1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/c06d7cef9125/ changeset: c06d7cef9125 user: greg date: 2012-02-08 19:46:14 summary: When handling datatype conflicts always override previously loaded datatypes with the datatype currently being loaded. Use the same behavior for sniffers. affected #: 2 files

diff -r 7c7b3f6ebbdbef5e9101c09037905a01511e9b9c -r c06d7cef9125577820006c607c0628b4940ca57d lib/galaxy/app.py --- a/lib/galaxy/app.py +++ b/lib/galaxy/app.py @@ -57,7 +57,7 @@ # This will also load proprietary datatype converters and display applications. self.installed_repository_manager.load_proprietary_datatypes() # Load the data types in the Galaxy distribution, which are defined in self.config.datatypes_config. - self.datatypes_registry.load_datatypes( self.config.root, self.config.datatypes_config, override_conflicts=True ) + self.datatypes_registry.load_datatypes( self.config.root, self.config.datatypes_config ) galaxy.model.set_datatypes_registry( self.datatypes_registry ) # Security helper self.security = security.SecurityHelper( id_secret=self.config.id_secret )

diff -r 7c7b3f6ebbdbef5e9101c09037905a01511e9b9c -r c06d7cef9125577820006c607c0628b4940ca57d lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py +++ b/lib/galaxy/datatypes/registry.py @@ -26,8 +26,6 @@ self.converter_deps = {} self.available_tracks = [] self.set_external_metadata_tool = None - # Keep a list of datatypes with loaded sniffers for handling potential conflicts. - self.datatype_sniffers = [] self.sniff_order = [] self.upload_file_formats = [] # Datatype elements defined in local datatypes_conf.xml that contain display applications. @@ -49,7 +47,7 @@ self.datatype_elems = [] self.sniffer_elems = [] self.xml_filename = None - def load_datatypes( self, root_dir=None, config=None, imported_modules=None, deactivate=False, override_conflicts=False ): + def load_datatypes( self, root_dir=None, config=None, imported_modules=None, deactivate=False ): """ Parse a datatypes XML file located at root_dir/config. If imported_modules is received, it is a list of imported datatypes class files included in an installed tool shed repository. @@ -100,13 +98,10 @@ else: # Keep an in-memory list of datatype elems to enable persistence. self.datatype_elems.append( elem ) - if extension and extension in self.datatypes_by_extension and not override_conflicts: - if deactivate: - # We are deactivating an installed tool shed repository, so eliminate the datatype from the registry. - self.log.debug( "Removing datatype with extension '%s' from the registry." % extension ) - del self.datatypes_by_extension[ extension ] - else: - self.log.debug( "Ignoring datatype with extension '%s' from %s because the registry already contains a datatype with that extension." % ( extension, config ) ) + if extension and extension in self.datatypes_by_extension and deactivate: + # We are deactivating an installed tool shed repository, so eliminate the datatype from the registry. + self.log.debug( "Removing datatype with extension '%s' from the registry." % extension ) + del self.datatypes_by_extension[ extension ] elif extension and ( dtype or type_extension ): if dtype: fields = dtype.split( ':' ) @@ -120,8 +115,7 @@ datatype_class = getattr( imported_module, datatype_class_name ) break if datatype_class is None: - # The datatype class name must be contained in one of the datatype - # modules in the Galaxy distribution. + # The datatype class name must be contained in one of the datatype modules in the Galaxy distribution. fields = datatype_module.split( '.' ) module = __import__( fields.pop(0) ) for mod in fields: @@ -131,52 +125,48 @@ datatype_class = self.datatypes_by_extension[type_extension].__class__ if make_subclass: datatype_class = type( datatype_class_name, (datatype_class,), {} ) - if extension not in self.datatypes_by_extension or override_conflicts: - if extension in self.datatypes_by_extension: - self.log.warning( "Overriding conflicting extension '%s', using datatype with same extension from %s." % ( extension, config ) ) - self.datatypes_by_extension[ extension ] = datatype_class() - if mimetype is None: - # Use default mime type as per datatype spec - mimetype = self.datatypes_by_extension[extension].get_mime() - self.mimetypes_by_extension[extension] = mimetype - if hasattr( datatype_class, "get_track_type" ): - self.available_tracks.append( extension ) - if display_in_upload: - self.upload_file_formats.append( extension ) - # Max file size cut off for setting optional metadata - self.datatypes_by_extension[extension].max_optional_metadata_filesize = elem.get( 'max_optional_metadata_filesize', None ) - for converter in elem.findall( 'converter' ): - # Build the list of datatype converters which will later be loaded - # into the calling app's toolbox. - converter_config = converter.get( 'file', None ) - target_datatype = converter.get( 'target_datatype', None ) - depends_on = converter.get( 'depends_on', None ) - if depends_on and target_datatype: - if extension not in self.converter_deps: - self.converter_deps[extension] = {} - self.converter_deps[extension][target_datatype] = depends_on.split(',') - if converter_config and target_datatype: - if imported_modules: - self.proprietary_converters.append( ( converter_config, extension, target_datatype ) ) - else: - self.converters.append( ( converter_config, extension, target_datatype ) ) - for composite_file in elem.findall( 'composite_file' ): - # add composite files - name = composite_file.get( 'name', None ) - if name is None: - self.log.warning( "You must provide a name for your composite_file (%s)." % composite_file ) - optional = composite_file.get( 'optional', False ) - 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' ): + if extension in self.datatypes_by_extension: + self.log.warning( "Overriding conflicting datatype with extension '%s', using datatype from %s." % ( extension, config ) ) + self.datatypes_by_extension[ extension ] = datatype_class() + if mimetype is None: + # Use default mime type as per datatype spec + mimetype = self.datatypes_by_extension[extension].get_mime() + self.mimetypes_by_extension[extension] = mimetype + if hasattr( datatype_class, "get_track_type" ): + self.available_tracks.append( extension ) + if display_in_upload: + self.upload_file_formats.append( extension ) + # Max file size cut off for setting optional metadata + self.datatypes_by_extension[extension].max_optional_metadata_filesize = elem.get( 'max_optional_metadata_filesize', None ) + for converter in elem.findall( 'converter' ): + # Build the list of datatype converters which will later be loaded into the calling app's toolbox. + converter_config = converter.get( 'file', None ) + target_datatype = converter.get( 'target_datatype', None ) + depends_on = converter.get( 'depends_on', None ) + if depends_on and target_datatype: + if extension not in self.converter_deps: + self.converter_deps[extension] = {} + self.converter_deps[extension][target_datatype] = depends_on.split(',') + if converter_config and target_datatype: if imported_modules: - if elem not in self.proprietary_display_app_containers: - self.proprietary_display_app_containers.append( elem ) + self.proprietary_converters.append( ( converter_config, extension, target_datatype ) ) else: - if elem not in self.display_app_containers: - self.display_app_containers.append( elem ) - else: - self.log.debug( "Ignoring datatype with extension '%s' from %s because the registry already contains a datatype with that extension." % ( extension, config ) ) + self.converters.append( ( converter_config, extension, target_datatype ) ) + for composite_file in elem.findall( 'composite_file' ): + # add composite files + name = composite_file.get( 'name', None ) + if name is None: + self.log.warning( "You must provide a name for your composite_file (%s)." % composite_file ) + optional = composite_file.get( 'optional', False ) + 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' ): + if imported_modules: + if elem not in self.proprietary_display_app_containers: + self.proprietary_display_app_containers.append( elem ) + else: + if elem not in self.display_app_containers: + self.display_app_containers.append( elem ) except Exception, e: if deactivate: self.log.warning( "Error deactivating datatype with extension '%s': %s" % ( extension, str( e ) ) ) @@ -202,26 +192,33 @@ module = imported_module break if module is None: - # The datatype class name must be contained in one of the datatype - # modules in the Galaxy distribution. + # The datatype class name must be contained in one of the datatype modules in the Galaxy distribution. module = __import__( datatype_module ) for comp in datatype_module.split( '.' )[ 1: ]: module = getattr( module, comp ) aclass = getattr( module, datatype_class_name )() + # See if we have a conflicting sniffer already loaded. + conflict_loc = None + conflict = False + for conflict_loc, sniffer_class in enumerate( self.sniff_order ): + if sniffer_class.__class__ == aclass.__class__: + conflict = True + break if deactivate: - self.sniff_order.remove( aclass ) - self.datatype_sniffers.remove( dtype ) + for sniffer_class in self.sniff_order: + if sniffer_class.__class__ == aclass.__class__: + self.sniff_order.remove( sniffer_class ) + break self.log.debug( "Deactivated sniffer for datatype '%s'" % dtype ) else: - if override_conflicts and dtype in self.datatype_sniffers: + if conflict: + # We have a conflicting sniffer, so replace the one previously loaded. + del self.sniff_order[ conflict_loc ] self.sniff_order.append( aclass ) - self.log.debug( "Loaded additional sniffer for datatype '%s'" % dtype ) - elif dtype not in self.datatype_sniffers: - self.datatype_sniffers.append( dtype ) + self.log.debug( "Replaced conflicting sniffer for datatype '%s'" % dtype ) + else: self.sniff_order.append( aclass ) self.log.debug( "Loaded sniffer for datatype '%s'" % dtype ) - else: - self.log.debug( "Ignoring sniffer for datatype '%s' because the registry already contains one." % dtype ) except Exception, exc: if deactivate: self.log.warning( "Error deactivating sniffer for datatype '%s': %s" % ( dtype, str( exc ) ) )

Repository URL: https://bitbucket.org/galaxy/galaxy-central/

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