1 new changeset in galaxy-central:
http://bitbucket.org/galaxy/galaxy-central/changeset/ef955e304925/ changeset: ef955e304925 user: greg date: 2011-08-26 22:04:53 summary: Eliminate the code for the long-unused tool shed datatypes. affected #: 3 files (247 bytes)
--- a/lib/galaxy/webapps/community/app.py Fri Aug 26 15:59:29 2011 -0400 +++ b/lib/galaxy/webapps/community/app.py Fri Aug 26 16:04:53 2011 -0400 @@ -13,8 +13,6 @@ self.config = config.Configuration( **kwargs ) self.config.check() config.configure_logging( self.config ) - # Set up datatypes registry - self.datatypes_registry = galaxy.datatypes.registry.Registry( self.config.root, self.config.datatypes_config ) # Determine the database url if self.config.database_connection: db_url = self.config.database_connection
--- a/lib/galaxy/webapps/community/config.py Fri Aug 26 15:59:29 2011 -0400 +++ b/lib/galaxy/webapps/community/config.py Fri Aug 26 16:04:53 2011 -0400 @@ -70,7 +70,6 @@ self.screencasts_url = kwargs.get( 'screencasts_url', None ) self.log_events = False self.cloud_controller_instance = False - self.datatypes_config = kwargs.get( 'datatypes_config_file', 'datatypes_conf.xml' ) # Proxy features self.apache_xsendfile = kwargs.get( 'apache_xsendfile', False ) self.nginx_x_accel_redirect_base = kwargs.get( 'nginx_x_accel_redirect_base', False )
--- a/lib/galaxy/webapps/community/datatypes/__init__.py Fri Aug 26 15:59:29 2011 -0400 +++ /dev/null Thu Jan 01 00:00:00 1970 +0000 @@ -1,196 +0,0 @@ -import sys, logging, tarfile -from galaxy.util import parse_xml -from galaxy.util.bunch import Bunch - -log = logging.getLogger( __name__ ) - -if sys.version_info[:2] == ( 2, 4 ): - from galaxy import eggs - eggs.require( 'ElementTree' ) - from elementtree import ElementTree -else: - from xml.etree import ElementTree - -class DatatypeVerificationError( Exception ): - pass - -class Registry( object ): - def __init__( self, root_dir=None, config=None ): - self.datatypes_by_extension = {} - if root_dir and config: - # Parse datatypes_conf.xml - tree = parse_xml( config ) - root = tree.getroot() - # Load datatypes and converters from config - log.debug( 'Loading datatypes from %s' % config ) - registration = root.find( 'registration' ) - for elem in registration.findall( 'datatype' ): - try: - extension = elem.get( 'extension', None ) - dtype = elem.get( 'type', None ) - model_object = elem.get( 'model', None ) - if extension and dtype: - fields = dtype.split( ':' ) - datatype_module = fields[0] - datatype_class = fields[1] - fields = datatype_module.split( '.' ) - module = __import__( fields.pop(0) ) - for mod in fields: - module = getattr( module, mod ) - self.datatypes_by_extension[extension] = getattr( module, datatype_class )() - log.debug( 'Loaded datatype: %s' % dtype ) - if model_object: - model_module, model_class = model_object.split( ':' ) - fields = model_module.split( '.' ) - module = __import__( fields.pop(0) ) - for mod in fields: - module = getattr( module, mod ) - self.datatypes_by_extension[extension].model_object = getattr( module, model_class ) - log.debug( 'Added model class: %s to datatype: %s' % ( model_class, dtype ) ) - except Exception, e: - log.warning( 'Error loading datatype "%s", problem: %s' % ( extension, str( e ) ) ) - def get_datatype_by_extension( self, ext ): - return self.datatypes_by_extension.get( ext, None ) - def get_datatype_extensions( self ): - rval = [] - for ext, datatype in self.datatypes_by_extension.items(): - rval.append( ext ) - return rval - -class Tool( object ): - def __init__( self, model_object=None ): - self.model_object = model_object - self.label = 'Tool' - def verify( self, f, xml_files=[], tool_tags={} ): - # xml_files and tool_tags will only be received if we're called from the ToolSuite.verify() method. - try: - tar = tarfile.open( f.name ) - except tarfile.ReadError, e: - raise DatatypeVerificationError( 'Error reading the archive, problem: %s' % str( e ) ) - if not xml_files: - # Make sure we're not uploading a tool suite - if filter( lambda x: x.lower().find( 'suite_config.xml' ) >= 0, tar.getnames() ): - raise DatatypeVerificationError( 'The archive includes a suite_config.xml file, so set the upload type to "Tool Suite".' ) - xml_files = filter( lambda x: x.lower().endswith( '.xml' ), tar.getnames() ) - if not xml_files: - raise DatatypeVerificationError( 'The archive does not contain any xml config files.' ) - for xml_file in xml_files: - try: - tree = ElementTree.parse( tar.extractfile( xml_file ) ) - root = tree.getroot() - except Exception, e: - raise DatatypeVerificationError( 'Error parsing file "%s", problem: %s' % ( str( xml_file ), str( e ) ) ) - if root.tag == 'tool': - if 'id' not in root.keys(): - raise DatatypeVerificationError( "Tool xml file (%s) does not include the required 'id' attribute in the <tool> tag" % str( xml_file ) ) - if 'name' not in root.keys(): - raise DatatypeVerificationError( "Tool xml file (%s) does not include the required 'name' attribute in the <tool> tag" % str( xml_file ) ) - if 'version' not in root.keys(): - raise DatatypeVerificationError( "Tool xml file (%s) does not include the required 'version' attribute in the <tool> tag" % str( xml_file ) ) - if tool_tags: - # We are verifying the tools inside a tool suite, so the current tag should have been found in the suite_config.xml - # file parsed in the ToolSuite verify() method. The tool_tags dictionary should include a key matching the current - # tool Id, and a tuple value matching the tool name and version. - if root.attrib[ 'id' ] not in tool_tags: - raise DatatypeVerificationError( 'Tool Id (%s) is not included in the suite_config.xml file.' % \ - ( str( root.attrib[ 'id' ] ) ) ) - tup = tool_tags[ root.attrib[ 'id' ] ] - if root.attrib[ 'name' ] != tup[ 0 ]: - raise DatatypeVerificationError( 'Tool name (%s) differs between suite_config.xml and the tool config file for tool Id (%s).' % \ - ( str( root.attrib[ 'name' ] ), str( root.attrib[ 'id' ] ) ) ) - if root.attrib[ 'version' ] != tup[ 1 ]: - raise DatatypeVerificationError( 'Tool version (%s) differs between suite_config.xml and the tool config file for tool Id (%s).' % \ - ( str( root.attrib[ 'version' ] ), str( root.attrib[ 'id' ] ) ) ) - else: - # We are not verifying a tool suite, so we'll create a bunch for returning to the caller. - tool_bunch = Bunch() - try: - tool_bunch.id = root.attrib['id'] - tool_bunch.name = root.attrib['name'] - tool_bunch.version = root.attrib['version'] - except KeyError, e: - raise DatatypeVerificationError( 'Tool XML file does not conform to the specification. Missing required <tool> tag attribute: %s' % str( e ) ) - tool_bunch.description = '' - desc_tag = root.find( 'description' ) - if desc_tag is not None: - description = desc_tag.text - if description: - tool_bunch.description = description.strip() - tool_bunch.message = 'Tool: %s %s, Version: %s, Id: %s' % \ - ( str( tool_bunch.name ), str( tool_bunch.description ), str( tool_bunch.version ), str( tool_bunch.id ) ) - return tool_bunch - else: - # TODO: should we verify files that are not tool configs? - log.debug( "The file named (%s) is not a tool config, so skipping verification." % str( xml_file ) ) - def create_model_object( self, datatype_bunch ): - if self.model_object is None: - raise Exception( 'No model object configured for %s, check the datatype configuration file' % self.__class__.__name__ ) - if datatype_bunch is None: - # TODO: do it automatically - raise Exception( 'Unable to create %s model object without passing in data' % self.__class__.__name__ ) - o = self.model_object() - o.create_from_datatype( datatype_bunch ) - return o - -class ToolSuite( Tool ): - def __init__( self, model_object=None ): - self.model_object = model_object - self.label = 'Tool Suite' - def verify( self, f ): - """ - A sample tool suite config: - <suite id="onto_toolkit" name="ONTO Toolkit" version="1.0"> - <description>ONTO-Toolkit is a collection of Galaxy tools which support the manipulation of bio-ontologies.</description> - <tool id="get_ancestor_terms" name="Get the ancestor terms of a given OBO term" version="1.0.0"> - <description>Collects the ancestor terms from a given term in the given OBO ontology</description> - </tool> - <tool id="get_child_terms" name="Get the child terms of a given OBO term" version="1.0.0"> - <description>Collects the child terms from a given term in the given OBO ontology</description> - </tool> - </suite> - """ - try: - tar = tarfile.open( f.name ) - except tarfile.ReadError: - raise DatatypeVerificationError( 'The archive is not a readable tar file.' ) - suite_config = filter( lambda x: x.lower().find( 'suite_config.xml' ) >=0, tar.getnames() ) - if not suite_config: - raise DatatypeVerificationError( 'The archive does not contain the required suite_config.xml config file. If you are uploading a single tool archive, set the upload type to "Tool".' ) - suite_config = suite_config[ 0 ] - # Parse and verify suite_config - archive_ok = False - try: - tree = ElementTree.parse( tar.extractfile( suite_config ) ) - root = tree.getroot() - archive_ok = True - except: - log.exception( 'fail:' ) - if archive_ok and root.tag == 'suite': - suite_bunch = Bunch() - try: - suite_bunch.id = root.attrib['id'] - suite_bunch.name = root.attrib['name'] - suite_bunch.version = root.attrib['version'] - except KeyError, e: - raise DatatypeVerificationError( 'The file named tool-suite.xml does not conform to the specification. Missing required <suite> tag attribute: %s' % str( e ) ) - suite_bunch.description = '' - desc_tag = root.find( 'description' ) - if desc_tag is not None: - description = desc_tag.text - if description: - suite_bunch.description = description.strip() - suite_bunch.message = 'Tool suite: %s %s, Version: %s, Id: %s' % \ - ( str( suite_bunch.name ), str( suite_bunch.description ), str( suite_bunch.version ), str( suite_bunch.id ) ) - # Create a dictionary of the tools in the suite where the keys are tool_ids and the - # values are tuples of tool name and version - tool_tags = {} - for elem in root.findall( 'tool' ): - tool_tags[ elem.attrib['id'] ] = ( elem.attrib['name'], elem.attrib['version'] ) - else: - raise DatatypeVerificationError( "The file named %s is not a valid tool suite config." % str( suite_config ) ) - # Verify all included tool config files - xml_files = filter( lambda x: x.lower().endswith( '.xml' ) and x.lower() != 'suite_config.xml', tar.getnames() ) - if not xml_files: - raise DatatypeVerificationError( 'The archive does not contain any tool config (xml) files.' ) - Tool.verify( self, f, xml_files=xml_files, tool_tags=tool_tags ) - return suite_bunch
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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