moving queries to DAOs

dspace-api/src/main/java/org/dspace/content/BitstreamServiceImpl.java

@@ -401,6 +401,11 @@ public class BitstreamServiceImpl extends DSpaceObjectServiceImpl<Bitstream> imp
         return bitstreamDAO.countByStoreNumber(context, storeNumber);
     }
 
+    @Override
+    public int countTotal(Context context) throws SQLException {
+        return bitstreamDAO.countRows(context);
+    }
+
     @Override
     public Bitstream findByIdOrLegacyId(Context context, String id) throws SQLException {
         if(StringUtils.isNumeric(id))
@@ -418,4 +423,19 @@ public class BitstreamServiceImpl extends DSpaceObjectServiceImpl<Bitstream> imp
         return bitstreamDAO.findByLegacyId(context, id, Bitstream.class);
 
     }
+
+    @Override
+    public int countDeletedBitstreams(Context context) throws SQLException {
+        return bitstreamDAO.countDeleted(context);
+    }
+
+    @Override
+    public int countBitstreamsWithoutPolicy(Context context) throws SQLException {
+        return bitstreamDAO.countWithNoPolicy(context);
+    }
+
+    @Override
+    public List<Bitstream> getNotReferencedBitstreams(Context context) throws SQLException {
+        return bitstreamDAO.getNotReferencedBitstreams(context);
+    }
 }

dspace-api/src/main/java/org/dspace/content/BundleServiceImpl.java

@@ -428,4 +428,9 @@ public class BundleServiceImpl extends DSpaceObjectServiceImpl<Bundle> implement
     public Bundle findByLegacyId(Context context, int id) throws SQLException {
         return bundleDAO.findByLegacyId(context, id, Bundle.class);
     }
+
+    @Override
+    public int countTotal(Context context) throws SQLException {
+        return bundleDAO.countRows(context);
+    }
 }

dspace-api/src/main/java/org/dspace/content/CollectionServiceImpl.java

@@ -762,6 +762,11 @@ public class CollectionServiceImpl extends DSpaceObjectServiceImpl<Collection> i
         return collectionDAO.findByGroup(context, group);
     }
 
+    @Override
+    public List<Collection> findCollectionsWithSubscribers(Context context) throws SQLException {
+        return collectionDAO.findCollectionsWithSubscribers(context);
+    }
+
     @Override
     public DSpaceObject getAdminObject(Context context, Collection collection, int action) throws SQLException {
         DSpaceObject adminObject = null;
@@ -831,4 +836,14 @@ public class CollectionServiceImpl extends DSpaceObjectServiceImpl<Collection> i
     public Collection findByLegacyId(Context context, int id) throws SQLException {
         return collectionDAO.findByLegacyId(context, id, Collection.class);
     }
+
+    @Override
+    public int countTotal(Context context) throws SQLException {
+        return collectionDAO.countRows(context);
+    }
+
+    @Override
+    public List<Map> getCollectionsWithBitstreamSizesTotal(Context context) throws SQLException {
+        return collectionDAO.getCollectionsWithBitstreamSizesTotal(context);
+    }
 }

dspace-api/src/main/java/org/dspace/content/CommunityServiceImpl.java

@@ -670,4 +670,9 @@ public class CommunityServiceImpl extends DSpaceObjectServiceImpl<Community> imp
     public Community findByLegacyId(Context context, int id) throws SQLException {
         return communityDAO.findByLegacyId(context, id, Community.class);
     }
+
+    @Override
+    public int countTotal(Context context) throws SQLException {
+        return communityDAO.countRows(context);
+    }
 }

dspace-api/src/main/java/org/dspace/content/ItemServiceImpl.java

@@ -1152,4 +1152,19 @@ public class ItemServiceImpl extends DSpaceObjectServiceImpl<Item> implements It
     {
         return itemDAO.findByLastModifiedSince(context, last);
     }
+
+    @Override
+    public int countTotal(Context context) throws SQLException {
+        return itemDAO.countRows(context);
+    }
+
+    @Override
+    public int getNotArchivedItemsCount(Context context) throws SQLException {
+        return itemDAO.countNotArchived(context);
+    }
+
+    @Override
+    public int countWithdrawnItems(Context context) throws SQLException {
+        return itemDAO.countWithdrawn(context);
+    }
 }

dspace-api/src/main/java/org/dspace/content/MetadataValueServiceImpl.java

@@ -110,4 +110,9 @@ public class MetadataValueServiceImpl implements MetadataValueService {
         return metadataValueDAO.getMinimum(context,
                 metadataFieldId);
     }
+
+    @Override
+    public int countTotal(Context context) throws SQLException {
+        return metadataValueDAO.countRows(context);
+    }
 }

dspace-api/src/main/java/org/dspace/content/WorkspaceItemServiceImpl.java

@@ -26,6 +26,7 @@ import org.springframework.beans.factory.annotation.Autowired;
 import java.io.IOException;
 import java.sql.SQLException;
 import java.util.List;
+import java.util.Map;
 
 /**
  * Service implementation for the WorkspaceItem object.
@@ -216,6 +217,16 @@ public class WorkspaceItemServiceImpl implements WorkspaceItemService {
         itemService.delete(context, item);
     }
 
+    @Override
+    public int countTotal(Context context) throws SQLException {
+        return workspaceItemDAO.countRows(context);
+    }
+
+    @Override
+    public List<Map> getStageReachedCounts(Context context) throws SQLException {
+        return workspaceItemDAO.getStageReachedCounts(context);
+    }
+
     @Override
     public void deleteWrapper(Context context, WorkspaceItem workspaceItem) throws SQLException, AuthorizeException {
         // Check authorisation. We check permissions on the enclosed item.

dspace-api/src/main/java/org/dspace/content/dao/BitstreamDAO.java

@@ -41,4 +41,12 @@ public interface BitstreamDAO extends DSpaceObjectLegacySupportDAO<Bitstream> {
     public Iterator<Bitstream> findByStoreNumber(Context context, Integer storeNumber) throws SQLException;
 
     public Long countByStoreNumber(Context context, Integer storeNumber) throws SQLException;
+
+    int countRows(Context context) throws SQLException;
+
+    int countDeleted(Context context) throws SQLException;
+
+    int countWithNoPolicy(Context context) throws SQLException;
+
+    List<Bitstream> getNotReferencedBitstreams(Context context) throws SQLException;
 }

dspace-api/src/main/java/org/dspace/content/dao/BundleDAO.java

@@ -8,6 +8,9 @@
 package org.dspace.content.dao;
 
 import org.dspace.content.Bundle;
+import org.dspace.core.Context;
+
+import java.sql.SQLException;
 
 /**
  * Database Access Object interface class for the Bundle object.
@@ -17,4 +20,5 @@ import org.dspace.content.Bundle;
  * @author kevinvandevelde at atmire.com
  */
 public interface BundleDAO extends DSpaceObjectLegacySupportDAO<Bundle> {
+    int countRows(Context context) throws SQLException;
 }

dspace-api/src/main/java/org/dspace/content/dao/CollectionDAO.java

@@ -16,6 +16,7 @@ import org.dspace.eperson.Group;
 
 import java.sql.SQLException;
 import java.util.List;
+import java.util.Map;
 
 /**
  * Database Access Object interface class for the Collection object.
@@ -37,4 +38,10 @@ public interface CollectionDAO extends DSpaceObjectLegacySupportDAO<Collection>
     public List<Collection> findAuthorized(Context context, EPerson ePerson, List<Integer> actions) throws SQLException;
 
     List<Collection> findAuthorizedByGroup(Context context, EPerson ePerson, List<Integer> actions) throws SQLException;
+
+    List<Collection> findCollectionsWithSubscribers(Context context) throws SQLException;
+
+    int countRows(Context context) throws SQLException;
+
+    List<Map> getCollectionsWithBitstreamSizesTotal(Context context) throws SQLException;
 }

dspace-api/src/main/java/org/dspace/content/dao/CommunityDAO.java

@@ -36,4 +36,6 @@ public interface CommunityDAO extends DSpaceObjectLegacySupportDAO<Community> {
     public List<Community> findAuthorized(Context context, EPerson ePerson, List<Integer> actions) throws SQLException;
 
     public List<Community> findAuthorizedByGroup(Context context, EPerson currentUser, List<Integer> actions) throws SQLException;
+
+    int countRows(Context context) throws SQLException;
 }

dspace-api/src/main/java/org/dspace/content/dao/ItemDAO.java

@@ -70,4 +70,10 @@ public interface ItemDAO extends DSpaceObjectLegacySupportDAO<Item>
     public Iterator<Item> findAll(Context context, boolean archived,
             boolean withdrawn, boolean discoverable, Date lastModified)
             throws SQLException;
+
+    int countRows(Context context) throws SQLException;
+
+    int countNotArchived(Context context) throws SQLException;
+
+    int countWithdrawn(Context context) throws SQLException;
 }

dspace-api/src/main/java/org/dspace/content/dao/MetadataValueDAO.java

@@ -32,4 +32,6 @@ public interface MetadataValueDAO extends GenericDAO<MetadataValue> {
 
     public MetadataValue getMinimum(Context context, int metadataFieldId)
             throws SQLException;
+
+    int countRows(Context context) throws SQLException;
 }

dspace-api/src/main/java/org/dspace/content/dao/WorkspaceItemDAO.java

@@ -16,6 +16,7 @@ import org.dspace.eperson.EPerson;
 
 import java.sql.SQLException;
 import java.util.List;
+import java.util.Map;
 
 /**
  * Database Access Object interface class for the WorkspaceItem object.
@@ -37,4 +38,8 @@ public interface WorkspaceItemDAO extends GenericDAO<WorkspaceItem> {
     public List<WorkspaceItem> findWithSupervisedGroup(Context context) throws SQLException;
 
     public List<WorkspaceItem> findBySupervisedGroupMember(Context context, EPerson ePerson) throws SQLException;
+
+    int countRows(Context context) throws SQLException;
+
+    List<Map> getStageReachedCounts(Context context) throws SQLException;
 }

dspace-api/src/main/java/org/dspace/content/dao/impl/BitstreamDAOImpl.java

@@ -13,6 +13,7 @@ import org.dspace.content.Community;
 import org.dspace.content.Item;
 import org.dspace.content.dao.BitstreamDAO;
 import org.dspace.core.AbstractHibernateDSODAO;
+import org.dspace.core.Constants;
 import org.dspace.core.Context;
 import org.hibernate.Criteria;
 import org.hibernate.Query;
@@ -119,4 +120,31 @@ public class BitstreamDAOImpl extends AbstractHibernateDSODAO<Bitstream> impleme
         criteria.add(Restrictions.eq("storeNumber", storeNumber));
         return countLong(criteria);
     }
+
+    @Override
+    public int countRows(Context context) throws SQLException {
+        return count(createQuery(context, "SELECT count(*) from Bitstream"));
+    }
+
+    @Override
+    public int countDeleted(Context context) throws SQLException {
+        return count(createQuery(context, "SELECT count(*) FROM Bitstream b WHERE b.deleted=true"));
+    }
+
+    @Override
+    public int countWithNoPolicy(Context context) throws SQLException {
+        Query query = createQuery(context,"SELECT count(bit.id) from Bitstream bit where bit.deleted<>true and bit.id not in" +
+                " (select res.dSpaceObject from ResourcePolicy res where res.resourceTypeId = :typeId )" );
+        query.setParameter("typeId", Constants.BITSTREAM);
+        return count(query);
+    }
+
+    @Override
+    public List<Bitstream> getNotReferencedBitstreams(Context context) throws SQLException {
+        return list(createQuery(context,"select bit from Bitstream bit where bit.deleted != true" +
+                " and bit.id not in (select bit2.id from Bundle bun join bun.bitstreams bit2)" +
+                " and bit.id not in (select com.logo.id from Community com)" +
+                " and bit.id not in (select col.logo.id from Collection col)" +
+                " and bit.id not in (select bun.primaryBitstream.id from Bundle bun)"));
+    }
 }

dspace-api/src/main/java/org/dspace/content/dao/impl/BundleDAOImpl.java

@@ -10,6 +10,9 @@ package org.dspace.content.dao.impl;
 import org.dspace.content.Bundle;
 import org.dspace.content.dao.BundleDAO;
 import org.dspace.core.AbstractHibernateDSODAO;
+import org.dspace.core.Context;
+
+import java.sql.SQLException;
 
 /**
  * Hibernate implementation of the Database Access Object interface class for the Bundle object.
@@ -21,5 +24,8 @@ import org.dspace.core.AbstractHibernateDSODAO;
 public class BundleDAOImpl extends AbstractHibernateDSODAO<Bundle> implements BundleDAO {
 
 
-
+    @Override
+    public int countRows(Context context) throws SQLException {
+        return count(createQuery(context, "SELECT count(*) from Bundle"));
+    }
 }

dspace-api/src/main/java/org/dspace/content/dao/impl/CollectionDAOImpl.java

@@ -20,10 +20,12 @@ import org.hibernate.Criteria;
 import org.hibernate.Query;
 import org.hibernate.criterion.Disjunction;
 import org.hibernate.criterion.Restrictions;
+import org.hibernate.transform.Transformers;
 
 import java.sql.SQLException;
 import java.util.Arrays;
 import java.util.List;
+import java.util.Map;
 
 /**
  * Hibernate implementation of the Database Access Object interface class for the Collection object.
@@ -158,6 +160,19 @@ public class CollectionDAOImpl extends AbstractHibernateDSODAO<Collection> imple
 
     }
 
-
+    @Override
-
+    public List<Collection> findCollectionsWithSubscribers(Context context) throws SQLException {
+        return list(createQuery(context, "SELECT DISTINCT col FROM Subscription s join  s.collection col"));
+    }
+
+    @Override
+    public int countRows(Context context) throws SQLException {
+        return count(createQuery(context, "SELECT count(*) FROM Collection"));
+    }
+
+    @Override
+    public List<Map> getCollectionsWithBitstreamSizesTotal(Context context) throws SQLException {
+        String q = "select col as collection, sum(bit.sizeBytes) as totalBytes from Item i join i.collections col join i.bundles bun join bun.bitstreams bit group by col";
+        return createQuery(context, q).setResultTransformer(Transformers.ALIAS_TO_ENTITY_MAP).list();
+    }
 }

dspace-api/src/main/java/org/dspace/content/dao/impl/CommunityDAOImpl.java

@@ -160,4 +160,9 @@ public class CommunityDAOImpl extends AbstractHibernateDSODAO<Community> impleme
         hibernateQuery.setParameter("eperson_id", ePerson.getID());
         return list(hibernateQuery);
     }
+
+    @Override
+    public int countRows(Context context) throws SQLException {
+        return count(createQuery(context, "SELECT count(*) FROM Community"));
+    }
 }

dspace-api/src/main/java/org/dspace/content/dao/impl/ItemDAOImpl.java

@@ -246,4 +246,19 @@ public class ItemDAOImpl extends AbstractHibernateDSODAO<Item> implements ItemDA
         query.setTimestamp("last_modified", since);
         return iterate(query);
     }
+
+    @Override
+    public int countRows(Context context) throws SQLException {
+        return count(createQuery(context, "SELECT count(*) FROM Item"));
+    }
+
+    @Override
+    public int countNotArchived(Context context) throws SQLException {
+        return count(createQuery(context, "SELECT count(*) FROM Item i WHERE i.inArchive=false AND i.withdrawn=false"));
+    }
+
+    @Override
+    public int countWithdrawn(Context context) throws SQLException {
+        return count(createQuery(context, "SELECT count(*) FROM Item i WHERE i.withdrawn=true"));
+    }
 }

dspace-api/src/main/java/org/dspace/content/dao/impl/MetadataValueDAOImpl.java

@@ -66,4 +66,9 @@ public class MetadataValueDAOImpl extends AbstractHibernateDAO<MetadataValue> im
         query.setMaxResults(1);
         return (MetadataValue) query.uniqueResult();
     }
+
+    @Override
+    public int countRows(Context context) throws SQLException {
+        return count(createQuery(context, "SELECT count(*) FROM MetadataValue"));
+    }
 }

dspace-api/src/main/java/org/dspace/content/dao/impl/WorkspaceItemDAOImpl.java

@@ -18,9 +18,11 @@ import org.hibernate.Criteria;
 import org.hibernate.Query;
 import org.hibernate.criterion.Order;
 import org.hibernate.criterion.Restrictions;
+import org.hibernate.transform.Transformers;
 
 import java.sql.SQLException;
 import java.util.List;
+import java.util.Map;
 
 /**
  * Hibernate implementation of the Database Access Object interface class for the WorkspaceItem object.
@@ -82,4 +84,16 @@ public class WorkspaceItemDAOImpl extends AbstractHibernateDAO<WorkspaceItem> im
         return list(criteria);
     }
 
+    @Override
+    public int countRows(Context context) throws SQLException {
+        return count(createQuery(context, "SELECT count(*) from WorkspaceItem"));
+    }
+
+    @Override
+    public List<Map> getStageReachedCounts(Context context) throws SQLException {
+        return createQuery(context,"SELECT wi.stageReached as stage_reached, count(*) as cnt from WorkspaceItem wi" +
+                " group by wi.stageReached order by wi.stageReached").setResultTransformer(Transformers.ALIAS_TO_ENTITY_MAP)
+                .list();
+    }
+
 }

dspace-api/src/main/java/org/dspace/content/service/BitstreamService.java

@@ -178,4 +178,12 @@ public interface BitstreamService extends DSpaceObjectService<Bitstream>, DSpace
     public Iterator<Bitstream> findByStoreNumber(Context context, Integer storeNumber) throws SQLException;
 
     public Long countByStoreNumber(Context context, Integer storeNumber) throws SQLException;
+
+    int countTotal(Context context) throws SQLException ;
+
+    int countDeletedBitstreams(Context context) throws SQLException;
+
+    int countBitstreamsWithoutPolicy(Context context) throws SQLException;
+
+    List<Bitstream> getNotReferencedBitstreams(Context context) throws SQLException;
 }

dspace-api/src/main/java/org/dspace/content/service/BundleService.java

@@ -105,4 +105,6 @@ public interface BundleService extends DSpaceObjectService<Bundle>, DSpaceObject
      * @throws AuthorizeException If the user can't make the changes
      */
     public void setOrder(Context context, Bundle bundle, UUID bitstreamIds[]) throws AuthorizeException, SQLException;
+
+    int countTotal(Context context) throws SQLException;
 }

dspace-api/src/main/java/org/dspace/content/service/CollectionService.java

@@ -19,6 +19,7 @@ import java.io.IOException;
 import java.io.InputStream;
 import java.sql.SQLException;
 import java.util.List;
+import java.util.Map;
 import java.util.MissingResourceException;
 
 /**
@@ -285,7 +286,7 @@ public interface CollectionService extends DSpaceObjectService<Collection>, DSpa
      * collections a person is an editor for.
      *
      * @param context
-     * @param comm
+     * @param community
      *            (optional) restrict search to a community, else null
      * @param actionID
      *            of the action
@@ -296,4 +297,10 @@ public interface CollectionService extends DSpaceObjectService<Collection>, DSpa
     public List<Collection> findAuthorized(Context context, Community community, int actionID) throws java.sql.SQLException;
 
     public Collection findByGroup(Context context, Group group) throws SQLException;
+
+    List<Collection> findCollectionsWithSubscribers(Context context) throws SQLException;
+
+    int countTotal(Context context) throws SQLException;
+
+    List<Map> getCollectionsWithBitstreamSizesTotal(Context context) throws SQLException;
 }

dspace-api/src/main/java/org/dspace/content/service/CommunityService.java

@@ -255,4 +255,6 @@ public interface CommunityService extends DSpaceObjectService<Community>, DSpace
     public List<Community> findAuthorized(Context context, List<Integer> actions) throws SQLException;
 
     public List<Community> findAuthorizedGroupMapped(Context context, List<Integer> actions) throws SQLException;
+
+    int countTotal(Context context) throws SQLException;
 }

dspace-api/src/main/java/org/dspace/content/service/ItemService.java

@@ -459,4 +459,10 @@ public interface ItemService extends DSpaceObjectService<Item>, DSpaceObjectLega
      * @return total items
      */
     public int countItems(Context context, Community community) throws SQLException;
+
+    int countTotal(Context context) throws SQLException;
+
+    int getNotArchivedItemsCount(Context context) throws SQLException;
+
+    int countWithdrawnItems(Context context) throws SQLException;
 }

dspace-api/src/main/java/org/dspace/content/service/MetadataValueService.java

@@ -91,4 +91,6 @@ public interface MetadataValueService {
      */
     public MetadataValue getMinimum(Context context, int metadataFieldId)
             throws SQLException;
+
+    int countTotal(Context context) throws SQLException;
 }

dspace-api/src/main/java/org/dspace/content/service/WorkspaceItemService.java

@@ -18,6 +18,7 @@ import org.dspace.workflow.WorkflowItem;
 import java.io.IOException;
 import java.sql.SQLException;
 import java.util.List;
+import java.util.Map;
 
 /**
  * Service interface class for the WorkspaceItem object.
@@ -124,4 +125,8 @@ public interface WorkspaceItemService extends InProgressSubmissionService<Worksp
      * notwithstanding.)
      */
     public void deleteAll(Context context, WorkspaceItem workspaceItem) throws SQLException, AuthorizeException, IOException;
+
+    int countTotal(Context context) throws SQLException;
+
+    List<Map> getStageReachedCounts(Context context) throws SQLException;
 }

dspace-api/src/main/java/org/dspace/eperson/EPersonServiceImpl.java

@@ -367,6 +367,11 @@ public class EPersonServiceImpl extends DSpaceObjectServiceImpl<EPerson> impleme
         }
     }
 
+    @Override
+    public List<EPerson> findEPeopleWithSubscription(Context context) throws SQLException {
+        return ePersonDAO.findAllSubscribers(context);
+    }
+
     @Override
     public void updateLastModified(Context context, EPerson dso) throws SQLException {
         //Not used
@@ -393,4 +398,9 @@ public class EPersonServiceImpl extends DSpaceObjectServiceImpl<EPerson> impleme
     public List<EPerson> findNotActiveSince(Context context, Date date) throws SQLException {
         return ePersonDAO.findNotActiveSince(context, date);
     }
+
+    @Override
+    public int countTotal(Context context) throws SQLException {
+        return ePersonDAO.countRows(context);
+    }
 }

dspace-api/src/main/java/org/dspace/eperson/GroupServiceImpl.java

@@ -377,6 +377,11 @@ public class GroupServiceImpl extends DSpaceObjectServiceImpl<Group> implements
         }
     }
 
+    @Override
+    public List<Group> getEmptyGroups(Context context) throws SQLException {
+        return groupDAO.getEmptyGroups(context);
+    }
+
     /**
      * Update the group - writing out group object and EPerson list if necessary
      */
@@ -607,4 +612,9 @@ public class GroupServiceImpl extends DSpaceObjectServiceImpl<Group> implements
     public Group findByLegacyId(Context context, int id) throws SQLException {
         return groupDAO.findByLegacyId(context, id, Group.class);
     }
+
+    @Override
+    public int countTotal(Context context) throws SQLException {
+        return groupDAO.countRows(context);
+    }
 }

dspace-api/src/main/java/org/dspace/eperson/dao/EPersonDAO.java

@@ -43,4 +43,8 @@ public interface EPersonDAO extends DSpaceObjectDAO<EPerson>, DSpaceObjectLegacy
     public List<EPerson> findNotActiveSince(Context context, Date date) throws SQLException;
 
     public List<EPerson> findAll(Context context, MetadataField metadataFieldSort, String sortColumn) throws SQLException;
+
+    public List<EPerson> findAllSubscribers(Context context) throws SQLException;
+
+    int countRows(Context context) throws SQLException;
 }

dspace-api/src/main/java/org/dspace/eperson/dao/GroupDAO.java

@@ -37,4 +37,8 @@ public interface GroupDAO extends DSpaceObjectDAO<Group>, DSpaceObjectLegacySupp
     public List<Group> findByEPerson(Context context, EPerson ePerson) throws SQLException;
 
     public List getGroup2GroupResults(Context context, boolean flushQueries) throws SQLException;
+
+    List<Group> getEmptyGroups(Context context) throws SQLException;
+
+    int countRows(Context context) throws SQLException;
 }

dspace-api/src/main/java/org/dspace/eperson/dao/impl/EPersonDAOImpl.java

@@ -145,4 +145,14 @@ public class EPersonDAOImpl extends AbstractHibernateDSODAO<EPerson> implements
 
         return query;
     }
+
+    @Override
+    public List<EPerson> findAllSubscribers(Context context) throws SQLException {
+        return list(createQuery(context, "SELECT DISTINCT e from Subscription s join s.ePerson e"));
+    }
+
+    @Override
+    public int countRows(Context context) throws SQLException {
+        return count(createQuery(context, "SELECT count(*) FROM EPerson"));
+    }
 }

dspace-api/src/main/java/org/dspace/eperson/dao/impl/GroupDAOImpl.java

@@ -153,4 +153,13 @@ public class GroupDAOImpl extends AbstractHibernateDSODAO<Group> implements Grou
         return sqlQuery.list();
     }
 
+    @Override
+    public List<Group> getEmptyGroups(Context context) throws SQLException {
+        return list(createQuery(context, "SELECT g from Group g where g.epeople is EMPTY"));
+    }
+
+    @Override
+    public int countRows(Context context) throws SQLException {
+        return count(createQuery(context, "SELECT count(*) FROM Group"));
+    }
 }

dspace-api/src/main/java/org/dspace/eperson/service/EPersonService.java

@@ -201,4 +201,8 @@ public interface EPersonService extends DSpaceObjectService<EPerson>, DSpaceObje
     public List<String> getDeleteConstraints(Context context, EPerson ePerson) throws SQLException;
 
     public List<EPerson> findByGroups(Context c, Set<Group> groups) throws SQLException;
+
+    List<EPerson> findEPeopleWithSubscription(Context context) throws SQLException;
+
+    int countTotal(Context context) throws SQLException;
 }

dspace-api/src/main/java/org/dspace/eperson/service/GroupService.java

@@ -204,4 +204,8 @@ public interface GroupService extends DSpaceObjectService<Group>, DSpaceObjectLe
      * @throws AuthorizeException
      */
     public void initDefaultGroupNames(Context context) throws SQLException, AuthorizeException;
+
+    List<Group> getEmptyGroups(Context context) throws SQLException;
+
+    int countTotal(Context context) throws SQLException;
 }

dspace-api/src/main/java/org/dspace/handle/HandleServiceImpl.java

@@ -399,4 +399,9 @@ public class HandleServiceImpl implements HandleService
 
         return handlePrefix + (handlePrefix.endsWith("/") ? "" : "/") + id;
     }
+
+    @Override
+    public int countTotal(Context context) throws SQLException {
+        return handleDAO.countRows(context);
+    }
 }

dspace-api/src/main/java/org/dspace/handle/dao/HandleDAO.java

@@ -33,4 +33,6 @@ public interface HandleDAO extends GenericDAO<Handle> {
     public long countHandlesByPrefix(Context context, String prefix) throws SQLException;
 
     int updateHandlesWithNewPrefix(Context context, String newPrefix, String oldPrefix) throws SQLException;
+
+    int countRows(Context context) throws SQLException;
 }

dspace-api/src/main/java/org/dspace/handle/dao/impl/HandleDAOImpl.java

@@ -67,4 +67,9 @@ public class HandleDAOImpl extends AbstractHibernateDAO<Handle> implements Handl
         query.setString("oldPrefix", oldPrefix);
         return query.executeUpdate();
     }
+
+    @Override
+    public int countRows(Context context) throws SQLException {
+        return count(createQuery(context, "SELECT count(*) FROM Handle"));
+    }
 }

dspace-api/src/main/java/org/dspace/handle/service/HandleService.java

@@ -184,4 +184,6 @@ public interface HandleService {
     public int updateHandlesWithNewPrefix(Context context, String newPrefix, String oldPrefix) throws SQLException;
 
     public void modifyHandleDSpaceObject(Context context, String handle, DSpaceObject newOwner) throws SQLException;
+
+    int countTotal(Context context) throws SQLException;
 }

dspace-api/src/main/java/org/dspace/health/Core.java

@@ -1,185 +0,0 @@
-/**
- * The contents of this file are subject to the license and copyright
- * detailed in the LICENSE and NOTICE files at the root of the source
- * tree and available online at
- *
- * http://www.dspace.org/license/
- */
-package org.dspace.health;
-
-import org.apache.commons.io.FileUtils;
-import org.dspace.app.util.CollectionDropDown;
-import org.dspace.content.*;
-import org.dspace.content.Collection;
-import org.dspace.content.factory.ContentServiceFactory;
-import org.dspace.content.service.*;
-import org.dspace.core.AbstractHibernateDAO;
-import org.dspace.core.Constants;
-import org.dspace.core.Context;
-import org.dspace.eperson.Group;
-
-import java.sql.SQLException;
-import java.util.*;
-
-/**
- * @author LINDAT/CLARIN dev team
- */
-public class Core {
-
-    private static AbstractHibernateDAO dao = new AbstractHibernateDAO<Object>(){};
-    private static ItemService itemService = ContentServiceFactory.getInstance().getItemService();
-    private static CommunityService communityService = ContentServiceFactory.getInstance().getCommunityService();
-
-    private final Context context;
-
-    public Core(Context context){
-        this.context = context;
-    }
-
-    // get info
-    //
-    public  String getCollectionSizesInfo() throws SQLException {
-        final StringBuffer ret = new StringBuffer();
-        List<Object[]> col_bitSizes = query("select col, sum(bit.sizeBytes) as sum from Item i join i.collections col join i.bundles bun join bun.bitstreams bit group by col");
-        long total_size = 0;
-
-        Collections.sort(col_bitSizes, new Comparator<Object[]>() {
-            @Override
-            public int compare(Object[] o1, Object[] o2) {
-                try {
-                    return CollectionDropDown.collectionPath((Collection) o1[0]).compareTo(
-                        CollectionDropDown.collectionPath((Collection) o2[0])
-                    );
-                } catch (Exception e) {
-                    ret.append(e.getMessage());
-                }
-                return 0;
-            }
-        });
-        for (Object[] row : col_bitSizes) {
-            Long size = (Long) row[1];
-            total_size += size;
-            Collection col = (Collection) row[0];
-            ret.append(String.format(
-                    "\t%s:  %s\n", CollectionDropDown.collectionPath(col), FileUtils.byteCountToDisplaySize((long) size)));
-        }
-        ret.append(String.format(
-                "Total size:              %s\n", FileUtils.byteCountToDisplaySize(total_size)));
-
-        ret.append(String.format(
-                "Resource without policy: %d\n", getBitstreamsWithoutPolicyCount()));
-
-        ret.append(String.format(
-                "Deleted bitstreams:      %d\n", getBitstreamsDeletedCount()));
-
-        String list_str = "";
-        List<UUID> bitstreamOrphans = getBitstreamOrphansRows();
-        for (UUID id : bitstreamOrphans) {
-            list_str += String.format("%d, ", id);
-        }
-        ret.append(String.format(
-                "Orphan bitstreams:       %d [%s]\n", bitstreamOrphans.size(), list_str));
-
-        return ret.toString();
-    }
-
-    public  String getObjectSizesInfo() throws SQLException {
-        String ret = "";
-        for (String tb : new String[] { "Bitstream", "Bundle", "Collection",
-            "Community", "MetadataValue", "EPerson", "Item", "Handle",
-            "Group", "BasicWorkflowItem", "WorkspaceItem", }) {
-            int count = count("SELECT COUNT(*) from " + tb);
-            ret += String.format("Count %-14s: %s\n", tb,
-                String.valueOf(count));
-        }
-        return ret;
-    }
-
-
-    // get objects
-    //
-
-    public  List<Object[]> getWorkspaceItemsRows() throws SQLException {
-        return query("SELECT wi.stageReached, count(*) as cnt from WorkspaceItem wi group by wi.stageReached order by wi.stageReached");
-    }
-
-    public  List<UUID> getBitstreamOrphansRows() throws SQLException {
-        return query("select bit.id from Bitstream bit where bit.deleted != true" +
-                " and bit.id not in (select bit2.id from Bundle bun join bun.bitstreams bit2)" +
-                " and bit.id not in (select com.logo.id from Community com)" +
-                " and bit.id not in (select col.logo.id from Collection col)" +
-                " and bit.id not in (select bun.primaryBitstream.id from Bundle bun)");
-    }
-
-    // get sizes
-    //
-
-    public  int getWorkflowItemsCount() throws SQLException {
-        return count("SELECT count(*) FROM BasicWorkflowItem");
-    }
-
-    public  int getNotArchivedItemsCount() throws SQLException {
-        return count(
-            "SELECT count(*) FROM Item i WHERE i.inArchive=false AND i.withdrawn=false");
-    }
-
-    public  int getWithdrawnItemsCount() throws SQLException {
-        return count("SELECT count(*) FROM Item i WHERE i.withdrawn=true");
-    }
-
-    public  int getBitstreamsWithoutPolicyCount() throws SQLException {
-        return count("SELECT count(bit.id) from Bitstream bit where bit.deleted<>true and bit.id not in" +
-                " (select res.dSpaceObject from ResourcePolicy res where res.resourceTypeId=" + Constants.BITSTREAM +")");
-    }
-
-    public  int getBitstreamsDeletedCount() throws SQLException {
-        return count("SELECT count(*) FROM Bitstream b WHERE b.deleted=true");
-    }
-
-    // get more complex information
-    //
-
-    public  List<Map.Entry<String, Integer>> getCommunities()
-        throws SQLException {
-
-        List<Map.Entry<String, Integer>> cl = new java.util.ArrayList<>();
-        List<Community> top_communities = communityService.findAllTop(context);
-        for (Community c : top_communities) {
-            cl.add(
-                new java.util.AbstractMap.SimpleEntry<>(c.getName(), itemService.countItems(context, c))
-            );
-        }
-        return cl;
-    }
-
-    public  List<String> getEmptyGroups() throws SQLException {
-        List<String> ret = new ArrayList<>();
-        List<Group> emptyGroups = query("SELECT g from Group g where g.epeople is EMPTY");
-        for (Group group : emptyGroups) {
-            ret.add(String.format("id=%s;name=%s", group.getID(), group.getName() ));
-        }
-        return ret;
-    }
-
-    public  List<UUID> getSubscribers() throws SQLException {
-        return query("SELECT DISTINCT e.id from Subscription s join s.ePerson e");
-    }
-
-    public  List<UUID> getSubscribedCollections() throws SQLException {
-        return query("SELECT DISTINCT col.id FROM Subscription s join  s.collection col");
-    }
-
-    //
-    //
-
-     int count(String query) throws SQLException {
-        return dao.count(dao.createQuery(context, query));
-    }
-
-     List query(String query) throws SQLException {
-        return dao.createQuery(context, query).list();
-    }
-}
-
-
-

dspace-api/src/main/java/org/dspace/health/ItemCheck.java

@@ -8,24 +8,50 @@
 package org.dspace.health;
 
 
+import org.apache.commons.io.FileUtils;
+import org.dspace.app.util.CollectionDropDown;
+import org.dspace.content.*;
+import org.dspace.content.Collection;
+import org.dspace.content.factory.ContentServiceFactory;
+import org.dspace.content.service.*;
 import org.dspace.core.Context;
+import org.dspace.eperson.factory.EPersonServiceFactory;
+import org.dspace.eperson.service.EPersonService;
+import org.dspace.eperson.service.GroupService;
+import org.dspace.handle.factory.HandleServiceFactory;
+import org.dspace.handle.service.HandleService;
+import org.dspace.workflowbasic.factory.BasicWorkflowServiceFactory;
+import org.dspace.workflowbasic.service.BasicWorkflowItemService;
 
 import java.sql.SQLException;
-import java.util.Map;
+import java.util.*;
 
 /**
  * @author LINDAT/CLARIN dev team
  */
 public class ItemCheck extends Check {
 
+    private BitstreamService bitstreamService = ContentServiceFactory.getInstance().getBitstreamService();
+    private BundleService bundleService =  ContentServiceFactory.getInstance().getBundleService();
+    private CollectionService collectionService = ContentServiceFactory.getInstance().getCollectionService();
+    private CommunityService communityService = ContentServiceFactory.getInstance().getCommunityService();
+    private MetadataValueService metadataValueService = ContentServiceFactory.getInstance().getMetadataValueService();
+    private ItemService itemService = ContentServiceFactory.getInstance().getItemService();
+    private WorkspaceItemService workspaceItemService = ContentServiceFactory.getInstance().getWorkspaceItemService();
+    private BasicWorkflowItemService basicWorkflowItemService = BasicWorkflowServiceFactory.getInstance().getBasicWorkflowItemService();
+    private HandleService handleService = HandleServiceFactory.getInstance().getHandleService();
+    private EPersonService ePersonService = EPersonServiceFactory.getInstance().getEPersonService();
+    private GroupService groupService = EPersonServiceFactory.getInstance().getGroupService();
+
+
+
     @Override
     public String run( ReportInfo ri ) {
         String ret = "";
         int tot_cnt = 0;
         Context context = new Context();
-        Core core = new Core(context);
         try {
-            for (Map.Entry<String, Integer> name_count : core.getCommunities()) {
+            for (Map.Entry<String, Integer> name_count : getCommunities(context)) {
                 ret += String.format("Community [%s]: %d\n",
                     name_count.getKey(), name_count.getValue());
                 tot_cnt += name_count.getValue();
@@ -36,7 +62,7 @@ public class ItemCheck extends Check {
 
         try {
             ret += "\nCollection sizes:\n";
-            ret += core.getCollectionSizesInfo();
+            ret += getCollectionSizesInfo(context);
         } catch (SQLException e) {
             error(e);
         }
@@ -45,32 +71,119 @@ public class ItemCheck extends Check {
             "\nPublished items (archived, not withdrawn): %d\n", tot_cnt);
         try {
             ret += String.format(
-                "Withdrawn items: %d\n", core.getWithdrawnItemsCount());
+                "Withdrawn items: %d\n", itemService.countWithdrawnItems(context));
             ret += String.format(
                 "Not published items (in workspace or workflow mode): %d\n",
-                core.getNotArchivedItemsCount());
+                itemService.getNotArchivedItemsCount(context));
 
-            for (Object[] row : core.getWorkspaceItemsRows()) {
+            for (Map row : workspaceItemService.getStageReachedCounts(context)) {
                 ret += String.format("\tIn Stage %s: %s\n",
-                    row[0],// "stage_reached"),
+                    row.get("stage_reached"),
-                    row[1]// "cnt")
+                    row.get("cnt")
                 );
             }
 
             ret += String.format(
                 "\tWaiting for approval (workflow items): %d\n",
-                core.getWorkflowItemsCount());
+                basicWorkflowItemService.countTotal(context));
 
         } catch (SQLException e) {
             error(e);
         }
 
         try {
-            ret += core.getObjectSizesInfo();
+            ret += getObjectSizesInfo(context);
             context.complete();
         } catch (SQLException e) {
             error(e);
         }
         return ret;
     }
+
+
+    public  String getObjectSizesInfo(Context context) throws SQLException {
+        StringBuilder sb = new StringBuilder();
+        sb.append(String.format("Count %-14s: %s\n", "Bitstream",
+                    String.valueOf(bitstreamService.countTotal(context))));
+        sb.append(String.format("Count %-14s: %s\n", "Bundle",
+                String.valueOf(bundleService.countTotal(context))));
+        sb.append(String.format("Count %-14s: %s\n", "Collection",
+                String.valueOf(collectionService.countTotal(context))));
+        sb.append(String.format("Count %-14s: %s\n", "Community",
+                String.valueOf(communityService.countTotal(context))));
+        sb.append(String.format("Count %-14s: %s\n", "MetadataValue",
+                String.valueOf(metadataValueService.countTotal(context))));
+        sb.append(String.format("Count %-14s: %s\n", "EPerson",
+                String.valueOf(ePersonService.countTotal(context))));
+        sb.append(String.format("Count %-14s: %s\n", "Item",
+                String.valueOf(itemService.countTotal(context))));
+        sb.append(String.format("Count %-14s: %s\n", "Handle",
+                String.valueOf(handleService.countTotal(context))));
+        sb.append(String.format("Count %-14s: %s\n", "Group",
+                String.valueOf(groupService.countTotal(context))));
+        sb.append(String.format("Count %-14s: %s\n", "BasicWorkflowItem",
+                String.valueOf(basicWorkflowItemService.countTotal(context))));
+        sb.append(String.format("Count %-14s: %s\n", "WorkspaceItem",
+                String.valueOf(workspaceItemService.countTotal(context))));
+        return sb.toString();
+    }
+
+    public  String getCollectionSizesInfo(Context context) throws SQLException {
+        final StringBuffer ret = new StringBuffer();
+        List<Map> colBitSizes = collectionService.getCollectionsWithBitstreamSizesTotal(context);
+        long total_size = 0;
+
+        Collections.sort(colBitSizes, new Comparator<Map>() {
+            @Override
+            public int compare(Map o1, Map o2) {
+                try {
+                    return CollectionDropDown.collectionPath((Collection) o1.get("collection")).compareTo(
+                            CollectionDropDown.collectionPath((Collection) o2.get("collection"))
+                    );
+                } catch (Exception e) {
+                    ret.append(e.getMessage());
+                }
+                return 0;
+            }
+        });
+        for (Map row : colBitSizes) {
+            Long size = (Long) row.get("totalBytes");
+            total_size += size;
+            Collection col = (Collection) row.get("collection");
+            ret.append(String.format(
+                    "\t%s:  %s\n", CollectionDropDown.collectionPath(col), FileUtils.byteCountToDisplaySize((long) size)));
+        }
+        ret.append(String.format(
+                "Total size:              %s\n", FileUtils.byteCountToDisplaySize(total_size)));
+
+        ret.append(String.format(
+                "Resource without policy: %d\n", bitstreamService.countBitstreamsWithoutPolicy(context)));
+
+        ret.append(String.format(
+                "Deleted bitstreams:      %d\n", bitstreamService.countDeletedBitstreams(context)));
+
+        String list_str = "";
+        List<Bitstream> bitstreamOrphans = bitstreamService.getNotReferencedBitstreams(context);
+        for (Bitstream orphan : bitstreamOrphans) {
+            UUID id = orphan.getID();
+            list_str += String.format("%d, ", id);
+        }
+        ret.append(String.format(
+                "Orphan bitstreams:       %d [%s]\n", bitstreamOrphans.size(), list_str));
+
+        return ret.toString();
+    }
+
+    public  List<Map.Entry<String, Integer>> getCommunities(Context context)
+            throws SQLException {
+
+        List<Map.Entry<String, Integer>> cl = new java.util.ArrayList<>();
+        List<Community> top_communities = communityService.findAllTop(context);
+        for (Community c : top_communities) {
+            cl.add(
+                    new java.util.AbstractMap.SimpleEntry<>(c.getName(), itemService.countItems(context, c))
+            );
+        }
+        return cl;
+    }
 }

dspace-api/src/main/java/org/dspace/health/UserCheck.java

@@ -8,17 +8,21 @@
 package org.dspace.health;
 
 
-import org.apache.commons.lang.StringUtils;
+import org.dspace.content.Collection;
+import org.dspace.content.DSpaceObject;
+import org.dspace.content.factory.ContentServiceFactory;
+import org.dspace.content.service.CollectionService;
 import org.dspace.core.Context;
 import org.dspace.eperson.EPerson;
+import org.dspace.eperson.Group;
 import org.dspace.eperson.factory.EPersonServiceFactory;
 import org.dspace.eperson.service.EPersonService;
+import org.dspace.eperson.service.GroupService;
 
 import java.sql.SQLException;
 import java.util.HashMap;
 import java.util.List;
 import java.util.Map;
-import java.util.UUID;
 
 /**
  * @author LINDAT/CLARIN dev team
@@ -26,11 +30,12 @@ import java.util.UUID;
 public class UserCheck extends Check {
 
     private static final EPersonService ePersonService = EPersonServiceFactory.getInstance().getEPersonService();
+    private static final GroupService groupService = EPersonServiceFactory.getInstance().getGroupService();
+    private static final CollectionService collectionService = ContentServiceFactory.getInstance().getCollectionService();
 
     @Override
     public String run( ReportInfo ri ) {
         Context context = new Context();
-        Core core = new Core(context);
         String ret = "";
         Map<String, Integer> info = new HashMap<String, Integer>();
         try {
@@ -81,20 +86,23 @@ public class UserCheck extends Check {
 
         try {
             // empty group
-            List<String> egs = core.getEmptyGroups();
+            List<Group> emptyGroups = groupService.getEmptyGroups(context);
-            ret += String.format(
+            ret += String.format("Empty groups: #%d\n    ", emptyGroups.size());
-                "Empty groups: #%d\n    %s\n",
+            for (Group group : emptyGroups) {
-                egs.size(), StringUtils.join(egs, ",\n    "));
+                ret += String.format("id=%s;name=%s,\n    ", group.getID(), group.getName() );
+            }
 
-            List<UUID> subs = core.getSubscribers();
+            //subscribers
+            List<EPerson> subscribers = ePersonService.findEPeopleWithSubscription(context);
             ret += String.format(
                 "Subscribers: #%d [%s]\n",
-                subs.size(), StringUtils.join(subs, ", "));
+                subscribers.size(), formatIds(subscribers));
 
-            subs = core.getSubscribedCollections();
+            //subscribed collections
+            List<Collection> subscribedCols = collectionService.findCollectionsWithSubscribers(context);
             ret += String.format(
                 "Subscribed cols.: #%d [%s]\n",
-                subs.size(), StringUtils.join(subs, ", "));
+                subscribedCols.size(), formatIds(subscribedCols));
 
             context.complete();
 
@@ -104,4 +112,13 @@ public class UserCheck extends Check {
 
         return ret;
     }
+
+    private String formatIds(List<? extends DSpaceObject> objects){
+        StringBuilder ids = new StringBuilder();
+        for(DSpaceObject o : objects){
+            ids.append(o.getID())
+                    .append(", ");
+        }
+        return ids.toString();
+    }
 }

dspace-api/src/main/java/org/dspace/workflowbasic/BasicWorkflowItemServiceImpl.java

@@ -151,4 +151,9 @@ public class BasicWorkflowItemServiceImpl implements BasicWorkflowItemService {
     public List<BasicWorkflowItem> findByOwner(Context context, EPerson ePerson) throws SQLException {
         return workflowItemDAO.findByOwner(context, ePerson);
     }
+
+    @Override
+    public int countTotal(Context context) throws SQLException {
+        return workflowItemDAO.countRows(context);
+    }
 }

dspace-api/src/main/java/org/dspace/workflowbasic/dao/BasicWorkflowItemDAO.java

@@ -35,4 +35,6 @@ public interface BasicWorkflowItemDAO extends GenericDAO<BasicWorkflowItem> {
     public List<BasicWorkflowItem> findByPooledTasks(Context context, EPerson ePerson) throws SQLException;
 
     public List<BasicWorkflowItem> findByOwner(Context context, EPerson ePerson) throws SQLException;
+
+    int countRows(Context context) throws SQLException;
 }

dspace-api/src/main/java/org/dspace/workflowbasic/dao/impl/BasicWorkflowItemDAOImpl.java

@@ -74,4 +74,9 @@ public class BasicWorkflowItemDAOImpl extends AbstractHibernateDAO<BasicWorkflow
         criteria.add(Restrictions.eq("owner", ePerson));
         return list(criteria);
     }
+
+    @Override
+    public int countRows(Context context) throws SQLException {
+        return count(createQuery(context, "SELECT count(*) FROM BasicWorkflowItem"));
+    }
 }

dspace-api/src/main/java/org/dspace/workflowbasic/service/BasicWorkflowItemService.java

@@ -27,4 +27,6 @@ public interface BasicWorkflowItemService extends WorkflowItemService<BasicWorkf
     public List<BasicWorkflowItem> findPooledTasks(Context context, EPerson ePerson) throws SQLException;
 
     public List<BasicWorkflowItem> findByOwner(Context context, EPerson ePerson) throws SQLException;
+
+    int countTotal(Context context) throws SQLException;
 }