@Override
@RunAsSystem
public void initialize() {
Resource resource = new ClassPathResource("roc-curve.R");
if (resource.exists()) {
long count =
dataService.count(
Script.ENTITY_NAME, new QueryImpl().eq(Script.NAME, ROC_CURVE_SCRIPT_NAME));
if (count == 0) {
Entity scriptType =
dataService.findOne(ScriptType.ENTITY_NAME, new QueryImpl().eq(ScriptType.NAME, "R"));
if (scriptType == null) throw new UnknownEntityException("ScriptType R does not exist!");
String scriptContent;
try {
scriptContent =
FileCopyUtils.copyToString(new InputStreamReader(resource.getInputStream(), "UTF-8"));
} catch (IOException e) {
throw new UncheckedIOException(e);
}
if (dataService.count(
ScriptParameter.ENTITY_NAME,
new QueryImpl().eq(ScriptParameter.NAME, ROC_CURVE_SCRIPT_PARAMETER))
== 0) {
dataService.add(
ScriptParameter.ENTITY_NAME,
new MapEntity(ImmutableMap.of(ScriptParameter.NAME, ROC_CURVE_SCRIPT_PARAMETER)));
}
Entity scriptParameterEntity =
dataService.findOne(
ScriptParameter.ENTITY_NAME,
new QueryImpl().eq(ScriptParameter.NAME, ROC_CURVE_SCRIPT_PARAMETER));
MapEntity scriptEntity = new MapEntity();
scriptEntity.set(Script.NAME, ROC_CURVE_SCRIPT_NAME);
scriptEntity.set(Script.GENERATE_TOKEN, true);
scriptEntity.set(Script.TYPE, scriptType);
scriptEntity.set(Script.RESULT_FILE_EXTENSION, "png");
scriptEntity.set(Script.CONTENT, scriptContent);
scriptEntity.set(Script.PARAMETERS, Arrays.asList(scriptParameterEntity));
dataService.add(Script.ENTITY_NAME, scriptEntity);
LOG.info("Script entity \"roc\" has been added to the database!");
} else {
LOG.info("Script entity \"roc\" already exists in the database!");
}
} else {
LOG.info("R script \"roc-curve.R\" does not exist on classpath!");
}
}
@RunAsSystem
public FileIngestJob createJob(FileIngestJobExecution fileIngestJobExecution) {
dataService.add(FileIngestJobExecutionMetaData.ENTITY_NAME, fileIngestJobExecution);
String username = fileIngestJobExecution.getUser();
Progress progress = new ProgressImpl(fileIngestJobExecution, jobExecutionUpdater, mailSender);
TransactionTemplate transactionTemplate = new TransactionTemplate(transactionManager);
RunAsUserToken runAsAuthentication =
new RunAsUserToken(
"Job Execution",
username,
null,
userDetailsService.loadUserByUsername(username).getAuthorities(),
null);
Entity fileIngestEntity = fileIngestJobExecution.getFileIngest();
Entity targetEntityEntity = fileIngestEntity.getEntity(FileIngestMetaData.ENTITY_META_DATA);
String targetEntityName = targetEntityEntity.getString(EntityMetaDataMetaData.FULL_NAME);
String url = fileIngestEntity.getString(FileIngestMetaData.URL);
String loader = fileIngestEntity.getString(FileIngestMetaData.LOADER);
String failureEmail = fileIngestEntity.getString(FileIngestMetaData.FAILURE_EMAIL);
return new FileIngestJob(
progress,
transactionTemplate,
runAsAuthentication,
fileIngester,
targetEntityName,
url,
loader,
failureEmail,
fileIngestJobExecution.getIdentifier());
}
private Entity upsert(EntityMapping entityMapping) {
List<Entity> attributeMappingEntities =
attributeMappingRepository.upsert(entityMapping.getAttributeMappings());
Entity entityMappingEntity;
if (entityMapping.getIdentifier() == null) {
entityMapping.setIdentifier(idGenerator.generateId());
entityMappingEntity = toEntityMappingEntity(entityMapping, attributeMappingEntities);
dataService.add(entityMappingMetaData.getName(), entityMappingEntity);
} else {
entityMappingEntity = toEntityMappingEntity(entityMapping, attributeMappingEntities);
dataService.update(entityMappingMetaData.getName(), entityMappingEntity);
}
return entityMappingEntity;
}
private void replaceUserPermissions(
List<UserAuthority> entityAuthorities, String userId, String authorityType) {
MolgenisUser molgenisUser =
dataService.findOne(MolgenisUser.ENTITY_NAME, userId, MolgenisUser.class);
if (molgenisUser == null) throw new RuntimeException("unknown user id [" + userId + "]");
// inject user
for (UserAuthority entityAuthority : entityAuthorities)
entityAuthority.setMolgenisUser(molgenisUser);
// delete old plugin authorities
List<? extends Authority> oldEntityAuthorities =
getUserPermissions(molgenisUser, authorityType);
if (oldEntityAuthorities != null && !oldEntityAuthorities.isEmpty())
dataService.delete(UserAuthority.ENTITY_NAME, oldEntityAuthorities);
// insert new plugin authorities
if (!entityAuthorities.isEmpty()) dataService.add(UserAuthority.ENTITY_NAME, entityAuthorities);
}
private void replaceGroupPermissions(
List<GroupAuthority> entityAuthorities, String groupId, String authorityPrefix) {
MolgenisGroup molgenisGroup =
dataService.findOne(MolgenisGroup.ENTITY_NAME, groupId, MolgenisGroup.class);
if (molgenisGroup == null) throw new RuntimeException("unknown group id [" + groupId + "]");
// inject user
for (GroupAuthority entityAuthority : entityAuthorities)
entityAuthority.setMolgenisGroup(molgenisGroup);
// delete old plugin authorities
List<Authority> oldEntityAuthorities = getGroupPermissions(molgenisGroup, authorityPrefix);
if (oldEntityAuthorities != null && !oldEntityAuthorities.isEmpty())
dataService.delete(GroupAuthority.ENTITY_NAME, oldEntityAuthorities);
// insert new plugin authorities
if (!entityAuthorities.isEmpty())
dataService.add(GroupAuthority.ENTITY_NAME, entityAuthorities);
}
@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;
}