/** * Test loading sample information file from a sql database, using a profile * * @throws Exception */ @Test public void testLoadSampleInfoProfile() throws Exception { AttributeManager.getInstance().clearAllAttributes(); String path = TestUtils.DATA_DIR + "sql/sampleinfo_brca_sif_profile.dbxml"; int expectedTracks = 0; List<Track> tracks = trackLoader.load(new ResourceLocator(path), genome); assertEquals(expectedTracks, tracks.size()); String[] attrNames = "TCGA_EXPERIMENT TCGA_BATCH TUMOR_NORMAL BIRDSEED_GENDER LEVEL2_NOISE LEVEL3_SEGMENT_COUNT PURITY PLOIDY DELTA CANCER_DNA_FRACTION SUBCLONAL_GENOME_FRACTION" .split("\\s+"); Set<String> expAttrNames = new HashSet<String>(Arrays.asList(attrNames)); List<String> actAttrNames = AttributeManager.getInstance().getAttributeNames(); actAttrNames.remove("NAME"); actAttrNames.remove("DATA TYPE"); actAttrNames.remove("DATA FILE"); assertEquals(actAttrNames.size(), expAttrNames.size()); for (String attrName : actAttrNames) { assertTrue(expAttrNames.contains(attrName)); } }
public void call(Call call) throws AssertionFailedError { if (pendingCalls.isEmpty() || !pendingCalls.get(0).equals(call)) fail(stateMessage(new StringBuilder("Unexpected call: ").append(call))); receivedCalls.add(pendingCalls.remove(0)); }