@Test
public final void testDeleteWithPropertiesButParentPreserved() {
final IExternalDataDAO externalDataDAO = daoFactory.getExternalDataDAO();
final ExternalDataPE deletedData = findExternalData(CHILD_CODE);
// Deleted data set should have all collections which prevent it from deletion empty.
assertTrue(deletedData.getChildren().isEmpty());
// delete
externalDataDAO.delete(deletedData);
// test successful deletion of data set
assertNull(externalDataDAO.tryGetByTechId(TechId.create(deletedData)));
// test successful deletion of data set properties
assertFalse(deletedData.getProperties().isEmpty());
List<EntityTypePropertyTypePE> retrievedPropertyTypes =
daoFactory
.getEntityPropertyTypeDAO(EntityKind.DATA_SET)
.listEntityPropertyTypes(deletedData.getEntityType());
for (DataSetPropertyPE property : deletedData.getProperties()) {
int index = retrievedPropertyTypes.indexOf(property.getEntityTypePropertyType());
EntityTypePropertyTypePE retrievedPropertyType = retrievedPropertyTypes.get(index);
assertFalse(retrievedPropertyType.getPropertyValues().contains(property));
}
// deleted sample had parent connected that should not have been deleted
// NOTE: somehow cannot get parents even though connection is the same as with children
// DataPE parent = deletedData.tryGetParent();
// assertNotNull(parent);
// assertNotNull(externalDataDAO.tryGetByTechId(new TechId(HibernateUtils.getId(parent))));
findExternalData(PARENT_CODE);
}
@Test
public final void testListExternalData() {
testCreateDataSetWithSample();
final IExternalDataDAO externalDataDAO = daoFactory.getExternalDataDAO();
List<ExternalDataPE> list = externalDataDAO.listExternalData(pickASample());
assertEquals(1, list.size());
ExternalDataPE dataSet = list.get(0);
assertEquals("abcd", dataSet.getLocation());
assertEquals(BooleanOrUnknown.U, dataSet.getComplete());
}
@Test(expectedExceptions = DataIntegrityViolationException.class)
public final void testDeleteFailWithChildrenDatasets() {
final IExternalDataDAO externalDataDAO = daoFactory.getExternalDataDAO();
final ExternalDataPE deletedData = findExternalData(PARENT_CODE);
// Deleted data set should have 'child' data sets which prevent it from deletion.
assertFalse(deletedData.getChildren().isEmpty());
// delete
externalDataDAO.delete(deletedData);
}
@Test
public void testUpdateOfDataSetFailWithSampleConnectedWhenThereIsParent() {
final IExternalDataDAO externalDataDAO = daoFactory.getExternalDataDAO();
// try to update dataset connected with a parent - connecting with a sample should fail
final ExternalDataPE dataSetConnectedWithParent = findExternalData(CHILD_CODE);
assertFalse(dataSetConnectedWithParent.getParents().isEmpty());
dataSetConnectedWithParent.setSampleAcquiredFrom(pickASample());
externalDataDAO.updateDataSet(dataSetConnectedWithParent);
assertCommitFailsWithBothSampleAndParentConnectionForDataSet(CHILD_CODE);
}
@Test
public void testUpdateOfDataSetFailWithParentAddedWhenIsSampleConnected() {
final IExternalDataDAO externalDataDAO = daoFactory.getExternalDataDAO();
// try to update dataset connected with a sample - adding a parent should fail
final ExternalDataPE dataSetConnectedWithSample = findExternalData(PARENT_CODE);
assertNotNull(dataSetConnectedWithSample.tryGetSample());
final ExternalDataPE anotherDataSet = findExternalData("20081105092159111-1");
dataSetConnectedWithSample.addParent(anotherDataSet);
externalDataDAO.updateDataSet(dataSetConnectedWithSample);
assertCommitFailsWithBothSampleAndParentConnectionForDataSet(PARENT_CODE);
}
@Test
public void testCreateDataSetFailWithBothSampleAndParent() {
final IExternalDataDAO externalDataDAO = daoFactory.getExternalDataDAO();
// try to create a dataset connected with a sample and a parent at the same time
final String dataSetCode = daoFactory.getPermIdDAO().createPermId();
final SamplePE sample = pickASample();
ExternalDataPE parentData = findExternalData(PARENT_CODE);
ExternalDataPE externalData = createExternalData(dataSetCode, sample);
externalData.addParent(parentData);
externalDataDAO.createDataSet(externalData);
assertCommitFailsWithBothSampleAndParentConnectionForDataSet(dataSetCode);
}
@Test
public void testUpdateDataSetWithParent() {
final IExternalDataDAO externalDataDAO = daoFactory.getExternalDataDAO();
// try to add a parent to a data set that already had one
final ExternalDataPE dataSetConnectedWithParent = findExternalData(CHILD_CODE);
assertFalse(dataSetConnectedWithParent.getParents().isEmpty());
final ExternalDataPE anotherDataSet = findExternalData("20081105092159111-1");
dataSetConnectedWithParent.addParent(anotherDataSet);
externalDataDAO.updateDataSet(dataSetConnectedWithParent);
ExternalDataPE dataSet = (ExternalDataPE) externalDataDAO.tryToFindDataSetByCode(CHILD_CODE);
assertEquals(dataSetConnectedWithParent.getParents().size(), dataSet.getParents().size());
Set<DataPE> extractedParents = dataSet.getParents();
for (DataPE parent : dataSetConnectedWithParent.getParents()) {
assertTrue(extractedParents.contains(parent));
}
assertTrue(extractedParents.contains(anotherDataSet));
}
@Test
public void testUpdateDataSetAquiredFromSample() {
IExternalDataDAO externalDataDAO = daoFactory.getExternalDataDAO();
DataPE data = new DataPE();
String dataSetCode = daoFactory.getPermIdDAO().createPermId();
data.setCode(dataSetCode);
data.setDataSetType(getDataSetType(DataSetTypeCode.UNKNOWN));
data.setExperiment(pickAnExperiment());
data.setSampleAcquiredFrom(pickASample());
data.setPlaceholder(true);
data.setDataStore(pickADataStore());
data.setModificationDate(new Date());
externalDataDAO.createDataSet(data);
ExternalDataPE externalData = new ExternalDataPE();
externalData.setId(externalDataDAO.tryToFindDataSetByCode(dataSetCode).getId());
externalData.setCode(dataSetCode);
externalData.setDataSetType(getDataSetType(DataSetTypeCode.UNKNOWN));
externalData.setDataStore(pickADataStore());
externalData.setExperiment(pickAnExperiment());
externalData.setSampleAcquiredFrom(pickASample());
externalData.setFileFormatType(pickAFileFormatType());
externalData.setLocatorType(pickALocatorType());
externalData.setLocation("abcd");
externalData.setComplete(BooleanOrUnknown.U);
externalData.setStorageFormatVocabularyTerm(pickAStorageFormatVocabularyTerm());
externalData.setPlaceholder(true);
final Date modificationTimestamp = data.getModificationDate();
externalData.setModificationDate(modificationTimestamp);
externalDataDAO.updateDataSet(externalData);
ExternalDataPE dataSet = (ExternalDataPE) externalDataDAO.tryToFindDataSetByCode(dataSetCode);
assertEquals(externalData.getCode(), dataSet.getCode());
assertEquals(externalData.getDataSetType(), dataSet.getDataSetType());
assertEquals(externalData.getExperiment(), dataSet.getExperiment());
assertEquals(externalData.getFileFormatType(), dataSet.getFileFormatType());
assertEquals(externalData.getLocatorType(), dataSet.getLocatorType());
assertEquals(externalData.getLocation(), dataSet.getLocation());
assertEquals(externalData.getComplete(), dataSet.getComplete());
assertEquals(externalData.getStorageFormat(), dataSet.getStorageFormat());
assertEquals(externalData.isPlaceholder(), dataSet.isPlaceholder());
assertEquals(externalData.isMeasured(), dataSet.isMeasured());
assertFalse(externalData.getModificationDate().equals(modificationTimestamp));
}
private void assertDataEqual(ExternalDataPE externalData, ExternalDataPE dataSet) {
assertEquals(externalData.getCode(), dataSet.getCode());
assertEquals(externalData.getDataSetType(), dataSet.getDataSetType());
assertEquals(externalData.getExperiment(), dataSet.getExperiment());
assertEquals(externalData.getFileFormatType(), dataSet.getFileFormatType());
assertEquals(externalData.getLocatorType(), dataSet.getLocatorType());
assertEquals(externalData.getLocation(), dataSet.getLocation());
assertEquals(externalData.getComplete(), dataSet.getComplete());
assertEquals(externalData.getStorageFormat(), dataSet.getStorageFormat());
assertEquals(externalData.isPlaceholder(), dataSet.isPlaceholder());
assertEquals(externalData.isMeasured(), dataSet.isMeasured());
assertEquals(externalData.tryGetSample(), dataSet.tryGetSample());
}
private ExternalDataPE createExternalData(String dataSetCode, SamplePE sampleOrNull) {
ExternalDataPE externalData = new ExternalDataPE();
externalData.setCode(dataSetCode);
externalData.setDataSetType(getDataSetType(DataSetTypeCode.UNKNOWN));
externalData.setExperiment(pickAnExperiment());
if (sampleOrNull != null) {
externalData.setSampleAcquiredFrom(sampleOrNull);
} else {
externalData.setDerived(true);
}
externalData.setFileFormatType(pickAFileFormatType());
externalData.setLocatorType(pickALocatorType());
externalData.setLocation("abcd");
externalData.setComplete(BooleanOrUnknown.U);
externalData.setStorageFormatVocabularyTerm(pickAStorageFormatVocabularyTerm());
externalData.setPlaceholder(true);
externalData.setDataStore(pickADataStore());
return externalData;
}