@Override public void entityProcessComplete(CAS cas) { try { CasIOUtil.writeXmi(cas, file); } catch (IOException e) { e.printStackTrace(); } }
@Override public void process(JCas jCas) throws AnalysisEngineProcessException { try { File xmiFile = getXmiFile(jCas); CasIOUtil.writeXmi(jCas, xmiFile); } catch (IOException e) { throw new AnalysisEngineProcessException(e); } }
@Override public void process(JCas jCas) throws AnalysisEngineProcessException { try { File xmiFile = getXmiFile(jCas); CasIOUtil.writeXmi(jCas, xmiFile); } catch (IOException e) { throw new AnalysisEngineProcessException(e); } }
/** * * @param aJCas * the source JCas * @param aFile * the file to write to * @throws IOException * if there is a problem writing the file * @deprecated Use {@link CasIOUtils#save(CAS, OutputStream, org.apache.uima.cas.SerialFormat)} * with {@link SerialFormat#XMI} instead. */ @Deprecated public static void writeXmi(JCas aJCas, File aFile) throws IOException { CasIOUtil.writeXmi(aJCas.getCas(), aFile); }
@Override public void process(JCas jCas) throws AnalysisEngineProcessException { SourceDocumentInformation sourceDocInfo = null; FSIndex annoIndex = jCas.getAnnotationIndex(SourceDocumentInformation.type); Iterator annoIter = annoIndex.iterator(); if (annoIter.hasNext()) { sourceDocInfo = (SourceDocumentInformation) annoIter.next(); } String FileName = new File(sourceDocInfo.getUri()).getName(); try { CasIOUtil.writeXmi(jCas, new File(outputDirectory, FileName + ".xmi")); } catch (IOException e) { e.printStackTrace(); } } }
public static void main(String[] args) throws Exception { System.out.println("Started " + ClinicalPipelineWithUmls.class.getCanonicalName() + " at " + new Date()); //String documentText = "Text of document to test goes here, such as the following. No edema, some soreness, denies pain."; //InputStream inStream = InputStreamCollectionReader.convertToByteArrayInputStream(documentText); //CollectionReader collectionReader = InputStreamCollectionReader.getCollectionReader(inStream); CollectionReaderDescription collectionReader = FilesCollectionReader.getDescription(AssertionConst.CORPUS_WO_GOLD_STD_TO_RUN_THROUGH_CTAKES); System.out.println("Reading from directory: " + AssertionConst.CORPUS_WO_GOLD_STD_TO_RUN_THROUGH_CTAKES); System.out.println("Outputting to directory: " + AssertionConst.evalOutputDir); AnalysisEngineDescription pipelineIncludingUmlsDictionaries = AnalysisEngineFactory.createEngineDescription( "desc/analysis_engine/AggregatePlaintextUMLSProcessor"); for(JCas jCas : SimplePipeline.iteratePipeline(collectionReader, pipelineIncludingUmlsDictionaries)){ CasIOUtil.writeXmi(jCas, new File(AssertionConst.evalOutputDir, DocumentIDAnnotationUtil.getDocumentID(jCas) + ".xmi")); } System.out.println("Done at " + new Date()); }
public static void main(String[] args) throws Exception { System.out.println("Started " + ClinicalPipelineWithUmls.class.getCanonicalName() + " at " + new Date()); //String documentText = "Text of document to test goes here, such as the following. No edema, some soreness, denies pain."; //InputStream inStream = InputStreamCollectionReader.convertToByteArrayInputStream(documentText); //CollectionReader collectionReader = InputStreamCollectionReader.getCollectionReader(inStream); CollectionReaderDescription collectionReader = FilesCollectionReader.getDescription(AssertionConst.CORPUS_WO_GOLD_STD_TO_RUN_THROUGH_CTAKES); System.out.println("Reading from directory: " + AssertionConst.CORPUS_WO_GOLD_STD_TO_RUN_THROUGH_CTAKES); System.out.println("Outputting to directory: " + AssertionConst.evalOutputDir); AnalysisEngineDescription pipelineIncludingUmlsDictionaries = AnalysisEngineFactory.createEngineDescription( "desc/analysis_engine/AggregatePlaintextUMLSProcessor"); for(JCas jCas : SimplePipeline.iteratePipeline(collectionReader, pipelineIncludingUmlsDictionaries)){ CasIOUtil.writeXmi(jCas, new File(AssertionConst.evalOutputDir, DocumentIDAnnotationUtil.getDocumentID(jCas) + ".xmi")); } System.out.println("Done at " + new Date()); }
public static void main(String[] args) throws UIMAException, IOException, CmdLineException { Options options = new Options(); CmdLineParser parser = new CmdLineParser(options); parser.parseArgument(args); CollectionReaderDescription collectionReader = CollectionReaderFactory.createReaderDescriptionFromPath( "../ctakes-core/desc/collection_reader/FilesInDirectoryCollectionReader.xml", ConfigParameterConstants.PARAM_INPUTDIR, options.inputDirectory ); // make sure the model parameters match those used for training AnalysisEngineDescription relationExtractor = AnalysisEngineFactory.createEngineDescriptionFromPath( "desc/analysis_engine/RelationExtractorAggregate.xml"); int fileNum = 0; for(JCas jcas : SimplePipeline.iteratePipeline(collectionReader, relationExtractor)){ CasIOUtil.writeXmi(jcas, new File(options.outputDirectory, String.format("%d.txt", fileNum++))); } } }
public static void main(String[] args) throws UIMAException, IOException, CmdLineException { Options options = new Options(); CmdLineParser parser = new CmdLineParser(options); parser.parseArgument(args); CollectionReaderDescription collectionReader = CollectionReaderFactory.createReaderDescriptionFromPath( "../ctakes-core/desc/collection_reader/FilesInDirectoryCollectionReader.xml", ConfigParameterConstants.PARAM_INPUTDIR, options.inputDirectory ); // make sure the model parameters match those used for training AnalysisEngineDescription relationExtractor = AnalysisEngineFactory.createEngineDescriptionFromPath( "desc/analysis_engine/RelationExtractorAggregate.xml"); int fileNum = 0; for(JCas jcas : SimplePipeline.iteratePipeline(collectionReader, relationExtractor)){ CasIOUtil.writeXmi(jcas, new File(options.outputDirectory, String.format("%d.txt", fileNum++))); } } }
engine.process(jCas); documentID.setDocumentID(textFile.getName()); CasIOUtil.writeXmi(jCas, new File("/tmp", textFile.toURI().toString()));
engine.process(jCas); documentID.setDocumentID(textFile.getName()); CasIOUtil.writeXmi(jCas, new File("/tmp", textFile.toURI().toString()));
CasIOUtil.writeXmi(jCas, new File(evaluationOutputDirectory, sourceFileName + ".xmi"));
CasIOUtil.writeXmi(jCas, new File(evaluationOutputDirectory, sourceFileName + ".xmi"));