details: http://www.bx.psu.edu/hg/galaxy/rev/b8d25aabb98d changeset: 3670:b8d25aabb98d user: Dan Blankenberg dan@bx.psu.edu date: Tue Apr 20 11:47:51 2010 -0400 description: Make failing to load datatype converters and display applications more graceful when given nonexistent file paths. A missing converter will still allow the application to start and a missing display application will not prevent a datatype from loading.
diffstat:
lib/galaxy/datatypes/registry.py | 46 ++++++++++++++++++++++----------------- 1 files changed, 26 insertions(+), 20 deletions(-)
diffs (63 lines):
diff -r e47ff545931f -r b8d25aabb98d lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py Mon Apr 19 17:41:35 2010 -0400 +++ b/lib/galaxy/datatypes/registry.py Tue Apr 20 11:47:51 2010 -0400 @@ -90,20 +90,22 @@ mimetype = composite_file.get( 'mimetype', None ) self.datatypes_by_extension[extension].add_composite_file( name, optional=optional, mimetype=mimetype ) for display_app in elem.findall( 'display' ): - display_file = display_app.get( 'file', None ) - assert display_file is not None, "A file must be specified for a datatype display tag." - inherit = galaxy.util.string_as_bool( display_app.get( 'inherit', 'False' ) ) - display_app = DisplayApplication.from_file( os.path.join( self.display_applications_path, display_file ), self ) - if display_app: - if display_app.id in self.display_applications: - #if we already loaded this display application, we'll use the first one again - display_app = self.display_applications[ display_app.id ] - self.log.debug( "Loaded display application '%s' for datatype '%s', inherit=%s" % ( display_app.id, extension, inherit ) ) - self.display_applications[ display_app.id ] = display_app #Display app by id - self.datatypes_by_extension[ extension ].add_display_application( display_app ) - if inherit and ( self.datatypes_by_extension[extension], display_app ) not in inherit_display_application_by_class: - #subclass inheritance will need to wait until all datatypes have been loaded - inherit_display_application_by_class.append( ( self.datatypes_by_extension[extension], display_app ) ) + display_file = os.path.join( self.display_applications_path, display_app.get( 'file', None ) ) + try: + inherit = galaxy.util.string_as_bool( display_app.get( 'inherit', 'False' ) ) + display_app = DisplayApplication.from_file( display_file, self ) + if display_app: + if display_app.id in self.display_applications: + #if we already loaded this display application, we'll use the first one again + display_app = self.display_applications[ display_app.id ] + self.log.debug( "Loaded display application '%s' for datatype '%s', inherit=%s" % ( display_app.id, extension, inherit ) ) + self.display_applications[ display_app.id ] = display_app #Display app by id + self.datatypes_by_extension[ extension ].add_display_application( display_app ) + if inherit and ( self.datatypes_by_extension[extension], display_app ) not in inherit_display_application_by_class: + #subclass inheritance will need to wait until all datatypes have been loaded + inherit_display_application_by_class.append( ( self.datatypes_by_extension[extension], display_app ) ) + except: + self.log.exception( "error reading display application from path: %s" % display_file ) except Exception, e: self.log.warning( 'Error loading datatype "%s", problem: %s' % ( extension, str( e ) ) ) # Handle display_application subclass inheritance here: @@ -290,12 +292,16 @@ tool_config = elem[0] source_datatype = elem[1] target_datatype = elem[2] - converter = toolbox.load_tool( os.path.join( self.datatype_converters_path, tool_config ) ) - toolbox.tools_by_id[converter.id] = converter - if source_datatype not in self.datatype_converters: - self.datatype_converters[source_datatype] = odict() - self.datatype_converters[source_datatype][target_datatype] = converter - self.log.debug( "Loaded converter: %s", converter.id ) + converter_path = os.path.join( self.datatype_converters_path, tool_config ) + try: + converter = toolbox.load_tool( converter_path ) + toolbox.tools_by_id[converter.id] = converter + if source_datatype not in self.datatype_converters: + self.datatype_converters[source_datatype] = odict() + self.datatype_converters[source_datatype][target_datatype] = converter + self.log.debug( "Loaded converter: %s", converter.id ) + except: + self.log.exception( "error reading converter from path: %s" % converter_path )
def load_external_metadata_tool( self, toolbox ): """Adds a tool which is used to set external metadata"""