1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/d9c384f7a754/ changeset: d9c384f7a754 user: greg date: 2012-07-05 15:42:11 summary: Make sure there is an entry for the main public Galaxy tool shed in the tool_sheds_conf.xml file when attempting to determine if tools migrated from the distribution to the tool shed are missing and need to be installed. affected #: 1 file
diff -r 456f11df0b53897086257b952457d615b3942539 -r d9c384f7a75435173817754300f8e7bef12d8840 lib/galaxy/tool_shed/migrate/common.py --- a/lib/galaxy/tool_shed/migrate/common.py +++ b/lib/galaxy/tool_shed/migrate/common.py @@ -21,39 +21,44 @@ root = tree.getroot() tool_shed = root.get( 'name' ) tool_shed_url = get_tool_shed_url_from_tools_xml_file_path( app, tool_shed ) - for elem in root: - if elem.tag == 'repository': - tool_dependencies = [] - tool_dependencies_dict = {} - repository_name = elem.get( 'name' ) - changeset_revision = elem.get( 'changeset_revision' ) - url = '%s/repository/get_tool_dependencies?name=%s&owner=%s&changeset_revision=%s&webapp=install_manager&no_reset=true' % \ - ( tool_shed_url, repository_name, REPOSITORY_OWNER, changeset_revision ) - response = urllib2.urlopen( url ) - text = response.read() - response.close() - if text: - tool_dependencies_dict = tool_shed_decode( text ) - for dependency_key, requirements_dict in tool_dependencies_dict.items(): - tool_dependency_name = requirements_dict[ 'name' ] - tool_dependency_version = requirements_dict[ 'version' ] - tool_dependency_type = requirements_dict[ 'type' ] - tool_dependency_readme = requirements_dict.get( 'readme', '' ) - tool_dependencies.append( ( tool_dependency_name, tool_dependency_version, tool_dependency_type, tool_dependency_readme ) ) - for tool_elem in elem.findall( 'tool' ): - migrated_tool_configs_dict[ tool_elem.get( 'file' ) ] = tool_dependencies - # Parse the proprietary tool_panel_configs (the default is tool_conf.xml) and generate the list of missing tool config file names. - missing_tool_configs_dict = odict() - for tool_panel_config in tool_panel_configs: - tree = util.parse_xml( tool_panel_config ) - root = tree.getroot() + if tool_shed_url: for elem in root: - if elem.tag == 'tool': - missing_tool_configs_dict = check_tool_tag_set( elem, migrated_tool_configs_dict, missing_tool_configs_dict ) - elif elem.tag == 'section': - for section_elem in elem: - if section_elem.tag == 'tool': - missing_tool_configs_dict = check_tool_tag_set( section_elem, migrated_tool_configs_dict, missing_tool_configs_dict ) + if elem.tag == 'repository': + tool_dependencies = [] + tool_dependencies_dict = {} + repository_name = elem.get( 'name' ) + changeset_revision = elem.get( 'changeset_revision' ) + url = '%s/repository/get_tool_dependencies?name=%s&owner=%s&changeset_revision=%s&webapp=install_manager&no_reset=true' % \ + ( tool_shed_url, repository_name, REPOSITORY_OWNER, changeset_revision ) + response = urllib2.urlopen( url ) + text = response.read() + response.close() + if text: + tool_dependencies_dict = tool_shed_decode( text ) + for dependency_key, requirements_dict in tool_dependencies_dict.items(): + tool_dependency_name = requirements_dict[ 'name' ] + tool_dependency_version = requirements_dict[ 'version' ] + tool_dependency_type = requirements_dict[ 'type' ] + tool_dependency_readme = requirements_dict.get( 'readme', '' ) + tool_dependencies.append( ( tool_dependency_name, tool_dependency_version, tool_dependency_type, tool_dependency_readme ) ) + for tool_elem in elem.findall( 'tool' ): + migrated_tool_configs_dict[ tool_elem.get( 'file' ) ] = tool_dependencies + # Parse the proprietary tool_panel_configs (the default is tool_conf.xml) and generate the list of missing tool config file names. + missing_tool_configs_dict = odict() + for tool_panel_config in tool_panel_configs: + tree = util.parse_xml( tool_panel_config ) + root = tree.getroot() + for elem in root: + if elem.tag == 'tool': + missing_tool_configs_dict = check_tool_tag_set( elem, migrated_tool_configs_dict, missing_tool_configs_dict ) + elif elem.tag == 'section': + for section_elem in elem: + if section_elem.tag == 'tool': + missing_tool_configs_dict = check_tool_tag_set( section_elem, migrated_tool_configs_dict, missing_tool_configs_dict ) + else: + exception_msg = '\n\nThe entry for the main Galaxy tool shed at %s is missing from the %s file. ' % ( tool_shed, app.config.tool_sheds_config ) + exception_msg += 'The entry for this tool shed must always be available in this file, so re-add it before attempting to start your Galaxy server.\n' + raise Exception( exception_msg ) return missing_tool_configs_dict def check_tool_tag_set( elem, migrated_tool_configs_dict, missing_tool_configs_dict ): file_path = elem.get( 'file', None ) @@ -76,8 +81,9 @@ config_filenames.append( config_filename ) return config_filenames def get_tool_shed_url_from_tools_xml_file_path( app, tool_shed ): + search_str = '://%s' % tool_shed for shed_name, shed_url in app.tool_shed_registry.tool_sheds.items(): - if shed_url.find( tool_shed ) >= 0: + if shed_url.find( search_str ) >= 0: if shed_url.endswith( '/' ): shed_url = shed_url.rstrip( '/' ) return shed_url
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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