1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/857a60e69c7a/ changeset: 857a60e69c7a user: greg date: 2013-01-09 15:20:58 summary: Fix for correctly positioning tool shed repository tools in the proper tool panel location when the repository is being installed or reinstalled. affected #: 1 file diff -r be29d1334c08ec3e32290feab9a6da7bda9862ec -r 857a60e69c7aee92f67f37311a40a825b40a6481 lib/galaxy/util/shed_util.py --- a/lib/galaxy/util/shed_util.py +++ b/lib/galaxy/util/shed_util.py @@ -184,17 +184,17 @@ instance and when uninstalled repositories are being reinstalled. """ message = '' - # The following list will be maintained within this method to contain all created or updated tool shed repositories, including repository - # dependencies that may not be installed. + # The following list will be maintained within this method to contain all created or updated tool shed repositories, including repository dependencies + # that may not be installed. all_created_or_updated_tool_shed_repositories = [] - # There will be a one-to-one mapping between items in created_or_updated_tool_shed_repositories and tool_panel_section_keys. The following - # list will filter out repository dependencies that are not to be installed. + # There will be a one-to-one mapping between items in 3 lists: created_or_updated_tool_shed_repositories, tool_panel_section_keys and filtered_repo_info_dicts. + # The 3 lists will filter out repository dependencies that are not to be installed. created_or_updated_tool_shed_repositories = [] tool_panel_section_keys = [] - # Repositories will be filtered (e.g., if already installed, etc), so filter the associated repo_info_dicts accordingly. + # Repositories will be filtered (e.g., if already installed, if elected to not be installed, etc), so filter the associated repo_info_dicts accordingly. filtered_repo_info_dicts = [] - # Discover all repository dependencies and retrieve information for installing them. Even if the user elected to not install repository dependencies, - # we have to make sure all repository dependency objects exist so that the appropriate repository dependency relationships can be built. + # Discover all repository dependencies and retrieve information for installing them. Even if the user elected to not install repository dependencies we have + # to make sure all repository dependency objects exist so that the appropriate repository dependency relationships can be built. all_repo_info_dicts = get_required_repo_info_dicts( tool_shed_url, repo_info_dicts ) if not all_repo_info_dicts: # No repository dependencies were discovered so process the received repositories. @@ -215,9 +215,12 @@ tool_panel_section=tool_panel_section, new_tool_panel_section=new_tool_panel_section ) if reinstalling or install_repository_dependencies: + # If the user elected to install repository dependencies, all items in the all_repo_info_dicts list will be processed. However, if + # repository dependencies are not to be installed, only those items contained in the received repo_info_dicts list will be processed. if is_in_repo_info_dicts( repo_info_dict, repo_info_dicts ) or install_repository_dependencies: if installed_tool_shed_repository.status in [ trans.model.ToolShedRepository.installation_status.ERROR, trans.model.ToolShedRepository.installation_status.UNINSTALLED ]: + # The current tool shed repository is not currently installed, so we can update it's record in the database. can_update = True name = installed_tool_shed_repository.name description = installed_tool_shed_repository.description @@ -225,13 +228,19 @@ metadata_dict = installed_tool_shed_repository.metadata dist_to_shed = installed_tool_shed_repository.dist_to_shed else: - # There is a repository already installed which is a dependency of the repository being reinstalled. + # The tool shed repository currently being processed is already installed or is in the process of being installed, so it's record + # in the database cannot be updated. can_update = False else: + # This block will be reached only if reinstalling is True, install_repository_dependencies is False and is_in_repo_info_dicts is False. + # The tool shed repository currently being processed must be a repository dependency that the user elected to not install, so it's + # record in the database cannot be updated. can_update = False else: + # This block will be reached only if reinstalling is False and install_repository_dependencies is False. This implies that the tool shed + # repository currently being processed has already been installed. if len( all_repo_info_dicts ) == 1: - # An attempt is being made to install a tool shed repository into a Galaxy instance when the same repository was previously installed. + # If only a single repository is being installed, return an informative message to the user. message += "Revision <b>%s</b> of tool shed repository <b>%s</b> owned by <b>%s</b> " % ( changeset_revision, name, repository_owner ) if installed_changeset_revision != changeset_revision: message += "was previously installed using changeset revision <b>%s</b>. " % installed_changeset_revision @@ -247,26 +256,24 @@ created_or_updated_tool_shed_repositories.append( installed_tool_shed_repository ) tool_panel_section_keys.append( tool_panel_section_key ) return created_or_updated_tool_shed_repositories, tool_panel_section_keys, all_repo_info_dicts, filtered_repo_info_dicts, message - elif is_in_repo_info_dicts( repo_info_dict, repo_info_dicts ): - can_update = True else: + # We're in the process of installing multiple tool shed repositories into Galaxy. Since the repository currently being processed + # has already been installed, skip it and process the next repository in the list. can_update = False else: - # A tool shed repository is being installed into a Galaxy instance for the first time. We may have the case where a repository - # is being reinstalled where because the repository being newly installed here may be a dependency of the repository being reinstalled. + # A tool shed repository is being installed into a Galaxy instance for the first time, or we're attempting to install it or reinstall it resulted + # in an error. In the latter case, the repository record in the database has no metadata and it's status has been set to 'New'. In either case, + # the repository's database record may be updated. can_update = True installed_changeset_revision = changeset_revision metadata_dict = {} dist_to_shed = False if can_update: + # The database record for the tool shed repository currently being processed can be updated. if reinstalling or install_repository_dependencies: # Get the repository metadata to see where it was previously located in the tool panel. - installed_tool_shed_repository = suc.get_repository_for_dependency_relationship( app=trans.app, - tool_shed=tool_shed_url, - name=name, - owner=repository_owner, - changeset_revision=changeset_revision ) if installed_tool_shed_repository: + # The tool shed repository status is one of 'New', 'Uninstalled', or 'Error'. tool_section, new_tool_panel_section, tool_panel_section_key = \ handle_tool_panel_selection( trans=trans, metadata=installed_tool_shed_repository.metadata, @@ -274,6 +281,8 @@ tool_panel_section=tool_panel_section, new_tool_panel_section=new_tool_panel_section ) else: + # We're installing a new tool shed repository that does not yet have a database record. This repository is a repository dependency + # of a different repository being installed. if new_tool_panel_section: section_id = new_tool_panel_section.lower().replace( ' ', '_' ) tool_panel_section_key = 'section_%s' % str( section_id ) @@ -282,6 +291,7 @@ else: tool_panel_section_key = None else: + # We're installing a new tool shed repository that does not yet have a database record. if new_tool_panel_section: section_id = new_tool_panel_section.lower().replace( ' ', '_' ) tool_panel_section_key = 'section_%s' % str( section_id ) @@ -300,9 +310,11 @@ current_changeset_revision=changeset_revision, owner=repository_owner, dist_to_shed=False ) + # Add the processed tool shed repository to the list of all processed repositories maintained within this method. all_created_or_updated_tool_shed_repositories.append( tool_shed_repository ) - # Only append the tool_shed_repository to the list of created_or_updated_tool_shed_repositories if it is supposed to be installed. + # Only append the tool shed repository to the list of created_or_updated_tool_shed_repositories if it is supposed to be installed. if install_repository_dependencies or is_in_repo_info_dicts( repo_info_dict, repo_info_dicts ): + # Keep the one-to-one mapping between items in 3 lists. created_or_updated_tool_shed_repositories.append( tool_shed_repository ) tool_panel_section_keys.append( tool_panel_section_key ) filtered_repo_info_dicts.append( encoding_util.tool_shed_encode( repo_info_dict ) ) Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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