Changeset 6283

Timestamp:

Jun 10, 2021, 9:24:05 AM (2 years ago)

Author:

Nicklas Nordborg

Message:

References #1315: Support more item types in the outtake wizard

The pick list protocol should now work also for Lysate and FlowThrough outtakes.

Location:

extensions/net.sf.basedb.reggie/branches/4.31-stable

Files:

• resources/outtake/picklist.js (modified) (3 diffs)
• resources/outtake/picklist2.jsp (modified) (1 diff)
• src/net/sf/basedb/reggie/servlet/OuttakeServlet.java (modified) (2 diffs)

extensions/net.sf.basedb.reggie/branches/4.31-stable/resources/outtake/picklist.js

@@ -98 +98 @@
     
     var list = response.list;
-    Doc.element('targetAmount').innerHTML = Reggie.formatNumber(list.TargetAmount, ' µg', 1);
-    Doc.element('targetVolume').innerHTML = Reggie.formatNumber(list.TargetVolume, ' µl', 1);
-    Doc.element('targetConcentration').innerHTML = Reggie.formatNumber(1000 * list.TargetAmount / list.TargetVolume, ' ng/µl', 2);
+    var needTargetAmount = list.TargetAmount > 0;
+    var needTargetVolume = list.TargetVolume > 0;
+    
+    if (needTargetAmount)
+    {
+      Doc.element('targetAmount').innerHTML = Reggie.formatNumber(list.TargetAmount, ' µg', 1);
+    }
+    else
+    {
+      Doc.hide('targetAmountSection');
+    }
+    if (needTargetVolume)
+    {
+      Doc.element('targetVolume').innerHTML = Reggie.formatNumber(list.TargetVolume, ' µl', 1);
+    }
+    else
+    {
+      Doc.hide('targetVolumeSection');
+    }
+    if (needTargetAmount && needTargetVolume)
+    {
+      Doc.element('targetConcentration').innerHTML = Reggie.formatNumber(1000 * list.TargetAmount / list.TargetVolume, ' ng/µl', 2);
+    }
+    else
+    {
+      Doc.hide('targetConcentrationSection');
+    }
     
     var aliquots = response.aliquots;
@@ -168 +192 @@
       {
         dilution = a.dilution;
-        if (dilution.amount < list.TargetAmount) 
-        {
-          // Not enough remaining quantity -- take as much as possible
-          remarks[remarks.length] = 'Remain: ' + Reggie.formatNumber(dilution.amount, ' µg', 1);
-        }
-        else if (dilution.amount > list.TargetAmount)
-        {
-          // Typically happens to avoid taking less than 1µl
-          remarks[remarks.length] = 'Large mix: ' + Reggie.formatNumber(dilution.amount, ' µg', 1);
+        if (needTargetAmount)
+        {
+          if (dilution.amount < list.TargetAmount) 
+          {
+            // Not enough remaining quantity -- take as much as possible
+            remarks[remarks.length] = 'Remain: ' + Reggie.formatNumber(dilution.amount, ' µg', 1);
+          }
+          else if (dilution.amount > list.TargetAmount)
+          {
+            // Typically happens to avoid taking less than 1µl
+            remarks[remarks.length] = 'Large mix: ' + Reggie.formatNumber(dilution.amount, ' µg', 1);
+          }
+        }
+        else if (needTargetVolume)
+        {
+          if (dilution.volume < list.TargetVolume)
+          {
+            // Not enough remaining quantity -- take as much as possible
+            remarks[remarks.length] = 'Remain: ' + Reggie.formatNumber(dilution.volume, ' µl', 1);
+          }
         }
         if (dilution.water < 0)
@@ -183 +218 @@
           remarks[remarks.length] = 'Conc: ' + Reggie.formatNumber(p.NdConc, ' ng/µl', 2);
           dilution.water = null;
+        }
+      }
+      else
+      {
+        if (!p.remainingQuantity) 
+        {
+          remarks[remarks.length] = 'Remain: unknown';
+        }
+        else if (!p.NdConc)
+        {
+          remarks[remarks.length] = 'Conc: unknown';
         }
       }

extensions/net.sf.basedb.reggie/branches/4.31-stable/resources/outtake/picklist2.jsp

@@ -152 +152 @@
     <td><%=HTML.encodeTags(workList.getName())%></td>
   </tr>
-  <tr>
+  <tr id="targetAmountSection">
     <th>Target amount</th>
     <td><span id="targetAmount"></span></td>
   </tr>
-  <tr>
+  <tr id="targetVolumeSection">
     <th>Target volume</th>
     <td><span id="targetVolume"></span></td>
   </tr>
-  <tr>
+  <tr id="targetConcentrationSection">
     <th>Target concentration</th>
     <td><span id="targetConcentration"></span></td>

extensions/net.sf.basedb.reggie/branches/4.31-stable/src/net/sf/basedb/reggie/servlet/OuttakeServlet.java

@@ -296 +296 @@
           Float ndConc = (Float)Annotationtype.ND_CONC.getAnnotationValue(dc, parent);
           
-          if (remain != null && ndConc != null)
-          {
-            Dilution d = new Dilution(targetAmount, targetVolume, ndConc, remain);
-            jsonA.put("dilution", d.asJSONObject());
+          if (targetAmount != null && targetVolume != null)
+          {
+            // Aliquots should be normalized
+            if (remain != null && ndConc != null)
+            {
+              Dilution d = new Dilution(targetAmount, targetVolume, ndConc, remain);
+              jsonA.put("dilution", d.asJSONObject());
+            }
+          }
+          else if (targetVolume != null)
+          {
+            if (remain != null)
+            {
+              // A specific volume is needed (remaining quantity is expcted to be µl)
+              Dilution d = new Dilution(targetVolume, remain);
+              jsonA.put("dilution", d.asJSONObject());
+            }
           }
           
@@ -766 +779 @@
     
     /**
+      Use a fixed target volume. If remaining quantity is lower
+      we can't take more of course.
+      @since 4.31.3
+    */
+    Dilution(float targetVolume, float remainingQuantity)
+    {
+      this.remainingQuantity = remainingQuantity;
+      this.conc = Float.NaN;
+      
+      this.volume = Math.min(targetVolume, remainingQuantity);
+      this.water = Float.NaN;
+      this.amount = Float.NaN;
+    }
+    
+    /**
       Create a new dilution calculation.
       @param targetAmount The target amount (µg)