Package org.apache.ctakes.core.resource

Examples of org.apache.ctakes.core.resource.FileResource

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    IndexReader indexReader;
    String indexDirAbsPath = null;
    try {
     
      // ohnlp Bugs tracker ID: 3425014 SNOMED lucene dictionary lookup hardcodes resource path
      FileResource fResrc = (FileResource) aCtx.getResourceObject(SNOMED_CODE_LIST_CONFIG_PARM);
      if (fResrc == null) logger.error("Unable to find config parm " + SNOMED_CODE_LIST_CONFIG_PARM +  ".");
      File indexDir = fResrc.getFile();
      indexDirAbsPath = indexDir.getAbsolutePath();

      try {
        logger.info("Using lucene index: " + indexDir.getAbsolutePath());
      }
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   * Reads configuration parameters.
   */
  private void configInit() throws ResourceInitializationException
  {
    try {
    FileResource fResrc = (FileResource) iv_context.getResourceObject("LookupDescriptor");
    File descFile = fResrc.getFile();

      iv_logger.info("Parsing descriptor: " + descFile.getAbsolutePath());
      iv_lookupSpecSet = LookupParseUtilities.parseDescriptor(descFile, iv_context);
    }
    catch (Exception e) {
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      }
      //      if(printModels){
      //        pathTreeOut = new PrintWriter(outputDir + "/" + CorefConsts.NE + "/matrix.out");
      //      }
      stopwords = new HashSet<String>();
      FileResource r = (FileResource) super.getUimaContext().getResourceObject("stopWords");
      BufferedReader br = new BufferedReader(new FileReader(r.getFile()));
      String l;
      while ((l = br.readLine())!=null) {
        l = l.trim();
        if (l.length()==0) continue;
        int i = l.indexOf('|');
        if (i > 0)
          stopwords.add(l.substring(0,i).trim());
        else if (i < 0)
          stopwords.add(l.trim());
      }
      File anaphModFile = FileLocator.locateFile("anaphoricity.mayo.rbf.model");
      svm_model anaphModel = svm.svm_load_model(anaphModFile.getAbsolutePath());
      vecCreator = new SvmVectorCreator(stopwords, anaphModel);
      r = (FileResource) super.getUimaContext().getResourceObject("treeFrags");
      Scanner scanner = new Scanner(r.getFile());
      if(useFrags){
        treeFrags = new ArrayList<String>();
        while(scanner.hasNextLine()){
          String line = scanner.nextLine();
          treeFrags.add(line.split(" ")[1]);
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    //    coref_idx = labels[0]==1 ? 0 : 1;

    // Load stop words list
    try {
      stopwords = new HashSet<String>();
      FileResource r = (FileResource) uc.getResourceObject("stopWords");
      Scanner scanner = new Scanner(r.getFile());
      String l;
      while (scanner.hasNextLine()) {
        l = scanner.nextLine().trim();
        if (l.length()==0) continue;
        int i = l.indexOf('|');
        if (i > 0)
          stopwords.add(l.substring(0,i).trim());
        else if (i < 0)
          stopwords.add(l.trim());
      }
      vecCreator = new org.apache.ctakes.coreference.util.SvmVectorCreator(stopwords, mod_anaphoricity);

      treeFrags = new ArrayList<String>();
      r = (FileResource) uc.getResourceObject("frags");
      if(r != null){
        scanner = new Scanner(r.getFile());
        while(scanner.hasNextLine()){
          String line = scanner.nextLine();
          treeFrags.add(line.split(" ")[1]);
        }
        vecCreator.setFrags(treeFrags);
      }
      logger.info("Stop words list loaded: " + r.getFile().getAbsolutePath());
    } catch (Exception e) {
      e.printStackTrace();
      logger.error("Error loading stop words list");
    }
  }
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         final Object minimumSpan = uimaContext.getConfigParameterValue( MIN_SPAN_PRP_KEY );
         if ( minimumSpan != null ) {
            _minimumLookupSpan = parseInt( minimumSpan, MIN_SPAN_PRP_KEY, _minimumLookupSpan );
         }
         _logger.info( "Using minimum lookup token span: " + _minimumLookupSpan );
         final FileResource fileResource = (FileResource) uimaContext.getResourceObject( DICTIONARY_DESCRIPTOR_KEY );
         final File descriptorFile = fileResource.getFile();
         _dictionarySpec = DictionaryDescriptorParser.parseDescriptor( descriptorFile, uimaContext );
      } catch ( ResourceAccessException raE ) {
         throw new ResourceInitializationException( raE );
      } catch ( AnnotatorContextException acE ) {
         throw new ResourceInitializationException( acE );
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      IndexReader indexReader;
      String indexDirAbsPath = null;
      try {

         // ohnlp Bugs tracker ID: 3425014 SNOMED lucene dictionary lookup hardcodes resource path
         FileResource fResrc = (FileResource) aCtx.getResourceObject( SNOMED_CODE_LIST_CONFIG_PARM );
         if ( fResrc == null ) {
            logger.error( "Unable to find config parm " + SNOMED_CODE_LIST_CONFIG_PARM + "." );
         }
         File indexDir = fResrc.getFile();
         indexDirAbsPath = indexDir.getAbsolutePath();

         try {
            logger.info( "Using lucene index: " + indexDir.getAbsolutePath() );
         } catch ( Exception e ) {
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   * Reads configuration parameters.
   */
  private void configInit() throws ResourceInitializationException
  {
    try {
    FileResource fResrc = (FileResource) iv_context.getResourceObject("LookupDescriptor");
    File descFile = fResrc.getFile();

      iv_logger.info("Parsing descriptor: " + descFile.getAbsolutePath());
      iv_lookupSpecSet = LookupParseUtilities.parseDescriptor(descFile, iv_context);
    }
    catch (Exception e) {
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   /**
    * Reads configuration parameters.
    */
   private void configInit( final UimaContext uimaContext ) throws ResourceInitializationException {
      try {
         final FileResource fResrc = (FileResource) uimaContext.getResourceObject("LookupDescriptor");
         final File descFile = fResrc.getFile();
         _logger.info( "Parsing descriptor: " + descFile.getAbsolutePath() );
         _lookupSpecSet = LookupParseUtilities.parseDescriptor( descFile, uimaContext );
      } catch ( ResourceAccessException raE ) {
         // thrown by uimaContext.getResourceObject
         throw new ResourceInitializationException( raE );
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            queryPrepStmt = conn.prepareStatement(sql);

            String fileResrcName = (String) getConfigParameterValue(PARAM_VALUE_FILE_RESRC);
            if ((fileResrcName != null) && (fileResrcName.trim().length() > 0))
            {
                FileResource fileResrc = (FileResource) getUimaContext().getResourceObject(fileResrcName);
                if (fileResrc != null)
                {
                    loadValueFile(fileResrc.getFile());
                    usePrepStmtVals = true;
                } else
                {
                    throw new Exception("Failed to get " + fileResrcName
                            + " from ResourceManager");
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    try
    {
      //String conWordsFileName = (String) aContext.getConfigParameterValue("ConWordsFile");
      //conWords = readLinesFromFile(FileLocator.locateFile(conWordsFileName.replaceAll(apiMacroHome, ".")).getAbsolutePath());
     
      FileResource fResrc = (FileResource) aContext.getResourceObject("negationContradictionWordsKey");
      File conWordsFile = fResrc.getFile();
      conWords = readLinesFromFile(conWordsFile.getAbsolutePath());
     
    }
    catch (Exception ace)
    {
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Related Classes of org.apache.ctakes.core.resource.FileResource

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  • org.apache.ctakes.coreference.ae.MipacqMarkablePairGenerator
  • org.apache.ctakes.coreference.ae.MipacqSvmChainCreator
  • org.apache.ctakes.coreference.cc.ODIEVectorFileWriter
  • org.apache.ctakes.dictionary.lookup.ae.DictionaryLookupAnnotator
  • org.apache.ctakes.dictionary.lookup.ae.ThreadedDictionaryLookupAnnotator
  • org.apache.ctakes.dictionary.lookup.ae.UmlsToSnomedLuceneConsumerImpl
  • org.apache.ctakes.dictionary.lookup2.ae.AbstractJCasTermAnnotator
  • org.apache.ctakes.padtermspotter.ae.PADHitAnnotator
  • org.apache.ctakes.padtermspotter.ae.SubSectionAnnotator
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