/**
* 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));
}
