Changeset 6082

Timestamp:

Aug 14, 2012, 3:54:00 PM (11 years ago)

Author:

Nicklas Nordborg

Message:

References #1707: Make it possible for a derived bioassay to have multiple physical bioassays as parents

Changed the database schema and implemented API methods for this. The web GUI has been updated, but some things are still broken. Eg. it is not possible to select an extract (will fix this in #1708) or inherit annotations correctly. Item overview and batch importers have not been fixed.

Code for updating an existing installation is also missing, so do not try this since it will probably break several things and cause data loss.

Location:

trunk

Files:

• src/core/common-queries.xml (modified) (2 diffs)
• src/core/net/sf/basedb/core/DerivedBioAssay.java (modified) (13 diffs)
• src/core/net/sf/basedb/core/Install.java (modified) (1 diff)
• src/core/net/sf/basedb/core/PhysicalBioAssay.java (modified) (3 diffs)
• src/core/net/sf/basedb/core/Update.java (modified) (4 diffs)
• src/core/net/sf/basedb/core/data/DerivedBioAssayData.java (modified) (5 diffs)
• src/core/net/sf/basedb/core/data/PhysicalBioAssayData.java (modified) (2 diffs)
• src/test/TestDerivedBioAssay.java (modified) (4 diffs)
• src/test/TestTag.java (modified) (1 diff)
• www/views/derivedbioassays/edit_bioassay.jsp (modified) (17 diffs)
• www/views/derivedbioassays/index.jsp (modified) (3 diffs)
• www/views/derivedbioassays/list_bioassays.jsp (modified) (5 diffs)
• www/views/derivedbioassays/view_bioassay.jsp (modified) (3 diffs)
• www/views/physicalbioassays/index.jsp (modified) (1 diff)
• www/views/physicalbioassays/list_bioassays.jsp (modified) (3 diffs)

trunk/src/core/common-queries.xml

@@ -1397 +1397 @@
       SELECT {1}
       FROM DerivedBioAssayData dba
-      WHERE dba.physicalBioAssay = :bioAssay
-      AND dba.parent is null
+      INNER JOIN dba.physicalBioAssays pba
+      WHERE pba = :bioAssay
+      AND dba.root = true
     </sql>
     <description>
@@ -1410 +1411 @@
       SELECT {1}
       FROM DerivedBioAssayData dba
-      WHERE dba.parent = :bioAssay
+      INNER JOIN dba.parents p
+      WHERE p = :bioAssay
     </sql>
     <description>

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

@@ -22 +22 @@
 package net.sf.basedb.core;
 
+import java.util.ArrayList;
 import java.util.Collection;
-import java.util.Collections;
 import java.util.Date;
 import java.util.HashSet;
@@ -29 +29 @@
 
 import net.sf.basedb.core.data.ArrayBatchData;
+import net.sf.basedb.core.data.ArrayDesignData;
 import net.sf.basedb.core.data.ArraySlideData;
 import net.sf.basedb.core.data.DerivedBioAssayData;
@@ -98 +99 @@
   
   /**
+    Create a new parent-less derived bioassay. Parent items can be 
+    added by calling {@link #addPhysicalBioAssay(PhysicalBioAssay)} or
+    {@link #addParent(DerivedBioAssay)}.
+    @param dc The <code>DbControl</code> which will be used for
+      permission checking and database access
+    @param isRoot TRUE if the new item is a root derived bioassay
+      (eg. it have physical bioassays as parent items)
+    @param job The job that created the new bioassay
+    @return A new DerivedBioAssay item
+    @since 3.2
+  */
+  public static DerivedBioAssay getNew(DbControl dc, boolean isRoot, Job job)
+  {
+    DerivedBioAssay dbas = dc.newItem(DerivedBioAssay.class);
+    dbas.setName("New derived bioassay");
+    dbas.getData().setRoot(isRoot);
+    dbas.getData().setEntryDate(new Date());
+    dbas.getData().setJob(job == null ? null : job.getData());
+    return dbas;
+    
+  }
+  
+  /**
     Create a new (root) derived bioassay from a physical bioassay.
     @param dc The <code>DbControl</code> which will be used for
@@ -107 +131 @@
   public static DerivedBioAssay getNew(DbControl dc, PhysicalBioAssay bioAssay, Job job)
   {
-    if (bioAssay == null) throw new InvalidUseOfNullException("bioAssay");
-    bioAssay.checkPermission(Permission.USE);
-    
-    DerivedBioAssay dbas = dc.newItem(DerivedBioAssay.class);
-    dbas.setName("New derived bioassay");
-    dbas.getData().setPhysicalBioAssay(bioAssay.getData());
-    dbas.getData().setEntryDate(new Date());
-    dbas.getData().setJob(job == null ? null : job.getData());
+    DerivedBioAssay dbas = getNew(dc, true, job);
+    dbas.addPhysicalBioAssay(bioAssay);
     return dbas;
   }
@@ -128 +146 @@
   public static DerivedBioAssay getNew(DbControl dc, DerivedBioAssay parent, Job job)
   {
-    if (parent == null) throw new InvalidUseOfNullException("parent");
-    parent.checkPermission(Permission.USE);
-    
-    DerivedBioAssay dbas = dc.newItem(DerivedBioAssay.class);
-    dbas.setName("New derived bioassay");
-    dbas.getData().setParent(parent.getData());
-    dbas.getData().setPhysicalBioAssay(parent.getData().getPhysicalBioAssay());
-    dbas.getData().setExtract(parent.getData().getExtract());
-    dbas.getData().setEntryDate(new Date());
-    dbas.getData().setJob(job == null ? null : job.getData());
+    DerivedBioAssay dbas = getNew(dc, false, job);
+    dbas.addParent(parent);
     return dbas;
   }
@@ -238 +248 @@
         SELECT {1}
         FROM DerivedBioAssayData dba
-        WHERE dba.parent = :bioAssay
+        INNER JOIN dba.parents p
+        WHERE p = :bioAssay
       */
       query.setEntity("bioAssay", this.getData());
@@ -295 +306 @@
   */
   /**
-    Get the extract and parent bioassay set or physical bioassay.
+    Get the extract and parent bioassays or physical bioassays.
   */
   @Override
@@ -306 +317 @@
       if (isRoot())
       {
-        annotatable.add(getPhysicalBioAssay());
+        ItemQuery<PhysicalBioAssay> query = getPhysicalBioAssays();
+        query.include(Include.ALL);
+        annotatable.addAll(query.list(getDbControl()));
       }
       else
       {
-        annotatable.add(getParent());
+        ItemQuery<DerivedBioAssay> query = getParents();
+        query.include(Include.ALL);
+        annotatable.addAll(query.list(getDbControl()));
       }
       if (getData().getExtract() != null) annotatable.add(getExtract());
@@ -394 +409 @@
   public Collection<FileSet> getParentFileSets()
   {
-    DerivedBioAssay parent = getParent();
+    ItemQuery<DerivedBioAssay> query = getParents();
+    query.include(Include.ALL);
     Collection<FileSet> parents = null;
-    if (parent != null && parent.hasFileSet())
-    {
-      parents = Collections.singleton(parent.getFileSet());
+    for (DerivedBioAssay parent : query.list(getDbControl()))
+    {
+      if (parent.hasFileSet())
+      {
+        if (parents == null) parents = new ArrayList<FileSet>();
+        parents.add(parent.getFileSet());
+      }
     }
     return parents;
@@ -408 +428 @@
     bioassay set. This property is always inherited down to child events 
     so this method never return null.
-  */
+    @deprecated In 3.2, replaced with {@link #getPhysicalBioAssays()}.
+    @return Always null
+  */
+  @Deprecated
   public PhysicalBioAssay getPhysicalBioAssay()
   {
-    return getDbControl().getItem(PhysicalBioAssay.class, getData().getPhysicalBioAssay());
-  }
+    return null;
+  }
+  
+  /**
+    Add a physical bioassay as a parent to this derived bioassay.
+    Note! Physical bioassays can only be added if this derived bioassay
+    is a root bioassay. The physical bioassay for non-root derived
+    bioassays are automatically assigned.
+    @param bioAssay The parent bioassay to add 
+    @since 3.2
+  */
+  public void addPhysicalBioAssay(PhysicalBioAssay bioAssay)
+    throws PermissionDeniedException, InvalidDataException
+  {
+    checkPermission(Permission.WRITE);
+    if (!isRoot()) throw new PermissionDeniedException("Can't add physical bioassay to non-root derived bioassay");
+    if (bioAssay == null) throw new InvalidUseOfNullException("bioAssay");
+    bioAssay.checkPermission(Permission.USE);
+    getData().getPhysicalBioAssays().add(bioAssay.getData());
+  }
+  
+  /**
+    Remove a physical bioassay as a parent item for this derived
+    bioassay.
+    Note! Physical bioassays can only be removed if this derived bioassay
+    is a root bioassay. The physical bioassay for non-root derived
+    bioassays are automatically assigned.
+    @param bioAssay The parent bioassay to remove from this bioassay
+    @since 3.2
+  */
+  public void removePhysicalBioAssay(PhysicalBioAssay bioAssay)
+    throws PermissionDeniedException, InvalidDataException
+  {
+    checkPermission(Permission.WRITE);
+    if (!isRoot()) throw new PermissionDeniedException("Can't remove physical bioassay from non-root derived bioassay");
+    if (bioAssay == null) throw new InvalidUseOfNullException("bioAssay");
+    getData().getPhysicalBioAssays().remove(bioAssay.getData());
+  }
+  
+  /**
+    Get a query that returns the physical bioassays used to create
+    this derived bioassay.
+    @return An <code>ItemQuery</code> object
+    @since 3.2
+  */
+  public ItemQuery<PhysicalBioAssay> getPhysicalBioAssays()
+  {
+    ItemQuery<PhysicalBioAssay> query = PhysicalBioAssay.getQuery();
+    query.joinPermanent(Hql.innerJoin("derivedBioAssays", Item.DERIVEDBIOASSAY.getAlias()));
+    query.restrictPermanent(
+      Restrictions.eq(
+        Hql.alias(Item.DERIVEDBIOASSAY.getAlias()), 
+        Hql.entity(this)
+      )
+    );
+    return query;
+  }
+
   
   /**
     Get the parent derived bioassay set.    
     @return The parent bioassay set or null if this item is a root bioassay set
-  */
+    @deprecated In 3.2, replaced with {@link #getParents()}
+    @return Always null
+  */
+  @Deprecated
   public DerivedBioAssay getParent()
   {
-    return getDbControl().getItem(DerivedBioAssay.class, getData().getParent());
-  }
-
-  /**
-    Check if this bioassay set is derived from a physical bioassay or from another
-    bioassay set.
+    return null;
+  }
+
+  
+  /**
+    Add a derived bioassay as a parent to this derived bioassay.
+    Note! Derived bioassays can only be added if this derived bioassay
+    is not a root bioassay. The physical bioassays are automatically assigned.
+    @param bioAssay The parent bioassay to add 
+    @since 3.2
+  */
+  public void addParent(DerivedBioAssay bioAssay)
+    throws PermissionDeniedException, InvalidDataException
+  {
+    checkPermission(Permission.WRITE);
+    if (isRoot()) throw new PermissionDeniedException("Root derived bioassays can't have parent derived bioassays");
+    if (bioAssay == null) throw new InvalidUseOfNullException("bioAssay");
+    if (this.equals(bioAssay)) throw new InvalidDataException("Can't add self as parent: " + this);
+    bioAssay.checkPermission(Permission.USE);
+    getData().getParents().add(bioAssay.getData());
+    getData().getPhysicalBioAssays().addAll(bioAssay.getData().getPhysicalBioAssays());
+  }
+
+  /**
+    Remove a derived bioassay as a parent item for this derived
+    bioassay.
+    Note! Derived bioassays can only be used as parents if this derived bioassay
+    is not a root bioassay. The physical bioassays are automatically assigned.
+    @param bioAssay The parent bioassay to remove from this bioassay
+    @since 3.2
+  */
+  public void removeParent(DerivedBioAssay bioAssay)
+    throws PermissionDeniedException, InvalidDataException
+  {
+    checkPermission(Permission.WRITE);
+    if (isRoot()) throw new PermissionDeniedException("Root derived bioassays can't have parent derived bioassays");
+    if (bioAssay == null) throw new InvalidUseOfNullException("bioAssay");
+    getData().getParents().remove(bioAssay.getData());
+  }
+
+  
+  /**
+    Get all parent derived bioassays.
+    @return A query returning all parent bioassays
+    @since 3.2
+  */
+  public ItemQuery<DerivedBioAssay> getParents()
+  {
+    ItemQuery<DerivedBioAssay> query = DerivedBioAssay.getQuery();
+    query.joinPermanent(Hql.innerJoin("children", "c"));
+    query.restrictPermanent(
+      Restrictions.eq(
+        Hql.alias("c"),
+        Hql.entity(this)
+      )
+    );
+    return query;
+  }
+
+  
+  /**
+    Check if this bioassay set is derived from one or more physical bioassays or 
+    from derived bioassays. A root derived bioassay can only have physical bioassays
+    as parent items. A non-root derived bioassay can only have other derived
+    bioassays as parents, but the core keep automatically keep track of the
+    physical bioassays.
     @return TRUE if this is a root bioassay set derived form a physical bioassay
   */
   public boolean isRoot()
   {
-    return getData().getParent() == null;
+    return getData().isRoot();
   }
   
@@ -466 +608 @@
   {
     ItemQuery<DerivedBioAssay> query = DerivedBioAssay.getQuery();
+    query.joinPermanent(Hql.innerJoin("parents", "p"));
     query.restrictPermanent(
       Restrictions.eq(
-        Hql.property("parent"),
+        Hql.alias("p"),
         Hql.entity(this)
       )
@@ -571 +714 @@
     Get the array design connected to this derived bioassay by 
     following the path from the physical bioassay to the array slide to 
-    the array batch  to the array design.
+    the array batch  to the array design. If this derived bioasay
+    has multiple parents that are linked to different array designs,
+    null is returned.
     @return The array design, or null if no array design is connected
     @throws PermissionDeniedException If the logged in user doesn't have 
@@ -580 +725 @@
     throws PermissionDeniedException, BaseException
   {
-    PhysicalBioAssayData pba = getData().getPhysicalBioAssay();
-    if (pba == null) return null;
-    ArraySlideData slide = pba.getArraySlide();
-    if (slide == null) return null;
-    ArrayBatchData batch = slide.getArrayBatch();
-    if (batch == null) return null;
-    return getDbControl().getItem(ArrayDesign.class, batch.getArrayDesign());
+    ArrayDesignData uniqueDesign = null;
+    for (PhysicalBioAssayData pba : getData().getPhysicalBioAssays())
+    {
+      ArraySlideData slide = pba.getArraySlide();
+      if (slide == null) continue;
+      
+      ArrayBatchData batch = slide.getArrayBatch();
+      if (batch == null) continue;
+      
+      ArrayDesignData design = batch.getArrayDesign();
+      if (design == null) continue;
+      
+      if (uniqueDesign == null)
+      {
+        // First array design we see is (temporarily) accepted as the one to return
+        uniqueDesign = design;
+      }
+      else
+      {
+        // If the design are different, break out and return null
+        if (!design.equals(uniqueDesign)) return null;
+      }
+    }
+    
+    return getDbControl().getItem(ArrayDesign.class, uniqueDesign);
   }
 

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

@@ -119 +119 @@
     method.
   */
-  public static final int NEW_SCHEMA_VERSION = Integer.valueOf(108).intValue();
+  public static final int NEW_SCHEMA_VERSION = Integer.valueOf(109).intValue();
   
   public static synchronized int createTables(SchemaGenerator.Mode mode, ProgressReporter progress,

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

@@ -235 +235 @@
         SELECT {1}
         FROM DerivedBioAssayData dba
-        WHERE dba.physicalBioAssay = :bioAssay
-        AND dba.parent is null
+        INNER JOIN dba.physicalBioAssays pba
+        WHERE pba = :bioAssay
+        AND dba.root = true
       */
     query.setEntity("bioAssay", this.getData());
@@ -441 +442 @@
   {
     ItemQuery<DerivedBioAssay> query = DerivedBioAssay.getQuery();
-    query.restrictPermanent(
-      Restrictions.eq(
-        Hql.property("physicalBioAssay"), 
-        Hql.entity(this)
-      )
-    );
-    query.restrictPermanent(Restrictions.eq(Hql.property("parent"), null));
+    query.joinPermanent(Hql.innerJoin("physicalBioAssays", "pba"));
+    query.restrictPermanent(Restrictions.eq(Hql.alias("pba"), Hql.entity(this)));
+    query.restrictPermanent(Restrictions.eq(Hql.property("root"), Expressions.bool(true)));
     return query;
   }
@@ -467 +464 @@
       SELECT {1}
       FROM DerivedBioAssayData dba
-      WHERE dbs.physicalBioAssay = :bioAssay
-      AND dba.parent is null
+      INNER JOIN dba.physicalBioAssays pba
+      WHERE pba = :bioAssay
+      AND dba.root = true
     */
     query.setEntity("bioAssay", this.getData());

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

@@ -143 +143 @@
   </tr>
   <tr>
-    <td>107</td>
+    <td>108</td>
     <td>
       Added {@link BioPlateData#getSection()}, {@link BioPlateData#getTray()}
       and {@link BioPlateData#getPosition()}
       All existing bioplates get null values.
+    </td>
+  </tr>
+  <tr>
+    <td>109</td>
+    <td>
+      Added {@link DerivedBioAssayData#getPhysicalBioAssays()} and {@link DerivedBioAssayData#getParents()}
+      and removed <code>DerivedBioAssayData.getPhysicalBioAssay()</code> and 
+      <code>DerivedBioAssayData.getParent()</code>. Existing derived bioassays are updated.
     </td>
   </tr>
@@ -238 +246 @@
         schemaVersion = setSchemaVersionInTransaction(session, 108);
         progress_current += 2 * progress_step;
+      }
+      
+      if (schemaVersion < 109)
+      {
+        if (progress != null) progress.display((int)(progress_current), "--Updating schema version: " + schemaVersion + " -> 109...");
+        schemaVersion = updateToSchemaVersion109(session);
+        progress_current += progress_step;
       }
 
@@ -606 +621 @@
     return schemaVersion;
   }
+  
+  /**
+    Move derived bioassay parent items to different tables. Get rid of
+    old columns in the DerivedBioAssays table.
+    
+    @return The new schema version (=109)
+  */
+  private static int updateToSchemaVersion109(org.hibernate.Session session)
+    throws BaseException
+  {
+    final int schemaVersion = 109;
+    try
+    {
+  
+      // TODO - 1707
+      
+      // Update the schema version number
+      setSchemaVersionInTransaction(session, schemaVersion);
+  
+      log.info("updateToSchemaVersion109: OK");
+    }
+    catch (BaseException ex)
+    {
+      log.error("updateToSchemaVersion109: FAILED", ex);
+      throw ex;
+    }
+    return schemaVersion;
+  }
+
   
   // Item type codes for item types that was removed since BASE 2
@@ -1315 +1359 @@
         DerivedBioAssayData bioAssay = new DerivedBioAssayData();
         bioAssay.setEntryDate((Date)row[2]);
-        bioAssay.setPhysicalBioAssay(load(session, PhysicalBioAssayData.class, hybMap.get(row[3])));
+        bioAssay.setRoot(true);
+        bioAssay.getPhysicalBioAssays().add(load(session, PhysicalBioAssayData.class, hybMap.get(row[3])));
         bioAssay.setHardware(load(session, HardwareData.class, row[4]));
         bioAssay.setProtocol(load(session, ProtocolData.class, row[5]));

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

@@ -1 +1 @@
 /**
-  $Id: DerivedBioAssayData.java 5685 2011-08-04 10:58:23Z nicklas $
+  $Id$
 
   Copyright (C) 2011 Nicklas Nordborg
@@ -23 +23 @@
 
 import java.util.Date;
+import java.util.HashSet;
 import java.util.Set;
 
@@ -29 +30 @@
   @author Nicklas
   @since 3.0
-  @base.modified $Date: 2011-08-04 12:58:23 +0200 (to, 04 aug 2011) $
+  @base.modified $Date$
   @hibernate.class table="`DerivedBioAssays`" lazy="true"
   @see <a href="../../../../../../html/developer/api/data_api.bioassays.html">Developer documentation: Bioassays and raw data</a>
@@ -90 +91 @@
   // -------------------------------------------
 
-  private PhysicalBioAssayData bioAssay;
-  /**
-    Get the physical bioassay that is the direct or indirect parent bioassay set.
-    @hibernate.many-to-one column="`bioassay_id`" not-null="true" update="false" outer-join="false"
-  */
-  public PhysicalBioAssayData getPhysicalBioAssay()
-  {
-    return bioAssay;
-  }
-  public void setPhysicalBioAssay(PhysicalBioAssayData bioAssay)
-  {
-    this.bioAssay = bioAssay;
-  }
-
-  private DerivedBioAssayData parent;
-  /**
-    Get the bioassay that is the parent of this bioassay. Null if this bioassay was
-    created from a physical bioassay.
-    @hibernate.many-to-one column="`parent_id`" not-null="false" update="false" outer-join="false"
-  */
-  public DerivedBioAssayData getParent()
-  {
-    return parent;
-  }
-  public void setParent(DerivedBioAssayData parent)
-  {
-    this.parent = parent;
+  private boolean isRoot;
+  /**
+    A flag indicating if this is a root derived bioassay or not. A root
+    bioassay can only have physical bioassays as parents, while a non-root 
+    bioassay only can have other derived bioassays as parents (but the
+    physical bioassays collection should be automatically managed to reflect
+    the parents of the parents, etc.)
+    @since 3.2
+    @hibernate.property column="`is_root`" type="boolean" not-null="true" 
+  */
+  public boolean isRoot()
+  {
+    return isRoot;
+  }
+  public void setRoot(boolean isRoot)
+  {
+    this.isRoot = isRoot;
+  }
+  
+  private Set<PhysicalBioAssayData> physicalBioAssays;
+  /**
+    A set that manages the parent physical bioassays that this derived bioassay
+    is related to.
+    @since 3.2
+    @hibernate.set table="`ParentPhysicalBioAssays`" lazy="true"
+    @hibernate.collection-key column="`derivedbioassay_id`"
+    @hibernate.collection-many-to-many column="`physicalbioassay_id`" class="net.sf.basedb.core.data.PhysicalBioAssayData"
+  */
+  public Set<PhysicalBioAssayData> getPhysicalBioAssays()
+  {
+    if (physicalBioAssays == null) physicalBioAssays = new HashSet<PhysicalBioAssayData>();
+    return physicalBioAssays;
+  }
+  
+  void setPhysicalBioAssays(Set<PhysicalBioAssayData> physicalBioAssays)
+  {
+    this.physicalBioAssays = physicalBioAssays;
+  }
+  
+  private Set<DerivedBioAssayData> parents;
+  /**
+    A set that manages the parent bioassays that this derived bioassay
+    related to.
+    @since 3.2
+    @hibernate.set table="`ParentDerivedBioAssays`" lazy="true"
+    @hibernate.collection-key column="`derivedbioassay_id`"
+    @hibernate.collection-many-to-many column="`parentbioassay_id`" class="net.sf.basedb.core.data.DerivedBioAssayData"
+  */
+  public Set<DerivedBioAssayData> getParents()
+  {
+    if (parents == null) parents = new HashSet<DerivedBioAssayData>();
+    return parents;
+  }
+  void setParents(Set<DerivedBioAssayData> parents)
+  {
+    this.parents = parents;
   }
 
@@ -122 +152 @@
   /**
     This is the inverse end.
-    @see DerivedBioAssayData#getParent()
-    @hibernate.set lazy="true" inverse="true" 
-    @hibernate.collection-key column="`parent_id`"
-    @hibernate.collection-one-to-many class="net.sf.basedb.core.data.DerivedBioAssayData"
+    @see DerivedBioAssayData#getParents()
+    @hibernate.set table="`ParentDerivedBioAssays`" lazy="true" inverse="true" 
+    @hibernate.collection-key column="`parentbioassay_id`"
+    @hibernate.collection-many-to-many column="`derivedbioassay_id`" class="net.sf.basedb.core.data.DerivedBioAssayData"
   */
   Set<DerivedBioAssayData> getChildren()

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

@@ -105 +105 @@
   }
 
+  
   private Set<DerivedBioAssayData> rootDerivedBioAssays;
   /**
     This is the inverse end with an extra restriction 
     @see DerivedBioAssayData#getPhysicalBioAssay()
-    @hibernate.set lazy="true" inverse="true" where="`parent_id` is null"
-    @hibernate.collection-key column="`bioassay_id`"
-    @hibernate.collection-one-to-many class="net.sf.basedb.core.data.DerivedBioAssayData"
+    @hibernate.set table="`ParentPhysicalBioAssays`" lazy="true" inverse="true" 
+    @hibernate.collection-key column="`physicalbioassay_id`"
+    @hibernate.collection-many-to-many column="`derivedbioassay_id`" class="net.sf.basedb.core.data.DerivedBioAssayData" where="`is_root`"
   */
   Set<DerivedBioAssayData> getRootDerivedBioAssays()
@@ -125 +126 @@
   /**
     This is the inverse end.
-    @see DerivedBioAssayData#getPhysicalBioAssay()
-    @hibernate.set lazy="true" inverse="true" 
-    @hibernate.collection-key column="`bioassay_id`"
-    @hibernate.collection-one-to-many class="net.sf.basedb.core.data.DerivedBioAssayData"
+    @see DerivedBioAssayData#getPhysicalBioAssays()
+    @hibernate.set table="`ParentPhysicalBioAssays`" lazy="true" inverse="true" 
+    @hibernate.collection-key column="`physicalbioassay_id`"
+    @hibernate.collection-many-to-many column="`derivedbioassay_id`" class="net.sf.basedb.core.data.DerivedBioAssayData"
   */
   Set<DerivedBioAssayData> getDerivedBioAssays()

trunk/src/test/TestDerivedBioAssay.java

@@ -55 +55 @@
     
     // Children and bioassays
-    int child1 = test_create_child("Child #1", id, 0, 0, 0, 0, 0);
-    int child2 = test_create_child("Child #2", id, 0, 0, 0, 0, 0);
+    int child1 = test_create_child("Child #1", 0, 0, 0, 0, 0, id);
+    int child2 = test_create_child("Child #2", 0, 0, 0, 0, 0, id);
 
     // Listing
@@ -67 +67 @@
     TestDataFileType.test_set_file(Item.DERIVEDBIOASSAY, child1, DataFileType.SAM, samId);
     
+    // A more complex setup: 
+    // Extract #1 and #2 get four child items
+    // Two of each are put on two different physical bioassays
+    // A derived bioassay is created for each child extract (2+2=4)
+    // Two merged derived bioassays are created (one for each extract)
+    int tag1 = TestTag.test_create("T1", SystemItems.getId(Tag.BARCODE), false);
+    int tag2 = TestTag.test_create("T2", SystemItems.getId(Tag.BARCODE), false);
+    
+    int e1a1 = TestExtract.test_create(extractId1, "Extract #1.a1", SystemItems.getId(Extract.LIBRARY), tag1, false);
+    int e1a2 = TestExtract.test_create(extractId1, "Extract #1.a2", SystemItems.getId(Extract.LIBRARY), tag1, false);
+    int e1a3 = TestExtract.test_create(extractId1, "Extract #1.a3", SystemItems.getId(Extract.LIBRARY), tag1, false);
+    int e1a4 = TestExtract.test_create(extractId1, "Extract #1.a4", SystemItems.getId(Extract.LIBRARY), tag1, false);
+    int e2a1 = TestExtract.test_create(extractId2, "Extract #2.a1", SystemItems.getId(Extract.LIBRARY), tag2, false);
+    int e2a2 = TestExtract.test_create(extractId2, "Extract #2.a2", SystemItems.getId(Extract.LIBRARY), tag2, false);
+    int e2a3 = TestExtract.test_create(extractId2, "Extract #2.a3", SystemItems.getId(Extract.LIBRARY), tag2, false);
+    int e2a4 = TestExtract.test_create(extractId2, "Extract #2.a4", SystemItems.getId(Extract.LIBRARY), tag2, false);
+    
+    int flowCell1 = TestPhysicalBioAssay.test_create(0, "Flow cell #1", SystemItems.getId(PhysicalBioAssay.CLONAL_AMPLIFICATION), 2);
+    TestPhysicalBioAssay.test_add_extract(flowCell1, e1a1, 1, null);
+    TestPhysicalBioAssay.test_add_extract(flowCell1, e1a2, 2, null);
+    TestPhysicalBioAssay.test_add_extract(flowCell1, e2a1, 1, null);
+    TestPhysicalBioAssay.test_add_extract(flowCell1, e2a2, 2, null);
+
+    int flowCell2 = TestPhysicalBioAssay.test_create(0, "Flow cell #2", SystemItems.getId(PhysicalBioAssay.CLONAL_AMPLIFICATION), 2);
+    TestPhysicalBioAssay.test_add_extract(flowCell2, e1a3, 1, null);
+    TestPhysicalBioAssay.test_add_extract(flowCell2, e1a4, 2, null);
+    TestPhysicalBioAssay.test_add_extract(flowCell2, e2a3, 1, null);
+    TestPhysicalBioAssay.test_add_extract(flowCell2, e2a4, 2, null);
+
+    // Root derived bioassay -> one per flow cell
+    int root1 = test_create_root("Seq #1", flowCell1, SystemItems.getId(DerivedBioAssay.SEQUENCES), 0, 0, 0);
+    int root2 = test_create_root("Seq #2", flowCell2, SystemItems.getId(DerivedBioAssay.SEQUENCES), 0, 0, 0);
+    
+    // First child derived bioassay -> one per aliquot
+    int ARRANGEMENT = SystemItems.getId(DerivedBioAssay.ARRANGEMENT);
+    int bam1l1t1 = test_create_child("BAM #1.lane1.tag1", e1a1, ARRANGEMENT, 0, 0, 0, root1);
+    int bam1l1t2 = test_create_child("BAM #1.lane1.tag2", e2a1, ARRANGEMENT, 0, 0, 0, root1);
+    int bam1l2t1 = test_create_child("BAM #1.lane2.tag1", e1a2, ARRANGEMENT, 0, 0, 0, root1);
+    int bam1l2t2 = test_create_child("BAM #1.lane2.tag2", e2a2, ARRANGEMENT, 0, 0, 0, root1);
+
+    int bam2l1t1 = test_create_child("BAM #2.lane1.tag1", e1a3, ARRANGEMENT, 0, 0, 0, root2);
+    int bam2l1t2 = test_create_child("BAM #2.lane1.tag2", e2a3, ARRANGEMENT, 0, 0, 0, root2);
+    int bam2l2t1 = test_create_child("BAM #2.lane2.tag1", e1a4, ARRANGEMENT, 0, 0, 0, root2);
+    int bam2l2t2 = test_create_child("BAM #2.lane2.tag2", e2a4, ARRANGEMENT, 0, 0, 0, root2);
+    
+    // Merged child derived bioassay -> one per original extract
+    int merged1 = test_create_child("Extract #1.merged", extractId1, ARRANGEMENT, 0, 0, 0, bam1l1t1, bam1l2t1, bam2l1t1, bam2l2t1);
+    int merged2 = test_create_child("Extract #2.merged", extractId2, ARRANGEMENT, 0, 0, 0, bam1l1t2, bam1l2t2, bam2l1t2, bam2l2t2);
+    
     // Standard test: Delete
     if (TestUtil.waitBeforeDelete()) TestUtil.waitForEnter();
+    
+    test_delete(merged1);
+    test_delete(merged2);
+    test_delete(bam1l1t1);
+    test_delete(bam1l1t2);
+    test_delete(bam1l2t1);
+    test_delete(bam1l2t2);
+    test_delete(bam2l1t1);
+    test_delete(bam2l1t2);
+    test_delete(bam2l2t1);
+    test_delete(bam2l2t2);
+    test_delete(root1);
+    test_delete(root2);
+    TestPhysicalBioAssay.test_delete(flowCell1);
+    TestPhysicalBioAssay.test_delete(flowCell2);
+    
+    TestExtract.test_delete(e1a1);
+    TestExtract.test_delete(e1a2);
+    TestExtract.test_delete(e1a3);
+    TestExtract.test_delete(e1a4);
+    TestExtract.test_delete(e2a1);
+    TestExtract.test_delete(e2a2);
+    TestExtract.test_delete(e2a3);
+    TestExtract.test_delete(e2a4);
+    
+    TestTag.test_delete(tag1);
+    TestTag.test_delete(tag2);
+    
     test_delete(child1);
     test_delete(child2);
@@ -132 +209 @@
   }
 
-  static int test_create_child(String name, int parentId, int extractId, int subtypeId, 
-      int protocolId, int hardwareId, int softwareId)
-  {
-    if (parentId == 0) return 0;
+  static int test_create_child(String name, int extractId, int subtypeId, 
+      int protocolId, int hardwareId, int softwareId, int... parents)
+  {
+    if (parents == null || parents.length == 0) return 0;
     int id = 0;
     DbControl dc = null;
@@ -141 +218 @@
     {
       dc = TestUtil.getDbControl();
-      DerivedBioAssay dbas = DerivedBioAssay.getNew(dc, DerivedBioAssay.getById(dc, parentId), null);
+      DerivedBioAssay dbas = DerivedBioAssay.getNew(dc, false, null);
       dbas.setName(name);
       dbas.setDescription("Added at "+new Date());
+      for (int parentId: parents)
+      {
+        dbas.addParent(DerivedBioAssay.getById(dc, parentId));
+      }
+      
       if (extractId != 0)
       {

trunk/src/test/TestTag.java

@@ -68 +68 @@
       dc = TestUtil.getDbControl();
       Tag t = Tag.getNew(dc);
+      t.setName(name);
+      if (subtypeId != 0)
+      {
+        t.setItemSubtype(ItemSubtype.getById(dc, subtypeId));
+      }
       if (setAll)
       {
-        t.setName("Test tag");
         t.setDescription("Added at "+new Date());
       }

trunk/www/views/derivedbioassays/edit_bioassay.jsp

@@ -37 +37 @@
   import="net.sf.basedb.core.ItemResultList"
   import="net.sf.basedb.core.Include"
+  import="net.sf.basedb.core.Type"
+  import="net.sf.basedb.core.query.Expressions"
   import="net.sf.basedb.core.query.Orders"
   import="net.sf.basedb.core.query.Hql"
+  import="net.sf.basedb.core.query.Restrictions"
   import="net.sf.basedb.core.PermissionDeniedException"
   import="net.sf.basedb.core.BaseException"
@@ -73 +76 @@
   ItemSubtype currentSubtype = null;
 
-  boolean readCurrentPhysicalBioAssay = true;
-  PhysicalBioAssay currentPhysicalBioAssay = null;
-  
-  boolean readCurrentParentBioAssay = true;
-  DerivedBioAssay currentParentBioAssay = null;
-  
   boolean readCurrentExtract = true;
   Extract currentExtract = null;
@@ -91 +88 @@
   Software currentSoftware = null;
 
+  ItemQuery<PhysicalBioAssay> physicalQuery = null;
+  ItemQuery<DerivedBioAssay> parentQuery = null;
+  
+  Item parentType = null;
+  
   if (itemId == 0)
   {
     title = "New derived bioassay";
     cc.removeObject("item");
+    int parentId = Values.getInt(request.getParameter("parent_id"));
+    int physicalBioAssayId = Values.getInt(request.getParameter("physicalbioassay_id"));
     int currentSubtypeId = Values.getInt(request.getParameter("subtype_id"));
     List<ItemSubtype> relatedToParent = Collections.emptyList();
-    int parentId = Values.getInt(request.getParameter("parent_id"));
+    
     if (parentId != 0)
     {
-      currentParentBioAssay = DerivedBioAssay.getById(dc, parentId);
+      parentType = Item.DERIVEDBIOASSAY;
+      DerivedBioAssay dba = DerivedBioAssay.getById(dc, parentId);
+      parentQuery = DerivedBioAssay.getQuery();
+      parentQuery.restrict(Restrictions.eq(Hql.property("id"), Expressions.integer(parentId)));
       if (currentSubtypeId == 0)
       {
-        relatedToParent = ItemSubtype.getParentSubtypes(dc, currentParentBioAssay, Item.DERIVEDBIOASSAY);
-      }
-      try
-      {
-        currentPhysicalBioAssay = currentParentBioAssay.getPhysicalBioAssay();
-      }
-      catch (PermissionDeniedException ex)
-      {
-        readCurrentPhysicalBioAssay = false;
-      }
-      try
-      {
-        currentExtract = currentParentBioAssay.getExtract();
-      }
-      catch (PermissionDeniedException ex)
-      {}
-    }
-    else
-    {
-      int physicalBioAssayId = Values.getInt(request.getParameter("physicalbioassay_id"));
-      if (physicalBioAssayId != 0)
-      {
-        currentPhysicalBioAssay = PhysicalBioAssay.getById(dc, physicalBioAssayId);
-        if (currentSubtypeId == 0)
-        {
-          relatedToParent = ItemSubtype.getParentSubtypes(dc, currentPhysicalBioAssay, Item.DERIVEDBIOASSAY);
-        }
-      }
-    }
+        relatedToParent = ItemSubtype.getParentSubtypes(dc, dba, Item.DERIVEDBIOASSAY);
+      }
+    }
+    else if (physicalBioAssayId != 0)
+    {
+      parentType = Item.PHYSICALBIOASSAY;
+      PhysicalBioAssay pba = PhysicalBioAssay.getById(dc, physicalBioAssayId);
+      physicalQuery = PhysicalBioAssay.getQuery();
+      physicalQuery.restrict(Restrictions.eq(Hql.property("id"), Expressions.integer(physicalBioAssayId)));
+      if (currentSubtypeId == 0)
+      {
+        relatedToParent = ItemSubtype.getParentSubtypes(dc, pba, Item.DERIVEDBIOASSAY);
+      }
+    }
+    else if ("PHYISCALBIOASSAY".equals(request.getParameter("useParents")))
+    {
+      parentType = Item.PHYSICALBIOASSAY;
+      physicalQuery = PhysicalBioAssay.getQuery();
+      physicalQuery.restrict(Restrictions.in(Hql.property("id"), Expressions.parameter("selected")));
+      physicalQuery.setParameter("selected", sc.getCurrentContext(Item.PHYSICALBIOASSAY).getSelected(), Type.INT);
+    }
+    else if ("DERIVEDBIOASSAY".equals(request.getParameter("useParents")))
+    {
+      parentType = Item.DERIVEDBIOASSAY;
+      parentQuery = DerivedBioAssay.getQuery();
+      parentQuery.restrict(Restrictions.in(Hql.property("id"), Expressions.parameter("selected")));
+      parentQuery.setParameter("selected", cc.getSelected(), Type.INT);
+    }
+
     if (currentSubtypeId == 0) 
     {
@@ -155 +162 @@
     title = "Edit bioassay -- " + HTML.encodeTags(bioAssay.getName());
     
+    if (bioAssay.isRoot())
+    {
+      physicalQuery = bioAssay.getPhysicalBioAssays();
+      parentType = Item.PHYSICALBIOASSAY;
+    }
+    else
+    {
+      parentQuery = bioAssay.getParents();
+      parentType = Item.DERIVEDBIOASSAY;
+    }
+    
     try
     {
@@ -162 +180 @@
     {
       readCurrentSubtype = false;
-    }
-    try
-    {
-      currentParentBioAssay = bioAssay.getParent();
-    }
-    catch (PermissionDeniedException ex)
-    {
-      readCurrentParentBioAssay = false;
-    }
-    try
-    {
-      currentPhysicalBioAssay = bioAssay.getPhysicalBioAssay();
-    }
-    catch (PermissionDeniedException ex)
-    {
-      readCurrentPhysicalBioAssay = false;
     }
     try
@@ -227 +229 @@
 
   // Load recently used items
-  List<PhysicalBioAssay> recentPhysicalBioAssays = (List<PhysicalBioAssay>)cc.getRecent(dc, Item.PHYSICALBIOASSAY);
-  List<DerivedBioAssay> recentParentBioAssays = (List<DerivedBioAssay>)cc.getRecent(dc, Item.DERIVEDBIOASSAY);
   List<Protocol> recentProtocols = (List<Protocol>)cc.getRecent(dc, Item.PROTOCOL, currentSubtype);
   List<Hardware> recentHardware = (List<Hardware>)cc.getRecent(dc, Item.HARDWARE, currentSubtype);
@@ -243 +243 @@
   %>
   <base:page type="popup" title="<%=title%>">
-  <base:head scripts="tabcontrol.js,annotations.js,platforms.js,subtypes.js,ajax.js,json2.js" styles="tabcontrol.css">
+  <base:head scripts="tabcontrol.js,annotations.js,platforms.js,subtypes.js,ajax.js,json2.js,linkitems.js" styles="tabcontrol.css">
     <ext:scripts context="<%=jspContext%>" />
     <ext:stylesheets context="<%=jspContext%>" />
@@ -257 +257 @@
         return false;
       }
-      if (frm.isRoot)
-      {
-        if (frm.isRoot[0].checked)
-        {
-          if (frm.physicalbioassay_id.selectedIndex < 0)
-          {
-            alert("You must select a parent bioassay");
-            frm.physicalbioassay_id.focus();
-            return false;
-          }
-        }
-        else
-        {
-          if (frm.parent_id.selectedIndex < 0)
-          {
-            alert("You must select a parent bioassay");
-            frm.parent_id.focus();
-            return false;
-          }
-        }
-        
-      }
       return true;
     }
@@ -300 +278 @@
           frames.datafiles.writeFileActionsToForm(frm);
         }
-        if (frm.isRoot)
-        {
-          if (frm.isRoot[0].checked)
-          {
-            frm.parent_id.selectedIndex = -1; 
-          }
-          else
-          {
-            frm.physicalbioassay_id.selectedIndex = -1;
-          }
+        if (frm.addedPhysicalBioAssays)
+        {
+          frm.addedPhysicalBioAssays.value = Link.getActionIds(1, 'P').join(',');
+          frm.removedPhysicalBioAssays.value = Link.getActionIds(-1, 'P').join(',');
+        }
+        if (frm.addedParents)
+        {
+          frm.addedParents.value = Link.getActionIds(1, 'D').join(',');
+          frm.removedParents.value = Link.getActionIds(-1, 'D').join(',');
         }
         frm.submit();
@@ -362 +339 @@
     {
       var frm = document.forms['bioAssay'];
-      if (!frm.physicalbioassay_id) return;
       
       var parents = new Array();
       if (frm.isRoot[0].checked)
       {
-        var bioAssayId = Math.abs(parseInt(frm.physicalbioassay_id[frm.physicalbioassay_id.selectedIndex].value));
-        if (bioAssayId > 0) parents[parents.length] = 'PHYSICALBIOASSAY:'+bioAssayId;
+        var ids = Link.getListIds(frm.physicalBioAssays, 'P');
+        if (ids.length > 0)
+        {
+          parents[parents.length] = 'PHYSICALBIOASSAY:'+ids.join(':');
+        }
       }
       else
       {
-        var bioAssayId = Math.abs(parseInt(frm.parent_id[frm.parent_id.selectedIndex].value));
-        if (bioAssayId > 0) parents[parents.length] = 'DERIVEDBIOASSAY:'+bioAssayId;
+        var ids = Link.getListIds(frm.parents, 'D');
+        if (ids.length > 0)
+        {
+          parents[parents.length] = 'DERIVEDBIOASSAY:'+ids.join(':');
+        }
       }
       return parents;
@@ -459 +441 @@
       url += '&callback=setParentBioAssayCallback&resetTemporary=1';
       url += ItemSubtype.createRelatedFilter('bioAssay', 'DERIVEDBIOASSAY');
-      if (frm.parent_id.selectedIndex >= 0) 
-      {
-        var id = Math.abs(parseInt(frm.parent_id[frm.parent_id.selectedIndex].value));        
+      if (frm.parents.selectedIndex >= 0) 
+      {
+        var id = Math.abs(parseInt(frm.parents[frm.parents.selectedIndex].value));        
         url += '&item_id='+id;
       }
@@ -469 +451 @@
     {
       var frm = document.forms['bioAssay'];
-      var list = frm.parent_id;
+      var list = frm.parents;
       if (list.length < 1 || list[0].value == '0') // >
       {
@@ -536 +518 @@
     }
 
+    function addPhysicalBioAssayOnClick()
+    {
+      var frm = document.forms['bioAssay'];
+      var url = '../physicalbioassays/index.jsp?ID=<%=ID%>&cmd=UpdateContext&mode=selectmultiple';
+      url += '&callback=addPhysicalBioAssayCallback&resetTemporary=1';
+      url += ItemSubtype.createRelatedFilter('bioAssay', 'PHYSICALBIOASSAY');
+      Main.openPopup(url, 'AddPhysicalBioAssay', 1050, 700);
+    }
+    
+    function addPhysicalBioAssayCallback(pbaId, name)
+    {
+      var frm = document.forms['bioAssay'];
+      var item = Link.getItem('P', pbaId);
+      if (!item) item = new Item('P', pbaId, name);
+      Link.addItem(frm.physicalBioAssays, item);
+      parentsChanged = true;
+    }
+
+    function addParentOnClick()
+    {
+      var frm = document.forms['bioAssay'];
+      var url = 'index.jsp?ID=<%=ID%>&cmd=UpdateContext&mode=selectmultiple';
+      url += '&callback=addParentCallback&resetTemporary=1';
+      url += ItemSubtype.createRelatedFilter('bioAssay', 'DERIVEDBIOASSAY');
+      Main.openPopup(url, 'AddParentBioAssay', 1050, 700);
+    }
+    
+    function addParentCallback(dbaId, name)
+    {
+      var frm = document.forms['bioAssay'];
+      var item = Link.getItem('D', dbaId);
+      if (!item) item = new Item('D', dbaId, name);
+      Link.addItem(frm.parents, item);
+      parentsChanged = true;
+    }
+    
     function init()
     {
@@ -548 +566 @@
       }
       %>
+      initParents();
+      initPhysicalBioAssays();
       if (frm.isRoot) 
       {
@@ -556 +576 @@
         initExtracts();
       }
+    }
+    
+    function initPhysicalBioAssays()
+    {
+      var physicalBioAssays = document.forms['bioAssay'].physicalBioAssays;
+      <%
+      if (physicalQuery != null)
+      {
+        physicalQuery.include(Include.ALL);
+        physicalQuery.order(Orders.asc(Hql.property("name")));
+        ItemResultList<PhysicalBioAssay> physicalBioAssays = physicalQuery.list(dc);
+        for (PhysicalBioAssay pba : physicalBioAssays)
+        {
+          if (bioAssay != null)
+          {
+            %>
+            Link.addNewItem(physicalBioAssays, new Item('P', <%=pba.getId()%>, '<%=HTML.javaScriptEncode(pba.getName())%>'));
+            <%
+          }
+          else
+          {
+            %>
+            Link.addItem(physicalBioAssays, new Item('P', <%=pba.getId()%>, '<%=HTML.javaScriptEncode(pba.getName())%>'));
+            <%
+          }
+        }
+      }
+      %>
+    }
+    
+    function initParents()
+    {
+      var parents = document.forms['bioAssay'].parents;
+      <%
+      if (parentQuery != null)
+      {
+        parentQuery.include(Include.ALL);
+        parentQuery.order(Orders.asc(Hql.property("name")));
+        ItemResultList<DerivedBioAssay> parents = parentQuery.list(dc);
+        for (DerivedBioAssay dba : parents)
+        {
+          if (bioAssay != null)
+          {
+            %>
+            Link.addNewItem(parents, new Item('D', <%=dba.getId()%>, '<%=HTML.javaScriptEncode(dba.getName())%>'));
+            <%
+          }
+          else
+          {
+            %>
+            Link.addItem(parents, new Item('D', <%=dba.getId()%>, '<%=HTML.javaScriptEncode(dba.getName())%>'));
+            <%
+          }
+        }
+      }
+      %>
     }
     
@@ -593 +669 @@
       else
       {
-        if (currentParentBioAssay != null)
+        if (bioAssay.isRoot())
         {
           %>
-          extracts = getExtractsFromParentBioassay(<%=currentParentBioAssay.getId()%>);
+          extracts = getExtractsFromPhysicalBioAssays();
           <%
         }
-        else if (currentPhysicalBioAssay != null)
+        else
         {
           %>
-          extracts = getExtractsFromPhysicalBioAssay(<%=currentPhysicalBioAssay.getId()%>);
+          extracts = getExtractsFromParentBioassays();
           <%
         }
@@ -742 +818 @@
           <td>
             <input id="isRoot" type="radio" name="isRoot" value="1" 
-              <%=currentParentBioAssay == null ? "checked" : "" %>
+              <%=parentType == Item.PHYSICALBIOASSAY ? "checked" : "" %>
               onchange="isRootOnChange()"><label for="isRoot">Physical bioassay</label>
             <input id="isChild" type="radio" name="isRoot" value="0"
-              <%=currentParentBioAssay == null ? "" : "checked" %>
+              <%=parentType != Item.PHYSICALBIOASSAY ? "checked" : "" %>
               onchange="isRootOnChange()"><label for="isChild">Derived bioassay</label><br>
           </td>
           <td></td>
         </tr>
-        <tr id="physicalBioAssaySection" style="display: none;">
-          <th class="subprompt">- physical bioassay</th>
+        <%
+      }
+      %>
+      <%
+      if (bioAssay == null || bioAssay.isRoot())
+      {
+        %>
+        <tr id="physicalBioAssaySection">
+          <th class="subprompt">- physical bioassays</th>
           <td>
-            <base:select 
-              id="physicalbioassay_id"
-              clazz="selectionlist unchangeable"
-              required="true"
-              current="<%=currentPhysicalBioAssay%>"
-              recent="<%=recentPhysicalBioAssays%>"
-              newitem="true"
-              onselect="selectPhysicalBioAssayOnClick()"
-              onchange="physicalBioAssayOnChange()"
-            />
+            <div class="selectionlist">
+            <table>
+            <tr>
+            <td>
+              <select name="physicalBioAssays" size="4" multiple onchange="physicalBioAssayOnChange()">
+              </select>
+            </td>
+            <td>
+            <td style="vertical-align: top;">
+              <base:buttongroup vertical="true">
+                <base:button 
+                  subclass="leftaligned"
+                  style="width: 12em;"
+                  onclick="addPhysicalBioAssayOnClick()" 
+                  title="Add&nbsp;bioassays&hellip;" 
+                  tooltip="Add physical bioassays"
+                />
+                <base:button 
+                  subclass="leftaligned"
+                  style="width: 12em;"
+                  onclick="removePhysicalBioAssayOnClick()" 
+                  title="Remove" 
+                  tooltip="Remove the selected physical bioassays"
+                />
+              </base:buttongroup>
+              <input type="hidden" name="addedPhysicalBioAssays" value="">
+              <input type="hidden" name="removedPhysicalBioAssays" value="">
+            </td>
+            </tr>
+            </table>
+            </div>
           </td>
           <td></td>
         </tr>
-        <tr id="parentBioAssaySection" style="display: none;">
-          <th class="subprompt">- bioassay</th>
+        <%
+      }
+      if (bioAssay == null || !bioAssay.isRoot())
+      {
+        %>
+        <tr id="parentBioAssaySection">
+          <th class="subprompt">- bioassays</th>
           <td>
-            <base:select 
-              id="parent_id"
-              clazz="selectionlist unchangeable"
-              required="true"
-              current="<%=currentParentBioAssay%>"
-              recent="<%=recentParentBioAssays%>"
-              newitem="true"
-              onselect="selectParentBioAssayOnClick()"
-              onchange="parentBioAssayOnChange()"
-            />
+            <div class="selectionlist">
+            <table>
+            <tr>
+            <td>
+              <select name="parents" size="4" multiple onchange="parentsOnChange()">
+              </select>
+            </td>
+            <td>
+            <td style="vertical-align: top;">
+              <base:buttongroup vertical="true">
+                <base:button 
+                  subclass="leftaligned"
+                  style="width: 12em;"
+                  onclick="addParentOnClick()" 
+                  title="Add&nbsp;bioassays&hellip;" 
+                  tooltip="Add parent derived bioassays"
+                />
+                <base:button 
+                  subclass="leftaligned"
+                  style="width: 12em;"
+                  onclick="removeParentOnClick()" 
+                  title="Remove" 
+                  tooltip="Remove the selected derived bioassays"
+                />
+              </base:buttongroup>
+              <input type="hidden" name="addedParents" value="">
+              <input type="hidden" name="removedParents" value="">
+            </td>
+            </tr>
+            </table>
+            </div>
+            
           </td>
           <td></td>

trunk/www/views/derivedbioassays/index.jsp

@@ -179 +179 @@
     if (bas == null)
     {
-      int parentId = Values.getInt(request.getParameter("parent_id"));
-      int physicalBioAssayId = Values.getInt(request.getParameter("physicalbioassay_id"));
-      if (parentId == 0)
-      {
-        PhysicalBioAssay bioAssay = PhysicalBioAssay.getById(dc, physicalBioAssayId);
-        bas = DerivedBioAssay.getNew(dc, bioAssay, null);
-        cc.setRecent(bioAssay, maxRecent);
-      }
-      else
-      {
-        DerivedBioAssay parent = DerivedBioAssay.getById(dc, parentId);
-        bas = DerivedBioAssay.getNew(dc, parent, null);
-        cc.setRecent(parent, maxRecent);
-      }
+      bas = DerivedBioAssay.getNew(dc, Values.getBoolean(request.getParameter("isRoot")), null);
       dc.saveItem(bas);
       message = "Derived bioassay created";
@@ -247 +234 @@
         bas.setSoftware(sw);
         if (sw != null) cc.setRecent(sw, subtype, maxRecent);
+      }
+      
+      if (bas.isRoot())
+      {
+        // A root derived bioassay set may have physical bioassays as parents
+        String[] removePhysicalBioAssays = Values.getString(request.getParameter("removedPhysicalBioAssays")).split(",");
+        for (int i = 0; i < removePhysicalBioAssays.length; ++i)
+        {
+          int pbaId = Values.getInt(removePhysicalBioAssays[i], -1);
+          if (pbaId != -1) bas.removePhysicalBioAssay(PhysicalBioAssay.getById(dc, pbaId));
+        }
+        
+        String[] addPhysicalBioAssays = Values.getString(request.getParameter("addedPhysicalBioAssays")).split(",");
+        for (int i = 0; i < addPhysicalBioAssays.length; ++i)
+        {
+          int pbaId = Values.getInt(addPhysicalBioAssays[i], -1);
+          if (pbaId != -1) bas.addPhysicalBioAssay(PhysicalBioAssay.getById(dc, pbaId));
+        }
+      }
+      else
+      {
+        // A non-root derived bioassay set may have other derived bioassays as parents
+        String[] removeParents = Values.getString(request.getParameter("removedParents")).split(",");
+        for (int i = 0; i < removeParents.length; ++i)
+        {
+          int parentId = Values.getInt(removeParents[i], -1);
+          if (parentId != -1) bas.removeParent(DerivedBioAssay.getById(dc, parentId));
+        }
+        
+        String[] addParents = Values.getString(request.getParameter("addedParents")).split(",");
+        for (int i = 0; i < addParents.length; ++i)
+        {
+          int parentId = Values.getInt(addParents[i], -1);
+          if (parentId != -1) bas.addParent(DerivedBioAssay.getById(dc, parentId));
+        }
       }
       
@@ -422 +444 @@
     redirect = "../../common/plugin/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=ITEM&main_type=ANALYZE&title=Run+analysis+plugin";
   }
+  else if ("NewMergedDerivedBioAssay".equals(cmd))
+  {
+    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
+    cc.setId(0);
+    forward = editPage + "&useParents=DERIVEDBIOASSAY";
+  }
   else
   {

trunk/www/views/derivedbioassays/list_bioassays.jsp

@@ -95 +95 @@
   final ItemQuery<ItemSubtype> subtypesQuery = Base.getSubtypesQuery(itemType);
 
+  // Query for parent physical bioassays to the current bioassay
+  final ItemQuery<PhysicalBioAssay> physicalBioAssayQuery = PhysicalBioAssay.getQuery();
+  physicalBioAssayQuery.include(cc.getInclude());
+  physicalBioAssayQuery.join(Hql.innerJoin("derivedBioAssays", "dba"));
+  physicalBioAssayQuery.restrict(Restrictions.eq(Hql.alias("dba"), Expressions.parameter("bioAssay")));
+  physicalBioAssayQuery.order(Orders.asc(Hql.property("name"))); 
+
+  // Query for parent bioassays to the current bioassay
+  final ItemQuery<DerivedBioAssay> parentQuery = DerivedBioAssay.getQuery();
+  parentQuery.include(cc.getInclude());
+  parentQuery.join(Hql.innerJoin("children", "c"));
+  parentQuery.restrict(Restrictions.eq(Hql.alias("c"), Expressions.parameter("bioAssay")));
+  parentQuery.order(Orders.asc(Hql.property("name"))); 
+
   // Query for child bioassays to the current bioassay
   final ItemQuery<DerivedBioAssay> childQuery = DerivedBioAssay.getQuery();
   childQuery.include(cc.getInclude());
-  childQuery.restrict(Restrictions.eq(Hql.property("parent"), Expressions.parameter("bioAssay")));
+  childQuery.join(Hql.innerJoin("parents", "p"));
+  childQuery.restrict(Restrictions.eq(Hql.alias("p"), Expressions.parameter("bioAssay")));
   childQuery.order(Orders.asc(Hql.property("name"))); 
 
@@ -213 +228 @@
       Main.viewOrEditItem('<%=ID%>', 'RAWBIOASSAY', 0, true, '&bioassay_id='+parentId);
     }
+    function newMergedChild()
+    {
+      var frm = document.forms[formId];
+      Table.poolItems(submitPage, '<%=ID%>', formId, '<%=itemType.name()%>', 'NewMergedDerivedBioAssay');
+    }
     </script>
   </base:head>
@@ -271 +291 @@
       />
       <tbl:columndef 
-        id="physicalBioAssay"
-        property="physicalBioAssay.name"
-        datatype="string"
-        title="Physical bioassay"
-        sortable="true" 
-        filterable="true"
-        exportable="true"
-      />
-      <tbl:columndef 
-        id="parent"
-        property="parent.name"
-        datatype="string"
-        title="Parent bioassay"
-        sortable="true" 
+        id="physicalBioAssays"
+        property="&physicalBioAssays(name)"
+        datatype="string"
+        title="Physical bioassays"
+        filterable="true"
+        exportable="true"
+      />
+      <tbl:columndef 
+        id="parents"
+        property="&parents(name)"
+        datatype="string"
+        title="Parent bioassays"
         filterable="true"
         exportable="true"
@@ -437 +455 @@
             title="New&hellip;" 
             tooltip="<%=createPermission ? "Create new derived bioassay" : "You do not have permission to create derived bioassays"%>" 
+          />
+          <tbl:button 
+            disabled="<%=!createPermission%>" 
+            image="new_pooled.png" 
+            onclick="newMergedChild()" 
+            title="Merge&hellip;" 
+            tooltip="<%=createPermission ? "Create new merged bioassay" : "You do not have permission to create derived bioassay"%>" 
           />
           <tbl:button 
@@ -678 +703 @@
                   />
                 </tbl:cell>
-                <tbl:cell column="physicalBioAssay"
-                  ><base:propertyvalue 
-                    item="<%=item%>" 
-                    property="physicalBioAssay"
-                    enableEditLink="<%=mode.hasEditLink()%>" 
-                    enablePropertyLink="<%=mode.hasPropertyLink()%>"
-                  /></tbl:cell>
-                <tbl:cell column="parent"
-                  ><base:propertyvalue 
-                    item="<%=item%>" 
-                    property="parent"
-                    enableEditLink="<%=mode.hasEditLink()%>" 
-                    enablePropertyLink="<%=mode.hasPropertyLink()%>"
-                  /></tbl:cell>
+                <tbl:cell column="physicalBioAssays">
+                  <%
+                  physicalBioAssayQuery.setParameter("bioAssay", itemId, Type.INT);
+                  try
+                  {
+                    String separator = "";
+                    for (PhysicalBioAssay pba : physicalBioAssayQuery.list(dc))
+                    {
+                      out.write(separator);
+                      if (mode.hasPropertyLink())
+                      {
+                        out.write(Base.getLinkedName(ID, pba, false, mode.hasEditLink()));
+                      }
+                      else
+                      {
+                        out.write(HTML.encodeTags(pba.getName()));
+                      }
+                      separator = ", ";
+                    }
+                  }
+                  catch (Throwable t)
+                  {
+                    %>
+                    <div class="error"><%=t.getMessage()%></div>
+                    <%
+                  }
+                  %>              
+                </tbl:cell>
+                <tbl:cell column="parents">
+                  <%
+                  if (!item.isRoot())
+                  {
+                    parentQuery.setParameter("bioAssay", itemId, Type.INT);
+                    try
+                    {
+                      String separator = "";
+                      for (DerivedBioAssay dba : parentQuery.list(dc))
+                      {
+                        out.write(separator);
+                        if (mode.hasPropertyLink())
+                        {
+                          out.write(Base.getLinkedName(ID, dba, false, mode.hasEditLink()));
+                        }
+                        else
+                        {
+                          out.write(HTML.encodeTags(dba.getName()));
+                        }
+                        separator = ", ";
+                      }
+                    }
+                    catch (Throwable t)
+                    {
+                      %>
+                      <div class="error"><%=t.getMessage()%></div>
+                      <%
+                    }
+                  }
+                  %>              
+                </tbl:cell>
                 <tbl:cell column="extract"
                   ><base:propertyvalue 

trunk/www/views/derivedbioassays/view_bioassay.jsp

@@ -322 +322 @@
       </tr>
     </table>
-    <table style="width: 100%; height: 20em;" class="bottomborder">
+    <table style="width: 100%; height: 16em;" class="bottomborder">
     <tr valign="top">
       <td style="width: 50%; height: 100%;">
@@ -333 +333 @@
           <th>Type</th>
           <td><base:propertyvalue item="<%=bioAssay%>" property="itemSubtype" /></td>
-        </tr>
-        <tr>
-          <th>Physical bioassay</th>
-          <td><base:propertyvalue item="<%=bioAssay%>" property="physicalBioAssay" /></td>
-        </tr>
-        <tr>
-          <th>Parent bioassay</th>
-          <td><base:propertyvalue item="<%=bioAssay%>" property="parent" /></td>
         </tr>
         <tr>
@@ -491 +483 @@
       </div>
       <%
+      ItemQuery<PhysicalBioAssay> physicalQuery = bioAssay.getPhysicalBioAssays();
+      physicalQuery.include(Include.ALL);
+      physicalQuery.order(Orders.asc(Hql.property("name")));
+      ItemResultList<PhysicalBioAssay> physicalBioAssays = physicalQuery.list(dc);
+      %>
+      <base:section 
+        id="physicalBioAssays"
+        title="<%="Physical bioassays (" + physicalBioAssays.size() + ")"%>"
+        context="<%=cc%>"
+        >
+        <%
+        if (physicalBioAssays.size() == 0)
+        {
+          %>
+          <div class="messagecontainer note">
+          This bioassay doesn't have any parent physical bioassays
+          (or you don't have permission to view them).
+          </div>
+          <%
+        }
+        else
+        {
+          %>
+          <tbl:table
+            id="physicalBioAssays"
+            columns="all"
+            >
+            <tbl:columndef 
+              id="name"
+              title="Name"
+            />
+            <tbl:columndef 
+              id="itemSubtype"
+              title="Type"
+            />
+            <tbl:columndef 
+              id="description"
+              title="Description"
+            />
+            <tbl:data>
+              <tbl:headers>
+                <tbl:headerrow>
+                  <tbl:columnheaders />
+                </tbl:headerrow>
+              </tbl:headers>            
+              <tbl:rows>
+              <%
+              for (PhysicalBioAssay item : physicalBioAssays)
+              {
+                %>
+                <tbl:row>
+                  <tbl:cell column="name"><%=Base.getLinkedName(ID, item, false, true)%></tbl:cell>
+                  <tbl:cell column="itemSubtype"><base:propertyvalue item="<%=item%>" property="itemSubtype" /></tbl:cell>
+                  <tbl:cell column="description"><%=HTML.encodeTags(item.getDescription())%></tbl:cell>
+                </tbl:row>
+                <%
+              }
+              %>
+              </tbl:rows>
+            </tbl:data>
+          </tbl:table>
+          <%
+        }
+        %>
+      </base:section>
+      <%
+      if (!bioAssay.isRoot())
+      {
+        ItemQuery<DerivedBioAssay> parentQuery = bioAssay.getParents();
+        parentQuery.include(Include.ALL);
+        parentQuery.order(Orders.asc(Hql.property("name")));
+        ItemResultList<DerivedBioAssay> parents = parentQuery.list(dc);
+        %>
+        <base:section 
+          id="parents"
+          title="<%="Parent bioassays (" + parents.size() + ")"%>"
+          context="<%=cc%>"
+          >
+          <%
+          if (parents.size() == 0)
+          {
+            %>
+            <div class="messagecontainer note">
+            This bioassay doesn't have any parent bioassays
+            (or you don't have permission to view them).
+            </div>
+            <%
+          }
+          else
+          {
+            %>
+            <tbl:table
+              id="parents"
+              columns="all"
+              >
+              <tbl:columndef 
+                id="name"
+                title="Name"
+              />
+              <tbl:columndef 
+                id="itemSubtype"
+                title="Type"
+              />
+              <tbl:columndef 
+                id="description"
+                title="Description"
+              />
+              <tbl:data>
+                <tbl:headers>
+                  <tbl:headerrow>
+                    <tbl:columnheaders />
+                  </tbl:headerrow>
+                </tbl:headers>            
+                <tbl:rows>
+                <%
+                for (DerivedBioAssay item : parents)
+                {
+                  %>
+                  <tbl:row>
+                    <tbl:cell column="name"><%=Base.getLinkedName(ID, item, false, true)%></tbl:cell>
+                    <tbl:cell column="itemSubtype"><base:propertyvalue item="<%=item%>" property="itemSubtype" /></tbl:cell>
+                    <tbl:cell column="description"><%=HTML.encodeTags(item.getDescription())%></tbl:cell>
+                  </tbl:row>
+                  <%
+                }
+                %>
+                </tbl:rows>
+              </tbl:data>
+            </tbl:table>
+            <%
+          }
+          %>
+        </base:section>
+        <%
+      }
       ItemQuery<DerivedBioAssay> childQuery = bioAssay.getChildren();
       childQuery.include(Include.ALL);

trunk/www/views/physicalbioassays/index.jsp

@@ -417 +417 @@
     redirect = "../../common/plugin/index.jsp?ID="+ID+"&cmd=SelectPlugin&item_type="+itemType.name()+"&context_type=ITEM&main_type=OTHER&title=Run+plugin";
   }
+  else if ("NewMergedDerivedBioAssay".equals(cmd))
+  {
+    ItemContext cc = Base.getAndSetCurrentContext(sc, itemType, pageContext, defaultContext);
+    redirect = "../derivedbioassays/index.jsp?ID="+ID+"&cmd=NewItem&useParents=PHYISCALBIOASSAY";
+  }
   else
   {

trunk/www/views/physicalbioassays/list_bioassays.jsp

@@ -111 +111 @@
   final ItemQuery<DerivedBioAssay> dbasQuery = DerivedBioAssay.getQuery();
   dbasQuery.include(cc.getInclude());
-  dbasQuery.restrict(Restrictions.eq(Hql.property("physicalBioAssay"), Expressions.parameter("bioAssay")));
-  dbasQuery.restrict(Restrictions.eq(Hql.property("parent"), null));
+  dbasQuery.join(Hql.innerJoin("physicalBioAssays", "pba"));
+  dbasQuery.restrict(Restrictions.eq(Hql.alias("pba"), Expressions.parameter("bioAssay")));
+  dbasQuery.restrict(Restrictions.eq(Hql.property("root"), Expressions.bool(true)));
   dbasQuery.order(Orders.asc(Hql.property("name"))); 
   final boolean createDerivedBioAssayPermission = sc.hasPermission(Permission.CREATE, Item.DERIVEDBIOASSAY);  
@@ -217 +218 @@
     {
       Main.viewOrEditItem('<%=ID%>', 'DERIVEDBIOASSAY', 0, true, '&physicalbioassay_id='+bioAssayId);
+    }
+    function newMergedDerivedBioAssay()
+    {
+      Table.poolItems(submitPage, '<%=ID%>', formId, '<%=itemType.name()%>', 'NewMergedDerivedBioAssay');
     }
     </script>
@@ -425 +430 @@
             title="New&hellip;" 
             tooltip="<%=createPermission ? "Create new physical bioassay" : "You do not have permission to create physical bioassays"%>" 
+          />
+          <tbl:button
+            disabled="<%=!createDerivedBioAssayPermission %>"
+            image="add.png"
+            onclick="newMergedDerivedBioAssay()"
+            title="New derived bioassay&hellip;"
+            tooltip="<%=createDerivedBioAssayPermission ? "Create new derived bioassay from the selected physical bioassays" : "You do not have permission to create derived bioassays"%>"
           />
           <tbl:button