Examples of DateAnnotation

Examples of org.apache.ctakes.typesystem.type.textsem.DateAnnotation

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  @Test
  public void testParseDate() throws UIMAException {
      JCas jCas = JCasFactory.createJCasFromPath("src/main/resources/org/apache/ctakes/ytex/types/TypeSystem.xml");
      String date = (new java.util.Date()).toString();
      jCas.setDocumentText(date);
      DateAnnotation ctakesDate = new DateAnnotation(jCas);
      ctakesDate.setBegin(0);
      ctakesDate.setEnd(date.length());
      ctakesDate.addToIndexes();
      DateAnnotator dateAnnotator = new DateAnnotator();
      dateAnnotator.dateType = org.apache.ctakes.ytex.uima.types.Date.class.getName();
      dateAnnotator.process(jCas);
      AnnotationIndex<Annotation> ytexDates = jCas.getAnnotationIndex(org.apache.ctakes.ytex.uima.types.Date.type);
      Assert.assertTrue(ytexDates.iterator().hasNext());
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Examples of org.apache.ctakes.typesystem.type.textsem.DateAnnotation

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    try {
      Set<DateToken> dateTokenSet = iv_dateFSM.execute(baseTokenList);
      Iterator<DateToken> dateTokenItr = dateTokenSet.iterator();
      while (dateTokenItr.hasNext()) {
        DateToken dt = dateTokenItr.next();
        DateAnnotation dta = new DateAnnotation(jcas, dt.getStartOffset(), dt.getEndOffset());
        dta.addToIndexes();
      }

      Set<TimeToken> timeTokenSet = iv_timeFSM.execute(baseTokenList);
      Iterator<TimeToken> timeTokenItr = timeTokenSet.iterator();
      while (timeTokenItr.hasNext()) {
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Examples of org.apache.ctakes.typesystem.type.textsem.DateAnnotation

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              // accurately.
              boolean overrideDate = false;
              Iterator statusSpecialDateItr = FSUtil.getAnnotationsIteratorInSpan(jcas, DateAnnotation.type, ssid.getEnd(), drugTokenAnt.getBegin());
              while (statusSpecialDateItr.hasNext() && !overrideDate)
              {
                DateAnnotation specialDate = (DateAnnotation) statusSpecialDateItr.next();
                Iterator findLF = FSUtil.getAnnotationsIteratorInSpan(jcas,
                    NewlineToken.type, ssid.getEnd(), specialDate.getBegin());
                if (!findLF.hasNext())
                {
                  // if (specialDate.getEnd() <=
                  // drugTokenAnt.getBegin() ){
                  drugTokenAnt.setStartDate(specialDate.getCoveredText());
                  overrideDate = true;
                }
              }

              DrugChangeStatusAnnotation dsa = null;
View Full Code Here

Examples of org.apache.ctakes.typesystem.type.textsem.DateAnnotation

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              // accurately.
              boolean overrideDate = false;
              Iterator statusSpecialDateItr = FSUtil.getAnnotationsIteratorInSpan(jcas, DateAnnotation.type, ssid.getEnd(), drugTokenAnt.getBegin());
              while (statusSpecialDateItr.hasNext() && !overrideDate)
              {
                DateAnnotation specialDate = (DateAnnotation) statusSpecialDateItr.next();
                Iterator findLF = FSUtil.getAnnotationsIteratorInSpan(jcas,
                    NewlineToken.type, ssid.getEnd(), specialDate.getBegin());
                if (!findLF.hasNext())
                {
                  // if (specialDate.getEnd() <=
                  // drugTokenAnt.getBegin() ){
                  drugTokenAnt.setStartDate(specialDate.getCoveredText());
                  overrideDate = true;
                }
              }

              DrugChangeStatusAnnotation dsa = null;
View Full Code Here

Examples of org.apache.ctakes.typesystem.type.textsem.DateAnnotation

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    try {
      Set<DateToken> dateTokenSet = iv_dateFSM.execute(baseTokenList);
      Iterator<DateToken> dateTokenItr = dateTokenSet.iterator();
      while (dateTokenItr.hasNext()) {
        DateToken dt = dateTokenItr.next();
        DateAnnotation dta = new DateAnnotation(jcas, dt.getStartOffset(), dt.getEndOffset());
        dta.addToIndexes();
      }

      Set<TimeToken> timeTokenSet = iv_timeFSM.execute(baseTokenList);
      Iterator<TimeToken> timeTokenItr = timeTokenSet.iterator();
      while (timeTokenItr.hasNext()) {
View Full Code Here

Examples of org.apache.ctakes.typesystem.type.textsem.DateAnnotation

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    }
     
    Iterator dateTokenItr = FSUtil.getAnnotationsIteratorInSpan(jcas,
        DateAnnotation.type, beginPos, endPos);
    while (dateTokenItr.hasNext()){
      DateAnnotation focusToken = (DateAnnotation) dateTokenItr.next();
      String localDate = null;
      if ((localDate = findStartDateElement(jcas, focusToken.getBegin(),
          focusToken.getEnd())) == null) {

        startDate = new StartDateElement(focusToken.getCoveredText(),
            focusToken.getBegin(), focusToken.getEnd());
      } else {
        setStartDateElement(localDate, focusToken.getBegin(),
            focusToken.getEnd());
      }
    }
     
    Iterator doseTokenItr = FSUtil.getAnnotationsIteratorInSpan(jcas,
        DosagesAnnotation.type, beginPos, endPos);
    while (doseTokenItr.hasNext()){
      DosagesAnnotation focusToken = (DosagesAnnotation) doseTokenItr.next();
      String localDose = null;
      if ((localDose = findDosageElement(jcas, focusToken.getBegin(),
          focusToken.getEnd())) == null) {

        dosage = new DosageElement(focusToken.getCoveredText(),
            focusToken.getBegin(), focusToken.getEnd());
      } else {
        setDosageElement(localDose, focusToken.getBegin(),
            focusToken.getEnd());
       
      }
    }
    Iterator frequencyTokenItr = FSUtil.getAnnotationsIteratorInSpan(jcas,
        FrequencyAnnotation.type, beginPos, endPos);
    while (frequencyTokenItr.hasNext()){
      FrequencyAnnotation focusToken = (FrequencyAnnotation) frequencyTokenItr.next();
      String localFreq = null;
      if ((localFreq = findFrequencyElement(jcas, focusToken
          .getBegin(), focusToken.getEnd())) == null) {

        frequency = new FrequencyElement(focusToken
            .getCoveredText(), focusToken.getBegin(),
            focusToken.getEnd());
      } else if ((frequency != null && localFreq != null)
          && (frequency.getFrequencyMention().compareTo("") != 0)
          && (localFreq.compareTo("") != 0)
          && (parseIntValue(localFreq) > parseIntValue(frequency
              .getFrequencyMention()) && findMaxValue == true)) {
        // Need a way to find the largest frequency and/or convert
        // it to factor daily dosage

        setFrequencyElement(localFreq, focusToken.getBegin(),
            focusToken.getEnd());
    } else {
      setFrequencyElement(localFreq, focusToken.getBegin(),
          focusToken.getEnd());
    }
    } 
      Iterator frequencyUnitTokenItr = FSUtil.getAnnotationsIteratorInSpan(jcas,
          FrequencyUnitAnnotation.type, beginPos, endPos);
      while (frequencyUnitTokenItr.hasNext()){
        FrequencyUnitAnnotation focusToken = (FrequencyUnitAnnotation) frequencyUnitTokenItr.next();
        String localFreq = null;
        if ((localFreq = findFrequencyUnitElement(jcas,
                focusToken.getBegin(), focusToken.getEnd())) == null) {
          frequencyUnit = new FrequencyUnitElement(focusToken
              .getCoveredText(), focusToken.getBegin(),
              focusToken.getEnd());
        } else if (frequencyUnit == null
            && findMaxValue == true) {
          // Need a way to find the largest frequency and/or convert
          // it to factor daily dosage
          setFrequencyUnitElement(localFreq, focusToken.getBegin(),
              focusToken.getEnd());
        }
      }
      Iterator strengthUnitTokenItr = FSUtil.getAnnotationsIteratorInSpan(jcas, StrengthUnitAnnotation.type, beginPos, endPos);
      while (strengthUnitTokenItr.hasNext()){
        StrengthUnitAnnotation focusToken = (StrengthUnitAnnotation) strengthUnitTokenItr.next();
        setStrengthUnitElement(focusToken.getCoveredText(),
            focusToken.getBegin(), focusToken.getEnd());
      }
      Iterator strengthTokenItr = FSUtil.getAnnotationsIteratorInSpan(jcas, StrengthAnnotation.type, beginPos, endPos);
      while (strengthTokenItr.hasNext()){
        StrengthAnnotation focusToken = (StrengthAnnotation) strengthTokenItr.next();
        

            String localStrength = null;
            if ((localStrength = findStrengthElement(jcas, focusToken
                .getBegin(), focusToken.getEnd())) == null) {
              strength = new StrengthElement(focusToken.getCoveredText(),
                  focusToken.getBegin(), focusToken.getEnd());
            } else {
              if (strength != null) {
                // check for range and compare
                int spacePosition = strength.getStrengthMention()
                    .indexOf(" ");
                int spacePos = localStrength
                .indexOf(" ");
                if (spacePosition > 0 && spacePos > 0
                    && parseDoubleValue(strength
                        .getStrengthMention().substring(0,
                            spacePosition)) < parseDoubleValue(localStrength
                        .substring(0, localStrength
                            .indexOf(" ")))&& findMaxValue == true) {
                  setStrengthElement(localStrength, focusToken
                      .getBegin(), focusToken.getEnd());
                } else {
                  String stringRange = strength.getStrengthMention();
                  int hyphPosition = 0;
                  if ((stringRange.length() > 0)
                      && (stringRange.indexOf('-') > 0)) {
                    hyphPosition = stringRange.indexOf('-');
                    Double firstValue = new Double(
                        parseDoubleValue(stringRange
                            .subSequence(0, hyphPosition)));
                    Double secondValue = new Double(
                        parseDoubleValue(stringRange
                            .substring(hyphPosition + 2)));
                    if (firstValue.doubleValue() >= secondValue
                        .doubleValue() && findMaxValue == true) {
                      setStrengthElement(firstValue.toString(),
                          focusToken.getBegin(), focusToken
                              .getEnd());
                    } else {
                      setStrengthElement(firstValue.toString(),
                          focusToken.getBegin(), focusToken
                              .getEnd());
                    }
                  }
                }
              } else if ((localStrength.length() > 0)
                  && (localStrength.indexOf('-') > 0)) {

                int hyphPosition = 0;

                hyphPosition = localStrength.indexOf('-');
                Double firstValue = new Double(
                    parseDoubleValue(localStrength.subSequence(0,
                        hyphPosition)));
                Double secondValue = new Double(
                    parseDoubleValue(localStrength
                        .substring(hyphPosition + 2)));
                if (firstValue.doubleValue() >= secondValue
                    .doubleValue() && findMaxValue == true) {
                  setStrengthElement(firstValue.toString(),
                      focusToken.getBegin(), focusToken.getEnd());
                } else {
                  setStrengthElement(firstValue.toString(),
                      focusToken.getBegin(), focusToken.getEnd());
                }

                setStrengthElement(localStrength,
                    focusToken.getBegin(), focusToken.getEnd());
              } else {
                setStrengthElement(localStrength,
                    focusToken.getBegin(), focusToken.getEnd());
              }
            }
      }
      Iterator formTokenItr = FSUtil.getAnnotationsIteratorInSpan(jcas, FormAnnotation.type, beginPos, endPos);
      while (formTokenItr.hasNext()){
        FormAnnotation focusToken = (FormAnnotation) formTokenItr.next();
        String localForm = null;
        if ((localForm = findFormElement(jcas, focusToken.getBegin(),
            focusToken.getEnd())) == null) {
          form = new FormElement(focusToken.getCoveredText(),
              focusToken.getBegin(), focusToken.getEnd());
        } else {
          setFormElement(localForm, focusToken.getBegin(), focusToken
              .getEnd());
        }
      }
      Iterator routeTokenItr = FSUtil.getAnnotationsIteratorInSpan(jcas, RouteAnnotation.type, beginPos, endPos);
      while (routeTokenItr.hasNext()){
        RouteAnnotation focusToken = (RouteAnnotation) routeTokenItr.next();
        String localRoute = null;
        if ((localRoute = findRouteElement(jcas, focusToken.getBegin(),
            focusToken.getEnd())) == null) {
          route = new RouteElement(focusToken.getCoveredText(),
              focusToken.getBegin(), focusToken.getEnd());
        } else {
          setRouteElement(localRoute, focusToken.getBegin(),
              focusToken.getEnd());
        }
      }
      Iterator durationTokenItr = FSUtil.getAnnotationsIteratorInSpan(jcas, DurationAnnotation.type, beginPos, endPos);
      while (durationTokenItr.hasNext()){
        DurationAnnotation focusToken = (DurationAnnotation) durationTokenItr.next();
        String localDuration = null;
        if ((localDuration = findDurationElement(jcas, focusToken
            .getBegin(), focusToken.getEnd())) == null) {
          duration = new DurationElement(focusToken.getCoveredText(),
              focusToken.getBegin(), focusToken.getEnd());
        } else {
          setDurationElement(localDuration, focusToken.getBegin(),
              focusToken.getEnd());
        }
      }

     
 
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Examples of org.apache.ctakes.typesystem.type.textsem.DateAnnotation

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    Iterator firItr = FSUtil.getAnnotationsIteratorInSpan(jcas,
        DateAnnotation.type, beginOffset, endOffset + 1);

    while (firItr.hasNext()) {
      DateAnnotation da = (DateAnnotation) firItr.next();
      if (da.getBegin() == beginOffset)
        return da.getCoveredText();
    }
    return null;
  }
View Full Code Here

Examples of org.apache.ctakes.typesystem.type.textsem.DateAnnotation

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  private String findEndDateElement(JCas jcas, int beginOffset, int endOffset) {

    Iterator firItr = FSUtil.getAnnotationsInSpanIterator(jcas,
        DateAnnotation.type, beginOffset, endOffset + 1);
    while (firItr.hasNext()) {
      DateAnnotation da = (DateAnnotation) firItr.next();
      if (da.getBegin() == beginOffset)
        return da.getCoveredText();
    }
    return null;
  }
View Full Code Here

Examples of org.apache.ctakes.typesystem.type.textsem.DateAnnotation

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              // accurately.
              boolean overrideDate = false;
              Iterator statusSpecialDateItr = FSUtil.getAnnotationsIteratorInSpan(jcas, DateAnnotation.type, ssid.getEnd(), drugTokenAnt.getBegin());
              while (statusSpecialDateItr.hasNext() && !overrideDate)
              {
                DateAnnotation specialDate = (DateAnnotation) statusSpecialDateItr.next();
                Iterator findLF = FSUtil.getAnnotationsIteratorInSpan(jcas,
                    NewlineToken.type, ssid.getEnd(), specialDate.getBegin());
                if (!findLF.hasNext())
                {
                  // if (specialDate.getEnd() <=
                  // drugTokenAnt.getBegin() ){
                  drugTokenAnt.setStartDate(specialDate.getCoveredText());
                  overrideDate = true;
                }
              }

              DrugChangeStatusAnnotation dsa = null;
View Full Code Here

Examples of org.apache.ctakes.typesystem.type.textsem.DateAnnotation

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    try {
      Set<DateToken> dateTokenSet = iv_dateFSM.execute(baseTokenList);
      Iterator<DateToken> dateTokenItr = dateTokenSet.iterator();
      while (dateTokenItr.hasNext()) {
        DateToken dt = dateTokenItr.next();
        DateAnnotation dta = new DateAnnotation(jcas, dt.getStartOffset(), dt.getEndOffset());
        dta.addToIndexes();
      }

      Set<TimeToken> timeTokenSet = iv_timeFSM.execute(baseTokenList);
      Iterator<TimeToken> timeTokenItr = timeTokenSet.iterator();
      while (timeTokenItr.hasNext()) {
View Full Code Here
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