From 421e88cd0537d89dd2ba10ae4abae1b014d11574 Mon Sep 17 00:00:00 2001
From: Daniel Blankenberg <dan@bx.psu.edu>
Date: Tue, 13 May 2014 16:10:27 -0400
Subject: [PATCH] Display line errors in data table registry display
 encountered when loading a location file.

---
 lib/galaxy/tools/data/__init__.py              | 14 ++++++++------
 templates/admin/view_data_tables_registry.mako |  7 +++++--
 2 files changed, 13 insertions(+), 8 deletions(-)

diff --git a/lib/galaxy/tools/data/__init__.py b/lib/galaxy/tools/data/__init__.py
index 9055b7f6a8c..7e8f8aec900 100644
--- a/lib/galaxy/tools/data/__init__.py
+++ b/lib/galaxy/tools/data/__init__.py
@@ -285,8 +285,9 @@ class TabularToolDataTable( ToolDataTable ):
                         filename = corrected_filename
                         found = True
 
+            errors = []
             if found:
-                self.data.extend( self.parse_file_fields( open( filename ) ) )
+                self.data.extend( self.parse_file_fields( open( filename ), errors=errors ) )
                 self._update_version()
             else:
                 self.missing_index_file = filename
@@ -294,7 +295,7 @@ class TabularToolDataTable( ToolDataTable ):
 
             if filename not in self.filenames or not self.filenames[ filename ][ 'found' ]:
                 self.filenames[ filename ] = dict( found=found, filename=filename, from_shed_config=from_shed_config, tool_data_path=tool_data_path,
-                                                   config_element=config_element, tool_shed_repository=repo_info )
+                                                   config_element=config_element, tool_shed_repository=repo_info, errors=errors )
             else:
                 log.debug( "Filename '%s' already exists in filenames (%s), not adding", filename, self.filenames.keys() )
 
@@ -353,7 +354,7 @@ class TabularToolDataTable( ToolDataTable ):
         if 'name' not in self.columns:
             self.columns['name'] = self.columns['value']
 
-    def parse_file_fields( self, reader ):
+    def parse_file_fields( self, reader, errors=None ):
         """
         Parse separated lines from file and return a list of tuples.
 
@@ -371,9 +372,10 @@ class TabularToolDataTable( ToolDataTable ):
                 if self.largest_index < len( fields ):
                     rval.append( fields )
                 else:
-                    log.warn( "Line %i in tool data table '%s' is invalid (HINT: "
-                              "'%s' characters must be used to separate fields):\n%s"
-                              % ( ( i + 1 ), self.name, separator_char, line ) )
+                    line_error = "Line %i in tool data table '%s' is invalid (HINT: '%s' characters must be used to separate fields):\n%s" % ( ( i + 1 ), self.name, separator_char, line )
+                    if errors is not None:
+                        errors.append( line_error )
+                    log.warn( line_error )
         return rval
 
     def get_column_name_list( self ):
diff --git a/templates/admin/view_data_tables_registry.mako b/templates/admin/view_data_tables_registry.mako
index e6206257a4c..faf75f565f0 100644
--- a/templates/admin/view_data_tables_registry.mako
+++ b/templates/admin/view_data_tables_registry.mako
@@ -18,7 +18,7 @@
                 <th bgcolor="#D8D8D8">Name</th>
                 <th bgcolor="#D8D8D8">Filename</th>
                 <th bgcolor="#D8D8D8">Tool data path</th>
-                <th bgcolor="#D8D8D8">Missing index file</th>
+                <th bgcolor="#D8D8D8">Errors</th>
             </tr>
             %for data_table_elem_name, data_table in sorted_data_tables:
                 %if ctr % 2 == 1:
@@ -35,8 +35,11 @@
                         <td>${ file_dict.get( 'tool_data_path' ) | h }</td>
                         <td>
                             %if not file_dict.get( 'found' ):
-                                missing
+                                file missing
                             %endif
+                            %for error in file_dict.get( 'errors', [] ):
+                                ${ error | h } <br/>
+                            %endfor
                         </td>
                         </tr>
                     %endfor