Changeset 2141

Timestamp:

Nov 18, 2013, 2:36:50 PM (10 years ago)

Author:

Nicklas Nordborg

Message:

References #527: Implement manual pooled library selection

Selection of plate/pool in lab protocol wizard for pooling and pool registration wizard has been updated to ensure that manaully created pools can be properly selected. There was a problem with manual pools if all libraries came from the same library plate which caused the wizard to beleive that the pool was a "plate" pool. Added PoolIsManual annotation to be able to check for this case and also added a AnyToAny link to the library plate for "plate" pools.

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• resources/libprep/create_pools.jsp (modified) (2 diffs)
• resources/libprep/pool_protocol.jsp (modified) (6 diffs)
• resources/libprep/pool_registration.jsp (modified) (4 diffs)
• src/net/sf/basedb/reggie/dao/Annotationtype.java (modified) (1 diff)
• src/net/sf/basedb/reggie/servlet/InstallServlet.java (modified) (2 diffs)
• src/net/sf/basedb/reggie/servlet/PoolServlet.java (modified) (4 diffs)

extensions/net.sf.basedb.reggie/trunk/resources/libprep/create_pools.jsp

@@ -139 +139 @@
   submitInfo.flagged = [];
   var frm = document.forms['reggie'];
+  var libPlate = frm.bioplate[frm.bioplate.selectedIndex].bioplate;
   submitInfo.targetVolumeInPoolPerLib = parseFloat(frm.target_volume.value);
   submitInfo.targetPoolMolarity = TARGET_MOLARITY_IN_POOL;
@@ -152 +153 @@
     poolInfo.comment = frm['comment.'+poolNo].value;
     poolInfo.ebVolumeExtra = POOL_DATA[poolNo].ebVolumeExtra;
+    poolInfo.libPlate = libPlate.id;
     poolInfo.libs = [];
     poolInfo.excluded = [];

extensions/net.sf.basedb.reggie/trunk/resources/libprep/pool_protocol.jsp

@@ -52 +52 @@
       var pool = pools[poolNo];
       // Shortcut to single-plate pools
-      var libPlateForPool = pool.libPlates.length == 1 ? pool.libPlates[0] : null;
-      pool.libPlate = libPlateForPool
+      var libPlateForPool = pool.libPlates.length == 1 && !pool.isManual ? pool.libPlates[0] : null;
+      pool.libPlate = libPlateForPool;
     
       // If the pool has a single library bioplate add it to the selection list
       // If the pool doesn't have a single library bioplate, nothing is added to
-      // the list and the pool can only be selected when the 'multiple' option is
+      // the list and the pool can only be selected when the 'manual' option is
       // active for the bioplates list
       if (libPlateForPool != null && !libPlates[libPlateForPool.name])
@@ -128 +128 @@
     if (addPool)
     {
-      frm.pools[frm.pools.length] = new Option(pool.name, pool.id, libPlateId);
+      var name = pool.name;
+      if (pool.libPlate == null)
+      {
+        
+        name += ' - ';
+        var numPlates = pool.libPlates.length;
+        var title = '';
+        if (numPlates <= 2)
+        {
+          for (var plateNo=0; plateNo < numPlates; plateNo++)
+          {
+            var libPlate = pool.libPlates[plateNo];
+            if (plateNo > 0) name += ', ';
+            name += libPlate.name;
+          }
+        }
+        else
+        {
+          name += pool.libPlates[0].name + ' + ' + (numPlates-1) + ' more...';
+          for (var plateNo=0; plateNo < numPlates; plateNo++)
+          {
+            var libPlate = pool.libPlates[plateNo];
+            if (plateNo > 0) title += ', ';
+            title += libPlate.name;
+          }
+        }
+      }
+
+      frm.pools[frm.pools.length] = new Option(name, pool.id, libPlateId || frm.pools.length == 0);
     }
   }
@@ -135 +163 @@
   if (libPlateId)
   {
-    frm.pools.disabled = true;
+    //frm.pools.disabled = true;
     Main.removeClass(document.getElementById('plateview'), 'disabled');
   }
@@ -153 +181 @@
   if (libPlateId == 0)
   {
-    // 'multiple' option selected, check that at least one pool is selected
+    // 'manual' option selected, check that at least one pool is selected
     var numSelectedPools = 0;
     for (var poolNo = 0; poolNo < frm.pools.length; poolNo++)
@@ -213 +241 @@
         <td class="input">
           <select style="width:90%;" name="bioplate" id="bioplate" onchange="bioplateOnChange()">
-            <option value="0">- multiple -
+            <option value="0">- manual pools -
           </select>
-          <br>
-          <i>- or -</i>
         </td>
         <td class="status" id="bioplate.status"></td>
@@ -222 +248 @@
           Select the library bioplate that should be pooled in this step. The list contains
           all plates with pools that has not yet been created (determined by abscense of creation date).
-          Use the <b>multiple</b> option to select pools with libraries from multiple plates.
+          Use the <b>manual pools</b> option to select pools that has been manually created.
         </td>
       </tr>

extensions/net.sf.basedb.reggie/trunk/resources/libprep/pool_registration.jsp

@@ -56 +56 @@
       
       // Shortcut to single-plate pools
-      var libPlateForPool = pool.libPlates.length == 1 ? pool.libPlates[0] : null;
+      var libPlateForPool = pool.libPlates.length == 1 && !pool.isManual ? pool.libPlates[0] : null;
       pool.libPlate = libPlateForPool
 
       // If the pool has a single library bioplate add it to the selection list
       // If the pool doesn't have a single library bioplate, nothing is added to
-      // the list and the pool can only be selected when the 'multiple' option is
+      // the list and the pool can only be selected when the 'manual pools' option is
       // active for the bioplates list
       if (libPlateForPool != null && !libPlates[libPlateForPool.name])
@@ -133 +133 @@
     if (addPool)
     {
-      var option = new Option(pool.name, pool.id, libPlateId);
+      var name = pool.name;
+      if (pool.libPlate == null)
+      {
+        
+        name += ' - ';
+        var numPlates = pool.libPlates.length;
+        var title = '';
+        if (numPlates <= 2)
+        {
+          for (var plateNo=0; plateNo < numPlates; plateNo++)
+          {
+            var libPlate = pool.libPlates[plateNo];
+            if (plateNo > 0) name += ', ';
+            name += libPlate.name;
+          }
+        }
+        else
+        {
+          name += pool.libPlates[0].name + ' + ' + (numPlates-1) + ' more...';
+          for (var plateNo=0; plateNo < numPlates; plateNo++)
+          {
+            var libPlate = pool.libPlates[plateNo];
+            if (plateNo > 0) title += ', ';
+            title += libPlate.name;
+          }
+        }
+      }
+
+      var option = new Option(name, pool.id, libPlateId || frm.pools.length == 0);
       option.pool = pool;
       frm.pools[frm.pools.length] = option;
@@ -425 +453 @@
         <td class="input">
           <select style="width:90%;" name="bioplate" id="bioplate" onchange="bioplateOnChange()">
-            <option value="0">- multiple -
+            <option value="0">- manual pools -
           </select>
-          <br>
-          <i>- or -</i>
         </td>
         <td class="status" id="bioplate.status"></td>
@@ -434 +460 @@
           Select the library bioplate that should be pooled in this step. The list contains
           all plates with pools that has not yet been created (determined by abscense of creation date).
-          Use the <b>multiple</b> option to select pools with libraries from multiple plates.
+          Use the <b>manual pools</b> option to select pools that has been manually created.
         </td>
       </tr>

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/dao/Annotationtype.java

@@ -605 +605 @@
   public static final Annotationtype POOL_TARGET_MOLARITY =
     new Annotationtype("PoolTargetMolarity", Type.FLOAT, Item.EXTRACT);
+
+  /**
+    The "PoolIsManual" annotation, used for extracts (PooledLibrary).
+    Store a flag indicating if the pool is manaually created. If not set,
+    it is asssumed that the pool is created from an entire library working plate.
+    @since 2.14
+  */
+  public static final Annotationtype POOL_IS_MANUAL =
+    new Annotationtype("PoolIsManual", Type.BOOLEAN, Item.EXTRACT);
+
   
   /**

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/InstallServlet.java

@@ -278 +278 @@
         jsonChecks.add(checkAnnotationType(dc, Annotationtype.POOL_TARGET_VOLUME_PER_LIB, 1, null, effectiveOptions, createIfMissing));
         jsonChecks.add(checkAnnotationType(dc, Annotationtype.POOL_TARGET_MOLARITY, 1, null, effectiveOptions, createIfMissing));
+        jsonChecks.add(checkAnnotationType(dc, Annotationtype.POOL_IS_MANUAL, 1, null, effectiveOptions, createIfMissing));
         jsonChecks.add(checkAnnotationType(dc, Annotationtype.POOL_MIXING_STRATEGY, 1, 
             new ValueOptions(PooledLibrary.MIXING_STRATEGY_FIXED, PooledLibrary.MIXING_STRATEGY_DYNAMIC),
@@ -384 +385 @@
         jsonChecks.add(checkAnnotationTypeCategory(dc, Subtype.POOLED_LIBRARY, createIfMissing,
             Annotationtype.POOL_MOLARITY, Annotationtype.POOL_CONC, Annotationtype.POOL_TARGET_VOLUME_PER_LIB,
-            Annotationtype.POOL_TARGET_MOLARITY,
+            Annotationtype.POOL_TARGET_MOLARITY, Annotationtype.POOL_IS_MANUAL,
             Annotationtype.POOL_MIXING_STRATEGY, Annotationtype.POOL_DATE, Annotationtype.OPERATOR,
             Annotationtype.FLAG, Annotationtype.AUTO_PROCESSING));

extensions/net.sf.basedb.reggie/trunk/src/net/sf/basedb/reggie/servlet/PoolServlet.java

@@ -19 +19 @@
 
 
+
 import net.sf.basedb.clients.web.util.HTML;
+import net.sf.basedb.core.AnyToAny;
 import net.sf.basedb.core.Application;
 import net.sf.basedb.core.BioMaterialEvent;
@@ -274 +276 @@
           pool.loadAnnotations(dc, "molarity", Annotationtype.POOL_MOLARITY, null);
           pool.loadAnnotations(dc, "conc", Annotationtype.POOL_CONC, null);
+          pool.loadAnnotations(dc, "isManual", Annotationtype.POOL_IS_MANUAL, null);
           pool.setAnnotation("remainingQuantity", pool.getExtract().getRemainingQuantity());
           pool.setAnnotation("comments", pool.getExtract().getDescription());
@@ -391 +394 @@
           JSONArray jsonExcluded = (JSONArray)jsonPool.get("excluded");
           
+          Number libPlateId = (Number)jsonPool.get("libPlate");
+          
           // Create PooledLibrary item
           Extract pool = Extract.getNew(dc);
@@ -399 +404 @@
           Annotationtype.POOL_TARGET_MOLARITY.setAnnotationValue(dc, pool, targetPoolMolarity.floatValue());
           Annotationtype.POOL_MIXING_STRATEGY.setAnnotationValue(dc, pool, mixingStrategy);
+          
+          // Link with library plate
+          if (libPlateId != null)
+          {
+            BioPlate libPlate = BioPlate.getById(dc, libPlateId.intValue());
+            AnyToAny libPlateLink = AnyToAny.getNew(dc, pool, libPlate, "LibPlate", true);
+            dc.saveItemIf(pool, libPlateLink, false);
+            jsonMessages.add("Linked pool " + pool.getName() + " with " + libPlateLink);
+          }
+          else
+          {
+            Annotationtype.POOL_IS_MANUAL.setAnnotationValue(dc, pool, true);
+          }
           
           BioMaterialEvent poolEvent = pool.getCreationEvent();