PanelManager(AuthorizationManager authorizationManager, AuditManager auditManager, CatalogManager catalogManager, DBAdaptorFactory catalogDBAdaptorFactory, CatalogIOManagerFactory ioManagerFactory, Configuration configuration) { super(authorizationManager, auditManager, catalogManager, catalogDBAdaptorFactory, ioManagerFactory, configuration); this.userManager = catalogManager.getUserManager(); this.studyManager = catalogManager.getStudyManager(); }
FileManager(AuthorizationManager authorizationManager, AuditManager auditManager, CatalogManager catalogManager, DBAdaptorFactory catalogDBAdaptorFactory, CatalogIOManagerFactory ioManagerFactory, Configuration configuration) { super(authorizationManager, auditManager, catalogManager, catalogDBAdaptorFactory, ioManagerFactory, configuration); file = new FileMetadataReader(this.catalogManager); this.userManager = catalogManager.getUserManager(); }
SampleManager(AuthorizationManager authorizationManager, AuditManager auditManager, CatalogManager catalogManager, DBAdaptorFactory catalogDBAdaptorFactory, CatalogIOManagerFactory ioManagerFactory, Configuration configuration) { super(authorizationManager, auditManager, catalogManager, catalogDBAdaptorFactory, ioManagerFactory, configuration); this.userManager = catalogManager.getUserManager(); this.studyManager = catalogManager.getStudyManager(); }
IndividualManager(AuthorizationManager authorizationManager, AuditManager auditManager, CatalogManager catalogManager, DBAdaptorFactory catalogDBAdaptorFactory, CatalogIOManagerFactory ioManagerFactory, Configuration configuration) { super(authorizationManager, auditManager, catalogManager, catalogDBAdaptorFactory, ioManagerFactory, configuration); this.userManager = catalogManager.getUserManager(); this.studyManager = catalogManager.getStudyManager(); }
public QueryResult<Group> getGroup(String studyStr, String groupId, String sessionId) throws CatalogException { String userId = catalogManager.getUserManager().getUserId(sessionId); Study study = resolveId(studyStr, userId); authorizationManager.checkCanViewStudy(study.getUid(), userId); // Fix the groupId if (groupId != null && !groupId.startsWith("@")) { groupId = "@" + groupId; } return studyDBAdaptor.getGroup(study.getUid(), groupId, Collections.emptyList()); }
@Test public void testLogin() throws Exception { catalogManager.getUserManager().login("user", PASSWORD); thrown.expect(CatalogAuthenticationException.class); thrown.expectMessage(allOf(containsString("Incorrect"), containsString("password"))); catalogManager.getUserManager().login("user", "fakePassword"); }
public QueryResult<PermissionRule> getPermissionRules(String studyStr, Study.Entity entry, String sessionId) throws CatalogException { String userId = catalogManager.getUserManager().getUserId(sessionId); Study study = resolveId(studyStr, userId); authorizationManager.checkCanViewStudy(study.getUid(), userId); return studyDBAdaptor.getPermissionRules(study.getUid(), entry); }
@Test public void createFileNoStudyMember() throws CatalogException, IOException { String newUser = "newUser"; catalogManager.getUserManager().create(newUser, newUser, "asda@mail.com", password, "org", 1000L, Account.FULL, null, null); String sessionId = catalogManager.getUserManager().login(newUser, password); thrown.expect(CatalogAuthorizationException.class); catalogManager.getFileManager().createFolder(studyFqn, Paths.get("data/my_folder/").toString(), null, false, null, QueryOptions.empty(), sessionId); }
@Test public void addExistingUserToRole() throws CatalogException { String newUser = "newUser"; catalogManager.getUserManager().create(newUser, newUser, "email@ccc.ccc", password, "ASDF", null, Account.FULL, null, null); Study.StudyAclParams aclParams = new Study.StudyAclParams("", AclParams.Action.ADD, AuthorizationManager.ROLE_ANALYST); catalogManager.getStudyManager().updateAcl(Arrays.asList(studyFqn), newUser, aclParams, ownerSessionId).get(0); }
@Test public void readFileNoStudyMember() throws CatalogException, IOException { String newUser = "newUser"; catalogManager.getUserManager().create(newUser, newUser, "asda@mail.com", password, "org", 1000L, Account.FULL, null, null); String sessionId = catalogManager.getUserManager().login(newUser, password); thrown.expect(CatalogAuthorizationException.class); catalogManager.getFileManager().get(studyFqn, data, null, sessionId); }
@Test public void testCreateExistingUser() throws Exception { thrown.expect(CatalogException.class); thrown.expectMessage(containsString("already exists")); catalogManager.getUserManager().create("user", "User Name", "mail@ebi.ac.uk", PASSWORD, "", null, Account.FULL, null, null); }
@Test public void readSampleExternalUser() throws CatalogException, IOException { String newUser = "newUser"; catalogManager.getUserManager().create(newUser, newUser, "asda@mail.com", password, "org", 1000L, Account.FULL, null, null); String sessionId = catalogManager.getUserManager().login(newUser, password); thrown.expect(CatalogAuthorizationException.class); catalogManager.getSampleManager().get(studyFqn, smp2.getId(), null, sessionId); }
public QueryResult<ClinicalAnalysis> count(String studyStr, Query query, String sessionId) throws CatalogException { String userId = catalogManager.getUserManager().getUserId(sessionId); Study study = catalogManager.getStudyManager().resolveId(studyStr, userId); fixQueryObject(query, study, sessionId); query.append(ClinicalAnalysisDBAdaptor.QueryParams.STUDY_UID.key(), study.getUid()); QueryResult<Long> queryResultAux = clinicalDBAdaptor.count(query, userId, StudyAclEntry.StudyPermissions.VIEW_CLINICAL_ANALYSIS); return new QueryResult<>("count", queryResultAux.getDbTime(), 0, queryResultAux.first(), queryResultAux.getWarningMsg(), queryResultAux.getErrorMsg(), Collections.emptyList()); }
public void markDeletedPermissionRule(String studyStr, Study.Entity entry, String permissionRuleId, PermissionRule.DeleteAction deleteAction, String sessionId) throws CatalogException { ParamUtils.checkObj(entry, "entry"); ParamUtils.checkObj(deleteAction, "Delete action"); ParamUtils.checkObj(permissionRuleId, "permission rule id"); String userId = catalogManager.getUserManager().getUserId(sessionId); Study study = resolveId(studyStr, userId); authorizationManager.checkCanUpdatePermissionRules(study.getUid(), userId); studyDBAdaptor.markDeletedPermissionRule(study.getUid(), entry, permissionRuleId, deleteAction); }
private void setUpCatalogManager(CatalogManager catalogManager) throws IOException, CatalogException { catalogManager.getUserManager().create("user", "User Name", "mail@ebi.ac.uk", PASSWORD, "", null, Account.FULL, null, null); sessionIdUser = catalogManager.getUserManager().login("user", PASSWORD); String projectId = catalogManager.getProjectManager().create("1000G", "Project about some genomes", "", "ACME", "Homo sapiens", null, null, "GRCh38", new QueryOptions(), sessionIdUser).first().getId(); catalogManager.getStudyManager().create(projectId, "phase1", null, "Phase 1", Study.Type.TRIO, null, "Done", null, null, null, null, null, null, null, null, sessionIdUser); }
public void setUpCatalogManager(CatalogManager catalogManager) throws IOException, CatalogException { catalogManager.getUserManager().create("user", "User Name", "mail@ebi.ac.uk", PASSWORD, "", null, Account.FULL, null, null); sessionIdUser = catalogManager.getUserManager().login("user", PASSWORD); String projectId = catalogManager.getProjectManager().create("1000G", "Project about some genomes", "", "ACME", "Homo sapiens", null, null, "GRCh38", new QueryOptions(), sessionIdUser).first().getId(); catalogManager.getStudyManager().create(projectId, "phase1", null, "Phase 1", Study.Type.TRIO, null, "Done", null, null, null, null, null, null, null, null, sessionIdUser); }
public void fillMissing(String studyStr, boolean overwrite, ObjectMap config, String sessionId) throws CatalogException, IllegalAccessException, InstantiationException, ClassNotFoundException, StorageEngineException { String userId = catalogManager.getUserManager().getUserId(sessionId); Study study = catalogManager.getStudyManager().resolveId(studyStr, userId); DataStore dataStore = getDataStore(study.getFqn(), sessionId); VariantStorageEngine variantStorageEngine = storageEngineFactory.getVariantStorageEngine(dataStore.getStorageEngine(), dataStore.getDbName()); variantStorageEngine.fillMissing(study.getFqn(), config, overwrite); }
public void setUpCatalogManager(CatalogManager catalogManager) throws IOException, CatalogException { catalogManager.getUserManager().create("user", "User Name", "mail@ebi.ac.uk", PASSWORD, "", null, Account.FULL, null, null); sessionIdUser = catalogManager.getUserManager().login("user", PASSWORD); String projectId = catalogManager.getProjectManager().create("1000G", "Project about some genomes", "", "ACME", "Homo sapiens", null, null, "GRCh38", new QueryOptions(), sessionIdUser).first().getId(); catalogManager.getStudyManager().create(projectId, "phase1", null, "Phase 1", Study.Type.TRIO, null, "Done", null, null, null, null, null, null, null, null, sessionIdUser); }
@Before public void setUp() throws IOException, CatalogException { catalogManager = catalogManagerResource.getCatalogManager(); panelManager = catalogManager.getPanelManager(); setUpCatalogManager(catalogManager); adminToken = catalogManager.getUserManager().login("admin", "admin"); }
@Test public void readSampleSharedForOthersNotWithStudyPermissions() throws CatalogException, IOException { // Add a new user to a new group String newUser = "newUser"; catalogManager.getUserManager().create(newUser, newUser, "asda@mail.com", password, "org", 1000L, Account.FULL, null, null); String sessionId = catalogManager.getUserManager().login(ownerUser, password); catalogManager.getStudyManager().updateGroup(studyFqn, "@members", new GroupParams(newUser, GroupParams.Action.ADD), ownerSessionId); QueryResult<Sample> sample = catalogManager.getSampleManager().get(studyFqn, smp6.getId(), null, sessionId); assertEquals(1, sample.getNumResults()); }