Changeset 3734

Timestamp:

Sep 14, 2007, 3:51:04 PM (15 years ago)

Author:

Johan Enell

Message:

Fixes #760

File:

• branches/2.4-stable/src/plugins/core/net/sf/basedb/plugins/Base1PluginExecuter.java (modified) (7 diffs)

branches/2.4-stable/src/plugins/core/net/sf/basedb/plugins/Base1PluginExecuter.java

@@ -55 +55 @@
 import net.sf.basedb.core.PositionBatcher;
 import net.sf.basedb.core.ProgressReporter;
+import net.sf.basedb.core.Reporter;
 import net.sf.basedb.core.RequestInformation;
 import net.sf.basedb.core.SpotBatcher;
@@ -62 +63 @@
 import net.sf.basedb.core.Type;
 import net.sf.basedb.core.User;
+import net.sf.basedb.core.data.ReporterData;
 import net.sf.basedb.core.plugin.About;
 import net.sf.basedb.core.plugin.AboutImpl;
@@ -565 +567 @@
       permissions.add(new Permissions(Item.PLUGINCONFIGURATION, EnumSet.of(Permission.WRITE), null));
       permissions.add(new Permissions(Item.RAWBIOASSAY, null, EnumSet.of(Permission.READ)));
+      permissions.add(new Permissions(Item.REPORTER, null, EnumSet.of(Permission.READ)));
       permissions.add(new Permissions(Item.EXTRAVALUETYPE, null, EnumSet.of(Permission.CREATE, Permission.USE)));
       permissions.add(new Permissions(Item.USER, null, EnumSet.of(Permission.READ)));
@@ -1309 +1312 @@
 
     HashMap<String, BioAssay> idMap = new HashMap<String, BioAssay>();
-    HashMap<Integer, Integer> posMap = new HashMap<Integer, Integer>();
+    HashMap<Integer, ReporterData> posRepMap = new HashMap<Integer, ReporterData>();
     HashMap<String, ExtraValueType> evtMap = new HashMap<String, ExtraValueType>();
 
@@ -1378 +1381 @@
         }
         spotBatcher = bas.getSpotBatcher();
-//        posBatcher = bas.getPositionBatcher();
 
         for (String assayId : assays)
@@ -1506 +1508 @@
               spotBatcher.insert(ba.getDataCubeColumnNo(), position, intensities);
               
-//              if (posMap.containsKey(position))
-//              {
-//                if (!posMap.get(position).equals(reporter))
-//                  throw new BaseException("Invalid data. Position, "+position+", occurs twice with different reporter data.");
-//                
-//              }
-//              else
-//              {
-//                posMap.put(position, reporter);
-//                posBatcher.insert(position, Reporter.getById(dc, reporter));
-//              }
+              if (posRepMap.containsKey(position))
+              {
+                if (!reporter.equals(posRepMap.get(position).getId()))
+                  throw new BaseException("Invalid data. Position, "+position+", occurs twice with different reporter data.");
+              }
+              else
+              {
+                posRepMap.put(position, Reporter.getById(dc, reporter));
+              }
+              
               for (int i = 0; i < evBatcher.size(); i++)
               {
@@ -1535 +1536 @@
       }
     }
+
+    //Batch reporters
+    int it = 0;
+    if (bas != null)
+    {
+      posBatcher = bas.getPositionBatcher();
+      for (Integer position : posRepMap.keySet())
+      {
+        System.out.println(it++ + "\t" +position);
+        try
+        {
+          posBatcher.insert(position, posRepMap.get(position));
+        }
+        catch (BaseException e)
+        {
+          System.out.println(position+"\t"+posRepMap.get(position));
+          throw e;
+        }
+      }
+    }
+    
     // save bas
     if (bas != null)