Ejemplo n.º 1
0
  public void testWriteAssayProperties() throws AtlasLoaderException {
    // create investigation
    MAGETABInvestigation investigation = new MAGETABInvestigation();
    investigation.IDF.experimentalFactorType.add("Type");
    investigation.IDF.experimentalFactorName.add("Type");

    Assay assay = new Assay("TEST-ASSAY");

    AssayNode assayNode = new AssayNode();
    FactorValueAttribute fva = new FactorValueAttribute();
    fva.type = "Type";
    fva.setAttributeValue("specific factor value");
    assayNode.factorValues.add(fva);

    final LoaderDAO dao = MockFactory.createLoaderDAO();

    AssayAndHybridizationStep.writeAssayProperties(investigation, assay, assayNode, dao);

    // now get properties of assay - we should have one matching our factor value
    assertSame("Wrong number of properties", assay.getProperties().size(), 1);
    for (AssayProperty p : assay.getProperties()) {
      assertEquals("Wrong property name", p.getName(), "type");
      assertEquals("Wrong property value", p.getValue(), "specific factor value");
    }
  }
Ejemplo n.º 2
0
  public void testWriteSampleProperties() throws AtlasLoaderException {
    // create investigation
    MAGETABInvestigation investigation = new MAGETABInvestigation();

    Sample sample = new Sample("TEST-SAMPLE");

    SourceNode sourceNode = new SourceNode();
    CharacteristicsAttribute fva = new CharacteristicsAttribute();
    fva.type = "Type";
    fva.setAttributeValue("specific factor value");
    sourceNode.characteristics.add(fva);

    new SourceStep().readSampleProperties(sample, sourceNode, MockFactory.createLoaderDAO());

    // now get properties of assay - we should have one matching our factor value
    assertSame("Wrong number of properties", sample.getProperties().size(), 1);
    for (SampleProperty p : sample.getProperties()) {
      assertEquals("Wrong property name", p.getName(), "type");
      assertEquals("Wrong property value", p.getValue(), "specific factor value");
    }
  }