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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.

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Daniel Blankenberg
2010-04-20 11:47:51 -04:00
parent a02d4d7f9c
commit 20b11ad6d1
1 changed files with 26 additions and 20 deletions
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lib/galaxy/datatypes/registry.py
+26 -20
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@@ -90,20 +90,22 @@ class Registry( object ):
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 @@ class Registry( object ):
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"""