Changeset 4630

Timestamp:

Nov 7, 2008, 9:36:37 AM (15 years ago)

Author:

Nicklas Nordborg

Message:

Fixes #1133: Experimental factors - inherit annotations

Location:

trunk

Files:

• src/core/net/sf/basedb/core/AnnotationSet.java (modified) (6 diffs)
• src/core/net/sf/basedb/util/AnnotationUtil.java (added)
• www/views/experiments/index.jsp (modified) (1 diff)
• www/views/experiments/view_experiment.jsp (modified) (9 diffs)

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

@@ -23 +23 @@
 package net.sf.basedb.core;
 
+import java.util.Collections;
 import java.util.LinkedList;
 import java.util.List;
@@ -37 +38 @@
 import net.sf.basedb.core.data.AnnotationSetData;
 import net.sf.basedb.core.data.AnnotationTypeData;
+import net.sf.basedb.util.AnnotationUtil;
+import net.sf.basedb.util.filter.Filter;
 
 /**
@@ -220 +223 @@
     throws PermissionDeniedException, BaseException
   {
+    return getItem(null);
+  }
+  
+  /**
+    Get the item this annotation set belongs to using a specific 
+    DbControl for database access. If the item has already been loaded
+    it is re-loaded by the given DbControl.
+    
+    @param dc An open DbControl, or null to use the current DbControl associated
+      with this annotation set
+    @return The <code>Annotatable</code> item
+    @since 2.9
+  */
+  public Annotatable getItem(DbControl dc)
+    throws PermissionDeniedException, BaseException
+  {
     if (item == null)
     { 
+      if (dc == null) dc = getDbControl();
       Item type = getItemType();
-      DbControl dc = getDbControl();
       String hql = "SELECT item"+
         " FROM "+type.getDataClass().getName()+" item"+
@@ -230 +249 @@
       query.setEntity("annotationSet", this.getData());
       item = (Annotatable)dc.getItem(type.getItemClass(), HibernateUtil.loadData(type.getDataClass(), query));
+    }
+    else if (dc != null)
+    {
+      item = (Annotatable)getItemType().getById(dc, item.getId());
     }
     return item;
@@ -355 +378 @@
   {
     if (annotationType == null) throw new InvalidUseOfNullException("annotationType");
+    if (!isInDatabase()) return Collections.emptyList();
     // List for storing the result
     List<Annotation> annotations = new LinkedList<Annotation>();
@@ -612 +636 @@
   }
 
+  /**
+    Automatically inherit all annotations of the specified annotation
+    type from parent items unless this annotation set already contains
+    an annotation of the specified type.
+    <p>
+    This method will only consider parent items that the logged in user
+    has access to with USE permission.
+    <p>
+    This method may result in inheriting multiple annotations (from different
+    parent items) of the specified annotation type.
+    
+    @param dc The DbControl to use for database access
+    @param annotationType The annotation type to look for
+    @param preferAnnotationSet If TRUE, the entire annotation set containing the
+      found annotation is inherited, otherwise only the found annotation is inherited
+    @since 2.9
+  */
+  public int autoInherit(DbControl dc, final AnnotationType annotationType, boolean preferAnnotationSet)
+  {
+    if (findAnnotations(dc, annotationType, null).size() > 0) return 0;
+    int numInherited = 0;
+    Annotatable item = getItem(dc);
+    
+    // Filter that only returns items that are annotated with the specified
+    // annotation type and for which the logged in user has USE permission
+    Filter<Annotatable> filter = new Filter<Annotatable>()
+    {
+      @Override
+      public boolean evaluate(Annotatable a)
+      {
+        return a.isAnnotated() && 
+          a.hasPermission(Permission.USE) && 
+          a.getAnnotationSet().hasAnnotation(annotationType);
+      }
+    };
+    
+    // This will find all parent items that we should inherit from
+    Set<Annotatable> allParents = AnnotationUtil.getAllAnnotatableParentItems(dc, item, filter);
+    for (Annotatable parent : allParents)
+    {
+      AnnotationSet pas = parent.getAnnotationSet();
+      numInherited++;
+      if (preferAnnotationSet)
+      {
+        inheritAnnotationSet(pas);
+      }
+      else
+      {
+        inheritAnnotation(pas.getAnnotation(annotationType));
+      }
+    }
+    return numInherited;
+  }
+  
   /**
     Copy annotations from another annotatable item to this annotation set.

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 ("AutoInherit".equals(cmd))
+  {
+    // Display the edit page for a single item (should be opened in a popup)
+    dc = sc.newDbControl();
+    Experiment exp = Experiment.getById(dc, Values.getInt(itemId));
+    AnnotationType at = AnnotationType.getById(dc, Values.getInt(request.getParameter("annotationtype_id")));
+    ItemQuery<RawBioAssay> query = exp.getRawBioAssays();
+    query.include(Include.ALL);
+    query.setItemPermission(Permission.WRITE);
+    int numInherited = 0;
+    int numRawBioAssays = 0;
+    for (RawBioAssay rba : query.list(dc))
+    {
+      numRawBioAssays++;
+      numInherited += rba.getAnnotationSet().autoInherit(dc, at, false);
+    }
+    dc.commit();
+    message = numInherited + " annotation(s) inherited by " + numRawBioAssays + " raw bioassay(s)";
+  }
   else
   {

trunk/www/views/experiments/view_experiment.jsp

@@ -103 +103 @@
   Map<AnnotationType, Set<Object>> usedFactorValues = 
     new HashMap<AnnotationType, Set<Object>>();
+  Map<AnnotationType, Integer> factorValuesCount = new HashMap<AnnotationType, Integer>();
   %>
 
@@ -193 +194 @@
       var div = document.getElementById('usedvalues.'+annotationTypeId);
       div.innerHTML = values;
+    }
+    function showStatus(annotationTypeId, numTotal, numInherited)
+    {
+      var sss = document.getElementById('status.'+annotationTypeId);
+      var html;
+      if (numTotal == numInherited)
+      {
+        html = '<img src="../../images/ok.gif" title="All ' + numTotal + 
+          ' raw bioassays have a value for this experimental factor">';
+      }
+      else
+      {
+        var numMissing = numTotal - numInherited;
+        html = '<a href="javascript:autoInherit('+annotationTypeId+')"' + 
+          ' title="Click for automatic inheritation of annotations from parents"';
+        html += '<img src="../../images/warning.gif" border="0">&nbsp;' + numMissing + ' missing</a>';
+      }
+      sss.innerHTML = html;
+    }
+    function autoInherit(annotationTypeId)
+    {
+      var url = 'index.jsp?ID=<%=ID%>&cmd=AutoInherit&item_id=<%=itemId%>&annotationtype_id=' + annotationTypeId;
+      Main.openPopup(url, 'AutoInherit', 400, 200);
     }
     </script>
@@ -424 +448 @@
           title="Description"
         />
+        <tbl:columndef 
+          id="status"
+          title="Status"
+        />
         <tbl:data>
           <tbl:columns>
@@ -433 +461 @@
             Type valueType = item.getValueType();
             usedFactorValues.put(item, new HashSet<Object>());
+            factorValuesCount.put(item, 0);
             Formatter formatter = FormatterFactory.getTypeFormatter(sc, valueType);
             %>
@@ -462 +491 @@
                 %>
               </tbl:cell>
+              <tbl:cell column="status"><div id="status.<%=item.getId()%>"></div></tbl:cell>
             </tbl:row>
             <%
@@ -469 +499 @@
         </tbl:data>
         </tbl:table>
+        <base:icon image="warning.gif" /> = Some raw bioassays are missing this factor value;
+          click to automatically try to inherit annotations from parents<br>
+        <base:icon image="ok.gif" /> = All raw bioassays have a value for this factor
         </base:section>
         <%
@@ -552 +585 @@
                     List values = a.getValues();
                     usedFactorValues.get(at).addAll(values);
+                    factorValuesCount.put(at, factorValuesCount.get(at)+1);
                     Annotatable aItem = null;
                     try
@@ -715 +749 @@
     {
       <%
+      int numRawBioAssays = rawBioAssays.size();
       for (Map.Entry<AnnotationType, Set<Object>> entry : usedFactorValues.entrySet())
       {
         AnnotationType at = entry.getKey();
+        int numRawBioAssaysWithFactor = factorValuesCount.get(at);
         Type valueType = at.getValueType();
         if (at.isEnumeration() || (valueType != Type.TEXT && valueType != Type.STRING))
@@ -728 +764 @@
           %>
           setUsedFactorValue(<%=at.getId()%>, '<%=HTML.javaScriptEncode(formattedValues)%>');
+          showStatus(<%=at.getId()%>, <%=numRawBioAssays%>, <%=numRawBioAssaysWithFactor%>);
           <%
         }