projects.put(userSession.getKey(), catalogManager.getProjectManager().create("default", "DefaultProject", "Description", "Organization", "Homo sapiens", null, null, "GrCh38", new QueryOptions(), userSession.getValue()).first().getFqn());
@Test public void testCreateProject() throws Exception { String projectAlias = "projectAlias_ASDFASDF"; catalogManager.getProjectManager().create(projectAlias, "Project", "", "", "Homo sapiens", null, null, "GRCh38", new QueryOptions(), sessionIdUser); thrown.expect(CatalogDBException.class); thrown.expectMessage(containsString("already exists")); catalogManager.getProjectManager().create(projectAlias, "Project", "", "", "Homo sapiens", null, null, "GRCh38", new QueryOptions(), sessionIdUser); }
@Before public void setUp() throws IOException, CatalogException, URISyntaxException { catalogManager = catalogManagerExternalResource.getCatalogManager(); catalogManager.getUserManager().create("user", "User Name", "mail@ebi.ac.uk", PASSWORD, "", null, Account.FULL, null, null); sessionIdUser = catalogManager.getUserManager().login("user", PASSWORD); project = catalogManager.getProjectManager().create("1000G", "Project about some genomes", "", "ACME", "Homo sapiens", null, null, "GRCh38", new QueryOptions(), sessionIdUser).first(); study = catalogManager.getStudyManager().create(project.getId(), "phase1", null, "Phase 1", Study.Type.TRIO, null, "Done", null, null, null, null, null, null, null, null, sessionIdUser).first(); folder = catalogManager.getFileManager().createFolder(study.getId(), Paths.get("data/vcf/").toString(), null, true, null, QueryOptions.empty(), sessionIdUser).first(); Path vcfPath = catalogManagerExternalResource.getOpencgaHome().resolve(VCF_FILE_NAME); Files.copy(this.getClass().getClassLoader().getResourceAsStream("biofiles/" + VCF_FILE_NAME), vcfPath, StandardCopyOption.REPLACE_EXISTING); vcfFileUri = vcfPath.toUri(); Path bamPath = catalogManagerExternalResource.getOpencgaHome().resolve(BAM_FILE_NAME); Files.copy(this.getClass().getClassLoader().getResourceAsStream("biofiles/" + BAM_FILE_NAME), bamPath, StandardCopyOption.REPLACE_EXISTING); bamFileUri = bamPath.toUri(); }
@Before public void setUp() throws IOException, CatalogException { catalogManager = catalogManagerExternalResource.getCatalogManager(); catalogManager.getUserManager().create("user", "User Name", "mail@ebi.ac.uk", PASSWORD, "", null, Account.FULL, null, null); sessionIdUser = catalogManager.getUserManager().login("user", PASSWORD); project = catalogManager.getProjectManager().create("1000G", "Project about some genomes", "", "ACME", "Homo sapiens", null, null, "GRCh38", new QueryOptions(), sessionIdUser).first(); study = catalogManager.getStudyManager().create(project.getId(), "phase1", null, "Phase 1", Study.Type.TRIO, null, "Done", null, null, null, null, null, null, null, null, sessionIdUser).first(); folder = catalogManager.getFileManager().createFolder(study.getId(), Paths.get("data/test/folder/").toString(), null, true, null, QueryOptions.empty(), sessionIdUser).first(); directory = catalogManagerExternalResource.getOpencgaHome().resolve("catalog_scan_test_folder").toAbsolutePath(); if (directory.toFile().exists()) { IOUtils.deleteDirectory(directory); } Files.createDirectory(directory); }
@BeforeClass public static void beforeClass() throws IOException, CatalogException, URISyntaxException { Configuration configuration = Configuration.load(CatalogSampleAnnotationsLoaderTest.class.getClassLoader() .getClass().getResource("/configuration-test.yml").openStream()); configuration.getAdmin().setAlgorithm("HS256"); catalogManager = new CatalogManager(configuration); catalogManager.deleteCatalogDB(true); catalogManager.installCatalogDB("dummy", "admin"); loader = new CatalogSampleAnnotationsLoader(catalogManager); String pedFileName = "20130606_g1k.ped"; URL pedFileURL = CatalogSampleAnnotationsLoader.class.getClassLoader().getResource(pedFileName); pedigree = loader.readPedigree(pedFileURL.getPath()); userId = "user1"; catalogManager.getUserManager().create(userId, userId, "asdasd@asd.asd", userId, "", -1L, Account.FULL, QueryOptions.empty(), null); sessionId = catalogManager.getUserManager().login(userId, userId); Project project = catalogManager.getProjectManager().create("def", "default", "", "ACME", "Homo sapiens", null, null, "GRCh38", new QueryOptions(), sessionId).getResult().get(0); Study study = catalogManager.getStudyManager().create(project.getFqn(), "def", null, "default", Study.Type.FAMILY, null, "", null, null, null, null, null, null, null, null, sessionId).getResult().get(0); studyId = study.getFqn(); pedFile = catalogManager.getFileManager().create(studyId, File.Type.FILE, File.Format.PED, File.Bioformat .OTHER_PED, "data/" + pedFileName, null, "", null, 0, -1, null, (long) -1, null, null, true, null, null, sessionId) .getResult().get(0); new FileUtils(catalogManager).upload(pedFileURL.toURI(), pedFile, null, sessionId, false, false, false, true, 10000000); pedFile = catalogManager.getFileManager().get(studyId, pedFile.getPath(), null, sessionId).getResult().get(0); }
@Test public void createStudyFailMoreThanOneProject() throws CatalogException { catalogManager.getProjectManager().incrementRelease(project1, sessionIdUser); catalogManager.getProjectManager().create("1000G2", "Project about some genomes", "", "ACME", "Homo sapiens", null, null, "GRCh38", new QueryOptions(), sessionIdUser); // Create a new study without providing the project. It should raise an error because the user owns more than one project thrown.expect(CatalogException.class); thrown.expectMessage("More than one project found"); catalogManager.getStudyManager().create(null, "phasexx", 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); }
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); }
projectId = catalogManager.getProjectManager().create("p1", "p1", "Project 1", "ACME", "Homo sapiens", null, null, "GRCh38", new QueryOptions(), sessionId).first().getId(); Study study = catalogManager.getStudyManager().create(projectId, "s1", null, "s1", Study.Type.CASE_CONTROL, null, "Study " +
userSessionId = catalogManager.getUserManager().login("user", "asdf"); String projectId = catalogManager.getProjectManager().create("proj", "proj", "", "", "Homo sapiens", null, null, "GRCh38", new QueryOptions(), userSessionId).getResult().get(0).getId(); Study study = catalogManager.getStudyManager().create(projectId, "std", "std", "std", Study.Type.CONTROL_SET, null, "", null, null,
catalog.getProjectManager().create("p1", "p1", "", null, "hsapiens", "Homo Sapiens", null, "GRCh38", null, sessionId); catalog.getStudyManager().create("p1", "s1", null, "s1", Study.Type.CONTROL_SET, null, null, null, null, null, null, null, null, null, null, sessionId); catalog.getStudyManager().create("p1", "s2", null, "s2", Study.Type.CONTROL_SET, null, null, null, null, null, null, null, null, null, null, sessionId); catalog.getCohortManager().create("s1", new Cohort().setId(StudyEntry.DEFAULT_COHORT).setSamples(samples), null, sessionId); catalog.getProjectManager().create("p2", "p2", "", null, "hsapiens", "Homo Sapiens", null, "GRCh38", null, sessionId); catalog.getStudyManager().create("p2", "p2s2", null, "s1", Study.Type.CONTROL_SET, null, null, null, null, null, null, null, null, null, null, sessionId);
public void setUpCatalogManager(CatalogManager catalogManager) throws IOException, CatalogException { catalogManager.getUserManager().create("user", "User Name", "mail@ebi.ac.uk", PASSWORD, "", null, Account.FULL, null, null); catalogManager.getUserManager().create("user2", "User2 Name", "mail2@ebi.ac.uk", PASSWORD, "", null, Account.FULL, null, null); catalogManager.getUserManager().create("user3", "User3 Name", "user.2@e.mail", PASSWORD, "ACME", null, Account.FULL, null, null); sessionIdUser = catalogManager.getUserManager().login("user", PASSWORD); sessionIdUser2 = catalogManager.getUserManager().login("user2", PASSWORD); sessionIdUser3 = catalogManager.getUserManager().login("user3", PASSWORD); project1 = catalogManager.getProjectManager().create("1000G", "Project about some genomes", "", "ACME", "Homo sapiens", null, null, "GRCh38", new QueryOptions(), sessionIdUser).first().getId(); project2 = catalogManager.getProjectManager().create("pmp", "Project Management Project", "life art intelligent system", "myorg", "Homo sapiens", null, null, "GRCh38", new QueryOptions(), sessionIdUser2).first().getId(); project3 = catalogManager.getProjectManager().create("p1", "project 1", "", "", "Homo sapiens", null, null, "GRCh38", new QueryOptions(), sessionIdUser3).first().getId(); studyId = catalogManager.getStudyManager().create(project1, "phase1", null, "Phase 1", Study.Type.TRIO, null, "Done", null, null, null, null, null, null, null, null, sessionIdUser).first().getFqn(); studyId2 = catalogManager.getStudyManager().create(project1, "phase3", null, "Phase 3", Study.Type.CASE_CONTROL, null, "d", null, null, null, null, null, null, null, null, sessionIdUser).first().getFqn(); studyId3 = catalogManager.getStudyManager().create(project2, "s1", null, "Study 1", Study.Type.CONTROL_SET, null, "", null, null, null, null, null, null, null, null, sessionIdUser2).first().getFqn(); }
sessionId = catalogManager.getUserManager().login(userId, "user"); projectAlias = "p1"; projectId = catalogManager.getProjectManager().create(projectAlias, projectAlias, "Project 1", "ACME", "Homo sapiens", null, null, "GRCh38", new QueryOptions(), sessionId).first().getId(); Study study = catalogManager.getStudyManager().create(projectId, "s1", "s1", "s1", Study.Type.CASE_CONTROL, null,
externalSessionId = catalogManager.getUserManager().login(externalUser, password); p1 = catalogManager.getProjectManager().create("p1", "p1", null, null, "Homo sapiens", null, null, "GRCh38", new QueryOptions(), ownerSessionId).first().getId(); Study study = catalogManager.getStudyManager().create(p1, "studyFqn", "studyFqn", "studyFqn", Study.Type.CASE_CONTROL, null, null,
sessionIdUser3 = catalogManager.getUserManager().login("user3", PASSWORD); Project project = catalogManager.getProjectManager().create("1000G", "Project about some genomes", "", "ACME", "Homo sapiens", null, null, "GRCh38", new QueryOptions(), sessionIdOwner).first(); studyFqn = catalogManager.getStudyManager().create(project.getFqn(), "phase1", null, "Phase 1", Study.Type.TRIO, null, "Done", null,
sessionIdUser3 = catalogManager.getUserManager().login("user3", PASSWORD); project1 = catalogManager.getProjectManager().create("1000G", "Project about some genomes", "", "ACME", "Homo sapiens", null, null, "GRCh38", new QueryOptions(), sessionIdUser).first().getId(); project2 = catalogManager.getProjectManager().create("pmp", "Project Management Project", "life art intelligent system", "myorg", "Homo sapiens", null, null, "GRCh38", new QueryOptions(), sessionIdUser2).first().getId(); catalogManager.getProjectManager().create("p1", "project 1", "", "", "Homo sapiens", null, null, "GRCh38", new QueryOptions(), sessionIdUser3).first();
@Test public void updateOrganismInProject() throws CatalogException { Project pr = catalogManager.getProjectManager().create("project2", "Project about some genomes", "", "ACME", "Homo sapiens", null, null, "GRCh38", null, sessionIdUser).first();