Changeset 234 for trunk/uk/ac/scri/batchimporter/src/sbrn

Timestamp:

Feb 14, 2007, 2:51:39 PM (16 years ago)

Author:

mbayer

Message:

error handling improved

Location:

trunk/uk/ac/scri/batchimporter/src/sbrn/base

Files:

• BatchDataImport.java (modified) (5 diffs)
• PluginConfigDetector.java (modified) (1 diff)

trunk/uk/ac/scri/batchimporter/src/sbrn/base/BatchDataImport.java

@@ -200 +200 @@
     System.out.println("dir = " + dir.getName());
 
-    //get the raw data type
+    //get the raw data type from the experiment
     RawDataType rawDataType = experiment.getRawDataType(); 
     System.out.println("rawDataType = " + rawDataType.getName());
@@ -247 +247 @@
             }
             //if it's a cel file, add it to the dataFiles array
-            if(extension.equalsIgnoreCase("cel"))
+            else if(extension.equalsIgnoreCase("cel"))
             {
                 System.out.println("setting dataFiles["+dataFileCount+"] to file " + file.getName());
                 dataFiles[dataFileCount] = file;
                 dataFileCount++;
+            }
+            //if it is neither a cel file nor a cdf file then the user must have defined the Experiment as
+            //being Affy but the data they are importing is not Affy
+            //in that case we need to throw an Exception and abort the whole import
+            else
+            {
+              throw new Exception("data file is not Affymetrix cel file but Experiment was defined as Affymetrix data type");
             }
           }
@@ -277 +284 @@
       File exampleFile = fileList.get(0);
       System.out.println("exampleFile = " + exampleFile.getName());
-
-      //only do this for non-Affy data types
+      
+      //check we don't have a discrepancy between the raw data type and the data files here
+      //if users have specified a non-affy data type and the data is affy we need to abort the import with an appropriate error
+      //get the current file and check its extension
+      String exampleFileName = exampleFile.getName();
+      String exampleFileExtension = exampleFileName.substring(exampleFileName.lastIndexOf(".")+1);
+      if(exampleFileExtension.equalsIgnoreCase("cdf") || exampleFileExtension.equalsIgnoreCase("cel"))
+      {
+        throw new Exception("Affymetrix data found but Experiment data type was specified as non-Affy");
+      }
+
+      //for non-Affy data types, find a suitable plugin configuration
       PluginConfiguration importConfig = null;
       if (!rawDataType.getName().equalsIgnoreCase("affymetrix"))
@@ -286 +303 @@
         importConfig = detector.detectPluginConfig(exampleFile);      
         System.out.println("PluginConfiguration importConfig = " + importConfig);
+        
+        //now need to figure out the raw data type to make sure it matches that of the Experiment we are importing into
+        //this can be done by looking at the plugin config which should have it stored in it
+        List rdtVal = importConfig.getParameterValues("rawDataType");
+        String rawDataTypeStr = (String)rdtVal.get(0);
+        System.out.println("rawDataType detected from files = " + rawDataTypeStr);  
+        //compare this to the raw data type of the experiment
+        if(!rawDataType.getName().equalsIgnoreCase(rawDataTypeStr))
+        {
+          throw new Exception("raw data types of experiment and data files do not match");
+        }
+        
       }
 
@@ -374 +403 @@
       }
       
+      //make sure we have a working dbcontrol object
+      if(dc.isClosed())
+        dc = sc.newDbControl();     
       //commit the changes to the database
       dc.commit();

trunk/uk/ac/scri/batchimporter/src/sbrn/base/PluginConfigDetector.java

@@ -79 +79 @@
       pc = configList.get(0);
     }
-    catch (Exception x)
+    catch (IndexOutOfBoundsException x)
     {
       x.printStackTrace();
-      throw new Exception(x);
+      throw new Exception("no suitable plugin configuration found for this data type");
     }
     finally