1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/c4ced3262d0d/ changeset: c4ced3262d0d user: greg date: 2012-09-13 21:31:56 summary: Another fix for handling Galaxy's ToolDataTableManager correctly in the tool shed. affected #: 4 files diff -r 2551b8632edea0df8b71ef6b426e30b7159153a4 -r c4ced3262d0d50719dd5d7d24ed10627b75d67ba lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -340,9 +340,6 @@ correction_msg = "This file refers to a file named <b>%s</b>. " % str( index_file ) correction_msg += "Upload a file named <b>%s.sample</b> to the repository to correct this error." % str( index_file_name ) invalid_files_and_errors_tups.append( ( tool_config_name, correction_msg ) ) - if webapp == 'community': - # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. - reset_tool_data_tables( app ) return invalid_files_and_errors_tups def config_elems_to_xml_file( app, config_elems, config_filename, tool_path ): # Persist the current in-memory list of config_elems to a file named by the value of config_filename. @@ -583,31 +580,6 @@ else: tool_dependencies_dict[ 'set_environment' ] = [ requirements_dict ] return tool_dependencies_dict -def generate_tool_dependency_metadata( tool_dependencies_config, metadata_dict ): - """ - 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, - then update the received metadata_dict with information from the parsed tool_dependencies_config. - """ - try: - tree = ElementTree.parse( tool_dependencies_config ) - except Exception, e: - log.debug( "Exception attempting to parse tool_dependencies.xml: %s" %str( e ) ) - return metadata_dict - root = tree.getroot() - ElementInclude.include( root ) - tool_dependencies_dict = {} - if can_generate_tool_dependency_metadata( root, metadata_dict ): - for elem in root: - if elem.tag == 'package': - tool_dependencies_dict = generate_package_dependency_metadata( elem, tool_dependencies_dict ) - elif elem.tag == 'set_environment': - tool_dependencies_dict = generate_environment_dependency_metadata( elem, tool_dependencies_dict ) - # Handle tool dependency installation via other means here (future). - if tool_dependencies_dict: - metadata_dict[ 'tool_dependencies' ] = tool_dependencies_dict - if tool_dependencies_dict: - metadata_dict[ 'tool_dependencies' ] = tool_dependencies_dict - return metadata_dict def generate_metadata_for_changeset_revision( app, repository_clone_url, relative_install_dir=None, repository_files_dir=None, resetting_all_metadata_on_repository=False, webapp='galaxy' ): """ @@ -621,6 +593,7 @@ invalid_tool_configs = [] tool_dependencies_config = None original_tool_data_path = app.config.tool_data_path + original_tool_data_table_config_path = app.config.tool_data_table_config_path if resetting_all_metadata_on_repository: if not relative_install_dir: raise Exception( "The value of repository.repo_path must be sent when resetting all metadata on a repository." ) @@ -630,12 +603,14 @@ files_dir = repository_files_dir # Since we're working from a temporary directory, we can safely copy sample files included in the repository to the repository root. app.config.tool_data_path = repository_files_dir + app.config.tool_data_table_config_path = repository_files_dir else: # Use a temporary working directory to copy all sample files. work_dir = tempfile.mkdtemp() # All other files are on disk in the repository's repo_path, which is the value of relative_install_dir. files_dir = relative_install_dir app.config.tool_data_path = work_dir + app.config.tool_data_table_config_path = work_dir # Handle proprietary datatypes, if any. datatypes_config = get_config_from_disk( 'datatypes_conf.xml', files_dir ) if datatypes_config: @@ -719,11 +694,9 @@ metadata_dict = generate_tool_dependency_metadata( tool_dependencies_config, metadata_dict ) if invalid_tool_configs: metadata_dict [ 'invalid_tools' ] = invalid_tool_configs - if webapp == 'community' and resetting_all_metadata_on_repository: - # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. - reset_tool_data_tables( app ) - # Reset the value of the app's tool_data_path to it's original value. - app.config.tool_data_path = original_tool_data_path + # Reset the value of the app's tool_data_path and tool_data_table_config_path to their respective original values. + app.config.tool_data_path = original_tool_data_path + app.config.tool_data_table_config_path = original_tool_data_table_config_path return metadata_dict, invalid_file_tups def generate_package_dependency_metadata( elem, tool_dependencies_dict ): """The value of package_name must match the value of the "package" type in the tool config's <requirements> tag set.""" @@ -741,6 +714,31 @@ if requirements_dict: tool_dependencies_dict[ dependency_key ] = requirements_dict return tool_dependencies_dict +def generate_tool_dependency_metadata( tool_dependencies_config, metadata_dict ): + """ + 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, + then update the received metadata_dict with information from the parsed tool_dependencies_config. + """ + try: + tree = ElementTree.parse( tool_dependencies_config ) + except Exception, e: + log.debug( "Exception attempting to parse tool_dependencies.xml: %s" %str( e ) ) + return metadata_dict + root = tree.getroot() + ElementInclude.include( root ) + tool_dependencies_dict = {} + if can_generate_tool_dependency_metadata( root, metadata_dict ): + for elem in root: + if elem.tag == 'package': + tool_dependencies_dict = generate_package_dependency_metadata( elem, tool_dependencies_dict ) + elif elem.tag == 'set_environment': + tool_dependencies_dict = generate_environment_dependency_metadata( elem, tool_dependencies_dict ) + # Handle tool dependency installation via other means here (future). + if tool_dependencies_dict: + metadata_dict[ 'tool_dependencies' ] = tool_dependencies_dict + if tool_dependencies_dict: + metadata_dict[ 'tool_dependencies' ] = tool_dependencies_dict + return metadata_dict def generate_tool_guid( repository_clone_url, tool ): """ Generate a guid for the installed tool. It is critical that this guid matches the guid for diff -r 2551b8632edea0df8b71ef6b426e30b7159153a4 -r c4ced3262d0d50719dd5d7d24ed10627b75d67ba lib/galaxy/webapps/community/controllers/admin.py --- a/lib/galaxy/webapps/community/controllers/admin.py +++ b/lib/galaxy/webapps/community/controllers/admin.py @@ -696,7 +696,7 @@ owner = repository_name_owner_list[ 1 ] repository = get_repository_by_name_and_owner( trans, name, owner ) try: - invalid_file_tups = reset_all_metadata_on_repository( trans, trans.security.encode_id( repository.id ) ) + invalid_file_tups, metadata_dict = reset_all_metadata_on_repository( trans, trans.security.encode_id( repository.id ) ) if invalid_file_tups: message = generate_message_for_invalid_tools( invalid_file_tups, repository, None, as_html=False ) log.debug( message ) diff -r 2551b8632edea0df8b71ef6b426e30b7159153a4 -r c4ced3262d0d50719dd5d7d24ed10627b75d67ba lib/galaxy/webapps/community/controllers/common.py --- a/lib/galaxy/webapps/community/controllers/common.py +++ b/lib/galaxy/webapps/community/controllers/common.py @@ -937,7 +937,9 @@ clean_repository_metadata( trans, id, changeset_revisions ) # Set tool version information for all downloadable changeset revisions. Get the list of changeset revisions from the changelog. reset_all_tool_versions( trans, id, repo ) - return invalid_file_tups + # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. + reset_tool_data_tables( trans.app ) + return invalid_file_tups, metadata_dict def set_repository_metadata( trans, repository, content_alert_str='', **kwd ): """ Set metadata using the repository's current disk files, returning specific error messages (if any) to alert the repository owner that the changeset @@ -1000,6 +1002,8 @@ if invalid_file_tups: message = generate_message_for_invalid_tools( invalid_file_tups, repository, metadata_dict ) status = 'error' + # Reset the tool_data_tables by loading the empty tool_data_table_conf.xml file. + reset_tool_data_tables( trans.app ) return message, status def set_repository_metadata_due_to_new_tip( trans, repository, content_alert_str=None, **kwd ): # Set metadata on the repository tip. diff -r 2551b8632edea0df8b71ef6b426e30b7159153a4 -r c4ced3262d0d50719dd5d7d24ed10627b75d67ba lib/galaxy/webapps/community/controllers/repository.py --- a/lib/galaxy/webapps/community/controllers/repository.py +++ b/lib/galaxy/webapps/community/controllers/repository.py @@ -1817,10 +1817,10 @@ status=status ) @web.expose def reset_all_metadata( self, trans, id, **kwd ): - invalid_file_tups = reset_all_metadata_on_repository( trans, id, **kwd ) + invalid_file_tups, metadata_dict = reset_all_metadata_on_repository( trans, id, **kwd ) if invalid_file_tups: repository = get_repository( trans, id ) - message = generate_message_for_invalid_tools( invalid_file_tups, repository, None ) + message = generate_message_for_invalid_tools( invalid_file_tups, repository, metadata_dict ) status = 'error' else: message = "All repository metadata has been reset." 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