Changeset 6326

Timestamp:

Jun 14, 2021, 9:06:23 AM (12 months ago)

Author:

Nicklas Nordborg

Message:

Merge Reggie 4.31.3 to the trunk

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• . (modified) (1 prop)
• README (modified) (1 diff)
• lib/compile/opengrid.jar (modified) (previous)
• resources/outtake/define.js (modified) (11 diffs)
• resources/outtake/define.jsp (modified) (6 diffs)
• resources/outtake/delivery_export.js (modified) (1 diff)
• resources/outtake/picklist.js (modified) (5 diffs)
• resources/outtake/picklist2.jsp (modified) (1 diff)
• resources/outtake/register.js (modified) (2 diffs)
• src/net/sf/basedb/reggie/dao/Annotationtype.java (modified) (1 diff)
• src/net/sf/basedb/reggie/servlet/InstallServlet.java (modified) (1 diff)
• src/net/sf/basedb/reggie/servlet/OuttakeServlet.java (modified) (16 diffs)

extensions/net.sf.basedb.reggie/trunk/README

@@ -2 +2 @@
 
  1. BASE 3.18.1
- 2. Open Grid Scheduler extension 1.2 must be installed
+ 2. Open Grid Scheduler extension 1.4 must be installed
  3. Thumbnails extension 1.2 must be installed
  

extensions/net.sf.basedb.reggie/trunk/resources/outtake/define.js

@@ -4 +4 @@
   var debug = 0;
   
-  var subtypeRNA = null;
-  var subtypeDNA = null;
+  var subtypeSelected = null;
   
   var sourceList;
@@ -12 +11 @@
   var targetAmountIsValid = false;
   var targetVolumeIsValid = false;
+
+  var needTargetAmount = true;
+  var needTargetVolume = true;
+  
   
   // Page initialization
@@ -18 +21 @@
     // Step 1
     Events.addEventHandler('step-1', 'wizard-validate', outtake.validateStep1);
+    Events.addEventHandler('outtakeType', 'change', outtake.outtakeTypeOnChange);
     Buttons.addClickHandler('sourceList.select', outtake.selectSourceList);
     Events.addEventHandler('sourceList', 'base-selected', outtake.sourceListSelected);
@@ -40 +44 @@
   }
 
+  outtake.outtakeTypeOnChange = function()
+  {
+    var frm = document.forms['reggie'];
+
+    subtypeSelected = null;
+    
+    var type = frm.outtakeType.value;
+    if (type == 'RNA' || type == 'DNA')
+    {
+      needTargetAmount = true;
+      needTargetVolume = true;
+    }
+    else
+    {
+      needTargetAmount = false;
+      needTargetVolume = true;
+    }
+    
+    Doc.showHide('targetAmountSection', needTargetAmount);
+    Doc.showHide('targetVolumeSection', needTargetVolume);
+    Doc.showHide('targetConcSection', needTargetVolume && needTargetAmount);
+    
+    if (frm.sourceList.value) outtake.sourceListSelected();
+  }
+
   outtake.selectSourceList = function()
   {
     var frm = document.forms['reggie'];
     
-    if (subtypeDNA == null) subtypeDNA = Reggie.getSubtypeInfo('DNA');
-    if (subtypeRNA == null) subtypeRNA = Reggie.getSubtypeInfo('RNA');
+    if (subtypeSelected == null) subtypeSelected = Reggie.getSubtypeInfo(frm.outtakeType.value);
     
     var url = '&resetTemporary=1';
@@ -54 +82 @@
     }
     url += '&tmpfilter:INT:memberType='+Data.int('page-data', 'extract-type');
-    url += '&tmpfilter:INT:itemSubtype='+encodeURIComponent(subtypeDNA.id+'|'+subtypeRNA.id);
+    url += '&tmpfilter:INT:itemSubtype='+encodeURIComponent(subtypeSelected.id);
     Dialogs.selectItem('ITEMLIST', 'sourceList', 0, url);
   }
@@ -68 +96 @@
     Doc.element('listConc').innerHTML = '';
 
-    var list = event.detail;
-    frm.sourceList[0] = new Option(list.name, list.id);
+    if (event)
+    {
+      var list = event.detail;
+      frm.sourceList[0] = new Option(list.name, list.id);
+      frm.sourceList.selectedIndex = 0;
+    }
     Wizard.setInputStatus('sourceList', 'checking', 'Checking list...');
     
     var url = '../Outtake.servlet?ID='+App.getSessionId();
     url += '&cmd=CheckSourceList';
-    url += '&listId='+list.id;
+    url += '&outtakeType='+frm.outtakeType.value;
+    url += '&listId='+frm.sourceList.value;
     Wizard.asyncJsonRequest(url, outtake.sourceListValidated);
-
   }
   
@@ -98 +130 @@
       listType += ' (' + Strings.encodeTags(sourceList.subtype.name) + ')';
     }
-    else if (sourceList.numDifferentSubtypes > 1)
-    {
-      Wizard.setInputStatus('listType', 'warning', 'The list have items of ' + sourceList.numDifferentSubtypes + ' different types');
-    }
-    
     Doc.element('listType').innerHTML = listType;
     Doc.element('listSize').innerHTML = sourceList.size;
     
-    var remainingQuantity = sourceList.remainingQuantity;
-    if (remainingQuantity)
-    {
-      Doc.element('listRemainingQuantity').innerHTML = 
-        Reggie.formatNumber(remainingQuantity.min, ' µg (min), ', 2) +
-        Reggie.formatNumber(remainingQuantity.max, ' µg (max)', 2);
-      
-      if (remainingQuantity.nulls > 0)
-      {
-        Wizard.setInputStatus('listRemainingQuantity', 'warning', remainingQuantity.nulls + ' items have unknown remaining quantity');
-      }
-    }
-    var conc = sourceList.conc;
-    if (conc)
-    {
-      Doc.element('listConc').innerHTML = 
-        Reggie.formatNumber(conc.min, ' ng/µl (min), ', 2) +
-        Reggie.formatNumber(conc.max, ' ng/µl (max)', 2);
-      
-      if (conc.nulls > 0)
-      {
-        Wizard.setInputStatus('listConc', 'warning', conc.nulls + ' items have unknown concentration');
-      }
-    }
+    if (needTargetAmount || needTargetVolume)
+    {
+      var remainingQuantity = sourceList.remainingQuantity;
+      if (remainingQuantity)
+      {
+        var remainingQuantityUnit = needTargetAmount ? ' µg' : ' µl';
+        Doc.element('listRemainingQuantity').innerHTML = 
+          Reggie.formatNumber(remainingQuantity.min, remainingQuantityUnit+' (min), ', 2) +
+          Reggie.formatNumber(remainingQuantity.max, remainingQuantityUnit+' (max)', 2);
+        
+        if (remainingQuantity.nulls > 0)
+        {
+          Wizard.setInputStatus('listRemainingQuantity', 'warning', remainingQuantity.nulls + ' items have unknown remaining quantity');
+        }
+      }
+    }
+    else
+    {
+      Doc.element('listRemainingQuantity').innerHTML = '';
+    }
+
+    if (needTargetAmount && needTargetVolume)
+    {
+      var conc = sourceList.cnc;
+      if (conc)
+      {
+        Doc.element('listConc').innerHTML = 
+          Reggie.formatNumber(conc.min, ' ng/µl (min), ', 2) +
+          Reggie.formatNumber(conc.max, ' ng/µl (max)', 2);
+        
+        if (ndConc.nulls > 0)
+        {
+          Wizard.setInputStatus('listConc', 'warning', conc.nulls + ' items have unknown concentration');
+        }
+      }
+    }
+    else
+    {
+      Doc.element('listConc').innerHTML = '';
+    }
+
 
     if (sourceList.size == 0)
@@ -148 +192 @@
       Wizard.showGoNextConfirmation(true, 'Confirm using the list with ' + sourceList.numDoNotUse + ' items marked as DoNotUse');
     }
-    else if (sourceList.numDifferentSubtype > 0)
-    {
-      Wizard.setInputStatus('sourceList', 'warning', 'Items in the list are not of the same subtype');
+    else if (sourceList.numIncorrectSubtype > 1)
+    {
+      Wizard.setInputStatus('sourceList', 'warning', 'The list have '+sourceList.numIncorrectSubtype+' items that are not '+frm.outtakeType.value);
     }
     else
@@ -237 +281 @@
     var targetConc = 1000 * targetAmount / targetVolume;
     
-    if (!isNaN(targetConc))
-    {
-      Doc.element('targetConcentration').innerHTML = Reggie.formatNumber(targetConc, ' ng/µl', 2);
+    if (needTargetAmount && needTargetVolume)
+    {
+      if (!isNaN(targetConc))
+      {
+        Doc.element('targetConcentration').innerHTML = Reggie.formatNumber(targetConc, ' ng/µl', 2);
+      }
     }
     
     if (sourceList)
     {
-      if (sourceList.remainingQuantity && sourceList.remainingQuantity.min < targetAmount)
-      {
-        Wizard.setInputStatus('targetAmount', 'warning', 'Some items in the list have less remaining quantity: '+ Reggie.formatNumber(sourceList.remainingQuantity.min, ' µg', 2));
+      if (needTargetAmount)
+      {
+        if (sourceList.remainingQuantity && sourceList.remainingQuantity.min < targetAmount)
+        {
+          Wizard.setInputStatus('targetAmount', 'warning', 'Some items in the list have less remaining quantity: '+ Reggie.formatNumber(sourceList.remainingQuantity.min, ' µg', 2));
+        }
       }
       
-      if (sourceList.conc && sourceList.conc.min < targetConc)
-      {
-        Wizard.setInputStatus('targetVolume', 'warning', 'Some items in the list has too low concentration: '+ Reggie.formatNumber(sourceList.conc.min, ' ng/µl', 2));
-      }
+      if (needTargetAmount && needTargetVolume)
+      {
+        if (sourceList.conc && sourceList.conc.min < targetConc)
+        {
+          Wizard.setInputStatus('targetVolume', 'warning', 'Some items in the list has too low concentration: '+ Reggie.formatNumber(sourceList.ndConc.min, ' ng/µl', 2));
+        }
+      }
+      else if (needTargetVolume)
+      {
+        if (sourceList.remainingQuantity && sourceList.remainingQuantity.min < targetVolume)
+        {
+          Wizard.setInputStatus('targetVolume', 'warning', 'Some items in the list have less remaining quantity: '+ Reggie.formatNumber(sourceList.remainingQuantity.min, ' µl', 2));
+        }
+      }
+
     }
   }
@@ -268 +329 @@
     valid &= sourceListIsValid;
     valid &= nameIsValid;
-    valid &= targetAmountIsValid;
-    valid &= targetVolumeIsValid;
+    if (needTargetAmount) valid &= targetAmountIsValid;
+    if (needTargetVolume) valid &= targetVolumeIsValid;
     
     if (!valid) event.preventDefault();
@@ -281 +342 @@
     
     submitInfo.sourceList = parseInt(frm.sourceList.value);
+    submitInfo.outtakeType = frm.outtakeType.value;
     submitInfo.outtakeName = frm.outtakeName.value;
-    submitInfo.targetAmount = parseFloat(frm.targetAmount.value);
-    submitInfo.targetVolume = parseFloat(frm.targetVolume.value);
+    if (needTargetAmount) 
+    {
+      submitInfo.targetAmount = parseFloat(frm.targetAmount.value);
+    }
+    if (needTargetVolume)
+    {
+      submitInfo.targetVolume = parseFloat(frm.targetVolume.value);
+    }
     submitInfo.comments = frm.comments.value;
 

extensions/net.sf.basedb.reggie/trunk/resources/outtake/define.jsp

@@ -55 +55 @@
         <td class="prompt">Outtake name</td>
         <td class="input"><input type="text" name="outtakeName" id="outtakeName"
-          class="auto-init required" data-auto-init="focus-on-enter" data-next-focus="sourceList.select"
+          class="auto-init required" data-auto-init="focus-on-enter" data-next-focus="outtakeType"
           maxlength="255"></td>
         <td class="status" id="outtakeName.status"></td>
@@ -63 +63 @@
           of the item list with aliquots.
         </td>
+      </tr>
+      <tr>
+        <td class="prompt">Outtake type</td>
+        <td class="input">
+          <select name="outtakeType" id="outtakeType" class="required auto-init"
+            data-auto-init="focus-on-enter" data-next-focus="sourceList.select"
+            style="width: 10em;">
+            <option value="DNA">DNA
+            <option value="RNA">RNA
+            <option value="LYSATE">Lysate
+            <option value="FLOWTHROUGH">FlowThrough
+          </select>
+        </td>
+        <td class="status" id="outtakeType.status"></td>
+        <td class="help">
+          <span id="outtakeType.message" class="message"></span>
+          Select the type of items in the outtake.
+        </td>
+        
       </tr>
       <tr class="align-top">
@@ -77 +96 @@
         <td class="help">
           <span id="sourceList.message" class="message"></span>
-          Select a source item list that contains either RNA or DNA items.
+          Select a source item list that contains items of the selected type.
         </td>
       </tr>
@@ -106 +125 @@
       </tr>
       </tbody>
-      <tr>
+      <tr id="targetAmountSection">
         <td class="prompt">Target amount</td>
         <td class="input"><input type="text" name="targetAmount" id="targetAmount"
@@ -118 +137 @@
         </td>
       </tr>
-      <tr>
+      <tr id="targetVolumeSection">
         <td class="prompt">Target volume</td>
         <td class="input"><input type="text" name="targetVolume" id="targetVolume"
@@ -126 +145 @@
         <td class="help">
           <span id="targetVolume.message" class="message"></span>
-          Specify the target volume in µl of the normalized aliquots.
+          Specify the target volume in µl of the aliquots.
         </td>
       </tr>
-      <tbody class="info-section">
+      <tbody class="info-section" id="targetConcSection">
       <tr>
         <td class="prompt">Target concentration</td>

extensions/net.sf.basedb.reggie/trunk/resources/outtake/delivery_export.js

@@ -38 +38 @@
       {
         var list = workLists[i];
-        var name = list.name + ' (' + list.size + ')';
+        var name = list.name + ' (' + list.size+(list.parentType?' '+list.parentType : '') + ')';
         var option = new Option(name, list.id);
         option.workList = list;

extensions/net.sf.basedb.reggie/trunk/resources/outtake/picklist.js

@@ -46 +46 @@
       {
         var list = workLists[i];
-        var name = list.name + ' (' + list.size + ')';
+        var name = list.name + ' (' + list.size+(list.parentType?' '+list.parentType : '') + ')';
         var option = new Option(name, list.id);
         option.workList = list;
@@ -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;
+    
+    Doc.element('parentType').innerHTML = Strings.encodeTags(list.parentType);
+    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;
@@ -108 +133 @@
     var lastStorageBox = -1;
     var numRows = 0;
-
-    var targetConc = 1000 * list.TargetAmount / list.TargetVolume; // ng/µl;
     
     for (var aliquotNo = 0; aliquotNo < aliquots.length; aliquotNo++)
@@ -168 +191 @@
       {
         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 +217 @@
           remarks[remarks.length] = 'Conc: ' + Reggie.formatNumber(p.conc, ' 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/trunk/resources/outtake/picklist2.jsp

@@ -153 +153 @@
   </tr>
   <tr>
+    <th>Parent item type</th>
+    <td><span id="parentType"></span></td>
+  </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/trunk/resources/outtake/register.js

@@ -49 +49 @@
       {
         var list = workLists[i];
-        var name = list.name + ' (' + list.size + ')';
+        var name = list.name + ' (' + list.size+(list.parentType?' '+list.parentType : '') + ')';
         var option = new Option(name, list.id);
         option.workList = list;
@@ -193 +193 @@
     {
       submitInfo.sampleConsumed = Doc.element('sampleConsumedYes').checked;
-      var except = [];
       submitInfo.except = Link.getIdsInList(frm.except, workList.itemType);
     }

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

@@ -1856 +1856 @@
   */
   public static final Annotationtype OUTTAKE_TARGET_VOLUME =
-      new Annotationtype("OuttakeTargetVolume", Type.FLOAT, false, Item.ITEMLIST);
-
+    new Annotationtype("OuttakeTargetVolume", Type.FLOAT, false, Item.ITEMLIST);
+
+  /**
+    Subtype of the parent items for the outtake aliquots.
+    @since 4.31.3
+  */
+  public static final Annotationtype OUTTAKE_PARENT_TYPE =
+    new Annotationtype("OuttakeParentType", Type.STRING, false, Item.ITEMLIST);
+    
   /**
     INCA2 diagnosis date annotation (provtagningsdatum). We need this to 

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

@@ -704 +704 @@
         jsonChecks.add(checkAnnotationType(dc, Annotationtype.OUTTAKE_TARGET_AMOUNT, 1, null, createIfMissing, effectivePermissionsUse));
         jsonChecks.add(checkAnnotationType(dc, Annotationtype.OUTTAKE_TARGET_VOLUME, 1, null, createIfMissing, effectivePermissionsUse));
+        jsonChecks.add(checkAnnotationType(dc, Annotationtype.OUTTAKE_PARENT_TYPE, 1, 
+            new ValueOptions("DNA", "RNA", "Lysate", "FlowThrough"), createIfMissing, effectivePermissionsUse));
         jsonChecks.add(checkAnnotationType(dc, Annotationtype.OUTTAKE_RESULT, 1, 
             new ValueOptions("Successful", "Failed"),

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

@@ -17 +17 @@
 import org.json.simple.JSONObject;
 
+import net.sf.basedb.core.AnyToAny;
 import net.sf.basedb.core.BioMaterial;
 import net.sf.basedb.core.BioMaterialEvent;
@@ -89 +90 @@
 
         int listId = Values.getInt(req.getParameter("listId"));
+        ItemSubtype outtakeType = Subtype.getByCName(req.getParameter("outtakeType")).get(dc);
         
         ItemList list = ItemList.getById(dc, listId);
@@ -94 +96 @@
         ItemSubtype memberSubtype = list.getItemSubtype();
         
-        Set<ItemSubtype> memberSubtypes = new HashSet<>();
-        if (memberSubtype != null) memberSubtypes.add(memberSubtype);
-
         JSONObject jsonList = new JSONObject();
         jsonList.put("id", list.getId());
@@ -106 +105 @@
         {
           int numDoNotUse = 0;
+          int numIncorrectSubtype = 0;
           ItemQuery<Extract> memberQuery = list.getMembers();
           memberQuery.setIncludes(Reggie.INCLUDE_IN_CURRENT_PROJECT);
@@ -121 +121 @@
             conc.add(c);
             
-            ItemSubtype subtype = e.getItemSubtype();
-            memberSubtypes.add(subtype);
+            ItemSubtype subtype = e.getItemSubtype();         
+            if (!outtakeType.equals(subtype))
+            {
+              numIncorrectSubtype++;
+            }
             
             if (Annotationtype.DO_NOT_USE.getAnnotationValue(dc, e) != null)
@@ -133 +136 @@
           jsonList.put("conc", conc.asJSONObject());
           jsonList.put("numDoNotUse", numDoNotUse);
-        }
-        
-        jsonList.put("numDifferentSubtypes", memberSubtypes.size());
-        if (memberSubtypes.size() == 1)
-        {
-          memberSubtype = memberSubtypes.iterator().next();
+          jsonList.put("numIncorrectSubtype", numIncorrectSubtype);
+        }
+        
+        if (memberSubtype != null)
+        {
           jsonList.put("subtype", Subtype.get(memberSubtype).asJSONObject(dc));
         }
@@ -181 +183 @@
           jsonList.put("size", list.getSize());
           jsonList.put("comments", list.getDescription());
+          jsonList.put("parentType", Annotationtype.OUTTAKE_PARENT_TYPE.getAnnotationValue(dc, list));
           jsonLists.add(jsonList);
         }
@@ -268 +271 @@
         jsonList.put("TargetAmount", targetAmount);
         jsonList.put("TargetVolume", targetVolume);
+        jsonList.put("parentType", Annotationtype.OUTTAKE_PARENT_TYPE.getAnnotationValue(dc, manager, list));
         
         ItemQuery<Extract> memberQuery = list.getMembers();
@@ -298 +302 @@
           if (conc == null) conc = (Float)Annotationtype.QUBIT_CONC.getAnnotationValue(dc, parent);
           
-          if (remain != null && conc != null)
-          {
-            Dilution d = new Dilution(targetAmount, targetVolume, conc, remain);
-            jsonA.put("dilution", d.asJSONObject());
+          if (targetAmount != null && targetVolume != null)
+          {
+            // Aliquots should be normalized
+            if (remain != null && conc != null)
+            {
+              Dilution d = new Dilution(targetAmount, targetVolume, conc, 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());
+            }
           }
           
@@ -328 +345 @@
         
         ItemList workList = ItemList.getById(dc, workListId);
-        
+        Float targetAmount = (Float)Annotationtype.OUTTAKE_TARGET_AMOUNT.getAnnotationValue(dc, workList);
+        Float targetVolume = (Float)Annotationtype.OUTTAKE_TARGET_VOLUME.getAnnotationValue(dc, workList);
+      
         ItemQuery<Extract> memberQuery = workList.getMembers();
         memberQuery.setIncludes(Reggie.INCLUDE_IN_CURRENT_PROJECT);
@@ -346 +365 @@
         
         TableWriter tw = new TableWriter(out);
-        tw.tablePrintData("Name", "Box", "Position", "Quantity (µg)", "Concentration (ng/µl)");
-        Object[] data = new Object[5];
+        Object[] data = null;
+        if (targetAmount != null && targetVolume != null)
+        {
+          tw.tablePrintData("Name", "Box", "Position", "Quantity (µg)", "Concentration (ng/µl)");
+          data = new Object[5];
+        }
+        else
+        {
+          tw.tablePrintData("Name", "Box", "Position", "Quantity (µl)");
+          data = new Object[4];
+        }
         
         Iterator<Extract> it = memberQuery.iterate(dc);
@@ -363 +391 @@
           data[2] = well.getCoordinate();
           data[3] = Values.formatNumber(aliquot.getRemainingQuantity(), 1);
-          data[4] = Values.formatNumber((Float)Annotationtype.DILUTION_CONC.getAnnotationValue(dc, aliquot), 1);
+          if (data.length > 4)
+          {
+            data[4] = Values.formatNumber((Float)Annotationtype.DILUTION_CONC.getAnnotationValue(dc, aliquot), 1);
+          }
           tw.tablePrintData(data);
         }
@@ -427 +458 @@
         String comments = (String)jsonReq.get("comments");
         
-        float targetAmount = ((Number)jsonReq.get("targetAmount")).floatValue();
-        float targetVolume = ((Number)jsonReq.get("targetVolume")).floatValue();
+        Number targetAmount = (Number)jsonReq.get("targetAmount");
+        Number targetVolume = (Number)jsonReq.get("targetVolume");
+        ItemSubtype outtakeType = Subtype.getByCName((String)jsonReq.get("outtakeType")).get(dc);
         
         ItemList aliquotList = ItemList.getNew(dc, sourceList.getMemberType());
@@ -436 +468 @@
         dc.saveItem(aliquotList);
         
+        AnyToAny sourceLink = AnyToAny.getNew(dc, aliquotList, sourceList, "Source list", false);
+        sourceLink.setDescription("This is the source list that contain parent items for the aliquots in this list");
+        dc.saveItem(sourceLink);
+        
         Annotationtype.OUTTAKE_TARGET_AMOUNT.setAnnotationValue(dc, aliquotList, targetAmount);
         Annotationtype.OUTTAKE_TARGET_VOLUME.setAnnotationValue(dc, aliquotList, targetVolume);
+        Annotationtype.OUTTAKE_PARENT_TYPE.setAnnotationValue(dc, aliquotList, outtakeType.getName());
         
         // Query for finding existing child aliquots
@@ -585 +622 @@
           if (conc == null) conc = (Float)Annotationtype.QUBIT_CONC.getAnnotationValue(dc, parent);
           
-          if (remain != null && conc != null)
-          {
-            boolean isException = except.contains(aliquot.getId());
-            if (isException) numExceptions++;
-            
-            if (sampleConsumed != isException)
+          if (targetAmount != null && targetVolume != null)
+          {
+            if (remain != null && conc != null)
             {
-              Dilution d = new Dilution(targetAmount, targetVolume, conc, remain);
-              creationEvent.getEventSource(parent).setUsedQuantity(d.amount);
-              aliquot.setOriginalQuantity(d.amount);
-              Annotationtype.DILUTION_CONC.setAnnotationValue(dc, aliquot, d.getDilutedConc());
-              //jsonMessages.add(aliquot.getId() + ":" + aliquot.getName() + ": " + ndConc + "--" + d.getDilutedConc() + ":"+isException);
+              boolean isException = except.contains(aliquot.getId());
+              if (isException) numExceptions++;
+              
+              if (sampleConsumed != isException)
+              {
+                Dilution d = new Dilution(targetAmount, targetVolume, conc, remain);
+                creationEvent.getEventSource(parent).setUsedQuantity(d.amount);
+                aliquot.setOriginalQuantity(d.amount);
+                Annotationtype.DILUTION_CONC.setAnnotationValue(dc, aliquot, d.getDilutedConc());
+                //jsonMessages.add(aliquot.getId() + ":" + aliquot.getName() + ": " + ndConc + "--" + d.getDilutedConc() + ":"+isException);
+              }
+              else
+              {
+                // jsonMessages.add(aliquot.getId() + ":" + aliquot.getName() + " not consumed: " + isException);
+              }
             }
-            else
+          }
+          else if (targetVolume != null)
+          {
+            if (remain != null)
             {
-              // jsonMessages.add(aliquot.getId() + ":" + aliquot.getName() + " not consumed: " + isException);
+              boolean isException = except.contains(aliquot.getId());
+              if (isException) numExceptions++;
+              if (sampleConsumed != isException)
+              {
+                Dilution d = new Dilution(targetVolume, remain);
+                creationEvent.getEventSource(parent).setUsedQuantity(d.volume);
+                aliquot.setOriginalQuantity(d.volume);
+                //jsonMessages.add(aliquot.getId() + ":" + aliquot.getName() + ": " + d.volume + ":"+isException);
+              }
+              else
+              {
+                //jsonMessages.add(aliquot.getId() + ":" + aliquot.getName() + " not consumed: " + isException);
+              }
             }
           }
@@ -769 +828 @@
     
     /**
+      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)