if (StringUtils.isEmpty(family.getId())) { throw new CatalogException("Missing family id"); QueryResult<Family> familyQueryResult = catalogManager.getFamilyManager().get(study.getFqn(), family.getId(), new QueryOptions(), sessionId); if (familyQueryResult.getNumResults() == 0) { throw new CatalogException("Family " + family.getId() + " not found"); throw new CatalogException("Family " + family.getId() + " does not have any members associated"); Individual fullMember = memberMap.get(selectedMember.getId()); if (fullMember == null) { throw new CatalogException("Member " + selectedMember.getId() + " does not belong to family " + family.getId());
private void validateFamilyAndProband(ClinicalAnalysis clinicalAnalysis, Study study, String sessionId) throws CatalogException { if (clinicalAnalysis.getFamily() != null && StringUtils.isNotEmpty(clinicalAnalysis.getFamily().getId())) { MyResource<Family> familyResource = catalogManager.getFamilyManager().getUid(clinicalAnalysis.getFamily().getId(), study.getFqn(), sessionId); clinicalAnalysis.setFamily(familyResource.getResource()); // Check the proband is an actual member of the family Query query = new Query() .append(FamilyDBAdaptor.QueryParams.UID.key(), familyResource.getResource().getUid()) .append(FamilyDBAdaptor.QueryParams.MEMBER_UID.key(), clinicalAnalysis.getProband().getUid()); QueryResult<Family> count = catalogManager.getFamilyManager().count(study.getFqn(), query, sessionId); if (count.getNumTotalResults() == 0) { throw new CatalogException("The member " + clinicalAnalysis.getProband().getId() + " does not belong to the family " + clinicalAnalysis.getFamily().getId()); } } }
public static Pedigree getPedigreeFromFamily(Family family) { List<Individual> members = family.getMembers(); Map<String, Member> individualMap = new HashMap<>(); // Parse all the individuals for (Individual member : members) { Member individual = new Member( member.getId(), member.getName(), null, null, member.getMultiples(), Member.Sex.getEnum(member.getSex().toString()), member.getLifeStatus(), Member.AffectionStatus.getEnum(member.getAffectationStatus().toString()), member.getPhenotypes(), member.getAttributes()); individualMap.put(individual.getId(), individual); } // Fill parent information for (Individual member : members) { if (member.getFather() != null && StringUtils.isNotEmpty(member.getFather().getId())) { individualMap.get(member.getId()).setFather(individualMap.get(member.getFather().getId())); } if (member.getMother() != null && StringUtils.isNotEmpty(member.getMother().getId())) { individualMap.get(member.getId()).setMother(individualMap.get(member.getMother().getId())); } } List<Member> individuals = new ArrayList<>(individualMap.values()); return new Pedigree(family.getId(), individuals, family.getPhenotypes(), family.getAttributes()); }
if (clinicalAnalysis.getFamily() == null || StringUtils.isEmpty(clinicalAnalysis.getFamily().getId())) { throw new AnalysisException("Missing family in clinical analysis " + clinicalAnalysisId);
auditManager.recordDeletion(AuditRecord.Resource.family, family.getUid(), userId, null, updateParams, null, null); } else { failedList.add(new WriteResult.Fail(family.getId(), "Unknown reason")); failedList.add(new WriteResult.Fail(family.getId(), e.getMessage())); logger.debug("Cannot delete family {}: {}", family.getId(), e.getMessage(), e);
public QueryResult<Family> create(String studyStr, Family family, QueryOptions options, String sessionId) throws CatalogException { String userId = catalogManager.getUserManager().getUserId(sessionId); Study study = catalogManager.getStudyManager().resolveId(studyStr, userId); authorizationManager.checkStudyPermission(study.getUid(), userId, StudyAclEntry.StudyPermissions.WRITE_FAMILIES); ParamUtils.checkObj(family, "family"); ParamUtils.checkAlias(family.getId(), "id"); family.setName(ParamUtils.defaultObject(family.getName(), family.getId())); family.setMembers(ParamUtils.defaultObject(family.getMembers(), Collections.emptyList())); family.setPhenotypes(ParamUtils.defaultObject(family.getPhenotypes(), Collections.emptyList())); family.setDisorders(ParamUtils.defaultObject(family.getDisorders(), Collections.emptyList())); family.setCreationDate(TimeUtils.getTime()); family.setDescription(ParamUtils.defaultString(family.getDescription(), "")); family.setStatus(new Family.FamilyStatus()); family.setAnnotationSets(ParamUtils.defaultObject(family.getAnnotationSets(), Collections.emptyList())); family.setRelease(catalogManager.getStudyManager().getCurrentRelease(study, userId)); family.setVersion(1); family.setAttributes(ParamUtils.defaultObject(family.getAttributes(), Collections.emptyMap())); List<VariableSet> variableSetList = validateNewAnnotationSetsAndExtractVariableSets(study.getUid(), family.getAnnotationSets()); autoCompleteFamilyMembers(family, study, sessionId); validateFamily(family); validateMultiples(family); validatePhenotypes(family); validateDisorders(family); createMissingMembers(family, study, sessionId); options = ParamUtils.defaultObject(options, QueryOptions::new); family.setUuid(UUIDUtils.generateOpenCGAUUID(UUIDUtils.Entity.FAMILY)); QueryResult<Family> queryResult = familyDBAdaptor.insert(study.getUid(), family, variableSetList, options); auditManager.recordCreation(AuditRecord.Resource.family, queryResult.first().getId(), userId, queryResult.first(), null, null); return queryResult; }
throw new CatalogException("Individual could not be extracted from family " + family.getId() + ". " + "Individual not deleted"); + "following members: {}", individual.getId(), family.getId(), family.getMembers().stream().map(Individual::getId).collect(Collectors.toList())); throw new CatalogException("Internal error: Could not delete individual");
if (clinicalAnalysis.getFamily() == null || StringUtils.isEmpty(clinicalAnalysis.getFamily().getId())) { throw new AnalysisException("Missing family in clinical analysis " + clinicalAnalysisId);
@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()); }