Changeset 6694

Timestamp:

Jan 26, 2015, 3:41:25 PM (8 years ago)

Author:

Nicklas Nordborg

Message:

References #1908: Batch inheriting multiple annotations

Added InheritAnnotationsManager, InheritSpecification and a few other changes.

A test case has been implemented from the raw bioassays lists page which allows the user to select one or more annotation types to inherit to the selected raw bioassays. It is possible to select if existing inherited annotations should be removed or if new annotations should be inherited. For each annotation type is possible to select the parent type to inherit from (to avoid duplicate inheritance).

Location:

trunk

Files:

• src/core/net/sf/basedb/core/SimpleProgressReporter.java (modified) (2 diffs)
• src/core/net/sf/basedb/util/annotations (added)
• src/core/net/sf/basedb/util/annotations/InheritAnnotationsManager.java (added)
• src/core/net/sf/basedb/util/annotations/InheritSpecification.java (added)
• src/core/net/sf/basedb/util/annotations/RunnableInheritAnnotationsManager.java (added)
• www/common/annotations/ajax.jsp (added)
• www/common/annotations/batch_inherit.js (added)
• www/common/annotations/batch_inherit.jsp (added)
• www/common/annotations/index.jsp (modified) (2 diffs)
• www/common/progress_reporter.js (modified) (1 diff)
• www/common/progress_reporter.jsp (modified) (3 diffs)
• www/images/inherit.png (added)
• www/include/scripts/main-2.js (modified) (3 diffs)
• www/include/scripts/table.js (modified) (1 diff)
• www/views/rawbioassays/bioassays.js (modified) (1 diff)
• www/views/rawbioassays/index.jsp (modified) (2 diffs)
• www/views/rawbioassays/list_rawbioassays.jsp (modified) (3 diffs)

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

@@ -40 +40 @@
   private String message;
   private int percent;
+  private Throwable error;
   
   
@@ -85 +86 @@
     return percent;
   }
+  
+  /**
+    Set an error that happened while processing some action that
+    was reported via this progress reporter.
+    @since 3.5
+  */
+  public void setError(Throwable error)
+  {
+    this.error = error;
+  }
+  
+  /**
+    Get error that happened while processing some action that
+    was reported via this progress reporter.
+    @since 3.5
+  */
+  public Throwable getError()
+  {
+    return error;
+  }
 }

trunk/www/common/annotations/index.jsp

@@ -29 +29 @@
   import="net.sf.basedb.core.ItemContext"
   import="net.sf.basedb.core.BasicItem"
+  import="net.sf.basedb.core.AnnotatedItem"
   import="net.sf.basedb.core.Annotation"
   import="net.sf.basedb.core.AnnotationType"
   import="net.sf.basedb.core.Annotatable"
+  import="net.sf.basedb.core.ItemSubtype"
   import="net.sf.basedb.core.BaseException"
+  import="net.sf.basedb.core.SimpleProgressReporter"
+  import="net.sf.basedb.core.snapshot.SnapshotManager"
+  import="net.sf.basedb.util.annotations.RunnableInheritAnnotationsManager"
+  import="net.sf.basedb.util.annotations.InheritAnnotationsManager"
+  import="net.sf.basedb.util.annotations.InheritSpecification"
   import="net.sf.basedb.clients.web.Base"
   import="net.sf.basedb.clients.web.WebException"
   import="net.sf.basedb.util.Values"
   import="net.sf.basedb.clients.web.util.HTML"
+  import="java.util.Set"
+  import="java.util.List"
+  import="java.util.ArrayList"
+  
+  
 %>
 <%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
@@ -82 +94 @@
     message = "Annotations saved";
   }
+  else if ("BatchInherit".equals(cmd))
+  {
+    final Item itemType = Item.valueOf(request.getParameter("item_type"));
+    final String subContext = Values.getString(request.getParameter("subcontext"), "");
+    final ItemContext cc = sc.getCurrentContext(itemType, subContext);
+    
+    newDc = sc.newDbControl();
+
+    Set<AnnotatedItem> items = (Set<AnnotatedItem>)cc.getObject("AnnotatedItems");
+    cc.removeObject("AnnotatedItems");
+    
+    RunnableInheritAnnotationsManager manager = new RunnableInheritAnnotationsManager(sc);
+    manager.addAllItems(items);
+    
+    for (Integer atId : Values.getInt(request.getParameter("annotationTypes").split(",")))
+    {
+      AnnotationType at = AnnotationType.getById(newDc, atId);
+      InheritSpecification spec = new InheritSpecification(at);
+      String action = request.getParameter("action_"+atId);
+      
+      if ("remove".equals(action))
+      {
+        spec.setRemove(true);
+      }
+      else
+      {
+        int subtypeId = Values.getInt(request.getParameter("from_"+atId));
+        boolean noDup = Values.getBoolean(request.getParameter("nodup_"+atId));
+        boolean replaceExisting = Values.getBoolean(request.getParameter("replace_"+atId));
+        if (subtypeId != 0)
+        {
+          spec.setItemSubtype(ItemSubtype.getById(newDc, subtypeId));
+        }
+        spec.setNoDuplicates(noDup);
+        spec.setReplaceExisting(replaceExisting);
+      }
+      manager.addSpecification(spec);
+      
+      //System.out.println("at:" + atId + "; " + action + "; from=" + from + "; noDup="+noDup + "; replace="+replaceExisting);
+    }
+    newDc.commit();
+    
+    SimpleProgressReporter progress = new SimpleProgressReporter(null);
+    sc.setSessionSetting("progress.inherit-annotations", progress);
+    manager.setProgressReporter(progress);
+    new Thread(manager).start();
+    
+    redirect = "../../common/progress_reporter.jsp?ID="+ID+
+      "&progress=inherit-annotations&title=Inheriting annotations to " + items.size() + " items";
+
+  }
   else
   {

trunk/www/common/progress_reporter.js

@@ -34 +34 @@
     
     var percentDone = Data.int(document.body, 'percent-done');
-    setTimeout(percentDone < 100 ? progress.reload : App.closeWindow, 1500);
+    var isError = Data.int(document.body, 'is-error');
+    if (!isError)
+    {
+      setTimeout(percentDone < 100 ? progress.reload : App.closeWindow, 1500);
+    }
+    else
+    {
+      Doc.addClass('progress-bar', 'failed');
+      Doc.hide('info');
+    }
   }
   

trunk/www/common/progress_reporter.jsp

@@ -41 +41 @@
   String message = null;
   int percentDone = 0;
+  boolean isError = false;
   if (progress != null)
   {
@@ -53 +54 @@
   {
     sc.setSessionSetting("progress." + progressName, null);
+    isError = progress.getError() != null;
   }
 %>
 <base:page type="popup" title="<%=title%>">
 <base:head styles="progressbar.css" scripts="~progress_reporter.js" />
-<base:body data-percent-done="<%=percentDone %>">
+<base:body data-percent-done="<%=percentDone %>" data-is-error="<%=isError ? 1 : 0 %>">
   <h1><%=title%></h1>
   <div class="content">
   
     <table class="fullcc bg-filled-50 bottomborder"><tr><td>
-      <table class="progressbar" style="margin: auto;">
+      <table class="progressbar" style="margin: auto;" id="progress-bar">
       <tr>
       <td>
@@ -78 +80 @@
       <br><br>
       
-      <div align="center">
+      <div align="center" id="info">
       <i>Closing this window will NOT abort the process</i>
       </div>

trunk/www/include/scripts/main-2.js

@@ -1154 +1154 @@
     var regexp = Data.get(target, 'regexp');
     Table.setOwnerOfItems(tableId, regexp);
+  }
+
+  /**
+    Event handler that opens the 'Batch inherit anntations' dialog
+    for all selected items in a table. Usually attached to 
+    an 'Inherit annotations' button on a list page. The table id must be specifed
+    in the 'data-table-id' attribute.
+  */
+  buttons.inheritAnnotations = function(event)
+  {
+    var target = event.currentTarget;
+    var tableId = Data.get(target, 'table-id');
+    var regexp = Data.get(target, 'regexp');
+    Table.inheritAnnotations(tableId, regexp);
   }
 
@@ -2739 +2753 @@
     label when the checkbox/radiobutton is disabled
   */
-  internal.linkCheckboxesWithLabels = function()
-  {
-    var labels = document.getElementsByTagName('label');
+  forms.linkCheckboxesWithLabels = function(element)
+  {
+    if (!element) element = document;
+    var labels = element.getElementsByTagName('label');
     if (labels.length > 0)
     {
@@ -2792 +2807 @@
   }
   
-  Doc.addFinalizer(internal.linkCheckboxesWithLabels);
+  Doc.addFinalizer(forms.linkCheckboxesWithLabels);
     
   return forms;

trunk/www/include/scripts/table.js

@@ -616 +616 @@
 
   /**
+    Open a popup dialog that allows a user to bathc inherit annotations
+    to all items that are selected in the given table. 
+    @param tableDiv The ID or main table element
+    @param regexp An optional regular expression matching the names
+      of checkboxes that can be selected, if not specified it matches
+      checkboxes with numeric names (eg. the name is the id of the item
+      in the table)
+   */
+  table.inheritAnnotations = function(tableDiv, regexp)
+  {
+    tableDiv = Doc.element(tableDiv);
+    if (!table.checkIfSelected(tableDiv, regexp))
+    {
+      return;
+    }
+    table.submitToPopup(tableDiv, 'InheritAnnotations', 750, 500);
+  }
+
+  
+  /**
     Open a popup window for selecting a plug-in that can run in the 
     current list context

trunk/www/views/rawbioassays/bioassays.js

@@ -102 +102 @@
       Buttons.addClickHandler('btnShareItems', Buttons.shareItems, tableAttributes);
       Buttons.addClickHandler('btnSetOwner', Buttons.setOwnerOfItems, tableAttributes);
+      Buttons.addClickHandler('btnInheritAnnotations', Buttons.inheritAnnotations, tableAttributes);
       Buttons.addClickHandler('btnColumns', Buttons.configureColumns, tableAttributes);
       Buttons.addClickHandler('btnExport', Buttons.runListPlugin, tableAttributes);

trunk/www/views/rawbioassays/index.jsp

@@ -49 +49 @@
   import="net.sf.basedb.core.ItemResultIterator"
   import="net.sf.basedb.core.OwnedItem"
+  import="net.sf.basedb.core.AnnotatedItem"
   import="net.sf.basedb.core.Permission"
   import="net.sf.basedb.core.ItemContext"
@@ -497 +498 @@
     redirect = "../../common/ownership/ownership.jsp?ID="+ID+"&item_type="+itemType.name();
   }
+  else if ("InheritAnnotations".equals(cmd))
+  {
+    // Change owner of items selected on a list page
+    dc = sc.newDbControl();
+    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
+    Set<AnnotatedItem> items = new HashSet<AnnotatedItem>();
+    for (Integer id : cc.getSelected())
+    {
+      if (id != null) items.add((AnnotatedItem)itemType.getById(dc, id));
+    }
+    dc.close();
+    cc.setObject("AnnotatedItems", items);
+    redirect = "../../common/annotations/batch_inherit.jsp?ID="+ID+"&item_type="+itemType.name();
+  }
   else if ("ExportItems".equals(cmd))
   {

trunk/www/views/rawbioassays/list_rawbioassays.jsp

@@ -407 +407 @@
       {
         AnnotationType at = loader.getAnnotationType();
+        Formatter formatter = FormatterFactory.getTypeFormatter(sc, at.getValueType());
         Enumeration<String, String> annotationEnum = null;
         if (at.isEnumeration())
@@ -430 +431 @@
           filterable="true" 
           exportable="true"
+          formatter="<%=formatter%>"
           unit="<%=at.getDefaultUnit()%>"
         />
@@ -499 +501 @@
             tooltip="Create a new experiment from the selected raw bioassays"
             visible="<%=sc.hasPermission(Permission.CREATE, Item.EXPERIMENT)%>"
+          />
+          <tbl:button
+            id="btnInheritAnnotations"
+            image="inherit.png"
+            title="Inherit annotations&hellip;"
+            tooltip="Batch inherit annotations from parent items"
           />
           <tbl:button