public List<QueryResult<SampleAclEntry>> getAcls(String studyStr, List<String> sampleList, String member, boolean silent, String sessionId) throws CatalogException { List<QueryResult<SampleAclEntry>> sampleAclList = new ArrayList<>(sampleList.size()); for (String sample : sampleList) { try { MyResource<Sample> resource = getUid(sample, studyStr, sessionId); QueryResult<SampleAclEntry> allSampleAcls; if (StringUtils.isNotEmpty(member)) { allSampleAcls = authorizationManager.getSampleAcl(resource.getStudy().getUid(), resource.getResource().getUid(), resource.getUser(), member); } else { allSampleAcls = authorizationManager.getAllSampleAcls(resource.getStudy().getUid(), resource.getResource().getUid(), resource.getUser()); } allSampleAcls.setId(sample); sampleAclList.add(allSampleAcls); } catch (CatalogException e) { if (silent) { sampleAclList.add(new QueryResult<>(sample, 0, 0, 0, "", e.toString(), new ArrayList<>(0))); } else { throw e; } } } return sampleAclList; }
for (Sample sample : individual.getSamples()) { try { MyResource<Sample> resource = catalogManager.getSampleManager().getUid(sample.getId(), studyStr, sessionId); existingSampleIds.add(resource.getResource().getUid()); } catch (CatalogException e) {
@Test public void createClinicalAnalysisNoFamilyTest() throws CatalogException { QueryResult<ClinicalAnalysis> dummyEnvironment = createDummyEnvironment(false); assertEquals(1, dummyEnvironment.getNumResults()); assertEquals(0, dummyEnvironment.first().getInterpretations().size()); assertEquals(catalogManager.getIndividualManager().getUid("child1", STUDY, sessionIdUser).getResource().getUid(), dummyEnvironment.first().getProband().getUid()); assertEquals(1, dummyEnvironment.first().getProband().getSamples().size()); assertEquals(catalogManager.getSampleManager().getUid("sample2", STUDY, sessionIdUser).getResource().getUid(), dummyEnvironment.first().getProband().getSamples().get(0).getUid()); }
@Test public void createClinicalAnalysisTest() throws CatalogException { QueryResult<ClinicalAnalysis> dummyEnvironment = createDummyEnvironment(true); assertEquals(1, dummyEnvironment.getNumResults()); assertEquals(0, dummyEnvironment.first().getInterpretations().size()); assertEquals("family", dummyEnvironment.first().getFamily().getId()); assertEquals(5, dummyEnvironment.first().getFamily().getMembers().size()); assertNotNull(dummyEnvironment.first().getProband()); assertEquals("child1", dummyEnvironment.first().getProband().getId()); assertEquals(1, dummyEnvironment.first().getProband().getSamples().size()); assertEquals("sample2", dummyEnvironment.first().getProband().getSamples().get(0).getId()); assertEquals(catalogManager.getSampleManager().getUid("sample2", STUDY, sessionIdUser).getResource().getUid(), dummyEnvironment.first().getProband().getSamples().get(0).getUid()); }
@Test public void updateSubjectsNoFamilyTest() throws CatalogException { createDummyEnvironment(false); ObjectMap params = new ObjectMap(ClinicalAnalysisDBAdaptor.QueryParams.PROBAND.key(), new Individual().setId("child1").setSamples(Arrays.asList(new Sample().setId("sample2")))); QueryResult<ClinicalAnalysis> updateResult = catalogManager.getClinicalAnalysisManager().update(STUDY, "analysis", params, QueryOptions.empty(), sessionIdUser); assertEquals(1, updateResult.getNumResults()); assertEquals(0, updateResult.first().getInterpretations().size()); assertEquals(catalogManager.getIndividualManager().getUid("child1", STUDY, sessionIdUser).getResource().getUid(), updateResult.first().getProband().getUid()); assertEquals(1, updateResult.first().getProband().getSamples().size()); assertEquals(catalogManager.getSampleManager().getUid("sample2", STUDY, sessionIdUser).getResource().getUid(), updateResult.first().getProband().getSamples().get(0).getUid()); }
options = ParamUtils.defaultObject(options, QueryOptions::new); MyResource<Sample> resource = getUid(entryStr, studyStr, sessionId);
@Test public void updateSubjectsAndFamilyTest() throws CatalogException { createDummyEnvironment(false); ObjectMap params = new ObjectMap() .append(ClinicalAnalysisDBAdaptor.QueryParams.PROBAND.key(), new Individual().setId("child1").setSamples(Arrays.asList(new Sample().setId("sample2")))) .append(ClinicalAnalysisDBAdaptor.QueryParams.FAMILY.key(), new Family().setId("family")); QueryResult<ClinicalAnalysis> updateResult = catalogManager.getClinicalAnalysisManager().update(STUDY, "analysis", params, QueryOptions.empty(), sessionIdUser); assertEquals(1, updateResult.getNumResults()); assertEquals(0, updateResult.first().getInterpretations().size()); assertEquals(catalogManager.getFamilyManager().getUid("family", STUDY, sessionIdUser).getResource().getUid(), updateResult.first().getFamily().getUid()); assertEquals(catalogManager.getIndividualManager().getUid("child1", STUDY, sessionIdUser).getResource().getUid(), updateResult.first().getProband().getUid()); assertEquals(1, updateResult.first().getProband().getSamples().size()); assertEquals(catalogManager.getSampleManager().getUid("sample2", STUDY, sessionIdUser).getResource().getUid(), updateResult.first().getProband().getSamples().get(0).getUid()); }
MyResource<Sample> sampleResource = catalogManager.getSampleManager().getUid(query.getString("sample"), study.getFqn(), sessionId); query.put(ClinicalAnalysisDBAdaptor.QueryParams.SAMPLE_UID.key(), sampleResource.getResource().getUid());