Examples with FIELD_BIOPSY_DATE com.hartwig.hmftools.patientdb.readers.BiopsyReader.FIELD_BIOPSY_DATE used on opensource projects

Example 1 with FIELD_BIOPSY_DATE

use of com.hartwig.hmftools.patientdb.readers.BiopsyReader.FIELD_BIOPSY_DATE 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;
}