1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/5c9971aba1b4/ changeset: 5c9971aba1b4 user: greg date: 2012-12-21 15:00:34 summary: Fix for setting tool versions for tools contained in tool shed repositories installed into a Galaxy instance. affected #: 2 files
diff -r 0a3e4bc2b5a510820b8aba73b78433db810a3481 -r 5c9971aba1b4f4062e27dcbdd9262e3e81c88ddf lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -852,6 +852,60 @@ if k not in [ 'id', 'version', 'name' ]: return True return False +def populate_containers_dict_from_repository_metadata( trans, tool_shed_url, tool_path, repository ): + """ + Retrieve necessary information from the received repository's metadata to populate the containers_dict for display. This methos is called only + from Galaxy and not the tool shed. + """ + metadata = repository.metadata + if metadata: + datatypes = metadata.get( 'datatypes', None ) + invalid_tools = metadata.get( 'invalid_tools', None ) + if repository.has_readme_files: + readme_files_dict = suc.build_readme_files_dict( repository.metadata, tool_path ) + else: + readme_files_dict = None + repository_dependencies = metadata.get( 'repository_dependencies', None ) + repository_dependencies_dict_for_display = {} + if repository_dependencies: + # We need to add a root_key entry to the repository_dependencies dictionary since it will not be included in the installed tool + # shed repository metadata. + root_key = container_util.generate_repository_dependencies_key_for_repository( repository.tool_shed, + repository.name, + repository.owner, + repository.installed_changeset_revision ) + rd_tups_for_display = [] + rd_tups = repository_dependencies[ 'repository_dependencies' ] + repository_dependencies_dict_for_display[ 'root_key' ] = root_key + repository_dependencies_dict_for_display[ root_key ] = rd_tups + repository_dependencies_dict_for_display[ 'description' ] = repository_dependencies[ 'description' ] + all_tool_dependencies = metadata.get( 'tool_dependencies', None ) + tool_dependencies, missing_tool_dependencies = get_installed_and_missing_tool_dependencies( trans, repository, all_tool_dependencies ) + valid_tools = metadata.get( 'tools', None ) + workflows = metadata.get( 'workflows', None ) + containers_dict = suc.build_repository_containers_for_galaxy( trans=trans, + toolshed_base_url=tool_shed_url, + repository_name=repository.name, + repository_owner=repository.owner, + changeset_revision=repository.installed_changeset_revision, + repository=repository, + datatypes=datatypes, + invalid_tools=invalid_tools, + missing_tool_dependencies=missing_tool_dependencies, + readme_files_dict=readme_files_dict, + repository_dependencies=repository_dependencies_dict_for_display, + tool_dependencies=tool_dependencies, + valid_tools=valid_tools, + workflows=workflows ) + else: + containers_dict = dict( datatypes=None, + invalid_tools=None, + readme_files_dict=None, + repository_dependencies=None, + tool_dependencies=None, + valid_tools=None, + workflows=None ) + return containers_dict def pull_repository( repo, repository_clone_url, ctx_rev ): """Pull changes from a remote repository to a local one.""" commands.pull( suc.get_configured_ui(), repo, source=repository_clone_url, rev=[ ctx_rev ] )
diff -r 0a3e4bc2b5a510820b8aba73b78433db810a3481 -r 5c9971aba1b4f4062e27dcbdd9262e3e81c88ddf lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -877,45 +877,7 @@ trans.sa_session.add( repository ) trans.sa_session.flush() message = "The repository information has been updated." - metadata = repository.metadata - datatypes = metadata.get( 'datatypes', None ) - invalid_tools = metadata.get( 'invalid_tools', None ) - if repository.has_readme_files: - readme_files_dict = suc.build_readme_files_dict( repository.metadata, tool_path ) - else: - readme_files_dict = None - repository_dependencies = metadata.get( 'repository_dependencies', None ) - repository_dependencies_dict_for_display = {} - if repository_dependencies: - # We need to add a root_key entry to the repository_dependencies dictionary since it will not be included in the installed tool - # shed repository metadata. - root_key = container_util.generate_repository_dependencies_key_for_repository( repository.tool_shed, - repository.name, - repository.owner, - repository.installed_changeset_revision ) - rd_tups_for_display = [] - rd_tups = repository_dependencies[ 'repository_dependencies' ] - repository_dependencies_dict_for_display[ 'root_key' ] = root_key - repository_dependencies_dict_for_display[ root_key ] = rd_tups - repository_dependencies_dict_for_display[ 'description' ] = repository_dependencies[ 'description' ] - all_tool_dependencies = metadata.get( 'tool_dependencies', None ) - tool_dependencies, missing_tool_dependencies = shed_util.get_installed_and_missing_tool_dependencies( trans, repository, all_tool_dependencies ) - valid_tools = metadata.get( 'tools', None ) - workflows = metadata.get( 'workflows', None ) - containers_dict = suc.build_repository_containers_for_galaxy( trans=trans, - toolshed_base_url=tool_shed_url, - repository_name=repository.name, - repository_owner=repository.owner, - changeset_revision=repository.installed_changeset_revision, - repository=repository, - datatypes=datatypes, - invalid_tools=invalid_tools, - missing_tool_dependencies=missing_tool_dependencies, - readme_files_dict=readme_files_dict, - repository_dependencies=repository_dependencies_dict_for_display, - tool_dependencies=tool_dependencies, - valid_tools=valid_tools, - workflows=workflows ) + containers_dict = shed_util.populate_containers_dict_from_repository_metadata( trans, tool_shed_url, tool_path, repository ) return trans.fill_template( '/admin/tool_shed_repository/manage_repository.mako', repository=repository, description=description, @@ -1668,7 +1630,10 @@ @web.expose @web.require_admin def set_tool_versions( self, trans, **kwd ): - # Get the tool_versions from the tool shed for each tool in the installed change set. + """ + Get the tool_versions from the tool shed for each tool in the installed revision of a selected tool shed repository and update the + metadata for the repository's revision in the Galaxy database. + """ repository = suc.get_installed_tool_shed_repository( trans, kwd[ 'id' ] ) tool_shed_url = suc.get_url_from_repository_tool_shed( trans.app, repository ) url = suc.url_join( tool_shed_url, @@ -1689,10 +1654,12 @@ status = 'error' shed_tool_conf, tool_path, relative_install_dir = suc.get_tool_panel_config_tool_path_install_dir( trans.app, repository ) repo_files_dir = os.path.abspath( os.path.join( relative_install_dir, repository.name ) ) + containers_dict = shed_util.populate_containers_dict_from_repository_metadata( trans, tool_shed_url, tool_path, repository ) return trans.fill_template( '/admin/tool_shed_repository/manage_repository.mako', repository=repository, description=repository.description, repo_files_dir=repo_files_dir, + containers_dict=containers_dict, message=message, status=status ) @web.json
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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