {
static interface Options {
@Option(
shortName = "i",
description = "specify the path to the directory containing the clinical notes to be processed")
public String getInputDirectory();
@Option(
shortName = "o",
description = "specify the path to the directory where the output xmi files are to be saved")
public String getOutputDirectory();
}
/**
* Preprocessing needed for relation extraction.
*/
protected static AggregateBuilder getPreprocessorAggregateBuilder()
throws Exception {
AggregateBuilder aggregateBuilder = new AggregateBuilder();
aggregateBuilder.add(ClinicalPipelineFactory.getDefaultPipeline());
// add semantic role labeler
aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(ClearNLPSemanticRoleLabelerAE.class));
aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(ConstituencyParser.class));
return aggregateBuilder;
}
protected static AggregateBuilder getLightweightPreprocessorAggregateBuilder() throws Exception{
AggregateBuilder aggregateBuilder = new AggregateBuilder();
/** Consider using ClinicalPipelineFactory.getDefaultPipeline()
*
*/
// identify segments; use simple segment annotator on non-mayo notes
// aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(SegmentsFromBracketedSectionTagsAnnotator.class));
aggregateBuilder.add(SimpleSegmentAnnotator.createAnnotatorDescription());
aggregateBuilder.add(SentenceDetector.createAnnotatorDescription());
aggregateBuilder.add(TokenizerAnnotatorPTB.createAnnotatorDescription());
aggregateBuilder.add(ContextDependentTokenizerAnnotator.createAnnotatorDescription());
aggregateBuilder.add(POSTagger.createAnnotatorDescription());
aggregateBuilder.add(Chunker.createAnnotatorDescription());
aggregateBuilder.add(ClearNLPDependencyParserAE.createAnnotatorDescription());
aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(ClearNLPSemanticRoleLabelerAE.class));
aggregateBuilder.add(AnalysisEngineFactory.createPrimitiveDescription(ConstituencyParser.class));
return aggregateBuilder;
}
protected static AnalysisEngine getXMIWriter(String outputDirectory) throws ResourceInitializationException{
return AnalysisEngineFactory.createPrimitive(
XWriter.class,
XWriter.PARAM_OUTPUT_DIRECTORY_NAME,
outputDirectory,
XWriter.PARAM_FILE_NAMER_CLASS_NAME,
DocIDFileNamer.class.getName()
);
}
public static class DocIDFileNamer implements XWriterFileNamer {
@Override
public String nameFile(JCas jCas) {
return DocumentIDAnnotationUtil.getDocumentID(jCas);
}
}
}