Example #1
0
 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();
   }
 }
Example #2
0
 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");
      }
    }
  }