@Override
public void onApplicationEvent(ContextRefreshedEvent event) {
// Run it as System
// Remember the original context
SecurityContext origCtx = SecurityContextHolder.getContext();
try {
// Set a SystemSecurityToken
SecurityContextHolder.setContext(SecurityContextHolder.createEmptyContext());
SecurityContextHolder.getContext().setAuthentication(new SystemSecurityToken());
Query q =
new QueryImpl()
.eq(ObservableFeature.DATATYPE, FieldTypeEnum.CATEGORICAL.toString().toLowerCase());
for (ObservableFeature categoricalFeature :
dataService.findAll(ObservableFeature.ENTITY_NAME, q, ObservableFeature.class)) {
OmxLookupTableRepository repo =
new OmxLookupTableRepository(
dataService, categoricalFeature.getIdentifier(), queryResolver);
dataService.addRepository(repo);
}
} finally {
// Set the original context back when method is finished
SecurityContextHolder.setContext(origCtx);
}
}
// RULE: Feature can only belong to one Protocol in a DataSet.(see issue #1136)
private void checkFeatureCanOnlyBelongToOneProtocolForOneDataSet() {
// RULE: Feature can only belong to one Protocol in a DataSet. Check it (see issue #1136)
Iterable<DataSet> dataSets = dataService.findAll(DataSet.ENTITY_NAME, DataSet.class);
for (DataSet dataSet : dataSets) {
List<Protocol> dataSetProtocols =
ProtocolUtils.getProtocolDescendants(dataSet.getProtocolUsed(), true);
for (Protocol protocol : dataSetProtocols) {
for (ObservableFeature feature : protocol.getFeatures()) {
for (Protocol p : dataSetProtocols) {
if (!p.equals(protocol) && p.getFeatures().contains(feature)) {
String message =
String.format(
"An ObservableFeature can only belong to one Protocol but feature '%s' belongs to both '%s' and '%s'",
feature.getIdentifier(), p.getIdentifier(), protocol.getIdentifier());
throw new MolgenisValidationException(
Sets.newHashSet(
new ConstraintViolation(
message, feature.getIdentifier(), feature, null, null, 0)));
}
}
}
}
}
}
public static void setUp(DataService dataService) throws Exception {
features0 = new ArrayList<ObservableFeature>();
features1 = new ArrayList<ObservableFeature>();
allEntities = new ArrayList<Entity>();
subProtocols = new ArrayList<Protocol>();
subProtocols1 = new ArrayList<Protocol>();
categories = new ArrayList<Category>();
feature0 = new ObservableFeature();
feature0.setId(0);
feature0.setName("featureName" + 0);
feature0.setIdentifier("feature" + 0);
feature1 = new ObservableFeature();
feature1.setId(1);
feature1.setName("featureName" + 1);
feature1.setIdentifier("feature" + 1);
features0.add(feature0);
features1.add(feature1);
protocol0 = new Protocol();
protocol0.setDescription("description0");
protocol0.setIdentifier("identifier0");
protocol0.setId(0);
protocol0.setFeatures(features0);
protocol1 = new Protocol();
protocol1.setDescription("description1");
protocol1.setIdentifier("identifier1");
protocol1.setId(1);
protocol1.setFeatures(features1);
subProtocols1.add(protocol1);
protocol2 = new Protocol();
protocol2.setDescription("description2");
protocol2.setIdentifier("identifier2");
protocol2.setSubprotocols(subProtocols1);
protocol2.setId(2);
protocol3 = new Protocol();
protocol3.setDescription("description3");
protocol3.setIdentifier("identifier3");
protocol3.setSubprotocols(subProtocols1);
protocol3.setId(3);
allEntities.add(protocol0);
allEntities.add(protocol1);
allEntities.add(protocol2);
allEntities.add(protocol3);
subProtocols.add(protocol0);
protocolUsed = new Protocol();
protocolUsed.setDescription("protocolUsed_description");
protocolUsed.setIdentifier("protocolUsed_identifier");
protocolUsed.setId(100);
protocolUsed.setSubprotocols(subProtocols);
allEntities.add(protocolUsed);
dataset = new DataSet();
dataset.setId(0);
dataset.setIdentifier("dataset" + 0);
dataset.setName("datasetname" + 0);
dataset.setProtocolUsed(protocolUsed);
observationSet0 = new ObservationSet();
observationSet0.setId(0);
observationSet0.setPartOfDataSet(dataset);
observationSets0 = new ArrayList<Entity>();
observationSets0.add(observationSet0);
observationSet1 = new ObservationSet();
observationSet1.setId(1);
ObservedValue observedValue0 = new ObservedValue();
observedValue0.setId(0);
observedValue0.setObservationSet(observationSet0);
observedValue0.setValue(new Value());
observedValue0.setFeature(feature0);
observedValue0.setObservationSet(observationSet0);
observedValues0 = new ArrayList<ObservedValue>();
observedValues0.add(observedValue0);
ObservedValue observedValue1 = new ObservedValue();
observedValue1.setId(1);
observedValue1.setObservationSet(observationSet1);
Value v1 = new Value();
v1.setId(1);
observedValue1.setValue(v1);
observedValue1.setFeature(feature1);
observedValue1.setObservationSet(observationSet1);
observedValues1 = new ArrayList<ObservedValue>();
observedValues1.add(observedValue1);
observationSets0 = new ArrayList<Entity>();
observationSets0.add(observationSet0);
category0 = new Category();
category0.setId(0);
category0.setIdentifier("category" + 0);
categories.add(category0);
List<DataSet> datasets = new ArrayList<DataSet>();
datasets.add(dataset);
when(dataService.findAllAsList(
DataSet.ENTITY_NAME, new QueryImpl().eq(DataSet.IDENTIFIER, "dataset1")))
.thenReturn(Arrays.<Entity>asList(dataset));
when(dataService.findAllAsList(
ObservedValue.ENTITY_NAME,
new QueryImpl().eq(ObservedValue.OBSERVATIONSET, observationSet0)))
.thenReturn(Arrays.<Entity>asList(observedValue0));
when(dataService.findAllAsList(
ObservationSet.ENTITY_NAME, new QueryImpl().eq(ObservationSet.PARTOFDATASET, 0)))
.thenReturn(Arrays.<Entity>asList(observationSet0));
}
@Override
@Transactional(rollbackFor = IOException.class)
public EntityImportReport doImport(
RepositoryCollection repositories, DatabaseAction databaseAction) throws IOException {
// All new repository identifiers
List<String> newRepoIdentifiers = new ArrayList<String>();
// First import entities, the data sheets are ignored in the entitiesimporter
EntityImportReport importReport = entitiesImporter.importEntities(repositories, databaseAction);
// RULE: Feature can only belong to one Protocol in a DataSet. Check it (see issue #1136)
checkFeatureCanOnlyBelongToOneProtocolForOneDataSet();
// Import data sheets
for (String name : repositories.getEntityNames()) {
Repository repository = repositories.getRepositoryByEntityName(name);
if (repository.getName().startsWith(DATASET_SHEET_PREFIX)) {
// Import DataSet sheet, create new OmxRepository
String identifier = repository.getName().substring(DATASET_SHEET_PREFIX.length());
if (!dataService.hasRepository(identifier)) {
dataService.addRepository(
new AggregateableCrudRepositorySecurityDecorator(
new OmxRepository(dataService, searchService, identifier, entityValidator)));
newRepoIdentifiers.add(identifier);
DataSet dataSet =
dataService.findOne(
DataSet.ENTITY_NAME,
new QueryImpl().eq(DataSet.IDENTIFIER, identifier),
DataSet.class);
List<Protocol> protocols =
ProtocolUtils.getProtocolDescendants(dataSet.getProtocolUsed());
List<ObservableFeature> categoricalFeatures = new ArrayList<ObservableFeature>();
for (Protocol protocol : protocols) {
List<ObservableFeature> observableFeatures = protocol.getFeatures();
if (observableFeatures != null) {
for (ObservableFeature observableFeature : observableFeatures) {
String dataType = observableFeature.getDataType();
FieldType type = MolgenisFieldTypes.getType(dataType);
if (type.getEnumType() == FieldTypeEnum.CATEGORICAL) {
categoricalFeatures.add(observableFeature);
}
}
}
}
for (ObservableFeature categoricalFeature : categoricalFeatures) {
if (!dataService.hasRepository(
OmxLookupTableEntityMetaData.createOmxLookupTableEntityMetaDataName(
categoricalFeature.getIdentifier()))) {
dataService.addRepository(
new OmxLookupTableRepository(
dataService, categoricalFeature.getIdentifier(), queryResolver));
newRepoIdentifiers.add(
OmxLookupTableEntityMetaData.createOmxLookupTableEntityMetaDataName(
categoricalFeature.getIdentifier()));
}
}
}
// Check if all column names in the excel sheet exist as attributes of the entity
Set<ConstraintViolation> violations = Sets.newLinkedHashSet();
EntityMetaData meta = dataService.getEntityMetaData(identifier);
for (AttributeMetaData attr : repository.getEntityMetaData().getAttributes()) {
if (meta.getAttribute(attr.getName()) == null) {
String message =
String.format(
"Unknown attributename '%s' for entity '%s'. Sheet: '%s'",
attr.getName(), meta.getName(), repository.getName());
violations.add(new ConstraintViolation(message, attr.getName(), null, null, meta, 0));
}
}
if (!violations.isEmpty()) {
throw new MolgenisValidationException(violations);
}
// Import data into new OmxRepository
try {
dataService.add(identifier, repository);
} catch (MolgenisValidationException e) {
// Add sheet info
for (ConstraintViolation violation : e.getViolations()) {
if (violation.getRownr() > 0) {
// Rownr +1 for header
violation.setImportInfo(
String.format(
"Sheet: '%s', row: %d", repository.getName(), violation.getRownr() + 1));
} else {
violation.setImportInfo(String.format("Sheet: '%s'", repository.getName()));
}
}
for (String newRepoIdentifier : newRepoIdentifiers) {
dataService.removeRepository(newRepoIdentifier);
}
throw e;
}
int count = (int) RepositoryUtils.count(repository);
importReport.addEntityCount(identifier, count);
importReport.addNrImported(count);
}
}
return importReport;
}