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;
}
private List<String> computeDiseaseFreeStatus(Map<String, DiseaseFreeData> diseaseFreeData) {
List<String> dfStatus = initializeList(canonicalPatientList.size());
for (String patientId : diseaseFreeData.keySet()) {
int dfStatusIndex = canonicalPatientList.indexOf(patientId);
DiseaseFreeData df = diseaseFreeData.get(patientId);
if (patientIsDiseaseFree(df)) {
dfStatus.set(dfStatusIndex, DiseaseFreeStatus.DISEASE_FREE.toString());
} else {
try {
Integer.parseInt(df.daysToNewTumorEventAfterInitialTreatment);
dfStatus.set(dfStatusIndex, DiseaseFreeStatus.DISEASED.toString());
} catch (NumberFormatException e) {
dfStatus.set(dfStatusIndex, ClinicalAttribute.NA);
}
}
}
return dfStatus;
}
private List<String> computeDiseaseFreeMonths(Map<String, DiseaseFreeData> diseaseFreeData) {
List<String> dfStatusMonths = initializeList(canonicalPatientList.size());
for (String patientId : diseaseFreeData.keySet()) {
int dfStatusMonthsIndex = canonicalPatientList.indexOf(patientId);
DiseaseFreeData df = diseaseFreeData.get(patientId);
try {
if (patientIsDiseaseFree(df)) {
dfStatusMonths.set(
dfStatusMonthsIndex, convertDaysToMonths(df.lastFollowUp, df.lastKnownAlive));
} else {
int dfStatusDays = Integer.parseInt(df.daysToNewTumorEventAfterInitialTreatment);
dfStatusMonths.set(
dfStatusMonthsIndex, convertDaysToMonths(Integer.toString(dfStatusDays)));
}
} catch (NumberFormatException e) {
dfStatusMonths.set(dfStatusMonthsIndex, ClinicalAttribute.NA);
}
}
return dfStatusMonths;
}
