1 new commit in galaxy-central:

https://bitbucket.org/galaxy/galaxy-central/changeset/1b6819e4598d/ changeset: 1b6819e4598d user: greg date: 2012-12-05 17:46:36 summary: Handle invalid repository dependency definitions. affected #: 2 files

diff -r 1b8fd73e2a5464fd2caab261dbf10017f119185d -r 1b6819e4598ddcc685cd8ab69667e2d8d7d952f0 lib/galaxy/util/shed_util_common.py --- a/lib/galaxy/util/shed_util_common.py +++ b/lib/galaxy/util/shed_util_common.py @@ -618,7 +618,7 @@ message = '' if not displaying_invalid_tool: if metadata_dict: - message += "Metadata was defined for some items in revision '%s'. " % str( repository.tip( trans.app ) ) + message += "Metadata may have been defined for some items in revision '%s'. " % str( repository.tip( trans.app ) ) message += "Correct the following problems if necessary and reset metadata.%s" % new_line else: message += "Metadata cannot be defined for revision '%s' so this revision cannot be automatically " % str( repository.tip( trans.app ) ) @@ -719,7 +719,9 @@ # See if we have a repository dependencies defined. if name == 'repository_dependencies.xml': path_to_repository_dependencies_config = os.path.join( root, name ) - metadata_dict = generate_repository_dependency_metadata( path_to_repository_dependencies_config, metadata_dict ) + metadata_dict, error_message = generate_repository_dependency_metadata( app, path_to_repository_dependencies_config, metadata_dict ) + if error_message: + invalid_file_tups.append( ( name, error_message ) ) # See if we have one or more READ_ME files. elif name.lower() in readme_file_names: relative_path_to_readme = get_relative_path_to_repository_file( root, @@ -812,29 +814,71 @@ if requirements_dict: tool_dependencies_dict[ dependency_key ] = requirements_dict return tool_dependencies_dict -def generate_repository_dependency_metadata( repository_dependencies_config, metadata_dict ): +def generate_repository_dependency_metadata( app, repository_dependencies_config, metadata_dict ): + """Generate a repository dependencies dictionary based on valid information defined in the received repository_dependencies_config.""" repository_dependencies_tups = [] + error_message = '' + config_file_name = strip_path( repository_dependencies_config ) try: # Make sure we're looking at a valid repository_dependencies.xml file. tree = util.parse_xml( repository_dependencies_config ) root = tree.getroot() is_valid = root.tag == 'repositories' except Exception, e: - log.debug( "Error parsing %s, exception: %s" % ( repository_dependencies_config, str( e ) ) ) + error_message = "Error parsing %s, exception: %s" % ( repository_dependencies_config, str( e ) ) + log.debug( error_message ) is_valid = False if is_valid: + sa_session = app.model.context.current for repository_elem in root.findall( 'repository' ): - repository_dependencies_tup = ( repository_elem.attrib[ 'toolshed' ], - repository_elem.attrib[ 'name' ], - repository_elem.attrib[ 'owner'], - repository_elem.attrib[ 'changeset_revision' ] ) - if repository_dependencies_tup not in repository_dependencies_tups: - repository_dependencies_tups.append( repository_dependencies_tup ) + toolshed = repository_elem.attrib[ 'toolshed' ] + name = repository_elem.attrib[ 'name' ] + owner = repository_elem.attrib[ 'owner'] + changeset_revision = repository_elem.attrib[ 'changeset_revision' ] + user = None + repository = None + # Repository dependencies are currentlhy supported only within a single tool shed. + if tool_shed_is_this_tool_shed( toolshed ): + try: + user = sa_session.query( app.model.User ) \ + .filter( app.model.User.table.c.username == owner ) \ + .one() + except Exception, e: + error_message = "Invalid owner %s defined for repository %s in config file %s. " % ( owner, name, config_file_name ) + error_message += "Repository dependencies will be ignored." + log.debug( error_message ) + return metadata_dict, error_message + if user: + try: + repository = sa_session.query( app.model.Repository ) \ + .filter( and_( app.model.Repository.table.c.name == name, + app.model.Repository.table.c.user_id == user.id ) ) \ + .first() + except: + error_message = "Invalid name %s or owner %s defined for repository in config file %s. " % ( name, owner, config_file_name ) + error_message += "Repository dependencies will be ignored." + log.debug( error_message ) + return metadata_dict, error_message + if repository: + repository_dependencies_tup = ( toolshed, name, owner, changeset_revision ) + if repository_dependencies_tup not in repository_dependencies_tups: + repository_dependencies_tups.append( repository_dependencies_tup ) + else: + error_message = "Invalid name %s or owner %s defined for repository in config file %s. " % ( name, owner, config_file_name ) + error_message += "Repository dependencies will be ignored." + log.debug( error_message ) + return metadata_dict, error_message + else: + # We have an invalid repository owner defined for an entry in repository_dependencies.xml. + config_file_name = strip_path( repository_dependencies_config ) + error_message = "Invalid username %s defined for owner of repository %s in config file %s. Repository dependencies will be ignored." % ( owner, name, config_file_name ) + log.debug( error_message ) + return metadata_dict, error_message if repository_dependencies_tups: repository_dependencies_dict = dict( description=root.get( 'description' ), repository_dependencies=repository_dependencies_tups ) metadata_dict[ 'repository_dependencies' ] = repository_dependencies_dict - return metadata_dict + return metadata_dict, error_message def generate_tool_dependency_metadata( app, repository, tool_dependencies_config, metadata_dict, original_repository_metadata=None ): """ If the combination of name, version and type of each element is defined in the <requirement> tag for at least one tool in the repository,

diff -r 1b8fd73e2a5464fd2caab261dbf10017f119185d -r 1b6819e4598ddcc685cd8ab69667e2d8d7d952f0 test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py --- a/test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py +++ b/test/tool_shed/functional/test_0010_repository_with_tool_dependencies.py @@ -38,7 +38,7 @@ self.upload_file( repository, 'freebayes/freebayes.xml', valid_tools_only=False, - strings_displayed=[ 'Metadata was defined', 'This file requires an entry', 'tool_data_table_conf' ], + strings_displayed=[ 'Metadata may have been defined', 'This file requires an entry', 'tool_data_table_conf' ], commit_message='Uploaded the tool xml.' ) self.display_manage_repository_page( repository, strings_displayed=[ 'Invalid tools' ], strings_not_displayed=[ 'Valid tools' ] ) tip = self.get_repository_tip( repository )

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

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