Changeset 4613

Timestamp:

Oct 29, 2008, 9:23:56 AM (14 years ago)

Author:

Nicklas Nordborg

Message:

Fixes #1129: Filtering of child/parent items in table listing

Biomaterials and the rest of the View menu.

Location:

trunk

Files:

• src/core/net/sf/basedb/core/data/BioMaterialData.java (modified) (2 diffs)
• src/core/net/sf/basedb/core/data/BioMaterialEventData.java (modified) (2 diffs)
• www/biomaterials/biosources/list_biosources.jsp (modified) (1 diff)
• www/biomaterials/extracts/list_extracts.jsp (modified) (1 diff)
• www/biomaterials/labeledextracts/list_labeledextracts.jsp (modified) (1 diff)
• www/biomaterials/samples/list_samples.jsp (modified) (3 diffs)
• www/views/experiments/index.jsp (modified) (1 diff)
• www/views/experiments/view_experiment.jsp (modified) (2 diffs)
• www/views/hybridizations/list_hybridizations.jsp (modified) (2 diffs)
• www/views/scans/list_scans.jsp (modified) (1 diff)

trunk/src/core/net/sf/basedb/core/data/BioMaterialData.java

@@ -22 +22 @@
 */
 package net.sf.basedb.core.data;
+
+import java.util.Set;
 
 /**
@@ -60 +62 @@
   }
 
+  private Set<MeasuredBioMaterialData> children;
+  /**
+    This is the inverse end. NOTE! This collection will not 
+    contained pooled children or hybridizations.
+    @see MeasuredBioMaterialData#getParent()
+    @since 2.9
+    @hibernate.set inverse="true" lazy="true"
+    @hibernate.collection-key column="`parent_id`"
+    @hibernate.collection-one-to-many class="net.sf.basedb.core.data.MeasuredBioMaterialData"
+  */
+  Set<MeasuredBioMaterialData> getChildren()
+  {
+    return children;
+  }
+  void setChildren(Set<MeasuredBioMaterialData> children)
+  {
+    this.children = children;
+  }
 
 }

trunk/src/core/net/sf/basedb/core/data/BioMaterialEventData.java

@@ -26 +26 @@
 import java.util.Map;
 import java.util.HashMap;
+import java.util.Set;
 
 /**
@@ -210 +211 @@
   }
   
+  private Set<MeasuredBioMaterialData> sourceBioMaterials;
+  /**
+    This is the inverse end. The children is the non-pooled biomaterials
+    that has this item as a parent.
+    @see MeasuredBioMaterialData#getParent()
+    @since 2.9
+    @hibernate.set table="`BioMaterialEventSources`" inverse="true" lazy="true"
+    @hibernate.collection-key column="`event_id`"
+    @hibernate.collection-many-to-many column="`biomaterial_id`" class="net.sf.basedb.core.data.MeasuredBioMaterialData"
+  */
+  Set<MeasuredBioMaterialData> getSourceBioMaterials()
+  {
+    return sourceBioMaterials;
+  }
+  void setSourceBioMaterials(Set<MeasuredBioMaterialData> sourceBioMaterials)
+  {
+    this.sourceBioMaterials = sourceBioMaterials;
+  }
 
 }

trunk/www/biomaterials/biosources/list_biosources.jsp

@@ -251 +251 @@
         id="samples"
         title="Samples"
+        property="&children(name)"
+        datatype="string"
+        filterable="true"
       />
       <tbl:columndef 

trunk/www/biomaterials/extracts/list_extracts.jsp

@@ -322 +322 @@
         id="parents"
         title="Parents"
+        property="&creationEvent.sourceBioMaterials(name)"
+        datatype="string"
+        filterable="true"
       />
       <tbl:columndef
         id="labeledextracts"
         title="Labeled extracts"
+        property="&children(name)"
+        datatype="string"
+        filterable="true"
       />
       <tbl:columndef 

trunk/www/biomaterials/labeledextracts/list_labeledextracts.jsp

@@ -330 +330 @@
         id="parents"
         title="Parents"
+        property="&creationEvent.sourceBioMaterials(name)"
+        datatype="string"
+        filterable="true"
       />
       <tbl:columndef
         id="hybridizations"
         title="Hybridizations"
+        property="&sourceEvents(event.hybridization.name)"
+        datatype="string"
+        filterable="true"
       />
       <tbl:columndef 

trunk/www/biomaterials/samples/list_samples.jsp

@@ -321 +321 @@
       />
       <tbl:columndef
+        id="bioSource"
+        title="Biosource"
+        property="parent.name"
+        datatype="string"
+        sortable="true" 
+        filterable="true"
+        exportable="true"
+      />
+      <tbl:columndef
         id="parents"
         title="Parents"
+        property="&creationEvent.sourceBioMaterials(name)"
+        datatype="string"
+        filterable="true"
       />
       <tbl:columndef
         id="extracts"
         title="Extracts"
+        property="&children(name)"
+        datatype="string"
+        filterable="true"
       />      
       <tbl:columndef 
@@ -571 +586 @@
                 <tbl:cell column="eventDate" value="<%=creationEvent.getEventDate()%>" />
                 <tbl:cell column="entryDate" value="<%=creationEvent.getEntryDate()%>" />
+                <tbl:cell column="bioSource"><base:propertyvalue item="<%=item%>" property="parent"/></tbl:cell>
                 <tbl:cell column="parents">
                   <%
-                  if (!item.isPooled())
-                  {
-                  %>
-                    <base:propertyvalue item="<%=item%>" property="parent"/>
-                  <%
-                  }
-                  else
+                  if (item.isPooled())
                   {
                     String separator = "";
@@ -601 +611 @@
                   }
                   %>
-                  </tbl:cell>
+                </tbl:cell>
                 <tbl:cell column="extracts">
                   <%

trunk/www/views/experiments/index.jsp

@@ -341 +341 @@
     redirect = "../../common/plugin/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=ITEM&main_type=OTHER&title=Run+plugin";
   }
+  else if ("DeleteAllRawData".equals(cmd))
+  {
+    dc = sc.newDbControl();
+    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
+    Experiment exp = Experiment.getById(dc, cc.getId());
+    List<RawBioAssay> all = new ArrayList<RawBioAssay>(exp.getRawBioAssays().list(dc));
+    for (RawBioAssay rba : all)
+    {
+      exp.removeRawBioAssay(rba);
+    }
+    dc.commit();
+    
+    dc = sc.newDbControl();
+    for (RawBioAssay rba : all)
+    {
+      rba = RawBioAssay.getById(dc, rba.getId());
+      rba.deleteRawData();
+    }
+    dc.commit();
+    
+    dc = sc.newDbControl();
+    exp = Experiment.getById(dc, cc.getId());
+    for (RawBioAssay rba : all)
+    {
+      exp.addRawBioAssay(rba);
+    }
+    dc.commit();
+    redirect = viewPage;
+  }
   else
   {

trunk/www/views/experiments/view_experiment.jsp

@@ -148 +148 @@
       location.href = '<%=root%>/analyze/index.jsp?ID=<%=ID%>&experiment_id=<%=itemId%>';
     }
+    function deleteAllRaw()
+    {
+      location.href = 'index.jsp?ID=<%=ID%>&cmd=DeleteAllRawData&item_id=<%=itemId%>';
+    }
     function viewBioAssaySets()
     {
@@ -271 +275 @@
         title="Help&hellip;"
         tooltip="Get help about this page"
+      />
+      <tbl:button
+        onclick="deleteAllRaw()"
+        title="Delete all raw data"
       />
       </tbl:toolbar>

trunk/www/views/hybridizations/list_hybridizations.jsp

@@ -266 +266 @@
         id="labeledExtracts"
         title="Labeled extracts"
+        property="&creationEvent.sourceBioMaterials(name)"
+        datatype="string"
+        filterable="true"
       />
       <tbl:columndef 
@@ -279 +282 @@
         id="scans"
         title="Scans"
+        property="&scans(name)"
+        datatype="string"
+        filterable="true"
       />
       <tbl:columndef 

trunk/www/views/scans/list_scans.jsp

@@ -270 +270 @@
         id="rawBioAssays"
         title="Raw bioassays"
+        property="&rawBioAssays(name)"
+        datatype="string"
+        filterable="true"
       />
       <tbl:columndef