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

Example 1 with EcrfDatamodelField

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

the class XMLEcrfDatamodelToEcrfFieldsTest method canConvertXMLObjectContainerToEcrfFields.

@Test
public void canConvertXMLObjectContainerToEcrfFields() {
    final String studyOID = "SE.Study";
    final String formOID = "FRM.Form";
    final String itemGroupOID = "GRP.ItemGroup";
    final String itemOID = "GRP.Item";
    final String description = "bla";
    final String codeListOID = "list";
    final String option1 = "x";
    final String option2 = "y";
    final List<StudyEvent> studyEvents = Lists.newArrayList(new ImmutableStudyEvent(studyOID, description, Lists.newArrayList(formOID)));
    final List<Form> forms = Lists.newArrayList(new ImmutableForm(formOID, description, Lists.newArrayList(itemGroupOID)));
    final List<ItemGroup> itemGroups = Lists.newArrayList(new ImmutableItemGroup(itemGroupOID, description, Lists.newArrayList(itemOID)));
    final List<Item> items = Lists.newArrayList(new ImmutableItem(itemOID, description, codeListOID));
    final Map<Integer, String> codeListItems = Maps.newHashMap();
    codeListItems.put(1, option1);
    codeListItems.put(2, option2);
    final List<CodeList> codeLists = Lists.newArrayList(new ImmutableCodeList(codeListOID, description, codeListItems));
    final XMLEcrfDatamodel datamodel = XMLEcrfDatamodel.of(studyEvents, forms, itemGroups, items, codeLists);
    final List<EcrfDatamodelField> fields = XMLEcrfDatamodelToEcrfFields.convert(datamodel);
    assertEquals(1, fields.size());
    final EcrfDatamodelField field = fields.get(0);
    assertEquals("STUDY.FORM.ITEMGROUP.ITEM", field.name());
    assertEquals(description, field.description());
    final Map<Integer, String> values = field.codeList();
    assertEquals(option1, values.get(1));
    assertEquals(option2, values.get(2));
}

Example 2 with EcrfDatamodelField

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

the class XMLEcrfDatamodelToEcrfFields method convert.

@NotNull
public static List<EcrfDatamodelField> convert(@NotNull final XMLEcrfDatamodel datamodel) {
    final List<EcrfDatamodelField> fields = Lists.newArrayList();
    for (final StudyEvent studyEvent : datamodel.studyEvents().values()) {
        for (final String formOID : studyEvent.formOIDs()) {
            final Form form = findByOID(datamodel.forms().values(), formOID);
            for (final String itemGroupOID : form.itemGroupOIDs()) {
                final ItemGroup itemGroup = findByOID(datamodel.itemGroups().values(), itemGroupOID);
                for (final String itemOID : itemGroup.itemOIDs()) {
                    final Item item = findByOID(datamodel.items().values(), itemOID);
                    Map<Integer, String> codeList = Maps.newHashMap();
                    String codeListOID = item.codeListOID();
                    if (codeListOID != null) {
                        final CodeList codeListObj = findByOID(datamodel.codeLists().values(), codeListOID);
                        codeList = codeListObj.values();
                    }
                    final EcrfDatamodelField field = new ImmutableEcrfDatamodelField(studyEvent.oid(), form.oid(), itemGroup.oid(), item.oid(), item.name(), codeList);
                    fields.add(field);
                }
            }
        }
    }
    return fields;
}

Example 3 with EcrfDatamodelField

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

the class XMLPatientReaderTest method canReadPatients.

@Test
public void canReadPatients() throws FileNotFoundException, XMLStreamException {
    final XMLInputFactory factory = XMLInputFactory.newInstance();
    final XMLStreamReader reader = factory.createXMLStreamReader(new FileInputStream(PATIENTS_TEST));
    final String studyOID = "SE.Study";
    final String formOID = "FRM.Form";
    final String itemGroupOID = "GRP.ItemGroup";
    final Map<Integer, String> codeListValues = Maps.newHashMap();
    codeListValues.put(1, "one");
    codeListValues.put(2, "two");
    codeListValues.put(3, "three");
    final String item1OID = "FLD.ItemGroup.field1";
    final String item2OID = "FLD.ItemGroup.field2";
    final String birthDateOID = "FLD.ItemGroup.BIRTHDTC";
    final String codeListOID = "codeList";
    final StudyEvent studyEvent = new ImmutableStudyEvent(studyOID, studyOID, Lists.newArrayList(formOID));
    final Form form = new ImmutableForm(formOID, formOID, Lists.newArrayList(itemGroupOID));
    final ItemGroup itemGroup = new ImmutableItemGroup(itemGroupOID, itemGroupOID, Lists.newArrayList(item1OID, item2OID, birthDateOID));
    final Item item1 = new ImmutableItem(item1OID, item1OID, codeListOID);
    final Item item2 = new ImmutableItem(item2OID, item2OID, "");
    final Item birthDate = new ImmutableItem(birthDateOID, birthDateOID, "");
    final CodeList codeList = new ImmutableCodeList(codeListOID, codeListOID, codeListValues);
    final List<EcrfPatient> patients = XMLPatientReader.readPatients(reader, XMLEcrfDatamodel.of(Lists.newArrayList(studyEvent), Lists.newArrayList(form), Lists.newArrayList(itemGroup), Lists.newArrayList(item1, item2, birthDate), Lists.newArrayList(codeList)), new ImmutableFormStatusModel(Maps.newHashMap()));
    final EcrfDatamodelField field1 = new ImmutableEcrfDatamodelField(studyOID, formOID, itemGroupOID, "FLD.ItemGroup.field1", "", codeListValues);
    final EcrfDatamodelField field2 = new ImmutableEcrfDatamodelField(studyOID, formOID, itemGroupOID, "FLD.ItemGroup.field2", "", Maps.newHashMap());
    final EcrfDatamodelField birthDateField = new ImmutableEcrfDatamodelField(studyOID, formOID, itemGroupOID, "FLD.ItemGroup.BIRTHDTC", "", Maps.newHashMap());
    // @formatter:off
    assertEquals(3, patients.size());
    assertEquals(4, patients.get(0).fields().size());
    assertEquals(PATIENT_1, patients.get(0).patientId());
    verifyFirstFieldValue("one", patients.get(0).fieldValuesByEcrfField(field1));
    verifyFirstFieldValue("hi", patients.get(0).fieldValuesByEcrfField(field2));
    verifyFirstFieldValue("2016-01-01", patients.get(0).fieldValuesByEcrfField(birthDateField));
    verifyFirstFieldValue("one", patients.get(0).studyEventsPerOID(studyOID).get(0).formsPerOID().get(formOID).get(0).itemGroupsPerOID().get(itemGroupOID).get(0).itemsPerOID().get(item1OID));
    verifyFirstFieldValue("hi", patients.get(0).studyEventsPerOID(studyOID).get(0).formsPerOID().get(formOID).get(0).itemGroupsPerOID().get(itemGroupOID).get(0).itemsPerOID().get(item2OID));
    verifyFirstFieldValue("2016-01-01", patients.get(0).studyEventsPerOID(studyOID).get(0).formsPerOID().get(formOID).get(0).itemGroupsPerOID().get(itemGroupOID).get(0).itemsPerOID().get(birthDateOID));
    assertEquals(1, patients.get(0).studyEventsPerOID().size());
    assertEquals(1, patients.get(0).studyEventsPerOID().get(studyOID).size());
    assertEquals(1, patients.get(0).studyEventsPerOID().get(studyOID).get(0).formsPerOID().get(formOID).size());
    assertEquals(1, patients.get(0).studyEventsPerOID().get(studyOID).get(0).formsPerOID().get(formOID).get(0).itemGroupsPerOID().get(itemGroupOID).size());
    assertEquals(4, patients.get(0).studyEventsPerOID().get(studyOID).get(0).formsPerOID().get(formOID).get(0).itemGroupsPerOID().get(itemGroupOID).get(0).itemsPerOID().size());
    assertEquals(4, patients.get(1).fields().size());
    assertEquals(PATIENT_2, patients.get(1).patientId());
    verifyFirstFieldValue("two", patients.get(1).studyEventsPerOID(studyOID).get(0).formsPerOID().get(formOID).get(0).itemGroupsPerOID().get(itemGroupOID).get(0).itemsPerOID().get(item1OID));
    verifyFirstFieldValue("hi there", patients.get(1).studyEventsPerOID(studyOID).get(0).formsPerOID().get(formOID).get(0).itemGroupsPerOID().get(itemGroupOID).get(0).itemsPerOID().get(item2OID));
    verifyFirstFieldValue("2016-01-01", patients.get(1).studyEventsPerOID(studyOID).get(0).formsPerOID().get(formOID).get(0).itemGroupsPerOID().get(itemGroupOID).get(0).itemsPerOID().get(birthDateOID));
    assertEquals(1, patients.get(1).studyEventsPerOID().size());
    assertEquals(1, patients.get(1).studyEventsPerOID().get(studyOID).size());
    assertEquals(1, patients.get(1).studyEventsPerOID().get(studyOID).get(0).formsPerOID().get(formOID).size());
    assertEquals(1, patients.get(1).studyEventsPerOID().get(studyOID).get(0).formsPerOID().get(formOID).get(0).itemGroupsPerOID().get(itemGroupOID).size());
    assertEquals(4, patients.get(1).studyEventsPerOID().get(studyOID).get(0).formsPerOID().get(formOID).get(0).itemGroupsPerOID().get(itemGroupOID).get(0).itemsPerOID().size());
// @formatter:on
}