mirror of
https://github.com/galaxyproject/galaxy.git
synced 2026-09-24 16:30:27 +08:00
Eliminate the code for the long-unused tool shed datatypes.
This commit is contained in:
Greg Von Kuster
@@ -13,8 +13,6 @@ class UniverseApplication( object ):
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self.config = config.Configuration( **kwargs )
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self.config.check()
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config.configure_logging( self.config )
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# Set up datatypes registry
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self.datatypes_registry = galaxy.datatypes.registry.Registry( self.config.root, self.config.datatypes_config )
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# Determine the database url
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if self.config.database_connection:
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db_url = self.config.database_connection
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@@ -70,7 +70,6 @@ class Configuration( object ):
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self.screencasts_url = kwargs.get( 'screencasts_url', None )
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self.log_events = False
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self.cloud_controller_instance = False
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self.datatypes_config = kwargs.get( 'datatypes_config_file', 'datatypes_conf.xml' )
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# Proxy features
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self.apache_xsendfile = kwargs.get( 'apache_xsendfile', False )
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self.nginx_x_accel_redirect_base = kwargs.get( 'nginx_x_accel_redirect_base', False )
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@@ -1,196 +0,0 @@
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import sys, logging, tarfile
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from galaxy.util import parse_xml
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from galaxy.util.bunch import Bunch
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log = logging.getLogger( __name__ )
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if sys.version_info[:2] == ( 2, 4 ):
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from galaxy import eggs
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eggs.require( 'ElementTree' )
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from elementtree import ElementTree
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else:
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from xml.etree import ElementTree
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class DatatypeVerificationError( Exception ):
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pass
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class Registry( object ):
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def __init__( self, root_dir=None, config=None ):
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self.datatypes_by_extension = {}
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if root_dir and config:
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# Parse datatypes_conf.xml
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tree = parse_xml( config )
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root = tree.getroot()
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# Load datatypes and converters from config
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log.debug( 'Loading datatypes from %s' % config )
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registration = root.find( 'registration' )
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for elem in registration.findall( 'datatype' ):
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try:
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extension = elem.get( 'extension', None )
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dtype = elem.get( 'type', None )
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model_object = elem.get( 'model', None )
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if extension and dtype:
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fields = dtype.split( ':' )
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datatype_module = fields[0]
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datatype_class = fields[1]
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fields = datatype_module.split( '.' )
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module = __import__( fields.pop(0) )
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for mod in fields:
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module = getattr( module, mod )
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self.datatypes_by_extension[extension] = getattr( module, datatype_class )()
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log.debug( 'Loaded datatype: %s' % dtype )
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if model_object:
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model_module, model_class = model_object.split( ':' )
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fields = model_module.split( '.' )
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module = __import__( fields.pop(0) )
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for mod in fields:
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module = getattr( module, mod )
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self.datatypes_by_extension[extension].model_object = getattr( module, model_class )
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log.debug( 'Added model class: %s to datatype: %s' % ( model_class, dtype ) )
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except Exception, e:
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log.warning( 'Error loading datatype "%s", problem: %s' % ( extension, str( e ) ) )
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def get_datatype_by_extension( self, ext ):
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return self.datatypes_by_extension.get( ext, None )
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def get_datatype_extensions( self ):
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rval = []
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for ext, datatype in self.datatypes_by_extension.items():
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rval.append( ext )
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return rval
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class Tool( object ):
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def __init__( self, model_object=None ):
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self.model_object = model_object
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self.label = 'Tool'
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def verify( self, f, xml_files=[], tool_tags={} ):
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# xml_files and tool_tags will only be received if we're called from the ToolSuite.verify() method.
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try:
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tar = tarfile.open( f.name )
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except tarfile.ReadError, e:
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raise DatatypeVerificationError( 'Error reading the archive, problem: %s' % str( e ) )
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if not xml_files:
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# Make sure we're not uploading a tool suite
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if filter( lambda x: x.lower().find( 'suite_config.xml' ) >= 0, tar.getnames() ):
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raise DatatypeVerificationError( 'The archive includes a suite_config.xml file, so set the upload type to "Tool Suite".' )
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xml_files = filter( lambda x: x.lower().endswith( '.xml' ), tar.getnames() )
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if not xml_files:
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raise DatatypeVerificationError( 'The archive does not contain any xml config files.' )
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for xml_file in xml_files:
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try:
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tree = ElementTree.parse( tar.extractfile( xml_file ) )
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root = tree.getroot()
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except Exception, e:
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raise DatatypeVerificationError( 'Error parsing file "%s", problem: %s' % ( str( xml_file ), str( e ) ) )
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if root.tag == 'tool':
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if 'id' not in root.keys():
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raise DatatypeVerificationError( "Tool xml file (%s) does not include the required 'id' attribute in the <tool> tag" % str( xml_file ) )
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if 'name' not in root.keys():
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raise DatatypeVerificationError( "Tool xml file (%s) does not include the required 'name' attribute in the <tool> tag" % str( xml_file ) )
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if 'version' not in root.keys():
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raise DatatypeVerificationError( "Tool xml file (%s) does not include the required 'version' attribute in the <tool> tag" % str( xml_file ) )
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if tool_tags:
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# We are verifying the tools inside a tool suite, so the current tag should have been found in the suite_config.xml
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# file parsed in the ToolSuite verify() method. The tool_tags dictionary should include a key matching the current
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# tool Id, and a tuple value matching the tool name and version.
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if root.attrib[ 'id' ] not in tool_tags:
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raise DatatypeVerificationError( 'Tool Id (%s) is not included in the suite_config.xml file.' % \
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( str( root.attrib[ 'id' ] ) ) )
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tup = tool_tags[ root.attrib[ 'id' ] ]
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if root.attrib[ 'name' ] != tup[ 0 ]:
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raise DatatypeVerificationError( 'Tool name (%s) differs between suite_config.xml and the tool config file for tool Id (%s).' % \
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( str( root.attrib[ 'name' ] ), str( root.attrib[ 'id' ] ) ) )
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if root.attrib[ 'version' ] != tup[ 1 ]:
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raise DatatypeVerificationError( 'Tool version (%s) differs between suite_config.xml and the tool config file for tool Id (%s).' % \
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( str( root.attrib[ 'version' ] ), str( root.attrib[ 'id' ] ) ) )
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else:
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# We are not verifying a tool suite, so we'll create a bunch for returning to the caller.
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tool_bunch = Bunch()
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try:
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tool_bunch.id = root.attrib['id']
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tool_bunch.name = root.attrib['name']
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tool_bunch.version = root.attrib['version']
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except KeyError, e:
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raise DatatypeVerificationError( 'Tool XML file does not conform to the specification. Missing required <tool> tag attribute: %s' % str( e ) )
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tool_bunch.description = ''
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desc_tag = root.find( 'description' )
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if desc_tag is not None:
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description = desc_tag.text
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if description:
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tool_bunch.description = description.strip()
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tool_bunch.message = 'Tool: %s %s, Version: %s, Id: %s' % \
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( str( tool_bunch.name ), str( tool_bunch.description ), str( tool_bunch.version ), str( tool_bunch.id ) )
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return tool_bunch
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else:
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# TODO: should we verify files that are not tool configs?
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log.debug( "The file named (%s) is not a tool config, so skipping verification." % str( xml_file ) )
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def create_model_object( self, datatype_bunch ):
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if self.model_object is None:
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raise Exception( 'No model object configured for %s, check the datatype configuration file' % self.__class__.__name__ )
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if datatype_bunch is None:
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# TODO: do it automatically
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raise Exception( 'Unable to create %s model object without passing in data' % self.__class__.__name__ )
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o = self.model_object()
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o.create_from_datatype( datatype_bunch )
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return o
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class ToolSuite( Tool ):
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def __init__( self, model_object=None ):
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self.model_object = model_object
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self.label = 'Tool Suite'
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def verify( self, f ):
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"""
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A sample tool suite config:
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<suite id="onto_toolkit" name="ONTO Toolkit" version="1.0">
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<description>ONTO-Toolkit is a collection of Galaxy tools which support the manipulation of bio-ontologies.</description>
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<tool id="get_ancestor_terms" name="Get the ancestor terms of a given OBO term" version="1.0.0">
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<description>Collects the ancestor terms from a given term in the given OBO ontology</description>
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</tool>
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<tool id="get_child_terms" name="Get the child terms of a given OBO term" version="1.0.0">
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<description>Collects the child terms from a given term in the given OBO ontology</description>
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</tool>
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</suite>
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"""
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try:
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tar = tarfile.open( f.name )
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except tarfile.ReadError:
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raise DatatypeVerificationError( 'The archive is not a readable tar file.' )
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suite_config = filter( lambda x: x.lower().find( 'suite_config.xml' ) >=0, tar.getnames() )
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if not suite_config:
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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".' )
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suite_config = suite_config[ 0 ]
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# Parse and verify suite_config
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archive_ok = False
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try:
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tree = ElementTree.parse( tar.extractfile( suite_config ) )
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root = tree.getroot()
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archive_ok = True
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except:
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log.exception( 'fail:' )
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if archive_ok and root.tag == 'suite':
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suite_bunch = Bunch()
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try:
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suite_bunch.id = root.attrib['id']
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suite_bunch.name = root.attrib['name']
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suite_bunch.version = root.attrib['version']
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except KeyError, e:
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raise DatatypeVerificationError( 'The file named tool-suite.xml does not conform to the specification. Missing required <suite> tag attribute: %s' % str( e ) )
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suite_bunch.description = ''
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desc_tag = root.find( 'description' )
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if desc_tag is not None:
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description = desc_tag.text
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if description:
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suite_bunch.description = description.strip()
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suite_bunch.message = 'Tool suite: %s %s, Version: %s, Id: %s' % \
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( str( suite_bunch.name ), str( suite_bunch.description ), str( suite_bunch.version ), str( suite_bunch.id ) )
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# Create a dictionary of the tools in the suite where the keys are tool_ids and the
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# values are tuples of tool name and version
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tool_tags = {}
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for elem in root.findall( 'tool' ):
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tool_tags[ elem.attrib['id'] ] = ( elem.attrib['name'], elem.attrib['version'] )
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else:
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raise DatatypeVerificationError( "The file named %s is not a valid tool suite config." % str( suite_config ) )
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# Verify all included tool config files
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xml_files = filter( lambda x: x.lower().endswith( '.xml' ) and x.lower() != 'suite_config.xml', tar.getnames() )
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if not xml_files:
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raise DatatypeVerificationError( 'The archive does not contain any tool config (xml) files.' )
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Tool.verify( self, f, xml_files=xml_files, tool_tags=tool_tags )
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return suite_bunch
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