/*
* 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 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());
}