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

Example 1 with BiopsyData

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

the class PatientReader method read.

@NotNull
public Patient read(@NotNull final EcrfPatient ecrfPatient, @NotNull final List<SampleData> sequencedSamples) throws IOException {
    LOGGER.info("Reading patient " + ecrfPatient.patientId() + " with samples: " + sequencedSamples);
    final BaselineData baselineData = cpctPatientReader.read(ecrfPatient);
    final PreTreatmentData preTreatmentData = preTreatmentReader.read(ecrfPatient);
    final List<BiopsyData> clinicalBiopsies = BiopsyReader.read(ecrfPatient);
    final List<BiopsyTreatmentData> treatments = biopsyTreatmentReader.read(ecrfPatient);
    final List<BiopsyTreatmentResponseData> treatmentResponses = BiopsyTreatmentResponseReader.read(ecrfPatient);
    final List<TumorMarkerData> tumorMarkers = TumorMarkerReader.read(ecrfPatient);
    final MatchResult<BiopsyData> matchedBiopsies = BiopsyMatcher.matchBiopsiesToTumorSamples(ecrfPatient.patientId(), sequencedSamples, clinicalBiopsies);
    final MatchResult<BiopsyTreatmentData> matchedTreatments = TreatmentMatcher.matchTreatmentsToBiopsies(ecrfPatient.patientId(), clinicalBiopsies, treatments);
    final MatchResult<BiopsyTreatmentResponseData> matchedResponses = TreatmentResponseMatcher.matchTreatmentResponsesToTreatments(ecrfPatient.patientId(), treatments, treatmentResponses);
    final List<ValidationFinding> findings = Lists.newArrayList();
    findings.addAll(matchedBiopsies.findings());
    findings.addAll(matchedTreatments.findings());
    findings.addAll(matchedResponses.findings());
    return new Patient(ecrfPatient.patientId(), baselineData, preTreatmentData, sequencedSamples, matchedBiopsies.values(), matchedTreatments.values(), matchedResponses.values(), tumorMarkers, findings);
}

Example 2 with BiopsyData

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

the class PatientValidator method validateInformedConsentDate.

@NotNull
static List<ValidationFinding> validateInformedConsentDate(@NotNull final String patientIdentifier, @NotNull final BaselineData baselineData, @NotNull final List<BiopsyData> biopsies) {
    final List<ValidationFinding> findings = Lists.newArrayList();
    final LocalDate informedConsentDate = baselineData.informedConsentDate();
    if (informedConsentDate != null && !biopsies.isEmpty()) {
        final List<BiopsyData> biopsiesPriorToInformedConsent = biopsies.stream().filter(biopsy -> {
            final LocalDate biopsyDate = biopsy.date();
            return biopsyDate != null && biopsyDate.isBefore(informedConsentDate);
        }).collect(Collectors.toList());
        if (biopsiesPriorToInformedConsent.size() > 0) {
            final String detailsMessage = "informedConsentDate: " + informedConsentDate + ". biopsies: " + biopsiesPriorToInformedConsent.stream().map(BiopsyData::toString).collect(Collectors.toList());
            FormStatusState best = baselineData.informedConsentStatus();
            boolean locked = baselineData.informedConsentLocked();
            for (BiopsyData biopsy : biopsies) {
                best = FormStatusState.best(best, biopsy.formStatus());
                locked = locked || biopsy.formLocked();
            }
            findings.add(ValidationFinding.of(ECRF_LEVEL, patientIdentifier, fields(FIELD_INFORMED_CONSENT_DATE, FIELD_BIOPSY_DATE), "at least 1 biopsy taken before informed consent date", best, locked, detailsMessage));
        }
    }
    return findings;
}

Example 3 with BiopsyData

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

the class PatientReaderTest method canReadCpctPatientBiopsies.

@Test
public void canReadCpctPatientBiopsies() {
    final CpctEcrfModel model = loadTestEcrf();
    assertEquals(1, model.patientCount());
    final EcrfPatient cpctPatient = model.patients().iterator().next();
    final List<BiopsyData> biopsies = BiopsyReader.read(cpctPatient);
    assertEquals(1, biopsies.size());
    assertEquals("Soft tissue", biopsies.get(0).site());
    assertEquals("near right scapula", biopsies.get(0).location());
    assertEquals(LocalDate.parse("2012-02-17", DATE_FORMATTER), biopsies.get(0).date());
}

Example 4 with BiopsyData

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

the class TreatmentMatcher method matchTreatmentsToBiopsies.

@NotNull
public static MatchResult<BiopsyTreatmentData> matchTreatmentsToBiopsies(@NotNull final String patientId, @NotNull final List<BiopsyData> biopsies, @NotNull final List<BiopsyTreatmentData> treatments) {
    final List<BiopsyTreatmentData> matchedTreatments = Lists.newArrayList();
    final List<ValidationFinding> findings = Lists.newArrayList();
    List<BiopsyData> remainingBiopsies = biopsies;
    for (final BiopsyTreatmentData treatment : treatments) {
        final String treatmentGiven = treatment.treatmentGiven();
        if (treatmentGiven == null || treatmentGiven.toLowerCase().equals("no")) {
            matchedTreatments.add(treatment);
            continue;
        }
        final Map<Boolean, List<BiopsyData>> partitions = remainingBiopsies.stream().collect(Collectors.partitioningBy(clinicalBiopsy -> isPossibleMatch(clinicalBiopsy.date(), treatment.startDate())));
        final List<BiopsyData> possibleMatches = partitions.get(true);
        if (possibleMatches.size() == 0) {
            findings.add(treatmentMatchFinding(patientId, "no biopsy match for treatment", treatment.toString()));
            matchedTreatments.add(treatment);
        } else if (possibleMatches.size() > 1) {
            findings.add(treatmentMatchFinding(patientId, "multiple biopsy matches for treatment", treatment + ". biopsies:  " + possibleMatches.stream().map(BiopsyData::toString).collect(Collectors.toList())));
            matchedTreatments.add(treatment);
        } else if (possibleMatches.get(0).date() == null) {
            findings.add(treatmentMatchFinding(patientId, "treatment matched biopsy with null date.", treatment.toString()));
            matchedTreatments.add(treatment);
        } else {
            final BiopsyData clinicalBiopsy = possibleMatches.get(0);
            matchedTreatments.add(ImmutableBiopsyTreatmentData.builder().from(treatment).biopsyId(clinicalBiopsy.id()).build());
            remainingBiopsies = partitions.get(false);
        }
    }
    return new MatchResult<>(matchedTreatments, findings);
}

Example 5 with BiopsyData

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

the class BiopsyReader method read.

@NotNull
static List<BiopsyData> read(@NotNull final EcrfPatient patient) {
    final List<BiopsyData> biopsies = Lists.newArrayList();
    for (final EcrfStudyEvent studyEvent : patient.studyEventsPerOID(STUDY_BIOPSY)) {
        for (final EcrfForm form : studyEvent.nonEmptyFormsPerOID(FORM_BIOPS, false)) {
            String biopsyTaken = null;
            String biopsyEvaluable = null;
            // KODU: This works as there is generally a 1:N relation between BIOPSY and BIOPSIES item groups.
            for (final EcrfItemGroup biopsyGroup : form.nonEmptyItemGroupsPerOID(ITEMGROUP_BIOPSY, false)) {
                biopsyTaken = biopsyGroup.readItemString(FIELD_BIOPSY_TAKEN, 0, false);
                biopsyEvaluable = biopsyGroup.readItemString(FIELD_BIOPSY_EVALUABLE, 0, false);
            }
            for (final EcrfItemGroup biopsiesGroup : form.nonEmptyItemGroupsPerOID(ITEMGROUP_BIOPSIES, false)) {
                final LocalDate date = biopsiesGroup.readItemDate(FIELD_BIOPSY_DATE, 0, DATE_FORMATTER, false);
                final String location = biopsiesGroup.readItemString(FIELD_LOCATION, 0, false);
                final String site = biopsiesGroup.readItemString(FIELD_SITE, 0, false);
                final String siteOther = biopsiesGroup.readItemString(FIELD_SITE_OTHER, 0, false);
                final String finalSite = (site == null || site.trim().toLowerCase().startsWith("other")) ? siteOther : site;
                BiopsyData biopsy = ImmutableBiopsyData.of(date, biopsyTaken, biopsyEvaluable, finalSite, location, form.status(), form.locked());
                // form needed to be created for every treatment response.
                if (!isDuplicate(biopsies, biopsy) && !isEmpty(biopsy)) {
                    biopsies.add(biopsy);
                }
            }
        }
    }
    return biopsies;
}