// test multiple derived data with no scan , multiple normalizations.
@Test
public void testNoScanWithNorm() {
MageTabDocumentSet ds = getDocumentSet(TestMageTabSets.MULTI_NO_SCAN_2_INPUT_SET);
CaArrayFileSet fileSet = TestMageTabSets.getFileSet(ds);
CaArrayTranslationResult result = this.translator.translate(ds, fileSet);
Experiment experiment = result.getInvestigations().iterator().next();
Hybridization hyb = experiment.getHybridizations().iterator().next();
checkPaCollection(hyb.getProtocolApplications(), "Scan");
RawArrayData rad = hyb.getRawDataCollection().iterator().next();
checkPaCollection(
rad.getProtocolApplications(),
"normalization-protocol-1",
"normalization-protocol-2",
"derived-data-protocol-1",
"derived-data-protocol-2");
for (DerivedArrayData d : hyb.getDerivedDataCollection()) {
if (d.getName().equals("test.data")) {
checkPaCollection(d.getProtocolApplications());
} else if (d.getName().equals("test2.data")) {
checkPaCollection(d.getProtocolApplications());
} else {
fail(d.getName());
}
}
}
// test normalization protocols end up in raw data.
@Test
public void testNormal_3() {
MageTabDocumentSet ds = getDocumentSet(TestMageTabSets.NORMAL_3_INPUT_SET);
CaArrayFileSet fileSet = TestMageTabSets.getFileSet(ds);
CaArrayTranslationResult result = this.translator.translate(ds, fileSet);
Experiment experiment = result.getInvestigations().iterator().next();
Hybridization hyb = experiment.getHybridizations().iterator().next();
RawArrayData rad = hyb.getRawDataCollection().iterator().next();
checkPaCollection(rad.getProtocolApplications(), "TRANPRTCL10656", "derived-data-protocol");
DerivedArrayData dad = hyb.getDerivedDataCollection().iterator().next();
checkPaCollection(dad.getProtocolApplications());
}
@Test
public void testNoNormNoDerivedData() {
MageTabDocumentSet ds = getDocumentSet(TestMageTabSets.NO_DERIVED_2_INPUT_SET);
CaArrayFileSet fileSet = TestMageTabSets.getFileSet(ds);
CaArrayTranslationResult result = this.translator.translate(ds, fileSet);
Experiment experiment = result.getInvestigations().iterator().next();
Hybridization hyb = experiment.getHybridizations().iterator().next();
checkPaCollection(hyb.getProtocolApplications(), "Scan");
RawArrayData rad = hyb.getRawDataCollection().iterator().next();
checkPaCollection(rad.getProtocolApplications(), "TRANPRTCL10656");
assertTrue(hyb.getDerivedDataCollection().isEmpty());
}
/*
* Tests to make sure that Characteristic categories with various forms of
* "external id", regardless of spaces and case, get translated into the
* "externalId" attribute of the biomaterial.
*/
@Test
public void testExternalIds() {
MageTabDocumentSet ds = getDocumentSet(TestMageTabSets.EXTERNAL_ID_1_INPUT_SET);
CaArrayFileSet fileSet = TestMageTabSets.getFileSet(ds);
CaArrayTranslationResult result = this.translator.translate(ds, fileSet);
Experiment experiment = result.getInvestigations().iterator().next();
Source src = experiment.getSources().iterator().next();
String sourceExternalId = src.getExternalId();
assertTrue(SOURCE_1_EXTERNAL_ID.equals(sourceExternalId));
Sample sampl = experiment.getSamples().iterator().next();
String sampleExternalId = sampl.getExternalId();
assertTrue(SAMPLE_1_EXTERNAL_ID.equals(sampleExternalId));
}
@Test
public void testNormal_1() {
MageTabDocumentSet ds = getDocumentSet(TestMageTabSets.NORMAL_1_INPUT_SET);
CaArrayFileSet fileSet = TestMageTabSets.getFileSet(ds);
CaArrayTranslationResult result = this.translator.translate(ds, fileSet);
Experiment experiment = result.getInvestigations().iterator().next();
Hybridization hyb = experiment.getHybridizations().iterator().next();
checkPaCollection(hyb.getProtocolApplications(), "Scan");
for (RawArrayData rad : hyb.getRawDataCollection()) {
if (rad.getName().equals("test1.CEL")) {
checkPaCollection(rad.getProtocolApplications());
} else if (rad.getName().equals("test2.CEL")) {
checkPaCollection(rad.getProtocolApplications(), "TRANPRTCL10656");
} else {
fail(rad.getName());
}
}
DerivedArrayData dad = hyb.getDerivedDataCollection().iterator().next();
checkPaCollection(dad.getProtocolApplications());
}