Beispiel #1
0
 /*
  * 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));
 }
Beispiel #2
0
  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());
  }