Changeset 5664

Timestamp:

Jun 23, 2011, 11:53:05 AM (12 years ago)

Author:

Nicklas Nordborg

Message:

References #1153: Handling short read transcript sequence data

Updated web gui for extracts to handle the new parent item scheme. Some minor changes to the sample and physical bioassay gui also that among other things fixes some export issues.

Location:

trunk

Files:

• src/clients/web/net/sf/basedb/clients/web/plugins/ItemQueryLoader.java (modified) (2 diffs)
• src/clients/web/net/sf/basedb/clients/web/plugins/ParentBioMaterialLoader.java (modified) (4 diffs)
• src/core/net/sf/basedb/util/formatter/ItemTypeFormatter.java (added)
• www/biomaterials/extracts/edit_extract.jsp (modified) (21 diffs)
• www/biomaterials/extracts/index.jsp (modified) (9 diffs)
• www/biomaterials/extracts/list_extracts.jsp (modified) (8 diffs)
• www/biomaterials/extracts/view_extract.jsp (modified) (11 diffs)
• www/biomaterials/samples/edit_sample.jsp (modified) (2 diffs)
• www/biomaterials/samples/index.jsp (modified) (4 diffs)
• www/biomaterials/samples/list_samples.jsp (modified) (6 diffs)
• www/biomaterials/samples/view_sample.jsp (modified) (2 diffs)
• www/include/styles/table.css (modified) (1 diff)
• www/views/physicalbioassays/view_bioassay.jsp (modified) (6 diffs)

trunk/src/clients/web/net/sf/basedb/clients/web/plugins/ItemQueryLoader.java

@@ -36 +36 @@
   @base.modified $Date$
 */
-public class ItemQueryLoader 
-  implements DataLoader<BasicItem<?>>
+public class ItemQueryLoader<T extends BasicItem>
+  implements DataLoader<T>
 {
   private final ItemQuery<?> query;
@@ -55 +55 @@
 
   @Override
-  public Object getData(ExportedProperty exportedProperty, BasicItem<?> item)
+  public Object getData(ExportedProperty exportedProperty, T item)
     throws Exception
   {

trunk/src/clients/web/net/sf/basedb/clients/web/plugins/ParentBioMaterialLoader.java

@@ -24 +24 @@
 import net.sf.basedb.core.BioMaterial;
 import net.sf.basedb.core.DbControl;
-import net.sf.basedb.core.Include;
 import net.sf.basedb.core.ItemQuery;
 import net.sf.basedb.core.MeasuredBioMaterial;
@@ -36 +35 @@
 
 public class ParentBioMaterialLoader 
-  implements DataLoader<MeasuredBioMaterial<?>>
+  extends ItemQueryLoader<MeasuredBioMaterial>
 {
 
-  public ParentBioMaterialLoader()
-  {}
+  public ParentBioMaterialLoader(ItemQuery<? extends BioMaterial> query, String parameterName)
+  {
+    super(query, parameterName);
+  }
   
-  @SuppressWarnings("unchecked")
   @Override
-  public Object getData(ExportedProperty exportedProperty, MeasuredBioMaterial<?> item) 
+  public Object getData(ExportedProperty exportedProperty, MeasuredBioMaterial item) 
     throws Exception
   {
@@ -57 +57 @@
       try
       {
-        parents = exportedProperty.propertyPath.getValue(dc, item);
+        parents = item.getParent();
       }
       catch(Throwable e)
@@ -64 +64 @@
     else
     {
-      ItemQuery<? extends BioMaterial> pooledQuery = item.getCreationEvent().getSources();
-      pooledQuery.include(Include.ALL);
-      parents = pooledQuery.list(dc);
+      parents = super.getData(exportedProperty, item);
     }
     return parents;

trunk/www/biomaterials/extracts/edit_extract.jsp

@@ -29 +29 @@
   import="net.sf.basedb.core.DbControl"
   import="net.sf.basedb.core.Item"
+  import="net.sf.basedb.core.Type"
   import="net.sf.basedb.core.ItemContext"
   import="net.sf.basedb.core.SystemItems"
@@ -48 +49 @@
   import="net.sf.basedb.core.query.Orders"
   import="net.sf.basedb.core.query.Hql"
+  import="net.sf.basedb.core.query.Expressions"
+  import="net.sf.basedb.core.query.Restrictions"
   import="net.sf.basedb.clients.web.Base"
   import="net.sf.basedb.clients.web.util.HTML"
@@ -81 +84 @@
   BioMaterialEvent creationEvent = null;
   Date eventDate = null;
-  boolean isPooled = false;
+  Item parentType = null;
   boolean lockEventProperties = false;
   
@@ -144 +147 @@
     }
     int sampleId = Values.getInt(request.getParameter("sample_id"));
+    int extractId = Values.getInt(request.getParameter("extract_id"));
     if (sampleId != 0)
     {
       currentSample  = Sample.getById(dc, sampleId);
-      isPooled = false;
+      parentType = Item.SAMPLE;
       name = currentSample.getName() + ".e" + (currentSample.countExtracts() + 1);      
     }
-    else if(Values.getBoolean(request.getParameter("pooled")))
-    {
-      isPooled = true;
+    else if (extractId != 0)
+    {
+      parentType = Item.EXTRACT;
+      Extract e = Extract.getById(dc, extractId);
+      name = e.getName() + ".e" + (e.countExtracts()+1);
+      extractsQuery = Extract.getQuery();
+      extractsQuery.restrict(Restrictions.eq(Hql.property("id"), Expressions.integer(extractId)));
+    }
+    else if (Values.getBoolean(request.getParameter("pooled")))
+    {
+      parentType = Item.EXTRACT;
       name = Values.getString(cc.getPropertyValue("name"), "New pooled extract");
+      extractsQuery = Extract.getQuery();
+      extractsQuery.restrict(Restrictions.in(Hql.property("id"), Expressions.parameter("selected")));
+      extractsQuery.setParameter("selected", cc.getSelected(), Type.INT);
     }
     else
     {
-      isPooled = Values.getBoolean(cc.getPropertyValue("pooled"));
       name = Values.getString(cc.getPropertyValue("name"), "New extract");
     }
@@ -171 +185 @@
     creationEvent = extract.getCreationEvent();
     eventDate = creationEvent.getEventDate();
-    isPooled = extract.isPooled();
     name = extract.getName();
     lockEventProperties = !creationEvent.hasPermission(Permission.WRITE);
@@ -205 +218 @@
     try
     {
-      currentSample = extract.getSample();
-      if (currentSample != null) usedFromSample = creationEvent.getUsedQuantity(currentSample);
+      if (parentType == Item.SAMPLE)
+      {
+        currentSample = (Sample)extract.getParent();
+        if (currentSample != null) 
+        {
+          usedFromSample = creationEvent.getUsedQuantity(currentSample);
+        }
+      }
     }
     catch (PermissionDeniedException ex)
@@ -228 +247 @@
   
     // Query to retrieve pooled extracts
-    extractsQuery = (ItemQuery<Extract>)creationEvent.getSources();
-    extractsQuery.include(Include.ALL);
-    extractsQuery.order(Orders.asc(Hql.property("name")));
-  
+    if (parentType == Item.EXTRACT)
+    {
+      extractsQuery = (ItemQuery<Extract>)creationEvent.getSources();
+    }
   }
   
@@ -329 +348 @@
       var frm = document.forms['extract'];
       var parents = new Array();
-      if (frm.pooled[0].checked)
+      if (frm.parentType[0].checked)
       {
         var sampleId = Math.abs(parseInt(frm.sample_id[frm.sample_id.selectedIndex].value));
@@ -488 +507 @@
     }
     
-    function pooledOnClick()
-    {
-      var frm = document.forms['extract'];
-      var isPooled = frm.pooled[1].checked;
-      frm.sample_id.disabled = isPooled;
-      frm.used_from_sample.disabled = isPooled;
-      frm.extracts.disabled = !isPooled;
-      frm.used_quantity.disabled = !isPooled;
+    function parentTypeOnClick()
+    {
+      var frm = document.forms['extract'];
+      var useExtracts = frm.parentType[1].checked;
+      frm.sample_id.disabled = useExtracts;
+      frm.used_from_sample.disabled = useExtracts;
+      frm.extracts.disabled = !useExtracts;
+      frm.used_quantity.disabled = !useExtracts;
       parentsChanged = true;
     }
@@ -506 +525 @@
     {
       var frm = document.forms['extract'];
-      if (frm.pooled[1].checked)
-      {
-        alert('This is a pooled extract, which cannot have a sample as it\'s parent');
-        return;
-      }
       var url = '../samples/index.jsp?ID=<%=ID%>&cmd=UpdateContext&mode=selectone';
       url += '&callback=setSampleCallback&resetTemporary=1';
@@ -532 +546 @@
       list[1].text = name;
       list.selectedIndex = 1;
+      frm.parentType[0].checked = true;
+      frm.parentType[1].checked = false;
+      parentTypeOnClick();
       parentsChanged = true;
     }
@@ -538 +555 @@
     {
       var frm = document.forms['extract'];
-      if (!frm.pooled[1].checked)
-      {
-        alert('This is not a pooled extract');
-        return;
-      }
       var url = 'index.jsp?ID=<%=ID%>&cmd=UpdateContext&mode=selectmultiple';
       url += '&callback=addExtractCallback&resetTemporary=1';
@@ -554 +566 @@
       if (!item) item = new Item('E', extractId, name+' [-]', '', '');
       Link.addItem(document.forms['extract'].extracts, item);
+      frm.parentType[0].checked = false;
+      frm.parentType[1].checked = true;
+      parentTypeOnClick();
       parentsChanged = true;
     }
@@ -618 +633 @@
       initBioWell();      
       initExtracts();
-      pooledOnClick();
+      parentTypeOnClick();
     }
     function initExtracts()
@@ -624 +639 @@
       var extracts = document.forms['extract'].extracts;
       <%
-      if (extract != null && extract.isPooled())
-      {
+      if (extractsQuery != null)
+      {
+        extractsQuery.include(Include.ALL);
+        extractsQuery.order(Orders.asc(Hql.property("name")));
         ItemResultList<Extract> extracts = extractsQuery.list(dc);
         for (Extract e : extracts)
         {
-          String usedQuantity = Values.formatNumber(creationEvent.getUsedQuantity(e), -1);
-          %>
-          Link.addNewItem(extracts, new Item('E', <%=e.getId()%>, '<%=HTML.javaScriptEncode(e.getName())%> [<%=usedQuantity%> µg]', '<%=usedQuantity%>'));
-          <%
-        }
-      }
-      else if (extract == null && Values.getBoolean(request.getParameter("pooled")))
-      {
-        for (int eId : cc.getSelected())
-        {
-          Extract extractToPool = Extract.getById(dc, eId);
-          %>
-          Link.addItem(extracts, new Item('E', <%=extractToPool.getId()%>, '<%=HTML.javaScriptEncode(extractToPool.getName())%> [-]', '', ''));
-          <%
+          if (extract != null)
+          {
+            String usedQuantity = Values.formatNumber(creationEvent.getUsedQuantity(e), -1);
+            %>
+            Link.addNewItem(extracts, new Item('E', <%=e.getId()%>, '<%=HTML.javaScriptEncode(e.getName())%> [<%=usedQuantity%> µg]', '<%=usedQuantity%>'));
+            <%
+          }
+          else
+          {
+            %>
+            Link.addItem(extracts, new Item('E', <%=e.getId()%>, '<%=HTML.javaScriptEncode(e.getName())%> [-]', '', ''));
+            <%
+            
+          }
         }
       }
@@ -821 +838 @@
       <table class="form" cellspacing=0>
       <tr>
-        <td class="prompt">Pooled</td>
+        <td class="prompt">Parent type</td>
         <td>
-          <input type="radio" name="pooled" value="0" onclick="pooledOnClick()"
-            <%=!isPooled ? "checked" : ""%>
-            >no
-          <input type="radio" name="pooled" value="1" onclick="pooledOnClick()"
-            <%=isPooled ? "checked" : ""%>
-            >yes
+          <input type="radio" name="parentType" id="parentType.sample" 
+            value="SAMPLE" onclick="parentTypeOnClick()"
+            <%=parentType != Item.EXTRACT ? "checked" : ""%>
+            ><label for="parentType.sample">Sample</label>
+          <input type="radio" name="parentType" id="parentType.extract" 
+            value="EXTRACT" onclick="parentTypeOnClick()"
+            <%=parentType == Item.EXTRACT ? "checked" : ""%>
+            ><label for="parentType.extract">Extract</label>
         </td>
       </tr>
@@ -837 +856 @@
             id="sample_id"
             clazz="selectionlist"
+            buttonstyle="width: 150px;"
+            buttonicon="add.png"
+            buttontitle="Select biosource&hellip;"
             required="false"
             current="<%=currentSample%>"
@@ -846 +868 @@
             onchange="sampleOnChange()"
           />
-          Used
+        </td>
+      </tr>
+      <tr>
+        <td class="subprompt">-</td>
+        <td>
+          used quantity
           <input <%=clazz%> type="text" name="used_from_sample" value="<%=Values.formatNumber(usedFromSample, -1)%>"
             size="12" maxlength="10" onkeypress="return Numbers.numberOnly(event)"
@@ -858 +885 @@
           <tr valign="top">
           <td>
-            <select name="extracts" size="5" multiple style="width: 20em;" 
+            <select name="extracts" size="5" multiple class="selectionlist" 
               onchange="extractsOnChange()">
-            </select>&nbsp;<br>
-            Used
-            <input <%=clazz%> type="text" name="used_quantity" value=""
-              size="12" maxlength="10" onkeypress="return Numbers.numberOnly(event)"
-              onkeyup="usedQuantityOnBlur()"
-            > (µg)
+            </select>&nbsp;
             <input type="hidden" name="modifiedExtracts" value="">
             <input type="hidden" name="removedExtracts" value="">
           </td>
           <td>
-            <table border="0">
-            <tr><td width="150"><base:button 
+            <table border="0" cellspacing="0" cellpadding="0">
+            <tr><td style="padding: 1px 0px 4px 0px;"><base:button 
+              style="width: 150px;"
               onclick="addExtractsOnClick()" 
               title="Add&nbsp;extracts&hellip;" 
@@ -877 +900 @@
               /></td></tr>
             <tr><td width="150"><base:button 
+              style="width: 150px;"
               onclick="removeOnClick()" 
               title="Remove" 
@@ -887 +911 @@
         </td>
       </tr>
+      <tr>
+        <td class="subprompt">-</td>
+        <td>used quantity
+        <input <%=clazz%> type="text" name="used_quantity" value=""
+              size="12" maxlength="10" onkeypress="return Numbers.numberOnly(event)"
+              onkeyup="usedQuantityOnBlur();"
+            > (µg)
+        </td>
+      </tr>         
       </table>
     </t:tab>

trunk/www/biomaterials/extracts/index.jsp

@@ -24 +24 @@
   @version 2.0
 --%>
-<%@page import="net.sf.basedb.core.BioMaterialEventSource"%>
 <%@ page pageEncoding="UTF-8" session="false"
   import="net.sf.basedb.core.SessionControl"
@@ -33 +32 @@
   import="net.sf.basedb.core.Extract"
   import="net.sf.basedb.core.BioMaterialEvent"
+  import="net.sf.basedb.core.BioMaterialEventSource"
   import="net.sf.basedb.core.BioPlateEventType"
   import="net.sf.basedb.core.BioWell"
@@ -61 +61 @@
   import="net.sf.basedb.util.formatter.NameableFormatter"
   import="net.sf.basedb.util.formatter.WellCoordinateFormatter"
+  import="net.sf.basedb.util.formatter.ItemTypeFormatter"
   import="net.sf.basedb.clients.web.formatter.FormatterFactory"
   import="net.sf.basedb.clients.web.plugins.ItemQueryLoader"
@@ -88 +89 @@
     cc.setObject("export.formatter.bioWell.column", new WellCoordinateFormatter(false));
     cc.setObject("export.formatter.&children(name)", new NameableFormatter());
-    cc.setObject("export.formatter.&creationEvent.sourceBioMaterials(name)", new NameableFormatter());
-    cc.setObject("export.formatter.&sourceEvents(event.physicalBioAssay.name)", new NameableFormatter());
-    cc.setObject("export.formatter.&sourceEvents(event.bioMaterial.name)", new NameableFormatter());
-    
+    cc.setObject("export.formatter.&creationEvent.sources(bioMaterial.name)", new NameableFormatter());
+    cc.setObject("export.formatter.&childCreationEvents(event.physicalBioAssay.name)", new NameableFormatter());
+    cc.setObject("export.formatter.&childCreationEvents(event.bioMaterial.name)", new NameableFormatter());
+    cc.setObject("export.formatter.parentType", new ItemTypeFormatter());
     
     String restrictionParameter = "extract";
@@ -99 +100 @@
     bioAssayQuery.join(Hql.innerJoin("creationEvent", "ce"));
     bioAssayQuery.join(Hql.innerJoin("ce", "sources", "src"));
-    bioAssayQuery.restrict(Restrictions.eq(Hql.index("src", null), Expressions.parameter(restrictionParameter)));
+    bioAssayQuery.restrict(Restrictions.eq(Hql.property("src", "bioMaterial"), Expressions.parameter(restrictionParameter)));
     bioAssayQuery.order(Orders.asc(Hql.property("name")));
     bioAssayQuery.include(cc.getInclude());
-    cc.setObject("export.dataloader.&sourceEvents(event.physicalBioAssay.name)", new ItemQueryLoader(bioAssayQuery, restrictionParameter));
+    cc.setObject("export.dataloader.&childCreationEvents(event.physicalBioAssay.name)", new ItemQueryLoader(bioAssayQuery, restrictionParameter));
 
     // Child extracts
@@ -108 +109 @@
     childExtractsQuery.join(Hql.innerJoin("creationEvent", "ce"));
     childExtractsQuery.join(Hql.innerJoin("ce", "sources", "src"));
-    childExtractsQuery.restrict(Restrictions.eq(Hql.index("src", null), Expressions.parameter(restrictionParameter)));
+    childExtractsQuery.restrict(Restrictions.eq(Hql.property("src", "bioMaterial"), Expressions.parameter(restrictionParameter)));
     childExtractsQuery.order(Orders.asc(Hql.property("name")));
     childExtractsQuery.include(cc.getInclude());
-    cc.setObject("export.dataloader.&sourceEvents(event.bioMaterial.name)", new ItemQueryLoader(childExtractsQuery, restrictionParameter));
+    cc.setObject("export.dataloader.&childCreationEvents(event.bioMaterial.name)", new ItemQueryLoader(childExtractsQuery, restrictionParameter));
     
-    // Parent extracts
+    // Parent items
     final ItemQuery<Extract> parentExtractsQuery = Extract.getQuery();
-    parentExtractsQuery.join(Hql.innerJoin("sourceEvents", "srcevt"));
-    parentExtractsQuery.join(Hql.innerJoin("srcevt", "event", "evt"));
+    parentExtractsQuery.join(Hql.innerJoin("childCreationEvents", "cce"));
+    parentExtractsQuery.join(Hql.innerJoin("cce", "event", "evt"));
     parentExtractsQuery.restrict(Restrictions.eq(Hql.property("evt", "bioMaterial"),  Expressions.parameter(restrictionParameter)));
     parentExtractsQuery.order(Orders.asc(Hql.property("name")));
     parentExtractsQuery.include(cc.getInclude());
-    cc.setObject("export.dataloader.&creationEvent.sourceBioMaterials(name)", new ItemQueryLoader(parentExtractsQuery, restrictionParameter));
+    cc.setObject("export.dataloader.&creationEvent.sources(bioMaterial.name)", new ParentBioMaterialLoader(parentExtractsQuery, restrictionParameter));
   }
 %>
@@ -277 +278 @@
   
       // Parents tab
-      extract.setPooled(Values.getBoolean(request.getParameter("pooled")));
-      if (!extract.isPooled())
+      Item parentType = Item.valueOf(request.getParameter("parentType"));
+      if (parentType == Item.SAMPLE)
       {
         int sampleId = Values.getInt(request.getParameter("sample_id"), -1);
@@ -284 +285 @@
         {
           Sample s = sampleId == 0 ? null : Sample.getById(dc, sampleId);
-          BioMaterialEventSource evtSrc = extract.setSample(s);
+          BioMaterialEventSource evtSrc = creationEvent.setSource(s);
           if (evtSrc != null)
           {
@@ -294 +295 @@
       else
       {
+        if (extract.getParentType() != Item.EXTRACT)
+        {
+          creationEvent.clearSources();
+        }
         String[] modifiedExtracts = Values.getString(request.getParameter("modifiedExtracts")).split(",");
         for (int i = 0; i < modifiedExtracts.length; ++i)

trunk/www/biomaterials/extracts/list_extracts.jsp

@@ -103 +103 @@
   final boolean createBioAssayPermission = sc.hasPermission(Permission.CREATE, Item.PHYSICALBIOASSAY);
 
+  // Child bioassays
   final ItemQuery<PhysicalBioAssay> bioAssayQuery = PhysicalBioAssay.getQuery();
   bioAssayQuery.join(Hql.innerJoin("creationEvent", "ce"));
   bioAssayQuery.join(Hql.innerJoin("ce", "sources", "src"));
-  bioAssayQuery.restrict(Restrictions.eq(Hql.index("src", null), Hql.entityParameter("extract", Item.EXTRACT)));
+  bioAssayQuery.restrict(Restrictions.eq(Hql.property("src", "bioMaterial"), Hql.entityParameter("extract", Item.EXTRACT)));
   bioAssayQuery.order(Orders.asc(Hql.property("name")));
   bioAssayQuery.include(cc.getInclude());
 
+  // Child extracts
   final ItemQuery<Extract> childExtractsQuery = Extract.getQuery();
   childExtractsQuery.join(Hql.innerJoin("creationEvent", "ce"));
   childExtractsQuery.join(Hql.innerJoin("ce", "sources", "src"));
-  childExtractsQuery.restrict(Restrictions.eq(Hql.index("src", null), Hql.entityParameter("extract", Item.EXTRACT)));
+  childExtractsQuery.restrict(Restrictions.eq(Hql.property("src", "bioMaterial"), Hql.entityParameter("extract", Item.EXTRACT)));
   childExtractsQuery.order(Orders.asc(Hql.property("name")));
   childExtractsQuery.include(cc.getInclude());
   
+  // Parent extracts
   final ItemQuery<Extract> parentExtractsQuery = Extract.getQuery();
   parentExtractsQuery.join(Hql.innerJoin("childCreationEvents", "cce"));
@@ -173 +176 @@
       Table.poolItems(submitPage, '<%=ID%>', formId, '<%=itemType.name()%>', 'NewPhysicalBioAssay');
     }
+    function newExtract(extractId)
+    {
+      Main.viewOrEditItem('<%=ID%>', 'EXTRACT', 0, true, '&extract_id='+extractId);
+    }
     function editItem(itemId)
     {
@@ -377 +384 @@
         formatter="<%=dateFormatter%>"
       />
-      <tbl:columndef 
-        id="pooled"
-        property="pooled"
-        datatype="boolean"
-        title="Pooled"
-        sortable="true" 
-        filterable="true"
-        exportable="true"
-      />
+      <%
+      Enumeration<String, String> parentTypes = new Enumeration<String, String>();
+      parentTypes.add(Integer.toString(Item.SAMPLE.getValue()), Item.SAMPLE.toString());
+      parentTypes.add(Integer.toString(Item.EXTRACT.getValue()), Item.EXTRACT.toString());
+      %>
       <tbl:columndef
-        id="sample"
-        title="Sample"
-        property="parent.name"
-        datatype="string"
-        sortable="true" 
-        filterable="true"
-        exportable="true"
+        id="parentType"
+        title="Parent type"
+        property="parentType"
+        enumeration="<%=parentTypes%>"
+        datatype="int"
+        filterable="true"
+        exportable="true"
+        sortable="true"
       />
       <tbl:columndef
         id="parents"
-        title="Parent extracts"
+        title="Parent items"
         property="&creationEvent.sources(bioMaterial.name)"
+        sortproperty="parent.name"
         datatype="string"
         filterable="true"
         exportable="true"
+        sortable="true"
       />
       <tbl:columndef
@@ -662 +668 @@
             {
               Extract item = extracts.next();
+              Item parentType = item.getParentType();
               BioMaterialEvent creationEvent = item.getCreationEvent();
               int itemId = item.getId();
@@ -727 +734 @@
                 <tbl:cell column="originalQuantity"><%=Values.formatNumber(item.getOriginalQuantity(), 2)%></tbl:cell>
                 <tbl:cell column="remainingQuantity"><%=Values.formatNumber(item.getRemainingQuantity(), 2)%></tbl:cell>
-                <tbl:cell column="pooled"><%=item.isPooled()%></tbl:cell>
                 <tbl:cell column="protocol"
                   ><base:propertyvalue 
@@ -737 +743 @@
                 <tbl:cell column="eventDate" value="<%=creationEvent.getEventDate()%>" />
                 <tbl:cell column="entryDate" value="<%=creationEvent.getEntryDate()%>" />
-                <tbl:cell column="sample"><base:propertyvalue item="<%=item%>" property="parent"/></tbl:cell>
+                <tbl:cell column="parentType"><%=parentType == null ? "" : parentType.toString() %></tbl:cell>
                 <tbl:cell column="parents">
                   <%
-                  if (item.isPooled())
+                  if (item.hasSingleParent() || item.getParentType() == null)
+                  {
+                    %>
+                    <base:propertyvalue item="<%=item%>" property="parent"/>
+                    <%
+                  }
+                  else
                   {
                     String separator = "";
@@ -759 +771 @@
                   }
                   %>
+                  <%=parentType != null ? "<span class=\"itemtype\">(" + parentType + ")</span>" : "" %>
                 </tbl:cell>
                 <tbl:cell column="children">
@@ -778 +791 @@
                   }
                   %>
+                  <base:icon
+                    image="add.png" 
+                    onclick="<%="newExtract("+itemId+")"%>" 
+                    tooltip="Create new child extract" 
+                    visible="<%=mode.hasEditLink() && createPermission && usePermission %>"
+                  />
                 </tbl:cell>
                 <tbl:cell column="physicalBioAssays">

trunk/www/biomaterials/extracts/view_extract.jsp

@@ -30 +30 @@
   import="net.sf.basedb.core.Group"
   import="net.sf.basedb.core.Item"
+  import="net.sf.basedb.core.CommonItem"
   import="net.sf.basedb.core.ItemContext"
   import="net.sf.basedb.core.ItemProxy"
@@ -36 +37 @@
   import="net.sf.basedb.core.PhysicalBioAssay"
   import="net.sf.basedb.core.Sample"
+  import="net.sf.basedb.core.BioMaterial"
   import="net.sf.basedb.core.BioMaterialEvent"
+  import="net.sf.basedb.core.BioMaterialEventSource"
   import="net.sf.basedb.core.BioWell"
   import="net.sf.basedb.core.MultiPermissions"
@@ -44 +47 @@
   import="net.sf.basedb.core.ItemQuery"
   import="net.sf.basedb.core.ItemResultList"
+  import="net.sf.basedb.core.SpecialQuery"
   import="net.sf.basedb.core.Include"
+  import="net.sf.basedb.core.query.ResultList"
   import="net.sf.basedb.core.query.Orders"
   import="net.sf.basedb.core.query.Hql"
@@ -124 +129 @@
       Main.viewOrEditItem('<%=ID%>', '<%=itemType.name()%>', <%=itemId%>, true);
     }
+    function newExtract()
+    {
+      Main.viewOrEditItem('<%=ID%>', 'EXTRACT', 0, true, '&extract_id=<%=itemId%>');
+    }
     function shareItem()
     {
@@ -230 +239 @@
         title="Set owner&hellip;"
         tooltip="<%=setOwnerPermission ? "Change owner of this item" : "You do not have permission to change ownership of this item"%>"
+      />
+      <tbl:button
+        image="add.png"
+        onclick="newExtract()"
+        title="New child extract&hellip;"
+        tooltip="Create a new child extract from this extract"
+        visible="<%=sc.hasPermission(Permission.CREATE, Item.EXTRACT) && usePermission%>"
       />
       <tbl:button
@@ -311 +327 @@
         <td><%=dateFormatter.format(creationEvent.getEntryDate())%></td>
       </tr>
-      <%
-      if (!extract.isPooled())
-      {
-        %>
-        <tr>
-          <td class="prompt">Sample</td>
-          <td><base:propertyvalue item="<%=extract%>" property="parent"/> 
-            <%
-            try
-            {
-            %>
-              <%=extract.getSample() != null ? "(" + Values.formatNumber(creationEvent.getUsedQuantity(extract.getSample()), 2, " µg") + ")" : ""%>
-            <%
-            }
-            catch (PermissionDeniedException ex)
-            {}
-            %>  
-
-          </td>
-        </tr>
-        <%
-      }
-      %>
       <tr>
         <td class="prompt">Protocol</td>
@@ -378 +371 @@
   
       <%
-      if (extract.isPooled())
-      {
-        ItemQuery<Extract> extractsQuery = (ItemQuery<Extract>)creationEvent.getSources();
-        extractsQuery.include(Include.ALL);
-        extractsQuery.order(Orders.asc(Hql.property("name")));
-        ItemResultList<Extract> extracts = extractsQuery.list(dc);
-        %>
-        <h4 class="docked">Pooled from extracts</h4>
-        <tbl:table
-          id="pooled"
-          clazz="itemlist"
-          columns="all"
+      SpecialQuery<BioMaterialEventSource> sourceQuery = creationEvent.getEventSources();
+      sourceQuery.order(Orders.asc(Hql.property("bioMaterial.name")));
+      ResultList<BioMaterialEventSource> sources = sourceQuery.list(dc);
+      if (sources.size() == 0)
+      {
+        %>
+        <h4>Parent items</h4>
+        This extract doesn't have any parent items
+        (or, you don't have permission to view them).
+        <%
+      }
+      else
+      {
+        %>
+        <base:section 
+          id="parentsSection" 
+          title="<%="Parent items (" + sources.size() + ")"%>"
+          context="<%=cc%>"
           >
-        <tbl:columndef 
-          id="name"
-          title="Name"
-        />
-        <tbl:columndef 
-          id="quantity"
-          title="Used quantity (µg)"
-        />
-        <tbl:columndef 
-          id="description"
-          title="Description"
-        />
-        <tbl:data>
-          <tbl:columns>
-          </tbl:columns>
-          <tbl:rows>
-          <%
-          for (Extract item : extracts)
-          {
-            %>
-            <tbl:row>
-              <tbl:cell column="name"><base:icon 
+          <tbl:table
+            id="parents"
+            clazz="itemlist"
+            columns="all"
+            >
+          <tbl:columndef 
+            id="name"
+            title="Name"
+          />
+          <tbl:columndef 
+            id="type"
+            title="Type"
+          />
+          <tbl:columndef 
+            id="quantity"
+            title="Used quantity (µg)"
+          />
+          <tbl:columndef 
+            id="description"
+            title="Description"
+          />
+          <tbl:data>
+            <tbl:columns>
+            </tbl:columns>
+            <tbl:rows>
+            <%
+            for (BioMaterialEventSource item : sources)
+            {
+              BioMaterial bm = null;
+              try
+              {
+                bm = item.getBioMaterial();
+              }
+              catch (PermissionDeniedException ex)
+              {}
+              %>
+              <tbl:row>
+                <tbl:cell column="name"><base:icon 
                   image="deleted.gif" 
                   tooltip="This item has been scheduled for deletion" 
-                  visible="<%=item.isRemoved()%>"
-                /><%=Base.getLinkedName(ID, item, false, true)%></tbl:cell>
-              <tbl:cell column="quantity"><%=Values.formatNumber(creationEvent.getUsedQuantity(item), 2)%></tbl:cell>
-              <tbl:cell column="description"><%=HTML.encodeTags(item.getDescription())%></tbl:cell>
-            </tbl:row>
-            <%
-          }
-          %>
+                  visible="<%=bm != null && bm.isRemoved()%>"
+                  /><%=Base.getLinkedName(ID, bm, bm == null, true)%></tbl:cell>
+                <tbl:cell column="type"><%=bm != null ? bm.getType() : "" %></tbl:cell>
+                <tbl:cell column="quantity"><%=Values.formatNumber(item.getUsedQuantity(), 2)%></tbl:cell>
+                <tbl:cell column="description"><%=HTML.encodeTags(bm == null ? "" : bm.getDescription())%></tbl:cell>
+              </tbl:row>
+              <%
+            }
+            %>
           </tbl:rows>
-        </tbl:data>
-        </tbl:table>
-        <%
-      }
-
-      // Extracts this item is pooled in.
-      ItemQuery<BioMaterialEvent> poolingQuery = extract.getPoolingEvents();
-      ItemResultList<BioMaterialEvent> poolingEvents = poolingQuery.list(dc);
-      if (poolingEvents.size() == 0)
-      {
-        %>
-        <h4>Pooled in extracts</h4>
-        No extracts have been pooled from this extract
+          </tbl:data>
+          </tbl:table>
+        </base:section>
+        <%
+      }
+      
+      SpecialQuery<BioMaterialEventSource> childQuery = extract.getChildCreationEvents();
+      childQuery.join(Hql.innerJoin("es", "event", "evt", true));
+      childQuery.join(Hql.leftJoin("evt", "bioMaterial", "bm", null, true));
+      childQuery.join(Hql.leftJoin("evt", "physicalBioAssay", "pba", null, true));
+      childQuery.order(Orders.asc(Hql.property("pba", "name")));
+      childQuery.order(Orders.asc(Hql.property("bm", "name")));
+      ResultList<BioMaterialEventSource> children = childQuery.list(dc);
+      if (children.size() == 0)
+      {
+        %>
+        <h4>Child items</h4>
+        No child items have been created from this extract
         (or, you don't have permission to view them).
         <%
@@ -444 +465 @@
         %>
         <base:section 
-          id="pooledSection" 
-          title="<%="Pooled in extracts (" + poolingEvents.size() + ")"%>"
+          id="childSection" 
+          title="<%="Child items (" + children.size() + ")"%>"
           context="<%=cc%>"
           >
           <tbl:table 
-            id="poolChilds"
+            id="children"
             clazz="itemlist"
             columns="all"
@@ -458 +479 @@
             />
             <tbl:columndef 
-              id="quantity"
-              title="Original quantity (µg)"
+              id="type"
+              title="Type"
             />
             <tbl:columndef 
-              id="parents"
-              title="Used extracts[quantity]" 
+              id="quantity"
+              title="Used quantity (µg)"
             />
             <tbl:columndef 
@@ -473 +494 @@
               <tbl:rows>
               <%
-              for (BioMaterialEvent poolEvt : poolingEvents)
+              for (BioMaterialEventSource item : children)
               {
-                ItemQuery<Extract> extractsQuery = (ItemQuery<Extract>)poolEvt.getSources();
-                Extract child = (Extract)poolEvt.getBioMaterial();
-                extractsQuery.include(Include.ALL);
-                extractsQuery.order(Orders.asc(Hql.property("name")));
-                ItemResultList<Extract> parentExtracts = extractsQuery.list(dc);
+                CommonItem child = null;
+                try
+                {
+                  BioMaterialEvent evt = item.getEvent();
+                  if (evt.getEventType() == BioMaterialEvent.Type.BIOASSAY)
+                  {
+                    child = evt.getPhysicalBioAssay();
+                  }
+                  else
+                  {
+                    child = evt.getBioMaterial();
+                  }
+                }
+                catch (PermissionDeniedException ex)
+                {}
                 %>
                 <tbl:row>
-                  <tbl:cell column="name">
-                    <base:icon 
+                  <tbl:cell column="name"><base:icon 
                       image="deleted.gif" 
                       tooltip="This item has been scheduled for deletion" 
-                      visible="<%=child.isRemoved()%>"
-                    />
-                    <%=Base.getLinkedName(ID, child, false, true)%>
-                  </tbl:cell>
-                  <tbl:cell column="quantity"><%=Values.formatNumber(child.getOriginalQuantity(), 2)%></tbl:cell>
-                  <tbl:cell column="parents">
-                  <%
-                  String separator = "";
-                  for (Extract parent : parentExtracts)
-                  {
-                    out.write(separator);
-                    if (parent.equals(extract))
-                        out.write(HTML.encodeTags(parent.getName()));
-                    else                    
-                      out.write(Base.getLinkedName(ID, parent, false, true));
-                    out.write("[" + Values.formatNumber(poolEvt.getUsedQuantity(parent), 2) + "µg]");
-                    separator = ", ";
-                  }
-                  %>
-                  </tbl:cell>
-                  <tbl:cell column="description"><%=HTML.encodeTags(child.getDescription())%></tbl:cell>
+                      visible="<%=child != null && child.isRemoved()%>"
+                    /><%=Base.getLinkedName(ID, child, child == null, true)%></tbl:cell>
+                  <tbl:cell column="type"><%=child != null ? child.getType() : "" %></tbl:cell>
+                  <tbl:cell column="quantity"><%=Values.formatNumber(item.getUsedQuantity(), 2)%></tbl:cell>
+                  <tbl:cell column="description"><%=HTML.encodeTags(child == null ? "" : child.getDescription())%></tbl:cell>
                 </tbl:row>
                 <%
@@ -517 +531 @@
         <%
       }
-      
-      ItemQuery<PhysicalBioAssay> bioAssayQuery = extract.getPhysicalBioAssays();
-      bioAssayQuery.include(Include.ALL);
-      bioAssayQuery.order(Orders.asc(Hql.property("name")));
-      ItemResultList<PhysicalBioAssay> bioAssays = bioAssayQuery.list(dc);
-      if (bioAssays.size() == 0)
-      {
-        %>
-        <h4>Physical bioassays</h4>
-        No bioassays have been created from this extract
-        (or you don't have the permission to view them)
-        <%
-      }
-      else
-      {
-        %>
-        <base:section 
-          id="bioAssaysSection" 
-          title="<%="Physical bioassays (" + bioAssays.size() + ")"%>"
-          context="<%=cc%>"
-          >
-          <tbl:table
-            id="bioAssays"
-            clazz="itemlist"
-            columns="all"
-            >
-            <tbl:columndef
-              id="name"
-              title="Name"
-            />          
-            <tbl:columndef 
-              id="quantity"
-              title="Used quantity (µg)"
-            />
-            <tbl:columndef
-              id="description"
-              title="Description"
-            />
-            <tbl:data>
-              <tbl:columns></tbl:columns>
-              <tbl:rows>
-                <%
-                for (PhysicalBioAssay pba : bioAssays)
-                {
-                  %>
-                  <tbl:row>
-                    <tbl:cell column="name"><base:icon 
-                      image="deleted.gif" 
-                      tooltip="This item has been scheduled for deletion" 
-                      visible="<%=pba.isRemoved()%>"
-                    /><%=Base.getLinkedName(ID, pba, false, true)%></tbl:cell>
-                    <tbl:cell column="quantity"><%=Values.formatNumber(pba.getCreationEvent().getUsedQuantity(extract), 2)%></tbl:cell>
-                    <tbl:cell column="description"><%=HTML.encodeTags(pba.getDescription())%></tbl:cell>
-                  </tbl:row>
-                  <%
-                }
-                %>
-              </tbl:rows>
-            </tbl:data>
-          </tbl:table>
-        </base:section>
-        <%
-      }     
       %>
       <jsp:include page="../../common/anytoany/list_anytoany.jsp">

trunk/www/biomaterials/samples/edit_sample.jsp

@@ -469 +469 @@
     {
       var frm = document.forms['sample'];
-      var useSamples = frm.parentType[1].checked
+      var useSamples = frm.parentType[1].checked;
       frm.biosource_id.disabled = useSamples;
       frm.samples.disabled = !useSamples;
@@ -815 +815 @@
           <td>
             <table border="0" cellspacing="0" cellpadding="0">
-            <tr><td style="padding: 1px 0px 4px 0px; width: 150px;"><base:button 
+            <tr><td style="padding: 1px 0px 4px 0px;"><base:button 
+              style="width: 150px;"
               onclick="addSamplesOnClick()" 
               title="Add&nbsp;samples&hellip;" 

trunk/www/biomaterials/samples/index.jsp

@@ -61 +61 @@
   import="net.sf.basedb.util.formatter.WellCoordinateFormatter"
   import="net.sf.basedb.util.formatter.NameableFormatter"
+  import="net.sf.basedb.util.formatter.ItemTypeFormatter"
   import="net.sf.basedb.clients.web.formatter.FormatterFactory"
 
@@ -91 +92 @@
     cc.setObject("export.formatter.&childCreationEvents(event.bioMaterial.name)", new NameableFormatter());
     cc.setObject("export.formatter.&children(name)", new NameableFormatter());
+    cc.setObject("export.formatter.parentType", new ItemTypeFormatter());
     
     // Register dataloaders
@@ -118 +120 @@
     parentSamplesQuery.order(Orders.asc(Hql.property("name")));
     parentSamplesQuery.include(cc.getInclude());
-    cc.setObject("export.dataloader.&creationEvent.sources(bioMaterial.name)", new ItemQueryLoader(parentSamplesQuery, sampleParameter));
+    cc.setObject("export.dataloader.&creationEvent.sources(bioMaterial.name)", new ParentBioMaterialLoader(parentSamplesQuery, sampleParameter));
   } 
 %>
@@ -264 +266 @@
   
       // Parents tab
-      //sample.setPooled(Values.getBoolean(request.getParameter("pooled")));
       Item parentType = Item.valueOf(request.getParameter("parentType"));
       if (parentType == Item.BIOSOURCE)

trunk/www/biomaterials/samples/list_samples.jsp

@@ -101 +101 @@
   final ItemQuery<AnnotationType> annotationTypeQuery = Base.getAnnotationTypesQuery(itemType);
   final ItemQuery<ItemSubtype> subtypesQuery = Base.getSubtypesQuery(itemType);
+  
+  // Child extracts
   final ItemQuery<Extract> extractQuery = Extract.getQuery();
   extractQuery.include(cc.getInclude());
@@ -107 +109 @@
   final boolean createExtractPermission = sc.hasPermission(Permission.CREATE, Item.EXTRACT);
 
+  // Child samples
   final ItemQuery<Sample> childSamplesQuery = Sample.getQuery();
   childSamplesQuery.join(Hql.innerJoin("creationEvent", "ce"));
@@ -114 +117 @@
   childSamplesQuery.include(cc.getInclude());
   
+  // Parent samples
   final ItemQuery<Sample> parentSamplesQuery = Sample.getQuery();
   parentSamplesQuery.join(Hql.innerJoin("childCreationEvents", "cce"));
@@ -377 +381 @@
         exportable="true"
         formatter="<%=dateFormatter%>"
+      />
+      <%
+      Enumeration<String, String> parentTypes = new Enumeration<String, String>();
+      parentTypes.add(Integer.toString(Item.BIOSOURCE.getValue()), Item.BIOSOURCE.toString());
+      parentTypes.add(Integer.toString(Item.SAMPLE.getValue()), Item.SAMPLE.toString());
+      %>
+      <tbl:columndef
+        id="parentType"
+        title="Parent type"
+        property="parentType"
+        enumeration="<%=parentTypes%>"
+        datatype="int"
+        filterable="true"
+        exportable="true"
+        sortable="true"
       />
       <tbl:columndef
@@ -756 +775 @@
                 <tbl:cell column="eventDate" value="<%=creationEvent.getEventDate()%>" />
                 <tbl:cell column="entryDate" value="<%=creationEvent.getEntryDate()%>" />
+                <tbl:cell column="parentType"><%=parentType == null ? "" : parentType.toString() %></tbl:cell>
                 <tbl:cell column="parents">
                   <%
-                  if (item.hasSingleParent() || item.getParentType() == null)
+                  if (item.hasSingleParent() || parentType == null)
                   {
                     %>
@@ -783 +803 @@
                   }
                   %>
+                  <%=parentType != null ? "<span class=\"itemtype\">(" + parentType + ")</span>" : "" %>
                 </tbl:cell>
                 <tbl:cell column="children">

trunk/www/biomaterials/samples/view_sample.jsp

@@ -373 +373 @@
       {
         %>
+        <h4>Parent items</h4>
+        This sample doesn't have any parent items
+        (or, you don't have permission to view them).
         <%
       }
@@ -439 +442 @@
       }
       
-      // Samples this item is pooled in.
       SpecialQuery<BioMaterialEventSource> childQuery = sample.getChildCreationEvents();
       childQuery.join(Hql.innerJoin("es", "event", "evt", true));

trunk/www/include/styles/table.css

@@ -199 +199 @@
 }
 
-
+.itemlist .itemtype {
+  font-size: 10px;
+  color: #777777;
+}
+

trunk/www/views/physicalbioassays/view_bioassay.jsp

@@ -35 +35 @@
   import="net.sf.basedb.core.PhysicalBioAssay"
   import="net.sf.basedb.core.ArraySlide"
+  import="net.sf.basedb.core.BioMaterial"
   import="net.sf.basedb.core.BioMaterialEvent"
   import="net.sf.basedb.core.BioMaterialEventSource"
@@ -46 +47 @@
   import="net.sf.basedb.core.MultiPermissions"
   import="net.sf.basedb.core.ItemQuery"
+  import="net.sf.basedb.core.SpecialQuery"
   import="net.sf.basedb.core.Include"
-  import="net.sf.basedb.core.ItemResultList"
   import="net.sf.basedb.core.ItemResultList"
   import="net.sf.basedb.core.PermissionDeniedException"
@@ -56 +57 @@
   import="net.sf.basedb.core.query.Orders"
   import="net.sf.basedb.core.query.Hql"
+  import="net.sf.basedb.core.query.ResultList"
   import="net.sf.basedb.clients.web.Base"
   import="net.sf.basedb.clients.web.ChangeHistoryUtil"
@@ -326 +328 @@
       
       <%
-      ItemQuery<Extract> extractsQuery = (ItemQuery<Extract>)creationEvent.getSources();
-      extractsQuery.include(Include.ALL);
-      extractsQuery.order(Orders.asc(Hql.property("srcevt", "position")));
-      extractsQuery.order(Orders.asc(Hql.property("name")));
-      ItemResultList<Extract> extracts = extractsQuery.list(dc);
-      if (extracts.size() == 0)
+      SpecialQuery<BioMaterialEventSource> sourceQuery = creationEvent.getEventSources();
+      sourceQuery.order(Orders.asc(Hql.property("position")));
+      sourceQuery.order(Orders.asc(Hql.property("bioMaterial.name")));
+      ResultList<BioMaterialEventSource> sources = sourceQuery.list(dc);
+      if (sources.size() == 0)
       {
         %>
@@ -344 +345 @@
         <base:section
           id="extractSection"
-          title="<%="Extracts (" + extracts.size() + ")"%>"
+          title="<%="Extracts (" + sources.size() + ")"%>"
           context="<%=cc%>"
           >
@@ -378 +379 @@
             <tbl:rows>
             <%
-            for (Extract item : extracts)
+            for (BioMaterialEventSource item : sources)
             {
-              BioMaterialEventSource evtSrc = creationEvent.getEventSource(item);
+              BioMaterial bm = null;
+              try
+              {
+                bm = item.getBioMaterial();
+              }
+              catch (PermissionDeniedException ex)
+              {}
               %>
               <tbl:row>
-                <tbl:cell column="position"><%=evtSrc.getPosition()%></tbl:cell>
+                <tbl:cell column="position"><%=item.getPosition()%></tbl:cell>
                 <tbl:cell column="name"><base:icon 
                     image="deleted.gif" 
                     tooltip="This item has been scheduled for deletion" 
-                    visible="<%=item.isRemoved()%>"
-                  /><%=Base.getLinkedName(ID, item, false, true)%></tbl:cell>
-                <tbl:cell column="tag"><base:propertyvalue item="<%=item%>" property="tag" /></tbl:cell>
-                <tbl:cell column="quantity"><%=Values.formatNumber(evtSrc.getUsedQuantity(), 2)%></tbl:cell>
-                <tbl:cell column="description"><%=HTML.encodeTags(item.getDescription())%></tbl:cell>
+                    visible="<%=bm != null && bm.isRemoved()%>"
+                  /><%=Base.getLinkedName(ID, bm, bm == null, true)%></tbl:cell>
+                <tbl:cell column="tag" visible="<%=bm != null && bm.getType() == Item.EXTRACT%>"><base:propertyvalue item="<%=bm%>" property="tag" /></tbl:cell>
+                <tbl:cell column="quantity"><%=Values.formatNumber(item.getUsedQuantity(), 2)%></tbl:cell>
+                <tbl:cell column="description"><%=HTML.encodeTags(bm == null ? "" : bm.getDescription())%></tbl:cell>
               </tbl:row>
               <%