public QueryResult<Individual> get(long studyId, Query query, QueryOptions options, String sessionId) throws CatalogException { return get(String.valueOf(studyId), query, options, sessionId); }
Query query = new Query(IndividualDBAdaptor.QueryParams.SAMPLES.key(), aclParams.getSample()); QueryOptions options = new QueryOptions(QueryOptions.INCLUDE, IndividualDBAdaptor.QueryParams.ID.key()); QueryResult<Individual> indQueryResult = catalogManager.getIndividualManager().get(studyStr, query, options, sessionId);
.append(IndividualDBAdaptor.QueryParams.SAMPLES.key(), query.getString(IndividualDBAdaptor.QueryParams.SAMPLES.key())); QueryOptions options = new QueryOptions(QueryOptions.INCLUDE, IndividualDBAdaptor.QueryParams.UID.key()); QueryResult<Individual> individualResult = catalogManager.getIndividualManager().get(study.getFqn(), newQuery, options, sessionId);
@Test public void readIndividualStudyManager() throws CatalogException { catalogManager.getIndividualManager().get(null, ind2, null, studyAdmin1SessionId); }
@Test public void readIndividualByReadingSomeSample() throws CatalogException { catalogManager.getIndividualManager().get(null, ind1, null, memberSessionId); }
QueryResult<Individual> individualQueryResult = catalogManager.getIndividualManager().get(study.getFqn(), query, new QueryOptions(), sessionId); for (Individual individual : individualQueryResult.getResult()) {
private void fillIndividuals(String studyId, List<org.opencb.biodata.models.metadata.Individual> individuals) throws CatalogException { Map<String, org.opencb.biodata.models.metadata.Individual> individualMap = individuals .stream() .collect(Collectors.toMap(org.opencb.biodata.models.metadata.Individual::getId, i -> i)); Query query = new Query(IndividualDBAdaptor.QueryParams.ID.key(), new ArrayList<>(individualMap.keySet())); List<Individual> catalogIndividuals = catalogManager.getIndividualManager().get(studyId, query, INDIVIDUAL_QUERY_OPTIONS, sessionId) .getResult(); for (Individual catalogIndividual : catalogIndividuals) { org.opencb.biodata.models.metadata.Individual individual = individualMap.get(catalogIndividual.getName()); individual.setSex(catalogIndividual.getSex().name()); // individual.setFamily(catalogIndividual.getFamily()); individual.setPhenotype(catalogIndividual.getAffectationStatus().toString()); if (catalogIndividual.getMother() != null) { individual.setMother(catalogIndividual.getMother().getId()); } if (catalogIndividual.getFather() != null) { individual.setFather(catalogIndividual.getFather().getId()); } } }
@Test public void readIndividualForbidden() throws CatalogException { thrown.expect(CatalogAuthorizationException.class); catalogManager.getIndividualManager().get(null, ind2, null, externalSessionId); }
Query query = new Query(IndividualDBAdaptor.QueryParams.ID.key(), sampleAclParams.getIndividual()); QueryOptions options = new QueryOptions(QueryOptions.INCLUDE, IndividualDBAdaptor.QueryParams.SAMPLES.key()); QueryResult<Individual> indQueryResult = catalogManager.getIndividualManager().get(studyStr, query, options, sessionId);
@Test public void readAllIndividuals() throws CatalogException { assertEquals(2, catalogManager.getIndividualManager().get(studyFqn, new Query(), null, ownerSessionId).getNumResults()); assertEquals(2, catalogManager.getIndividualManager().get(studyFqn, new Query(), null, studyAdmin1SessionId).getNumResults()); assertEquals(0, catalogManager.getIndividualManager().get(studyFqn, new Query(), null, externalSessionId).getNumResults()); }
QueryResult<Individual> individualQueryResult = catalogManager.getIndividualManager().get(study.getFqn(), member.getId(), new QueryOptions(), sessionId); if (individualQueryResult.getNumResults() == 0) { if (ListUtils.isNotEmpty(samples) && samples.get(0).getUid() <= 0) { QueryResult<Individual> individualQueryResult = catalogManager.getIndividualManager().get(study.getFqn(), finalMember.getId(), new QueryOptions(QueryOptions.INCLUDE, IndividualDBAdaptor.QueryParams.SAMPLES.key()), sessionId);
@Test public void testCreateSampleWithIndividual() throws CatalogException { String individualId = catalogManager.getIndividualManager().create(studyFqn, new Individual().setId("Individual1"), new QueryOptions(), sessionIdUser).first().getId(); String sampleId1 = catalogManager.getSampleManager().create(studyFqn, new Sample() .setId("SAMPLE_1") .setIndividual(new Individual().setId(individualId)), new QueryOptions(), sessionIdUser).first().getId(); QueryResult<Individual> individualQueryResult = catalogManager.getIndividualManager().get(studyFqn, individualId, QueryOptions.empty(), sessionIdUser); assertEquals(sampleId1, individualQueryResult.first().getSamples().get(0).getId()); // Create sample linking to individual based on the individual name String sampleId2 = catalogManager.getSampleManager().create(studyFqn, new Sample() .setId("SAMPLE_2") .setIndividual(new Individual().setId("Individual1")), new QueryOptions(), sessionIdUser).first().getId(); individualQueryResult = catalogManager.getIndividualManager().get(studyFqn, individualId, QueryOptions.empty(), sessionIdUser); assertEquals(2, individualQueryResult.first().getSamples().size()); assertTrue(individualQueryResult.first().getSamples().stream().map(Sample::getId).collect(Collectors.toSet()).containsAll( Arrays.asList(sampleId1, sampleId2) )); }
), QueryOptions.empty(), sessionIdUser); QueryResult<Individual> individualQueryResult = catalogManager.getIndividualManager().get(studyFqn, individualId, new QueryOptions(QueryOptions.INCLUDE, SampleDBAdaptor.QueryParams.ANNOTATION_SETS.key()), sessionIdUser); assertEquals(1, individualQueryResult.first().getAnnotationSets().size());
QueryResult<Individual> individualQueryResult = catalogManager.getIndividualManager().get(studyStr, sample.getIndividual().getId(), new QueryOptions(QueryOptions.INCLUDE, Arrays.asList(
ind = catalogManager.getIndividualManager().get(studyFqn, ind.getId(), null, sessionIdUser).first(); check.accept(sample.getAnnotationSets().get(0)); check.accept(ind.getAnnotationSets().get(0)); ind = catalogManager.getIndividualManager().get(studyFqn, ind.getId(), null, sessionIdUser).first(); check.accept(sample.getAnnotationSets().get(0)); check.accept(ind.getAnnotationSets().get(0)); ind = catalogManager.getIndividualManager().get(studyFqn, ind.getId(), null, sessionIdUser).first(); check.accept(sample.getAnnotationSets().get(0)); check.accept(ind.getAnnotationSets().get(0)); ind = catalogManager.getIndividualManager().get(studyFqn, ind.getId(), null, sessionIdUser).first(); check.accept(sample.getAnnotationSets().get(0)); check.accept(ind.getAnnotationSets().get(0));
individuals = catalogManager.getIndividualManager().get(studyFqn, new Query(IndividualDBAdaptor.QueryParams.ANNOTATION.key(), variableSet.getId() + ":NAME=~^INDIVIDUAL_"), null, sessionIdUser) assertTrue(individuals.containsAll(Arrays.asList("INDIVIDUAL_1", "INDIVIDUAL_2", "INDIVIDUAL_3"))); individuals = catalogManager.getIndividualManager().get(studyFqn, new Query(IndividualDBAdaptor.QueryParams.ANNOTATION.key(), variableSet.getId() + ":AGE>10"), null, sessionIdUser) .getResult().stream().map(Individual::getName).collect(Collectors.toList()); assertTrue(individuals.containsAll(Arrays.asList("INDIVIDUAL_2", "INDIVIDUAL_3"))); individuals = catalogManager.getIndividualManager().get(studyFqn, new Query(IndividualDBAdaptor.QueryParams.ANNOTATION.key(), variableSet.getId() + ":AGE>10;" + variableSet.getId() + ":PHEN=CASE"), null, sessionIdUser)
QueryResult<Individual> newIndividualQueryResult = catalogManager.getIndividualManager().get(studyStr, individualStr, indOptions, sessionId);