@Before public void setUp() throws Exception { DummyProjectMetadataAdaptor.clear(); DummyStudyConfigurationAdaptor.clear(); scm = new StudyConfigurationManager(new DummyProjectMetadataAdaptor(), new DummyStudyConfigurationAdaptor(), new DummyVariantFileMetadataDBAdaptor()); }
@Override public StudyConfigurationManager getStudyConfigurationManager() throws StorageEngineException { return new StudyConfigurationManager(new DummyProjectMetadataAdaptor(), new DummyStudyConfigurationAdaptor(), new DummyVariantFileMetadataDBAdaptor()); } }
@Override default void clearDB(String dbName) throws Exception { DummyProjectMetadataAdaptor.clear(); DummyStudyConfigurationAdaptor.clear(); }
@After public void tearDown() throws Exception { DummyProjectMetadataAdaptor.writeAndClear(catalogManagerExternalResource.getOpencgaHome()); DummyStudyConfigurationAdaptor.writeAndClear(catalogManagerExternalResource.getOpencgaHome()); }
@Override public StudyConfigurationManager getStudyConfigurationManager() { return new StudyConfigurationManager(new DummyProjectMetadataAdaptor(), new DummyStudyConfigurationAdaptor(), new DummyVariantFileMetadataDBAdaptor()); }
@After public void tearDown() throws Exception { DummyStudyConfigurationAdaptor.clear(); }
@After public void tearDown() throws Exception { DummyProjectMetadataAdaptor.writeAndClear(getTmpRootDir()); DummyStudyConfigurationAdaptor.writeAndClear(getTmpRootDir()); }
@Before public void setUp() throws Exception { DummyStudyConfigurationAdaptor.clear(); scm = new StudyConfigurationManager(new DummyProjectMetadataAdaptor(), new DummyStudyConfigurationAdaptor(), new DummyVariantFileMetadataDBAdaptor()); parser = new VariantMongoDBQueryParser(scm); scm.updateStudyConfiguration(newStudyConfiguration(1, Arrays.asList(1, 2, 3, 4), false), null); scm.updateStudyConfiguration(newStudyConfiguration(2, Arrays.asList(1, 2, 3, 4), true), null); }
@Before public void init() throws StorageEngineException { scm = new StudyConfigurationManager(new DummyProjectMetadataAdaptor(), new DummyStudyConfigurationAdaptor(), new DummyVariantFileMetadataDBAdaptor()); scm.createStudy(studyName); solrQueryParser = new SolrQueryParser(scm); }
@Test public void testExportImport() throws Exception { String export = Paths.get(opencga.createTmpOutdir(studyId, "_EXPORT_", sessionId)).resolve("export.json.gz").toString(); variantManager.exportData(export, VariantOutputFormat.JSON_GZ, studyId, sessionId); DummyStudyConfigurationAdaptor.clear(); variantManager.importData(URI.create(export), studyId2, sessionId); }
@After public void tearDown() throws Exception { DummyStudyConfigurationAdaptor.writeAndClear(opencga.getOpencgaHome()); DummyVariantFileMetadataDBAdaptor.writeAndClear(opencga.getOpencgaHome()); DummyProjectMetadataAdaptor.writeAndClear(opencga.getOpencgaHome()); }
@Before public void setUp() throws Exception { scm = new StudyConfigurationManager(new DummyProjectMetadataAdaptor(), new DummyStudyConfigurationAdaptor(), new DummyVariantFileMetadataDBAdaptor()); sc = new StudyConfiguration(1, "S1"); sc.getIndexedFiles().add(1); sc.getIndexedFiles().add(2); sc.getSamplesInFiles().put(1, new LinkedHashSet<>(listOf(1, 2, 3))); sc.getSamplesInFiles().put(2, new LinkedHashSet<>(listOf(4, 5, 6))); sc.getSampleIds().put("S1", 1); sc.getSampleIds().put("S2", 2); sc.getSampleIds().put("S3", 3); sc.getSampleIds().put("S4", 4); sc.getSampleIds().put("S5", 5); sc.getSampleIds().put("S6", 6); sc.getSampleIds().put("S7", 7); sc.getAttributes().put(VariantStorageEngine.Options.MERGE_MODE.key(), VariantStorageEngine.MergeMode.BASIC); scm.updateStudyConfiguration(sc, null); final GenomeHelper genomeHelper = new GenomeHelper(new Configuration()); converter = new HBaseToStudyEntryConverter(genomeHelper.getColumnFamily(), scm, null); }
@Test public void testExportSomeSamplesImport() throws Exception { String export = Paths.get(opencga.createTmpOutdir(studyId, "_EXPORT_", sessionId)).resolve("export.avro").toString(); List<Sample> samples = catalogManager.getSampleManager().get(studyId, new Query(), new QueryOptions(), sessionId).getResult(); List<String> someSamples = samples.stream().limit(samples.size() / 2).map(Sample::getId).collect(Collectors.toList()); Query query = new Query(VariantQueryParam.INCLUDE_STUDY.key(), studyId) .append(VariantQueryParam.INCLUDE_SAMPLE.key(), someSamples); QueryOptions queryOptions = new QueryOptions(); variantManager.exportData(export, VariantOutputFormat.AVRO, query, queryOptions, sessionId); DummyStudyConfigurationAdaptor.clear(); variantManager.importData(URI.create(export), studyId2, sessionId); } }
@Before public void setUp() throws Exception { scm = new StudyConfigurationManager(new DummyProjectMetadataAdaptor(), new DummyStudyConfigurationAdaptor(), new DummyVariantFileMetadataDBAdaptor()); Study study = catalogManager.getStudyManager().get(studyId, null, sessionId).first(); StudyConfiguration studyConfigurationToReturn = new StudyConfiguration((int) study.getUid(), "user@p1:s1"); studyConfigurationToReturn.setIndexedFiles(indexedFiles); for (File file : files) { if (indexedFiles.contains(((int) file.getUid()))) { studyConfigurationToReturn.getFileIds().put(file.getName(), ((int) file.getUid())); } } scm.updateStudyConfiguration(studyConfigurationToReturn, null); // checkStudyConfiguration(study, studyConfigurationToReturn); }
factory.unregisterVariantStorageEngine(DummyVariantStorageEngine.STORAGE_ENGINE_ID); DummyStudyConfigurationAdaptor.clear();