Changeset 3004

Timestamp:

Dec 6, 2006, 4:06:47 PM (16 years ago)

Author:

Martin Svensson

Message:

Fixes #374 Restoring a Bioassayset or Transformation restores
all child bioassay sets and transformations but not the parents

Restoring directories and files had a strange behavior too. It is also fixed in this commit.

Location:

trunk

Files:

• src/core/net/sf/basedb/util/RemovableUtil.java (modified) (7 diffs)
• www/filemanager/files/index.jsp (modified) (2 diffs)

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

@@ -82 +82 @@
     @param dc The database control to use when accessing the database
     @param itemType The itemType to delete
-    @param items A set of the selected items in the list
+    @param items A set of ids from the items that shall be deleted.
     @param removed True if the items should be deleted. False if the items should be restored.
-    @return An int[2] where [0] is the number of removed items, including the parent.
-      and [1] is the total number of subitems that were included in the selection
+    @return An int[2] where [0] is the number of removed/restored items, including the parent
+      and [1] is the total number of items that were included in the selection.
     @throws BaseException If there is an error
   */
@@ -91 +91 @@
     throws BaseException
   {
-    int[] numRemoved = {0,0};
+    int[] numTotalCount = {0,0};
     for (Integer id : items)
     {     
+      int[] numHandled = {0,0};
       if (id != null)
-      {
-        int[] subRemovedCount = {0, 0}; 
+      {        
         Removable item = (Removable)itemType.getById(dc, id);
-        subRemovedCount = removeSubItems(dc, item, removed);
-        numRemoved[0] += subRemovedCount[0];
-        numRemoved[1] += subRemovedCount[1];
-        
-        numRemoved[0] += setRemovedFlag(item, removed) ? 1 : 0;       
-      }
-    }
-    return numRemoved;
+        numHandled = removeDependingItems(dc, item, removed);
+        if ((item instanceof Directory || item instanceof File) && !removed)
+        {
+          int[] numRestored = {0,0};
+          Directory dir = null;
+          
+          if (item instanceof Directory)
+          {
+            dir = ((Directory)item).getParent();
+          }
+          else 
+          {
+            dir = ((File)item).getDirectory();
+          }         
+          numRestored = restorePath(dir);
+          numHandled[0] += numRestored[0];
+          numHandled[1] += numRestored[1];
+        }
+        numHandled[0] += setRemovedFlag(item, removed) ? 1 : 0;       
+      }
+      numTotalCount[0] += numHandled[0];
+      numTotalCount[1] += numHandled[1];
+    }
+    return numTotalCount;
   } 
   
-
   public static int delete(DbControl dc, Item itemType, Set<Integer> items)
     throws BaseException
@@ -128 +143 @@
     }
     return numDeleted;
+  }
+  
+  /**
+    Restores the path to a directory
+      @param parentDir The Directory that is being restored
+      @return An int[2] were [0] is the number of restored directories and
+        [1] is the total number of directories.
+  */
+  private static int[] restorePath(Directory parentDir)
+  {
+    int[] countRestored = {0,0};
+    if (!parentDir.isRootDirectory())
+    {
+      countRestored = restorePath(parentDir.getParent());
+    }
+    countRestored[1]++;
+    countRestored[0] += setRemovedFlag(parentDir, false) ? 1 : 0;
+    
+    return countRestored;
   }
   
@@ -140 +174 @@
     @throws BaseException If there is an error
   */
-  private static int[] removeSubItems(DbControl dc, Removable parent, boolean removed)
+  private static int[] removeDependingItems(DbControl dc, Removable item, boolean removed)
     throws BaseException
   {
@@ -147 +181 @@
     
     /**
-      parent is a <code>Directory</code>
+      item is a <code>Directory</code>
     */
-    if (parent instanceof Directory)
-    {
-      ItemQuery<Directory> subDirQuery = ((Directory)parent).getSubDirectories();
-      ItemQuery<File> fileQuery = ((Directory)parent).getFiles();
+    if (item instanceof Directory)
+    {
+      ItemQuery<Directory> subDirQuery = ((Directory)item).getSubDirectories();
+      ItemQuery<File> fileQuery = ((Directory)item).getFiles();
       
       ItemResultList<Directory> subDirectories = null;
@@ -160 +194 @@
       fileQuery.include(Include.REMOVED, Include.MINE, Include.OTHERS, Include.SHARED);
                   
+      int totalFiles = 0;
+      int totalDirectories = 0;
+      
       try
       {
@@ -170 +207 @@
       if (files != null)
       {
+        totalFiles = files.size();
         for (File file : files)
         {
           numItemsRemoved += setRemovedFlag(file, removed) ? 1 : 0;
-        }
-        numSubItemsRemoved[1] += files.size();
+        }       
       }
       
       if (subDirectories != null)
       {
+        totalDirectories = subDirectories.size();
         for (Directory dir : subDirectories)
         {
-          numSubItemsRemoved = removeSubItems(dc, dir, removed);
+          numSubItemsRemoved = removeDependingItems(dc, dir, removed);          
           numItemsRemoved += setRemovedFlag(dir, removed) ? 1 : 0;
-        }
-        numSubItemsRemoved[1] += subDirectories.size();
-      }
-    }
-    
+        }       
+        numSubItemsRemoved[1] += totalFiles + totalDirectories;
+      }
+    }
+      
     /**
-      parent is a <code>Transformation</code>
+      item is a <code>Transformation</code>
     */
-    else if (parent instanceof Transformation)
-    {
-      ItemQuery<BioAssaySet> bioAssayQuery = ((Transformation)parent).getProducts();      
-      ItemResultList<BioAssaySet> bioAssaySets = null;
-      
-      bioAssayQuery.include(Include.REMOVED,Include.MINE, Include.OTHERS, Include.SHARED);
+    else if (item instanceof Transformation)
+    {
+      if (removed)
+      {
+        ItemQuery<BioAssaySet> bioAssayQuery = ((Transformation)item).getProducts();      
+        ItemResultList<BioAssaySet> bioAssaySets = null;
+        
+        bioAssayQuery.include(Include.REMOVED,Include.MINE, Include.OTHERS, Include.SHARED);
+        
+        try
+        {
+          bioAssaySets = bioAssayQuery.list(dc);
+        }
+        catch (BaseException ex)
+        {}
+        
+        if (bioAssaySets != null)
+        {
+          for (BioAssaySet bsa : bioAssaySets)
+          {
+            numSubItemsRemoved = removeDependingItems(dc, bsa, removed);
+            numItemsRemoved  += setRemovedFlag(bsa, removed) ? 1 : 0;
+          }
+          numSubItemsRemoved[1] += bioAssaySets.size();
+        }     
+      }
+      else
+      {
+        Transformation tf = (Transformation)item;
+        BioAssaySet bas = tf.getSource();
+        // The transformation is not a root transformation
+        if (bas != null)
+        {
+          numSubItemsRemoved = removeDependingItems(dc, bas, removed);
+          numItemsRemoved += setRemovedFlag(bas, removed) ? 1 : 0;
+          numSubItemsRemoved[1]++;
+        }
+      }
+    }
+    
+    
+    /**
+      item is a <code>BioAssaySet</code>
+    */
+    else if (item instanceof BioAssaySet)
+    {
+      if (removed)
+      {
+        ItemQuery<Transformation> transformationQuery = ((BioAssaySet)item).getTransformations();
+        ItemResultList<Transformation> transformations = null;
+        
+        transformationQuery.include(Include.REMOVED,Include.MINE, Include.OTHERS, Include.SHARED);
+        
+        try
+        {
+          transformations = transformationQuery.list(dc);
+        }
+        catch (BaseException ex)
+        {}
+        
+        if (transformations != null)
+        {
+          for (Transformation tf : transformations)
+          {
+            numSubItemsRemoved = removeDependingItems(dc, tf, removed);
+            numItemsRemoved += setRemovedFlag(tf, removed) ? 1 : 0;
+          }
+          numSubItemsRemoved[1] += transformations.size();
+        }           
+      }
+      else
+      {
+        BioAssaySet bas = (BioAssaySet)item;
+        Transformation tf = bas.getTransformation();
+        if (tf != null)
+        {
+          numSubItemsRemoved = removeDependingItems(dc, tf, removed);
+          numItemsRemoved += setRemovedFlag(tf, removed) ? 1 : 0;
+          numSubItemsRemoved[1]++;
+        }
+      }
+    }
+    
+    /**
+      item is an <code>Experiment</code>
+    */
+    else if (item instanceof Experiment)
+    {
+      ItemQuery<Transformation> transformationQuery = ((Experiment)item).getRootTransformations();
+      ItemResultList<Transformation> transformations = null;
+      
+      transformationQuery.include(Include.REMOVED,Include.MINE, Include.OTHERS, Include.SHARED);
       
       try
       {
-        bioAssaySets = bioAssayQuery.list(dc);
+        transformations = transformationQuery.list(dc);
       }
       catch (BaseException ex)
       {}
       
-      if (bioAssaySets != null)
-      {
-        for (BioAssaySet bsa : bioAssaySets)
-        {
-          numSubItemsRemoved = removeSubItems(dc, bsa, removed);
-          numItemsRemoved  += setRemovedFlag(bsa, removed) ? 1 : 0;
-        }
-        numSubItemsRemoved[1] += bioAssaySets.size();
-      }     
-    }
-    
-    /**
-      parent is a <code>BioAssaySet</code>
-    */
-    else if (parent instanceof BioAssaySet)
-    {
-      ItemQuery<Transformation> transformationQuery = ((BioAssaySet)parent).getTransformations();
-      ItemResultList<Transformation> transformations = null;
-      
-      transformationQuery.include(Include.REMOVED,Include.MINE, Include.OTHERS, Include.SHARED);
-      
-      try
-      {
-        transformations = transformationQuery.list(dc);
-      }
-      catch (BaseException ex)
-      {}
-      
       if (transformations != null)
       {
         for (Transformation tf : transformations)
         {
-          numSubItemsRemoved = removeSubItems(dc, tf, removed);
-          numItemsRemoved += setRemovedFlag(tf, removed) ? 1 : 0;
-        }
-        numSubItemsRemoved[1] += transformations.size();
-      }           
-    }
-    
-    /**
-      parent is an <code>Experiment</code>
-    */
-    else if (parent instanceof Experiment)
-    {
-      ItemQuery<Transformation> transformationQuery = ((Experiment)parent).getRootTransformations();
-      ItemResultList<Transformation> transformations = null;
-      
-      transformationQuery.include(Include.REMOVED,Include.MINE, Include.OTHERS, Include.SHARED);
-      
-      try
-      {
-        transformations = transformationQuery.list(dc);
-      }
-      catch (BaseException ex)
-      {}
-      
-      if (transformations != null)
-      {
-        for (Transformation tf : transformations)
-        {
-          numSubItemsRemoved = removeSubItems(dc, tf, removed);
+          numSubItemsRemoved = removeDependingItems(dc, tf, removed);
           numItemsRemoved += setRemovedFlag(tf, removed) ? 1 : 0;
         }

trunk/www/filemanager/files/index.jsp

@@ -208 +208 @@
     dc = sc.newDbControl();
     ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
-    RemovableUtil.setRemoved(dc, itemType, Collections.singleton(cc.getId()), false);
+    RemovableUtil.removeRecursively(dc, itemType, Collections.singleton(cc.getId()), false);
     dc.commit();
     redirect = viewPage;
@@ -218 +218 @@
     ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
     int numTotal = cc.getSelected().size()+dirContext.getSelected().size();
-    int[] numRemoved = RemovableUtil.removeRecursively(dc, Item.DIRECTORY, dirContext.getSelected(), false);
-    numRemoved[0] += RemovableUtil.setRemoved(dc, itemType, cc.getSelected(), false);
-    numTotal += numRemoved[1];
-    dc.commit();
-    if (numTotal != numRemoved[0])
-    {
-      message = (numRemoved[0] == 0 ? "No" : "Only "+numRemoved[0]+" of "+numTotal) + " items could be restored, because you have no WRITE permission";
+    int numRemoved = 0;
+    int[] numDirRemoved = RemovableUtil.removeRecursively(dc, Item.DIRECTORY, dirContext.getSelected(), false);
+    int[] numFileRemoved = RemovableUtil.removeRecursively(dc, itemType, cc.getSelected(), false);
+    numTotal += numDirRemoved[1] + numFileRemoved[1];
+    numRemoved = numDirRemoved[0] + numFileRemoved[0];
+    
+    dc.commit();
+    if (numTotal != numRemoved)
+    {
+      message = (numRemoved == 0 ? "No" : "Only "+numRemoved+" of "+numTotal) + " items could be restored, because you have no WRITE permission";
     }
     redirect = listPage+(message != null ? "&popmessage="+HTML.urlEncode(message) : "");