Changeset 6962

Timestamp:

Oct 1, 2015, 2:29:38 PM (6 years ago)

Author:

Nicklas Nordborg

Message:

References #1941: Store experimental factor values as part experiments

Using a different "Edit" icon for cloned annotations that are out-of-sync.

Location:

trunk

Files:

• src/core/net/sf/basedb/core/snapshot/AnnotationSnapshot.java (modified) (1 diff)
• www/common/annotations/list_annotations.jsp (modified) (3 diffs)
• www/common/overview/info.jsp (modified) (3 diffs)
• www/images/edit-outofsync.png (added)
• www/views/experiments/bioassays/view_bioassay.jsp (modified) (2 diffs)
• www/views/experiments/rootrawbioassays/view_bioassay.jsp (modified) (6 diffs)
• www/views/experiments/view_experiment.jsp (modified) (2 diffs)

trunk/src/core/net/sf/basedb/core/snapshot/AnnotationSnapshot.java

@@ -524 +524 @@
   
   /**
+    A primary or inherited annotation is always up-to-date. A cloned annotation
+    is up-to-date if the link to the source annotation exists and the source
+    annotation has a date equal to or before the cloned annotation.
+    @since 3.6
+  */
+  public boolean isUpToDate()
+  {
+    boolean upToDate = true;
+    if (source == Annotation.Source.CLONED)
+    {
+      AnnotationSnapshot inherited = getInheritedFrom();
+      Date cloned = getThisLastUpdate();
+      Date source = inherited != null ? inherited.getThisLastUpdate() : null;
+      upToDate = cloned != null && source != null && !source.after(cloned);
+    }
+    return upToDate;
+  }
+  
+  /**
     Get the id of the item this annotation belongs to. 
     @deprecated In 3.6, use {@link #getThisItemId()} or 

trunk/www/common/annotations/list_annotations.jsp

@@ -510 +510 @@
               String description = HTML.encodeTags(at.getDescription());
               Date lastModified = a.getThisLastUpdate();
-              boolean isUpToDate = true;
+              boolean isUpToDate = a.isUpToDate();
               
               // Which item are we inheriting from?
@@ -522 +522 @@
                 {
                   lastModified = from.getThisLastUpdate();
-                }
-                else
-                {
-                  isUpToDate = !lastModified.before(from.getThisLastUpdate());
                 }
                 try
@@ -557 +553 @@
                   <%=values == null || values.size() == 0 ? 
                     "<i>- no values -</i>" : Values.getString(values, ", ", true, formatter)%>
-                  <base:icon image="edit.png" subclass="edit-annotation auto-init link" 
+                  <base:icon image="<%=isUpToDate ? "edit.png" : "edit-outofsync.png"%>" 
+                    subclass="edit-annotation auto-init link" 
                     data-auto-init="edit-annotation" 
                     data-annotation="<%= a.getThisAnnotationId()%>"

trunk/www/common/overview/info.jsp

@@ -449 +449 @@
                 // Inheritance information
                 Date lastModified = snapshot.getThisLastUpdate();
-                boolean isUpToDate = true;
+                boolean isUpToDate = snapshot.isUpToDate();
                 AnnotationSnapshot inherited = snapshot.getInheritedFrom();
                 Annotatable inheritedFrom = null;
@@ -457 +457 @@
                   {
                     lastModified = inherited.getThisLastUpdate();
-                  }
-                  else
-                  {
-                    isUpToDate = !lastModified.before(inherited.getThisLastUpdate());
                   }
                   try
@@ -481 +477 @@
                     <%=Values.getString(values, ", ", true, formatter)%>
                     <base:icon id="<%=Integer.toString(snapshot.getThisAnnotationId())%>" 
-                      image="edit.png" subclass="edit-annotation auto-init" data-auto-init="edit-annotation"
+                      image="<%=isUpToDate ? "edit.png" : "edit-outofsync.png"%>" 
+                      subclass="edit-annotation auto-init" 
+                      data-auto-init="edit-annotation"
                       data-item-type="<%=annotatable.getType().name()%>" 
                       data-item-id="<%=annotatable.getId()%>" 

trunk/www/views/experiments/bioassays/view_bioassay.jsp

@@ -293 +293 @@
                         {
                           List values = a.getActualValues();
+                          boolean isUpToDate = a.isUpToDate();
                           %>
                           <tbl:cellvalue list="<%=values%>" suffix="<%=unitSymbol%>"/>
@@ -303 +304 @@
                             data-annotation="<%=a.getThisAnnotationId()%>"
                             visible="<%=writePermission%>"
-                            image="edit.png" 
+                            image="<%=isUpToDate ? "edit.png" : "edit-outofsync.png"%>" 
                             tooltip="Modify the values of this experimental factor"
                           />

trunk/www/views/experiments/rootrawbioassays/view_bioassay.jsp

@@ -105 +105 @@
     manager.getSnapshot(dc, bioAssay.getAnnotationSet().getId()) : null;
 
+  Formatter<Date> dateTimeFormatter = FormatterFactory.getDateTimeFormatter(sc);
   final boolean writePermission = bioAssay.hasPermission(Permission.WRITE);
   Map<Plugin.MainType, Integer> pluginCount = PluginDefinition.countPlugins(dc, guiContext);
@@ -244 +245 @@
               id="note"
               title="Note"
+            />
+            <tbl:columndef
+              id="lastModified"
+              title="Last modified"
+              formatter="<%=dateTimeFormatter %>"
             />
             <tbl:columndef 
@@ -283 +289 @@
 
                     Date lastModified = a.getThisLastUpdate();
-                    boolean isUpToDate = true;
+                    boolean isUpToDate = a.isUpToDate();
                     AnnotationSnapshot inherited = a.getInheritedFrom();
                     if (inherited != null)
@@ -291 +297 @@
                       {
                         lastModified = inherited.getThisLastUpdate();
-                      }
-                      else
-                      {
-                        isUpToDate = !lastModified.before(inherited.getThisLastUpdate());
                       }
                       try
@@ -323 +325 @@
                         <%=Values.getString(values, ", ", true, formatter)%>
                         <base:icon id="<%=Integer.toString(a.getThisAnnotationId())%>"
-                          image="edit.png" subclass="edit-experimental-factor auto-init" data-auto-init="edit-experimental-factor"
+                          image="<%=isUpToDate ? "edit.png" : "edit-outofsync.png"%>" 
+                          subclass="edit-experimental-factor auto-init" 
+                          data-auto-init="edit-experimental-factor"
                           data-item-type="ROOTRAWBIOASSAY" 
                           data-item-id="<%=itemId%>" 
@@ -348 +352 @@
                       </tbl:cell>
                       <tbl:cell column="note"><%=a.getSource() == Annotation.Source.CLONED ? "Cloned" + (isUpToDate ? "; up-to-date" : "; modified") : "" %></tbl:cell>
+                      <tbl:cell column="lastModified" value="<%=lastModified %>" />
                     </tbl:row>
                     <%

trunk/www/views/experiments/view_experiment.jsp

@@ -556 +556 @@
                         factorValuesCount.put(at, factorValuesCount.get(at)+1);
                         List values = a.getActualValues();
+                        boolean isUpToDate = a.isUpToDate();
                         usedFactorValues.get(at).addAll(values);
                         %>
@@ -567 +568 @@
                           data-annotation="<%=a.getThisAnnotationId()%>"
                           visible="<%=writePermission%>"
-                          image="edit.png" 
+                          image="<%=isUpToDate ? "edit.png" : "edit-outofsync.png"%>" 
                           tooltip="Modify the values of this experimental factor"
                         />