1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/changeset/04229b267b3e/ changeset: 04229b267b3e user: dan date: 2012-10-09 16:27:54 summary: Some cleanup for shed_util.py affected #: 1 file diff -r 429e895ee1b3bfb2fea1632d34a01d54faeac866 -r 04229b267b3e8dd112d3e66fd6826d2f66404424 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -387,8 +387,6 @@ else: tmp_url = repository_clone_url return tmp_url -def tool_shed_from_repository_clone_url( repository_clone_url ): - return clean_repository_clone_url( repository_clone_url ).split( 'repos' )[ 0 ].rstrip( '/' ) def clean_tool_shed_url( tool_shed_url ): if tool_shed_url.find( ':' ) > 0: # Eliminate the port, if any, since it will result in an invalid directory name. @@ -1772,42 +1770,6 @@ config_elems.remove( config_elem ) # Persist the altered in-memory version of the tool config. config_elems_to_xml_file( trans.app, config_elems, shed_tool_conf, tool_path ) -def update_in_shed_tool_config( app, repository ): - # A tool shed repository is being updated so change the shed_tool_conf file. Parse the config file to generate the entire list - # of config_elems instead of using the in-memory list. - shed_conf_dict = repository.get_shed_config_dict( app ) - shed_tool_conf = shed_conf_dict[ 'config_filename' ] - tool_path = shed_conf_dict[ 'tool_path' ] - - #hack for 'trans.app' used in lots of places. These places should just directly use app - trans = util.bunch.Bunch() - trans.app = app - - tool_panel_dict = generate_tool_panel_dict_from_shed_tool_conf_entries( trans, repository ) - repository_tools_tups = get_repository_tools_tups( app, repository.metadata ) - cleaned_repository_clone_url = clean_repository_clone_url( generate_clone_url( trans, repository ) ) - tool_shed = tool_shed_from_repository_clone_url( cleaned_repository_clone_url ) - owner = repository.owner - if not owner: - owner = get_repository_owner( cleaned_repository_clone_url ) - guid_to_tool_elem_dict = {} - for tool_config_filename, guid, tool in repository_tools_tups: - guid_to_tool_elem_dict[ guid ] = generate_tool_elem( tool_shed, repository.name, repository.changeset_revision, repository.owner or '', tool_config_filename, tool, None ) - config_elems = [] - tree = util.parse_xml( shed_tool_conf ) - root = tree.getroot() - for elem in root: - if elem.tag == 'section': - for i, tool_elem in enumerate( elem ): - guid = tool_elem.attrib.get( 'guid' ) - if guid in guid_to_tool_elem_dict: - elem[i] = guid_to_tool_elem_dict[ guid ] - elif elem.tag == 'tool': - guid = elem.attrib.get( 'guid' ) - if guid in guid_to_tool_elem_dict: - elem = guid_to_tool_elem_dict[ guid ] - config_elems.append( elem ) - config_elems_to_xml_file( app, config_elems, shed_tool_conf, tool_path ) def remove_from_tool_panel( trans, repository, shed_tool_conf, uninstall ): """A tool shed repository is being deactivated or uninstalled so handle tool panel alterations accordingly.""" # Determine where the tools are currently defined in the tool panel and store this information so the tools can be displayed @@ -2016,6 +1978,8 @@ elif c not in [ '\r' ]: translated.append( '' ) return ''.join( translated ) +def tool_shed_from_repository_clone_url( repository_clone_url ): + return clean_repository_clone_url( repository_clone_url ).split( 'repos' )[ 0 ].rstrip( '/' ) def translate_string( raw_text, to_html=True ): if raw_text: if to_html: @@ -2086,6 +2050,42 @@ sa_session.delete( tool_dependency ) sa_session.flush() return new_tool_dependency +def update_in_shed_tool_config( app, repository ): + # A tool shed repository is being updated so change the shed_tool_conf file. Parse the config file to generate the entire list + # of config_elems instead of using the in-memory list. + shed_conf_dict = repository.get_shed_config_dict( app ) + shed_tool_conf = shed_conf_dict[ 'config_filename' ] + tool_path = shed_conf_dict[ 'tool_path' ] + + #hack for 'trans.app' used in lots of places. These places should just directly use app + trans = util.bunch.Bunch() + trans.app = app + + tool_panel_dict = generate_tool_panel_dict_from_shed_tool_conf_entries( trans, repository ) + repository_tools_tups = get_repository_tools_tups( app, repository.metadata ) + cleaned_repository_clone_url = clean_repository_clone_url( generate_clone_url( trans, repository ) ) + tool_shed = tool_shed_from_repository_clone_url( cleaned_repository_clone_url ) + owner = repository.owner + if not owner: + owner = get_repository_owner( cleaned_repository_clone_url ) + guid_to_tool_elem_dict = {} + for tool_config_filename, guid, tool in repository_tools_tups: + guid_to_tool_elem_dict[ guid ] = generate_tool_elem( tool_shed, repository.name, repository.changeset_revision, repository.owner or '', tool_config_filename, tool, None ) + config_elems = [] + tree = util.parse_xml( shed_tool_conf ) + root = tree.getroot() + for elem in root: + if elem.tag == 'section': + for i, tool_elem in enumerate( elem ): + guid = tool_elem.attrib.get( 'guid' ) + if guid in guid_to_tool_elem_dict: + elem[i] = guid_to_tool_elem_dict[ guid ] + elif elem.tag == 'tool': + guid = elem.attrib.get( 'guid' ) + if guid in guid_to_tool_elem_dict: + elem = guid_to_tool_elem_dict[ guid ] + config_elems.append( elem ) + config_elems_to_xml_file( app, config_elems, shed_tool_conf, tool_path ) def update_repository( repo, ctx_rev=None ): """ Update the cloned repository to changeset_revision. It is critical that the installed repository is updated to the desired Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. You are receiving this because you have the service enabled, addressing the recipient of this email.