// 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));
}
private void mergeFactors(Experiment originalExperiment, Experiment translatedExperiment) {
for (final Factor translatedFactor : translatedExperiment.getFactors()) {
boolean isNewFactor = true;
final Set<Factor> originalFactors = originalExperiment.getFactors();
for (final Factor originalFactor : originalFactors) {
if (originalFactor.getName().equals(translatedFactor.getName())) {
isNewFactor = false;
for (final AbstractFactorValue newValue : translatedFactor.getFactorValues()) {
newValue.setFactor(originalFactor);
}
break;
}
}
if (isNewFactor) {
originalFactors.add(translatedFactor);
}
}
}
private void mergeExperimentContacts(
Experiment originalExperiment, Experiment translatedExperiment) {
for (final ExperimentContact translatedEc : translatedExperiment.getExperimentContacts()) {
final List<ExperimentContact> originalExperimentContacts =
originalExperiment.getExperimentContacts();
boolean isNewEc = true;
for (final ExperimentContact originalEc : originalExperimentContacts) {
if (originalEc.equalsBaseContact(translatedEc)) {
isNewEc = false;
break;
}
}
if (isNewEc) {
translatedEc.setExperiment(originalExperiment);
originalExperimentContacts.add(translatedEc);
}
}
}
@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());
}
private void mergeTranslatedData(Experiment originalExperiment, Experiment translatedExperiment) {
originalExperiment.getArrayDesigns().addAll(translatedExperiment.getArrayDesigns());
originalExperiment.setDate(translatedExperiment.getDate());
originalExperiment.setDescription(translatedExperiment.getDescription());
mergeFactors(originalExperiment, translatedExperiment);
originalExperiment
.getExperimentDesignTypes()
.addAll(translatedExperiment.getExperimentDesignTypes());
originalExperiment.getNormalizationTypes().addAll(translatedExperiment.getNormalizationTypes());
originalExperiment.getPublications().addAll(translatedExperiment.getPublications());
originalExperiment
.getQualityControlTypes()
.addAll(translatedExperiment.getQualityControlTypes());
originalExperiment.getReplicateTypes().addAll(translatedExperiment.getReplicateTypes());
mergeExperimentContacts(originalExperiment, translatedExperiment);
originalExperiment.getHybridizations().addAll(translatedExperiment.getHybridizations());
this.projectDao.save(originalExperiment.getHybridizations());
for (final LabeledExtract le : translatedExperiment.getLabeledExtracts()) {
le.setExperiment(originalExperiment);
originalExperiment.getLabeledExtracts().add(le);
}
this.projectDao.save(originalExperiment.getLabeledExtracts());
for (final Extract e : translatedExperiment.getExtracts()) {
e.setExperiment(originalExperiment);
originalExperiment.getExtracts().add(e);
}
this.projectDao.save(originalExperiment.getExtracts());
for (final Sample s : translatedExperiment.getSamples()) {
s.setExperiment(originalExperiment);
originalExperiment.getSamples().add(s);
}
this.projectDao.save(originalExperiment.getSamples());
for (final Source s : translatedExperiment.getSources()) {
s.setExperiment(originalExperiment);
originalExperiment.getSources().add(s);
}
this.projectDao.save(originalExperiment.getSources());
}