Esempio n. 1
0
  /**
   * 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));
  }