Changeset 5456

Timestamp:

Oct 28, 2010, 2:12:26 PM (12 years ago)

Author:

Nicklas Nordborg

Message:

References #1532: Add bioplate type to bioplates

Added BioPlateType?.getLockMode() and Well.getOriginalBioMaterial() link. Extended test programs to makes sure locking is working as expected. Changes to the gui are not yet complete. The JSPs compiles but locking options are not considered.

Location:

trunk

Files:

• src/core/common-queries.xml (modified) (1 diff)
• src/core/net/sf/basedb/core/BioPlate.java (modified) (1 diff)
• src/core/net/sf/basedb/core/BioPlateType.java (modified) (1 diff)
• src/core/net/sf/basedb/core/BioWell.java (modified) (3 diffs)
• src/core/net/sf/basedb/core/Install.java (modified) (3 diffs)
• src/core/net/sf/basedb/core/MeasuredBioMaterial.java (modified) (4 diffs)
• src/core/net/sf/basedb/core/Update.java (modified) (2 diffs)
• src/core/net/sf/basedb/core/data/BioPlateTypeData.java (modified) (1 diff)
• src/core/net/sf/basedb/core/data/BioWellData.java (modified) (1 diff)
• src/test/TestBioPlate.java (modified) (7 diffs)
• src/test/TestBioPlateType.java (modified) (6 diffs)
• src/test/net/sf/basedb/test/roles/PowerUserTest.java (modified) (5 diffs)
• www/biomaterials/bioplates/view_bioplate.jsp (modified) (4 diffs)
• www/biomaterials/bioplates/wells/list_biowells.jsp (modified) (3 diffs)
• www/biomaterials/bioplatetypes/edit_platetype.jsp (modified) (1 diff)
• www/biomaterials/bioplatetypes/index.jsp (modified) (1 diff)
• www/biomaterials/bioplatetypes/list_platetypes.jsp (modified) (1 diff)
• www/biomaterials/bioplatetypes/view_platetype.jsp (modified) (1 diff)
• www/biomaterials/extracts/edit_extract.jsp (modified) (1 diff)
• www/biomaterials/extracts/view_extract.jsp (modified) (1 diff)
• www/biomaterials/labeledextracts/edit_labeledextract.jsp (modified) (1 diff)
• www/biomaterials/labeledextracts/view_labeledextract.jsp (modified) (1 diff)
• www/biomaterials/samples/edit_sample.jsp (modified) (1 diff)
• www/biomaterials/samples/view_sample.jsp (modified) (1 diff)

trunk/src/core/common-queries.xml

@@ -3821 +3821 @@
   </query>
 
+  <query id="CLEAR_ORIGINAL_BIOMATERIAL_ON_BIOWELLS" type="HQL">
+    <sql>
+      UPDATE BioWellData bw
+      SET bw.originalBioMaterial = null
+      WHERE bw.originalBioMaterial = :bioMaterial
+    </sql>
+    <description>
+      An HQL update-query that for a given biomaterial clears the 
+      link on all biowells were it is set as the original biomaterial.
+    </description>
+  </query>
+
 </predefined-queries>

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

@@ -158 +158 @@
   /**
     Check if there are any <code>MeasuredBioMaterial</code> on
-    this plate or if this plate has any child plates (note that
-    child events may exists but they are automatically deleted)
+    this plate.
    */
   @Override

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

@@ -238 +238 @@
   
   /**
-    A flag indicating if plates with this type have locked wells or not.
-    If the wells are locked it is not possible to change the biomaterial
-    in them.
-    @return TRUE if the wells should be locked, FALSE otherwise
-  */
-  public boolean getLockedWells()
-  {
-    return getData().getLockedWells();
-  }
-  /**
-    Set the flag to lock/unlock wells on the plates of this type.
-  */
-  public void setLockedWells(boolean lockedWells)
-  {
-    checkPermission(Permission.WRITE);
-    getData().setLockedWells(lockedWells);
+    Get the lock mode for wells located on plates of this plate type.
+    The lock mode determines if biomaterial may be changed in the
+    well.
+    
+    @return A lock mode
+  */
+  public BioWell.LockMode getLockMode()
+  {
+    return BioWell.LockMode.fromValue(getData().getLockMode());
+  }
+  /**
+    Set the lock mode for wells on plates of this plate type.
+    @param lockMode A lock mode, null is not allowed
+  */
+  public void setLockMode(BioWell.LockMode lockMode)
+  {
+    checkPermission(Permission.WRITE);
+    if (lockMode == null) throw new InvalidUseOfNullException("lockMode");
+    getData().setLockMode(lockMode.getValue());
   }
   

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

@@ -23 +23 @@
 
 import net.sf.basedb.core.data.BioWellData;
+import net.sf.basedb.core.data.MeasuredBioMaterialData;
 import net.sf.basedb.core.data.SharedData;
 import net.sf.basedb.core.query.Hql;
@@ -28 +29 @@
 import net.sf.basedb.util.Coordinate;
 
+import java.util.HashMap;
+import java.util.Map;
 import java.util.Set;
 
@@ -208 +211 @@
   
   /**
-    Is this well locked or not? A well is locked if there is biomaterial in it and
-    the plate type has locked wells.
+    If the original biomaterial in this well has been moved to
+    another plate (eg. for final storage in a freezer). This property
+    is only defined for well with lock mode={@link LockMode#LOCKED_AFTER_MOVE}.
+    @return TRUE if the original biomaterial has been moved
     @since 2.16
-    @see BioPlateType#getLockedWells()
-  */
-  public boolean isLocked()
-  {
-    return getData().getBioPlate().getBioPlateType().getLockedWells() && getData().getBioMaterial() != null;
-  }
+  */
+  public boolean hasBeenMoved()
+  {
+    return getData().getBioMaterial() == null && getData().getOriginalBioMaterial() != null;
+  }
+  
+  /**
+    Get the original biomaterial that was placed in this biowell. This
+    property is only defined for well with lock mode={@link LockMode#LOCKED_AFTER_MOVE}
+    after the biomaterial has been moved.
+    
+    @return The original biomaterial
+    @since 2.16
+  */
+  public MeasuredBioMaterial getOriginalBioMaterial()
+  {
+    return getDbControl().getItem(MeasuredBioMaterial.class, getData().getOriginalBioMaterial());
+  }
+  
+  /**
+    The lock mode for a well is determined by the plate's bio
+    plate type. See {@link BioPlateType#getLockMode()}. The lock-mode
+    is used to determine if the well can be assigned to a biomaterial
+    or not.
+  
+    @since 2.16
+  */
+  public enum LockMode
+  {
+    /**
+      The well is not locked. It is possible to change the biomaterial
+      any number of times.
+    */
+    UNLOCKED(0)
+    {
+      /**
+        @return Always true
+      */
+      @Override
+      boolean canClear(BioWellData well)
+      {
+        return true;
+      }
+      /**
+        @return Always true
+      */
+      @Override
+      boolean canAdd(BioWellData well)
+      {
+        return true;
+      }
+    },
+    
+    /**
+      It is allowed to add biomaterial once to the well. It can not be replaced
+      by a new biomaterial but it is possible to clear it. The original biomaterial
+      is then saved in the {@link BioWell#getOriginalBioMaterial()}.
+    */
+    LOCKED_AFTER_MOVE(1)
+    {
+      /**
+        @return Always true
+      */
+      @Override
+      boolean canClear(BioWellData well)
+      {
+        return true;
+      }
+      /**
+        Can only add if there is no original biomaterial.
+      */
+      @Override
+      boolean canAdd(BioWellData well)
+      {
+        return well.getOriginalBioMaterial() == null;
+      }
+      /**
+        This lockmode will save the original biomaterial in 
+        {@link BioWell#getOriginalBioMaterial()} when it is cleared.
+        After that, it is not possible to add biomaterial to the well again.
+      */
+      @Override
+      void onClear(BioWellData well, MeasuredBioMaterialData biomaterial)
+      {
+        well.setOriginalBioMaterial(biomaterial);
+      }
+    },
+    
+    /**
+      It is allowed to add biomaterial once to the well. It can't be replaced
+      by a new biomaterial and it is not possible to clear it. It is possible to
+      add biomaterial to empty wells at any time.
+    */
+    LOCKED_AFTER_ADD(2) 
+    {
+      /**
+        @return Always false
+      */
+      @Override
+      boolean canClear(BioWellData well)
+      {
+        return false;
+      }
+      /**
+        @return Always true
+      */
+      @Override
+      boolean canAdd(BioWellData well)
+      {
+        return true;
+      }
+    },
+
+    /**
+      It is allowed to add biomaterial once to the well, but it most be done
+      at the same time the plate is creted. Once the transaction has been
+      committed to the database, all wells become locked.
+    */
+    LOCKED_AFTER_CREATE(3) 
+    {
+      /**
+        @return Always false
+      */
+      @Override
+      boolean canClear(BioWellData well)
+      {
+        return false;
+      }
+      /**
+        Can only add to unsaved items.
+      */
+      @Override
+      boolean canAdd(BioWellData well)
+      {
+        return well.getId() == 0;
+      }
+    };    
+    
+    /**
+      Maps an integer to a lock mode.
+    */
+    private static final Map<Integer, LockMode> valueMapping = new HashMap<Integer, LockMode>();
+    
+    static
+    {
+      for (LockMode lockMode : LockMode.values())
+      {
+        LockMode lm = valueMapping.put(lockMode.getValue(), lockMode);
+        assert lm == null : "Another lock mode with the value "+lockMode.getValue()+" already exists";
+      }
+    }
+    
+    /**
+      The integer value of this lock mode. 
+    */
+    private final int value;
+    
+    private LockMode(int value)
+    {
+      this.value = value;
+    }
+    
+    /**
+      Get the integer value that is used when storing a lock mode to the database.
+      @return The integer value for this lock mode
+    */
+    public int getValue()
+    {
+      return value;
+    }
+
+    /**
+      Get the <code>Lock mode</code> object when you know the integer code.
+      
+      @param value The integer value
+      @return The location for the integer value
+    */
+    public static LockMode fromValue(int value)
+    {
+      LockMode lockMode = valueMapping.get(value);
+      assert lockMode != null : "lockMode == null for value "+value;
+      return lockMode;
+    }
+
+    /**
+      Is it allowed to clear a well that already has biomaterial in it? If
+      this method is called with an empty well as parameter the result
+      is undefined.
+      @param well The biowell, which should already have biomaterial in it
+    */
+    public boolean canClear(BioWell well)
+    {
+      return canClear(well.getData());
+    }
+    
+    abstract boolean canClear(BioWellData well);
+    
+    /**
+      Called when a well is cleared from an existing biomaterial. The
+      default implementation of this method does nothing, but it may be
+      overriden by some lock modes.
+      
+      @param well The well that is cleared
+      @param biomaterial The biomaterial that is currently located on the well
+    */
+    void onClear(BioWellData well, MeasuredBioMaterialData biomaterial)
+    {}
+
+    /**
+      Is it allowed to add biomaterial to the (empty) well? If this
+      method is called with a non-empty well as parameter the result
+      is undefined.
+      @param well An empty biowell
+    */
+    public boolean canAdd(BioWell well)
+    {
+      return canAdd(well.getData());
+    }
+    
+    abstract boolean canAdd(BioWellData well);
+
+    /**
+      Called when biomaterial is added to a well. The
+      default implementation of this method does nothing, but it may be
+      overriden by some lock modes.
+      
+      @param well The well the biomaterial is added to
+      @param biomaterial The biomaterial that is going to be added to the well
+    */
+    void onAdd(BioWellData well, MeasuredBioMaterialData biomaterial)
+    {}
+    
+  }
+  
 }

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

@@ -583 +583 @@
       progressStep++;
       if (progress != null) progress.display((int)(progressStep*progress_factor), "--Creating bioplate types...");
-      BioPlateTypeData storagePlate = createBioPlateType("Storage plate", "A generic storage plate for all types of biomaterial.", null, false);
-      BioPlateTypeData sampleReactionPlate = createBioPlateType("Sample reaction plate", "A generic reaction plate for samples.", Item.SAMPLE, true);
-      BioPlateTypeData extractReactionPlate = createBioPlateType("Extract reaction plate", "A generic reaction plate for extracts.", Item.EXTRACT, true);
+      BioPlateTypeData storagePlate = createBioPlateType("Storage plate", "A generic storage plate for all types of biomaterial.", 
+          null, BioWell.LockMode.UNLOCKED);
+      BioPlateTypeData sampleReactionPlate = createBioPlateType("Sample reaction plate", "A generic reaction plate for samples.", 
+          Item.SAMPLE, BioWell.LockMode.LOCKED_AFTER_ADD);
+      BioPlateTypeData extractReactionPlate = createBioPlateType("Extract reaction plate", "A generic reaction plate for extracts.", 
+          Item.EXTRACT, BioWell.LockMode.LOCKED_AFTER_ADD);
       BioPlateTypeData labeledExtractReactionPlate = 
-        createBioPlateType("Labeled extract reaction plate", "A generic reaction plate for labeled extracts.", Item.LABELEDEXTRACT, true);
+        createBioPlateType("Labeled extract reaction plate", "A generic reaction plate for labeled extracts.", 
+            Item.LABELEDEXTRACT, BioWell.LockMode.LOCKED_AFTER_ADD);
       
       // Labels
@@ -1788 +1792 @@
   */
   private static BioPlateTypeData createBioPlateType(String name, String description, 
-    Item biomaterialType, boolean lockedWells)
+    Item biomaterialType, BioWell.LockMode lockedMode)
     throws BaseException
   {
@@ -1815 +1819 @@
         pt.setDescription(description);
         pt.setBioMaterialType(biomaterialType == null ? null : biomaterialType.getValue());
-        pt.setLockedWells(lockedWells);
+        pt.setLockMode(lockedMode.getValue());
         HibernateUtil.saveData(session, pt);
         HibernateUtil.commit(tx);

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

@@ -132 +132 @@
     {
       getCreationEvent().clearSources();
+      org.hibernate.Query query = HibernateUtil.getPredefinedQuery(getDbControl().getHibernateSession(), 
+          "CLEAR_ORIGINAL_BIOMATERIAL_ON_BIOWELLS");
+      /*
+        UPDATE BioWellData bw
+        SET bw.originalBioMaterial = null
+        WHERE bw.originalBioMaterial = :bioMaterial
+      */
+      query.setEntity("bioMaterial", getData());
+      query.executeUpdate();
     }
   }
@@ -344 +353 @@
   
   /**
-    Sets the <code>BioWell</code> where this biomaterial is located. This
-    method also updates the plate event associated with the creation event
-    of this biomaterial, if the new well is located on a plate which was 
-    created by an event.
+    Sets the <code>BioWell</code> where this biomaterial is located. 
     
       @param well The <code>BioWell</code> to set.
@@ -362 +368 @@
   {
     checkPermission(Permission.WRITE);
-    BioWellData currentWell = getData().getBioWell();
+    MeasuredBioMaterialData myData = getData();
+    BioWellData currentWell = myData.getBioWell();
     BioWellData newWell = well != null ? well.getData() : null;
     if (EqualsHelper.equals(currentWell, newWell)) return; // early exit if no change
     
     // Check if current biowell is locked
-    if (currentWell != null)
+    if (currentWell != null && currentWell.getId() != 0)
     {
       BioPlateData currentPlate = currentWell.getBioPlate();
-      if (currentPlate.getBioPlateType().getLockedWells())
+      BioWell.LockMode lockMode = BioWell.LockMode.fromValue(currentPlate.getBioPlateType().getLockMode());
+      
+      if (!lockMode.canClear(currentWell))
       {
         throw new PermissionDeniedException(Permission.WRITE, this + 
-            ". Wells on plate '" + currentPlate.getName() + "'' are locked.");
-      }
+            ". Well on plate '" + currentPlate.getName() + "'' is locked: " + currentWell);
+      }
+      lockMode.onClear(currentWell, myData);
     }
     
@@ -397 +407 @@
           Item.fromValue(biomaterialType));
       }
+      // Check that the lock mode allows adding biomaterial to the well
+      BioWell.LockMode lockMode = BioWell.LockMode.fromValue(newPlateType.getLockMode());
+      if (!lockMode.canAdd(newWell))
+      {
+        throw new PermissionDeniedException(Permission.WRITE, this + 
+            ". Well on plate '" + newPlate.getName() + "'' is locked: " + well);
+      }
+      lockMode.onAdd(newWell, myData);
     }
     if (currentWell != null) currentWell.setBioMaterial(null);
-    if (newWell != null) newWell.setBioMaterial(getData());
-    getData().setBioWell(newWell);
+    if (newWell != null) newWell.setBioMaterial(myData);
+    myData.setBioWell(newWell);
   }
   

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

@@ -41 +41 @@
 import net.sf.basedb.core.data.BioPlateData;
 import net.sf.basedb.core.data.BioPlateTypeData;
+import net.sf.basedb.core.data.BioWellData;
 import net.sf.basedb.core.data.ChangeHistoryData;
 import net.sf.basedb.core.data.ChangeHistoryDetailData;
@@ -882 +883 @@
     <td>80</td>
     <td>
-      Added {@link BioPlateTypeData}.
+      Added {@link BioPlateTypeData}, {@link BioWellData#getOriginalBioMaterial()}.
       All existing bio plates are assigned "Storage plate" as their
       plate type.

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

@@ -101 +101 @@
   }
 
-  private boolean lockedWells;
+  private int lockMode;
   /**
-    If bioplates that uses this type must have locked wells or not.
-    @hibernate.property column="`locked_wells`" type="boolean" not-null="true"
+    A flag indicating if plates with this type have locked wells or not.
+    0 = not locked; 1 = locked-after-move; 2 = locked-after-add; 3=locked-after-create
+    @hibernate.property column="`lock_mode`" type="int" not-null="true"
   */
-  public boolean getLockedWells()
+  public int getLockMode()
   {
-    return lockedWells;
+    return lockMode;
   }
-  public void setLockedWells(boolean lockedWells)
+  public void setLockMode(int lockMode)
   {
-    this.lockedWells = lockedWells;
+    this.lockMode = lockMode;
   }
   

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

@@ -80 +80 @@
   }
   
+  private MeasuredBioMaterialData originalBioMaterial;
+  /**
+    The {@link MeasuredBioMaterialData} used in this well.
+    @since 2.16
+    @hibernate.many-to-one column="`original_biomaterial_id`" not-null="false" outer-join="false"
+  */
+  public MeasuredBioMaterialData getOriginalBioMaterial()
+  {
+    return originalBioMaterial;
+  }
+  public void setOriginalBioMaterial(MeasuredBioMaterialData originalBioMaterial)
+  {
+    this.originalBioMaterial = originalBioMaterial;
+  }
+  
   private MeasuredBioMaterialData bioMaterial;
   /**

trunk/src/test/TestBioPlate.java

@@ -71 +71 @@
     write_header();
     
-    int sampleId = TestSample.test_create(0, "Sample A", true);
+    int sampleId = TestSample.test_create(0, "Sample A.1", true);
+    int sample2Id = TestSample.test_create(0, "Sample A.2", true);
+    int sample3Id = TestSample.test_create(0, "Sample A.3", true);
     int extractId = TestExtract.test_create(sampleId, true);
     int labelId = TestLabel.test_create(true);
@@ -83 +85 @@
     // Standard tests: create, load, list
     int plateGeometryId = TestPlateGeometry.test_create(8, 12, false);
-    int bioPlateTypeId = TestBioPlateType.test_create("Test for bioplate", null, false);
+    int bioPlateTypeId = TestBioPlateType.test_create("Test for bioplate", null, BioWell.LockMode.UNLOCKED);
+    int addOnlyTypeId = TestBioPlateType.test_create("Add-only plate type", null, BioWell.LockMode.LOCKED_AFTER_ADD);
+    int moveTypeId = TestBioPlateType.test_create("Move plate type", null, BioWell.LockMode.LOCKED_AFTER_MOVE);
     int id = test_create("Test BioPlate", plateGeometryId, bioPlateTypeId, freezerId, true);
+    int id2 = test_create("Add-only plate", plateGeometryId, addOnlyTypeId, 0, false);
+    int id3 = test_create("Move plate", plateGeometryId, moveTypeId, 0, false);
     test_load(id);
     test_list(-1);
     
-    // Wells
-    test_set_well(id, 0, 0, Item.SAMPLE, sampleId);
-    test_set_well(id, 0, 1, Item.EXTRACT, extractId);
+    // Wells -- unlocked plate
+    boolean FAIL = true;
+    test_set_well(id, 0, 0, Item.SAMPLE, sampleId, !FAIL);
+    test_set_well(id, 0, 1, Item.EXTRACT, extractId, !FAIL);
     test_list_wells(id, 2);
+    test_clear_well(id, 0, 0, !FAIL);
+    test_clear_well(id, 0, 1, !FAIL);
+    test_list_wells(id, 0);
+    
+    // Wells -- add-only plate
+    test_set_well(id2, 0, 0, Item.SAMPLE, sample2Id, !FAIL);
+    test_clear_well(id2, 0, 0, FAIL);
+    test_set_well(id2, 0, 0, Item.SAMPLE, sample3Id, FAIL);
+    
+    // Wells -- locked-after-move plate
+    test_set_well(id3, 0, 0, Item.SAMPLE, sample3Id, !FAIL);
+    test_clear_well(id3, 0, 0, !FAIL);
+    test_list_wells(id3, 0);
+    test_list_original_biomaterial(id3, 1);
+    test_set_well(id3, 0, 0, Item.SAMPLE, sample3Id, FAIL);
     
     if (TestUtil.waitBeforeDelete()) TestUtil.waitForEnter();
@@ -99 +121 @@
     TestExtract.test_delete(extractId);
     TestSample.test_delete(sampleId);
+    TestSample.test_delete(sample2Id);
+    TestSample.test_delete(sample3Id);
     test_delete(id);
+    test_delete(id2);
+    test_delete(id3);
+    
     TestPlateGeometry.test_delete(plateGeometryId);
     TestBioPlateType.test_delete(bioPlateTypeId);
+    TestBioPlateType.test_delete(addOnlyTypeId);
+    TestBioPlateType.test_delete(moveTypeId);
     TestHardware.test_delete(freezerId);
     TestProtocol.test_delete(protocolId);
@@ -283 +312 @@
   {
     if (!TestUtil.getSilent()) System.out.println(i+":\t"+well.getId()+"\t["+well.getRow()+
-        ","+well.getColumn()+"]\t"+well.getBioMaterial());
-  }
-
-  
-  static int test_set_well(int bioPlateId, int row, int column, Item bioMaterialType, int bioMaterialId)
+        ","+well.getColumn()+"]\t"+well.getBioMaterial()+"\t"+well.getOriginalBioMaterial());
+  }
+
+  
+  static int test_set_well(int bioPlateId, int row, int column, Item bioMaterialType, int bioMaterialId, boolean shouldFail)
   {
     if (bioPlateId == 0 || bioMaterialId == 0)
@@ -297 +326 @@
     try
     {
-      dc = TestUtil.getDbControl();
-      BioPlate plate = BioPlate.getById(dc, bioPlateId);
-      MeasuredBioMaterial bm = (MeasuredBioMaterial)bioMaterialType.getById(dc, bioMaterialId);
-      BioWell well = plate.getBioWell(row, column);
-      bm.setBioWell(well);
-      dc.commit();
-      wellId = well.getId();
-      write("--Set well " + plate + "[" + row + "," + column + "] OK");
+      Throwable t = null;
+      BioPlate plate = null;
+      try
+      {
+        dc = TestUtil.getDbControl();
+        plate = BioPlate.getById(dc, bioPlateId);
+        MeasuredBioMaterial bm = (MeasuredBioMaterial)bioMaterialType.getById(dc, bioMaterialId);
+        BioWell well = plate.getBioWell(row, column);
+        bm.setBioWell(well);
+        dc.commit();
+        wellId = well.getId();
+      }
+      catch (Throwable t1)
+      {
+        t = t1;
+      }
+      if (shouldFail)
+      {
+        if (t == null) throw new RuntimeException("Well shuld be locked");
+        write("--Set well " + plate + "[" + row + "," + column + "] OK (well was locked)");
+      }
+      else
+      {
+        if (t != null) throw t;
+        write("--Set well " + plate + "[" + row + "," + column + "] OK");
+      }
     }
     catch (Throwable ex)
@@ -318 +365 @@
     return wellId;
   }
+  
+  
+  static void test_clear_well(int bioPlateId, int row, int column, boolean shouldFail)
+  {
+    if (bioPlateId == 0) return;
+    int wellId = 0;
+    DbControl dc = null;
+    try
+    {
+      Throwable t = null;
+      BioPlate plate = null;
+      try
+      {
+        dc = TestUtil.getDbControl();
+        plate = BioPlate.getById(dc, bioPlateId);
+        BioWell well = plate.getBioWell(row, column);
+        well.getBioMaterial().setBioWell(null);
+        dc.commit();
+      }
+      catch (Throwable t1)
+      {
+        t = t1;
+      }
+      if (shouldFail)
+      {
+        if (t == null) throw new RuntimeException("Well shuld be locked");
+        write("--Clear well " + plate + "[" + row + "," + column + "] OK (well was locked)");
+      }
+      else
+      {
+        if (t != null) throw t;
+        write("--Clear well " + plate + "[" + row + "," + column + "] OK");
+      }
+    }
+    catch (Throwable ex)
+    {
+      write("--Clear well BioPlate[id=" + bioPlateId + "][" + row + "," + column + "] FAILED");
+      ex.printStackTrace();
+      ok = false;
+    }
+    finally
+    {
+      if (dc != null) dc.close();
+    }
+  }
+
   
   static void test_list_wells(int bioPlateId, int expectedResults)
@@ -356 +449 @@
     }
   }
-  
+
+  static void test_list_original_biomaterial(int bioPlateId, int expectedResults)
+  {
+    if (bioPlateId == 0) return;
+    DbControl dc = null;
+    try
+    {
+      dc = TestUtil.getDbControl();
+      BioPlate plate = BioPlate.getById(dc, bioPlateId);
+      ItemResultList<BioWell> wells = plate.getBioWells().list(dc);
+      int numWells = 0;
+      for (int i = 0; i<wells.size(); i++)
+      {
+        BioWell well = wells.get(i);
+        if (well.getOriginalBioMaterial() != null)
+        {
+          write_item(i, well);
+          numWells++;
+        }
+      }
+      if (expectedResults >=0 && expectedResults != numWells)
+      {
+        throw new BaseException("Expected " + expectedResults + " results, " +
+            "not " + numWells);
+      }
+      write ("--List wells with original biomaterial OK (" + numWells +")");
+    }
+    catch (Throwable ex)
+    {
+      write("--List wells with original biomaterial FAILED");
+      ex.printStackTrace();
+      ok = false;
+    }
+    finally
+    {
+      if (dc != null) dc.close();
+    }
+  }
+
   
   static List<Integer> test_fill(int bioPlateId, Item itemType, String rootName, int labelId)

trunk/src/test/TestBioPlateType.java

@@ -4 +4 @@
 import net.sf.basedb.core.BaseException;
 import net.sf.basedb.core.BioPlateType;
+import net.sf.basedb.core.BioWell;
 import net.sf.basedb.core.DbControl;
 import net.sf.basedb.core.Item;
@@ -49 +50 @@
     write_header();
     // Standard tests: create, load, list
-    int id = test_create("Free for all", null, false);
-    int id2 = test_create("Locked samples", Item.SAMPLE, true);
+    int id = test_create("Free for all", null, BioWell.LockMode.UNLOCKED);
+    int id2 = test_create("Locked samples", Item.SAMPLE, BioWell.LockMode.LOCKED_AFTER_ADD);
+    int id3 = test_create("Moveable samples", Item.SAMPLE, BioWell.LockMode.LOCKED_AFTER_MOVE);
     test_load(id);
     test_list(-1);
@@ -58 +60 @@
     test_delete(id);
     test_delete(id2);
+    test_delete(id3);
     write("++Testing bioplate types "+(ok ? "OK" : "Failed")+"\n");
     return ok;
   }
 
-  static int test_create(String name, Item bioMaterialType, boolean lockedWells)
+  static int test_create(String name, Item bioMaterialType, BioWell.LockMode lockMode)
   {
     if (!TestUtil.hasPermission(Permission.CREATE, Item.BIOPLATETYPE)) return 0;
@@ -74 +77 @@
       pt.setDescription("Added at "+new Date());
       pt.setBioMaterialType(bioMaterialType);
-      pt.setLockedWells(lockedWells);
+      pt.setLockMode(lockMode);
       dc.saveItem(pt);
       dc.commit();
@@ -181 +184 @@
     if (!TestUtil.getSilent())
     {
-      System.out.println("   \tID \tName      \tDescription\tBiomaterial type\tLocked wells");
+      System.out.println("   \tID \tName      \tDescription\tBiomaterial type\tLock mode");
       System.out.println("-- \t-- \t--------- \t-----------\t----------------\t------------");
     }
@@ -189 +192 @@
   {
     if (!TestUtil.getSilent()) System.out.println(i+":\t"+pt.getId()+"\t"+pt.getName()+"\t"+pt.getDescription()+
-      "\t"+pt.getBioMaterialType()+"\t"+pt.getLockedWells());
+      "\t"+pt.getBioMaterialType()+"\t"+pt.getLockMode());
   }
   static void write(String message)

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

@@ -32 +32 @@
 import net.sf.basedb.core.ArraySlide;
 import net.sf.basedb.core.BioPlateType;
+import net.sf.basedb.core.BioWell;
 import net.sf.basedb.core.DataFileType;
 import net.sf.basedb.core.DbControl;
@@ -78 +79 @@
   <li>Create annotation types: {@link #createAnnotationType(DbControl, String, Type, Unit, Object[], Item[])}
   <li>Create plate type: {@link #createPlateType(DbControl, String, int, int)}
-  <li>Create bioplate type: {@link #createBioPlateType(DbControl, String, Item, boolean)}
+  <li>Create bioplate type: {@link #createBioPlateType(DbControl, String, Item, BioWell.LockMode)}
   <li>Create file formats for import:
   <li>Import plates:
@@ -154 +155 @@
       
       PlateType plateType = createPlateType(dc, "Plate type A", 16, 24);
-      BioPlateType bioPlateType = createBioPlateType(dc, "Bioplate type A", null, false);
+      BioPlateType bioPlateType = createBioPlateType(dc, "Bioplate type A", null, BioWell.LockMode.UNLOCKED);
       
       PluginConfiguration platesImporter = PluginUtil.createPluginConfiguration(dc, "Plates for project A", 
@@ -395 +396 @@
     Create a bioplate type.
   */
-  public static BioPlateType createBioPlateType(DbControl dc, String name, Item bioMaterialType, boolean lockedWells)
+  public static BioPlateType createBioPlateType(DbControl dc, String name, Item bioMaterialType, BioWell.LockMode lockMode)
   {
     TestUtil.write("--Creating bioplate type: " + name + "\n");
@@ -402 +403 @@
     pt.setName(name);
     pt.setBioMaterialType(bioMaterialType);
-    pt.setLockedWells(lockedWells);
+    pt.setLockMode(lockMode);
     dc.saveItem(pt);
     return pt;

trunk/www/biomaterials/bioplates/view_bioplate.jsp

@@ -152 +152 @@
       location.href = 'wells/index.jsp?ID=<%=ID%>&bioplate_id=<%=itemId%>';
     }
-    function viewEvents()
-    {
-      location.href = 'events/index.jsp?ID=<%=ID%>&cmd=List&bioplate_id=<%=itemId%>';
-    }
     function switchTab(tabControlId, tabId)
     {
@@ -161 +157 @@
       {
         location.href = 'index.jsp?ID=<%=ID%>&cmd=ViewItem&item_id=<%=itemId%>&tab='+tabId;
-      }
-      else if (tabId == 'events')
-      {
-        viewEvents();
       }
       else if (tabId == 'wells')
@@ -407 +399 @@
             BioWell well = bioplate.getBioWell(r, c);
             boolean isEmpty = well.isEmpty();
-            boolean editable = well.hasPermission(Permission.USE) && !well.isLocked();
+            boolean editable = well.hasPermission(Permission.USE); // && !well.isLocked();
             MeasuredBioMaterial bm = null;
             String cls = "well";
@@ -606 +598 @@
       </t:tab>
       <t:tab id="wells" title="Wells" />
-      <t:tab id="events" title="Events" />
       <t:tab id="history" title="Change history" 
         tooltip="Displays a log of all modifications made to this item"

trunk/www/biomaterials/bioplates/wells/list_biowells.jsp

@@ -99 +99 @@
   final boolean createPermission = bioplate.hasPermission(Permission.WRITE);
   final boolean deletePermission = createPermission;
-  final boolean lockedWells = bioPlateType.getLockedWells();
+  final boolean lockedWells = false; //bioPlateType.getLockedWells();
 
   Enumeration<String, String> rows = new Enumeration<String,String>();
@@ -164 +164 @@
       {
         location.href = '../index.jsp?ID=<%=ID%>&cmd=ViewItem&item_id=<%=bioPlateId%>&tab='+tabId;
-      }
-      else if (tabId == 'events')
-      {
-        location.href = '../events/index.jsp?ID=<%=ID%>&bioplate_id=<%=bioPlateId%>';
       }
       else
@@ -505 +501 @@
   
     </t:tab>
-    <t:tab id="events" title="Events" />
     <t:tab id="history" title="Change history" 
         tooltip="Displays a log of all modifications made to this item"

trunk/www/biomaterials/bioplatetypes/edit_platetype.jsp

@@ -74 +74 @@
     bioPlateType = BioPlateType.getById(dc, itemId);
     bioPlateType.checkPermission(Permission.WRITE);
-    isLocked = bioPlateType.getLockedWells();
+    //isLocked = bioPlateType.getLockedWells();
     cc.setObject("item", bioPlateType);
     title = "Edit bio plate type -- " + HTML.encodeTags(bioPlateType.getName());

trunk/www/biomaterials/bioplatetypes/index.jsp

@@ -148 +148 @@
     plateType.setName(Values.getStringOrNull(request.getParameter("name")));
     plateType.setDescription(Values.getStringOrNull(request.getParameter("description")));
-    plateType.setLockedWells(Values.getBoolean(request.getParameter("lockedWells")));
+//    plateType.setLockedWells(Values.getBoolean(request.getParameter("lockedWells")));
     dc.commit();
     cc.removeObject("item");

trunk/www/biomaterials/bioplatetypes/list_platetypes.jsp

@@ -400 +400 @@
                 <tbl:cell column="id"><%=item.getId()%></tbl:cell>
                 <tbl:cell column="bioMaterialType"><%=item.getBioMaterialType() == null ? "<i>- any -</i>" : item.getBioMaterialType().toString() %></tbl:cell>
-                <tbl:cell column="lockedWells"><%=item.getLockedWells() ? "yes" : "no" %></tbl:cell>
+                <tbl:cell column="lockedWells"><% //item.getLockedWells() ? "yes" : "no" %></tbl:cell>
                 <tbl:cell column="description"><%=HTML.encodeTags(item.getDescription())%></tbl:cell>
               </tbl:row>

trunk/www/biomaterials/bioplatetypes/view_platetype.jsp

@@ -220 +220 @@
       <tr>
         <td class="prompt">Locked wells</td>
-        <td><%=plateType.getLockedWells() ? "yes" : "no"%></td>
+        <td><% //plateType.getLockedWells() ? "yes" : "no"%></td>
       </tr>
       <tr>

trunk/www/biomaterials/extracts/edit_extract.jsp

@@ -176 +176 @@
       {
         currentBioPlate = currentBioWell.getPlate();
-        lockedWell = currentBioWell.isLocked();
+        lockedWell = false; //currentBioWell.isLocked();
       }
     }

trunk/www/biomaterials/extracts/view_extract.jsp

@@ -354 +354 @@
               %>
               [<%=rowFormatter.format(bw.getRow())%>,<%=columnFormatter.format(bw.getColumn())%>]
-              <base:icon image="locked.gif"  visible="<%=bw.isLocked() %>"/>
+              <base:icon image="locked.gif"  visible="<% //bw.isLocked() %>"/>
             <%
             }

trunk/www/biomaterials/labeledextracts/edit_labeledextract.jsp

@@ -200 +200 @@
       {
         currentBioPlate = currentBioWell.getPlate();
-        lockedWell = currentBioWell.isLocked();
+        lockedWell = false; //currentBioWell.isLocked();
       }
     }

trunk/www/biomaterials/labeledextracts/view_labeledextract.jsp

@@ -357 +357 @@
               %>
               [<%=rowFormatter.format(bw.getRow())%>,<%=columnFormatter.format(bw.getColumn())%>]
-              <base:icon image="locked.gif"  visible="<%=bw.isLocked() %>"/>
+              <base:icon image="locked.gif"  visible="<% // bw.isLocked() %>"/>
             <%
             }

trunk/www/biomaterials/samples/edit_sample.jsp

@@ -177 +177 @@
       {
         currentBioPlate = currentBioWell.getPlate();
-        lockedWell = currentBioWell.isLocked();
+        lockedWell = false; //currentBioWell.isLocked();
       }
     }

trunk/www/biomaterials/samples/view_sample.jsp

@@ -339 +339 @@
               %>
               [<%=rowFormatter.format(bw.getRow())%>,<%=columnFormatter.format(bw.getColumn())%>]
-              <base:icon image="locked.gif"  visible="<%=bw.isLocked() %>"/>
+              <base:icon image="locked.gif"  visible="<% //bw.isLocked() %>"/>
             <%
             }