コード例 #1
0
 private boolean vitalStatusChanged(String value1, String value2) {
   return ((VitalStatusAlive.has(value1)
           || VitalStatusDead.has(value1)
           || VitalStatusAlive.has(value2)
           || VitalStatusDead.has(value2))
       && !value1.equals(value2));
 }
コード例 #2
0
 private boolean patientIsDiseaseFree(DiseaseFreeData df) {
   return (VitalStatusAlive.has(df.vitalStatus)
       && (df.daysToNewTumorEventAfterInitialTreatment.equals(
               MissingAttributeValues.NULL.toString())
           || df.daysToNewTumorEventAfterInitialTreatment.equals(
               MissingAttributeValues.getNotAvailable())));
 }
コード例 #3
0
  private String returnHigherPrecendenceString(String value1, String value2) {
    if (value1.equals(value2)) {
      return value1;
    } else if (oneStringEmpty(value1, value2)) {
      return returnNonEmptyString(value1, value2);
    } else if (vitalStatusChanged(value1, value2)) {
      if (VitalStatusAlive.has(value1) && VitalStatusDead.has(value2))
        return VitalStatusDead.DEAD.toString(); // alive - dead --> dead
      if (VitalStatusDead.has(value1) && VitalStatusAlive.has(value2))
        return VitalStatusDead.DEAD.toString(); // dead - alive --> dead
      if (VitalStatusAlive.has(value1) && !VitalStatusDead.has(value2))
        return VitalStatusAlive.ALIVE.toString(); // alive - [Not Available] --> alive
      if (VitalStatusDead.has(value1) && !VitalStatusAlive.has(value2))
        return VitalStatusDead.DEAD.toString(); // dead - [Not Available] --> dead
      if (!VitalStatusAlive.has(value1) && VitalStatusAlive.has(value2))
        return VitalStatusAlive.ALIVE.toString(); // [Not Available] - alive --> alive
      if (!VitalStatusAlive.has(value1) && VitalStatusDead.has(value2))
        return VitalStatusDead.DEAD.toString(); // [Not Available] - deade --> dead
      return VitalStatusDead.DEAD.toString();
    } else if (missingAttributeChanged(value1, value2)) {
      return returnHigherPrecedenceMissingAttribute(value1, value2);
    }

    assert true == false : String.format("returnHigherPrecendenceString, %s, %s", value1, value2);
    return MissingAttributeValues.MISSING.toString();
  }
コード例 #4
0
 private List<String> computeOverallSurvivalStatus(Map<String, SurvivalData> survivalData) {
   List<String> osStatus = initializeList(canonicalPatientList.size());
   for (String patientId : survivalData.keySet()) {
     int osStatusIndex = canonicalPatientList.indexOf(patientId);
     SurvivalData sd = survivalData.get(patientId);
     if (VitalStatusAlive.has(sd.vitalStatus)) {
       osStatus.set(osStatusIndex, VitalStatusAlive.LIVING.toString());
     } else if (VitalStatusDead.has(sd.vitalStatus)) {
       osStatus.set(osStatusIndex, VitalStatusDead.DECEASED.toString());
     } else {
       osStatus.set(osStatusIndex, ClinicalAttribute.NA);
     }
   }
   return osStatus;
 }
コード例 #5
0
  private List<String> computeOverallSurvivalMonths(Map<String, SurvivalData> survivalData) {
    List<String> osStatusMonths = initializeList(canonicalPatientList.size());
    for (String patientId : survivalData.keySet()) {
      int osStatusMonthsIndex = canonicalPatientList.indexOf(patientId);
      SurvivalData sd = survivalData.get(patientId);
      if (VitalStatusAlive.has(sd.vitalStatus)) {
        osStatusMonths.set(
            osStatusMonthsIndex, convertDaysToMonths(sd.lastFollowUp, sd.lastKnownAlive));
      } else if (VitalStatusDead.has(sd.vitalStatus)) {
        osStatusMonths.set(osStatusMonthsIndex, convertDaysToMonths(sd.daysToDeath));
      } else {
        osStatusMonths.set(osStatusMonthsIndex, ClinicalAttribute.NA);
      }
    }

    return osStatusMonths;
  }