private boolean vitalStatusChanged(String value1, String value2) {
return ((VitalStatusAlive.has(value1)
|| VitalStatusDead.has(value1)
|| VitalStatusAlive.has(value2)
|| VitalStatusDead.has(value2))
&& !value1.equals(value2));
}
private boolean patientIsDiseaseFree(DiseaseFreeData df) {
return (VitalStatusAlive.has(df.vitalStatus)
&& (df.daysToNewTumorEventAfterInitialTreatment.equals(
MissingAttributeValues.NULL.toString())
|| df.daysToNewTumorEventAfterInitialTreatment.equals(
MissingAttributeValues.getNotAvailable())));
}
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();
}
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;
}
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;
}