Changeset 3190 for trunk/src

Timestamp:

Mar 13, 2007, 11:05:42 AM (16 years ago)

Author:

Johan Enell

Message:

Merged log:branches/2.2.2#3116:3186 to trunk.

Location:

trunk/src

Files:

• clients/web/net/sf/basedb/clients/web/formatter/FormatterSettings.java (modified) (1 diff)
• core/common-queries.xml (modified) (2 diffs)
• core/net/sf/basedb/core/Group.java (modified) (3 diffs)
• core/net/sf/basedb/core/Install.java (modified) (1 diff)
• core/net/sf/basedb/core/Keyring.java (modified) (5 diffs)
• core/net/sf/basedb/core/Trashcan.java (modified) (1 diff)
• core/net/sf/basedb/core/Update.java (modified) (6 diffs)
• core/net/sf/basedb/core/User.java (modified) (3 diffs)
• core/net/sf/basedb/core/query/Hql.java (modified) (3 diffs)
• core/net/sf/basedb/core/query/HqlEntityExpression.java (modified) (5 diffs)
• core/net/sf/basedb/util/Values.java (modified) (2 diffs)
• core/net/sf/basedb/util/overview/ExperimentOverview.java (modified) (4 diffs)

trunk/src/clients/web/net/sf/basedb/clients/web/formatter/FormatterSettings.java

@@ -80 +80 @@
   {
     sc.setUserClientSetting("formatter.number.decimals", Integer.toString(numDecimals));
-    sc.setSessionSetting("formatter.number", null);
+    sc.setSessionSetting("formatter.double", null);
+    sc.setSessionSetting("formatter.float", null);
   }
   

trunk/src/core/common-queries.xml

@@ -202 +202 @@
     <description>
       Load the ID of all users which has a quota group from one of the given groups.
+    </description>
+  </query>
+
+  <query id="GET_USER_IDS_FOR_PROJECT" type="HQL">
+    <sql>
+      SELECT up.userId
+      FROM UserProjects up
+      WHERE up.projectId = :projectId
+    </sql>
+    <description>
+      Load the ID of all users which are direct member of the given project
+    </description>
+  </query>
+
+  <query id="GET_GROUP_IDS_FOR_PROJECT" type="HQL">
+    <sql>
+      SELECT gp.groupId
+      FROM GroupProjects gp
+      WHERE gp.projectId = :projectId
+    </sql>
+    <description>
+      Load the ID of all groups which are direct member of the given project
     </description>
   </query>
@@ -2523 +2545 @@
   </query>
 
-  <query id="GET_SUM_USED_QUANTITY_EVENTS" type="HQL">
-    <sql>
-      SELECT evt.bioMaterial, SUM(evt.usedQuantity)
+  <query id="GET_USED_QUANTITY_EVENTS" type="HQL">
+    <sql>
+      SELECT evt.bioMaterial, evt.usedQuantity
       FROM BioMaterialEventData evt
-      GROUP BY evt.bioMaterial
-    </sql>
-    <description>
-      A HQL query that loads the sum of the used quantity 
-      grouped by the biomaterial for all BioMaterialEvent:s.
-    </description>
-  </query>
-  
-  <query id="GET_SUM_USED_QUANTITY_SOURCES" type="HQL">
-    <sql>
-      SELECT index(src), SUM(src.usedQuantity)
+    </sql>
+    <description>
+      A HQL query that loads the biomaterial and the used quantity 
+      for all BioMaterialEvent:s.
+    </description>
+  </query>
+  
+  <query id="GET_USED_QUANTITY_SOURCES" type="HQL">
+    <sql>
+      SELECT index(src), src.usedQuantity
       FROM BioMaterialEventData evt
       JOIN evt.sources src
-      GROUP BY index(src)
-    </sql>
-    <description>
-      A HQL query that loads the sum of the used quantity 
-      grouped by the biomaterial for all sources to
-      BioMaterialEvent:s.
+    </sql>
+    <description>
+      A HQL query that loads the used quantity 
+      for all sources to BioMaterialEvent:s.
     </description>
   </query>

trunk/src/core/net/sf/basedb/core/Group.java

@@ -29 +29 @@
 import net.sf.basedb.core.query.Hql;
 
+import java.util.Collection;
 import java.util.HashSet;
 import java.util.Set;
@@ -124 +125 @@
   public static Set<Integer> getGroupsRecursive(DbControl dc, Set<Integer> groups)
   {
+    return getGroupsRecursive(dc.getHibernateSession(), groups);
+  }
+
+  static Set<Integer> getGroupsRecursive(org.hibernate.Session session, Collection<Integer> groups)
+  {
     Set<Integer> allGroups = new HashSet<Integer>(groups);
     if (allGroups.size() > 0)
     {
       
-      org.hibernate.Query query = HibernateUtil.getPredefinedQuery(dc.getHibernateSession(), 
+      org.hibernate.Query query = HibernateUtil.getPredefinedQuery(session, 
         "GET_CHILDGROUPS_IDS_FOR_GROUPS");
       /*
@@ -143 +149 @@
     return allGroups;
   }
+
   
   /**

trunk/src/core/net/sf/basedb/core/Install.java

@@ -102 +102 @@
     method.
   */
-  public static final int NEW_SCHEMA_VERSION = 29;
-
+  public static final int NEW_SCHEMA_VERSION = 30;
+  
   public static synchronized void createTables(boolean update, final ProgressReporter progress)
     throws BaseException

trunk/src/core/net/sf/basedb/core/Keyring.java

@@ -450 +450 @@
     Load all users which are member of at least one group where the
     logged in user is also a member and put that information
-    in the {@link #users} variable.
+    in the {@link #users} variable. If a project is active, also load the members
+    and owner of that project.
   */
   private void loadUsers(org.hibernate.Session session)
     throws BaseException
   {
-    Set<Integer> temp;
+    Set<Integer> temp = new HashSet<Integer>();
     try
     {
@@ -468 +469 @@
         */
         query.setParameterList("groups", groups, org.hibernate.Hibernate.INTEGER);
-        temp = new HashSet<Integer>(HibernateUtil.loadList(Integer.class, query));
+        temp.addAll(HibernateUtil.loadList(Integer.class, query));
         
         // Get the users that have a quota group among the same groups
@@ -479 +480 @@
         query.setParameterList("groups", groups, org.hibernate.Hibernate.INTEGER);
         temp.addAll(HibernateUtil.loadList(Integer.class, query));
+      }
+      
+      if (projectId != 0)
+      {
+        // Get the owner of the active project
+        ProjectData pd = HibernateUtil.loadData(session, ProjectData.class, projectId);
+        temp.add(pd.getOwner().getId());
         
-        users = Collections.unmodifiableSet(temp);
-      }
+        // Get direct members of the active project
+        org.hibernate.Query query = HibernateUtil.getPredefinedQuery(session, "GET_USER_IDS_FOR_PROJECT");
+        /*
+          SELECT up.userId
+          FROM UserProjects up
+          WHERE up.projectId = :projectId
+        */
+        query.setInteger("projectId", projectId);
+        temp.addAll(HibernateUtil.loadList(Integer.class, query));
+        
+        // Get groups that are direct members of the active project
+        query = HibernateUtil.getPredefinedQuery(session, "GET_GROUP_IDS_FOR_PROJECT");
+        /*
+          SELECT gp.groupId
+          FROM GroupProjects gp
+          WHERE gp.projectId = :projectId
+        */
+        query.setInteger("projectId", projectId);
+        // Load the direct groups and subgroups
+        Set<Integer> projectGroups = Group.getGroupsRecursive(session, HibernateUtil.loadList(Integer.class, query));
+
+        // Load users that are members of the project groups
+        temp.addAll(User.getAllMembers(session, projectGroups));
+        
+      }
+      users = Collections.unmodifiableSet(temp);
     }
     catch (HibernateException ex)
@@ -717 +749 @@
   {
     if (getReload() && !reload()) projectData = null;
+    int oldProjectId = projectId;
     if (projectData == null)
     {
@@ -725 +758 @@
     {
       projectId = projectData.getId();
-      org.hibernate.Session session = null;
-      org.hibernate.Transaction tx = null;
-      try
-      {
-        session = HibernateUtil.newSession();
-        tx = HibernateUtil.newTransaction(session);
-        loadMaxProjectPermission(session, projectData);
-        loadProjectKeys(session);
-      }
-      catch (BaseException ex)
-      {
-        projectId = 0;
-        maxProjectPermission = 0;
-        throw ex;
-      }
-      finally
-      {
-        if (tx != null) HibernateUtil.commit(tx);
-        if (session != null) HibernateUtil.close(session);
-      }
-    }
+    }
+    reload = projectId != oldProjectId;
   }
   

trunk/src/core/net/sf/basedb/core/Trashcan.java

@@ -90 +90 @@
             if (item.hasPermission(Permission.DELETE)) 
             {
-              if (!useLimit || (index >= firstItem && index < lastItem))
+              SharedItem parent = item instanceof ChildItem ? 
+                  dc.getItem(SharedItem.class, ((ChildItem)item).getSharedParent()) : null; 
+              
+              if ( (parent != null && parent.isOwner()) || (parent == null))
               {
-                items.add((Removable)item);
+                if (!useLimit || (index >= firstItem && index < lastItem))
+                {
+                  items.add((Removable)item);
+                }
+                index++;
+                totalItems++;
               }
-              index++;
-              totalItems++;
             }
           }

trunk/src/core/net/sf/basedb/core/Update.java

@@ -346 +346 @@
   <tr>
     <td>29</td>
+    <td>
+      No changes at all except increasing the schema version number. 
+      The veryfication of remaining quantity is moved to next update of schema version. 
+    </td>
+  </tr>
+  
+  <tr>
+    <td>30</td>
     <td>
       No schema change as such, but we need to verify and possibly update the
@@ -505 +513 @@
       }
       
+      
+      if (schemaVersion < 30)
+      {
+        if (progress != null) progress.display((int)(29*progress_factor), "--Updating schema version: " + schemaVersion + " -> 30...");      
+        schemaVersion = updateToSchemaVersion30(session);
+      }
+      
       /*
-      if (schemaVersion < 30)
-      {
-        if (progress != null) progress.display((int)(29*progress_factor), "--Updating schema version: " + schemaVersion + " -> 30...");
-        schemaVersion = setSchemaVersionInTransaction(session, 30);
+      if (schemaVersion < 31)
+      {
+        if (progress != null) progress.display((int)(30*progress_factor), "--Updating schema version: " + schemaVersion + " -> 30...");
+        schemaVersion = setSchemaVersionInTransaction(session, 31);
         - or - 
-        schemaVersion = updateToSchemaVersion30(session);
+        schemaVersion = updateToSchemaVersion31(session);
       }
       ... etc... 
@@ -1071 +1086 @@
   /**
     Vefify and update the remaining quantity of all biomaterials.
-    @return The new schema version (=29)
+    @return The new schema version (=30)
   */
-  private static int updateToSchemaVersion29(org.hibernate.Session session)
+  private static int updateToSchemaVersion30(org.hibernate.Session session)
     throws BaseException
   {
-    final int schemaVersion = 29;
+    final int schemaVersion = 30;
     
     org.hibernate.Transaction tx = null;
@@ -1086 +1101 @@
       Map<MeasuredBioMaterialData, Float> remaining = new HashMap<MeasuredBioMaterialData, Float>(); 
       
-      // Load sum of used quantity for all events
+      // Load used quantity for all events
       org.hibernate.Query eventQuery = HibernateUtil.getPredefinedQuery(session, 
-        "GET_SUM_USED_QUANTITY_EVENTS");
-      /*
-        SELECT evt.bioMaterial, SUM(evt.usedQuantity)
-        FROM BioMaterialEventData evt
-        GROUP BY evt.bioMaterial
-      */
-      // Load sum of used quantity for sources to all events
+        "GET_USED_QUANTITY_EVENTS");
+        /*       
+          SELECT evt.bioMaterial, evt.usedQuantity
+          FROM BioMaterialEventData evt
+        */
+      
+      // Load used quantity for sources to all events
       org.hibernate.Query sourcesQuery = HibernateUtil.getPredefinedQuery(session, 
-        "GET_SUM_USED_QUANTITY_SOURCES");
+        "GET_USED_QUANTITY_SOURCES");
         /*
-          SELECT index(src), SUM(src.usedQuantity)
+          SELECT index(src), src.usedQuantity
           FROM BioMaterialEventData evt
-          JOIN evt.sources src
-          GROUP BY index(src)
+          JOIN evt.sources src          
          */
       List<Object[]> events = HibernateUtil.loadList(Object[].class, eventQuery);
@@ -1107 +1121 @@
       
       // Calculate the remaining quantity for each biomaterial
-      // o[0] = biomaterial, o[1] = sum of used quantity
+      // o[0] = biomaterial, o[1] = used quantity     
       for (Object[] o : events)
       {
-        MeasuredBioMaterialData bioMaterial = (MeasuredBioMaterialData)o[0];
-        Double sumUsedQuantity = (Double)o[1];
-        if (sumUsedQuantity != null)
+        MeasuredBioMaterialData bioMaterial = (MeasuredBioMaterialData)o[0];        
+        Float usedQuantity = (Float)o[1];       
+        if (usedQuantity != null)
         {
           Float currentRemaining = remaining.get(bioMaterial);
           if (currentRemaining == null) currentRemaining = 0.0f;
-          currentRemaining = currentRemaining - sumUsedQuantity.floatValue();
+          currentRemaining = currentRemaining - usedQuantity;
           remaining.put(bioMaterial, currentRemaining);
         }
@@ -1143 +1157 @@
       // Commit the changes
       HibernateUtil.commit(tx);
-      log.info("updateToSchemaVersion29: OK");
+      log.info("updateToSchemaVersion30: OK");
     }
     catch (BaseException ex)
     {
       if (tx != null) HibernateUtil.rollback(tx); 
-      log.error("updateToSchemaVersion29: FAILED", ex);
+      log.error("updateToSchemaVersion30: FAILED", ex);
       throw ex;
     }

trunk/src/core/net/sf/basedb/core/User.java

@@ -36 +36 @@
 
 import java.util.ArrayList;
+import java.util.Collection;
 import java.util.Date;
 import java.util.HashSet;
@@ -124 +125 @@
   public static Set<Integer> getAllMembers(DbControl dc, Set<Integer> groupIds)
   {
+    return getAllMembers(dc.getHibernateSession(), groupIds);
+  }
+  
+  static Set<Integer> getAllMembers(org.hibernate.Session session, Collection<Integer> groupIds)
+  {
     Set<Integer> userIds = new HashSet<Integer>();
     if (groupIds != null && groupIds.size() > 0)
     {
-      org.hibernate.Session session = dc.getHibernateSession();
       // Get the users which are members of the same groups
       org.hibernate.Query query = HibernateUtil.getPredefinedQuery(session, "GET_USER_IDS_FOR_GROUPS");
@@ -149 +154 @@
     }
     return userIds;
-    
-  }
+  }
+
   
   /**

trunk/src/core/net/sf/basedb/core/query/Hql.java

@@ -27 +27 @@
 import net.sf.basedb.core.InvalidDataException;
 import net.sf.basedb.core.InvalidUseOfNullException;
+import net.sf.basedb.core.data.BasicData;
 
 import java.util.regex.Pattern;
@@ -55 +56 @@
 
   /**
-    Create an expression representing an item. In the query the actual
-    value used is the id of the entity. See {@link #property(String, String)}
-    for a code example.
+    Create an expression representing an item which is a subclass of BasicItem. 
+    In the query the actual value used is the id of the entity. 
+    See {@link #property(String, String)} for a code example.
 
     @param entity The entity
-    @throws InvalidDataException If the etity is null
+    @throws InvalidDataException If the entity is null
+    @see #entity(BasicData)
   */
   public static Expression entity(BasicItem entity)
@@ -69 +71 @@
   }
   
+  /**
+    Create an expression representing an item which is a subclass of BasicData,
+    for example a reporter. In the query the actual value used is the id of the entity. 
+    See {@link #property(String, String)} for a code example.
+  
+    @param entity The entity
+    @throws InvalidDataException If the entity is null
+    @see #entity(BasicItem)
+    @since 2.2.2
+  */
+  public static Expression entity(BasicData entity)
+    throws InvalidDataException
+  {
+    if (entity == null) throw new InvalidUseOfNullException("entity");
+    return new HqlEntityExpression(entity);
+  }
+    
   /**
     Same as <code>property(null, property)</code>.

trunk/src/core/net/sf/basedb/core/query/HqlEntityExpression.java

@@ -29 +29 @@
 import net.sf.basedb.core.BasicItem;
 import net.sf.basedb.core.BaseException;
+import net.sf.basedb.core.data.BasicData;
 
 /**
@@ -39 +40 @@
   @version 2.0
   @see Hql#entity(BasicItem)
+  @see Hql#entity(BasicData)
   @base.modified $Date$
 */
@@ -44 +46 @@
   implements Expression
 {
-  private final BasicItem item;
+  private final int id;
+  private final String item;
 
   HqlEntityExpression(BasicItem item)
   {
-    this.item = item;
+    this.id = item.getId();
+    this.item = item.toString();
+  }
+  
+  /**
+    @since 2.2.2
+  */
+  HqlEntityExpression(BasicData data)
+  {
+    this.id = data.getId();
+    this.item = data.toString();
   }
 
@@ -60 +73 @@
     if (query.getQueryType() == QueryType.HQL)
     {
-      return Integer.toString(item.getId());
+      return Integer.toString(id);
     }
     else
@@ -81 +94 @@
   public String toString()
   {
-    return item.toString();
+    return item;
   }
   // -------------------------------------------

trunk/src/core/net/sf/basedb/util/Values.java

@@ -628 +628 @@
       result.append(lNumber).append(".");
       String theDecimals = Long.toString(Math.round(fNumber*exp-lNumber*exp)); 
-      result.append(theDecimals);
       if (theDecimals.length() < decimals) 
       {
@@ -636 +635 @@
         }
       }
+      result.append(theDecimals);
     }
     if (unit != null) result.append(unit);

trunk/src/core/net/sf/basedb/util/overview/ExperimentOverview.java

@@ -281 +281 @@
     this.annotatableParents = new HashMap<Annotatable, Set<Annotatable>>();
     
-    // Load 'Required for MIAME' annotation types
+    // Load 'Required for MIAME' annotation types (parameter='false' must also be set)
     ItemQuery<AnnotationType> query = initQuery(AnnotationType.getQuery(null), "name");
     query.restrict(
       Restrictions.eq(
         Hql.property("requiredForMiame"), 
-        Expressions.parameter("flag", true, Type.BOOLEAN)
+        Expressions.parameter("miameFlag", true, Type.BOOLEAN)
+      )
+    );
+    query.restrict(
+      Restrictions.eq(
+        Hql.property("protocolParameter"), 
+        Expressions.parameter("parameterFlag", false, Type.BOOLEAN)
       )
     );
@@ -619 +625 @@
       for (Node factorNode : efNode.getChildren())
       {
-        Node annotationNode = annotationsNode.getChild("annotationtype." + factorNode.getItem().getId());
+        Node annotationNode = annotationsNode == null ? 
+            null : annotationsNode.getChild("annotationtype." + factorNode.getItem().getId());
         if (annotationNode == null)
         {
@@ -1541 +1548 @@
           failures.add(new Failure(Validator.MISSING_PARAMETER, parentNode, 
             "Missing parameter value: " + pp.getName(), 
-            new Fix("Add parameter value", parentItem, pp, false)));
+            new Fix("Add parameter value for: " + pp.getName(), parentItem, pp, false)));
         }
       }
@@ -1579 +1586 @@
         {
           AnnotationType at = a.getAnnotationType();
-          if (protocol == null || protocol.isParameter(at))
+          // Protocol parameters are handled elsewhere
+          if (protocol == null || !protocol.isParameter(at))
           {
             Node atNode = new Node("annotationtype."+at.getId(), at.getName(), annotationsNode, at);