Examples with FORM_TREATMENT com.hartwig.hmftools.patientdb.readers.BiopsyTreatmentReader.FORM_TREATMENT used on opensource projects

Example 1 with FORM_TREATMENT

use of com.hartwig.hmftools.patientdb.readers.BiopsyTreatmentReader.FORM_TREATMENT in project hmftools by hartwigmedical.

the class PatientValidator method validateTreatmentResponses.

@NotNull
@VisibleForTesting
static List<ValidationFinding> validateTreatmentResponses(@NotNull final String patientIdentifier, @NotNull final List<BiopsyTreatmentData> treatments, @NotNull final List<BiopsyTreatmentResponseData> responses) {
    final List<ValidationFinding> findings = Lists.newArrayList();
    for (int i = 0; i < responses.size(); i++) {
        findings.addAll(validateTreatmentResponse(patientIdentifier, responses.get(i), i == 0));
    }
    Collections.sort(treatments);
    Collections.sort(responses);
    if (treatments.isEmpty() && !responses.isEmpty()) {
        findings.add(ValidationFinding.of(ECRF_LEVEL, patientIdentifier, FORM_TREATMENT, "treatment response filled in, but treatment data missing", FormStatusState.UNKNOWN, false));
    }
    if (!treatments.isEmpty() && !responses.isEmpty()) {
        final LocalDate firstResponseDate = responses.get(0).date();
        final LocalDate firstTreatmentStart = treatments.get(0).startDate();
        if (firstResponseDate != null && firstTreatmentStart != null && firstResponseDate.isAfter(firstTreatmentStart)) {
            findings.add(ValidationFinding.of(ECRF_LEVEL, patientIdentifier, fields(FORM_TREATMENT, FORM_TUMOR_MEASUREMENT), "first (baseline) measurement date is after first treatment start", FormStatusState.best(treatments.get(0).formStatus(), responses.get(0).formStatus()), treatments.get(0).formLocked() || responses.get(0).formLocked(), "first treatment response: " + firstResponseDate + "; first treatment start: " + firstTreatmentStart));
        }
    }
    final List<BiopsyTreatmentData> treatmentsMissingResponse = treatments.stream().filter(treatment -> shouldHaveResponse(treatment) && !hasResponse(treatment.id(), responses)).collect(Collectors.toList());
    if (treatmentsMissingResponse.size() > 0) {
        findings.add(ValidationFinding.of(ECRF_LEVEL, patientIdentifier, FORM_TUMOR_MEASUREMENT, "no treatment response for at least 1 treatment", FormStatusState.UNKNOWN, false, "treatments " + treatmentsMissingResponse.stream().map(BiopsyTreatmentData::toString).collect(Collectors.toList()) + " should have response since they lasted more than " + Config.IMMEDIATE_TREATMENT_END_THRESHOLD + " days and started more than " + Config.START_DATE_RESPONSE_THRESHOLD + " days ago"));
    }
    return findings;
}

Example 2 with FORM_TREATMENT

use of com.hartwig.hmftools.patientdb.readers.BiopsyTreatmentReader.FORM_TREATMENT in project hmftools by hartwigmedical.

the class PatientValidator method validateTreatments.

@NotNull
@VisibleForTesting
static List<ValidationFinding> validateTreatments(@NotNull final String patientIdentifier, @NotNull final List<BiopsyTreatmentData> treatments) {
    final List<ValidationFinding> findings = Lists.newArrayList();
    treatments.forEach(treatment -> findings.addAll(validateTreatmentData(patientIdentifier, treatment)));
    Collections.sort(treatments);
    if (treatments.size() > 1) {
        for (int index = 1; index < treatments.size(); index++) {
            final BiopsyTreatmentData currentTreatment = treatments.get(index);
            final LocalDate startDate = currentTreatment.startDate();
            final LocalDate previousTreatmentEnd = treatments.get(index - 1).endDate();
            if (startDate != null && (previousTreatmentEnd == null || startDate.isBefore(previousTreatmentEnd))) {
                findings.add(ValidationFinding.of(ECRF_LEVEL, patientIdentifier, FORM_TREATMENT, "subsequent treatment starts before the end of previous treatment", currentTreatment.formStatus(), currentTreatment.formLocked()));
            }
        }
        final List<BiopsyTreatmentData> nonFinishedTreatments = treatments.stream().filter(treatment -> treatment.endDate() == null).collect(Collectors.toList());
        if (nonFinishedTreatments.size() > 1) {
            nonFinishedTreatments.forEach(treatment -> findings.add(ValidationFinding.of(ECRF_LEVEL, patientIdentifier, FORM_TREATMENT, "end of at least 1 non-final treatment is missing", treatment.formStatus(), treatment.formLocked())));
        }
    }
    return findings;
}