Changeset 1986

Timestamp:

May 21, 2013, 2:34:28 PM (9 years ago)

Author:

Nicklas Nordborg

Message:

References #473: Register library processing results

Show warning if trying to register a library plate without any quality control PDF files attached to it. Registration is still possible.

Added "manual select" functionality for registering quality control PDF:s to a library plate. This allows a PDF file to be attached to a plate at any time.

Location:

extensions/net.sf.basedb.reggie/trunk

Files:

• resources/libprep/lib_registration.jsp (modified) (2 diffs)
• resources/libprep/libqc_registration.jsp (modified) (6 diffs)
• src/net/sf/basedb/reggie/servlet/LibPrepServlet.java (modified) (3 diffs)

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

@@ -49 +49 @@
     {
       var bioplate = bioplates[i];
-      var option = new Option(bioplate.name, bioplate.id);
-      option.comments = bioplate.comments;
+      var warning = bioplate.numFiles == 0 ? ' ( ! )' : '';
+      var option = new Option(bioplate.name + warning, bioplate.id);
+      option.bioplate = bioplate;
       plates.options[plates.length] = option;
     }
@@ -214 +215 @@
 {
   var frm = document.forms['reggie'];
+  var selectedPlate = frm.bioplate[frm.bioplate.selectedIndex].bioplate;
+  if (selectedPlate.numFiles == 0)
+  {
+    setInputStatus('bioplate', 'No quality control PDF has been registered for this plate', 'warning');
+  }
+  else
+  {
+    setInputStatus('bioplate', '', 'valid');
+  }
 }
 

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

@@ -32 +32 @@
 var currentStep = 1;
 
+var bioplateIsValid = false;
 var pdfQcIsValid = false;
 var qcDateIsValid = false;
@@ -53 +54 @@
       plates.options[plates.length] = option;
     }
-    bioplateIsValid = true;
-    setInputStatus('bioplate', '', 'valid');
-    bioPlateOnChange();
-  }
-  else
-  {
-    var msg = 'No Library bioplates available for processing.';
-    setFatalError(msg);
-    return;
-  }
-
-  // All is ok
+  }
+
   frm.bioplate.focus();
+  bioPlateOnChange();
 }
 
@@ -115 +107 @@
 function gotoStep2()
 {
+  if (!bioplateIsValid) return;
   var frm = document.forms['reggie']; 
   frm.bioplate.disabled = true;
@@ -131 +124 @@
 {
   var frm = document.forms['reggie'];
+  bioplateIsValid = false;
+
+  if (frm.bioplate.length == 0)
+  {
+    setInputStatus('bioplate', 'No Library plate available for processing.', 'invalid');
+    return;
+  }
+  
+  bioplateIsValid = true;
+  setInputStatus('bioplate', '', 'valid');
 }
 
@@ -294 +297 @@
 }
 
+function selectLibPlate()
+{
+  var frm = document.forms['reggie'];
+  if (frm.bioplate.disabled) return;
+    
+  var url = getRoot() + 'biomaterials/bioplates/index.jsp?ID=<%=ID%>&cmd=UpdateContext&mode=selectone&callback=setLibPlateCallback';
+  url += '&tmpfilter:STRING:bioPlateType.name=Library+plate';
+  Main.openPopup(url, 'SelectLibPlate', 1000, 700);
+}
+function setLibPlateCallback(id, name)
+{
+  var frm = document.forms['reggie'];
+  var plateList = frm.bioplate;
+  for (var i = 0; i < plateList.length; i++)
+  {
+    if (plateList[i].value == id)
+    {
+      plateList[i].selected = true;
+      return;
+    }
+  }
+  
+  var option = new Option(name, id, true, true);
+  plateList[plateList.length] = option;
+  bioPlateOnChange();
+}
 
 </script>
@@ -334 +363 @@
         <td class="input"><select class="required" style="width:90%;" 
             name="bioplate" id="bioplate" onchange="bioPlateOnChange()"></select>
+            
+          <base:buttongroup style="margin-top: 0.5em;">
+            <base:button title="Select manually&hellip;" onclick="selectLibPlate()" id="btnSelectLibPlate" />
+          </base:buttongroup>
         </td>
         <td class="status" id="bioplate.status"></td>

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

@@ -34 +34 @@
 import net.sf.basedb.core.File;
 import net.sf.basedb.core.InvalidDataException;
+import net.sf.basedb.core.Item;
 import net.sf.basedb.core.ItemQuery;
 import net.sf.basedb.core.ItemSubtype;
@@ -44 +45 @@
 import net.sf.basedb.core.plugin.ParameterValues;
 import net.sf.basedb.core.query.Annotations;
+import net.sf.basedb.core.query.Expressions;
 import net.sf.basedb.core.query.Hql;
 import net.sf.basedb.core.query.Orders;
@@ -183 +185 @@
         for (BioPlate plate : plates)
         {
+          ItemQuery<AnyToAny> fileQuery = AnyToAny.getLinksFrom(plate);
+          Restrictions.eq(Hql.property("toType"), Expressions.integer(Item.FILE.getValue()));
+          long fileCount = fileQuery.count(dc);
+
           JSONObject jsonPlate = new JSONObject();
           jsonPlate.put("id", plate.getId());
           jsonPlate.put("name", plate.getName());
           jsonPlate.put("comments", plate.getDescription());
+          jsonPlate.put("numFiles", fileCount);
           jsonPlate.put("poolSchema", Annotationtype.POOL_SCHEMA.getAnnotationValue(dc, plate));
           jsonPlate.put("barcodeVariant", Annotationtype.BARCODE_VARIANT.getAnnotationValue(dc, plate));