1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/5c5249fac5c8/ changeset: 5c5249fac5c8 user: greg date: 2012-12-05 16:46:50 summary: Handle exceptions when parsing proprietary tool_data_table_conf.xml.sample files in the tool shed, and use the webapp's configured tool_data_path when configuring and loading the ToolDataTableManager. affected #: 1 file
diff -r e40fdd5f6e8936f936f7118b0b9521f7379972ee -r 5c5249fac5c8893a8da13043b8cc1ba23d3b303e lib/galaxy/tools/data/__init__.py --- a/lib/galaxy/tools/data/__init__.py +++ b/lib/galaxy/tools/data/__init__.py @@ -77,8 +77,15 @@ </table>
""" - tree = util.parse_xml( config_filename ) - root = tree.getroot() + error_message = '' + table_elems = [] + try: + tree = util.parse_xml( config_filename ) + root = tree.getroot() + except Exception, e: + error_message = 'Error attempting to parse file %s: %s' % ( str( os.path.split( config_filename )[ 1 ] ), str( e ) ) + log.debug( error_message ) + return table_elems, error_message # Make a copy of the current list of data_table_elem_names so we can persist later if changes to the config file are necessary. original_data_table_elem_names = [ name for name in self.data_table_elem_names ] if root.tag == 'tables': @@ -86,7 +93,6 @@ tool_data_path=tool_data_path, from_shed_config=True ) else: - table_elems = [] type = root.get( 'type', 'tabular' ) assert type in tool_data_table_types, "Unknown data table type '%s'" % type table_elems.append( root ) @@ -101,7 +107,7 @@ if persist and self.data_table_elem_names != original_data_table_elem_names: # Persist Galaxy's version of the changed tool_data_table_conf.xml file. self.to_xml_file( shed_tool_data_table_config ) - return table_elems + return table_elems, error_message def to_xml_file( self, shed_tool_data_table_config ): """Write the current in-memory version of the shed_tool_data_table_conf.xml file to disk.""" full_path = os.path.abspath( shed_tool_data_table_config ) @@ -146,8 +152,8 @@
def __init__( self, config_element, tool_data_path ): super( TabularToolDataTable, self ).__init__( config_element, tool_data_path ) - self.configure_and_load( config_element ) - def configure_and_load( self, config_element ): + self.configure_and_load( config_element, tool_data_path ) + def configure_and_load( self, config_element, tool_data_path ): """ Configure and load table from an XML element. """ @@ -157,9 +163,16 @@ self.parse_column_spec( config_element ) # Read every file all_rows = [] - found = False for file_element in config_element.findall( 'file' ): - filename = file_element.get( 'path' ) + found = False + if tool_data_path: + # We're loading a tool in the tool shed, so we cannot use the Galaxy tool-data + # directory which is hard-coded into the tool_data_table_conf.xml entries. + filepath = file_element.get( 'path' ) + filename = os.path.split( filepath )[ 1 ] + filename = os.path.join( tool_data_path, filename ) + else: + filename = file_element.get( 'path' ) if os.path.exists( filename ): found = True all_rows.extend( self.parse_file_fields( open( filename ) ) )
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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