Changeset 3583

Timestamp:

Jul 20, 2007, 11:44:17 AM (16 years ago)

Author:

Martin Svensson

Message:

References #686 Jep Formula Filter and JepExtraValueCalculator? can now work on subset of bioassays

Location:

trunk

Files:

• src/core/net/sf/basedb/core/plugin/AbstractAnalysisPlugin.java (modified) (1 diff)
• src/plugins/core/net/sf/basedb/plugins/FormulaFilter.java (modified) (5 diffs)
• src/plugins/core/net/sf/basedb/plugins/JepExtraValueCalculator.java (modified) (6 diffs)
• www/plugins/net/sf/basedb/plugins/jep_extra_value_calculator.jsp (modified) (8 diffs)

trunk/src/core/net/sf/basedb/core/plugin/AbstractAnalysisPlugin.java

@@ -211 +211 @@
   }
   
-  protected static final String SOURCE_BIOASSAYS = "source_subset";
+  protected static final String SOURCE_BIOASSAYS = "bioAssays";
   
   /**

trunk/src/plugins/core/net/sf/basedb/plugins/FormulaFilter.java

@@ -33 +33 @@
 import net.sf.basedb.core.IntegerParameterType;
 import net.sf.basedb.core.Item;
-import net.sf.basedb.core.ItemParameterType;
 import net.sf.basedb.core.Job;
 import net.sf.basedb.core.Permission;
@@ -142 +141 @@
       // Get all parameters
       BioAssaySet source = getSourceBioAssaySet(dc);
-      List<BioAssay> bioAssays = (List<BioAssay>)job.getValues("bioAssays");
+      List<BioAssay> bioAssays = getSourceBioAssays(dc);
       String expression = (String)job.getValue("expression");
       Integer includeLimit = (Integer)job.getValue("includeLimit");
@@ -149 +148 @@
       String childDescription = (String)job.getValue("childDescription");
       
-      // Reattach bioassays
-      if (bioAssays != null)
-      {
-        for (BioAssay ba : bioAssays)
-        {
-          dc.reattachItem(ba);
-        }
-      }
-      
-      // and, the current job
+      // get the current job
       Job currentJob = getCurrentJob(dc);
       
@@ -244 +234 @@
         // Source bioassay set and bioassays
         storeValue(job, request, ri.getParameter(SOURCE_BIOASSAYSET));
-        storeValues(job, request, ri.getParameter("bioAssays"));
+        storeValues(job, request, ri.getParameter(SOURCE_BIOASSAYS));
         
         // Filter expression and options
@@ -283 +273 @@
         // Source bioassay set and bioassay parameters
         parameters.add(getSourceBioAssaySetParameter(null, null));
-        PluginParameter<BioAssay> bioAssaysParameter = new PluginParameter<BioAssay>(
-          "bioAssays", "Source bioassays", "Select the bioassays that should be filtered. " + 
-          "If no bioassay is selected all will be filtered.",
-          new ItemParameterType<BioAssay>(BioAssay.class, null, false, 0, 
-              bas.getBioAssays().list(dc)
-        ));
-        parameters.add(bioAssaysParameter);
+        parameters.add(getSourceBioAssaysParameter(null, null));
         
         // Filter expression and options

trunk/src/plugins/core/net/sf/basedb/plugins/JepExtraValueCalculator.java

@@ -33 +33 @@
 
 import net.sf.basedb.core.BaseException;
+import net.sf.basedb.core.BioAssay;
 import net.sf.basedb.core.BioAssaySet;
 import net.sf.basedb.core.DbControl;
@@ -58 +59 @@
 import net.sf.basedb.core.query.Dynamic;
 import net.sf.basedb.core.query.Expression;
+import net.sf.basedb.core.query.Expressions;
 import net.sf.basedb.core.query.Hql;
 import net.sf.basedb.core.query.Orders;
+import net.sf.basedb.core.query.Restrictions;
 import net.sf.basedb.core.query.Selects;
 import net.sf.basedb.util.BioAssaySetUtil;
@@ -145 +148 @@
       // Get all parameters
       BioAssaySet source = getSourceBioAssaySet(dc);
+      List<BioAssay> bioAssays = getSourceBioAssays(dc);
       ExtraValueType extraValueType = (ExtraValueType)job.getValue("extraValueType");
       String expression = (String)job.getValue("expression");
@@ -162 +166 @@
       Expression extraExpression = BioAssaySetUtil.createJepExpression(dc, source, expression, false);
       query.select(Selects.expression(extraExpression, "xtra"));
+      // If one or more bioassays are selected-restrict to them.
+      if (bioAssays != null && !bioAssays.isEmpty())
+      {
+        Expression[] selectedColumns = new Expression[bioAssays.size()];
+        for (int i=0; i<selectedColumns.length; i++)
+        {
+          BioAssay ba = bioAssays.get(i);
+          selectedColumns[i] = Expressions.integer(ba.getDataCubeColumnNo());
+        }       
+        query.restrict(Restrictions.in(
+            Dynamic.column(VirtualColumn.COLUMN), 
+            selectedColumns));
+      }
 
       if (progress != null) progress.display(10, "Calculating extra value ("+source.getNumSpots()+" total)...");
@@ -217 +234 @@
         storeValue(job, request, getSourceBioAssaySetParameter(null, null));
         
+        // Subset of bioassays
+        storeValue(job, request, this.getSourceBioAssaysParameter(null, null));
+        
         // ExtraValueType
         storeValue(job, request, extraValueTypeParameter);
@@ -247 +267 @@
         // Source bioassay set
         parameters.add(getSourceBioAssaySetParameter(null, null));
+        
+        // Sub set of bioassays
+        parameters.add(getSourceBioAssaysParameter(null, null));
         
         // Extra value types

trunk/www/plugins/net/sf/basedb/plugins/jep_extra_value_calculator.jsp

@@ -28 +28 @@
   import="net.sf.basedb.core.SessionControl"
   import="net.sf.basedb.core.DbControl"
+  import="net.sf.basedb.core.BioAssay"
   import="net.sf.basedb.core.Item"
   import="net.sf.basedb.core.ItemContext"
@@ -38 +39 @@
   import="net.sf.basedb.core.ItemResultList"
   import="net.sf.basedb.core.Include"
+  import="net.sf.basedb.core.Type"
   import="net.sf.basedb.core.query.Orders"
+  import="net.sf.basedb.core.query.Restrictions"
+  import="net.sf.basedb.core.query.Expressions" 
   import="net.sf.basedb.core.query.Hql"
   import="net.sf.basedb.clients.web.Base"
@@ -81 +85 @@
   RawDataType rdt = source.getRawDataType();
   
+  //Find selected bioassays
+  List<BioAssay> bioAssays = null;
+  if (job != null) bioAssays = (List<BioAssay>)job.getParameterValues("bioAssays");
+  if (bioAssays == null)
+  {
+    ItemContext bioAssayContext = sc.getCurrentContext(Item.BIOASSAY);
+    ItemQuery<BioAssay> bioAssayQuery = null;
+    if (bioAssayContext.getSelected().size() > 0)
+    {
+      bioAssayQuery = source.getBioAssays();
+      bioAssayQuery.restrict(
+        Restrictions.in(Hql.property("id"), Expressions.parameter("selected"))
+      );
+      bioAssayQuery.setParameter("selected", bioAssayContext.getSelected(), Type.INT);
+      bioAssays = bioAssayQuery.list(dc);
+    }
+  }
+  
   // Current parameter values
   ExtraValueType currentExtraValueType = (ExtraValueType)job.getParameterValue("extraValueType");
@@ -105 +127 @@
   %>
   <base:page type="popup" title="Calculate extra value">
-  <base:head styles="parameters.css">
+  <base:head scripts="linkitems.js" styles="parameters.css">
     <script language="JavaScript">
     function hideErrorList()
@@ -154 +176 @@
     {
       var frm = document.forms['extraValue'];
-      if (frm['parameter:extraValueType'].selectedIndex < 0)
+      if (!frm.allBioAssays.checked && frm.bioAssays.length == 0)
+      {
+        alert('You have not selected any bioassays');
+        return false;
+      }
+      else if (frm['parameter:extraValueType'].selectedIndex < 0)
       {
         alert('You must select a type');
@@ -185 +212 @@
       {
         var frm = document.forms['extraValue'];
+        if (!frm.allBioAssays.checked)
+        {
+          var ids = Link.getListIds(frm.bioAssays, 'R');
+          for (var i = 0; i < ids.length; i++)
+          {
+            Forms.createHidden(frm, 'parameter:bioAssays', ids[i]);
+          }
+        }
         frm.submit();
       }
@@ -192 +227 @@
       location = 'index.jsp?ID=<%=ID%>&cmd=CancelWizard';
     }
+    function allBioAssaysOnClick()
+    {
+      var frm = document.forms['extraValue'];
+      frm.bioAssays.disabled = frm.allBioAssays.checked;
+    }
+    function addBioAssaysOnClick()
+    {
+      var frm = document.forms['extraValue'];
+      if (frm.allBioAssays.checked)
+      {
+        return;
+      }
+      var ids = Link.getListIds(frm.bioAssays, 'R');
+      var excludes = ids.join(',');
+      var url = '../../views/experiments/bioassays/index.jsp?ID=<%=ID%>&cmd=UpdateContext&mode=selectmultiple&callback=addBioAssayCallback&bioassayset_id=<%=source.getId()%>';
+      url += "&exclude="+excludes;
+      Main.openPopup(url, 'AddBioAssays', 1000, 700);
+    }
+    function addBioAssayCallback(bioAssayId, name)
+    {
+      var item = Link.getItem('R', bioAssayId);
+      if (!item) item = new Item('R', bioAssayId, name);
+      Link.addItem(document.forms['extraValue'].bioAssays, item);
+    }
+    function removeBioAssaysOnClick()
+    {
+      var frm = document.forms['extraValue'];
+      if (frm.allBioAssays.checked)
+      {
+        return;
+      }
+      Link.removeSelected(frm.bioAssays);
+    }
+    function init()
+    {
+      initBioAssays();
+    }
+    
+    function initBioAssays()
+    {
+      var frm = document.forms['extraValue'];
+      <%
+      if (bioAssays != null)
+      {
+        for (BioAssay ba : bioAssays)
+        {
+          %>
+          Link.addNewItem(frm.bioAssays, new Item('R', <%=ba.getId()%>, '<%=HTML.javaScriptEncode(ba.getName())%>'));
+          <%
+        }
+      }
+      %>
+      frm.allBioAssays.checked = frm.bioAssays.length == 0;
+      allBioAssaysOnClick();
+    }
     </script>
   </base:head>
-  <base:body>
+  <base:body onload="init()">
     <form name="extraValue" action="index.jsp" method="get" onsubmit="return false;">
     <input type="hidden" name="ID" value="<%=ID%>">
@@ -244 +334 @@
         <td class="prompt">Source bioassay set</td>
         <td><%=HTML.encodeTags(source.getName())%></td>
+      </tr>
+      <tr valign="top">
+      <td class="prompt">Bioassays</td>
+        <td>
+          <input type="checkbox" name="allBioAssays" 
+            onclick="allBioAssaysOnClick()"><a 
+            href="javascript:document.forms['extraValue'].allBioAssays.click()">All bioassays</a><br>
+          <table border="0" cellspacing="0" cellpadding="0">
+          <tr valign="top">
+          <td>
+            <select name="bioAssays" size="5" multiple style="width: 20em;">
+            </select>
+          </td>
+          <td>
+            <table border="0">
+            <tr><td width="150"><base:button 
+              onclick="addBioAssaysOnClick()" 
+              title="Add&nbsp;bioassays&hellip;" 
+              tooltip="Add bioassays"
+              /></td></tr>
+            <tr><td width="150"><base:button 
+              onclick="removeBioAssaysOnClick()" 
+              title="Remove" 
+              tooltip="Remove the selected bioassays"
+            /></td></tr>
+            </table>
+          </td>
+          </tr>
+          </table>
+        </td>
       </tr>
       <tr>