Examples with ContainmentExpression org.ehrbase.client.aql.containment.ContainmentExpression used on opensource projects

Example 1 with ContainmentExpression

use of org.ehrbase.client.aql.containment.ContainmentExpression in project openEHR_SDK by ehrbase.

the class ContainmentBinder method handleContainmentDto.

public void handleContainmentDto(ContainmentDto dto, MutablePair<ContainmentExpression, Map<Integer, Containment>> result) {
    ContainmentExpression containmentExpression;
    Map<Integer, Containment> containmentMap = new HashMap<>();
    ContainmentExpression containmentExpression1;
    Containment containment = new Containment(dto.getArchetypeId());
    containmentExpression1 = containment;
    containmentMap.put(dto.getId(), containment);
    if (dto.getContains() != null) {
        Pair<ContainmentExpression, Map<Integer, Containment>> pair = buildContainment(dto.getContains());
        containment.setContains(pair.getLeft());
        containmentMap.putAll(pair.getRight());
    }
    containmentExpression = containmentExpression1;
    result.setLeft(containmentExpression);
    result.setRight(containmentMap);
}

Example 2 with ContainmentExpression

use of org.ehrbase.client.aql.containment.ContainmentExpression in project openEHR_SDK by ehrbase.

the class CoronaTestIT method testCoronaWithJoin.

@Test
@Ignore
public void testCoronaWithJoin() throws IOException {
    ehr = openEhrClient.ehrEndpoint().createEhr();
    Composition composition = new CanonicalJson().unmarshal(IOUtils.toString(CompositionTestDataCanonicalJson.CORONA.getStream(), StandardCharsets.UTF_8), Composition.class);
    Flattener flattener = new Flattener(new TestDataTemplateProvider());
    CoronaAnamneseComposition coronaAnamneseComposition = flattener.flatten(composition, CoronaAnamneseComposition.class);
    openEhrClient.compositionEndpoint(ehr).mergeCompositionEntity(coronaAnamneseComposition);
    openEhrClient.compositionEndpoint(ehr).mergeCompositionEntity(TestData.buildEhrbaseBloodPressureSimpleDeV0());
    assertThat(openEhrClient.compositionEndpoint(ehr).find(coronaAnamneseComposition.getVersionUid().getUuid(), CoronaAnamneseComposition.class)).isNotNull();
    CoronaAnamneseCompositionContainment coronaAnamneseCompositionContainment = CoronaAnamneseCompositionContainment.getInstance();
    SymptomeSectionContainment symptomeSectionContainment = SymptomeSectionContainment.getInstance();
    HustenObservationContainment hustenObservationContainment = HustenObservationContainment.getInstance();
    FieberOderErhohteKorpertemperaturObservationContainment fieberOderErhohteKorpertemperaturObservationContainment = FieberOderErhohteKorpertemperaturObservationContainment.getInstance();
    HeiserkeitObservationContainment heiserkeitObservationContainment = HeiserkeitObservationContainment.getInstance();
    RisikogebietSectionContainment risikogebietSectionContainment = RisikogebietSectionContainment.getInstance();
    ReisefallObservationContainment reisefallObservationContainment = ReisefallObservationContainment.getInstance();
    // @formatter:off
    ContainmentExpression containmentExpression = coronaAnamneseCompositionContainment.contains(symptomeSectionContainment.contains(hustenObservationContainment).and(risikogebietSectionContainment.contains(reisefallObservationContainment)));
    // @formatter:on
    EntityQuery<Record3<VorhandenDefiningCode, Language, Language>> entityQuery = Query.buildEntityQuery(containmentExpression, hustenObservationContainment.VORHANDEN_DEFINING_CODE, coronaAnamneseCompositionContainment.LANGUAGE, reisefallObservationContainment.LANGUAGE);
    Parameter<UUID> ehrIdParameter = entityQuery.buildParameter();
    entityQuery.where(Condition.equal(EhrFields.EHR_ID(), ehrIdParameter));
    /*
        Select
              o0/data[at0001]/events[at0002]/data[at0003]/items[at0022]/items[at0005]/value/defining_Code as F0,
              c1/language as F1,
              o2/language as F2
              from EHR e
              contains COMPOSITION c1[openEHR-EHR-COMPOSITION.report.v1] contains (
                                                                                    (SECTION s3[openEHR-EHR-SECTION.adhoc.v1] contains
                                                                                                                                    OBSERVATION o0[openEHR-EHR-OBSERVATION.symptom_sign_screening.v0] )
                                                                                    and
                                                                                    ( SECTION s4[openEHR-EHR-SECTION.adhoc.v1] contains
                                                                                                                                    OBSERVATION o2[openEHR-EHR-OBSERVATION.travel_event.v0] )
                                                                                   )
             where e/ehr_id/value = $parm0
         */
    List<Record3<VorhandenDefiningCode, Language, Language>> actual = openEhrClient.aqlEndpoint().execute(entityQuery, ehrIdParameter.setValue(ehr));
    assertThat(actual).extracting(Record3::value1, Record3::value2, Record3::value3).containsExactlyInAnyOrder(new Tuple(VorhandenDefiningCode.VORHANDEN, Language.DE, Language.DE));
}

Example 3 with ContainmentExpression

use of org.ehrbase.client.aql.containment.ContainmentExpression in project openEHR_SDK by ehrbase.

the class EntityQueryTest method buildAqlWithNativePath.

@Test
public void buildAqlWithNativePath() {
    BefundObservationContainment befundObservationContainment = BefundObservationContainment.getInstance();
    ProVirusClusterContainment proVirusClusterContainment = ProVirusClusterContainment.getInstance();
    ProbeClusterContainment probeClusterContainment = ProbeClusterContainment.getInstance();
    Containment compositionContainment = new Containment("COMPOSITION");
    ContainmentExpression containment = compositionContainment.contains(befundObservationContainment).contains(proVirusClusterContainment.and(probeClusterContainment));
    EntityQuery<Record3<String, TemporalAccessor, UUID>> entityQuery = Query.buildEntityQuery(containment, proVirusClusterContainment.VIRUS_VALUE, probeClusterContainment.ZEITPUNKT_DER_PROBENENTNAHME_VALUE, new NativeSelectAqlField<>(compositionContainment, "/uid/value", "uid", UUID.class));
    entityQuery.where(Condition.equal(new NativeSelectAqlField<>(compositionContainment, "/name/value", String.class), "Mikrobiologischer Befund"));
    assertThat(entityQuery.buildAql()).isEqualTo("Select c0/items[at0024]/value/value as virusValue, c1/items[at0015]/value/value as zeitpunktDerProbenentnahmeValue, c2/uid/value as uid " + "from EHR e " + "contains COMPOSITION c2 " + "contains OBSERVATION o3[openEHR-EHR-OBSERVATION.laboratory_test_result.v1] " + "contains (CLUSTER c0[openEHR-EHR-CLUSTER.laboratory_test_analyte.v1] and CLUSTER c1[openEHR-EHR-CLUSTER.specimen.v1]) " + "where c2/name/value = 'Mikrobiologischer Befund'");
}

Example 4 with ContainmentExpression

use of org.ehrbase.client.aql.containment.ContainmentExpression in project openEHR_SDK by ehrbase.

the class CoronaTestIT method testNUMResearchCase_5.

/**
 * see https://wiki.vitagroup.ag/display/NUM/Research+Repository
 *
 * Containment test:
 *
 * contains COMPOSITION c[openEHR-EHR-COMPOSITION.event_summary.v0]
 * contains
 * (CLUSTER n[openEHR-EHR-CLUSTER.case_identification.v0]
 * and ADMIN_ENTRY u[openEHR-EHR-ADMIN_ENTRY.hospitalization.v0]
 * contains (CLUSTER a[openEHR-EHR-CLUSTER.location.v1]))
 */
@Test
public void testNUMResearchCase_5() {
    ehr = openEhrClient.ehrEndpoint().createEhr();
    openEhrClient.compositionEndpoint(ehr).mergeCompositionEntity(TestData.buildTestPatientenaufenthaltComposition());
    // build AQL
    PatientenaufenthaltCompositionContainment patientenaufenthaltCompositionContainment = PatientenaufenthaltCompositionContainment.getInstance();
    AbteilungsfallClusterContainment abteilungsfallClusterContainment = AbteilungsfallClusterContainment.getInstance();
    VersorgungsortAdminEntryContainment versorgungsortAdminEntryContainment = VersorgungsortAdminEntryContainment.getInstance();
    StandortClusterContainment standortClusterContainment = StandortClusterContainment.getInstance();
    ContainmentExpression containmentExpression = patientenaufenthaltCompositionContainment.contains(abteilungsfallClusterContainment.and(versorgungsortAdminEntryContainment.contains(standortClusterContainment)));
    // select set values from test data
    EntityQuery<Record3<TemporalAccessor, TemporalAccessor, String>> entityQuery = Query.buildEntityQuery(containmentExpression, versorgungsortAdminEntryContainment.BEGINN_VALUE, versorgungsortAdminEntryContainment.ENDE_VALUE, versorgungsortAdminEntryContainment.GRUND_DES_AUFENTHALTES_VALUE);
    Parameter<UUID> ehrIdParameter = entityQuery.buildParameter();
    entityQuery.where(Condition.equal(EhrFields.EHR_ID(), ehrIdParameter));
    List<Record3<TemporalAccessor, TemporalAccessor, String>> actual = openEhrClient.aqlEndpoint().execute(entityQuery, ehrIdParameter.setValue(ehr));
    assertThat(actual).extracting(Record3::value1, Record3::value2, Record3::value3).containsExactlyInAnyOrder(new Tuple(new DvDateTime("2020-01-01T10:00Z").getValue(), new DvDateTime("2020-01-01T12:00Z").getValue(), "test value"));
}

Example 5 with ContainmentExpression

use of org.ehrbase.client.aql.containment.ContainmentExpression in project openEHR_SDK by ehrbase.

the class CoronaTestIT method testNUMResearchCase_8.

/**
 * see https://wiki.vitagroup.ag/display/NUM/Research+Repository
 *
 * Containment test UC 8:
 *
 * contains COMPOSITION c
 * contains OBSERVATION v[openEHR-EHR-OBSERVATION.laboratory_test_result.v1]
 * contains (
 * CLUSTER h[openEHR-EHR-CLUSTER.laboratory_test_panel.v0] and
 * CLUSTER x[openEHR-EHR-CLUSTER.specimen.v1] and
 * CLUSTER q[openEHR-EHR-CLUSTER.laboratory_test_analyte.v1])
 */
@Test
public void testNUMResearchCase_8() {
    VirologischerBefundComposition virologischerBefundComposition = TestData.buildTestVirologischerBefundComposition();
    assertThat(virologischerBefundComposition.getBefund()).isNotNull();
    ehr = openEhrClient.ehrEndpoint().createEhr();
    openEhrClient.compositionEndpoint(ehr).mergeCompositionEntity(virologischerBefundComposition);
    // build AQL expression
    Containment compositionContainment = new Containment("COMPOSITION");
    BefundObservationContainment befundObservationContainment = BefundObservationContainment.getInstance();
    ProbeClusterContainment probeClusterContainment = ProbeClusterContainment.getInstance();
    KulturClusterContainment kulturClusterContainment = KulturClusterContainment.getInstance();
    ProVirusClusterContainment proVirusClusterContainment = ProVirusClusterContainment.getInstance();
    ContainmentExpression containmentExpression = compositionContainment.contains(befundObservationContainment.contains(kulturClusterContainment.and(probeClusterContainment.and(proVirusClusterContainment))));
    EntityQuery<Record2<String, Long>> entityQuery = Query.buildEntityQuery(containmentExpression, proVirusClusterContainment.VIRUS_VALUE, proVirusClusterContainment.ANALYSEERGEBNIS_REIHENFOLGE_MAGNITUDE);
    Parameter<UUID> ehrIdParameter = entityQuery.buildParameter();
    entityQuery.where(Condition.equal(EhrFields.EHR_ID(), ehrIdParameter).and(Condition.equal(new NativeSelectAqlField<>(compositionContainment, "/name/value", String.class), "Virologischer Befund")));
    List<Record2<String, Long>> actual = openEhrClient.aqlEndpoint().execute(entityQuery, ehrIdParameter.setValue(ehr));
    // NB. At the moment, we cannot specify DISTINCT with SDK
    assertThat(actual).extracting(Record2::value1, Record2::value2).containsExactlyInAnyOrder(new Tuple("SARS-Cov-2", 32L), new Tuple("SARS-Cov-2", 34L), new Tuple("SARS-Cov-2", 32L), new Tuple("SARS-Cov-2", 34L));
}