1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/f37d9a0a1afc/ changeset: f37d9a0a1afc user: greg date: 2011-12-16 17:19:29 summary: Enhance the datatypes registry to: (a) enable use of config files that do not include a "sniffers" tag set section, (b) not load a datatypes if the registry already includes a datatype with that extension. affected #: 1 file
diff -r ef4a1377fcc62bad6feb11df126339c639b7e56a -r f37d9a0a1afc72945e1283195739fc31418dc934 lib/galaxy/datatypes/registry.py --- a/lib/galaxy/datatypes/registry.py +++ b/lib/galaxy/datatypes/registry.py @@ -62,7 +62,10 @@ mimetype = elem.get( 'mimetype', None ) display_in_upload = elem.get( 'display_in_upload', False ) make_subclass = galaxy.util.string_as_bool( elem.get( 'subclass', False ) ) - if extension and ( dtype or type_extension ): + if extension and extension in self.datatypes_by_extension: + self.log.debug( "Ignoring datatype with extension '%s' from '%s' because the registry already includes a datatype with that extension." \ + % ( extension, config ) ) + elif extension and ( dtype or type_extension ): if dtype: fields = dtype.split( ':' ) datatype_module = fields[0] @@ -142,23 +145,24 @@ d_type1.add_display_application( display_app ) # Load datatype sniffers from the config sniffers = root.find( 'sniffers' ) - for elem in sniffers.findall( 'sniffer' ): - dtype = elem.get( 'type', None ) - if dtype: - try: - fields = dtype.split( ":" ) - datatype_module = fields[0] - datatype_class = fields[1] - module = __import__( datatype_module ) - for comp in datatype_module.split('.')[1:]: - module = getattr(module, comp) - aclass = getattr( module, datatype_class )() - self.sniff_order.append( aclass ) - self.log.debug( 'Loaded sniffer for datatype: %s' % dtype ) - except Exception, exc: - self.log.warning( 'Error appending datatype %s to sniff_order, problem: %s' % ( dtype, str( exc ) ) ) - #default values - if len(self.datatypes_by_extension) < 1: + if sniffers: + for elem in sniffers.findall( 'sniffer' ): + dtype = elem.get( 'type', None ) + if dtype: + try: + fields = dtype.split( ":" ) + datatype_module = fields[0] + datatype_class = fields[1] + module = __import__( datatype_module ) + for comp in datatype_module.split('.')[1:]: + module = getattr(module, comp) + aclass = getattr( module, datatype_class )() + self.sniff_order.append( aclass ) + self.log.debug( 'Loaded sniffer for datatype: %s' % dtype ) + except Exception, exc: + self.log.warning( 'Error appending datatype %s to sniff_order, problem: %s' % ( dtype, str( exc ) ) ) + # Default values. + if not self.datatypes_by_extension: self.datatypes_by_extension = { 'ab1' : binary.Ab1(), 'axt' : sequence.Axt(),
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
--
This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.