1 new commit in galaxy-central:
https://bitbucket.org/galaxy/galaxy-central/changeset/34b8a00ea301/ changeset: 34b8a00ea301 user: greg date: 2012-12-20 16:44:45 summary: Fixes for handling tool dependencies and missing tool dependencies for installed tool shed repositories and tose being installed. affected #: 3 files
diff -r 8c3ad449b21d996f9f0a877daf3f76dc29f3b39d -r 34b8a00ea3016fd09fd069bd48fbc5f52877ebf7 lib/galaxy/util/shed_util_common.py --- a/lib/galaxy/util/shed_util_common.py +++ b/lib/galaxy/util/shed_util_common.py @@ -1749,14 +1749,31 @@ relative_install_dir = None shed_config_dict = repository.get_shed_config_dict( app ) if not shed_config_dict: - #just pick a semi-random shed config + # Just pick a semi-random shed config. for shed_config_dict in app.toolbox.shed_tool_confs: - if ( repository.dist_to_shed and shed_config_dict['config_filename'] == app.config.migrated_tools_config ) or ( not repository.dist_to_shed and shed_config_dict['config_filename'] != app.config.migrated_tools_config ): + if ( repository.dist_to_shed and shed_config_dict[ 'config_filename' ] == app.config.migrated_tools_config ) \ + or ( not repository.dist_to_shed and shed_config_dict[ 'config_filename' ] != app.config.migrated_tools_config ): break shed_tool_conf = shed_config_dict[ 'config_filename' ] tool_path = shed_config_dict[ 'tool_path' ] relative_install_dir = partial_install_dir return shed_tool_conf, tool_path, relative_install_dir +def get_tool_path_by_shed_tool_conf_filename( trans, shed_tool_conf ): + """ + Return the tool_path config setting for the received shed_tool_conf file by searching the tool box's in-memory list of shed_tool_confs for the + dictionary whose config_filename key has a value matching the received shed_tool_conf. + """ + for shed_tool_conf_dict in trans.app.toolbox.shed_tool_confs: + config_filename = shed_tool_conf_dict[ 'config_filename' ] + if config_filename == shed_tool_conf: + tool_path = shed_tool_conf_dict[ 'tool_path' ] + break + else: + file_name = strip_path( config_filename ) + if file_name == shed_tool_conf: + tool_path = shed_tool_conf_dict[ 'tool_path' ] + break + return tool_path def get_tool_shed_repository_by_shed_name_owner_changeset_revision( app, tool_shed, name, owner, changeset_revision ): # This method is used only in Galaxy, not the tool shed. sa_session = app.model.context.current
diff -r 8c3ad449b21d996f9f0a877daf3f76dc29f3b39d -r 34b8a00ea3016fd09fd069bd48fbc5f52877ebf7 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 @@ -898,7 +898,7 @@ 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 ) + 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 ) @@ -1126,7 +1126,7 @@ if ( not includes_tools and not includes_repository_dependencies ) or \ ( ( includes_tools or includes_repository_dependencies ) and kwd.get( 'select_tool_panel_section_button', False ) ): install_repository_dependencies = CheckboxField.is_checked( install_repository_dependencies ) - if includes_tools: + if includes_tool_dependencies: install_tool_dependencies = CheckboxField.is_checked( install_tool_dependencies ) shed_tool_conf = kwd[ 'shed_tool_conf' ] else: @@ -1134,17 +1134,7 @@ # If installing a repository that includes no tools, get the relative tool_path from the file to which the migrated_tools_config # setting points. shed_tool_conf = trans.app.config.migrated_tools_config - # Get the tool path by searching the list of shed_tool_confs for the dictionary that contains the information about shed_tool_conf. - for shed_tool_conf_dict in trans.app.toolbox.shed_tool_confs: - config_filename = shed_tool_conf_dict[ 'config_filename' ] - if config_filename == shed_tool_conf: - tool_path = shed_tool_conf_dict[ 'tool_path' ] - break - else: - file_name = suc.strip_path( config_filename ) - if file_name == shed_tool_conf: - tool_path = shed_tool_conf_dict[ 'tool_path' ] - break + tool_path = suc.get_tool_path_by_shed_tool_conf_filename( trans, shed_tool_conf ) created_or_updated_tool_shed_repositories, repo_info_dicts, filtered_repo_info_dicts, message = \ shed_util.create_repository_dependency_objects( trans, tool_path, tool_shed_url, repo_info_dicts, reinstalling=False ) if message and len( repo_info_dicts ) == 1: @@ -1232,6 +1222,8 @@ raw_text = response.read() response.close() readme_files_dict = from_json_string( raw_text ) + # Since we are installing a new repository, no tool dependencies will be considered "missing". Most of the repository contents + # are set to None since we don't yet know what they are. containers_dict = suc.build_repository_containers_for_galaxy( trans=trans, toolshed_base_url=tool_shed_url, repository_name=name, @@ -1247,7 +1239,13 @@ valid_tools=None, workflows=None ) else: - containers_dict = dict( readme_files_dict=None, repository_dependencies=None, tool_dependencies=None ) + containers_dict = dict( datatypes=None, + invalid_tools=None, + readme_files_dict=None, + repository_dependencies=None, + tool_dependencies=None, + valid_tools=None, + workflows=None ) # Handle tool dependencies chack box. if trans.app.config.tool_dependency_dir is None: if includes_tool_dependencies: @@ -1260,6 +1258,17 @@ install_tool_dependencies_check_box = CheckboxField( 'install_tool_dependencies', checked=install_tool_dependencies_check_box_checked ) # Handle repository dependencies check box. install_repository_dependencies_check_box = CheckboxField( 'install_repository_dependencies', checked=True ) + log.debug("PPPPP In prepare_for_install, containers_dict: %s" % str( containers_dict )) + """ + PPPPP In prepare_for_install, + containers_dict: + {'repository_dependencies': None, + 'missing_tool_dependencies': <galaxy.webapps.community.util.container_util.Folder object at 0x108a56f0>, + 'readme_files': None, + 'tool_dependencies': None} + FAIL + + """ return trans.fill_template( '/admin/tool_shed_repository/select_tool_panel_section.mako', encoded_repo_info_dicts=encoded_repo_info_dicts, includes_tools=includes_tools, @@ -1456,6 +1465,7 @@ includes_repository_dependencies = True else: includes_repository_dependencies = False + includes_tool_dependencies = tool_shed_repository.includes_tool_dependencies repo_info_dict = suc.create_repo_info_dict( trans=trans, repository_clone_url=repository_clone_url, changeset_revision=tool_shed_repository.installed_changeset_revision, @@ -1527,6 +1537,10 @@ all_tool_dependencies ) valid_tools = metadata.get( 'tools', None ) workflows = metadata.get( 'workflows', None ) + # All tool dependencies will be considered missing since we are reinstalling the repository. + for td in tool_dependencies: + missing_tool_dependencies.append( td ) + tool_dependencies = None containers_dict = suc.build_repository_containers_for_galaxy( trans=trans, toolshed_base_url=tool_shed_url, repository_name=tool_shed_repository.name, @@ -1538,16 +1552,22 @@ missing_tool_dependencies=missing_tool_dependencies, readme_files_dict=readme_files_dict, repository_dependencies=repository_dependencies, - tool_dependencies=tool_dependencies, + tool_dependencies=missing_tool_dependencies, valid_tools=valid_tools, workflows=workflows ) else: - containers_dict = dict( readme_files_dict=None, repository_dependencies=None, tool_dependencies=None ) + containers_dict = dict( datatypes=None, + invalid_tools=None, + readme_files_dict=None, + repository_dependencies=None, + tool_dependencies=None, + valid_tools=None, + workflows=None ) # Handle repository dependencies check box. install_repository_dependencies_check_box = CheckboxField( 'install_repository_dependencies', checked=True ) # Handle tool dependencies check box. if trans.app.config.tool_dependency_dir is None: - if tool_shed_repository.includes_tool_dependencies: + if includes_tool_dependencies: message += "Tool dependencies defined in this repository can be automatically installed if you set the value of your <b>tool_dependency_dir</b> " message += "setting in your Galaxy config file (universe_wsgi.ini) and restart your Galaxy server before installing the repository. " status = "warning"
diff -r 8c3ad449b21d996f9f0a877daf3f76dc29f3b39d -r 34b8a00ea3016fd09fd069bd48fbc5f52877ebf7 templates/webapps/community/repository/common.mako --- a/templates/webapps/community/repository/common.mako +++ b/templates/webapps/community/repository/common.mako @@ -509,7 +509,7 @@ </div></div> %endif - %if repository_dependencies_root_folder or tool_dependencies_root_folder: + %if repository_dependencies_root_folder or tool_dependencies_root_folder or missing_tool_dependencies_root_folder: <div class="toolForm"><div class="toolFormTitle">Dependencies of this repository</div><div class="toolFormBody">
Repository URL: https://bitbucket.org/galaxy/galaxy-central/
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