@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); }
@Test public void testByStepsMultiRelease() throws Exception { List<File> inputFiles = new ArrayList<>(); File transformFile; for (int i = 77; i <= 79; i++) { inputFiles.add(create("platinum/1K.end.platinum-genomes-vcf-NA128" + i + "_S1.genome.vcf.gz")); } for (File inputFile : inputFiles) { transformFile = transformFile(inputFile, new QueryOptions()); loadFile(transformFile, new QueryOptions(), outputId); opencga.getCatalogManager().getProjectManager().incrementRelease(projectAlias, sessionId); } int i = 1; for (File inputFile : inputFiles) { inputFile = opencga.getCatalogManager().getFileManager().get(studyId, inputFile.getId(), null, sessionId).first(); assertEquals(1, inputFile.getRelease()); assertEquals(i, inputFile.getIndex().getRelease()); i++; } variantManager.iterator(new Query(VariantQueryParam.STUDY.key(), studyId), new QueryOptions(), sessionId).forEachRemaining(variant -> { System.out.println("variant = " + variant); }); }
catalog.getCohortManager().create("s1", new Cohort().setId("c1").setSamples(Collections.emptyList()), null, sessionId); catalog.getProjectManager().incrementRelease("p1", sessionId); file3 = createFile("data/file3.vcf"); file4 = createFile("data/file4.vcf");
new QueryOptions(Constants.INCREMENT_VERSION, true), sessionIdUser); catalogManager.getProjectManager().incrementRelease(projectId, sessionIdUser); catalogManager.getProjectManager().incrementRelease(projectId, sessionIdUser); catalogManager.getSampleManager().update(studyFqn, "testSample", new ObjectMap(), new QueryOptions(Constants.INCREMENT_VERSION, true), sessionIdUser);