Changeset 2210

Timestamp:

May 3, 2006, 3:42:21 PM (17 years ago)

Author:

Nicklas Nordborg

Message:

Fixes #163: The tree of bioassay sets in the analysis should include
transformations as separate items

Location:

trunk

Files:

• src/clients/web/net/sf/basedb/clients/web/Base.java (modified) (4 diffs)
• www/views/experiments/bioassaysets/index.jsp (modified) (7 diffs)
• www/views/experiments/bioassaysets/list_bioassaysets.jsp (modified) (15 diffs)
• www/views/experiments/transformations (added)
• www/views/experiments/transformations/edit_transformation.jsp (added)
• www/views/experiments/transformations/index.jsp (added)
• www/views/experiments/transformations/view_transformation.jsp (added)

trunk/src/clients/web/net/sf/basedb/clients/web/Base.java

@@ -309 +309 @@
       sc.getCurrentContext(Item.DIRECTORY, subContext) : null; // Used in special case for file manager
     
+    ItemContext transformationContext = itemType == Item.BIOASSAYSET ?
+      sc.getCurrentContext(Item.TRANSFORMATION, subContext) : null; // Used in special case for analysis tree
+      
     // Detect if active project has changed and then set the include option
     int projectId = sc.getActiveProjectId();
@@ -395 +398 @@
         cc.getSelected().clear();
         if (dirContext != null) dirContext.getSelected().clear();
+        if (transformationContext != null) transformationContext.getSelected().clear();
         while (names.hasMoreElements())
         {
@@ -466 +470 @@
             }
           }
-          else if (name.startsWith("D:") && dirContext != null)
+          else if (dirContext != null && name.startsWith("D:"))
           {
             // Special case for file manager which lists both files and directories in the
@@ -472 +476 @@
             int id = Values.getInt(name.substring(2), -1);
             if (id != -1) dirContext.getSelected().add(id);
+          }
+          else if (transformationContext != null && name.startsWith("T:"))
+          {
+            // Special case for analysis tree which lists both bioassay sets and 
+            // transformations in the same list
+            int id = Values.getInt(name.substring(2), -1);
+            if (id != -1) transformationContext.getSelected().add(id);
           }
           else

trunk/www/views/experiments/bioassaysets/index.jsp

@@ -71 +71 @@
   private static final ItemContext defaultContext = Base.createDefaultContext("name", "name,transformation,spots,reporters,date,tools");
   private static final Item itemType = Item.BIOASSAYSET;
+  
+  
+  private void setClosed(HttpServletRequest request, ItemContext cc)
+  {
+    String closed = request.getParameter("closed");
+    if (closed != null)
+    {
+      cc.setObject("closed", new HashSet<String>(Arrays.asList(closed.split(","))));
+    }
+  }
 %>
 <%
@@ -111 +121 @@
     // Display the list page after updating the current context from the request parameters
     ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
-    String closed = request.getParameter("closed");
-    if (closed != null)
-    {
-      cc.setObject("closed", new HashSet<Integer>(Arrays.asList(Values.getInt(closed.split(",")))));
-    }
+    setClosed(request, cc);
     redirect = listPage;
   }
@@ -180 +186 @@
     dc = sc.newDbControl();
     ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
-    int numTotal = cc.getSelected().size();
+    ItemContext tc = sc.getCurrentContext(Item.TRANSFORMATION);
+    setClosed(request, cc);
+
+    int numTotal = cc.getSelected().size()+tc.getSelected().size();
     int numRemoved = RemovableUtil.setRemoved(dc, itemType, cc.getSelected(), true);
+    numRemoved += RemovableUtil.setRemoved(dc, Item.TRANSFORMATION, tc.getSelected(), true);
     dc.commit();
     if (numTotal != numRemoved)
@@ -203 +213 @@
     dc = sc.newDbControl();
     ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
-    int numTotal = cc.getSelected().size();
+    ItemContext tc = sc.getCurrentContext(Item.TRANSFORMATION);
+    setClosed(request, cc);
+
+    int numTotal = cc.getSelected().size()+tc.getSelected().size();
     int numRemoved = RemovableUtil.setRemoved(dc, itemType, cc.getSelected(), false);
+    numRemoved += RemovableUtil.setRemoved(dc, Item.TRANSFORMATION, tc.getSelected(), false);
     dc.commit();
     if (numTotal != numRemoved)
@@ -216 +230 @@
     // Run an export plugin in a list context
     ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
+    setClosed(request, cc);
     dc = sc.newDbControl();
     final Experiment experiment = Experiment.getById(dc, experimentId);
@@ -234 +249 @@
     // Run an import plugin in a list context
     ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
+    setClosed(request, cc);
     dc = sc.newDbControl();
     final Experiment experiment = Experiment.getById(dc, experimentId);
@@ -252 +268 @@
     // Run another plugin in a list context
     ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
+    setClosed(request, cc);
     dc = sc.newDbControl();
     final Experiment experiment = Experiment.getById(dc, experimentId);

trunk/www/views/experiments/bioassaysets/list_bioassaysets.jsp

@@ -31 +31 @@
   import="net.sf.basedb.core.Item"
   import="net.sf.basedb.core.ItemContext"
+  import="net.sf.basedb.core.BasicItem"
   import="net.sf.basedb.core.Experiment"
   import="net.sf.basedb.core.BioAssaySet"
+  import="net.sf.basedb.core.Transformation"
   import="net.sf.basedb.core.ItemQuery"
+  import="net.sf.basedb.core.Nameable"
   import="net.sf.basedb.core.ItemResultIterator"
   import="net.sf.basedb.core.ItemResultList"
@@ -43 +46 @@
   import="net.sf.basedb.core.query.Orders"
   import="net.sf.basedb.core.query.Hql"
+  import="net.sf.basedb.core.query.Restrictions"
   import="net.sf.basedb.core.plugin.GuiContext"
   import="net.sf.basedb.core.plugin.Plugin"
@@ -51 +55 @@
   import="net.sf.basedb.clients.web.util.Values"
   import="java.util.List"
+  import="java.util.ArrayList"
   import="java.util.LinkedList"
   import="java.util.Map"
@@ -67 +72 @@
 <%!
 
-private static void addToTree(Tree<BioAssaySet> tree, BioAssaySet bas)
+private static void addToTree(Tree<BasicItem> tree, BioAssaySet bas)
 {
   if (!tree.contains(bas))
   {
-    BioAssaySet source = bas.getTransformation().getSource();
-    Tree.Entry<BioAssaySet> parent = tree.getEntry(source);
+    Transformation transformation = bas.getTransformation();
+    Tree.Entry<BasicItem> parent = tree.getEntry(transformation);
     if (parent == null) 
     {
-      addToTree(tree, source);
-      parent = tree.getEntry(source);
+      addToTree(tree, transformation);
+      parent = tree.getEntry(transformation);
     }
     parent.addChild(bas);
@@ -82 +87 @@
 }
 
-private static Tree<BioAssaySet> getBioAssaySetTree(DbControl dc, ItemQuery<BioAssaySet> query)
+private static void addToTree(Tree<BasicItem> tree, Transformation transformation)
 {
-  Tree<BioAssaySet> tree = new Tree<BioAssaySet>(null);
-  ItemResultList<BioAssaySet> allBioAssaySets = query.list(dc);
+  if (!tree.contains(transformation))
+  {
+    BioAssaySet source = transformation.getSource();
+    Tree.Entry<BasicItem> parent = tree.getEntry(source);
+    if (parent == null) 
+    {
+      addToTree(tree, source);
+      parent = tree.getEntry(source);
+    }
+    parent.addChild(transformation);
+  }
+}
+
+private static Tree<BasicItem> getAnalysisTree(DbControl dc, ItemQuery<BioAssaySet> bioAssaySetQuery, ItemQuery<Transformation> transformationQuery)
+{
+  Tree<BasicItem> tree = new Tree<BasicItem>(null);
+  ItemResultList<BioAssaySet> allBioAssaySets = bioAssaySetQuery.list(dc);
+  List<Integer> ids = new ArrayList<Integer>(allBioAssaySets.size());
+  
   for (BioAssaySet bas : allBioAssaySets)
   {
     addToTree(tree, bas);
+    ids.add(bas.getId());
+  }
+  
+  transformationQuery.restrict(
+    Restrictions.in(
+      Hql.property("source.id"), 
+      Expressions.parameter("bioAssaySets", ids)
+    )
+  );
+  ItemResultList<Transformation> allTransformations = transformationQuery.list(dc);
+  for (Transformation t: allTransformations)
+  {
+    addToTree(tree, t);
   }
   return tree;
 }
-String generateTree(Tree<BioAssaySet> tree, BioAssaySet root, Collection<Integer> closed)
+String generateTree(Tree<BasicItem> tree, BasicItem root, Collection<String> closed)
 {
   StringBuilder sb = new StringBuilder();
-  Tree.Entry<BioAssaySet> rootEntry = tree.getEntry(root);
+  Tree.Entry<BasicItem> rootEntry = tree.getEntry(root);
   if (rootEntry == null) return "";
   
-  List<Tree.Entry<BioAssaySet>> children = rootEntry.getChildren();
+  List<Tree.Entry<BasicItem>> children = rootEntry.getChildren();
   if (children != null)
   {
-    for (Tree.Entry<BioAssaySet> child : children)
-    {
-      String folderIcon = "BioAssaySet";
-      BioAssaySet childBa = child.getNode();
-      sb.append("var ba").append(childBa.getId());
+    for (Tree.Entry<BasicItem> child : children)
+    {
+      BasicItem node = child.getNode();
+      int id = node.getId();
+      String var = node.getType().name() + "_" + id;
+      String name = ((Nameable)node).getName();
+      
+      String folderIcon = node.getType() == Item.BIOASSAYSET ?
+        "BioAssaySet" : "Transformation";
+      sb.append("var ").append(var);
       if (root == null)
       {
@@ -112 +152 @@
       else
       {
-        sb.append(" = JoustMenu.addChildItem(ba" + root.getId()); 
+        String rootVar = root.getType().name() + "_" + root.getId();
+        sb.append(" = JoustMenu.addChildItem(").append(rootVar); 
       }
       sb.append(",'").append(folderIcon).append("'");
-      sb.append(",'").append(HTML.javaScriptEncode(childBa.getName())).append("'");
-      sb.append(", 'itemOnClick(event, ").append(childBa.getId()).append(")', '', '").append(childBa.getId()).append("');\n");
-      if ((closed == null || !closed.contains(childBa.getId())) && child.getNumChildren() > 0)
-      {
-        sb.append("JoustMenu.menuItems[ba").append(childBa.getId()).append("].isOpen = true;\n");
-      }
-      sb.append(generateTree(tree, childBa, closed));
+      sb.append(",'").append(HTML.javaScriptEncode(name)).append("'");
+      sb.append(", 'itemOnClick(event, ").append(id).append(")', '', '").append(var).append("');\n");
+      if ((closed == null || !closed.contains(var)) && child.getNumChildren() > 0)
+      {
+        sb.append("JoustMenu.menuItems[").append(var).append("].isOpen = true;\n");
+      }
+      sb.append(generateTree(tree, node, closed));
     }
   }
@@ -132 +173 @@
 final String ID = sc.getId();
 final ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, null, null);
+final ItemContext tc = sc.getCurrentContext(Item.TRANSFORMATION);
 
 final ModeInfo mode = ModeInfo.get(request.getParameter("mode"));
@@ -137 +179 @@
 final String title = mode.generateTitle("bioassay set", "bioassay sets");
 final DbControl dc = sc.newDbControl();
-Tree<BioAssaySet> bioAssaySets = null;
+Tree<BasicItem> analysisTree = null;
 try
 {
@@ -146 +188 @@
 
   final ItemQuery<BioAssaySet> query = Base.getConfiguredQuery(cc, true, experiment.getBioAssaySets());
+  final ItemQuery<Transformation> transformationQuery = experiment.getTransformations();
   Map<Plugin.MainType, Integer> pluginCount = PluginDefinition.countPlugins(dc, guiContext);
   try
   {
-    bioAssaySets = getBioAssaySetTree(dc, query);
+    analysisTree = getAnalysisTree(dc, query, transformationQuery);
   }
   catch (Throwable t)
@@ -156 +199 @@
   }
   // Contains the ID:s of the bioassaysets that are closed in the tree
-  Collection<Integer> closed = (Collection<Integer>)cc.getObject("closed");
+  Collection<String> closed = (Collection<String>)cc.getObject("closed");
   int numListed = 0;
   %>
@@ -168 +211 @@
       Main.openPopup('index.jsp?ID=<%=ID%>&cmd=NewItem&experiment_id=<%=experimentId%>', 'NewBioAssaySet', 740, 540);
     }
-    function editItem(itemId)
+    function editBioAssaySet(itemId)
     {
       Main.openPopup('index.jsp?ID=<%=ID%>&cmd=EditItem&experiment_id=<%=experimentId%>&item_id='+itemId, 'EditBioAssaySet', 500, 300);
     }
-    function viewItem(itemId)
+    function viewBioAssaySet(itemId)
     {
       location.href = 'index.jsp?ID=<%=ID%>&cmd=ViewItem&experiment_id=<%=experimentId%>&item_id='+itemId;
     }
-    function itemOnClick(evt, itemId)
-    {
-      Table.itemOnClick(formId, evt, itemId, '<%=mode.getName()%>', viewItem, editItem, returnSelected);
+    function bioAssaySetOnClick(evt, itemId)
+    {
+      Table.itemOnClick(formId, evt, itemId, '<%=mode.getName()%>', viewBioAssaySet, editBioAssaySet, returnSelected);
+    }
+    function viewTransformation(itemId)
+    {
+      location.href = '../transformations/index.jsp?ID=<%=ID%>&cmd=ViewItem&experiment_id=<%=experimentId%>&item_id='+itemId;
+    }
+    function transformationOnClick(evt, itemId)
+    {
+      viewTransformation(itemId);
     }
     function deleteItems()
@@ -258 +309 @@
           frm.closed.value += menuItem.externalId+',';
         }
-//        alert(document.forms[formId].closed.value);
+        // alert(document.forms[formId].closed.value);
         this.updateIconsAndText(menuItemIndex);
       }
@@ -324 +375 @@
       }
 
-      <%=generateTree(bioAssaySets, null, closed)%>
+      <%=analysisTree == null ? "" : generateTree(analysisTree, null, closed)%>
       JoustMenu.draw('joust');
       
@@ -404 +455 @@
         datatype="int"
         title="Reporters"
-        sortable="true" 
-        filterable="true"
-        exportable="true"
-      />
-      <tbl:columndef 
-        id="transformation"
-        property="transformation.name"
-        datatype="string"
-        title="Transformation"
         sortable="true" 
         filterable="true"
@@ -537 +579 @@
           int index = cc.getPage()*cc.getRowsPerPage();
           int selectedItemId = cc.getId();
-          if (bioAssaySets != null)
+          if (analysisTree != null)
           {
-            Iterator<Tree.Entry<BioAssaySet>> baas = bioAssaySets.entryIterator();
+            Iterator<Tree.Entry<BasicItem>> baas = analysisTree.entryIterator();
             while (baas.hasNext())
             {
-              Tree.Entry<BioAssaySet> entry = baas.next();
-              BioAssaySet item = entry.getNode();
+              Tree.Entry<BasicItem> entry = baas.next();
+              BasicItem item = entry.getNode();
               if (item != null)
               {
-              int level = entry.getDepth() - 1;
-              int itemId = item.getId();
-              String name = HTML.encodeTags(item.getName());
-              index++;
-              numListed++;
-              boolean hasChildren = entry.getNumChildren() > 0;
-              boolean isFirstChild = entry.getParent().isFirstChild(item);
-              boolean isLastChild = entry.getParent().isLastChild(item);
-              String outlineIcon = "";
-              String docIcon = "";
-              if (hasChildren)
-              {
-                docIcon = "folderopen.gif";
-                outlineIcon = "minus";
-                if (isFirstChild && isLastChild)
+                int level = entry.getDepth() - 1;
+                int itemId = item.getId();
+                String joustId = item.getType().name() + "_" + itemId;
+                String name = HTML.encodeTags(((Nameable)item).getName());
+                String description = HTML.encodeTags(((Nameable)item).getDescription());
+                boolean removed = false;
+                Transformation t = null;
+                BioAssaySet bas = null;
+                String prefix = "";
+                ItemContext ccc = null;
+                String view = "";
+                String onClick = "";
+                if (item.getType() == Item.TRANSFORMATION)
                 {
-                  outlineIcon += "only.gif";
-                }
-                else if (isFirstChild)
-                {
-                  outlineIcon += "top.gif";
-                }
-                else if (isLastChild)
-                {
-                  outlineIcon += "bottom.gif";
+                  t = (Transformation)item;
+                  removed = t.isRemoved();
+                  prefix = "T:";
+                  ccc = tc;
+                  view = "View this transformation (use CTRL, ALT or SHIFT to edit)";
+                  onClick = "transformationOnClick";
                 }
                 else
                 {
-                  outlineIcon += ".gif";
+                  bas = (BioAssaySet)item;
+                  removed = bas.isRemoved();
+                  ccc = cc;
+                  view = "View this bioassay set (use CTRL, ALT or SHIFT to edit)";
+                  onClick = "bioAssaySetOnClick";
                 }
-              }
-              else
-              {
-                docIcon = "folderclosed.gif";
-                outlineIcon = "join";
-                if (isLastChild)
-                {
-                  outlineIcon += "bottom.gif";
-                }
-                else if (isFirstChild)
-                {
-                  outlineIcon += "top.gif";
-                }
-                else
-                {
-                  outlineIcon += ".gif";
-                }
-              }
-              %>
-              <tbl:row
-                id="<%="row."+itemId%>"
-                >
-                <tbl:header 
-                  clazz="index"
-                  ><%=index%></tbl:header>
-                <tbl:header 
-                  clazz="check" 
-                  visible="<%=mode.hasCheck()%>"
-                  ><input 
-                      type="checkbox" 
-                      name="<%=itemId%>" 
-                      value="<%=itemId%>" 
-                      title="<%=name%>" 
-                      <%=cc.getSelected().contains(itemId) ? "checked" : ""%>
-                    ></tbl:header>
-                <tbl:header 
-                  clazz="check" 
-                  visible="<%=mode.hasRadio()%>"
-                  ><input 
-                      type="radio" 
-                      name="item_id" 
-                      value="<%=itemId%>" 
-                      title="<%=name%>" 
-                      <%=selectedItemId == itemId ? "checked" : ""%>
-                    ></tbl:header>
-                <tbl:header 
-                  clazz="icons" 
-                  visible="<%=mode.hasIcons()%>"
-                  ><base:icon 
-                    image="deleted.gif" 
-                    tooltip="This item has been scheduled for deletion" 
-                    visible="<%=item.isRemoved()%>"
-                  />&nbsp;</tbl:header>
                 
-                <tbl:cell clazz="joustcell" column="name">
-                  <div id="tree.<%=itemId%>" class="link" onclick="itemOnClick(event, <%=itemId%>)" title="View this bioassay set (use CTRL, ALT or SHIFT to edit)">
-                    <img src="../../../images/joust/blank.gif" width="<%=level*18%>" height="1">
-                    <img src="../../../images/joust/<%=outlineIcon%>">
-                    <img src="../../../images/joust/<%=docIcon%>">
-                    <%=name%>
-                  </div>
-                </tbl:cell>
-                <tbl:cell column="spots"><%=item.getNumSpots()%></tbl:cell>
-                <tbl:cell column="reporters"><%=item.getNumReporters()%></tbl:cell>
-                <tbl:cell column="transformation"><base:propertyvalue item="<%=item%>" property="transformation.name" /></tbl:cell>
-                <tbl:cell column="date"><base:propertyvalue item="<%=item%>" property="transformation.job.ended" /></tbl:cell>
-                <tbl:cell column="plugin"><base:propertyvalue item="<%=item%>" property="transformation.job.pluginDefinition.name" /></tbl:cell>
-                <tbl:cell column="description"><%=HTML.encodeTags(item.getDescription())%></tbl:cell>
-                <tbl:cell column="tools">TODO</tbl:cell>
-              </tbl:row>
-              <%
+                index++;
+                numListed++;
+
+                %>
+                <tbl:row
+                  id="<%="row."+joustId%>"
+                  >
+                  <tbl:header 
+                    clazz="index"
+                    ><%=index%></tbl:header>
+                  <tbl:header 
+                    clazz="check" 
+                    visible="<%=mode.hasCheck()%>"
+                    ><input 
+                        type="checkbox" 
+                        name="<%=prefix+itemId%>" 
+                        value="<%=itemId%>" 
+                        title="<%=name%>" 
+                        <%=ccc.getSelected().contains(itemId) ? "checked" : ""%>
+                      ></tbl:header>
+                  <tbl:header 
+                    clazz="check" 
+                    visible="<%=mode.hasRadio()%>"
+                    ><input 
+                        type="radio" 
+                        name="item_id" 
+                        value="<%=itemId%>" 
+                        title="<%=name%>" 
+                        <%=selectedItemId == itemId ? "checked" : ""%>
+                      ></tbl:header>
+                  <tbl:header 
+                    clazz="icons" 
+                    visible="<%=mode.hasIcons()%>"
+                    ><base:icon 
+                      image="deleted.gif" 
+                      tooltip="This item has been scheduled for deletion" 
+                      visible="<%=removed%>"
+                    />&nbsp;</tbl:header>
+                  
+                  <tbl:cell clazz="joustcell" column="name">
+                    <div id="tree.<%=joustId%>" class="link" onclick="<%=onClick%>(event, <%=itemId%>)" title="<%=view%>">
+                      <%=name%>
+                    </div>
+                  </tbl:cell>
+                  <tbl:cell column="spots"><%=bas == null ? "" : bas.getNumSpots()%></tbl:cell>
+                  <tbl:cell column="reporters"><%=bas == null ? "" : bas.getNumReporters()%></tbl:cell>
+                  <%
+                  if (t != null)
+                  {
+                    %>
+                    <tbl:cell column="date"><base:propertyvalue item="<%=t%>" property="job.ended" /></tbl:cell>
+                    <tbl:cell column="plugin"><base:propertyvalue item="<%=t%>" property="job.pluginDefinition.name" /></tbl:cell>
+                    <%
+                  }
+                  else
+                  {
+                    %>
+                    <tbl:cell column="date">&nbsp;</tbl:cell>
+                    <tbl:cell column="plugin">&nbsp;</tbl:cell>
+                    <%
+                  }
+                  %>
+                  <tbl:cell column="description"><%=description%></tbl:cell>
+                  <tbl:cell column="tools">TODO</tbl:cell>
+                </tbl:row>
+                <%
               }
             }