Changeset 4857

Timestamp:

Mar 27, 2009, 12:47:31 PM (13 years ago)

Author:

Nicklas Nordborg

Message:

Fixes #1259: Exporting spot data (with table exporter): Bioassay column is numerated 1, 2, 3, ...

Also changed the list page to use the same formatter.

Location:

trunk

Files:

• src/core/net/sf/basedb/util/formatter/LookupFormatter.java (added)
• www/views/experiments/spotdata/index.jsp (modified) (3 diffs)
• www/views/experiments/spotdata/list_spotdata.jsp (modified) (6 diffs)

trunk/www/views/experiments/spotdata/index.jsp

@@ -36 +36 @@
   import="net.sf.basedb.clients.web.WebException"
   import="net.sf.basedb.util.Values"
+  import="net.sf.basedb.util.formatter.LookupFormatter"
   import="net.sf.basedb.clients.web.util.HTML"
   import="java.util.Map"
@@ -61 +62 @@
   }
   private static final Item itemType = Item.SPOTDATA;
+  
+  private static void registerExportFormatters(DbControl dc, ItemContext cc, 
+    BioAssaySet bas, BioAssay ba)
+  {
+    if (bas != null)
+    {
+      Map<Number, String> bioAssayMap = new HashMap<Number, String>();
+      for (BioAssay b : bas.getBioAssays().list(dc))
+      {
+        short columnNo = b.getDataCubeColumnNo();
+        String name = b.getName();
+        // Safety measure, since JDBC driver seems to return 'short' as 'int'
+        bioAssayMap.put(columnNo, name);
+        bioAssayMap.put((int)columnNo, name);
+      }
+      cc.setObject("export.formatter.COLUMN", new LookupFormatter(bioAssayMap));
+    }
+  }
 %>
 <%
@@ -122 +141 @@
     final DynamicSpotQuery query = ba != null ? ba.getSpotData() : bas.getSpotData();
     //cc.configureQuery(query, true);
+    registerExportFormatters(dc, cc, bas, ba);
     dc.close();
     cc.setQuery(query);

trunk/www/views/experiments/spotdata/list_spotdata.jsp

@@ -45 +45 @@
   import="net.sf.basedb.util.Enumeration"
   import="net.sf.basedb.util.ColorGenerator"
+  import="net.sf.basedb.util.formatter.LookupFormatter"
   import="net.sf.basedb.clients.web.Base"
   import="net.sf.basedb.clients.web.ModeInfo"
@@ -88 +89 @@
   final int experimentId = experiment.getId();
   final RawDataType rawDataType = bioAssaySet.getRawDataType();
-  Map<Short, String> bioAssayMap = null;
   
   final String subContext = rawDataType.getId();
@@ -119 +119 @@
   int numListed = 0;
   %>
+  
   <base:page title="<%=title%>">
   <base:head scripts="table.js,tabcontrol.js" styles="table.css,toolbar.css,headertabcontrol.css,path.css">
@@ -269 +270 @@
       if (bioAssay == null)
       {
-        bioAssayMap = new HashMap<Short, String>();
+        Map<Number, String> bioAssayMap = new HashMap<Number, String>();
         Enumeration<String, String> bioAssayEnum = new Enumeration<String, String>();
         for (BioAssay ba : bioAssaySet.getBioAssays().list(dc))
         {
-          short columnNo = ba.getDataCubeColumnNo(); 
-          bioAssayMap.put(columnNo, Base.getLinkedName(ID, ba, false, true));
+          short columnNo = ba.getDataCubeColumnNo();
+          String linkedBioAssay = Base.getLinkedName(ID, ba, false, true);
+          // Safety measure, since JDBC driver seems to return 'short' as 'int'
+          bioAssayMap.put(columnNo, linkedBioAssay);
+          bioAssayMap.put((int)columnNo, linkedBioAssay);
           bioAssayEnum.add(String.valueOf(columnNo), HTML.encodeTags(ba.getName()));
         }
@@ -287 +291 @@
           exportable="true"
           enumeration="<%=bioAssayEnum%>"
+          formatter="<%=new LookupFormatter<Number>(bioAssayMap)%>"
         />
         <%
@@ -373 +378 @@
                 for (String columnId : selected.selectedIds)
                 {
-                  Object value = item.getObject(i++);
-                  if ("COLUMN".equals(columnId))
-                  {
-                    short columnNo = ((Number)value).shortValue();
-                    value= bioAssayMap.get(columnNo);
-                  }
                   %>
-                  <tbl:cell column="<%=columnId%>" value="<%=value%>" />
+                  <tbl:cell column="<%=columnId%>" value="<%=item.getObject(i++)%>" />
                   <%
                 }