Changeset 3526

Timestamp:

Oct 5, 2015, 8:57:32 AM (7 years ago)

Author:

olle

Message:

Refs #801. Refs #816. Case summary updated to present information on fpa and fpb DNA aliquots in a separate section (initially the "Library" section will be used), instead of the "DNA" section:

1. JSP file case_summary.jsp in resources/reports/ updated with "Library" section (previously commented out), after the "DNA" section.
2. Javascript file case_summary.js in resources/reports/ updated in function caseInfoLoaded(response) to obtain information on fpa and fpb DNA aliquots from the CaseSummaryServlet response, and insert it in appropriate fields in the "Library" section of the case summary form. Code for barcode name updated to display "NA", if not defined.
3. Java servlet class/file CaseSummaryServlet.java in src/net/sf/basedb/servlet/ updated in protected method void doGet(HttpServletRequest req, HttpServletResponse resp) for command "GetCaseInfo" to send information on fpa and fpb DNA aliquots in new JSON object with key "lib". The barcode string is constructed based on the well location on the library plate.

Location:

extensions/net.sf.basedb.meludi/trunk

Files:

• resources/reports/case_summary.js (modified) (3 diffs)
• resources/reports/case_summary.jsp (modified) (2 diffs)
• src/net/sf/basedb/meludi/servlet/CaseSummaryServlet.java (modified) (2 diffs)

extensions/net.sf.basedb.meludi/trunk/resources/reports/case_summary.js

@@ -240 +240 @@
       Doc.hide('cdna-details');
     }
-    
+*/    
     var lib = response.lib;
     if (lib && lib.length > 0)
@@ -247 +247 @@
       for (var i = 0; i < lib.length; i++)
       {
-        var r = lib[i];
-        cs.addColumn('lib.name', cs.asLink('EXTRACT', r));
-        cs.addColumn('lib.registrationDate', cs.asDate(r.registrationDate));
-        cs.addColumn('lib.storageBox', cs.asBioPlateLocation(r.bioWell));
-        cs.addColumn('lib.result', (r.result && r.result != 'Successful') ? cs.asFailInfo(r.result, 'error.png') : null);
-        cs.addColumn('lib.cleanupDate', cs.asDate(r.cleanupDate)+cs.asLabEnvLink('http://givare2.onk.lu.se/', r.cleanupDate, 'Library cleanup: ' + r.name, 'thermometer.png'));
-        cs.addColumn('lib.remainingQuantity', cs.asQuantity(r.remainingQuantity, ' ng', 0.001));
-        cs.addColumn('lib.originalQuantity', cs.asQuantity(r.originalQuantity, ' ng', 0.001));
-        cs.addColumn('lib.barcode.name', r.barcode.name);
-        cs.addColumn('lib.ca_size', cs.asQuantity(r.ca_size, ''));
-        cs.addColumn('lib.molarity', cs.asQuantity(r.library_molarity_est, ' nM'));
-        cs.addColumn('lib.adapterFrac', cs.asPercent(r.library_frac_adpt));
-        cs.addColumn('lib.qubitconc', cs.asQuantity(r.qubitconc, ' ng/µl'));
-        cs.addColumn('lib.description', cs.truncate(r.description, truncateAt));
+        var d = lib[i];
+        var barcodeName = 'NA';
+        if (d.barcode != null)
+        {
+          barcodeName = d.barcode.name;
+        }
+        cs.addColumn('lib.name', cs.asLink('EXTRACT', d));
+        cs.addColumn('lib.registrationDate', cs.asDate(d.registrationDate));
+        cs.addColumn('lib.storageBox', cs.asBioPlateLocation(d.bioWell));
+        cs.addColumn('lib.result', (d.result && d.result != 'Successful') ? cs.asFailInfo(d.result, 'error.png') : null);
+        cs.addColumn('lib.cleanupDate', cs.asDate(d.cleanupDate)+cs.asLabEnvLink('http://givare2.onk.lu.se/', d.cleanupDate, 'Library cleanup: ' + d.name, 'thermometer.png'));
+        cs.addColumn('lib.remainingQuantity', cs.asQuantity(d.remainingQuantity, ' ng', 0.001));
+        cs.addColumn('lib.originalQuantity', cs.asQuantity(d.originalQuantity, ' ng', 0.001));
+        cs.addColumn('lib.barcode.name', barcodeName);
+        cs.addColumn('lib.ca_size', cs.asQuantity(d.ca_size, ''));
+        cs.addColumn('lib.molarity', cs.asQuantity(d.library_molarity_est, ' nM'));
+        cs.addColumn('lib.adapterFrac', cs.asPercent(d.library_frac_adpt));
+        cs.addColumn('lib.qubitconc', cs.asQuantity(d.qubitconc, ' ng/µl'));
+        cs.addColumn('lib.description', cs.truncate(d.description, truncateAt));
       }
     }
@@ -268 +273 @@
       Doc.hide('lib-details');
     }
-
+/*
     var pooledLib = response.pooledlib;
     if (pooledLib && pooledLib.length > 0)

extensions/net.sf.basedb.meludi/trunk/resources/reports/case_summary.jsp

@@ -487 +487 @@
           </div>
         </div>
-        
+--> 
         <div class="info-section" id="lib-info">
           <div>
@@ -537 +537 @@
           </div>
         </div>
-        
+<!--        
         <div class="info-section" id="pooledlib-info">
           <div>

extensions/net.sf.basedb.meludi/trunk/src/net/sf/basedb/meludi/servlet/CaseSummaryServlet.java

@@ -223 +223 @@
         {
           JSONArray jsonDna = new JSONArray();
+          JSONArray jsonLib = new JSONArray();
           for (Dna d : dna)
           {
@@ -237 +238 @@
               }
             }
-            jsonDna.add(jsonD);
+            if (d.getName().endsWith(".d"))
+            {
+              jsonDna.add(jsonD);
+            }
+            else if (d.getName().endsWith(".fpa") || d.getName().endsWith(".fpb"))
+            {
+              // Get BioWell row and column (0-based)
+              JSONObject jsonWell = new JSONObject();
+              JSONObject jsonDnaTmp = (JSONObject) d.asJSONObject();
+              jsonWell = (JSONObject) jsonDnaTmp.get("bioWell");
+              Integer row = null;
+              Integer col = null;
+              if (jsonWell != null)
+              {
+                row = (Integer) jsonWell.get("row");
+                col = (Integer) jsonWell.get("column");
+              }
+              // Add barcode name
+              JSONObject jsonBarcode = new JSONObject();
+              if (row != null && col != null)
+              {
+                String rowStr = "50" + (row + 1);
+                String colStr = "70" + (col + 1);
+                if (col > 8)
+                {
+                  colStr = "7" + (col + 1);
+                }
+                jsonBarcode.put("name", rowStr + "," + colStr);
+              }
+              jsonD.put("barcode", jsonBarcode);
+              jsonLib.add(jsonD);
+            }
           }
           jsonSections.add(loadSectionInfo(sc, "dna"));
           json.put("dna", jsonDna);
+          jsonSections.add(loadSectionInfo(sc, "lib"));
+          json.put("lib", jsonLib);
         }