Changeset 3532

Timestamp:

Oct 5, 2015, 4:23:47 PM (7 years ago)

Author:

olle

Message:

Refs #801. Refs #816. Case summary updated to present information on fpa and fpb DNA aliquot barcode tags as links to the corresponding Tag items:

1. Javascript file case_summary.js in resources/reports/ updated in function caseInfoLoaded(response) to present fpa and fpb aliquot barcode tags as links by calling function asLink(itemType, item, maxLength).
2. Java data access object class/file Barcode.java in src/net/sf/basedb/meludi/dao/ added. It contains among other methods one for retrieving a barcode Tag item from the database, if the name of the former is known.
3. Java servlet class/file CaseSummaryServlet.java in src/net/sf/basedb/meludi/servlet/ updated in protected method void doGet(HttpServletRequest req, HttpServletResponse resp) for command "GetCaseInfo" to send information on fpa and fpb DNA aliquot Illumina index 1 and 2 name and id in new JSON objects with keys "index1" and "index2", respectively. The barcode info 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) (2 diffs)
• src/net/sf/basedb/meludi/dao/Barcode.java (added)
• src/net/sf/basedb/meludi/servlet/CaseSummaryServlet.java (modified) (2 diffs)

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

@@ -248 +248 @@
       {
         var d = lib[i];
-        var barcodeName = 'NA';
-        if (d.barcode != null)
+        var barcodeInfo = 'NA';
+        if (d.index1 != null && d.index2 != null)
         {
-          barcodeName = d.barcode.name;
+          barcodeInfo = cs.asLink('TAG', d.index2) + ',' + cs.asLink('TAG', d.index1);
         }
         cs.addColumn('lib.name', cs.asLink('EXTRACT', d));
@@ -260 +260 @@
         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.barcode.name', barcodeInfo);
         cs.addColumn('lib.ca_size', cs.asQuantity(d.ca_size, ''));
         cs.addColumn('lib.molarity', cs.asQuantity(d.library_molarity_est, ' nM'));

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

@@ -34 +34 @@
 import net.sf.basedb.meludi.Site;
 import net.sf.basedb.meludi.dao.Annotationtype;
+import net.sf.basedb.meludi.dao.Barcode;
 import net.sf.basedb.meludi.dao.BioplateType;
 import net.sf.basedb.meludi.dao.Case;
@@ -248 +249 @@
               JSONObject jsonDnaTmp = (JSONObject) d.asJSONObject();
               jsonWell = (JSONObject) jsonDnaTmp.get("bioWell");
-              Integer row = null;
-              Integer col = null;
+              // Add barcode (Illumina index) info
               if (jsonWell != null)
               {
-                row = (Integer) jsonWell.get("row");
-                col = (Integer) jsonWell.get("column");
+                Integer row = (Integer) jsonWell.get("row");
+                Integer col = (Integer) jsonWell.get("column");
+                if (row != null)
+                {
+                  String rowStr = "A50" + (row + 1);
+                  Integer barcodeTagId = null;
+                  Barcode barcode = Barcode.findByName(dc, rowStr);
+                  if (barcode != null)
+                  {
+                    barcodeTagId = barcode.getTag().getId();
+                  }
+                  JSONObject jsonIndex2 = new JSONObject();
+                  jsonIndex2.put("name", rowStr);
+                  jsonIndex2.put("id", barcodeTagId);
+                  // Add Illumina Index 2 (row) barcode info
+                  jsonD.put("index2", jsonIndex2);
+                }
+                if (col != null)
+                {
+                  String colStr = "A70" + (col + 1);
+                  if (col > 8)
+                  {
+                    colStr = "A7" + (col + 1);
+                  }
+                  Integer barcodeTagId = null;
+                  Barcode barcode = Barcode.findByName(dc, colStr);
+                  if (barcode != null)
+                  {
+                    barcodeTagId = barcode.getTag().getId();
+                  }
+                  JSONObject jsonIndex1 = new JSONObject();
+                  jsonIndex1.put("name", colStr);
+                  jsonIndex1.put("id", barcodeTagId);
+                  // Add Illumina Index 1 (column) barcode info
+                  jsonD.put("index1", jsonIndex1);
+                }
               }
-              // 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);
             }