Changeset 6689

Timestamp:

Jan 21, 2015, 11:35:06 AM (8 years ago)

Author:

Nicklas Nordborg

Message:

References #1906: Display inherited annotations in list views

The "Configure columns" dialog can now be used to add inherited annotation columns. This must be enabled from the list page by setting <tbl:table ... data-inherited-annotations="true"> in the table definition.

First implementation is made in the list raw bioassays table.

Location:

trunk

Files:

• src/clients/web/net/sf/basedb/clients/web/Base.java (modified) (1 diff)
• www/common/columns/configure.js (modified) (3 diffs)
• www/common/columns/configure.jsp (modified) (5 diffs)
• www/include/scripts/table.js (modified) (1 diff)
• www/views/rawbioassays/list_rawbioassays.jsp (modified) (4 diffs)

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

@@ -1014 +1014 @@
 
   /**
+    Get a query returning all annotation types that are needed to display
+    inherited annotations for the given columns. The columns is a string with
+    comma-separated values that define the visible columns in a table.
+    Columns for inherited annotations are defined by 'ia'+<id>.
+    @since 3.5
+  */
+  public static ItemQuery<AnnotationType> getInheritedAnnotationColumns(String columns)
+  {
+    ItemQuery<AnnotationType> q = AnnotationType.getQuery(null);
+    q.order(Orders.asc(Hql.property("name")));
+    q.include(Include.ALL);
+    q.restrict(Restrictions.in(Hql.property("id"), Expressions.parameter("ids")));
+    List<Integer> ids = new ArrayList<Integer>();
+    ids.add(0);
+    if (columns != null)
+    {
+      for (String c : columns.split(","))
+      {
+        if (c.startsWith("ia")) ids.add(Integer.parseInt(c.substring(2)));
+      }
+    }
+    q.setParameter("ids", ids, Type.INT);
+    q.setCacheResult(true);
+    return q;
+  }
+  
+  /**
     Get a query that returns all subtypes for the given main item type.
     @param itemType The main item type

trunk/www/common/columns/configure.js

@@ -49 +49 @@
     Buttons.addClickHandler('btnSavePreset', configure.savePresetAs);
     Events.addEventHandler('presets', 'change', configure.presetOnChange);
+    if (Doc.element('selectAnnotationTypes'))
+    {
+      Buttons.addClickHandler('selectAnnotationTypes', configure.selectAnnotationTypes);
+      Events.addEventHandler('selectAnnotationTypes', 'base-selected', configure.annotationTypeSelected);
+    }
     
     Buttons.addClickHandler('moveUp', configure.moveVisibleUpOrDown);
@@ -146 +151 @@
     {
       var temp = [];
-      for (var i = 0; i < columnDefs.length; i++) // >
+      for (var i = 0; i < columnDefs.length; i++)
       {
         var col = columnDefs[i];
@@ -171 +176 @@
   }
 
+  
+  configure.selectAnnotationTypes = function(event)
+  {
+    var frm = document.forms['columns'];
+    var exclude = [];
+    for (var i = 0; i < frm.visible.length; i++)
+    {
+      if (frm.visible[i].value.indexOf('ia')==0)
+      {
+        exclude[exclude.length] = frm.visible[i].value.substring(2);
+      }
+    }
+    var url = '&exclude='+exclude.join(',');
+    Dialogs.selectItem('ANNOTATIONTYPE', event.currentTarget.id, 1, url);
+  }
+  
+  configure.annotationTypeSelected = function(event)
+  {
+    var frm = document.forms['columns'];
+    var item = event.detail;
+    var colId = 'ia'+item.id;
+    // Do not add duplicates
+    for (var i = 0; i < frm.visible.length; i++)
+    {
+      if (frm.visible[i].value == colId) return;
+    }
+    // Remove from 'hidden' list
+    for (var i = frm.hidden.length-1; i >= 0; i--)
+    {
+      if (frm.hidden[i].value == colId) frm.hidden[i] = null;
+    }
+    frm.visible[frm.visible.length] = new Option(item.name + ' [I]', colId);
+  }
+  
   /**
     Save the current selection and close the dialog.

trunk/www/common/columns/configure.jsp

@@ -46 +46 @@
 <%@ taglib prefix="base" uri="/WEB-INF/base.tld" %>
 <%@ taglib prefix="t" uri="/WEB-INF/tab.tld" %>
-
+<%@ taglib prefix="tbl" uri="/WEB-INF/table.tld" %>
 <%
 final SessionControl sc = Base.getExistingSessionControl(pageContext, true);
@@ -53 +53 @@
 final String subContext = Values.getString(request.getParameter("subcontext"), "");
 final String tableId = request.getParameter("table_id");
+final boolean enableInheritedAnnotations = Values.getBoolean(request.getParameter("enableInheritedAnnotations"));
 final ItemContext cc = sc.getCurrentContext(itemType, subContext);
 
@@ -59 +60 @@
 %>
   <base:page type="popup" title="Set column order and visibility">
-  <base:head scripts="~configure.js" />
+  <base:head scripts="~configure.js" styles="toolbar.css" />
   <base:body>
     <h1>Set column order and visiblity <base:help helpid="columns.configure" /></h1>
@@ -74 +75 @@
     <div class="content bg-filled-50 bottomborder">
     <table style="width: 100%; height: 100%;">
+    <%
+    if (enableInheritedAnnotations)
+    {
+      %>
+      <tr>
+        <td colspan="4" style="vertical-align: top;">
+        <tbl:toolbar subclass="bottomborder">
+          <tbl:button 
+            id="selectAnnotationTypes" 
+            image="add.png"
+            title="Add inherited annotations&hellip;" 
+            tooltip="Add columns for inherited annotations" 
+           />
+        </tbl:toolbar>
+        </td>
+      </tr>
+      <%
+    }
+    %>
     <tr>
       <td style="padding: 5px;">
@@ -121 +141 @@
         </select>
       </td>
-    </tr>   
+    </tr>
     <tr>
       <td colspan="4" >

trunk/www/include/scripts/table.js

@@ -418 +418 @@
     var itemType = Data.get(tableDiv, 'item-type');
     var subContext = Data.get(tableDiv, 'subcontext', '');
+    var enableInheritedAnnotations = Data.get(tableDiv, 'inherited-annotations');
     
     var url = App.getRoot()+'common/columns/configure.jsp?ID='+App.getSessionId();
     url += '&table_id='+tableDiv.id+'&item_type='+itemType+'&subcontext='+subContext;
+    if (enableInheritedAnnotations)
+    {
+      url += '&enableInheritedAnnotations='+encodeURIComponent(enableInheritedAnnotations);
+    }
     if (settingName) url += '&settingName='+settingName;
     Dialogs.openPopup(url, 'ConfigureColumns', 750, 450);

trunk/www/views/rawbioassays/list_rawbioassays.jsp

@@ -109 +109 @@
 try
 {
-  final ItemQuery<AnnotationType> annotationTypeQuery = Base.getAnnotationTypesQuery(itemType);
+  ItemQuery<AnnotationType> annotationTypeQuery = Base.getAnnotationTypesQuery(itemType);
   SnapshotManager manager = new SnapshotManager();
   for (AnnotationType at : annotationTypeQuery.list(dc))
   {
     annotationLoaders.add(new AnnotationLoaderUtil(dc, manager, at));
+  }
+  annotationTypeQuery = Base.getInheritedAnnotationColumns(cc.getSetting("columns"));
+  for (AnnotationType at : annotationTypeQuery.list(dc))
+  {
+    annotationLoaders.add(new AnnotationLoaderUtil(dc, manager, at, false, true));
   }
 
@@ -171 +176 @@
       item="<%=itemType%>"
       subclass="fulltable"
+      data-inherited-annotations="true"
       >
       <tbl:hidden 
@@ -414 +420 @@
         %>
         <tbl:columndef 
-          id="<%="at"+at.getId()%>"
-          title="<%=HTML.encodeTags(at.getName())+" [A]"%>" 
-          property="<%="#"+at.getId()%>"
+          id="<%=(loader.isSearchingInheritedAnnotations() ? "ia" : "at")+at.getId()%>"
+          title="<%=HTML.encodeTags(at.getName())+(loader.isSearchingInheritedAnnotations() ? " [I]" : " [A]")%>" 
+          property="<%=(loader.isSearchingInheritedAnnotations() ? "##" : "#")+at.getId()%>"
           annotation="true"
           datatype="<%=at.getValueType().getStringValue()%>"
           enumeration="<%=annotationEnum%>"
           smartenum="<%=at.getDisplayAsList() %>"
-          sortable="<%=at.getMultiplicity() == 1%>" 
+          sortable="<%=at.getMultiplicity() == 1 && !loader.isSearchingInheritedAnnotations()%>" 
           filterable="true" 
           exportable="true"
@@ -790 +796 @@
                       %>
                       <tbl:cell 
-                        column="<%="at"+loader.getId()%>"
+                        column="<%=(loader.isSearchingInheritedAnnotations() ? "ia" : "at")+loader.getId()%>"
                         ><tbl:cellvalue 
                           list="<%=loader.getValues()%>"