Changeset 5662

Timestamp:

Jun 20, 2011, 1:55:13 PM (12 years ago)

Author:

Nicklas Nordborg

Message:

References #1153: Handling short read transcript sequence data

Removed the old "hack" with UsedQuantity and the dummy column used to store the array index. This has now been replaced with BioMaterialEventSource which is almost a full-fledged item and it should be easier to handle and create queries using the information.

Location:

trunk

Files:

• src/core/net/sf/basedb/core/BioMaterialEvent.java (modified) (11 diffs)
• src/core/net/sf/basedb/core/BioMaterialEventSource.java (added)
• src/core/net/sf/basedb/core/Extract.java (modified) (3 diffs)
• src/core/net/sf/basedb/core/Sample.java (modified) (1 diff)
• src/core/net/sf/basedb/core/SpecialQuery.java (added)
• src/core/net/sf/basedb/core/data/BioMaterialData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/BioMaterialEventData.java (modified) (3 diffs)
• src/core/net/sf/basedb/core/data/BioMaterialEventSourceData.java (added)
• src/core/net/sf/basedb/core/data/BioMaterialSourceEventData.java (deleted)
• src/core/net/sf/basedb/core/data/MeasuredBioMaterialData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/UsedQuantity.java (deleted)
• src/core/net/sf/basedb/util/biomaterial/PooledChildrenTransformer.java (modified) (1 diff)
• src/core/net/sf/basedb/util/biomaterial/PooledParentsTransformer.java (modified) (1 diff)
• src/core/net/sf/basedb/util/overview/loader/PhysicalBioAssayLoader.java (modified) (1 diff)
• src/core/net/sf/basedb/util/overview/loader/RawBioAssayLoader.java (modified) (3 diffs)
• src/core/net/sf/basedb/util/transform (added)
• src/core/net/sf/basedb/util/transform/Transformer.java (added)
• src/plugins/core/net/sf/basedb/plugins/batchimport/ExtractImporter.java (modified) (3 diffs)
• src/plugins/core/net/sf/basedb/plugins/batchimport/HybridizationImporter.java (modified) (3 diffs)
• src/plugins/core/net/sf/basedb/plugins/batchimport/LabeledExtractImporter.java (modified) (3 diffs)
• src/plugins/core/net/sf/basedb/plugins/batchimport/PhysicalBioAssayImporter.java (modified) (3 diffs)
• src/plugins/core/net/sf/basedb/plugins/batchimport/SampleImporter.java (modified) (1 diff)
• src/test/TestExtract.java (modified) (2 diffs)
• src/test/TestPhysicalBioAssay.java (modified) (3 diffs)
• src/test/TestSample.java (modified) (1 diff)
• src/test/TestTag.java (modified) (1 diff)
• src/test/net/sf/basedb/test/roles/UserTest.java (modified) (3 diffs)
• www/biomaterials/extracts/index.jsp (modified) (3 diffs)
• www/biomaterials/extracts/list_extracts.jsp (modified) (4 diffs)
• www/biomaterials/samples/index.jsp (modified) (1 diff)
• www/biomaterials/samples/list_samples.jsp (modified) (3 diffs)
• www/biomaterials/samples/view_sample.jsp (modified) (5 diffs)
• www/biomaterials/wizards/index.jsp (modified) (4 diffs)
• www/views/physicalbioassays/edit_bioassay.jsp (modified) (2 diffs)
• www/views/physicalbioassays/index.jsp (modified) (2 diffs)
• www/views/physicalbioassays/list_bioassays.jsp (modified) (4 diffs)
• www/views/physicalbioassays/view_bioassay.jsp (modified) (4 diffs)

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

@@ -26 +26 @@
 import net.sf.basedb.core.query.Hql;
 
+import net.sf.basedb.core.data.BioMaterialData;
 import net.sf.basedb.core.data.BioMaterialEventData;
+import net.sf.basedb.core.data.BioMaterialEventSourceData;
 import net.sf.basedb.core.data.HardwareData;
 import net.sf.basedb.core.data.MeasuredBioMaterialData;
 import net.sf.basedb.core.data.ProtocolData;
 import net.sf.basedb.core.data.UserData;
-import net.sf.basedb.core.data.UsedQuantity;
 import net.sf.basedb.core.data.SharedData;
 
@@ -37 +38 @@
 import java.util.HashMap;
 import java.util.Date;
-import java.util.Iterator;
 
 /**
@@ -599 +599 @@
     else
     {
-      UsedQuantity used = getData().getSources().get((MeasuredBioMaterialData)bioMaterial.getData());
-      return used == null ? null : used.getUsedQuantity();
-    }
-  }
-  
-  /**
-    Get the source group of the biomaterial
-    @param bioMaterial The source biomaterial
-    @return The source group index or 0 if the biomaterial is not a source of this event
-    @since 2.6
-    @see #setSourceGroup(MeasuredBioMaterial, int)
-  */
-  public int getSourceGroup(MeasuredBioMaterial bioMaterial)
-  {
-    UsedQuantity used = getData().getSources().get(bioMaterial.getData());
-    return used != null ? used.getSourceGroup() : 0;
-  }
-  
-  /**
-    Add a source biomaterial to this event or update
-    the used quantity of an existing source. Sources can only be specified if
-    the produced biomaterial is a pooled biomaterial and this is a creation event.
-    
-    @param bioMaterial The biomaterial used as a source
-    @param usedQuantity The quantity that was used from the source biomaterial
-    @throws PermissionDeniedException If the logged in user doesn't have 
-      write permission for this event of use permission for the source
-    @throws InvalidDataException If this is not a creation event or 
-      if the produced biomaterial is not pooled or if the source
-      biomaterial is of another type
-    @throws BaseException If there is another error
-  */
-  public void addSource(MeasuredBioMaterial bioMaterial, Float usedQuantity)
-    throws PermissionDeniedException, InvalidDataException, BaseException
+      BioMaterialEventSourceData src = getData().getSources().get(bioMaterial.getData());
+      return src == null ? null : src.getUsedQuantity();
+    }
+  }
+  
+  /**
+    Get information about a biomaterial used as a source to this event.
+    @param bioMaterial The biomaterial
+    @return A BioMaterialEventSource object or null if the given biomaterial
+      is not a source to the event
+    @see #addSource(BioMaterial)
+  */
+  public BioMaterialEventSource getEventSource(BioMaterial bioMaterial)
+  {
+    BioMaterialEventSourceData src = getData().getSources().get(bioMaterial.getData());
+    return src == null ? null : new BioMaterialEventSource(getDbControl(), src); //(this);
+  }
+  
+  /**
+    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
+    @return A BioMaterialEventSource object
+  */
+  public BioMaterialEventSource addSource(BioMaterial bioMaterial)
   {
     checkPermission(Permission.RESTRICTED_WRITE);
@@ -638 +630 @@
     bioMaterial.checkPermission(Permission.USE);
     checkAllowedSource(bioMaterial);
-    MeasuredBioMaterialData data = (MeasuredBioMaterialData)bioMaterial.getData();
-    UsedQuantity used = getData().getSources().get(data);
-    if (used != null)
-    {
-      // There is already an entry for this biomaterial
-      if (used.getUsedQuantity() != null)
-      {
-        // Return the old value to the biomaterial
-        MeasuredBioMaterial.updateRemainingQuantity(getDbControl(), data, -used.getUsedQuantity());
-      }
-      // Set the new value
-      used.setUsedQuantity(usedQuantity);
-    }
-    else
-    {
-      // This is a new entry
-      used = new UsedQuantity(usedQuantity, 1); 
-      getData().getSources().put(data, used);
-    }
-    if (usedQuantity != null) 
-    {
-      // Take away the new used quantity from the biomaterial
-      MeasuredBioMaterial.updateRemainingQuantity(getDbControl(), data, usedQuantity);
-    }
-  }
-  
-  /**
-    Set the source group for a biomaterial that was used as a source in this event.
-    The source group value is used to group sources that are related. The only
-    example and use case is when using multi-array hybridizations
-    where it is essential to know which array a labeled extract goes on. The source
-    group is then simply the number of the array on the hybridization and should be
-    a value between 1 and {@link PhysicalBioAssay#getSize()}.
-    <p>
-    A single labeled extract can only be used in a single group. Experiments using a n-channel
-    platform and a common reference must first split the reference labeled extract
-    into individual labeled extracts. This can be done with the 'pooling' functionality.
-    <p>
-    If the source biomaterial has not been added with {@link #addSource(MeasuredBioMaterial, Float)}
-    this method will automatically add it with usedQuantity = null.
-  
-    @param bioMaterial The source biomaterial
-    @param sourceGroup The source group
-    @throws PermissionDeniedException If the logged in user doesn't have 
-      write permission for this event of use permission for the source
-    @throws InvalidDataException If this is not a creation event or 
-      if the produced biomaterial is not pooled or if the source
-      biomaterial is of another type
-    @since 2.6
-  */
-  public void setSourceGroup(MeasuredBioMaterial bioMaterial, int sourceGroup)
-    throws PermissionDeniedException, InvalidDataException, BaseException
-  {
-    checkPermission(Permission.RESTRICTED_WRITE);
-    if (bioMaterial == null) throw new InvalidUseOfNullException("bioMaterial");
-    MeasuredBioMaterialData data = (MeasuredBioMaterialData)bioMaterial.getData();
-
-    UsedQuantity used = getData().getSources().get(data);
-    if (used == null)
-    {
-      addSource(bioMaterial, null);
-      used = getData().getSources().get(data);
-    }
-    if (used != null)
-    {
-      used.setSourceGroup(sourceGroup);
-    }
-  }
-  
+    return addCheckedSource(bioMaterial);
+  }
+  
+  private BioMaterialEventSource addCheckedSource(BioMaterial bioMaterial)
+  {
+    BioMaterialData bmData = (BioMaterialData)bioMaterial.getData();
+    BioMaterialEventSourceData src = getData().getSources().get(bmData);
+    if (src == null)
+    {
+      src = new BioMaterialEventSourceData();
+      src.setBioMaterial(bmData);
+      src.setEvent(this.getData());
+      getData().getSources().put(bmData, src);
+    }
+    return new BioMaterialEventSource(getDbControl(), src);
+  }
+
   /**
     Remove a biomaterial used as a source. Sources can only be specified if
@@ -718 +658 @@
     @throws BaseException If there is another error
   */
-  public void removeSource(MeasuredBioMaterial bioMaterial)
+  public void removeSource(BioMaterial bioMaterial)
     throws PermissionDeniedException, InvalidDataException, BaseException
   {
@@ -724 +664 @@
     if (bioMaterial == null) throw new InvalidUseOfNullException("bioMaterial");
     checkAllowedSource(bioMaterial);
-    MeasuredBioMaterialData data = (MeasuredBioMaterialData)bioMaterial.getData();
-    UsedQuantity used = getData().getSources().remove(data);
-    Float usedQuantity = used == null ? null : used.getUsedQuantity();
-    if (usedQuantity != null) MeasuredBioMaterial.updateRemainingQuantity(getDbControl(), data, -usedQuantity);
+    BioMaterialData data = (BioMaterialData)bioMaterial.getData();
+    BioMaterialEventSourceData src = getData().getSources().remove(data);
+    if (src == null) return;
+    
+    if (src.getId() != 0) getDbControl().getHibernateSession().delete(src);
+    if (data instanceof MeasuredBioMaterialData)
+    {
+      Float used = src.getUsedQuantity();
+      if (used != null)
+      {
+        MeasuredBioMaterial.updateRemainingQuantity(getDbControl(), (MeasuredBioMaterialData)data, -used);
+      }
+    }
   }
 
@@ -739 +688 @@
     </ul>
   */
-  private void checkAllowedSource(MeasuredBioMaterial bioMaterial)
+  private void checkAllowedSource(BioMaterial bioMaterial)
     throws PermissionDeniedException, InvalidDataException, BaseException
   {
@@ -784 +733 @@
     Set a single source. This method is used for non-pooled biomaterial
     to specify the parent. 
-    @see Extract#setSample(Sample, Float)
-  */
-  void setSource(MeasuredBioMaterial bioMaterial, Float usedQuantity)
+    @see Extract#setSample(Sample)
+  */
+  BioMaterialEventSource setSource(MeasuredBioMaterial bioMaterial)
     throws PermissionDeniedException, InvalidDataException
   {
     clearSources();
-    if (bioMaterial != null)
-    {
-      MeasuredBioMaterialData data = (MeasuredBioMaterialData)bioMaterial.getData();
-      getData().getSources().put(data, new UsedQuantity(usedQuantity, 1));
-      if (usedQuantity != null) MeasuredBioMaterial.updateRemainingQuantity(getDbControl(), data, usedQuantity);
-    }
+    return bioMaterial == null ? null : addCheckedSource(bioMaterial);
   }
   
@@ -804 +748 @@
   void clearSources()
   {
-    Iterator<Map.Entry<MeasuredBioMaterialData, UsedQuantity>> i = getData().getSources().entrySet().iterator();
-    while (i.hasNext())
-    {
-      Map.Entry<MeasuredBioMaterialData, UsedQuantity> entry = i.next();
-      MeasuredBioMaterialData source = entry.getKey();
-      UsedQuantity used = entry.getValue();
-      Float usedQuantity = used == null ? null : used.getUsedQuantity();
-      if (usedQuantity != null) MeasuredBioMaterial.updateRemainingQuantity(getDbControl(), source, -usedQuantity);
-      i.remove();
-    }
+    DbControl dc = getDbControl();
+    for (BioMaterialEventSourceData src : getData().getSources().values())
+    {
+      BioMaterialData bioMaterial = src.getBioMaterial();
+      Float used = src.getUsedQuantity();
+      if (used != null && bioMaterial instanceof MeasuredBioMaterialData) 
+      {
+        MeasuredBioMaterial.updateRemainingQuantity(dc, (MeasuredBioMaterialData)bioMaterial, -used);
+      }
+      dc.getHibernateSession().delete(src);
+    }
+    getData().getSources().clear();
   }
 
   /**
     Get a query that return all biomaterials used as sources
-    for this event. To filter or sort on the used quantity or source group columns
-    use 'srcevt' as alias. For example to only return sources in source group 2
+    for this event. To filter or sort on the used quantity or position columns
+    use 'srcevt' as alias. For example to only return sources in position 2
     and to order the result by used quantity:
     <pre class="code">
 query = event.getSources();
 query.restrict(Expressions.gteq(
-  Hql.property("srcevt", "sourceGroup"), Expressions.integer(2))
+  Hql.property("srcevt", "position"), Expressions.integer(2))
 );
 query.order(Orders.asc(Hql.property("srcevt", "usedQuantity")));
@@ -870 +816 @@
     }
     
-    query.joinPermanent(Hql.innerJoin("sourceEvents", "srcevt"));
+    query.joinPermanent(Hql.innerJoin("childCreationEvents", "srcevt"));
     query.joinPermanent(Hql.innerJoin("srcevt", "event", TYPE.getAlias()));
     query.restrictPermanent(
@@ -882 +828 @@
   
   /**
+    Create a special query that return BioMaterialEventSource objects.
+    The objects are not {@link BasicItem}:s but can be used to get information
+    about and modify the source biomaterials used in the event. Note
+    that the query may return objects that link to biomaterial that the
+    logged in used doesn't have read access to.
+    @return A special query
+    @since 3.0
+  */
+  public SpecialQuery<BioMaterialEventSource> getEventSources()
+  {
+    SpecialQuery<BioMaterialEventSource> query = 
+      new SpecialQuery<BioMaterialEventSource>(null, "BioMaterialEventSourceData", "es", 
+          new BioMaterialEventSource.BioMaterialEventSourceTransformer());
+    query.restrictPermanent(Restrictions.eq(Hql.property("es", "event"), Hql.entity(this)));
+    return query;
+  }
+  
+  /**
     The maximum length of the comment about this event. Check the length
     against this value before calling the {@link #setComment(String)}

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

@@ -258 +258 @@
     of this extract.
     @param sample The new <code>Sample</code> item
-    @param usedQuantity The quantity that was used from the sample when 
-      the extract was created
     @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
-  */
-  public void setSample(Sample sample, Float usedQuantity)
+    @since 3.0
+  */
+  public BioMaterialEventSource setSample(Sample sample)
     throws PermissionDeniedException, InvalidDataException, BaseException
   {
@@ -275 +274 @@
     }
     getData().setParent(sample == null ? null : sample.getData());
-    getCreationEvent().setSource(sample, usedQuantity);
-  }
-  
-
-  public void setExtract(Extract extract, Float usedQuantity)
+    return getCreationEvent().setSource(sample);
+  }
+  
+
+  public BioMaterialEventSource setExtract(Extract extract)
     throws PermissionDeniedException, InvalidDataException, BaseException
   {
@@ -286 +285 @@
     
     getData().setPooled(true);
-
     getData().setParent(extract == null ? null : extract.getData());
-    getCreationEvent().setSource(extract, usedQuantity);
+    return getCreationEvent().setSource(extract);
   }
 

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

@@ -281 +281 @@
   {
     Extract e = Extract.getNew(getDbControl(), master);
-    e.setSample(this, usedQuantity);
+    e.setSample(this).setUsedQuantity(usedQuantity);
     return e;
   }

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

@@ -120 +120 @@
   }
   
+  private Set<BioMaterialEventSourceData> childCreationEvents;
+  /**
+    This is the inverse end.
+    @see BioMaterialEventSourceData#getBioMaterial()
+    @hibernate.set lazy="true" inverse="true"
+    @hibernate.collection-key column="`biomaterial_id`"
+    @hibernate.collection-one-to-many class="net.sf.basedb.core.data.BioMaterialEventSourceData"
+  */
+  Set<BioMaterialEventSourceData> getChildCreationEvents()
+  {
+    return childCreationEvents;
+  }
+  void setChildCreationEvents(Set<BioMaterialEventSourceData> childCreationEvents)
+  {
+    this.childCreationEvents = childCreationEvents;
+  }
+
 }

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

@@ -26 +26 @@
 import java.util.Map;
 import java.util.HashMap;
-import java.util.Set;
 
 /**
@@ -123 +122 @@
   private PhysicalBioAssayData bioassay;
   /**
-    Get the hybridization that was created by this event.
+    Get the physical bioassay that was created by this event.
     @hibernate.many-to-one column="`physicalbioassay_id`" not-null="false" outer-join="false" update="false"
   */
@@ -210 +209 @@
   }
   
-  private Map<MeasuredBioMaterialData, UsedQuantity> sources;
-  /**
-    Get a map containing the source biomaterials and the used quantity for
-    this event.
-    @hibernate.map table="`BioMaterialEventSources`" lazy="true" cascade="delete"
+  private Map<BioMaterialData, BioMaterialEventSourceData> sources;
+  /**
+    Get a map containing information about the source biomaterials used
+    in the event. This is only used for events that create child biomaterial or
+    physical bioassay. This is the inverse end. See
+    {@link BioMaterialEventSourceData#getEvent()}
+    @hibernate.map inverse="true" lazy="true" cascade="all"
     @hibernate.collection-key column="`event_id`"
-    @hibernate.index-many-to-many column="`biomaterial_id`" class="net.sf.basedb.core.data.MeasuredBioMaterialData"
-    @hibernate.collection-composite-element class="net.sf.basedb.core.data.UsedQuantity"
-  */
-  public Map<MeasuredBioMaterialData, UsedQuantity> getSources()
-  {
-    if (sources == null) sources = new HashMap<MeasuredBioMaterialData, UsedQuantity>();
+    @hibernate.index-many-to-many column="`biomaterial_id`" class="net.sf.basedb.core.data.BioMaterialData"
+    @hibernate.collection-one-to-many class="net.sf.basedb.core.data.BioMaterialEventSourceData"
+    @since 3.0
+  */
+  public Map<BioMaterialData, BioMaterialEventSourceData> getSources()
+  {
+    if (sources == null) 
+    {
+      sources = new HashMap<BioMaterialData, BioMaterialEventSourceData>();
+    }
     return sources;
   }
-  void setSources(Map<MeasuredBioMaterialData, UsedQuantity> sources)
+  void setSources(Map<BioMaterialData, BioMaterialEventSourceData> sources)
   {
     this.sources = sources;
   }
   
-  private Set<MeasuredBioMaterialData> sourceBioMaterials;
-  /**
-    This is the inverse end. The children is the non-pooled biomaterials
-    that has this item as a parent.
-    @see MeasuredBioMaterialData#getParent()
-    @since 2.9
-    @hibernate.set table="`BioMaterialEventSources`" inverse="true" lazy="true"
-    @hibernate.collection-key column="`event_id`"
-    @hibernate.collection-many-to-many column="`biomaterial_id`" class="net.sf.basedb.core.data.MeasuredBioMaterialData"
-  */
-  Set<MeasuredBioMaterialData> getSourceBioMaterials()
-  {
-    return sourceBioMaterials;
-  }
-  void setSourceBioMaterials(Set<MeasuredBioMaterialData> sourceBioMaterials)
-  {
-    this.sourceBioMaterials = sourceBioMaterials;
-  }
-
 }

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

@@ -133 +133 @@
   }
   
-  private Set<BioMaterialSourceEventData> sourceEvents;
-  /**
-    This is the inverse end.
-    @see BioMaterialEventData#getSources()
-    @hibernate.set table="`BioMaterialEventSources`" lazy="true" inverse="true"
-    @hibernate.collection-key column="`biomaterial_id`"
-    @hibernate.collection-composite-element class="net.sf.basedb.core.data.BioMaterialSourceEventData"
-    hibernate.collection-many-to-many column="`event_id`" class="net.sf.basedb.core.data.BioMaterialEventData"
-  */
-  Set<BioMaterialSourceEventData> getSourceEvents()
-  {
-    return sourceEvents;
-  }
-  void setSourceEvents(Set<BioMaterialSourceEventData> sourceEvents)
-  {
-    this.sourceEvents = sourceEvents;
-  }
-  
   private BioWellData bioWell;
   /**

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

@@ -61 +61 @@
     query.include(Include.ALL);
     query.join(Hql.innerJoin("creationEvent", "ce"));
-    query.join(Hql.innerJoin("ce", "sourceBioMaterials", "sbm"));
+    query.join(Hql.innerJoin("ce", "sources", "sbm"));
+    query.join(Hql.innerJoin("sbm", "bioMaterial", "bm"));
     query.restrict(
       Restrictions.in(
-        Hql.alias("sbm"), 
+        Hql.alias("bm"), 
         Expressions.parameter("sources")
       )

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

@@ -60 +60 @@
     this.query = query;
     query.include(Include.ALL);
-    query.join(Hql.innerJoin("sourceEvents", "se"));
-    query.join(Hql.innerJoin("se", "event", "evt"));
+    query.join(Hql.innerJoin("childCreationEvents", "ce"));
+    query.join(Hql.innerJoin("ce", "event", "evt"));
     query.restrict(
       Restrictions.in(

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

@@ -200 +200 @@
     {
       PhysicalBioAssay bioAssay = it.next();
-      int arrayNum = bioAssay.getCreationEvent().getSourceGroup(extract);
-      Object cacheKey = arrayNum == 0 ? bioAssay : new IndexedCacheKey(bioAssay, arrayNum);
+      int position = bioAssay.getCreationEvent().getEventSource(extract).getPosition();
+      Object cacheKey = position == 0 ? bioAssay : new IndexedCacheKey(bioAssay, position);
       if (folderNode == null)
       {

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

@@ -23 +23 @@
 
 
+import net.sf.basedb.core.BioMaterialEventSource;
 import net.sf.basedb.core.DbControl;
 import net.sf.basedb.core.DerivedBioAssay;
@@ -82 +83 @@
     // to be able to load the correct raw bioassays -- The same physical bioassay
     // may have other raw bioassays that are NOT related to the same extract
-    int arrayNum = 0;
+    int position = 0;
     PhysicalBioAssay pba = null;
     Node physicalBioAssayNode = bioAssayNode.getFirstParent(new ItemTypeFilter(Item.PHYSICALBIOASSAY));
@@ -92 +93 @@
         pba = (PhysicalBioAssay)physicalBioAssayNode.getItem(dc);
         Extract extract = (Extract)extractNode.getItem();
-        arrayNum = pba.getCreationEvent().getSourceGroup(extract);
+        BioMaterialEventSource eventSource = pba.getCreationEvent().getEventSource(extract);
+        position = eventSource == null ? 0 : eventSource.getPosition();
       }
     }
-    if (arrayNum > 0)
+    if (position > 0)
     {
-      query.restrict(Restrictions.eq(Hql.property("arrayNum"), Expressions.integer(arrayNum)));
+      query.restrict(Restrictions.eq(Hql.property("arrayNum"), Expressions.integer(position)));
     }
     

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

@@ -27 +27 @@
 
 import net.sf.basedb.core.BioMaterialEvent;
+import net.sf.basedb.core.BioMaterialEventSource;
 import net.sf.basedb.core.BioPlate;
 import net.sf.basedb.core.BioWell;
@@ -241 +242 @@
         Float usedQuantity = usedQuantityMapper == null ?
           null : usedQuantityMapper.getFloat(data);
-        if (nameOrId == null || sample != null) extract.setSample(sample, usedQuantity);
+        if (nameOrId == null || sample != null) 
+        {
+          BioMaterialEventSource evtSrc = extract.setSample(sample);
+          if (evtSrc != null) evtSrc.setUsedQuantity(usedQuantity);
+        }
       }
     }
@@ -266 +271 @@
         Float usedQuantity = usedQuantityMapper == null ?
             null : usedQuantityMapper.getFloat(data);
-        extract.getCreationEvent().addSource(parent, usedQuantity);
+        extract.getCreationEvent().addSource(parent).setUsedQuantity(usedQuantity);
         // Use same tag as parent if not yet set and not mapped in the file
         if (tagMapper == null && parent.getTag() != null && extract.getTag() == null)

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

@@ -29 +29 @@
 import net.sf.basedb.core.ArraySlide;
 import net.sf.basedb.core.BioMaterialEvent;
+import net.sf.basedb.core.BioMaterialEventSource;
 import net.sf.basedb.core.DbControl;
 import net.sf.basedb.core.Extract;
@@ -305 +306 @@
       {
         BioMaterialEvent creationEvent = hyb.getCreationEvent();
-        int currentIndex = creationEvent.getSourceGroup(parent);
+        BioMaterialEventSource eventSource = creationEvent.addSource(parent);
+        int currentIndex = eventSource.getPosition();
         Float usedQuantity = usedQuantityMapper == null ?
             null : usedQuantityMapper.getFloat(data);
-        creationEvent.addSource(parent, usedQuantity);
+        eventSource.setUsedQuantity(usedQuantity);
         if (arrayIndexMapper != null)
         {
@@ -321 +323 @@
                   "also associate it with array index " + arrayIndex);
             }
-            creationEvent.setSourceGroup(parent, arrayIndex);
+            eventSource.setPosition(arrayIndex);
           }
         }

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

@@ -27 +27 @@
 
 import net.sf.basedb.core.BioMaterialEvent;
+import net.sf.basedb.core.BioMaterialEventSource;
 import net.sf.basedb.core.BioPlate;
 import net.sf.basedb.core.BioWell;
@@ -244 +245 @@
         Float usedQuantity = usedQuantityMapper == null ?
           null : usedQuantityMapper.getFloat(data);
-        if (nameOrId == null || parent != null) extract.setExtract(parent, usedQuantity);
+        if (nameOrId == null || parent != null) 
+        {
+          BioMaterialEventSource evtSrc = extract.setExtract(parent);
+          if (evtSrc != null) evtSrc.setUsedQuantity(usedQuantity);
+        }
       }
     }
@@ -268 +273 @@
         Float usedQuantity = usedQuantityMapper == null ?
             null : usedQuantityMapper.getFloat(data);
-        extract.getCreationEvent().addSource(parent, usedQuantity);
+        extract.getCreationEvent().addSource(parent).setUsedQuantity(usedQuantity);
         // Use same tag as parent if not yet set and not mapped in the file
         if (labelMapper == null && parent.getTag() != null && extract.getTag() == null)

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

@@ -29 +29 @@
 import net.sf.basedb.core.ArraySlide;
 import net.sf.basedb.core.BioMaterialEvent;
+import net.sf.basedb.core.BioMaterialEventSource;
 import net.sf.basedb.core.DbControl;
 import net.sf.basedb.core.Extract;
@@ -301 +302 @@
       {
         BioMaterialEvent creationEvent = pba.getCreationEvent();
-        int currentPosition = creationEvent.getSourceGroup(parent);
-        Float usedQuantity = usedQuantityMapper == null ?
-            null : usedQuantityMapper.getFloat(data);
-        creationEvent.addSource(parent, usedQuantity);
+        BioMaterialEventSource eventSource = creationEvent.addSource(parent);
+        int currentPosition = eventSource.getPosition();
+        if (usedQuantityMapper != null)
+        {
+          eventSource.setUsedQuantity(usedQuantityMapper.getFloat(data));
+        }
         if (extractPositionMapper != null)
         {
@@ -317 +320 @@
                   "also associate it with position " + position);
             }
-            creationEvent.setSourceGroup(parent, position);
+            eventSource.setPosition(position);
           }
         }

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

@@ -351 +351 @@
         Float usedQuantity = usedQuantityMapper == null ?
             null : usedQuantityMapper.getFloat(data);
-        sample.getCreationEvent().addSource(parent, usedQuantity);
+        sample.getCreationEvent().addSource(parent).setUsedQuantity(usedQuantity);
       }
     }

trunk/src/test/TestExtract.java

@@ -97 +97 @@
         {
           Sample s = (Sample)parent;
-          e.setSample(s, 200.0f);
+          e.setSample(s).setUsedQuantity(200.0f);
         }
         else
         {
           e.setPooled(true);
-          e.getCreationEvent().addSource((MeasuredBioMaterial)parent,  200.0f);
+          e.getCreationEvent().addSource(parent).setUsedQuantity(200.0f);
         }
       }
@@ -153 +153 @@
         Extract s = Extract.getById(dc, sourceId);
         Float original = s.getOriginalQuantity();
-        evt.addSource(s, original == null ? null : original/2);
+        BioMaterialEventSource eventSource = evt.addSource(s);
+        if (original != null)
+        {
+          eventSource.setUsedQuantity(original/2);
+        }
       }
       dc.saveItem(e);

trunk/src/test/TestPhysicalBioAssay.java

@@ -106 +106 @@
       {
         Extract le = Extract.getById(dc, extractId);
-        evt.addSource(le, 100.0f);
+        BioMaterialEventSource eventSource = evt.addSource(le);
+        eventSource.setUsedQuantity(100.0f);
       }
       dc.saveItem(h);
@@ -265 +266 @@
   }
   
-  static void test_add_extract(int hybId, int extractId, int arrayNum, Float usedQuantity)
+  static void test_add_extract(int hybId, int extractId, int position, Float usedQuantity)
   {
     if (hybId == 0 || extractId == 0) return;
@@ -275 +276 @@
       Extract le = Extract.getById(dc, extractId);
       BioMaterialEvent event = h.getCreationEvent();
-      event.addSource(le, usedQuantity);
-      event.setSourceGroup(le, arrayNum);
+      BioMaterialEventSource eventSource = event.addSource(le);
+      eventSource.setUsedQuantity(usedQuantity);
+      eventSource.setPosition(position);
       dc.commit();
       write("--Add extract to bioassay OK");

trunk/src/test/TestSample.java

@@ -142 +142 @@
         Sample src = Sample.getById(dc, sourceId);
         Float original = src.getOriginalQuantity();
-        evt.addSource(src, original == null ? null : original/2);
+        BioMaterialEventSource eventSource = evt.addSource(src);
+        if (original != null)
+        {
+          eventSource.setUsedQuantity(original/2);
+        }
       }
       dc.saveItem(s);

trunk/src/test/TestTag.java

@@ -76 +76 @@
       dc.commit();
       id = t.getId();
+      dc = TestUtil.getDbControl();
+      dc.reattachItem(t, false);
       write_item(0, t);
       write("--Create tag OK");

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

@@ -398 +398 @@
     extract.setName(name);
     extract.setOriginalQuantity(100.0f);
-    extract.setSample(sample, 50.0f);
+    extract.setSample(sample).setUsedQuantity(50.0f);
     extract.getCreationEvent().setProtocol(Util.findProtocol(dc, "Extraction A"));
     dc.saveItem(extract);
@@ -418 +418 @@
     labeledExtract.setPooled(true);
     labeledExtract.getCreationEvent().setProtocol(Util.findProtocol(dc, "Labeling A"));
-    labeledExtract.getCreationEvent().addSource(extract, 50.0f);
+    labeledExtract.getCreationEvent().addSource(extract).setUsedQuantity(50.0f);
     dc.saveItem(labeledExtract);
     return labeledExtract;
@@ -450 +450 @@
     for (Extract le : extracts)
     {
-      creationEvent.addSource(le, 50.0f);
+      creationEvent.addSource(le).setUsedQuantity(50.0f);
     }
     dc.saveItem(hyb);

trunk/www/biomaterials/extracts/index.jsp

@@ -24 +24 @@
   @version 2.0
 --%>
+<%@page import="net.sf.basedb.core.BioMaterialEventSource"%>
 <%@ page pageEncoding="UTF-8" session="false"
   import="net.sf.basedb.core.SessionControl"
@@ -283 +284 @@
         {
           Sample s = sampleId == 0 ? null : Sample.getById(dc, sampleId);
-          extract.setSample(s, s == null ? null : Values.getFloat(request.getParameter("used_from_sample"), null));
+          BioMaterialEventSource evtSrc = extract.setSample(s);
+          if (evtSrc != null)
+          {
+            evtSrc.setUsedQuantity(Values.getFloat(request.getParameter("used_from_sample"), null));
+          }
           if (s != null) cc.setRecent(s, maxRecent);
         }
@@ -296 +301 @@
           {
             Extract e = Extract.getById(dc, eId);
-            creationEvent.addSource(e, Values.getFloat(request.getParameter("E"+eId), null));
+            creationEvent.addSource(e).setUsedQuantity(Values.getFloat(request.getParameter("E"+eId), null));
           }
         }

trunk/www/biomaterials/extracts/list_extracts.jsp

@@ -118 +118 @@
   
   final ItemQuery<Extract> parentExtractsQuery = Extract.getQuery();
-  parentExtractsQuery.join(Hql.innerJoin("sourceEvents", "srcevt"));
-  parentExtractsQuery.join(Hql.innerJoin("srcevt", "event", "evt"));
+  parentExtractsQuery.join(Hql.innerJoin("childCreationEvents", "cce"));
+  parentExtractsQuery.join(Hql.innerJoin("cce", "event", "evt"));
   parentExtractsQuery.restrict(Restrictions.eq(Hql.alias("evt"), Hql.entityParameter("creationEvent", Item.BIOMATERIALEVENT)));
   parentExtractsQuery.order(Orders.asc(Hql.property("name")));
@@ -398 +398 @@
         id="parents"
         title="Parent extracts"
-        property="&creationEvent.sourceBioMaterials(name)"
+        property="&creationEvent.sources(bioMaterial.name)"
         datatype="string"
         filterable="true"
@@ -406 +406 @@
         id="children"
         title="Child extracts"
-        property="&sourceEvents(event.bioMaterial.name)"
+        property="&childCreationEvents(event.bioMaterial.name)"
         datatype="string"
         filterable="true"
@@ -414 +414 @@
         id="physicalBioAssays"
         title="Physical bioassays"
-        property="&sourceEvents(event.physicalBioAssay.name)"
+        property="&childCreationEvents(event.physicalBioAssay.name)"
         datatype="string"
         filterable="true"

trunk/www/biomaterials/samples/index.jsp

@@ -284 +284 @@
           {
             Sample s = Sample.getById(dc, sId);
-            creationEvent.addSource(s, Values.getFloat(request.getParameter("S"+sId), null));
+            creationEvent.addSource(s).setUsedQuantity(Values.getFloat(request.getParameter("S"+sId), null));
           }
         }

trunk/www/biomaterials/samples/list_samples.jsp

@@ -115 +115 @@
   
   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.alias("evt"), Hql.entityParameter("creationEvent", Item.BIOMATERIALEVENT)));
   parentSamplesQuery.order(Orders.asc(Hql.property("name")));
@@ -395 +395 @@
         id="parents"
         title="Parent samples"
-        property="&creationEvent.sourceBioMaterials(name)"
+        property="&creationEvent.sources(bioMaterial.name)"
         datatype="string"
         filterable="true"
@@ -403 +403 @@
         id="children"
         title="Child samples"
-        property="&sourceEvents(event.bioMaterial.name)"
+        property="&childCreationEvents(event.bioMaterial.name)"
         datatype="string"
         filterable="true"

trunk/www/biomaterials/samples/view_sample.jsp

@@ -34 +34 @@
   import="net.sf.basedb.core.Sample"
   import="net.sf.basedb.core.BioSource"
+  import="net.sf.basedb.core.BioMaterial"
   import="net.sf.basedb.core.BioMaterialEvent"
+  import="net.sf.basedb.core.BioMaterialEventSource"
   import="net.sf.basedb.core.BioWell"
   import="net.sf.basedb.core.Protocol"
@@ -42 +44 @@
   import="net.sf.basedb.core.ItemQuery"
   import="net.sf.basedb.core.ItemResultList"
+  import="net.sf.basedb.core.query.ResultList"
+  import="net.sf.basedb.core.SpecialQuery"
   import="net.sf.basedb.core.Include"
   import="net.sf.basedb.core.MultiPermissions"
@@ -365 +369 @@
       if (sample.isPooled())
       {
-        ItemQuery<Sample> samplesQuery = (ItemQuery<Sample>)creationEvent.getSources();
-        samplesQuery.include(Include.ALL);
-        samplesQuery.order(Orders.asc(Hql.property("name")));
-        ItemResultList<Sample> samples = samplesQuery.list(dc);
+        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>
@@ -393 +396 @@
           <tbl:rows>
           <%
-          for (Sample item : samples)
+          for (BioMaterialEventSource item : sources)
           {
+            BioMaterial bm = null;
+            try
+            {
+              bm = item.getBioMaterial();
+            }
+            catch (PermissionDeniedException ex)
+            {}
             %>
             <tbl:row>
@@ -400 +410 @@
                   image="deleted.gif" 
                   tooltip="This item has been scheduled for deletion" 
-                  visible="<%=item.isRemoved()%>"
-                /><%=Base.getLinkedName(ID, item, false, true)%></tbl:cell>
-              <tbl:cell column="quantity"><%=Values.formatNumber(creationEvent.getUsedQuantity(item), 2)%></tbl:cell>
-              <tbl:cell column="description"><%=HTML.encodeTags(item.getDescription())%></tbl:cell>
+                  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>
             <%

trunk/www/biomaterials/wizards/index.jsp

@@ -22 +22 @@
   @author Nicklas
 --%>
+<%@page import="net.sf.basedb.core.BioMaterialEventSource"%>
 <%@ page pageEncoding="UTF-8" session="false"
   import="net.sf.basedb.core.SessionControl"
@@ -293 +294 @@
             if (isBioAssayEvent)
             {
-              pbaCreationEvent.addSource(parent, usedQuantity);
-              pbaCreationEvent.setSourceGroup(parent, column+1);
+              BioMaterialEventSource evtSrc = pbaCreationEvent.addSource(parent);
+              evtSrc.setUsedQuantity(usedQuantity);
+              evtSrc.setPosition(column+1);
             }
             else
@@ -308 +310 @@
               {
                 child = Extract.getNew(dc, destParticipant);
-                if (!pooled) ((Extract)child).setSample((Sample)parent, usedQuantity);
+                if (!pooled) ((Extract)child).setSample((Sample)parent).setUsedQuantity(usedQuantity);
               }
               /*
@@ -329 +331 @@
               if (pooled)
               {
-                child.getCreationEvent().addSource(parent, usedQuantity);
+                child.getCreationEvent().addSource(parent).setUsedQuantity(usedQuantity);
               }
               dc.saveItem(child);

trunk/www/views/physicalbioassays/edit_bioassay.jsp

@@ -35 +35 @@
   import="net.sf.basedb.core.PhysicalBioAssay"
   import="net.sf.basedb.core.BioMaterialEvent"
+  import="net.sf.basedb.core.BioMaterialEventSource"
   import="net.sf.basedb.core.ItemSubtype"
   import="net.sf.basedb.core.ArraySlide"
@@ -553 +554 @@
           else
           {
-            Float used = creationEvent.getUsedQuantity(extract);
+            BioMaterialEventSource evtSrc = creationEvent.getEventSource(extract);
+            Float used = evtSrc.getUsedQuantity();
             String usedQuantity = Values.formatNumber(used, -1);
             String usedWithUnit = used == null ? "-" : usedQuantity + " µg";
-            int arrayIndex = creationEvent.getSourceGroup(extract);
+            int position = evtSrc.getPosition();
             %>
-            Link.addNewItem(extracts, new Item('E', <%=extract.getId()%>, '<%=arrayIndex + ": " + HTML.javaScriptEncode(extract.getName())%> [<%=usedWithUnit%>]', '<%=usedQuantity%>:<%=arrayIndex%>'));
+            Link.addNewItem(extracts, new Item('E', <%=extract.getId()%>, '<%=position + ": " + HTML.javaScriptEncode(extract.getName())%> [<%=usedWithUnit%>]', '<%=usedQuantity%>:<%=position%>'));
             <%
           }

trunk/www/views/physicalbioassays/index.jsp

@@ -32 +32 @@
   import="net.sf.basedb.core.ArraySlide"
   import="net.sf.basedb.core.BioMaterialEvent"
+  import="net.sf.basedb.core.BioMaterialEventSource"
   import="net.sf.basedb.core.Extract"
   import="net.sf.basedb.core.Protocol"
@@ -242 +243 @@
           Float usedQuantity = Values.getFloat(extra[0], null);
           int position = extra.length > 1 ? Values.getInt(extra[1], 1) : 1;
-          creationEvent.addSource(e, usedQuantity);
-          creationEvent.setSourceGroup(e, position);
+          BioMaterialEventSource evtSrc = creationEvent.addSource(e);
+          evtSrc.setUsedQuantity(usedQuantity);
+          evtSrc.setPosition(position);
         }
       }

trunk/www/views/physicalbioassays/list_bioassays.jsp

@@ -33 +33 @@
   import="net.sf.basedb.core.DerivedBioAssaySet"
   import="net.sf.basedb.core.BioMaterialEvent"
+  import="net.sf.basedb.core.BioMaterialEventSource"
   import="net.sf.basedb.core.AnnotationType"
   import="net.sf.basedb.core.AnnotationSet"
@@ -100 +101 @@
   final ItemQuery<Extract> extractQuery = Extract.getQuery();
   extractQuery.include(cc.getInclude());
-  extractQuery.join(Hql.innerJoin("sourceEvents", "srcevt"));
-  extractQuery.join(Hql.innerJoin("srcevt", "event", "evt"));
+  extractQuery.join(Hql.innerJoin("childCreationEvents", "cce"));
+  extractQuery.join(Hql.innerJoin("cce", "event", "evt"));
   extractQuery.restrict(Restrictions.eq(Hql.property("evt", "physicalBioAssay"), Expressions.parameter("bioAssay")));
-  extractQuery.order(Orders.asc(Hql.property("srcevt", "sourceGroup")));
+  extractQuery.order(Orders.asc(Hql.property("cce", "position")));
   extractQuery.order(Orders.asc(Hql.property("name"))); 
 
@@ -292 +293 @@
         id="extracts"
         title="Extracts"
-        property="&creationEvent.sourceBioMaterials(name)"
+        property="&creationEvent.sources(bioMaterial.name)"
         datatype="string"
         filterable="true"
@@ -609 +610 @@
                       if (needIndex)
                       {
-                        out.write(creationEvent.getSourceGroup(extract) + ": ");
+                        out.write(creationEvent.getEventSource(extract).getPosition() + ": ");
                       }
                       if (mode.hasPropertyLink())

trunk/www/views/physicalbioassays/view_bioassay.jsp

@@ -36 +36 @@
   import="net.sf.basedb.core.ArraySlide"
   import="net.sf.basedb.core.BioMaterialEvent"
+  import="net.sf.basedb.core.BioMaterialEventSource"
   import="net.sf.basedb.core.Protocol"
   import="net.sf.basedb.core.DerivedBioAssaySet"
@@ -327 +328 @@
       ItemQuery<Extract> extractsQuery = (ItemQuery<Extract>)creationEvent.getSources();
       extractsQuery.include(Include.ALL);
-      extractsQuery.order(Orders.asc(Hql.property("srcevt", "sourceGroup")));
+      extractsQuery.order(Orders.asc(Hql.property("srcevt", "position")));
       extractsQuery.order(Orders.asc(Hql.property("name")));
       ItemResultList<Extract> extracts = extractsQuery.list(dc);
@@ -379 +380 @@
             for (Extract item : extracts)
             {
+              BioMaterialEventSource evtSrc = creationEvent.getEventSource(item);
               %>
               <tbl:row>
-                <tbl:cell column="position"><%=creationEvent.getSourceGroup(item)%></tbl:cell>
+                <tbl:cell column="position"><%=evtSrc.getPosition()%></tbl:cell>
                 <tbl:cell column="name"><base:icon 
                     image="deleted.gif" 
@@ -388 +390 @@
                   /><%=Base.getLinkedName(ID, item, false, true)%></tbl:cell>
                 <tbl:cell column="tag"><base:propertyvalue item="<%=item%>" property="tag" /></tbl:cell>
-                <tbl:cell column="quantity"><%=Values.formatNumber(creationEvent.getUsedQuantity(item), 2)%></tbl:cell>
+                <tbl:cell column="quantity"><%=Values.formatNumber(evtSrc.getUsedQuantity(), 2)%></tbl:cell>
                 <tbl:cell column="description"><%=HTML.encodeTags(item.getDescription())%></tbl:cell>
               </tbl:row>