Changeset 5663

Timestamp:

Jun 22, 2011, 4:03:17 PM (12 years ago)

Author:

Nicklas Nordborg

Message:

References #1153: Handling short read transcript sequence data

Changed the way parent biomaterials are handled. The pooled property has been replaced with parentType instead. There are two reasons:

1. Removing the LabeledExtract class has changed all to Extract items which are not pooled.
2. It doesn't make sense to talk about "pooled" biomaterials when there is only a single parent.

The web gui for biosources and samples have been updated. Extracts does not work yet.

Overview loaders have been updated.

Batch importers need to be fixed. They currently assume a single parent of the parent item type.

Also added some of the button/select taglibs to provide more control over the look and feel in some cases.

Location:

trunk

Files:

• src/clients/web/net/sf/basedb/clients/web/plugins/ParentBioMaterialLoader.java (modified) (3 diffs)
• src/clients/web/net/sf/basedb/clients/web/taglib/Button.java (modified) (3 diffs)
• src/clients/web/net/sf/basedb/clients/web/taglib/Select.java (modified) (6 diffs)
• src/core/common-queries.xml (modified) (1 diff)
• src/core/net/sf/basedb/core/BioMaterial.java (modified) (2 diffs)
• src/core/net/sf/basedb/core/BioMaterialEvent.java (modified) (15 diffs)
• src/core/net/sf/basedb/core/BioSource.java (modified) (1 diff)
• src/core/net/sf/basedb/core/Extract.java (modified) (7 diffs)
• src/core/net/sf/basedb/core/MeasuredBioMaterial.java (modified) (7 diffs)
• src/core/net/sf/basedb/core/Sample.java (modified) (5 diffs)
• src/core/net/sf/basedb/core/data/MeasuredBioMaterialData.java (modified) (2 diffs)
• src/core/net/sf/basedb/util/biomaterial/ChildrenTransformer.java (moved) (moved from trunk/src/core/net/sf/basedb/util/biomaterial/PooledChildrenTransformer.java) (2 diffs)
• src/core/net/sf/basedb/util/biomaterial/ExtractToSampleTransformer.java (modified) (1 diff)
• src/core/net/sf/basedb/util/biomaterial/ListUtil.java (modified) (5 diffs)
• src/core/net/sf/basedb/util/biomaterial/ParentsTransformer.java (moved) (moved from trunk/src/core/net/sf/basedb/util/biomaterial/PooledParentsTransformer.java) (2 diffs)
• src/core/net/sf/basedb/util/biomaterial/SampleToBioSourceTransformer.java (modified) (1 diff)
• src/core/net/sf/basedb/util/biomaterial/SampleToExtractTransformer.java (modified) (1 diff)
• src/core/net/sf/basedb/util/overview/loader/BioSourceLoader.java (modified) (1 diff)
• src/core/net/sf/basedb/util/overview/loader/ExtractLoader.java (modified) (5 diffs)
• src/core/net/sf/basedb/util/overview/loader/SampleLoader.java (modified) (7 diffs)
• src/plugins/core/net/sf/basedb/plugins/batchimport/ExtractImporter.java (modified) (6 diffs)
• src/plugins/core/net/sf/basedb/plugins/batchimport/LabeledExtractImporter.java (modified) (5 diffs)
• src/plugins/core/net/sf/basedb/plugins/batchimport/SampleImporter.java (modified) (5 diffs)
• src/test/TestExtract.java (modified) (15 diffs)
• src/test/TestGenericOverview.java (modified) (1 diff)
• src/test/TestPhysicalBioAssay.java (modified) (1 diff)
• src/test/TestSample.java (modified) (15 diffs)
• src/test/net/sf/basedb/test/roles/UserTest.java (modified) (3 diffs)
• www/WEB-INF/base.tld (modified) (1 diff)
• www/biomaterials/biosources/view_biosource.jsp (modified) (4 diffs)
• www/biomaterials/events/view_event.jsp (modified) (5 diffs)
• www/biomaterials/lists/index.jsp (modified) (1 diff)
• www/biomaterials/samples/edit_sample.jsp (modified) (20 diffs)
• www/biomaterials/samples/index.jsp (modified) (5 diffs)
• www/biomaterials/samples/list_samples.jsp (modified) (8 diffs)
• www/biomaterials/samples/view_sample.jsp (modified) (8 diffs)
• www/images/select.png (added)
• www/include/styles/main.css (modified) (1 diff)

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

@@ -22 +22 @@
 package net.sf.basedb.clients.web.plugins;
 
+import net.sf.basedb.core.BioMaterial;
 import net.sf.basedb.core.DbControl;
 import net.sf.basedb.core.Include;
@@ -48 +49 @@
     Object parents = null;
     DbControl dc = item.getDbControl();
-    if (item.isPooled())
+    if (item.getParentType() == null)
     {
-      ItemQuery<? extends MeasuredBioMaterial> pooledQuery = item.getCreationEvent().getSources();
-      pooledQuery.include(Include.ALL);
-      parents = pooledQuery.list(dc);
+      // No parents
     }
-    else
+    else if (item.hasSingleParent())
     {
       try
@@ -63 +62 @@
       {}
     }
+    else
+    {
+      ItemQuery<? extends BioMaterial> pooledQuery = item.getCreationEvent().getSources();
+      pooledQuery.include(Include.ALL);
+      parents = pooledQuery.list(dc);
+    }
     return parents;
   }

trunk/src/clients/web/net/sf/basedb/clients/web/taglib/Button.java

@@ -175 +175 @@
     defaultImages.put("remove", "remove.png");
     defaultImages.put("browse", "browse.png");
+    defaultImages.put("select", "select.png");
   }
   
@@ -316 +317 @@
       if (!isDisabled())
       {
-        sb.append(" onmouseover=\"this.className='").append(getClazz()).append("_hover';\"");
-        sb.append(" onmouseout=\"this.className='").append(getClazz()).append("';\"");
+        //sb.append(" onmouseover=\"this.className='").append(getClazz()).append("_hover';\"");
+        //sb.append(" onmouseout=\"this.className='").append(getClazz()).append("';\"");
       }
     }
@@ -332 +333 @@
         theImage = page.getRoot() + "images/" + theImage;
       }
-      sb.append("<table border=\"0\" cellspacing=\"0\" cellpadding=\"0\"><tr><td>");
+      sb.append("<table border=\"0\" cellspacing=\"0\" cellpadding=\"0\"><tr><td style=\"width: 20px;\">");
       sb.append("<img src=\"").append(theImage).append("\"");
       sb.append(" border=\"0\">");
-      sb.append("</td><td>");
+      sb.append("</td><td style=\"text-align: left;\">");
     }
     sb.append(getTitle());

trunk/src/clients/web/net/sf/basedb/clients/web/taglib/Select.java

@@ -59 +59 @@
       clazz=...
       style=...
+      buttonclass=...
+      buttonstyle=...
+      buttontitle=...
+      buttonicon=...
       required=true|false
       current=...
@@ -111 +115 @@
   </tr>
   <tr>
+    <td>buttonclass</td>
+    <td>buttonclass</td>
+    <td>no</td>
+    <td>
+      The value if this attribute goes directly into the standard HTML 
+      <code>class</code> attribute for the "Select" button part. This allows you to
+      apply different styles to the button. If the button is disabled "_disabled" is
+      appended to the class name.
+    </td>
+  </tr>
+  <tr>
+    <td>buttonstyle</td>
+    <td>-</td>
+    <td>no</td>
+    <td>
+      The value if this attribute goes directly into the standard HTML 
+      <code>style</code> attribute for the "Select" button part. This allows you to
+      apply different styles to the button. 
+    </td>
+  </tr>
+  <tr>
+    <td>buttontitle</td>
+    <td>Select</td>
+    <td>no</td>
+    <td>
+      The text on the "Select" button.
+    </td>
+  </tr>
+  <tr>
+    <td>buttonicon</td>
+    <td>select.png</td>
+    <td>no</td>
+    <td>
+      The icon to use on the "Select" button.
+    </td>
+  </tr>
+  <tr>
     <td>required</td>
     <td>false</td>
@@ -242 +283 @@
   private String style = null;
 
+  private String buttonclass = "buttonclass";
+  private String buttonstyle = null;
+  private String buttontitle = "Select&hellip;";
+  private String buttonicon = "select.png";
+  
   /**
     If a value is required or not.
@@ -331 +377 @@
     return style;
   }
+  /**
+    @since 3.0
+  */
+  public void setButtonclass(String clazz)
+  {
+    this.buttonclass = clazz;
+  }
+  /**
+    @since 3.0
+  */
+  public String getButtonclass()
+  {
+    return buttonclass;
+  }
+  /**
+    @since 3.0
+  */
+  public void setButtonstyle(String style)
+  {
+    this.buttonstyle = style;
+  }
+  /**
+    @since 3.0
+  */
+  public String getButtonstyle()
+  {
+    return buttonstyle;
+  }
+  /**
+    @since 3.0
+  */
+  public void setButtontitle(String title)
+  {
+    this.buttontitle = title;
+  }
+  /**
+    @since 3.0
+  */
+  public String getButtontitle()
+  {
+    return buttontitle;
+  }
+  /**
+    @since 3.0
+  */
+  public void setButtonicon(String icon)
+  {
+    this.buttonicon = icon;
+  }
+  /**
+    @since 3.0
+  */
+  public String getButtonicon()
+  {
+    return buttonicon;
+  }
   
   public void setRequired(boolean required)
@@ -454 +556 @@
   {
     if (!isVisible()) return SKIP_BODY;
-//    Page page = (Page)findAncestorWithClass(this, Page.class);
+    Page page = (Page)findAncestorWithClass(this, Page.class);
 
     tryGetDirectoryPath = true;
@@ -536 +638 @@
     {
       sb.append("<td>");
-      sb.append("<div class=\"buttonclass").append(disabled ? "_disabled": "").append("\"");
+      sb.append("<div class=\"").append(getButtonclass()).append(disabled ? "_disabled": "").append("\"");
       if (!disabled)
       {
-        sb.append(" onmouseover=\"this.className='buttonclass_hover';\" onmouseout=\"this.className='buttonclass';\"");
+        //sb.append(" onmouseover=\"this.className='buttonclass_hover';\" onmouseout=\"this.className='buttonclass';\"");
         sb.append(" onclick=\"").append(getOnselect()).append("\"");
       }
-      sb.append("><div class=\"buttonclass_inner\">Select&hellip;</div></div>");
+      if (getButtonstyle() != null)
+      {
+        sb.append("style=\"").append(getButtonstyle()).append("\"");
+      }
+      sb.append("><div class=\"").append(getButtonclass()).append("_inner\">");
+      String buttonImg = getButtonicon();
+      if (buttonImg != null)
+      {
+        if (!buttonImg.startsWith("/"))
+        {
+          buttonImg = page.getRoot() + "images/" + buttonImg;
+        }
+        sb.append("<table border=\"0\" cellspacing=\"0\" cellpadding=\"0\"><tr><td style=\"width: 20px;\">");
+        sb.append("<img src=\"").append(buttonImg).append("\" border=\"0\"></td><td style=\"text-align: left;\">");
+      }
+      sb.append(getButtontitle());
+      if (buttonImg != null)
+      {
+        sb.append("</td></tr></table>");
+      }
+      sb.append("</div></div>");
       sb.append("</td>\n");
     }

trunk/src/core/common-queries.xml

@@ -1091 +1091 @@
       FROM BioMaterialEventData bme
       JOIN bme.sources src
-      WHERE index(src) = :bioMaterial
+      WHERE src.bioMaterial = :bioMaterial
     </sql>
     <description>

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

@@ -26 +26 @@
 import net.sf.basedb.core.Transactional.Action;
 import net.sf.basedb.core.data.BioMaterialData;
+import net.sf.basedb.core.query.Hql;
+import net.sf.basedb.core.query.Restrictions;
 
 /**
@@ -167 +169 @@
   */
   public abstract long countChildren(boolean pooled);
+
+  /**
+    Get a query returning all events where this biomaterial has been used
+    as a source item.
+    @return A special query
+    @since 3.0
+  */
+  public SpecialQuery<BioMaterialEventSource> getChildCreationEvents()
+  {
+    SpecialQuery<BioMaterialEventSource> query = 
+      new SpecialQuery<BioMaterialEventSource>(null, "BioMaterialEventSourceData", "es", 
+          new BioMaterialEventSource.BioMaterialEventSourceTransformer());
+    query.restrictPermanent(Restrictions.eq(Hql.property("es", "bioMaterial"), Hql.entity(this)));
+    return query;
+  }
   
 }

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

@@ -331 +331 @@
   
     DbControl dc = getDbControl();
-    Subtypable parent = null;
-    ItemSubtype protocolSubtype = null;
-    ItemSubtype hardwareSubtype = null;
+    Subtypable createdItem = null;
     String defaultProtocolId = null;
     if (getEventType() == Type.BIOASSAY)
     {
-      parent = getPhysicalBioAssay();
+      createdItem = getPhysicalBioAssay();
     }
     else
     {
       MeasuredBioMaterial bioMaterial = getBioMaterial();
-      parent = bioMaterial;
-      Item parentType = parent.getType();
-      if (bioMaterial.isPooled())
-      {
-        defaultProtocolId = Protocol.POOLING;
-      }
-      else if (parentType == Item.SAMPLE)
+      createdItem = bioMaterial;
+      Item parentType = createdItem.getType();
+      if (parentType == Item.SAMPLE)
       {
         defaultProtocolId = Protocol.SAMPLING;
@@ -357 +351 @@
       }
     }
-    protocolSubtype = ItemSubtype.getRelatedSubtype(dc, parent, Item.PROTOCOL, SystemItems.getId(defaultProtocolId));
-    hardwareSubtype = ItemSubtype.getRelatedSubtype(dc, parent, Item.HARDWARE, 0);
-    
-    if (!protocolHasBeenSet && protocolSubtype != null)
-    {
-      ProtocolData protocol = 
-        (ProtocolData)activeProject.findDefaultData(Item.PROTOCOL, protocolSubtype.getData(), false);
-      if (protocol != null) getData().setProtocol(protocol);
-      protocolHasBeenSet = true;
-    }
-    if (!hardwareHasBeenSet && hardwareSubtype != null)
+    
+    if (!protocolHasBeenSet)
+    {
+      ItemSubtype protocolSubtype = 
+        ItemSubtype.getRelatedSubtype(dc, createdItem, Item.PROTOCOL, SystemItems.getId(defaultProtocolId));
+      if (protocolSubtype != null)
+      {
+        ProtocolData protocol = 
+          (ProtocolData)activeProject.findDefaultData(Item.PROTOCOL, protocolSubtype.getData(), false);
+        if (protocol != null)
+        {
+          getData().setProtocol(protocol);
+          protocolHasBeenSet = true;
+        }
+      }
+    }
+    if (!hardwareHasBeenSet)
     {
       HardwareData hardware = 
-        (HardwareData)activeProject.findDefaultData(Item.HARDWARE, hardwareSubtype.getData(), false);
-      if (hardware != null) getData().setHardware(hardware);
-      hardwareHasBeenSet = true;
+        (HardwareData)activeProject.findDefaultRelatedData(dc, createdItem, Item.HARDWARE, false);
+      if (hardware != null) 
+      {
+        getData().setHardware(hardware);
+        hardwareHasBeenSet = true;
+      }
     }
   }
@@ -618 +621 @@
   
   /**
-    Add a biomaterial as a source to this event. If the given biomaterial
-    already is a source, the existing information is returned.
-    
-    @param bioMaterial The biomaterial
+    Set a single parent item for this event. Any sources
+    that are currently associated with it are removed and
+    the used quantity is returned.
+    
+    @param parent The parent biomaterial, or null to remove all parents
+    @since 3.0
+  */
+  public BioMaterialEventSource setSource(BioMaterial parent)
+  {
+    checkPermission(Permission.RESTRICTED_WRITE);
+    if (parent != null) 
+    {
+      parent.checkPermission(Permission.USE);
+      checkAllowedSource(parent, false);
+    }
+    clearSources();
+    BioMaterialEventSource eventSource = null;
+    if (parent != null) 
+    {
+      eventSource = addCheckedSource(parent);
+    }
+    return eventSource;
+  }
+
+  /**
+    Add a biomaterial as a source to this event. If the given 
+    biomaterial already is a source, the existing information is 
+    returned. If this event already has sources the new source
+    must be of the same type as the existing sources and the
+    produced biomaterial.
+    
+    @param bioMaterial The biomaterial (null is not allowed)
     @return A BioMaterialEventSource object
+    @since 3.0
   */
   public BioMaterialEventSource addSource(BioMaterial bioMaterial)
@@ -629 +661 @@
     if (bioMaterial == null) throw new InvalidUseOfNullException("bioMaterial");
     bioMaterial.checkPermission(Permission.USE);
-    checkAllowedSource(bioMaterial);
+    
+    checkAllowedSource(bioMaterial, true);
     return addCheckedSource(bioMaterial);
   }
@@ -636 +669 @@
   {
     BioMaterialData bmData = (BioMaterialData)bioMaterial.getData();
-    BioMaterialEventSourceData src = getData().getSources().get(bmData);
+    
+    Map<BioMaterialData, BioMaterialEventSourceData> sources = getData().getSources();
+    
+    BioMaterialEventSourceData src = sources.get(bmData);
     if (src == null)
     {
@@ -642 +678 @@
       src.setBioMaterial(bmData);
       src.setEvent(this.getData());
-      getData().getSources().put(bmData, src);
-    }
+      sources.put(bmData, src);
+    }
+
+    if (getData().getBioMaterial() != null)
+    {
+      // If the product is a biomaterial we may need to set parent + parent type
+      MeasuredBioMaterialData product = getData().getBioMaterial();
+      if (sources.size() == 1)
+      {
+        // This is the first parent
+        product.setParentType(bioMaterial.getType().getValue());
+        product.setParent(bmData);
+      }
+      else
+      {
+        // Clear if we get more than one parent
+        product.setParent(null);
+      }
+    }
+
     return new BioMaterialEventSource(getDbControl(), src);
   }
@@ -657 +711 @@
       biomaterial is of another type
     @throws BaseException If there is another error
+    @since 3.0
   */
   public void removeSource(BioMaterial bioMaterial)
@@ -663 +718 @@
     checkPermission(Permission.RESTRICTED_WRITE);
     if (bioMaterial == null) throw new InvalidUseOfNullException("bioMaterial");
-    checkAllowedSource(bioMaterial);
     BioMaterialData data = (BioMaterialData)bioMaterial.getData();
-    BioMaterialEventSourceData src = getData().getSources().remove(data);
+    Map<BioMaterialData, BioMaterialEventSourceData> sources = getData().getSources();
+    BioMaterialEventSourceData src = sources.remove(data);
+    
+    if (sources.size() == 0)
+    {
+      if (getData().getBioMaterial() != null)
+      {
+        getData().getBioMaterial().setParentType(null);
+      }
+    }
+    
     if (src == null) return;
     
@@ -680 +744 @@
 
   /**
-    Check if the biomaterial is allowed as a source. It is allowed if:
-    <ul>
-    <li>This is a creation event
-    <li>The created biomaterial is pooled
-    <li>It is of the same type as the created biomaterial
-    <li>It is not the same item as the created biomaterial
-    </ul>
-  */
-  private void checkAllowedSource(BioMaterial bioMaterial)
+    Check if the biomaterial is allowed as a source.
+  */
+  private void checkAllowedSource(BioMaterial source, boolean forAdd)
     throws PermissionDeniedException, InvalidDataException, BaseException
   {
     Type eventType = getEventType();
+    Item sourceType = source.getType();
     switch (eventType)
     {
@@ -700 +759 @@
       case BIOASSAY:
       {
-        if (bioMaterial.getType() != Item.EXTRACT)
+        if (sourceType != Item.EXTRACT)
         {
           throw new InvalidDataException("The source for a physical bioassay must be an extract");
@@ -708 +767 @@
       case CREATION:
       {
-        MeasuredBioMaterial parent = getBioMaterial();
-        if (!parent.isPooled())
+        MeasuredBioMaterial product = getBioMaterial();
+        Item productType = product.getType();
+        Item parentType = product.getParentType();
+        
+        if (forAdd && parentType != null)
         {
-          throw new InvalidDataException("Non-pooled biomaterials can't have sources");
+          if (parentType != sourceType)
+          {
+            throw new InvalidDataException("Can't add '" + source.getName() + "' (" + sourceType + 
+                ") as parent since there is already a " + parentType + " parent");
+          }
         }
-        else if (bioMaterial.getType() != parent.getType())
+        
+        if (productType != sourceType)
         {
-          throw new InvalidDataException("The source biomaterial must be of the same type as the produced biomaterial");
+          if (productType == Item.EXTRACT && sourceType != Item.SAMPLE)
+          {
+            throw new InvalidDataException("The parent for an extract must be an extract or sample: " + source);
+          }
+          if (productType == Item.SAMPLE && sourceType != Item.BIOSOURCE)
+          {
+            throw new InvalidDataException("The parent for a sample must be a biosource or sample: " + source);
+          }
         }
-        else if (bioMaterial.equals(parent))
+        
+        if (source.equals(product))
         {
-          throw new InvalidDataException("The source biomaterial cannot be the same as the produced biomaterial");
+          throw new InvalidDataException("The parent biomaterial cannot be the same as the produced biomaterial: " + source);
         }
         break;
@@ -731 +806 @@
 
   /**
-    Set a single source. This method is used for non-pooled biomaterial
-    to specify the parent. 
-    @see Extract#setSample(Sample)
-  */
-  BioMaterialEventSource setSource(MeasuredBioMaterial bioMaterial)
-    throws PermissionDeniedException, InvalidDataException
-  {
-    clearSources();
-    return bioMaterial == null ? null : addCheckedSource(bioMaterial);
-  }
-  
-  /**
     Clear the sources collection and return the used quantities to
     the source biomaterials.
-  */
-  void clearSources()
+    @since 3.0
+  */
+  public void clearSources()
   {
     DbControl dc = getDbControl();
-    for (BioMaterialEventSourceData src : getData().getSources().values())
+    Map<BioMaterialData, BioMaterialEventSourceData> sources = getData().getSources();
+    for (BioMaterialEventSourceData src : sources.values())
     {
       BioMaterialData bioMaterial = src.getBioMaterial();
@@ -759 +824 @@
       dc.getHibernateSession().delete(src);
     }
-    getData().getSources().clear();
+    sources.clear();
+    if (getData().getBioMaterial() != null)
+    {
+      getData().getBioMaterial().setParentType(null);
+      getData().getBioMaterial().setParent(null);
+    }
   }
 
@@ -780 +850 @@
     @return An {@link ItemQuery} object
   */
-  public ItemQuery<? extends MeasuredBioMaterial> getSources()
-  {
-    ItemQuery<? extends MeasuredBioMaterial> query = null;
+  public ItemQuery<? extends BioMaterial> getSources()
+  {
+    ItemQuery<? extends BioMaterial> query = null;
     MeasuredBioMaterialData bioMaterialData = getData().getBioMaterial();
-    boolean pooled = bioMaterialData != null ? bioMaterialData.isPooled() : false;
-    Item parentType = Item.fromDataObject(bioMaterialData == null ? getData().getPhysicalBioAssay() : bioMaterialData);
+    Item parentType = null;
+    if (getEventType() == Type.BIOASSAY)
+    {
+      parentType = Item.EXTRACT;
+    }
+    else
+    {
+      Integer tmp = getData().getBioMaterial().getParentType();
+      parentType = tmp != null ? Item.fromValue(tmp) : Item.fromDataObject(getData().getBioMaterial());
+    }
     switch (parentType)
     {
+      case EXTRACT:
+      {
+        query = Extract.getQuery();
+        break;
+      }
       case SAMPLE:
       {
@@ -793 +876 @@
         break;
       }
-      case EXTRACT:
-      {
-        if (pooled)
-        {
-          query = Extract.getQuery();
-        }
-        else
-        {
-          query = Sample.getQuery();
-        }
-        break;
-      }
-      case PHYSICALBIOASSAY:
-      {
-        query = Extract.getQuery();
+      case BIOSOURCE:
+      {
+        query = BioSource.getQuery();
         break;
       }

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

@@ -185 +185 @@
   {
     Sample s= Sample.getNew(getDbControl());
-    s.setBioSource(this);
+    s.getCreationEvent().setSource(this);
     return s;
   }

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

@@ -28 +28 @@
 
 import java.util.Set;
-import java.util.HashSet;
 
 /**
@@ -143 +142 @@
   {
     return TYPE;
-  }
-  // -------------------------------------------
-  /*
-    From the Annotatable interface
-    -------------------------------------------
-  */
-  /**
-    Get the sample or pooled extracts.
-  */
-  public Set<Annotatable> getAnnotatableParents()
-    throws BaseException
-  {
-    Set<Annotatable> annotatable = new HashSet<Annotatable>();
-    try
-    {
-      if (isPooled())
-      {
-        ItemQuery<? extends MeasuredBioMaterial> query = getCreationEvent().getSources();
-        query.include(Include.ALL);
-        annotatable.addAll(query.list(getDbControl()));
-      }
-      else if (getData().getParent() != null)
-      {
-        annotatable.add(getSample());
-      }
-    }
-    catch (PermissionDeniedException ex)
-    {}
-    return annotatable;
   }
   // -------------------------------------------
@@ -228 +198 @@
   // -------------------------------------------
 
+  /**
+    Get the tag that has been applied to this extract in order
+    to be able to distinguish it from other extracts on a 
+    physical bioassay.
+    @return A tag or null if the extract is not tagged
+    @since 3.0
+  */
   public Tag getTag()
   {
@@ -233 +210 @@
   }
   
+  /**
+    Set the tag that was applied to this extract in order
+    to be able to distinguish it from other extracts on a 
+    physical bioassay.
+    @param tag The tag, or null if the extract is not tagged
+    @since 3.0
+  */
   public void setTag(Tag tag)
   {
@@ -239 +223 @@
     getData().setTag(tag == null ? null : tag.getData());
   }
-  
-  /**
-    Get the {@link Sample} that is the parent of this extract.
-    @return A <code>Sample</code> object or null if this is a pooled or
-      standalone extract
-    @throws PermissionDeniedException If the logged in user doesn't have read
-      permission for the sample
-    @throws BaseException If there is another error
-  */
-  public Sample getSample()
-    throws PermissionDeniedException, BaseException
-  {
-    return getDbControl().getItem(Sample.class, getData().getParent());
-  }
-
-  /**
-    Set the {@link Sample} item that is the parent
-    of this extract.
-    @param sample The new <code>Sample</code> item
-    @throws PermissionDeniedException If the logged in user doesn't have 
-      write permission for this extract or use permission for the sample
-    @throws InvalidDataException If this is a pooled extract
-    @throws BaseException If there is another error
-    @since 3.0
-  */
-  public BioMaterialEventSource setSample(Sample sample)
-    throws PermissionDeniedException, InvalidDataException, BaseException
-  {
-    checkPermission(Permission.WRITE);
-    if (sample != null) sample.checkPermission(Permission.USE);
-    if (isPooled())
-    {
-      throw new InvalidDataException("A pooled extract can't have a parent sample");
-    }
-    getData().setParent(sample == null ? null : sample.getData());
-    return getCreationEvent().setSource(sample);
-  }
-  
-
-  public BioMaterialEventSource setExtract(Extract extract)
-    throws PermissionDeniedException, InvalidDataException, BaseException
-  {
-    checkPermission(Permission.WRITE);
-    if (extract != null) extract.checkPermission(Permission.USE);
-    
-    getData().setPooled(true);
-    getData().setParent(extract == null ? null : extract.getData());
-    return getCreationEvent().setSource(extract);
-  }
-
   
   /**
@@ -322 +256 @@
       FROM BioMaterialEventData bme
       JOIN bme.sources src
-      WHERE index(src) = :bioMaterial
+      WHERE src.bioMaterial = :bioMaterial
     */
     query.setEntity("bioMaterial", this.getData());
@@ -330 +264 @@
   /**
     Count the number of child extracts. Since an extract
-    can't have non-pooled children, this method always return 
-    0 if pooled = false.
+    can only have other extracts as children, this method always return 
+    0 if extractsOnly = false.
     @since 2.16
   */
   @Override
-  public long countChildren(boolean pooled)
-  {
-    return pooled ? countExtracts() : 0;
+  public long countChildren(boolean extractsOnly)
+  {
+    return extractsOnly ? countExtracts() : 0;
   }
 

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

@@ -25 +25 @@
 
 import java.util.Date;
+import java.util.HashSet;
 import java.util.Set;
 
@@ -31 +32 @@
 import net.sf.basedb.core.data.BioWellData;
 import net.sf.basedb.core.data.MeasuredBioMaterialData;
-import net.sf.basedb.core.query.Expressions;
-import net.sf.basedb.core.query.Hql;
-import net.sf.basedb.core.query.Restrictions;
 import net.sf.basedb.util.EqualsHelper;
 
@@ -87 +85 @@
       FROM BioMaterialEventData bme
       JOIN bme.sources src
-      WHERE index(src) = :bioMaterial
+      WHERE src.bioMaterial = :bioMaterial
     */
     query.setEntity("bioMaterial", this.getData());
@@ -110 +108 @@
         FROM BioMaterialEventData bme
         JOIN bme.sources src
-        WHERE index(src) = :bioMaterial
+        WHERE src.bioMaterial = :bioMaterial
       */
     query.setEntity("bioMaterial", this.getData());
@@ -173 +171 @@
   // -------------------------------------------
   /*
+    From the Annotatable interface
+    -------------------------------------------
+  */
+  /**
+    Get the biosource or pooled samples.
+  */
+  public Set<Annotatable> getAnnotatableParents()
+    throws BaseException
+  {
+    Set<Annotatable> annotatable = new HashSet<Annotatable>();
+    try
+    {
+      if (getData().getParent() != null)
+      {
+        annotatable.add(getParent());
+      }
+      else if (getParentType() != null)
+      {
+        ItemQuery<? extends BioMaterial> query = getCreationEvent().getSources();
+        query.include(Include.ALL);
+        annotatable.addAll(query.list(getDbControl()));
+      }
+    }
+    catch (PermissionDeniedException ex)
+    {}
+    return annotatable;
+  }
+  // -------------------------------------------
+
+  
+  /*
     From the Subtypable interface
     -----------------------------
@@ -290 +319 @@
   
   /**
-    Check if this biomaterial was created by pooling or not.
-    @return TRUE if pooled, FALSE otherwise. 
-  */
-  public boolean isPooled()
-  {
-    return getData().isPooled();
-  }
-  
-  /**
-    Specify if this biomaterial was created by pooling or not. Changing this property
-    also clears the parent biomaterial and the sources collection for the creation event.
-    @param pooled set to TRUE if pooled, FALSE otherwise.
-    @throws PermissionDeniedException If the logged in user doesn't have
-      write permission
-    @throws BaseException If there is another error
-    @see BioMaterialEvent#getSources()
-  */
-  public void setPooled(boolean pooled)
-    throws PermissionDeniedException, BaseException
-  {
-    checkPermission(Permission.WRITE);
-    boolean current = getData().isPooled();
-    if (current != pooled) 
-    {
-      getCreationEvent().clearSources();
-      getData().setParent(null);
-      getData().setPooled(pooled);
-    }
+    Get the item type of the parent biomaterial. The parent type
+    must be either the same type as the current biomaterial or "one
+    step up" in the Extract -- Sample -- BioSource chain.
+    @return The parent type, or null if the biomaterial doesn't have any parents
+    @since 3.0
+  */
+  public Item getParentType()
+  {
+    Integer parentType = getData().getParentType();
+    return parentType == null ? null : Item.fromValue(parentType);
+  }
+
+  /**
+    Get the parent biomaterial if there is a single parent item only.
+    @return The parent biomaterial or null if there is not exactly one
+      parent
+    @since 3.0
+    @see #hasSingleParent()
+   */
+  public BioMaterial getParent()
+  {
+    return getDbControl().getItem(BioMaterial.class, getData().getParent());
+  }
+  
+  /**
+    Checks if this biomaterial has a single parent item or not.
+    @return TRUE if there is exactly one parent, FALSE if there are
+      0 or 2 or more parents
+    @since 3.0
+    @see #getParentType()
+  */
+  public boolean hasSingleParent()
+  {
+    return getData().getParent() != null;
   }
   
@@ -355 +390 @@
   {
     return BioMaterialEvent.getQuery(this);
-  }
-  
-  /**
-    Get a query that returns all events where this biomaterial
-    has been used as a source.
-      @return An {@link ItemQuery} object
-      @since 2.9
-   */
-  public ItemQuery<BioMaterialEvent> getPoolingEvents()
-  {
-    ItemQuery<BioMaterialEvent> query = new ItemQuery<BioMaterialEvent>(BioMaterialEvent.class, null);
-    query.setDistinct(true);  // Otherwise, the join to sources can result in one copy for each source
-    query.joinPermanent(Hql.leftJoin("sources", "src"));
-    query.joinPermanent(Hql.leftJoin("bioMaterial", "bm"));
-    query.restrictPermanent(
-      Restrictions.and(
-        Restrictions.eq(
-          Hql.index("src", null), 
-          Hql.entity(this)
-        ),
-        Restrictions.eq(
-          Hql.property("bm", "pooled"), 
-          Expressions.parameter("isPooled", true, Type.BOOLEAN)
-        ),
-        Restrictions.eq(
-          Hql.property("eventType"),
-          Expressions.integer(BioMaterialEvent.Type.CREATION.getValue())
-        )
-      )
-    );
-    return query;   
   }
   

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

@@ -28 +28 @@
 
 import java.util.Set;
-import java.util.HashSet;
 
 /**
@@ -130 +129 @@
   {
     return TYPE;
-  }
-  // -------------------------------------------
-  /*
-    From the Annotatable interface
-    -------------------------------------------
-  */
-  /**
-    Get the biosource or pooled samples.
-  */
-  public Set<Annotatable> getAnnotatableParents()
-    throws BaseException
-  {
-    Set<Annotatable> annotatable = new HashSet<Annotatable>();
-    try
-    {
-      if (isPooled())
-      {
-        ItemQuery<? extends MeasuredBioMaterial> query = getCreationEvent().getSources();
-        query.include(Include.ALL);
-        annotatable.addAll(query.list(getDbControl()));
-      }
-      else if (getData().getParent() != null)
-      {
-        annotatable.add(getBioSource());
-      }
-    }
-    catch (PermissionDeniedException ex)
-    {}
-    return annotatable;
   }
   // -------------------------------------------
@@ -216 +186 @@
 
   /**
-    Get the {@link BioSource} that is the parent of this sample.
-    @return A <code>BioSource</code> object or null if this is a pooled or
-      standalone sample
-    @throws PermissionDeniedException If the logged in user doesn't have read
-      permission for the biosource
-    @throws BaseException If there is another error
-  */
-  public BioSource getBioSource()
-    throws PermissionDeniedException, BaseException
-  {
-    return getDbControl().getItem(BioSource.class, getData().getParent());
-  }
-  
-  /**
-    Set the {@link BioSource} item that is the parent
-    of this sample.
-    @param bioSource The parent <code>BioSource</code> item
-    @throws PermissionDeniedException If the logged in user doesn't have 
-      write permission for this sample or use permission for the biosource
-    @throws InvalidDataException If this is a pooled sample
-    @throws BaseException If there is another error
-  */
-  public void setBioSource(BioSource bioSource)
-    throws PermissionDeniedException, InvalidDataException
-  {
-    checkPermission(Permission.WRITE);
-    if (bioSource != null) bioSource.checkPermission(Permission.USE);
-    if (isPooled())
-    {
-      throw new InvalidDataException("A pooled sample can't have a parent biosource");
-    }
-    getData().setParent(bioSource == null ? null : bioSource.getData());
-  }
-  
-  /**
     Create a new {@link Extract} from this sample.
     @param usedQuantity The quantity used from this sample or null
@@ -281 +216 @@
   {
     Extract e = Extract.getNew(getDbControl(), master);
-    e.setSample(this).setUsedQuantity(usedQuantity);
+    e.getCreationEvent().setSource(e).setUsedQuantity(usedQuantity);
     return e;
   }
@@ -366 +301 @@
   /**
     Count the number of child samples or extracts.
-    @param pooled TRUE = count child samples, FALSE = count child extracts
+    @param samples TRUE = count child samples, FALSE = count child extracts
     @since 2.16
   */
   @Override
-  public long countChildren(boolean pooled)
-  {
-    return pooled ? countSamples() : countExtracts();
+  public long countChildren(boolean samples)
+  {
+    return samples ? countSamples() : countExtracts();
   }
 

trunk/src/core/net/sf/basedb/core/data/MeasuredBioMaterialData.java

@@ -45 +45 @@
   private BioMaterialData parent;
   /**
-    Get the parent biomaterial. Used for non-pooled biomaterials. The
-    core must add logic to check that only a biomaterial of the parent
-    type is linked.
+    Get the parent biomaterial. Used when a biomaterial has a single parent item.
     @hibernate.many-to-one column="`parent_id`" not-null="false" outer-join="false"
   */
@@ -87 +85 @@
   }
   
-  private boolean pooled;
+  private Integer parentType;
   /**
-    If the biomaterial was created by pooling other biomaterials of the same type
-    or not.
-    @hibernate.property column="`pooled`" type="boolean" not-null="false"
+    Get the type of the parent item. Null if the biomaterial doesn't have any parents.
+    @hibernate.property column="`parent_type`" type="int" not-null="false"
+    @since 3.0
   */
-  public boolean isPooled()
+  public Integer getParentType()
   {
-    return pooled;
+    return parentType;
   }
-  public void setPooled(boolean pooled)
+  public void setParentType(Integer parentType)
   {
-    this.pooled = pooled;
+    this.parentType = parentType;
   }
+
   private BioMaterialEventData creationEvent;
   /**

trunk/src/core/net/sf/basedb/util/biomaterial/ChildrenTransformer.java

@@ -40 +40 @@
 /**
   Collection transformer that given a collection of biomaterials
-  finds all pooled children (of the same type).
+  finds all children of the same type.
 
   @author Nicklas
-  @version 2.10
+  @since 3.0
   @base.modified $Date$
 */
-public class PooledChildrenTransformer<I extends MeasuredBioMaterial>
+public class ChildrenTransformer<I extends MeasuredBioMaterial>
   implements CollectionTransformer<I, I>
 {
@@ -54 +54 @@
   private final boolean copySources;
   
-  public PooledChildrenTransformer(DbControl dc, boolean copySources, ItemQuery<I> query)
+  public ChildrenTransformer(DbControl dc, boolean copySources, ItemQuery<I> query)
   {
     this.dc = dc;

trunk/src/core/net/sf/basedb/util/biomaterial/ExtractToSampleTransformer.java

@@ -46 +46 @@
   parents to the extract. If you want to follow pooled extracts up
   to samples, you should combine this transformer
-  and a {@link PooledParentsTransformer} with the help of a
+  and a {@link ParentsTransformer} with the help of a
   {@link MultiStepCollectionTransformer}.
 

trunk/src/core/net/sf/basedb/util/biomaterial/ListUtil.java

@@ -132 +132 @@
     @param sourceItem The type of source items
     @param destinationItem The type of destination items
-    @param pooled If pooled children/parents should be considered or not
+    @param sameType If children/parents of the same type should be considered or not
     @return A collection transformer (never null)
   */
   @SuppressWarnings("unchecked")
-  public static CollectionTransformer createTransformer(DbControl dc, Item sourceItem, Item destinationItem, boolean pooled)
+  public static CollectionTransformer createTransformer(DbControl dc, Item sourceItem, Item destinationItem, boolean sameType)
   {
     // The allowed item types
@@ -167 +167 @@
         {
           // Moving down
-          if (pooled) transformers.add(new PooledChildrenTransformer<Sample>(dc, true, Sample.getQuery()));
+          if (sameType) transformers.add(new ChildrenTransformer<Sample>(dc, true, Sample.getQuery()));
           transformers.add(new SampleToExtractTransformer(dc));
         }
@@ -173 +173 @@
         {
           // Moving up
-          if (pooled) transformers.add(new PooledParentsTransformer<Sample>(dc, true, Sample.getQuery()));
+          if (sameType) transformers.add(new ParentsTransformer<Sample>(dc, true, Sample.getQuery()));
           transformers.add(new SampleToBioSourceTransformer(dc));
         }
@@ -182 +182 @@
         {
           // Moving down
-          if (pooled) transformers.add(new PooledChildrenTransformer<Extract>(dc, true, Extract.getQuery()));
+          if (sameType) transformers.add(new ChildrenTransformer<Extract>(dc, true, Extract.getQuery()));
         }
         else
         {
           // Moving up
-          if (pooled) transformers.add(new PooledParentsTransformer<Extract>(dc, true, Extract.getQuery()));
+          if (sameType) transformers.add(new ParentsTransformer<Extract>(dc, true, Extract.getQuery()));
           transformers.add(new ExtractToSampleTransformer(dc));
         }
@@ -201 +201 @@
     }
     
-    if (pooled && destinationItem != Item.BIOSOURCE)
+    if (sameType && destinationItem != Item.BIOSOURCE)
     {
       if (step == 1)
       {
         // Moving down
-        transformers.add(new PooledChildrenTransformer(dc, true, getQuery(destinationItem)));
+        transformers.add(new ChildrenTransformer(dc, true, getQuery(destinationItem)));
       }
       else
       {
         // Moving up
-        transformers.add(new PooledParentsTransformer(dc, true, getQuery(destinationItem)));
+        transformers.add(new ParentsTransformer(dc, true, getQuery(destinationItem)));
       }
     }

trunk/src/core/net/sf/basedb/util/biomaterial/ParentsTransformer.java

@@ -39 +39 @@
 
 /**
-  Collection transformer that given a collection of (pooled) 
-  biomaterials finds all parents (of the same type).
+  Collection transformer that given a collection of 
+  biomaterials finds all parents of the same type
 
   @author Nicklas
-  @version 2.10
+  @since 3.0
   @base.modified $Date$
 */
-public class PooledParentsTransformer<I extends MeasuredBioMaterial>
+public class ParentsTransformer<I extends MeasuredBioMaterial>
   implements CollectionTransformer<I, I>
 {
@@ -54 +54 @@
   private final boolean copySources;
   
-  public PooledParentsTransformer(DbControl dc, boolean copySources, ItemQuery<I> query)
+  public ParentsTransformer(DbControl dc, boolean copySources, ItemQuery<I> query)
   {
     this.dc = dc;

trunk/src/core/net/sf/basedb/util/biomaterial/SampleToBioSourceTransformer.java

@@ -46 +46 @@
   parents to the samples. If you want to follow pooled samples up
   to biosources, you should combine this transformer
-  and a {@link PooledParentsTransformer} with the help of a
+  and a {@link ParentsTransformer} with the help of a
   {@link MultiStepCollectionTransformer}.
 

trunk/src/core/net/sf/basedb/util/biomaterial/SampleToExtractTransformer.java

@@ -45 +45 @@
   children to the samples. If you want to include extracts that are
   children to pooled samples, you should combine this transformer
-  with a {@link PooledChildrenTransformer} with the help of a
+  with a {@link ChildrenTransformer} with the help of a
   {@link MultiStepCollectionTransformer}.
 

trunk/src/core/net/sf/basedb/util/overview/loader/BioSourceLoader.java

@@ -68 +68 @@
     {
       Sample sample = (Sample)sampleNode.getItem(dc);
-      bioSource = sample.getBioSource();
+      bioSource = (BioSource)sample.getParent();
     }
     catch (PermissionDeniedException ex)

trunk/src/core/net/sf/basedb/util/overview/loader/ExtractLoader.java

@@ -30 +30 @@
 import net.sf.basedb.core.ItemQuery;
 import net.sf.basedb.core.ItemResultIterator;
-import net.sf.basedb.core.RawBioAssay;
 import net.sf.basedb.core.Sample;
 import net.sf.basedb.util.overview.Fix;
@@ -106 +105 @@
     else if (parentItem == Item.EXTRACT)
     {
-      returnNode = createReverseNode((Extract)parentNode.getItem(dc), dc, context, parentNode);
+      Extract e = (Extract)parentNode.getItem(dc);
+      if (e.hasSingleParent())
+      {
+        createSingleParentReverseNode(e, dc, context, parentNode);
+      }
+      else
+      {
+        returnNode = createPooledReverseNode(e, dc, context, parentNode);
+      }
     }
     else if (parentItem == Item.DERIVEDBIOASSAY)
@@ -160 +167 @@
   {
     Extract extract = (Extract)extractNode.getItem();
-    if (extract.isPooled())
+    if (extract.getParentType() == Item.EXTRACT)
     {
       getNodeLoader(context, Item.EXTRACT).createReverseNode(dc, context, extractNode);
@@ -175 +182 @@
   */
   @SuppressWarnings("unchecked")
-  private Node createReverseNode(Extract product, DbControl dc, OverviewContext context, Node parentNode)
+  private Node createPooledReverseNode(Extract product, DbControl dc, OverviewContext context, Node parentNode)
   {
     NodeFactory<Extract> nf = getNodeFactory(dc, context);
@@ -212 +219 @@
 
   /**
+    Create a reverse-loading extract node from an extract. Eg. the child node
+    is the extract that is the parent of the (non-pooled) extract.
+  */
+  private Node createSingleParentReverseNode(Extract bioMaterial, DbControl dc, OverviewContext context, Node parentNode)
+  {
+    NodeFactory<Extract> nf = getNodeFactory(dc, context);
+    Extract extract = null;
+    boolean denied = false;
+    try
+    {
+      extract = (Extract)bioMaterial.getParent();
+    }
+    catch (PermissionDeniedException ex)
+    {
+      denied = true;
+    }
+    Node sampleNode = createItemNode(nf, extract, extract, denied, 
+        parentNode, ChildNodeDirection.REVERSE);
+    return sampleNode;
+  }
+
+  /**
     Create reverse-loading extract nodes from a physical bioassay. Eg. the child nodes
     are the extracts that has been used on a bioassay.

trunk/src/core/net/sf/basedb/util/overview/loader/SampleLoader.java

@@ -21 +21 @@
 */
 package net.sf.basedb.util.overview.loader;
+
+import java.util.Iterator;
 
 import net.sf.basedb.core.BioSource;
@@ -28 +30 @@
 import net.sf.basedb.core.ItemQuery;
 import net.sf.basedb.core.ItemResultIterator;
+import net.sf.basedb.core.MeasuredBioMaterial;
 import net.sf.basedb.core.PermissionDeniedException;
 import net.sf.basedb.core.Sample;
@@ -99 +102 @@
     if (parentType == Item.EXTRACT)
     {
-      returnNode = createReverseNode((Extract)parentNode.getItem(dc), dc, context, parentNode);
+      returnNode = createSingleParentReverseNode((Extract)parentNode.getItem(dc), dc, context, parentNode);
     }
     else if (parentType == Item.SAMPLE)
     {
-      returnNode = createReverseNode((Sample)parentNode.getItem(dc), dc, context, parentNode);
+      Sample s = (Sample)parentNode.getItem(dc);
+      if (s.hasSingleParent())
+      {
+        createSingleParentReverseNode(s, dc, context, parentNode);
+      }
+      else
+      {
+        returnNode = createPooledReverseNode(s, dc, context, parentNode);
+      }
     }
     return returnNode;
@@ -150 +161 @@
   {
     Sample sample = (Sample)sampleNode.getItem();
-    if (sample.isPooled())
+    if (sample.getParentType() == Item.SAMPLE)
     {
       getNodeLoader(context, Item.SAMPLE).createReverseNode(dc, context, sampleNode);
@@ -162 +173 @@
   
   /**
-    Create reverse-loading samples nodes of a pooled sample. Eg. the child nodes
-    are the source samples that was pooled to create the given product.
+    Create reverse-loading samples nodes of a sample with other sample(s) as parent items. 
+    Eg. the child nodes are the source sample(s) that was used to create the given product.
   */
   @SuppressWarnings("unchecked")
-  private Node createReverseNode(Sample product, DbControl dc, OverviewContext context, Node parentNode)
+  private Node createPooledReverseNode(Sample product, DbControl dc, OverviewContext context, Node parentNode)
   {
     NodeFactory<Sample> nf = getNodeFactory(dc, context);
     Node folderNode = null;
     ItemQuery<Sample> query = (ItemQuery<Sample>)context.initQuery(product.getCreationEvent().getSources(), "name");
-    ItemResultIterator<Sample> it = query.iterate(dc);
+    Iterator<Sample> it = query.iterate(dc);
     int numSamples = 0;
     while (it.hasNext())
@@ -202 +213 @@
 
   /**
-    Create a reverse-loading sample node from an extract. Eg. the child node
-    is the sample that is the parent of the (non-pooled) extract.
-  */
-  private Node createReverseNode(Extract extract, DbControl dc, OverviewContext context, Node parentNode)
+    Create a reverse-loading sample node from an extract or sample. Eg. the child node
+    is the sample that is the parent of the (non-pooled) extract/sample.
+  */
+  private Node createSingleParentReverseNode(MeasuredBioMaterial bioMaterial, DbControl dc, OverviewContext context, Node parentNode)
   {
     NodeFactory<Sample> nf = getNodeFactory(dc, context);
@@ -212 +223 @@
     try
     {
-      sample = extract.getSample();
+      sample = (Sample)bioMaterial.getParent();
     }
     catch (PermissionDeniedException ex)

trunk/src/plugins/core/net/sf/basedb/plugins/batchimport/ExtractImporter.java

@@ -202 +202 @@
     if (pooledMapper != null)
     {
-      extract.setPooled(Values.getBoolean(pooledMapper.getValue(data)));
+      //extract.setPooled(Values.getBoolean(pooledMapper.getValue(data)));
     }
 
@@ -216 +216 @@
     {
       String nameOrId = protocolMapper.getValue(data);
-      ItemSubtype type = ItemSubtype.getRelatedSubtype(dc, extract, Item.PROTOCOL, 
-          SystemItems.getId(extract.isPooled() ? Protocol.POOLING : Protocol.EXTRACTION));
+      ItemSubtype type = ItemSubtype.getRelatedSubtype(dc, extract, Item.PROTOCOL, SystemItems.getId(Protocol.EXTRACTION));
       Protocol protocol = findProtocol(dc, FallbackIdMethod.NAME_OR_EXTERNALID_OR_ID, nameOrId, type);
       if (nameOrId == null || protocol != null) creationEvent.setProtocol(protocol);
@@ -233 +232 @@
       }
     }
+    /*
     if (!extract.isPooled())
     {
+    */
       if (parentMapper != null)
       {
@@ -244 +245 @@
         if (nameOrId == null || sample != null) 
         {
-          BioMaterialEventSource evtSrc = extract.setSample(sample);
+          BioMaterialEventSource evtSrc = extract.getCreationEvent().setSource(sample);
           if (evtSrc != null) evtSrc.setUsedQuantity(usedQuantity);
         }
       }
+      /*
     }
     else
@@ -253 +255 @@
       updateMultiLineItem(dc, extract, data, 0);
     }
+    */
   }
   
@@ -262 +265 @@
     FlatFileParser.Data data, int multiLineNum)
   {
-    if (parentMapper != null && extract.isPooled())
+    if (parentMapper != null) // && extract.isPooled())
     {
       String nameOrId = parentMapper.getValue(data);

trunk/src/plugins/core/net/sf/basedb/plugins/batchimport/LabeledExtractImporter.java

@@ -206 +206 @@
     if (pooledMapper != null)
     {
-      extract.setPooled(Values.getBoolean(pooledMapper.getValue(data)));
+      //extract.setPooled(Values.getBoolean(pooledMapper.getValue(data)));
     }
     if (protocolMapper != null) 
     {
       String nameOrId = protocolMapper.getValue(data);
-      ItemSubtype type = ItemSubtype.getById(dc, 
-          SystemItems.getId(extract.isPooled() ? Protocol.POOLING : Protocol.LABELING));
+      ItemSubtype type = ItemSubtype.getById(dc, SystemItems.getId(Protocol.LABELING));
       Protocol protocol = findProtocol(dc, FallbackIdMethod.NAME_OR_EXTERNALID_OR_ID, nameOrId, type);
       if (nameOrId == null || protocol != null) creationEvent.setProtocol(protocol);
@@ -237 +236 @@
       }
     }
+    /*
     if (!extract.isPooled())
     {
+    */
       if (parentMapper != null)
       {
@@ -247 +248 @@
         if (nameOrId == null || parent != null) 
         {
-          BioMaterialEventSource evtSrc = extract.setExtract(parent);
+          BioMaterialEventSource evtSrc = extract.getCreationEvent().setSource(parent);
           if (evtSrc != null) evtSrc.setUsedQuantity(usedQuantity);
         }
       }
+      /*
     }
     else
@@ -256 +258 @@
       updateMultiLineItem(dc, extract, data, 0);
     }
+    */
   }
   
@@ -265 +268 @@
     FlatFileParser.Data data, int multiLineNum)
   {
-    if (parentMapper != null && extract.isPooled())
+    if (parentMapper != null) // && extract.isPooled())
     {
       String nameOrId = parentMapper.getValue(data);

trunk/src/plugins/core/net/sf/basedb/plugins/batchimport/SampleImporter.java

@@ -297 +297 @@
     if (pooledMapper != null)
     {
-      sample.setPooled(Values.getBoolean(pooledMapper.getValue(data)));
+      //sample.setPooled(Values.getBoolean(pooledMapper.getValue(data)));
     }
     if (protocolMapper != null) 
     {
       String nameOrId = protocolMapper.getValue(data);
-      ItemSubtype type = ItemSubtype.getRelatedSubtype(dc, sample, Item.PROTOCOL, 
-          SystemItems.getId(sample.isPooled() ? Protocol.POOLING : Protocol.SAMPLING));
+      ItemSubtype type = ItemSubtype.getRelatedSubtype(dc, sample, Item.PROTOCOL, SystemItems.getId(Protocol.SAMPLING));
       Protocol protocol = findProtocol(dc, FallbackIdMethod.NAME_OR_EXTERNALID_OR_ID, nameOrId, type);
       if (nameOrId == null || protocol != null) creationEvent.setProtocol(protocol);
@@ -319 +318 @@
       }
     }
+    /*
     if (!sample.isPooled())
     {
+    */
       if (parentMapper != null)
       {
@@ -326 +327 @@
         ItemSubtype type = ItemSubtype.getRelatedSubtype(dc, sample, Item.BIOSOURCE, 0);
         BioSource bioSource = findBioSource(dc, FallbackIdMethod.NAME_OR_EXTERNALID_OR_ID, nameOrId, type);
-        if (nameOrId == null || bioSource != null) sample.setBioSource(bioSource);
+        if (nameOrId == null || bioSource != null) sample.getCreationEvent().setSource(bioSource);
       }
+      /*
     }
     else
@@ -333 +335 @@
       updateMultiLineItem(dc, sample, data, 0);
     }
+    */
   }
   
@@ -342 +345 @@
     FlatFileParser.Data data, int multiLineNum)
   {
-    if (parentMapper != null && sample.isPooled())
+    if (parentMapper != null) // && sample.isPooled())
     {
       String nameOrId = parentMapper.getValue(data);

trunk/src/test/TestExtract.java

@@ -23 +23 @@
 */
 import net.sf.basedb.core.*;
-
+import net.sf.basedb.core.query.ResultList;
+import net.sf.basedb.util.biomaterial.ChildrenTransformer;
+import net.sf.basedb.util.biomaterial.ExtractToSampleTransformer;
+import net.sf.basedb.util.biomaterial.ParentsTransformer;
+import net.sf.basedb.util.biomaterial.SampleToExtractTransformer;
+
+import java.util.Collections;
 import java.util.Date;
+import java.util.LinkedHashSet;
 import java.util.Set;
 
@@ -47 +54 @@
     int tagId = TestTag.test_create("Test", SystemItems.getId(Tag.LABEL), true);
     int id = test_create(0, "Extract #1 (standalone)", 0, 0, true);
-    int id2 = test_create(sampleId, "Extract #2", 0, 0, false);
-    int id3 = test_create(id2, "Extract #3 (labeled)", SystemItems.getId(Extract.LABELED), tagId, false);
-    int id4 = test_create_pooled(id, id2, id3);
-
+    int id2 = test_create(sampleId, "Extract #2 (sample parent)", 0, 0, false);
+    int id3 = test_create(id, "Extract #3 (extract parent+labeled)", SystemItems.getId(Extract.LABELED), tagId, false);
+    int id4 = test_create_pooled("Extract #4 (pooled)", id, id2, id3);
+
+  
     test_load(id);
     test_list(-1);
@@ -56 +64 @@
     write_events_header();
     test_add_event(id, 100.0f);
-    test_list_events(id, 3);  // creation event, pooling event for id4, and extra event
+    test_list_events(id, 4);  // creation event, create event for id3+id4, and extra event
     
-    write_sources_header();
-    test_list_sources(id3, 1); // The sample
-    test_list_sources(id4, 3); // The three id, id2 and id3 extracts
-    test_list_pooledChildren(id2, 2);
-
+    write_parents_header();
+    test_list_sources(id4, 3); // The three id, id2 and id3 samples
+    test_list_children(id, 2); // id3 and id4
+
+    // Transformers
+    test_childrenTransformer(id, 2);
+    test_parentsTransformer(id4, 3);
+    test_extractToSampleTransformer(id2, 1);
+    test_sampleToExtractTransformer(sampleId, 1);
+
+    
     if (TestUtil.waitBeforeDelete()) TestUtil.waitForEnter();
     // Standard test: Delete
@@ -94 +108 @@
       {
         BioMaterial parent = BioMaterial.getById(dc, parentId);
-        if (parent.getType() == Item.SAMPLE)
-        {
-          Sample s = (Sample)parent;
-          e.setSample(s).setUsedQuantity(200.0f);
-        }
-        else
-        {
-          e.setPooled(true);
-          e.getCreationEvent().addSource(parent).setUsedQuantity(200.0f);
-        }
+        BioMaterialEventSource evtSrc = e.getCreationEvent().setSource(parent);
+        evtSrc.setUsedQuantity(200.0f);
       }
       if (subtypeId > 0)
@@ -134 +140 @@
   }
 
-  static int test_create_pooled(int... sourceIds)
+  static int test_create_pooled(String name, int... sourceIds)
   {
     if (!TestUtil.hasPermission(Permission.CREATE, Item.EXTRACT)) return 0;
@@ -143 +149 @@
       dc = TestUtil.getDbControl();
       Extract e = Extract.getNew(dc);
-      e.setName("Test pooled extract");
+      e.setName(name);
       e.setDescription("Added at "+new Date());
       e.setExternalId("POOLED-455-EXTRACT");
       e.setOriginalQuantity(500.0f);
-      e.setPooled(true);
       BioMaterialEvent evt = e.getCreationEvent();
       for (int sourceId : sourceIds)
@@ -289 +294 @@
     if (!TestUtil.getSilent())
     {
-      write("   \tID \tName      \tSubtype\tDescription\tExternal id\tPooled\tSample\tTag\tQuantity\tRemain");
-      write("-- \t-- \t--------- \t-------\t-----------\t-----------\t------\t------\t---\t--------\t------");
+      write("   \tID \tName      \tSubtype\tDescription\tExternal id\tParent type\tParent\tTag\tQuantity\tRemain");
+      write("-- \t-- \t--------- \t-------\t-----------\t-----------\t-----------\t------\t---\t--------\t------");
     }
   }
@@ -297 +302 @@
   {
     if (!TestUtil.getSilent()) System.out.println(i+":\t"+e.getId()+"\t"+e.getName()+"\t"+e.getItemSubtype()+"\t"+e.getDescription()+
-      "\t"+e.getExternalId()+"\t"+e.isPooled()+"\t"+e.getSample()+"\t"+e.getTag()+"\t"+e.getOriginalQuantity()+"\t"+e.getRemainingQuantity());
+      "\t"+e.getExternalId()+"\t"+e.getParentType()+"\t"+e.getParent()+"\t"+e.getTag()+"\t"+e.getOriginalQuantity()+"\t"+e.getRemainingQuantity());
   }
   static void write_events_header()
@@ -318 +323 @@
     if (!TestUtil.getSilent()) System.out.println(i+":\t"+h.getId()+"\t"+h.getName()+"\t"+h.getDescription());
   }
-  static void write_sources_header()
+
+  static void write_parents_header()
   {
     if (!TestUtil.getSilent())
     {
-      write("   \tID \tName      \tDescription\tExternal id\tPooled\tQuantity\tRemain\tUsed");
-      write("-- \t-- \t--------- \t-----------\t-----------\t------\t--------\t------\t----");
-    }
-  }
+      write("   \tID \tName      \tDescription\tExternal id\tQuantity\tRemain\tUsed");
+      write("-- \t-- \t--------- \t-----------\t-----------\t--------\t------\t----");
+    }
+  }
+
   static void write_item(int i, MeasuredBioMaterial b, BioMaterialEvent evt)
     throws BaseException
   {
     if (!TestUtil.getSilent()) System.out.println(i+":\t"+b.getId()+"\t"+b.getName()+"\t"+b.getDescription()+
-      "\t"+b.getExternalId()+"\t"+b.isPooled()+"\t"+b.getOriginalQuantity()+"\t"+b.getRemainingQuantity()+
+      "\t"+b.getExternalId()+"\t"+b.getParentType()+"\t"+b.getOriginalQuantity()+"\t"+b.getRemainingQuantity()+
       "\t"+evt.getUsedQuantity(b));
   }
@@ -402 +409 @@
     }
   }
-
+  
   static void test_list_sources(int extractId, int expectedResults)
   {
@@ -412 +419 @@
       Extract e = Extract.getById(dc, extractId);
       BioMaterialEvent evt = e.getCreationEvent();
-      ItemResultList<? extends MeasuredBioMaterial> l = evt.getSources().list(dc);
+      ResultList<BioMaterialEventSource> l = evt.getEventSources().list(dc);
       for (int i = 0; i<l.size(); i++)
       {
-        write_item(i, l.get(i), evt);
+        TestSample.write_item(i, l.get(i));
       }
       if (expectedResults >= 0 && expectedResults != l.size())
@@ -434 +441 @@
     }
   }
-  static void test_list_pooledChildren(int extractId, int expectedResults)
+
+  static void test_list_children(int extractId, int expectedResults)
   {
     if (extractId == 0) return;
@@ -442 +450 @@
       dc = TestUtil.getDbControl();
       Extract e = Extract.getById(dc, extractId);
-      ItemResultList<BioMaterialEvent> ev = e.getPoolingEvents().list(dc);
+      ItemResultList<Extract> ev = e.getChildExtracts().list(dc);
       
       for (int i=0; i<ev.size(); i++)
       {
-        write_item(i, (Extract)ev.get(i).getBioMaterial());
+        write_item(i, ev.get(i));
       }
       if (expectedResults >= 0 && expectedResults != ev.size())
@@ -452 +460 @@
         throw new BaseException("Expected "+expectedResults+" results, not "+ev.size());
       }
-      write("--List pools from extract OK ("+ev.size()+")");
-    }
-    catch (Throwable ex)
-    {
-      write("--List pools for extract FAILED");
-      ex.printStackTrace();
-      ok = false;
-    }
-    finally
-    {
-      if (dc != null) dc.close();
-    }
-  }
+      write("--List children for extract OK ("+ev.size()+")");
+    }
+    catch (Throwable ex)
+    {
+      write("--List children for extract FAILED");
+      ex.printStackTrace();
+      ok = false;
+    }
+    finally
+    {
+      if (dc != null) dc.close();
+    }
+  }
+
   
   static void test_list_bioassays(int extractId, int expectedResults)
@@ -497 +506 @@
   }
   
+  
+  static void test_childrenTransformer(int extractId, int expectedResults)
+  {
+    if (extractId == 0) return;
+    DbControl dc = null;
+    try
+    {
+      dc = TestUtil.getDbControl();
+      Extract e = Extract.getById(dc, extractId);
+      ChildrenTransformer<Extract> pct = new ChildrenTransformer<Extract>(dc, false, Extract.getQuery());
+      Set<Extract> children = new LinkedHashSet<Extract>();
+      pct.transform(Collections.singleton(e), children);
+
+      int i = 0;
+      for (Extract c : children)
+      {
+        write_item(i, c);
+        i++;
+      }
+      if (expectedResults >= 0 && expectedResults != children.size())
+      {
+        throw new BaseException("Expected "+expectedResults+" results, not "+children.size());
+      }
+      write("--List children for extract using transformer OK ("+children.size()+")");
+    }
+    catch (Throwable ex)
+    {
+      write("--List children for extract using transformer FAILED");
+      ex.printStackTrace();
+      ok = false;
+    }
+    finally
+    {
+      if (dc != null) dc.close();
+    }
+  }
+
+  static void test_parentsTransformer(int extractId, int expectedResults)
+  {
+    if (extractId == 0) return;
+    DbControl dc = null;
+    try
+    {
+      dc = TestUtil.getDbControl();
+      Extract e = Extract.getById(dc, extractId);
+      ParentsTransformer<Extract> pct = new ParentsTransformer<Extract>(dc, false, Extract.getQuery());
+      Set<Extract> parents = new LinkedHashSet<Extract>();
+      pct.transform(Collections.singleton(e), parents);
+
+      int i = 0;
+      for (Extract c : parents)
+      {
+        write_item(i, c);
+        i++;
+      }
+      if (expectedResults >= 0 && expectedResults != parents.size())
+      {
+        throw new BaseException("Expected "+expectedResults+" results, not "+parents.size());
+      }
+      write("--List parents for extract using transformer OK ("+parents.size()+")");
+    }
+    catch (Throwable ex)
+    {
+      write("--List parents for extract using transformer FAILED");
+      ex.printStackTrace();
+      ok = false;
+    }
+    finally
+    {
+      if (dc != null) dc.close();
+    }
+  }
+
+  static void test_extractToSampleTransformer(int extractId, int expectedResults)
+  {
+    if (extractId == 0) return;
+    DbControl dc = null;
+    try
+    {
+      dc = TestUtil.getDbControl();
+      Extract e = Extract.getById(dc, extractId);
+      ExtractToSampleTransformer pct = new ExtractToSampleTransformer(dc);
+      Set<Sample> parents = new LinkedHashSet<Sample>();
+      pct.transform(Collections.singleton(e), parents);
+
+      int i = 0;
+      for (Sample c : parents)
+      {
+        TestSample.write_item(i, c);
+        i++;
+      }
+      if (expectedResults >= 0 && expectedResults != parents.size())
+      {
+        throw new BaseException("Expected "+expectedResults+" results, not "+parents.size());
+      }
+      write("--List sample for extract using transformer OK ("+parents.size()+")");
+    }
+    catch (Throwable ex)
+    {
+      write("--List sample for extract using transformer FAILED");
+      ex.printStackTrace();
+      ok = false;
+    }
+    finally
+    {
+      if (dc != null) dc.close();
+    }
+  }
+
+  static void test_sampleToExtractTransformer(int sampleId, int expectedResults)
+  {
+    if (sampleId == 0) return;
+    DbControl dc = null;
+    try
+    {
+      dc = TestUtil.getDbControl();
+      Sample s = Sample.getById(dc, sampleId);
+      SampleToExtractTransformer pct = new SampleToExtractTransformer(dc);
+      Set<Extract> children = new LinkedHashSet<Extract>();
+      pct.transform(Collections.singleton(s), children);
+
+      int i = 0;
+      for (Extract c : children)
+      {
+        write_item(i, c);
+        i++;
+      }
+      if (expectedResults >= 0 && expectedResults != children.size())
+      {
+        throw new BaseException("Expected "+expectedResults+" results, not "+children.size());
+      }
+      write("--List extracts for sample using transformer OK ("+children.size()+")");
+    }
+    catch (Throwable ex)
+    {
+      write("--List extracts for sample using transformer FAILED");
+      ex.printStackTrace();
+      ok = false;
+    }
+    finally
+    {
+      if (dc != null) dc.close();
+    }
+  }
+  
+  
 }

trunk/src/test/TestGenericOverview.java

@@ -100 +100 @@
     int extract1 = TestExtract.test_create(sample1, "Extract GO #1", 0, 0, false);
     int extract2 = TestExtract.test_create(sample2, "Extract GO #2", 0, 0, false);
-    int extractPooled = TestExtract.test_create_pooled(extract1, extract2);
+    int extractPooled = TestExtract.test_create_pooled("Extract GO #3 (pooled)", extract1, extract2);
     
     // Array design

trunk/src/test/TestPhysicalBioAssay.java

@@ -251 +251 @@
       StringBuilder sb = new StringBuilder();
       sb.append("[");
-      for (MeasuredBioMaterial le : h.getCreationEvent().getSources().list(h.getDbControl()))
+      for (BioMaterial le : h.getCreationEvent().getSources().list(h.getDbControl()))
       {
         sb.append(le.toString());

trunk/src/test/TestSample.java

@@ -23 +23 @@
 */
 import net.sf.basedb.core.*;
-import net.sf.basedb.util.biomaterial.PooledChildrenTransformer;
-
-import java.util.ArrayList;
+import net.sf.basedb.core.query.ResultList;
+import net.sf.basedb.util.biomaterial.BioSourceToSampleTransformer;
+import net.sf.basedb.util.biomaterial.ChildrenTransformer;
+import net.sf.basedb.util.biomaterial.ParentsTransformer;
+import net.sf.basedb.util.biomaterial.SampleToBioSourceTransformer;
+
 import java.util.Collections;
 import java.util.Date;
-import java.util.List;
+import java.util.LinkedHashSet;
 import java.util.Set;
 
@@ -48 +51 @@
     write_header();
     // Standard tests: create, load, list
-    int id = test_create(0, null, true);
-    int id2 = test_create(0, null, false);
-    
     int bioSourceId = TestBioSource.test_create(null, false);
-    int id3 = test_create(bioSourceId, null, false);
-    int id4 = test_create_pooled(id, id2, id3);
+    int id = test_create(0, "Sample #1 (standalone)", true);
+    int id2 = test_create(bioSourceId, "Sample #2 (biosource parent)", false); 
+    int id3 = test_create(id, "Sample #3 (sample parent)", false);
+    int id4 = test_create_pooled("Sample #4 (pooled)", id, id2, id3);
 
     test_load(id);
@@ -60 +62 @@
     write_events_header();
     test_add_event(id, 100.0f);
-    test_list_events(id, 3);  // creation event, pooling event for id4, and extra event
+    test_list_events(id, 4);  // creation event, create event for id3+id4, and extra event
     
-    write_sources_header();
+    write_parents_header();
     test_list_sources(id4, 3); // The three id, id2 and id3 samples
-    test_list_pooledChildren(id2, 1);
-    test_pooledChildrenTransformer(id2, 1);
+    test_list_children(id, 2); // id3 and id4
+
+    // Transformers
+    test_childrenTransformer(id, 2);
+    test_parentsTransformer(id4, 3);
+    test_sampleToBioSourceTransformer(id2, 1);
+    test_bioSourceToSampleTransformer(bioSourceId, 1);
 
     // Standard test: Delete
@@ -79 +86 @@
   }
 
-  static int test_create(int bioSourceId, String name, boolean setAll)
+  static int test_create(int parentId, String name, boolean setAll)
   {
     if (!TestUtil.hasPermission(Permission.CREATE, Item.SAMPLE)) return 0;
@@ -95 +102 @@
         s.setOriginalQuantity(500.0f);
       }
-      if (bioSourceId != 0)
-      {
-        BioSource bs = BioSource.getById(dc, bioSourceId);
-        s.setBioSource(bs);
-        s.setName(bs.getName() + ".s");
+      if (parentId != 0)
+      {
+        BioMaterial parent = BioMaterial.getById(dc, parentId);
+        s.getCreationEvent().setSource(parent);
+        s.setName(parent.getName() + ".s");
       }
       if (name != null) s.setName(name);
@@ -123 +130 @@
   }
 
-  static int test_create_pooled(int... sourceIds)
+  static int test_create_pooled(String name, int... sourceIds)
   {
     if (!TestUtil.hasPermission(Permission.CREATE, Item.SAMPLE)) return 0;
@@ -132 +139 @@
       dc = TestUtil.getDbControl();
       Sample s = Sample.getNew(dc);
-      s.setName("Test pooled sample");
+      s.setName(name);
       s.setDescription("Added at "+new Date());
       s.setExternalId("POOLED-455-SAMPLE");
       s.setOriginalQuantity(500.0f);
-      s.setPooled(true);
       BioMaterialEvent evt = s.getCreationEvent();
       for (int sourceId : sourceIds)
@@ -277 +283 @@
     if (!TestUtil.getSilent())
     {
-      write("   \tID \tName      \tDescription\tExternal id\tBioSource\tQuantity\tRemain");
-      write("-- \t-- \t--------- \t-----------\t-----------\t---------\t--------\t------");
+      write("   \tID \tName      \tDescription\tExternal id\tParent\tQuantity\tRemain");
+      write("-- \t-- \t--------- \t-----------\t-----------\t------\t--------\t------");
     }
   }
@@ -285 +291 @@
   {
     if (!TestUtil.getSilent()) System.out.println(i+":\t"+s.getId()+"\t"+s.getName()+"\t"+s.getDescription()+
-      "\t"+s.getExternalId()+"\t"+s.getBioSource()+"\t"+s.getOriginalQuantity()+"\t"+s.getRemainingQuantity());
+      "\t"+s.getExternalId()+"\t"+s.getParent()+"\t"+s.getOriginalQuantity()+"\t"+s.getRemainingQuantity());
   }
   static void write_events_header()
@@ -301 +307 @@
       "\t"+evt.getEventDate()+"\t"+evt.getEntryDate()+"\t"+evt.getUsedQuantity(s)+"\t"+evt.getComment());
   }
-  static void write_sources_header()
+
+  static void write_parents_header()
   {
     if (!TestUtil.getSilent())
     {
-      write("   \tID \tName      \tDescription\tExternal id\tPooled\tQuantity\tRemain\tUsed");
-      write("-- \t-- \t--------- \t-----------\t-----------\t------\t--------\t------\t----");
-    }
-  }
-  static void write_item(int i, MeasuredBioMaterial b, BioMaterialEvent evt)
+      write("   \tID \tName      \tDescription\tExternal id\tQuantity\tRemain\tUsed");
+      write("-- \t-- \t--------- \t-----------\t-----------\t--------\t------\t----");
+    }
+  }
+
+  static void write_item(int i, BioMaterialEventSource evtSrc)
     throws BaseException
   {
-    if (!TestUtil.getSilent()) System.out.println(i+":\t"+b.getId()+"\t"+b.getName()+"\t"+b.getDescription()+
-      "\t"+b.getExternalId()+"\t"+b.isPooled()+"\t"+b.getOriginalQuantity()+"\t"+b.getRemainingQuantity()+
-      "\t"+evt.getUsedQuantity(b));
+    if (!TestUtil.getSilent()) 
+    {
+      MeasuredBioMaterial bm = (MeasuredBioMaterial)evtSrc.getBioMaterial();
+      System.out.println(i+":\t"+bm.getId()+"\t"+bm.getName()+"\t"+bm.getDescription()+
+          "\t"+bm.getExternalId()+"\t"+"\t"+bm.getOriginalQuantity()+"\t"+bm.getRemainingQuantity()+
+          "\t"+evtSrc.getUsedQuantity());
+    }
   }
 
@@ -395 +407 @@
       Sample s = Sample.getById(dc, sampleId);
       BioMaterialEvent evt = s.getCreationEvent();
-      ItemResultList<? extends MeasuredBioMaterial> l = evt.getSources().list(dc);
+      ResultList<BioMaterialEventSource> l = evt.getEventSources().list(dc);
       for (int i = 0; i<l.size(); i++)
       {
-        write_item(i, l.get(i), evt);
+        write_item(i, l.get(i));
       }
       if (expectedResults >= 0 && expectedResults != l.size())
@@ -417 +429 @@
     }
   }
-  static void test_list_pooledChildren(int sampleId, int expectedResults)
+
+  static void test_list_children(int sampleId, int expectedResults)
   {
     if (sampleId == 0) return;
@@ -425 +438 @@
       dc = TestUtil.getDbControl();
       Sample s = Sample.getById(dc, sampleId);
-      ItemResultList<BioMaterialEvent> ev = s.getPoolingEvents().list(dc);
+      ItemResultList<Sample> ev = s.getChildSamples().list(dc);
       
       for (int i=0; i<ev.size(); i++)
       {
-        write_item(i, (Sample)ev.get(i).getBioMaterial());
+        write_item(i, ev.get(i));
       }
       if (expectedResults >= 0 && expectedResults != ev.size())
@@ -435 +448 @@
         throw new BaseException("Expected "+expectedResults+" results, not "+ev.size());
       }
-      write("--List pools from sample OK ("+ev.size()+")");
-    }
-    catch (Throwable ex)
-    {
-      write("--List pools for sample FAILED");
-      ex.printStackTrace();
-      ok = false;
-    }
-    finally
-    {
-      if (dc != null) dc.close();
-    }
-  }
-
-  static void test_pooledChildrenTransformer(int sampleId, int expectedResults)
+      write("--List children for sample OK ("+ev.size()+")");
+    }
+    catch (Throwable ex)
+    {
+      write("--List children for sample FAILED");
+      ex.printStackTrace();
+      ok = false;
+    }
+    finally
+    {
+      if (dc != null) dc.close();
+    }
+  }
+  
+  static void test_childrenTransformer(int sampleId, int expectedResults)
   {
     if (sampleId == 0) return;
@@ -457 +470 @@
       dc = TestUtil.getDbControl();
       Sample s = Sample.getById(dc, sampleId);
-      PooledChildrenTransformer<Sample> pct = new PooledChildrenTransformer<Sample>(dc, false, Sample.getQuery());
-      List<Sample> children = new ArrayList<Sample>();
-      int numAdded = pct.transform(Collections.singleton(s), children);
-
-      for (int i=0; i<children.size(); i++)
-      {
-        write_item(i, children.get(i));
-      }
-      if (expectedResults >= 0 && expectedResults != numAdded && numAdded != children.size())
-      {
-        throw new BaseException("Expected "+expectedResults+" results, not "+numAdded);
-      }
-      write("--List pools from sample using transformer OK ("+numAdded+")");
-    }
-    catch (Throwable ex)
-    {
-      write("--List pools for sample using transformer FAILED");
-      ex.printStackTrace();
-      ok = false;
-    }
-    finally
-    {
-      if (dc != null) dc.close();
-    }
-  }
-
+      ChildrenTransformer<Sample> pct = new ChildrenTransformer<Sample>(dc, false, Sample.getQuery());
+      Set<Sample> children = new LinkedHashSet<Sample>();
+      pct.transform(Collections.singleton(s), children);
+
+      int i = 0;
+      for (Sample c : children)
+      {
+        write_item(i, c);
+        i++;
+      }
+      if (expectedResults >= 0 && expectedResults != children.size())
+      {
+        throw new BaseException("Expected "+expectedResults+" results, not "+children.size());
+      }
+      write("--List children for sample using transformer OK ("+children.size()+")");
+    }
+    catch (Throwable ex)
+    {
+      write("--List children for sample using transformer FAILED");
+      ex.printStackTrace();
+      ok = false;
+    }
+    finally
+    {
+      if (dc != null) dc.close();
+    }
+  }
+
+  static void test_parentsTransformer(int sampleId, int expectedResults)
+  {
+    if (sampleId == 0) return;
+    DbControl dc = null;
+    try
+    {
+      dc = TestUtil.getDbControl();
+      Sample s = Sample.getById(dc, sampleId);
+      ParentsTransformer<Sample> pct = new ParentsTransformer<Sample>(dc, false, Sample.getQuery());
+      Set<Sample> parents = new LinkedHashSet<Sample>();
+      pct.transform(Collections.singleton(s), parents);
+
+      int i = 0;
+      for (Sample c : parents)
+      {
+        write_item(i, c);
+        i++;
+      }
+      if (expectedResults >= 0 && expectedResults != parents.size())
+      {
+        throw new BaseException("Expected "+expectedResults+" results, not "+parents.size());
+      }
+      write("--List parents for sample using transformer OK ("+parents.size()+")");
+    }
+    catch (Throwable ex)
+    {
+      write("--List parents for sample using transformer FAILED");
+      ex.printStackTrace();
+      ok = false;
+    }
+    finally
+    {
+      if (dc != null) dc.close();
+    }
+  }
+
+  static void test_sampleToBioSourceTransformer(int sampleId, int expectedResults)
+  {
+    if (sampleId == 0) return;
+    DbControl dc = null;
+    try
+    {
+      dc = TestUtil.getDbControl();
+      Sample s = Sample.getById(dc, sampleId);
+      SampleToBioSourceTransformer pct = new SampleToBioSourceTransformer(dc);
+      Set<BioSource> parents = new LinkedHashSet<BioSource>();
+      pct.transform(Collections.singleton(s), parents);
+
+      int i = 0;
+      for (BioSource c : parents)
+      {
+        TestBioSource.write_item(i, c);
+        i++;
+      }
+      if (expectedResults >= 0 && expectedResults != parents.size())
+      {
+        throw new BaseException("Expected "+expectedResults+" results, not "+parents.size());
+      }
+      write("--List biosource for sample using transformer OK ("+parents.size()+")");
+    }
+    catch (Throwable ex)
+    {
+      write("--List biosource for sample using transformer FAILED");
+      ex.printStackTrace();
+      ok = false;
+    }
+    finally
+    {
+      if (dc != null) dc.close();
+    }
+  }
+
+  static void test_bioSourceToSampleTransformer(int bioSourceId, int expectedResults)
+  {
+    if (bioSourceId == 0) return;
+    DbControl dc = null;
+    try
+    {
+      dc = TestUtil.getDbControl();
+      BioSource bs = BioSource.getById(dc, bioSourceId);
+      BioSourceToSampleTransformer pct = new BioSourceToSampleTransformer(dc);
+      Set<Sample> children = new LinkedHashSet<Sample>();
+      pct.transform(Collections.singleton(bs), children);
+
+      int i = 0;
+      for (Sample c : children)
+      {
+        write_item(i, c);
+        i++;
+      }
+      if (expectedResults >= 0 && expectedResults != children.size())
+      {
+        throw new BaseException("Expected "+expectedResults+" results, not "+children.size());
+      }
+      write("--List sample for biosource using transformer OK ("+children.size()+")");
+    }
+    catch (Throwable ex)
+    {
+      write("--List sample for biosource using transformer FAILED");
+      ex.printStackTrace();
+      ok = false;
+    }
+    finally
+    {
+      if (dc != null) dc.close();
+    }
+  }
+  
 }

trunk/src/test/net/sf/basedb/test/roles/UserTest.java

@@ -376 +376 @@
     sample.setName(name);
     sample.setOriginalQuantity(100.0f);
-    sample.setBioSource(bioSource);
+    sample.getCreationEvent().setSource(bioSource);
     sample.getCreationEvent().setProtocol(Util.findProtocol(dc, "Sampling A"));
     dc.saveItem(sample);
@@ -398 +398 @@
     extract.setName(name);
     extract.setOriginalQuantity(100.0f);
-    extract.setSample(sample).setUsedQuantity(50.0f);
+    extract.getCreationEvent().setSource(sample).setUsedQuantity(50.0f);
     extract.getCreationEvent().setProtocol(Util.findProtocol(dc, "Extraction A"));
     dc.saveItem(extract);
@@ -416 +416 @@
     labeledExtract.setOriginalQuantity(100.0f);
     labeledExtract.setTag(label);
-    labeledExtract.setPooled(true);
     labeledExtract.getCreationEvent().setProtocol(Util.findProtocol(dc, "Labeling A"));
-    labeledExtract.getCreationEvent().addSource(extract).setUsedQuantity(50.0f);
+    labeledExtract.getCreationEvent().setSource(extract).setUsedQuantity(50.0f);
     dc.saveItem(labeledExtract);
     return labeledExtract;

trunk/www/WEB-INF/base.tld

@@ -383 +383 @@
     </attribute>
     <attribute>
+      <name>buttonclass</name>
+      <required>false</required>
+      <rtexprvalue>true</rtexprvalue>
+    </attribute>
+    <attribute>
+      <name>buttonstyle</name>
+      <required>false</required>
+      <rtexprvalue>true</rtexprvalue>
+    </attribute>
+    <attribute>
+      <name>buttontitle</name>
+      <required>false</required>
+      <rtexprvalue>true</rtexprvalue>
+    </attribute>
+    <attribute>
+      <name>buttonicon</name>
+      <required>false</required>
+      <rtexprvalue>true</rtexprvalue>
+    </attribute>
+    <attribute>
       <name>required</name>
       <required>false</required>

trunk/www/biomaterials/biosources/view_biosource.jsp

@@ -307 +307 @@
       {
         %>
-        <h4>Samples</h4>
+        <h4>Child samples</h4>
         No samples have been created from this biosource
         (or, you don't have permission to view them).
@@ -317 +317 @@
         <base:section 
           id="sampleSection" 
-          title="<%="Samples (" + samples.size() + ")"%>"
+          title="<%="Child samples (" + samples.size() + ")"%>"
           context="<%=cc%>"
           >
@@ -328 +328 @@
             id="name"
             title="Name"
+          />
+          <tbl:columndef 
+            id="type"
+            title="Type"
           />
           <tbl:columndef 
@@ -347 +351 @@
                     visible="<%=item.isRemoved()%>"
                   /><%=Base.getLinkedName(ID, item, false, true)%></tbl:cell>
+                  <tbl:cell column="type"><base:propertyvalue item="<%=item%>" property="itemSubtype" /></tbl:cell>
                 <tbl:cell column="description"><%=HTML.encodeTags(item.getDescription())%></tbl:cell>
               </tbl:row>

trunk/www/biomaterials/events/view_event.jsp

@@ -31 +31 @@
   import="net.sf.basedb.core.Permission"
   import="net.sf.basedb.core.Plate"
+  import="net.sf.basedb.core.BioMaterial"
   import="net.sf.basedb.core.BioMaterialEvent"
+  import="net.sf.basedb.core.BioMaterialEventSource"
   import="net.sf.basedb.core.BioPlateEventParticipant"
   import="net.sf.basedb.core.BioPlateEvent"
@@ -40 +42 @@
   import="net.sf.basedb.core.PermissionDeniedException"
   import="net.sf.basedb.core.ItemQuery"
+  import="net.sf.basedb.core.SpecialQuery"
   import="net.sf.basedb.core.ItemResultList"
   import="net.sf.basedb.core.Include"
@@ -45 +48 @@
   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.core.plugin.GuiContext"
   import="net.sf.basedb.core.plugin.Plugin"
@@ -277 +281 @@
           <%
         }
-        ItemQuery<? extends MeasuredBioMaterial> sourcesQuery = event.getSources();
-        sourcesQuery.include(Include.MINE, Include.SHARED, Include.IN_PROJECT, Include.OTHERS);
-        sourcesQuery.order(Orders.asc(Hql.property("name")));
-        ItemResultList<? extends MeasuredBioMaterial> sources = sourcesQuery.list(dc);
+        SpecialQuery<BioMaterialEventSource> sourcesQuery = event.getEventSources();
+        sourcesQuery.order(Orders.asc(Hql.property("bioMaterial.name")));
+        ResultList<BioMaterialEventSource> sources = sourcesQuery.list(dc);
         %>
         <tr>
@@ -286 +289 @@
           <td>
           <%
-          for (MeasuredBioMaterial s : sources)
+          for (BioMaterialEventSource evtSrc : sources)
           {
-            Item sourceType = s.getType();
+            BioMaterial source = null;
+            Item sourceType = null;
+            try
+            {
+              source = evtSrc.getBioMaterial();
+              sourceType = source.getType();
+            }
+            catch (PermissionDeniedException ex)
+            {}
             %>
-            <%=HTML.encodeTags(s.getName())%> (<%=sourceType%>),
-            <%=Values.formatNumber(event.getUsedQuantity(s), 2, " µg")%>
+            <%=Base.getLinkedName(ID, source, source == null, true)%>
+            <%=sourceType != null ? "(" + sourceType + ")" : "" %>
+            <%=Values.formatNumber(evtSrc.getUsedQuantity(), 2, " µg")%>
             <br>
             <%

trunk/www/biomaterials/lists/index.jsp

@@ -46 +46 @@
   import="net.sf.basedb.util.ShareableUtil"
   import="net.sf.basedb.util.OwnableUtil"
-  import="net.sf.basedb.util.biomaterial.BioSourceToSampleTransformer"
-  import="net.sf.basedb.util.biomaterial.SampleToExtractTransformer"
-  import="net.sf.basedb.util.biomaterial.PooledChildrenTransformer"
   import="net.sf.basedb.util.collections.CollectionTransformer"
   import="net.sf.basedb.util.biomaterial.ListUtil"

trunk/www/biomaterials/samples/edit_sample.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"
@@ -47 +48 @@
   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;
   String name = null;
   boolean lockEventProperties = false;
@@ -138 +141 @@
     }
     int bioSourceId = Values.getInt(request.getParameter("biosource_id"));
+    int sampleId = Values.getInt(request.getParameter("sample_id"));
     if (bioSourceId != 0)
     {
       currentBioSource = BioSource.getById(dc, bioSourceId);
-      isPooled = false;
+      parentType = Item.BIOSOURCE;
       name = currentBioSource.getName() + ".s" + (currentBioSource.countSamples() + 1);
+    }
+    else if (sampleId != 0)
+    {
+      parentType = Item.SAMPLE;
+      Sample s = Sample.getById(dc, sampleId);
+      name = s.getName() + ".s" + (s.countSamples()+1);
+      samplesQuery = Sample.getQuery();
+      samplesQuery.restrict(Restrictions.eq(Hql.property("id"), Expressions.integer(sampleId)));
     }
     else if (Values.getBoolean(request.getParameter("pooled")))
     {   
-      isPooled = true;
-      name = Values.getString(cc.getPropertyValue("name"),"New pooled sample");
+      parentType = Item.SAMPLE;
+      name = Values.getString(cc.getPropertyValue("name"), "New pooled sample");
+      samplesQuery = Sample.getQuery();
+      samplesQuery.restrict(Restrictions.in(Hql.property("id"), Expressions.parameter("selected")));
+      samplesQuery.setParameter("selected", cc.getSelected(), Type.INT);
     }
     else
     {
-      isPooled = Values.getBoolean(cc.getPropertyValue("pooled"));
       name = Values.getString(cc.getPropertyValue("name"), "New sample");
     }
@@ -165 +179 @@
     creationEvent = sample.getCreationEvent();
     eventDate = creationEvent.getEventDate();
-    isPooled = sample.isPooled();
+    parentType = sample.getParentType();
     name = sample.getName();
     lockEventProperties = !creationEvent.hasPermission(Permission.WRITE);
@@ -179 +193 @@
     }
 
-    
     try
     {
@@ -191 +204 @@
     try
     {
-      currentBioSource = sample.getBioSource();
+      if (parentType == Item.BIOSOURCE)
+      {
+        currentBioSource = (BioSource)sample.getParent();
+      }
     }
     catch (PermissionDeniedException ex)
@@ -213 +229 @@
     }
   
-    // Query to retrieve pooled samples
-    samplesQuery = (ItemQuery<Sample>)creationEvent.getSources();
-    samplesQuery.include(Include.ALL);
-    samplesQuery.order(Orders.asc(Hql.property("name")));
+    // Query to retrieve parent samples
+    if (parentType == Item.SAMPLE)
+    {
+      samplesQuery = (ItemQuery<Sample>)creationEvent.getSources();
+    }
   }
   
@@ -314 +331 @@
       var frm = document.forms['sample'];
       var parents = new Array();
-      if (frm.pooled[0].checked)
+      if (frm.parentType[0].checked)
       {
         var bioSourceId = Math.abs(parseInt(frm.biosource_id[frm.biosource_id.selectedIndex].value));
@@ -449 +466 @@
     }
     
-    function pooledOnClick()
-    {
-      var frm = document.forms['sample'];
-      var isPooled = frm.pooled[1].checked
-      frm.biosource_id.disabled = isPooled;
-      frm.samples.disabled = !isPooled;
-      frm.used_quantity.disabled = !isPooled;
+    function parentTypeOnClick()
+    {
+      var frm = document.forms['sample'];
+      var useSamples = frm.parentType[1].checked
+      frm.biosource_id.disabled = useSamples;
+      frm.samples.disabled = !useSamples;
+      frm.used_quantity.disabled = !useSamples;
       parentsChanged = true;
     }
@@ -465 +482 @@
     {
       var frm = document.forms['sample'];
-      if (frm.pooled[1].checked)
-      {
-        alert('This is a pooled sample, which cannot have a biosource as it\'s parent');
-        return;
-      }
-
       var url = '../biosources/index.jsp?ID=<%=ID%>&cmd=UpdateContext&mode=selectone';
       url += '&callback=setBioSourceCallback&resetTemporary=1';
@@ -492 +503 @@
       list[1].text = name;
       list.selectedIndex = 1;
+
+      frm.parentType[0].checked = true;
+      frm.parentType[1].checked = false;
+      parentTypeOnClick();
       parentsChanged = true;
     }
@@ -498 +513 @@
     {
       var frm = document.forms['sample'];
-      if (!frm.pooled[1].checked)
-      {
-        alert('This is not a pooled sample');
-        return;
-      }
-      
       var url = 'index.jsp?ID=<%=ID%>&cmd=UpdateContext&mode=selectmultiple';
       url += '&callback=addSampleCallback&resetTemporary=1';
@@ -511 +520 @@
     function addSampleCallback(sampleId, name)
     {
+      var frm = document.forms['sample'];
       var item = Link.getItem('S', sampleId);
       if (!item) item = new Item('S', sampleId, name+' [-]', '', '');
-      Link.addItem(document.forms['sample'].samples, item);
+      Link.addItem(frm.samples, item);
+      frm.parentType[0].checked = false;
+      frm.parentType[1].checked = true;
+      parentTypeOnClick();
       parentsChanged = true;
     }
@@ -567 +580 @@
       initBioWell();
       initSamples();
-      pooledOnClick();    
+      parentTypeOnClick();    
     }
     function initSamples()
@@ -573 +586 @@
       var samples = document.forms['sample'].samples;
       <%
-      if (sample != null && sample.isPooled())
-      {
+      if (samplesQuery != null)
+      {
+        samplesQuery.include(Include.ALL);
+        samplesQuery.order(Orders.asc(Hql.property("name")));
         ItemResultList<Sample> samples = samplesQuery.list(dc);
         for (Sample s : samples)
         {
-          String usedQuantity = Values.formatNumber(creationEvent.getUsedQuantity(s), -1);
-          %>
-          Link.addNewItem(samples, new Item('S', <%=s.getId()%>, '<%=HTML.javaScriptEncode(s.getName())%> [<%=usedQuantity%> µg]', '<%=usedQuantity%>'));
-          <%
-        }
-      }
-      else if (sample == null && Values.getBoolean(request.getParameter("pooled")))
-      {
-        for (int sid : cc.getSelected())
-        {
-          Sample sampleToPool = Sample.getById(dc, sid);
-          %>
-          Link.addItem(samples, new Item('S', <%=sampleToPool.getId()%>, '<%=HTML.javaScriptEncode(sampleToPool.getName())%> [-]', '', ''));
-          <%
+          if (sample != null)
+          {
+            String usedQuantity = Values.formatNumber(creationEvent.getUsedQuantity(s), -1);
+            %>
+            Link.addNewItem(samples, new Item('S', <%=s.getId()%>, '<%=HTML.javaScriptEncode(s.getName())%> [<%=usedQuantity%> µg]', '<%=usedQuantity%>'));
+            <%
+          }
+          else
+          {
+            %>
+            Link.addItem(samples, new Item('S', <%=s.getId()%>, '<%=HTML.javaScriptEncode(s.getName())%> [-]', '', ''));
+            <%
+          }
         }
       }
@@ -755 +769 @@
       <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.biosource" 
+            value="BIOSOURCE" onclick="parentTypeOnClick()"
+            <%=parentType != Item.SAMPLE ? "checked" : ""%>
+            ><label for="parentType.biosource">Biosource</label>
+          <input type="radio" name="parentType" id="parentType.sample" 
+            value="SAMPLE" onclick="parentTypeOnClick()"
+            <%=parentType == Item.SAMPLE ? "checked" : ""%>
+            ><label for="parentType.sample">Sample</label>
         </td>
       </tr>
@@ -771 +787 @@
             id="biosource_id"
             clazz="selectionlist"
+            buttonstyle="width: 150px;"
+            buttonicon="add.png"
+            buttontitle="Select biosource&hellip;"
             required="false"
             current="<%=currentBioSource%>"
@@ -788 +807 @@
           <tr valign="top">
           <td>
-            <select name="samples" size="5" multiple style="width: 20em;" 
+            <select name="samples" size="5" multiple class="selectionlist" 
               onchange="samplesOnChange()">
-            </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="modifiedSamples" value="">
             <input type="hidden" name="removedSamples" 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; width: 150px;"><base:button 
               onclick="addSamplesOnClick()" 
               title="Add&nbsp;samples&hellip;" 
               tooltip="Add samples"
               /></td></tr>
-            <tr><td width="150"><base:button 
+            <tr><td><base:button 
+              style="width: 150px;"
               onclick="removeOnClick()" 
               title="Remove" 
@@ -817 +832 @@
         </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/samples/index.jsp

@@ -88 +88 @@
     cc.setObject("export.formatter.bioWell.row", new WellCoordinateFormatter(true));
     cc.setObject("export.formatter.bioWell.column", new WellCoordinateFormatter(false));
-    cc.setObject("export.formatter.&creationEvent.sourceBioMaterials(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.bioMaterial.name)", new NameableFormatter());
     cc.setObject("export.formatter.&children(name)", new NameableFormatter());
     
@@ -106 +106 @@
     childSamplesQuery.join(Hql.innerJoin("creationEvent", "ce"));
     childSamplesQuery.join(Hql.innerJoin("ce", "sources", "src"));
-    childSamplesQuery.restrict(Restrictions.eq(Hql.index("src", null), Expressions.parameter(sampleParameter)));
+    childSamplesQuery.restrict(Restrictions.eq(Hql.property("src", "bioMaterial"), Expressions.parameter(sampleParameter)));
     childSamplesQuery.order(Orders.asc(Hql.property("name")));
     childSamplesQuery.include(cc.getInclude());
-    cc.setObject("export.dataloader.&sourceEvents(event.bioMaterial.name)", new ItemQueryLoader(childSamplesQuery, sampleParameter));
+    cc.setObject("export.dataloader.&childCreationEvents(event.bioMaterial.name)", new ItemQueryLoader(childSamplesQuery, sampleParameter));
     
     // Parent samples
     final ItemQuery<Sample> parentSamplesQuery = Sample.getQuery();
-    parentSamplesQuery.join(Hql.innerJoin("sourceEvents", "srcevt"));
-    parentSamplesQuery.join(Hql.innerJoin("srcevt", "event", "evt"));
+    parentSamplesQuery.join(Hql.innerJoin("childCreationEvents", "cce"));
+    parentSamplesQuery.join(Hql.innerJoin("cce", "event", "evt"));
     parentSamplesQuery.restrict(Restrictions.eq(Hql.property("evt", "bioMaterial"),  Expressions.parameter(sampleParameter)));
     parentSamplesQuery.order(Orders.asc(Hql.property("name")));
     parentSamplesQuery.include(cc.getInclude());
-    cc.setObject("export.dataloader.&creationEvent.sourceBioMaterials(name)", new ItemQueryLoader(parentSamplesQuery, sampleParameter));
+    cc.setObject("export.dataloader.&creationEvent.sources(bioMaterial.name)", new ItemQueryLoader(parentSamplesQuery, sampleParameter));
   } 
 %>
@@ -264 +264 @@
   
       // Parents tab
-      sample.setPooled(Values.getBoolean(request.getParameter("pooled")));
-      if (!sample.isPooled())
+      //sample.setPooled(Values.getBoolean(request.getParameter("pooled")));
+      Item parentType = Item.valueOf(request.getParameter("parentType"));
+      if (parentType == Item.BIOSOURCE)
       {
         int bioSourceId = Values.getInt(request.getParameter("biosource_id"), -1);
@@ -271 +272 @@
         {
           BioSource bs = bioSourceId == 0 ? null : BioSource.getById(dc, bioSourceId);
-          sample.setBioSource(bs);
+          creationEvent.setSource(bs);
           if (bs != null) cc.setRecent(bs, maxRecent);
         }
@@ -277 +278 @@
       else
       {
+        if (sample.getParentType() != Item.SAMPLE)
+        {
+          creationEvent.clearSources();
+        }
         String[] modifiedSamples = Values.getString(request.getParameter("modifiedSamples")).split(",");
         for (int i = 0; i < modifiedSamples.length; ++i)

trunk/www/biomaterials/samples/list_samples.jsp

@@ -110 +110 @@
   childSamplesQuery.join(Hql.innerJoin("creationEvent", "ce"));
   childSamplesQuery.join(Hql.innerJoin("ce", "sources", "src"));
-  childSamplesQuery.restrict(Restrictions.eq(Hql.index("src", null), Hql.entityParameter("sample", Item.SAMPLE)));
+  childSamplesQuery.restrict(Restrictions.eq(Hql.property("src", "bioMaterial"), Hql.entityParameter("sample", Item.SAMPLE)));
   childSamplesQuery.order(Orders.asc(Hql.property("name")));
   childSamplesQuery.include(cc.getInclude());
@@ -178 +178 @@
       Table.itemOnClick(formId, evt, itemId, '<%=mode.getName()%>', viewItem, editItem, returnSelected);
     }
+    function newSample(sampleId)
+    {
+      Main.viewOrEditItem('<%=ID%>', 'SAMPLE', 0, true, '&sample_id='+sampleId);
+    }
     function newExtract(sampleId)
     {
@@ -374 +378 @@
         formatter="<%=dateFormatter%>"
       />
-      <tbl:columndef 
-        id="pooled"
-        property="pooled"
-        datatype="boolean"
-        title="Pooled"
-        sortable="true" 
-        filterable="true"
-        exportable="true"
-      />
-      <tbl:columndef
-        id="bioSource"
-        title="Biosource"
-        property="parent.name"
-        datatype="string"
-        sortable="true" 
-        filterable="true"
-        exportable="true"
-      />
       <tbl:columndef
         id="parents"
-        title="Parent samples"
+        title="Parent items"
         property="&creationEvent.sources(bioMaterial.name)"
+        sortproperty="parent.name"
         datatype="string"
         filterable="true"
         exportable="true"
+        sortable="true"
       />
       <tbl:columndef
@@ -652 +640 @@
             {
               Sample item = samples.next();
+              Item parentType = item.getParentType();
               BioMaterialEvent creationEvent = item.getCreationEvent();
               int itemId = item.getId();
@@ -717 +706 @@
                 <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 
@@ -768 +756 @@
                 <tbl:cell column="eventDate" value="<%=creationEvent.getEventDate()%>" />
                 <tbl:cell column="entryDate" value="<%=creationEvent.getEntryDate()%>" />
-                <tbl:cell column="bioSource"><base:propertyvalue item="<%=item%>" property="parent"/></tbl:cell>
                 <tbl:cell column="parents">
                   <%
-                  if (item.isPooled())
+                  if (item.hasSingleParent() || item.getParentType() == null)
+                  {
+                    %>
+                    <base:propertyvalue item="<%=item%>" property="parent"/>
+                    <%
+                  }
+                  else
                   {
                     String separator = "";
@@ -788 +781 @@
                       separator = ", ";
                     }
-                    
                   }
                   %>
@@ -810 +802 @@
                   }
                   %>
+                  <base:icon
+                    image="add.png" 
+                    onclick="<%="newSample("+itemId+")"%>" 
+                    tooltip="Create new child sample" 
+                    visible="<%=mode.hasEditLink() && createPermission && usePermission %>"
+                  />
                 </tbl:cell>
                 <tbl:cell column="extracts">

trunk/www/biomaterials/samples/view_sample.jsp

@@ -133 +133 @@
       Main.viewOrEditItem('<%=ID%>', 'EXTRACT', 0, true, '&sample_id=<%=itemId%>');
     }
+    function newSample()
+    {
+      Main.viewOrEditItem('<%=ID%>', 'SAMPLE', 0, true, '&sample_id=<%=itemId%>');
+    }
     function deleteItem()
     {
@@ -234 +238 @@
       <tbl:button
         image="add.png"
+        onclick="newSample()"
+        title="New child sample&hellip;"
+        tooltip="Create a new child sample from this sample"
+        visible="<%=sc.hasPermission(Permission.CREATE, Item.SAMPLE) && usePermission%>"
+      />
+      <tbl:button
+        image="add.png"
         onclick="newExtract()"
-        title="New extract&hellip;"
+        title="New child extract&hellip;"
         tooltip="Create a new extract from this sample"
         visible="<%=sc.hasPermission(Permission.CREATE, Item.EXTRACT) && usePermission%>"
@@ -312 +323 @@
         <td><%=dateFormatter.format(creationEvent.getEntryDate())%></td>
       </tr>
-      <%
-      if (!sample.isPooled())
-      {
-        %>
-        <tr>
-          <td class="prompt">Biosource</td>
-          <td><base:propertyvalue item="<%=sample%>" property="parent" /></td>
-        </tr>
-        <%
-      }
-      %>
       <tr>
         <td class="prompt">Protocol</td>
@@ -367 +367 @@
   
       <%
-      if (sample.isPooled())
-      {
-        SpecialQuery<BioMaterialEventSource> sourceQuery = creationEvent.getEventSources();
-        sourceQuery.order(Orders.asc(Hql.property("bioMaterial.name")));
-        ResultList<BioMaterialEventSource> sources = sourceQuery.list(dc);
-        %>
-        <h4 class="docked">Pooled from samples</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)
+      {
+        %>
+        <%
+      }
+      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 (BioMaterialEventSource item : sources)
-          {
-            BioMaterial bm = null;
-            try
+          <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)
             {
-              bm = item.getBioMaterial();
+              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="<%=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>
+              <%
             }
-            catch (PermissionDeniedException ex)
-            {}
             %>
-            <tbl:row>
-              <tbl:cell column="name"><base:icon 
-                  image="deleted.gif" 
-                  tooltip="This item has been scheduled for deletion" 
-                  visible="<%=bm != null && bm.isRemoved()%>"
-                /><%=Base.getLinkedName(ID, bm, bm == null, true)%></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>
+            </tbl:rows>
+          </tbl:data>
+          </tbl:table>
+        </base:section>
         <%
       }
       
       // Samples this item is pooled in.
-      ItemQuery<BioMaterialEvent> poolingQuery = sample.getPoolingEvents();
-      ItemResultList<BioMaterialEvent> poolingEvents = poolingQuery.list(dc);
-      if (poolingEvents.size() == 0)
-      {
-        %>
-        <h4>Pooled in samples</h4>
-        No samples have been pooled from this sample
+      SpecialQuery<BioMaterialEventSource> childQuery = sample.getChildCreationEvents();
+      childQuery.join(Hql.innerJoin("es", "event", "evt", true));
+      childQuery.join(Hql.innerJoin("evt", "bioMaterial", "bm", true));
+      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 sample
         (or, you don't have permission to view them).
         <%
@@ -439 +457 @@
         %>
         <base:section 
-          id="pooledSection" 
-          title="<%="Pooled in samples (" + poolingEvents.size() + ")"%>"
+          id="childSection" 
+          title="<%="Child items (" + children.size() + ")"%>"
           context="<%=cc%>"
           >
           <tbl:table 
-            id="poolChilds"
+            id="children"
             clazz="itemlist"
             columns="all"
@@ -453 +471 @@
             />
             <tbl:columndef 
-              id="quantity"
-              title="Original quantity (µg)"
+              id="type"
+              title="Type"
             />
             <tbl:columndef 
-              id="parents"
-              title="Used samples[quantity]" 
+              id="quantity"
+              title="Used quantity (µg)"
             />
             <tbl:columndef 
@@ -468 +486 @@
               <tbl:rows>
               <%
-              for (BioMaterialEvent poolingEvt : poolingEvents)
+              for (BioMaterialEventSource item : children)
               {
-                Sample child = (Sample)poolingEvt.getBioMaterial();
-                ItemQuery<Sample> samplesQuery = (ItemQuery<Sample>)poolingEvt.getSources();
-                samplesQuery.include(Include.ALL);
-                samplesQuery.order(Orders.asc(Hql.property("name")));
-                ItemResultList<Sample> parentSamples = samplesQuery.list(dc);
+                BioMaterial bm = null;
+                try
+                {
+                  bm = item.getEvent().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 (Sample parent : parentSamples)
-                  {
-                    out.write(separator);
-                    if (parent.equals(sample))
-                        out.write(HTML.encodeTags(parent.getName()));
-                    else                    
-                      out.write(Base.getLinkedName(ID, parent, false, true));
-                    out.write("[" + Values.formatNumber(poolingEvt.getUsedQuantity(parent), 2) + "µg]");
-                    separator = ", ";
-                  }
-                  %>
-                  </tbl:cell>
-                  <tbl:cell column="description"><%=HTML.encodeTags(child.getDescription())%></tbl:cell>
+                      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>
                 <%
@@ -512 +515 @@
         <%
       }
-        
-      // Extracts created from this sample
-      ItemQuery<Extract> extractQuery = sample.getExtracts();
-      extractQuery.include(Include.ALL);
-      extractQuery.order(Orders.asc(Hql.property("name")));
-      ItemResultList<Extract> extracts = extractQuery.list(dc);
-      if (extracts.size() == 0)
-      {
-        %>
-        <h4>Extracts</h4>
-        No extracts have been created from this sample
-        (or, you don't have permission to view them).
-        <%
-      }
-      else
-      {
-        %>
-        <base:section 
-          id="extractSection" 
-          title="<%="Extracts (" + extracts.size() + ")"%>"
-          context="<%=cc%>"
-          >
-          <tbl:table
-            id="extracts"
-            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 (Extract e : extracts)
-                {
-                  %>
-                  <tbl:row>
-                    <tbl:cell column="name"><base:icon 
-                    image="deleted.gif" 
-                    tooltip="This item has been scheduled for deletion" 
-                    visible="<%=e.isRemoved()%>"
-                  /><%=Base.getLinkedName(ID, e, false, true)%></tbl:cell>
-                    <tbl:cell column="quantity"><%=Values.formatNumber(e.getCreationEvent().getUsedQuantity(sample), 2)%></tbl:cell>
-                    <tbl:cell column="description"><%=HTML.encodeTags(e.getDescription())%></tbl:cell>
-                  </tbl:row>
-                  <%
-                }
-                %>
-              </tbl:rows>
-            </tbl:data>
-          </tbl:table>
-        </base:section>
-        <%
-      }     
       %>
       <jsp:include page="../../common/anytoany/list_anytoany.jsp">

trunk/www/include/styles/main.css

@@ -345 +345 @@
 }
 
-.buttonclass_hover {
+.buttonclass:hover {
   background: #F0F0F0;
   border-top: 1px solid #333333;