Examples with BiopsyTreatmentData com.hartwig.hmftools.patientdb.data.BiopsyTreatmentData used on opensource projects

Example 6 with BiopsyTreatmentData

use of com.hartwig.hmftools.patientdb.data.BiopsyTreatmentData 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;
}

Example 7 with BiopsyTreatmentData

use of com.hartwig.hmftools.patientdb.data.BiopsyTreatmentData in project hmftools by hartwigmedical.

the class PatientValidator method validateDeathDate.

@NotNull
@VisibleForTesting
static List<ValidationFinding> validateDeathDate(@NotNull final String patientIdentifier, @NotNull final BaselineData baselineData, @NotNull final List<BiopsyTreatmentData> treatments) {
    final List<ValidationFinding> findings = Lists.newArrayList();
    final LocalDate deathDate = baselineData.deathDate();
    if (deathDate != null && !treatments.isEmpty()) {
        treatments.sort(comparing(BiopsyTreatmentData::endDate, nullsLast(naturalOrder())));
        final BiopsyTreatmentData lastTreatment = treatments.get(treatments.size() - 1);
        final LocalDate lastTreatmentEndDate = lastTreatment.endDate();
        final LocalDate firstTreatmentStart = treatments.get(0).startDate();
        if (lastTreatmentEndDate == null || lastTreatmentEndDate.isAfter(deathDate)) {
            String details = "death date (" + deathDate + ") before end of last treatment (" + lastTreatmentEndDate + ")" + " and start treatment is (" + firstTreatmentStart + ")";
            findings.add(ValidationFinding.of(ECRF_LEVEL, patientIdentifier, fields(FIELD_DEATH_DATE, FORM_TREATMENT), "death date before end of last treatment", FormStatusState.best(baselineData.deathStatus(), lastTreatment.formStatus()), baselineData.deathLocked() || lastTreatment.formLocked(), details));
        }
    }
    return findings;
}

Example 8 with BiopsyTreatmentData

use of com.hartwig.hmftools.patientdb.data.BiopsyTreatmentData in project hmftools by hartwigmedical.

the class TreatmentResponseMatcher method matchTreatmentResponsesToTreatments.

@NotNull
public static MatchResult<BiopsyTreatmentResponseData> matchTreatmentResponsesToTreatments(@NotNull String patientId, @NotNull List<BiopsyTreatmentData> treatments, @NotNull List<BiopsyTreatmentResponseData> responses) {
    final List<BiopsyTreatmentResponseData> matchedResponses = Lists.newArrayList();
    final List<ValidationFinding> findings = Lists.newArrayList();
    Collections.sort(responses);
    List<BiopsyTreatmentData> sortedTreatments = sortAndFilter(treatments);
    if (hasOverlappingTreatments(sortedTreatments)) {
        if (!responses.isEmpty()) {
            findings.add(responseMatchFinding(patientId, "treatments are overlapping. Cannot match any response.", "treatments: " + sortedTreatments));
        }
        return new MatchResult<>(responses, findings);
    }
    Iterator<BiopsyTreatmentData> treatmentIterator = sortedTreatments.iterator();
    BiopsyTreatmentData currentTreatment = treatmentIterator.hasNext() ? treatmentIterator.next() : null;
    LocalDate firstTreatmentStart = currentTreatment != null ? currentTreatment.startDate() : null;
    BiopsyTreatmentData nextTreatment = treatmentIterator.hasNext() ? treatmentIterator.next() : null;
    boolean hasNewBaselineResponseFound = false;
    for (BiopsyTreatmentResponseData response : responses) {
        LocalDate responseDate = response.date();
        if (responseMatchable(responseDate, firstTreatmentStart)) {
            LocalDate nextTreatmentStart = nextTreatment != null ? nextTreatment.startDate() : null;
            while (nextTreatmentStart != null && responseDate.isAfter(nextTreatmentStart)) {
                currentTreatment = nextTreatment;
                nextTreatment = treatmentIterator.hasNext() ? treatmentIterator.next() : null;
                nextTreatmentStart = nextTreatment != null ? nextTreatment.startDate() : null;
                hasNewBaselineResponseFound = false;
            }
            if (hasNewBaselineResponseFound) {
                matchedResponses.add(response);
                findings.add(responseMatchFinding(patientId, "response after new baseline and before next treatment", "response: " + response));
            } else {
                String actualResponse = response.response();
                if (actualResponse != null && actualResponse.equalsIgnoreCase("ne")) {
                    matchedResponses.add(response);
                    hasNewBaselineResponseFound = true;
                } else {
                    matchedResponses.add(ImmutableBiopsyTreatmentResponseData.builder().from(response).treatmentId(currentTreatment.id()).build());
                }
            }
        } else {
            matchedResponses.add(response);
        }
    }
    return new MatchResult<>(matchedResponses, findings);
}

Example 9 with BiopsyTreatmentData

use of com.hartwig.hmftools.patientdb.data.BiopsyTreatmentData in project hmftools by hartwigmedical.

the class BiopsyTreatmentReader method read.

@NotNull
List<BiopsyTreatmentData> read(@NotNull final EcrfPatient patient) throws IOException {
    final List<BiopsyTreatmentData> treatments = Lists.newArrayList();
    for (final EcrfStudyEvent studyEvent : patient.studyEventsPerOID(STUDY_AFTERBIOPT)) {
        for (final EcrfForm treatmentForm : studyEvent.nonEmptyFormsPerOID(FORM_TREATMENT, false)) {
            final String treatmentGiven = readTreatmentGiven(treatmentForm);
            final String radiotherapyGiven = readRadiotherapyGiven(treatmentForm);
            final List<DrugData> drugs = readDrugs(treatmentForm);
            treatments.add(ImmutableBiopsyTreatmentData.of(treatmentGiven, radiotherapyGiven, drugs, treatmentForm.status(), treatmentForm.locked()));
        }
    }
    return treatments;
}