public void _save() {
if (!em().contains(this)) {
em().persist(this);
PlayPlugin.postEvent("JPASupport.objectPersisted", this);
}
avoidCascadeSaveLoops.set(new HashSet<JPABase>());
try {
saveAndCascade(true);
} finally {
avoidCascadeSaveLoops.get().clear();
}
try {
em().flush();
} catch (PersistenceException e) {
if (e.getCause() instanceof GenericJDBCException) {
throw new PersistenceException(((GenericJDBCException) e.getCause()).getSQL(), e);
} else {
throw e;
}
}
avoidCascadeSaveLoops.set(new HashSet<JPABase>());
try {
saveAndCascade(false);
} finally {
avoidCascadeSaveLoops.get().clear();
}
}
public void _delete() {
try {
avoidCascadeSaveLoops.set(new HashSet<JPABase>());
try {
saveAndCascade(true);
} finally {
avoidCascadeSaveLoops.get().clear();
}
em().remove(this);
try {
em().flush();
} catch (PersistenceException e) {
if (e.getCause() instanceof GenericJDBCException) {
throw new PersistenceException(((GenericJDBCException) e.getCause()).getSQL(), e);
} else {
throw e;
}
}
avoidCascadeSaveLoops.set(new HashSet<JPABase>());
try {
saveAndCascade(false);
} finally {
avoidCascadeSaveLoops.get().clear();
}
PlayPlugin.postEvent("JPASupport.objectDeleted", this);
} catch (PersistenceException e) {
throw e;
} catch (Throwable e) {
throw new RuntimeException(e);
}
}
private void addResource(
Accessions accession,
IdentifierType resourceId,
DomainImportController controller,
String accesionNumber,
int recordNumber)
throws ImportException {
if (resourceId != null) {
String resourceId1;
String resourceId2 = null;
String resourceId3 = null;
String resourceId4 = null;
if (resourceId.getComposite() != null) {
resourceId1 =
StringHelper.trimToLength(
resourceId.getComposite(),
ATFieldInfo.checkFieldLength(
Resources.class, Resources.PROPERTYNAME_RESOURCE_IDENTIFIER_1));
} else {
resourceId1 = resourceId.getPart1();
resourceId2 = resourceId.getPart2();
resourceId3 = resourceId.getPart3();
resourceId4 = resourceId.getPart4();
}
ResourcesDAO resourceDao = new ResourcesDAO();
Resources resource;
if (resourceCreation.equalsIgnoreCase(AccessionImportXmlHandler.RESOURCE_CREATION_NONE)) {
resource =
resourceDao.lookupResource(
resourceId1, resourceId2, resourceId3, resourceId4, false, repository);
} else {
resource =
resourceDao.lookupResource(
resourceId1, resourceId2, resourceId3, resourceId4, true, repository);
}
if (resourceDao.getNewRecordCreated()
&& resourceCreation.equalsIgnoreCase(AccessionImportXmlHandler.RESOURCE_CREATION_FULL)) {
try {
resource = (Resources) resourceDao.findByPrimaryKeyLongSession(resource.getIdentifier());
resource.populateResourceFromAccession(accession);
resourceDao.updateLongSession(resource);
} catch (LookupException e) {
throw new ImportException(
"Error creating resource: " + resourceId + ", " + e.getMessage(), e);
} catch (PersistenceException e) {
throw new ImportException(
"Error creating resource: " + resourceId + ", " + e.getMessage(), e);
} catch (DuplicateLinkException e) {
throw new ImportException(
"Error creating resource: duplicate link" + resourceId + ", " + e.getMessage(), e);
}
}
if (resource != null) {
AccessionsResources accessionResource = new AccessionsResources(resource, accession);
accession.addAccessionsResources(accessionResource);
}
} else {
if (!resourceCreation.equalsIgnoreCase(AccessionImportXmlHandler.RESOURCE_CREATION_NONE)) {
controller.addLineToImportLog(
"Record # "
+ recordNumber
+ " - "
+ accesionNumber
+ " has no resource id so no resource record was created");
}
}
}