1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/9e985bee2041/ Changeset: 9e985bee2041 User: greg Date: 2013-07-09 17:54:49 Summary: Fixes for repairing an installed tool shed repository. Affected #: 4 files diff -r 86efa5ac1fae6fb46e7af9804e036a7ab44b0e26 -r 9e985bee20419c0cdbf76fadbe2448400820cbb9 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 @@ -589,14 +589,6 @@ else: kwd[ 'message' ] = 'All selected tool shed repositories are already installed.' kwd[ 'status' ] = 'error' - elif operation == "repair": - # In this case, tsridslist is ordered. - repositories_for_repair = [] - for tsr_id in tsridslist: - repository = trans.sa_session.query( trans.model.ToolShedRepository ).get( trans.security.decode_id( tsr_id ) ) - repositories_for_repair.append( repository ) - ordered_repo_info_dicts = kwd.get( 'ordered_repo_info_dicts', [] ) - self.repair_tool_shed_repositories( trans, repositories_for_repair, ordered_repo_info_dicts ) return self.repository_installation_grid( trans, **kwd ) @web.expose @@ -1159,23 +1151,29 @@ status=status ) ) tool_shed_repository = suc.get_installed_tool_shed_repository( trans, repository_id ) if kwd.get( 'repair_repository_button', False ): - repair_dict = kwd.get( 'repair_dict', None ) + encoded_repair_dict = kwd.get( 'repair_dict', None ) + if encoded_repair_dict: + repair_dict = encoding_util.tool_shed_decode( encoded_repair_dict ) + else: + repair_dict = None if not repair_dict: repair_dict = repository_util.get_repair_dict( trans, tool_shed_repository ) - ordered_tsr_ids = repair_dict.get( 'ordered_tsr_ids', [] ) - ordered_repo_info_dicts = repair_dict.get( 'ordered_repo_info_dicts', [] ) - if ordered_tsr_ids and ordered_repo_info_dicts: - return trans.response.send_redirect( web.url_for( controller='admin_toolshed', - action='manage_repositories', - operation='repair', - ordered_tsr_ids=ordered_tsr_ids, - ordered_repo_info_dicts=ordered_repo_info_dicts ) ) + ordered_tsr_ids = repair_dict.get( 'ordered_tsr_ids', [] ) + ordered_repo_info_dicts = repair_dict.get( 'ordered_repo_info_dicts', [] ) + if ordered_tsr_ids and ordered_repo_info_dicts: + repositories_for_repair = [] + for tsr_id in ordered_tsr_ids: + repository = trans.sa_session.query( trans.model.ToolShedRepository ).get( trans.security.decode_id( tsr_id ) ) + repositories_for_repair.append( repository ) + return self.repair_tool_shed_repositories( trans, repositories_for_repair, ordered_repo_info_dicts ) tool_shed_repository = suc.get_installed_tool_shed_repository( trans, repository_id ) repair_dict = repository_util.get_repair_dict( trans, tool_shed_repository ) + encoded_repair_dict = encoding_util.tool_shed_encode( repair_dict ) ordered_tsr_ids = repair_dict.get( 'ordered_tsr_ids', [] ) ordered_repo_info_dicts = repair_dict.get( 'ordered_repo_info_dicts', [] ) return trans.fill_template( 'admin/tool_shed_repository/repair_repository.mako', repository=tool_shed_repository, + encoded_repair_dict=encoded_repair_dict, repair_dict=repair_dict, message=message, status=status ) diff -r 86efa5ac1fae6fb46e7af9804e036a7ab44b0e26 -r 9e985bee20419c0cdbf76fadbe2448400820cbb9 lib/tool_shed/galaxy_install/repository_util.py --- a/lib/tool_shed/galaxy_install/repository_util.py +++ b/lib/tool_shed/galaxy_install/repository_util.py @@ -110,9 +110,9 @@ installed_repositories.append( installed_repository ) for rd_val in rd_vals: try: - tool_shed, name, owner, changeset_revision, prior_installation_required = container_util.get_components_from_key( rd_key ) + tool_shed, name, owner, changeset_revision, prior_installation_required = rd_val except: - tool_shed, name, owner, changeset_revision = container_util.get_components_from_key( rd_val ) + tool_shed, name, owner, changeset_revision = rd_val installed_repository = suc.get_tool_shed_repository_by_shed_name_owner_changeset_revision( trans.app, tool_shed, name, owner, changeset_revision ) if installed_repository not in installed_repositories: installed_repositories.append( installed_repository ) @@ -182,6 +182,7 @@ # tsr_ids to ensure all repositories are repaired in the required order. tsr_ids = [] repo_info_dicts = [] + tool_panel_section_keys = [] for installed_repository in installed_repositories: tsr_ids.append( trans.security.encode_id( installed_repository.id ) ) repository_clone_url = suc.generate_clone_url_for_installed_repository( trans.app, installed_repository ) @@ -189,8 +190,36 @@ metadata = installed_repository.metadata if metadata: tool_dependencies = metadata.get( 'tool_dependencies', None ) + tool_panel_section_dict = metadata.get( 'tool_panel_section', None ) + if tool_panel_section_dict: + # The installed_repository must be in the uninstalled state. The structure of tool_panel_section_dict is: + # {<tool guid> : [{ 'id':<section id>, 'name':<section name>, 'version':<section version>, 'tool_config':<tool config file name> }]} + # Here is an example: + # {"localhost:9009/repos/test/filter/Filter1/1.1.0": + # [{"id": "filter_and_sort", "name": "Filter and Sort", "tool_config": "filtering.xml", "version": ""}]} + # Currently all tools contained within an installed tool shed repository must be loaded into the same section in the tool panel, so we can + # get the section id of the first guid in the tool_panel_section_dict. In the future, we'll have to handle different sections per guid. + guid = tool_panel_section_dict.keys()[ 0 ] + section_dicts = tool_panel_section_dict[ guid ] + section_dict = section_dicts[ 0 ] + tool_panel_section_id = section_dict[ 'id' ] + tool_panel_section_name = section_dict[ 'name' ] + if tool_panel_section_id: + tool_panel_section_key, tool_panel_section = tool_util.get_or_create_tool_section( trans, + tool_panel_section_id=tool_panel_section_id, + new_tool_panel_section=tool_panel_section_name ) + tool_panel_section_keys.append( tool_panel_section_key ) + else: + # The tools will be loaded outside of any sections in the tool panel. + tool_panel_section_keys.append( None ) + else: + # The installed_repository must be in the installed state, so we can skip determining if it has tools that are displayed in a tool panel section + # since no changes will be made to it. + tool_panel_section_keys.append( None ) else: tool_dependencies = None + # The tools will be loaded outside of any sections in the tool panel. + tool_panel_section_keys.append( None ) repo_info_dict = create_repo_info_dict( trans=trans, repository_clone_url=repository_clone_url, changeset_revision=installed_repository.changeset_revision, @@ -202,11 +231,11 @@ tool_dependencies=tool_dependencies, repository_dependencies=repository_dependencies ) repo_info_dicts.append( repo_info_dict ) - # We don't consider tool_panel_section_keys since the repository database records already exist. - ordered_tsr_ids, ordered_repo_info_dicts, ordered_tool_panel_section_keys = order_components_for_installation( trans, - tsr_ids, - repo_info_dicts, - tool_panel_section_keys=None ) + ordered_tsr_ids, ordered_repo_info_dicts, ordered_tool_panel_section_keys = \ + order_components_for_installation( trans, + tsr_ids, + repo_info_dicts, + tool_panel_section_keys=tool_panel_section_keys ) repair_dict[ 'ordered_tsr_ids' ] = ordered_tsr_ids repair_dict[ 'ordered_repo_info_dicts' ] = ordered_repo_info_dicts repair_dict[ 'ordered_tool_panel_section_keys' ] = ordered_tool_panel_section_keys @@ -245,7 +274,7 @@ repository_dependencies=None ) return repo_info_dict, includes_tools, includes_tool_dependencies, includes_tools_for_display_in_tool_panel, has_repository_dependencies -def get_repository_components_for_installation( encoded_tsr_id, encoded_tsr_ids, repo_info_dicts, tool_panel_section_keys=None ): +def get_repository_components_for_installation( encoded_tsr_id, encoded_tsr_ids, repo_info_dicts, tool_panel_section_keys ): """ The received encoded_tsr_ids, repo_info_dicts, and tool_panel_section_keys are 3 lists that contain associated elements at each location in the list. This method will return the elements from repo_info_dicts and tool_panel_section_keys associated with the received encoded_tsr_id @@ -254,10 +283,7 @@ for index, tsr_id in enumerate( encoded_tsr_ids ): if tsr_id == encoded_tsr_id: repo_info_dict = repo_info_dicts[ index ] - if tool_panel_section_keys: - tool_panel_section_key = tool_panel_section_keys[ index ] - else: - tool_panel_section_key = None + tool_panel_section_key = tool_panel_section_keys[ index ] return repo_info_dict, tool_panel_section_key return None, None @@ -684,7 +710,7 @@ lock.release() return new_containers_dict -def order_components_for_installation( trans, tsr_ids, repo_info_dicts, tool_panel_section_keys=None ): +def order_components_for_installation( trans, tsr_ids, repo_info_dicts, tool_panel_section_keys ): """ Some repositories may have repository dependencies that are required to be installed before the dependent repository. This method will inspect the list of repositories about to be installed and make sure to order them appropriately. For each repository about to be installed, if required repositories are not @@ -713,16 +739,14 @@ tool_panel_section_keys=tool_panel_section_keys ) ordered_tsr_ids.append( prior_install_required_id ) ordered_repo_info_dicts.append( prior_repo_info_dict ) - if tool_panel_section_keys: - ordered_tool_panel_section_keys.append( prior_tool_panel_section_key ) + ordered_tool_panel_section_keys.append( prior_tool_panel_section_key ) repo_info_dict, tool_panel_section_key = get_repository_components_for_installation( tsr_id, tsr_ids, repo_info_dicts, tool_panel_section_keys=tool_panel_section_keys ) ordered_tsr_ids.append( tsr_id ) ordered_repo_info_dicts.append( repo_info_dict ) - if tool_panel_section_keys: - ordered_tool_panel_section_keys.append( tool_panel_section_key ) + ordered_tool_panel_section_keys.append( tool_panel_section_key ) return ordered_tsr_ids, ordered_repo_info_dicts, ordered_tool_panel_section_keys def populate_containers_dict_for_new_install( trans, tool_shed_url, tool_path, readme_files_dict, installed_repository_dependencies, missing_repository_dependencies, @@ -785,11 +809,11 @@ shed_tool_conf, tool_path, relative_install_dir = suc.get_tool_panel_config_tool_path_install_dir( trans.app, repository ) # Reset the repository attributes to the New state for installation. if metadata: - tool_panel_section_key = tool_util.handle_tool_panel_selection( trans, - metadata, - no_changes_checked=True, - tool_panel_section=None, - new_tool_panel_section=None ) + tool_section, new_tool_panel_section, tool_panel_section_key = tool_util.handle_tool_panel_selection( trans, + metadata, + no_changes_checked=True, + tool_panel_section=None, + new_tool_panel_section=None ) else: # The tools will be loaded outside of any sections in the tool panel. tool_panel_section_key = None diff -r 86efa5ac1fae6fb46e7af9804e036a7ab44b0e26 -r 9e985bee20419c0cdbf76fadbe2448400820cbb9 lib/tool_shed/util/tool_util.py --- a/lib/tool_shed/util/tool_util.py +++ b/lib/tool_shed/util/tool_util.py @@ -639,8 +639,7 @@ if 'tools' in metadata: # This forces everything to be loaded into the same section (or no section) in the tool panel. if no_changes_checked: - # Make sure the no_changes check box overrides the new_tool_panel_section if the user checked the check box and entered something - # into the field. + # Make sure the no_changes check box overrides the new_tool_panel_section if the user checked the check box and entered something into the field. new_tool_panel_section = None if 'tool_panel_section' in metadata: tool_panel_dict = metadata[ 'tool_panel_section' ] @@ -649,7 +648,7 @@ else: tool_panel_dict = generate_tool_panel_dict_for_new_install( metadata[ 'tools' ] ) if tool_panel_dict: - #tool_panel_dict is empty when tools exist but are not installed into a tool panel + # The tool_panel_dict is empty when tools exist but are not installed into a tool panel section. tool_section_dicts = tool_panel_dict[ tool_panel_dict.keys()[ 0 ] ] tool_section_dict = tool_section_dicts[ 0 ] original_section_id = tool_section_dict[ 'id' ] diff -r 86efa5ac1fae6fb46e7af9804e036a7ab44b0e26 -r 9e985bee20419c0cdbf76fadbe2448400820cbb9 templates/admin/tool_shed_repository/repair_repository.mako --- a/templates/admin/tool_shed_repository/repair_repository.mako +++ b/templates/admin/tool_shed_repository/repair_repository.mako @@ -25,7 +25,7 @@ <div class="toolForm"><div class="toolFormTitle">Repair tool shed repository '${repository.name}'</div><br/><br/> - <form name="repair_repository" id="repair_repository" action="${h.url_for( controller='admin_toolshed', action='repair_repository', id=trans.security.encode_id( repository.id ), repair_dict=repair_dict )}" method="post" > + <form name="repair_repository" id="repair_repository" action="${h.url_for( controller='admin_toolshed', action='repair_repository', id=trans.security.encode_id( repository.id ), repair_dict=encoded_repair_dict )}" method="post" ><% ordered_repo_info_dicts = repair_dict.get( 'ordered_repo_info_dicts', [] ) %><table class="grid"><tr><th bgcolor="#D8D8D8">Name</th><th bgcolor="#D8D8D8">Owner</th><th bgcolor="#D8D8D8">Changeset revision</th></tr> Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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