@Test
public void testLoadSIF() throws Exception {
String filepath = TestUtils.DATA_DIR + "sample/BRCA_sif.txt";
List<String> expectedAttributeNames =
Arrays.asList(
"TCGA_EXPERIMENT",
"TCGA_BATCH",
"TUMOR_NORMAL",
"BIRDSEED_GENDER",
"LEVEL2_NOISE",
"LEVEL3_SEGMENT_COUNT",
"PURITY PLOIDY",
"DELTA",
"CANCER_DNA_FRACTION",
"SUBCLONAL_GENOME_FRACTION");
tstLoadFi(filepath, 0, false); // Sample information file, shouldn't have tracks.
Set<String> attrNames = new HashSet<String>(AttributeManager.getInstance().getAttributeNames());
assertTrue(
attrNames.size()
>= expectedAttributeNames.size()); // Can be larger because of default attributes
for (String name : expectedAttributeNames) {
assertTrue(expectedAttributeNames.contains(name));
}
}
/**
* Test loading segmented data file from a sql database, using a profile
*
* @throws Exception
*/
@Test
public void testLoadSegProfile() throws Exception {
String path = TestUtils.DATA_DIR + "sql/seg_canFam2_profile.dbxml";
int expectedTracks = 6;
List<Track> tracks = trackLoader.load(new ResourceLocator(path), genome);
assertEquals(expectedTracks, tracks.size());
Set<String> expSampleIds =
new HashSet<String>(
Arrays.asList("0123-A", "0123-B-1", "0123-C-1", "0123-C-2", "0123-C-3"));
Set<String> actSampleIds = new HashSet<String>(5);
for (Track track : tracks) {
if (track instanceof DataSourceTrack) {
actSampleIds.add(track.getName());
}
}
assertEquals(expSampleIds, actSampleIds);
}
/**
* 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));
}
}