Changeset 736

Timestamp:

Aug 5, 2008, 1:54:30 PM (14 years ago)

Author:

Martin Svensson

Message:

Fixes #112. Changed the property validation when installing a data file-type which already exists.

File:

• plugins/base2/net.sf.basedb.illumina/trunk/src/net/sf/basedb/illumina/install/Install.java (modified) (3 diffs)

plugins/base2/net.sf.basedb.illumina/trunk/src/net/sf/basedb/illumina/install/Install.java

@@ -467 +467 @@
     //Data file types
     Map<String, DataFileType> dataFileTypes = new HashMap<String, DataFileType>();      
-    DataFileType bgx = createDataFileType(dc, 
-      Illumina.BGX_FILE_ID, "BGX file", "Illumina Sentrix Array binary manifest file", 
-      Item.ARRAYDESIGN, BGX_FILEYTPE_EXTENSION, reporterMapType, 
-      Illumina.BGX_VALIDATOR_METADATAREADER, Illumina.BGX_VALIDATOR_METADATAREADER,
-      jarPath, ignoreExistingItems);
+    DataFileType bgx = null;
+    //Create bgx-datafile type if there are one or more expression platforms.
+    if (largestNumOfStrips > 0)
+    {
+      bgx = createDataFileType(dc, 
+        Illumina.BGX_FILE_ID, "BGX file", "Illumina Sentrix Array binary manifest file", 
+        Item.ARRAYDESIGN, BGX_FILEYTPE_EXTENSION, reporterMapType, 
+        Illumina.BGX_VALIDATOR_METADATAREADER, Illumina.BGX_VALIDATOR_METADATAREADER,
+        jarPath, ignoreExistingItems);
+    }
     for (int i = 1; i <= largestNumOfStrips; i++ )
     {
@@ -739 +744 @@
   
   /**
-    Create a new data file type. If an item with the given external ID already exists
-    it will be updated if updateExistingItem=true, otherwise an ItemAlreadyExistsException
-    is thrown. If an existing item can't be updated, and ItemAlreadyExistsException 
-    is thrown.
+    Create a new data file type. If an item with the given external ID already exists and ignoreExistingItem=true
+    the existing data file type will be updated with new jarPath for validator and metadata reader and then returned, 
+    otherwise, if ignoreExistingItem=false, an ItemAlreadyExistsException is thrown. 
     @return The new or existing data file type
   */
@@ -759 +763 @@
         throw new ItemAlreadyExistsException(dft.getExternalId());
       }
-      
-      dft = DataFileType.getByExternalId(dc, externalId);
       if (extension != null && !extension.equals(dft.getExtension())) message += dft.getName() + " has invalid extension.\n";
       if (!itemType.equals(dft.getItemType())) message += dft.getName() + " has invalid item type.\n";
+      if (validatorClass != null && !validatorClass.equals(dft.getValidatorClass())) message += "Validator class used: " + dft.getValidatorClass() + ", expected: " + validatorClass;
+      if (metadataReaderClass != null && !metadataReaderClass.equals(dft.getMetadataReaderClass())) message += "Metadata class used: " + dft.getMetadataReaderClass() + ", expected: " + metadataReaderClass;
+      if (message != null) throw new ItemAlreadyExistsException(message + " The existing datafiletype, '" + dft.getName() + "' can not be used.");
+      
+      // Update the jar path of the data file type's meta-data reader and validator
       if (jarPath != null)
       {
-        if (dft.getMetadataReaderJarPath() == null)
-        {
-          dft.setMetadataReaderJarPath(jarPath);          
-        }
-        if (dft.getValidatorJarPath() == null)
-        {
-          dft.setValidatorJarPath(jarPath);   
-        }
-        if (!jarPath.equals(dft.getValidatorJarPath()) || !jarPath.equals(dft.getMetadataReaderJarPath()))
-        {
-          message += "Validator/meta-data reader has not the expected jar-path: " + jarPath + ".\n";
-        }
-      }
-      if (message != null) throw new ItemAlreadyExistsException(message + " The existing datafiletype, '" + dft.getName() + "' can not be used.");  
+        dft.setMetadataReaderJarPath(jarPath);
+        dft.setValidatorJarPath(jarPath);
+      }
     }
     catch (ItemNotFoundException infe)