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

Example 11 with EcrfItemGroup

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

the class CpctPatientReader method setRegistrationAndBirthData.

private static void setRegistrationAndBirthData(@NotNull final ImmutableBaselineData.Builder builder, @NotNull final EcrfStudyEvent studyEvent) {
    LocalDate registrationDate1 = null;
    LocalDate registrationDate2 = null;
    String birthYear1 = null;
    String birthYear2 = null;
    LocalDate birthYear3 = null;
    for (final EcrfForm eligibilityForm : studyEvent.nonEmptyFormsPerOID(FORM_ELIGIBILITY, false)) {
        for (final EcrfItemGroup eligibilityItemGroup : eligibilityForm.nonEmptyItemGroupsPerOID(ITEMGROUP_ELIGIBILITY, false)) {
            registrationDate1 = eligibilityItemGroup.readItemDate(FIELD_REGISTRATION_DATE1, 0, DATE_FORMATTER, false);
            birthYear2 = eligibilityItemGroup.readItemString(FIELD_BIRTH_YEAR2, 0, false);
            birthYear3 = eligibilityItemGroup.readItemDate(FIELD_BIRTH_YEAR3, 0, DATE_FORMATTER, false);
            builder.eligibilityStatus(eligibilityForm.status());
            builder.eligibilityLocked(eligibilityForm.locked());
        }
    }
    for (final EcrfForm selcritForm : studyEvent.nonEmptyFormsPerOID(FORM_SELCRIT, false)) {
        for (final EcrfItemGroup selcritItemGroup : selcritForm.nonEmptyItemGroupsPerOID(ITEMGROUP_SELCRIT, false)) {
            birthYear1 = selcritItemGroup.readItemString(FIELD_BIRTH_YEAR1, 0, false);
            if (registrationDate1 == null) {
                registrationDate2 = selcritItemGroup.readItemDate(FIELD_REGISTRATION_DATE2, 0, DATE_FORMATTER, false);
                builder.selectionCriteriaStatus(selcritForm.status());
                builder.selectionCriteriaLocked(selcritForm.locked());
            }
        }
    }
    final LocalDate registrationDate = registrationDate2 == null ? registrationDate1 : registrationDate2;
    final Integer birthYear = determineBirthYear(birthYear1, birthYear2, birthYear3);
    builder.registrationDate(registrationDate);
    builder.birthYear(birthYear);
}

Example 12 with EcrfItemGroup

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

the class BiopsyTreatmentResponseReaderTest method buildTestPatient.

@NotNull
private static EcrfPatient buildTestPatient() {
    final String patient = "dummy";
    EcrfItemGroup response1 = new EcrfItemGroup(patient);
    response1.addItem(BiopsyTreatmentResponseReader.FIELD_MEASUREMENT_DONE, "Yes");
    response1.addItem(BiopsyTreatmentResponseReader.FIELD_RESPONSE, "PR");
    EcrfForm form1 = new EcrfForm(patient, FormStatusState.SAVED, true);
    form1.addItemGroup(BiopsyTreatmentResponseReader.ITEMGROUP_TUMOR_MEASUREMENT, response1);
    EcrfItemGroup response2 = new EcrfItemGroup(patient);
    EcrfForm form2 = new EcrfForm(patient, FormStatusState.SAVED, true);
    form1.addItemGroup(BiopsyTreatmentResponseReader.ITEMGROUP_TUMOR_MEASUREMENT, response2);
    EcrfStudyEvent studyEvent = new EcrfStudyEvent(patient);
    studyEvent.addForm(BiopsyTreatmentResponseReader.FORM_TUMOR_MEASUREMENT, form1);
    studyEvent.addForm(BiopsyTreatmentResponseReader.FORM_TUMOR_MEASUREMENT, form2);
    Map<String, List<EcrfStudyEvent>> studyEvents = Maps.newHashMap();
    studyEvents.put(BiopsyTreatmentResponseReader.STUDY_TREATMENT, Lists.newArrayList(studyEvent));
    return new EcrfPatient(patient, studyEvents, Lists.newArrayList());
}

Example 13 with EcrfItemGroup

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

the class XMLPatientReader method readPatient.

@NotNull
private static EcrfPatient readPatient(@NotNull final XMLStreamReader reader, @NotNull final XMLEcrfDatamodel datamodel, @NotNull final FormStatusModel formStatusModel) throws XMLStreamException {
    final String patientId = toCPCTPatientId(reader.getAttributeValue("", PATIENT_ID_ATTRIBUTE));
    final Map<String, List<EcrfStudyEvent>> studyEventsPerOID = Maps.newHashMap();
    final List<EcrfDataField> fields = Lists.newArrayList();
    String currentStudyEventOID = Strings.EMPTY;
    String currentStudyEventIdx = Strings.EMPTY;
    String currentFormOID = Strings.EMPTY;
    String currentFormIdx = Strings.EMPTY;
    String currentItemGroupOID = Strings.EMPTY;
    String currentItemGroupIdx = Strings.EMPTY;
    EcrfStudyEvent currentStudy = new EcrfStudyEvent(patientId);
    EcrfForm currentForm = new EcrfForm(patientId, FormStatusState.UNKNOWN, false);
    EcrfItemGroup currentItemGroup = new EcrfItemGroup(patientId);
    while (reader.hasNext() && !isPatientEnd(reader)) {
        if (isStudyEventStart(reader)) {
            currentStudyEventOID = reader.getAttributeValue("", STUDY_EVENT_OID_ATTRIBUTE);
            currentStudyEventIdx = reader.getAttributeValue("", STUDY_EVENT_REPEAT_KEY_ATTRIBUTE);
            currentStudy = new EcrfStudyEvent(patientId);
            if (!studyEventsPerOID.containsKey(currentStudyEventOID)) {
                studyEventsPerOID.put(currentStudyEventOID, Lists.newArrayList());
            }
            studyEventsPerOID.get(currentStudyEventOID).add(currentStudy);
        } else if (isFormStart(reader)) {
            currentFormOID = reader.getAttributeValue("", FORM_OID_ATTRIBUTE);
            currentFormIdx = reader.getAttributeValue("", FORM_REPEAT_KEY_ATTRIBUTE);
            final String formName = datamodel.forms().get(currentFormOID).name();
            final String studyEventName = datamodel.studyEvents().get(currentStudyEventOID).name();
            final FormStatusKey formKey = new ImmutableFormStatusKey(patientId, formName, currentFormIdx, studyEventName, currentStudyEventIdx);
            final FormStatusData formStatus = formStatusModel.formStatuses().get(formKey);
            if (formStatus != null) {
                currentForm = new EcrfForm(patientId, formStatus.state(), formStatus.locked());
            } else {
                currentForm = new EcrfForm(patientId, FormStatusState.UNKNOWN, false);
            }
            currentStudy.addForm(currentFormOID, currentForm);
        } else if (isItemGroupStart(reader)) {
            currentItemGroupOID = reader.getAttributeValue("", ITEM_GROUP_OID_ATTRIBUTE);
            currentItemGroupIdx = reader.getAttributeValue("", ITEM_GROUP_REPEAT_KEY);
            currentItemGroup = new EcrfItemGroup(patientId);
            currentForm.addItemGroup(currentItemGroupOID, currentItemGroup);
        } else if (isFieldStart(reader)) {
            String OID = reader.getAttributeValue("", ITEM_OID_ATTRIBUTE);
            String value = Strings.EMPTY;
            try {
                value = datamodel.resolveValue(OID, reader.getAttributeValue("", ITEM_VALUE_ATTRIBUTE));
            } catch (EcrfResolveException exception) {
                LOGGER.warn("Resolve issue for " + patientId + ": " + exception.getMessage());
            }
            currentItemGroup.addItem(OID, value);
            fields.add(EcrfDataField.of(patientId, currentStudyEventOID, currentStudyEventIdx, currentFormOID, currentFormIdx, currentItemGroupOID, currentItemGroupIdx, OID, value, currentForm.status().stateString(), Boolean.toString(currentForm.locked())));
        }
        reader.next();
    }
    return new EcrfPatient(patientId, studyEventsPerOID, fields);
}