Examples with EcrfItemGroup com.hartwig.hmftools.common.ecrf.datamodel.EcrfItemGroup used on opensource projects

Example 1 with EcrfItemGroup

use of com.hartwig.hmftools.common.ecrf.datamodel.EcrfItemGroup in project hmftools by hartwigmedical.

the class BiopsyReaderTest method buildTestPatient.

@NotNull
private static EcrfPatient buildTestPatient() {
    final String patient = "dummy";
    EcrfItemGroup biopsy = new EcrfItemGroup(patient);
    biopsy.addItem(BiopsyReader.FIELD_BIOPSY_TAKEN, "Yes");
    biopsy.addItem(BiopsyReader.FIELD_BIOPSY_EVALUABLE, "Yes");
    // KODU: Create initial biopsy.
    EcrfItemGroup biopsies1 = new EcrfItemGroup(patient);
    biopsies1.addItem(BiopsyReader.FIELD_BIOPSY_DATE, "2017-11-10");
    biopsies1.addItem(BiopsyReader.FIELD_LOCATION, "liver");
    biopsies1.addItem(BiopsyReader.FIELD_SITE, "other");
    biopsies1.addItem(BiopsyReader.FIELD_SITE_OTHER, "body");
    EcrfForm form1 = new EcrfForm(patient, FormStatusState.SAVED, true);
    form1.addItemGroup(BiopsyReader.ITEMGROUP_BIOPSY, biopsy);
    form1.addItemGroup(BiopsyReader.ITEMGROUP_BIOPSIES, biopsies1);
    // KODU: Create empty 2nd biopsy
    EcrfItemGroup biopsies2 = new EcrfItemGroup(patient);
    EcrfForm form2 = new EcrfForm(patient, FormStatusState.SAVED, true);
    form2.addItemGroup(BiopsyReader.ITEMGROUP_BIOPSY, biopsy);
    form2.addItemGroup(BiopsyReader.ITEMGROUP_BIOPSIES, biopsies2);
    // KODU: Create duplicate 3rd biopsy
    EcrfItemGroup biopsies3 = new EcrfItemGroup(patient);
    biopsies3.addItem(BiopsyReader.FIELD_BIOPSY_DATE, "2017-11-10");
    biopsies3.addItem(BiopsyReader.FIELD_LOCATION, "liver");
    biopsies3.addItem(BiopsyReader.FIELD_SITE, "other");
    biopsies3.addItem(BiopsyReader.FIELD_SITE_OTHER, "body");
    EcrfForm form3 = new EcrfForm(patient, FormStatusState.SAVED, true);
    form3.addItemGroup(BiopsyReader.ITEMGROUP_BIOPSY, biopsy);
    form3.addItemGroup(BiopsyReader.ITEMGROUP_BIOPSIES, biopsies3);
    EcrfStudyEvent studyEvent = new EcrfStudyEvent(patient);
    studyEvent.addForm(BiopsyReader.FORM_BIOPS, form1);
    studyEvent.addForm(BiopsyReader.FORM_BIOPS, form2);
    studyEvent.addForm(BiopsyReader.FORM_BIOPS, form3);
    Map<String, List<EcrfStudyEvent>> studyEvents = Maps.newHashMap();
    studyEvents.put(BiopsyReader.STUDY_BIOPSY, Lists.newArrayList(studyEvent));
    return new EcrfPatient(patient, studyEvents, Lists.newArrayList());
}

Example 2 with EcrfItemGroup

use of com.hartwig.hmftools.common.ecrf.datamodel.EcrfItemGroup 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;
}

Example 3 with EcrfItemGroup

use of com.hartwig.hmftools.common.ecrf.datamodel.EcrfItemGroup in project hmftools by hartwigmedical.

the class BiopsyTreatmentReader method readDrugs.

@NotNull
private List<DrugData> readDrugs(@NotNull final EcrfForm treatmentForm) throws IOException {
    final List<DrugData> drugs = Lists.newArrayList();
    for (final EcrfItemGroup itemGroup : treatmentForm.nonEmptyItemGroupsPerOID(ITEMGROUP_SYSPOSTBIO, false)) {
        final LocalDate drugStart = itemGroup.readItemDate(FIELD_DRUG_START, 0, DATE_FORMATTER, false);
        final LocalDate drugEnd = itemGroup.readItemDate(FIELD_DRUG_END, 0, DATE_FORMATTER, false);
        String drugName = itemGroup.readItemString(FIELD_DRUG, 0, false);
        if (drugName == null || drugName.trim().toLowerCase().startsWith("other")) {
            drugName = itemGroup.readItemString(FIELD_DRUG_OTHER, 0, false);
        }
        final List<CuratedTreatment> curatedDrugs = drugName == null ? Lists.newArrayList() : treatmentCurator.search(drugName);
        drugs.add(ImmutableDrugData.of(drugName, drugStart, drugEnd, null, curatedDrugs));
    }
    return drugs;
}

Example 4 with EcrfItemGroup

use of com.hartwig.hmftools.common.ecrf.datamodel.EcrfItemGroup in project hmftools by hartwigmedical.

the class BiopsyTreatmentResponseReader method read.

@NotNull
static List<BiopsyTreatmentResponseData> read(@NotNull final EcrfPatient patient) {
    final List<BiopsyTreatmentResponseData> treatmentResponses = Lists.newArrayList();
    for (final EcrfStudyEvent studyEvent : patient.studyEventsPerOID(STUDY_TREATMENT)) {
        for (final EcrfForm form : studyEvent.nonEmptyFormsPerOID(FORM_TUMOR_MEASUREMENT, false)) {
            // KODU: There are generally multiple assessment dates per tumor measurement (one per target lesion)
            LocalDate assessmentDate = null;
            for (final EcrfItemGroup itemGroup : form.nonEmptyItemGroupsPerOID(ITEMGROUP_MEASUREMENT, false)) {
                final LocalDate date = itemGroup.readItemDate(FIELD_ASSESSMENT_DATE, 0, DATE_FORMATTER, false);
                if (date != null) {
                    assessmentDate = date;
                    break;
                }
            }
            LocalDate responseDate = null;
            String measurementDone = null;
            String boneOnlyDisease = null;
            String response = null;
            for (final EcrfItemGroup itemGroup : form.nonEmptyItemGroupsPerOID(ITEMGROUP_TUMOR_MEASUREMENT, false)) {
                final LocalDate responseDateValue = itemGroup.readItemDate(FIELD_RESPONSE_DATE, 0, DATE_FORMATTER, false);
                if (responseDateValue != null) {
                    responseDate = responseDateValue;
                }
                final String measurementDoneValue = itemGroup.readItemString(FIELD_MEASUREMENT_DONE, 0, false);
                if (measurementDoneValue != null) {
                    measurementDone = measurementDoneValue;
                }
                final String boneOnlyDiseaseValue = itemGroup.readItemString(FIELD_BONE_ONLY_DISEASE, 0, false);
                if (boneOnlyDiseaseValue != null) {
                    boneOnlyDisease = boneOnlyDiseaseValue;
                }
                final String responseValue = itemGroup.readItemString(FIELD_RESPONSE, 0, false);
                if (responseValue != null) {
                    response = responseValue;
                }
            }
            BiopsyTreatmentResponseData responseData = ImmutableBiopsyTreatmentResponseData.of(assessmentDate, responseDate, response, measurementDone, boneOnlyDisease, form.status(), form.locked());
            if (!isEmpty(responseData)) {
                treatmentResponses.add(responseData);
            }
        }
    }
    return treatmentResponses;
}

Example 5 with EcrfItemGroup

use of com.hartwig.hmftools.common.ecrf.datamodel.EcrfItemGroup in project hmftools by hartwigmedical.

the class CpctPatientReader method setDemographyData.

private void setDemographyData(@NotNull final ImmutableBaselineData.Builder builder, @NotNull final EcrfStudyEvent studyEvent) {
    for (final EcrfForm demographyForm : studyEvent.nonEmptyFormsPerOID(FORM_DEMOGRAPHY, false)) {
        for (final EcrfItemGroup demographyItemGroup : demographyForm.nonEmptyItemGroupsPerOID(ITEMGROUP_DEMOGRAPHY, false)) {
            builder.gender(demographyItemGroup.readItemString(FIELD_SEX, 0, false));
            builder.demographyStatus(demographyForm.status());
            builder.demographyLocked(demographyForm.locked());
        }
    }
}