Changeset 4614

Timestamp:

Oct 29, 2008, 9:58:38 AM (15 years ago)

Author:

Nicklas Nordborg

Message:

Fixes #1159: Annotation importer should detect non-existing column mappings

Location:

trunk/src/plugins/core/net/sf/basedb/plugins

Files:

• AbstractFlatFileImporter.java (modified) (2 diffs)
• AnnotationFlatFileImporter.java (modified) (2 diffs)

trunk/src/plugins/core/net/sf/basedb/plugins/AbstractFlatFileImporter.java

@@ -1171 +1171 @@
     throws InvalidDataException
   {
+    return checkColumnMapping(null, mapExpression, allowComplex, name);
+  }
+  
+  /**
+    Checks the syntax column mapping and verifies that the given file parser
+    has found the columns that are used in the file.
+    
+    @param ffp An optional flat file parser that should have parsed the file headers
+      with {@link FlatFileParser#parseHeaders()}
+    @param mapExpression The mapping expression
+    @param allowComplex If complex column mappings should be allowed
+    @param name The name of the column (used if an error message needs to be generated)
+    @return The mapping string
+    @throws InvalidDataException If the mapping isn't a valid column 
+      mapping or if the allowComplex parameter is false and the mapping is complex
+    @since 2.9
+  */
+  protected String checkColumnMapping(FlatFileParser ffp, String mapExpression, 
+    boolean allowComplex, String name)
+    throws InvalidDataException
+  {
+    System.out.println("checkMapping: ffp=" + ffp + "; expr=" + mapExpression + "; name=" + name);
+    
     if (mapExpression == null || mapExpression.length() == 0) 
     {
@@ -1197 +1220 @@
       }
     }
-    else
-    {
-      if (isJep)
+    
+    if (ffp != null)
+    {
+      try
       {
-        try
-        {
-          new JepMapper(mapExpression.substring(1), new ArrayList<String>(), null);
-        }
-        catch (Throwable t)
-        {
-          throw new InvalidDataException("Invalid expression for column '" +
-              name + "': " + mapExpression + " (" + t.getMessage() + ")");
-        }
+        Mapper m = ffp.getMapper(mapExpression);
+        System.out.println("Mapper: " + m);
+      }
+      catch (Throwable t)
+      {
+        throw new InvalidDataException("Invalid expression for column '" +
+            name + "': " + mapExpression + " (" + t.getMessage() + ")");
+      }
+    }
+    else if (isJep)
+    {
+      try
+      {
+        new JepMapper(mapExpression.substring(1), new ArrayList<String>(), null);
+      }
+      catch (Throwable t)
+      {
+        throw new InvalidDataException("Invalid expression for column '" +
+            name + "': " + mapExpression + " (" + t.getMessage() + ")");
       }
     }

trunk/src/plugins/core/net/sf/basedb/plugins/AnnotationFlatFileImporter.java

@@ -425 +425 @@
 
         ParameterValues wrapper = new ParameterValuesWrapper(request, job, configuration, forJob);
+        FlatFileParser parser = null;
         if (forJob)
         {
           // Check that file can be parsed with given regular expressions
-          FlatFileParser ffp = getInitializedFlatFileParser(wrapper);
+          parser = getInitializedFlatFileParser(wrapper);
           File f = (File)request.getParameterValue("file");
           InputStream in = f.getDownloadStream(0);
-          ffp.setInputStream(in, getCharset(request));
-          ffp.setDefaultNumberFormat(getNumberFormat());
-          FlatFileParser.LineType result = ffp.parseHeaders();
+          parser.setInputStream(in, getCharset(request));
+          parser.setDefaultNumberFormat(getNumberFormat());
+          FlatFileParser.LineType result = parser.parseHeaders();
           in.close();
           if (result == FlatFileParser.LineType.UNKNOWN)
           {
             response.setError("The file could not be parsed with the given settings, " +
-              "no data found after " + ffp.getLineCount() + " lines.", null);
+              "no data found after " + parser.getLineCount() + " lines.", null);
             return;
           }
           // Store column headers for use in the next configuration step
-          columnHeaders = ffp.getColumnHeaders();
+          columnHeaders = parser.getColumnHeaders();
         }
 
@@ -487 +488 @@
         // Check the mapping expressions
         boolean allowComplex = "allow".equals(request.getParameterValue(complexMappings.getName()));
-        checkColumnMapping(nameMapping, allowComplex, nameColumnMapping.getLabel());
-        checkColumnMapping(externalIdMapping, allowComplex, externalIdColumnMapping.getLabel());
-        checkColumnMapping(internalIdMapping, allowComplex, internalIdColumnMapping.getLabel());
+        checkColumnMapping(parser, nameMapping, allowComplex, nameColumnMapping.getLabel());
+        checkColumnMapping(parser, externalIdMapping, allowComplex, externalIdColumnMapping.getLabel());
+        checkColumnMapping(parser, internalIdMapping, allowComplex, internalIdColumnMapping.getLabel());
 
         // Everything is ok, save values