1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/a29d54619813/ Changeset: a29d54619813 User: greg Date: 2013-12-05 22:49:11 Summary: Send only a tool panel section id if selecting and existing section or a new tool panel section label when installing repositories that contain tools for display in the Galaxy tool panel from the tool shed. ToolSection objects are not passed at all, so the parameter names have been corrected for better identification. Affected #: 29 files diff -r 6be4eb823a7ea30f35411251900487ee92734b7e -r a29d54619813d5da992b897557162a360b8d610c lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py --- a/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py +++ b/lib/galaxy/webapps/galaxy/api/tool_shed_repositories.py @@ -264,7 +264,7 @@ no_tool_dependency_dir_message = "Tool dependencies can be automatically installed only if you set the value of your 'tool_dependency_dir' " no_tool_dependency_dir_message += "setting in your Galaxy configuration file (universe_wsgi.ini) and restart your Galaxy server." raise HTTPBadRequest( detail=no_tool_dependency_dir_message ) - new_tool_panel_section = payload.get( 'new_tool_panel_section_label', '' ) + new_tool_panel_section_label = payload.get( 'new_tool_panel_section_label', '' ) shed_tool_conf = payload.get( 'shed_tool_conf', None ) if shed_tool_conf: # Get the tool_path setting. @@ -282,15 +282,20 @@ raise HTTPBadRequest( detail="Missing required parameter 'shed_tool_conf'." ) tool_panel_section_id = payload.get( 'tool_panel_section_id', '' ) if tool_panel_section_id not in [ None, '' ]: - tool_panel_section = trans.app.toolbox.tool_panel[ tool_panel_section_id ] + if tool_panel_section_id not in trans.app.toolbox.tool_panel: + fixed_tool_panel_section_id = 'section_%s' % tool_panel_section_id + if fixed_tool_panel_section_id in trans.app.toolbox.tool_panel: + tool_panel_section_id = fixed_tool_panel_section_id + else: + tool_panel_section_id = '' else: - tool_panel_section = '' + tool_panel_section_id = '' # Build the dictionary of information necessary for creating tool_shed_repository database records for each repository being installed. installation_dict = dict( install_repository_dependencies=install_repository_dependencies, - new_tool_panel_section=new_tool_panel_section, + new_tool_panel_section_label=new_tool_panel_section_label, no_changes_checked=False, repo_info_dicts=repo_info_dicts, - tool_panel_section=tool_panel_section, + tool_panel_section_id=tool_panel_section_id, tool_path=tool_path, tool_shed_url=tool_shed_url ) # Create the tool_shed_repository database records and gather additional information for repository installation. @@ -307,17 +312,18 @@ install_repository_dependencies=install_repository_dependencies, install_tool_dependencies=install_tool_dependencies, message='', - new_tool_panel_section=new_tool_panel_section, + new_tool_panel_section_label=new_tool_panel_section_label, shed_tool_conf=shed_tool_conf, status='done', - tool_panel_section=tool_panel_section, + tool_panel_section_id=tool_panel_section_id, tool_panel_section_keys=tool_panel_section_keys, tool_path=tool_path, tool_shed_url=tool_shed_url ) # Prepare the repositories for installation. Even though this method receives a single combination of tool_shed_url, name, owner and # changeset_revision, there may be multiple repositories for installation at this point because repository dependencies may have added # additional repositories for installation along with the single specified repository. - encoded_kwd, query, tool_shed_repositories, encoded_repository_ids = repository_util.initiate_repository_installation( trans, installation_dict ) + encoded_kwd, query, tool_shed_repositories, encoded_repository_ids = \ + repository_util.initiate_repository_installation( trans, installation_dict ) # Some repositories may have repository dependencies that are required to be installed before the dependent repository, so we'll # order the list of tsr_ids to ensure all repositories install in the required order. tsr_ids = [ trans.security.encode_id( tool_shed_repository.id ) for tool_shed_repository in tool_shed_repositories ] diff -r 6be4eb823a7ea30f35411251900487ee92734b7e -r a29d54619813d5da992b897557162a360b8d610c 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 @@ -568,7 +568,10 @@ # Some repositories may have repository dependencies that are required to be installed before the dependent repository, so we'll # order the list of tsr_ids to ensure all repositories install in the required order. ordered_tsr_ids, ordered_repo_info_dicts, ordered_tool_panel_section_keys = \ - repository_util.order_components_for_installation( trans, tsr_ids, repo_info_dicts, tool_panel_section_keys=tool_panel_section_keys ) + repository_util.order_components_for_installation( trans, + tsr_ids, + repo_info_dicts, + tool_panel_section_keys=tool_panel_section_keys ) for tsr_id in ordered_tsr_ids: repository = trans.install_model.context.query( trans.install_model.ToolShedRepository ).get( trans.security.decode_id( tsr_id ) ) if repository.status in [ trans.install_model.ToolShedRepository.installation_status.NEW, @@ -816,8 +819,8 @@ has_repository_dependencies = util.string_as_bool( kwd.get( 'has_repository_dependencies', False ) ) install_repository_dependencies = kwd.get( 'install_repository_dependencies', '' ) # Every repository will be installed into the same tool panel section or all will be installed outside of any sections. - new_tool_panel_section = kwd.get( 'new_tool_panel_section', '' ) - tool_panel_section = kwd.get( 'tool_panel_section', '' ) + new_tool_panel_section_label = kwd.get( 'new_tool_panel_section_label', '' ) + tool_panel_section_id = kwd.get( 'tool_panel_section_id', '' ) tool_panel_section_keys = [] # One or more repositories may include tools, but not necessarily all of them. includes_tools = util.string_as_bool( kwd.get( 'includes_tools', False ) ) @@ -859,10 +862,10 @@ install_tool_dependencies = False tool_path = suc.get_tool_path_by_shed_tool_conf_filename( trans, shed_tool_conf ) installation_dict = dict( install_repository_dependencies=install_repository_dependencies, - new_tool_panel_section=new_tool_panel_section, + new_tool_panel_section_label=new_tool_panel_section_label, no_changes_checked=False, repo_info_dicts=repo_info_dicts, - tool_panel_section=tool_panel_section, + tool_panel_section_id=tool_panel_section_id, tool_path=tool_path, tool_shed_url=tool_shed_url ) created_or_updated_tool_shed_repositories, tool_panel_section_keys, repo_info_dicts, filtered_repo_info_dicts = \ @@ -877,10 +880,10 @@ install_repository_dependencies=install_repository_dependencies, install_tool_dependencies=install_tool_dependencies, message=message, - new_tool_panel_section=new_tool_panel_section, + new_tool_panel_section_label=new_tool_panel_section_label, shed_tool_conf=shed_tool_conf, status=status, - tool_panel_section=tool_panel_section, + tool_panel_section_id=tool_panel_section_id, tool_panel_section_keys=tool_panel_section_keys, tool_path=tool_path, tool_shed_url=tool_shed_url ) @@ -993,7 +996,7 @@ install_tool_dependencies_check_box=install_tool_dependencies_check_box, has_repository_dependencies=has_repository_dependencies, install_repository_dependencies_check_box=install_repository_dependencies_check_box, - new_tool_panel_section=new_tool_panel_section, + new_tool_panel_section_label=new_tool_panel_section_label, containers_dict=containers_dict, shed_tool_conf=shed_tool_conf, shed_tool_conf_select_field=shed_tool_conf_select_field, @@ -1012,7 +1015,7 @@ install_tool_dependencies_check_box=install_tool_dependencies_check_box, has_repository_dependencies=has_repository_dependencies, install_repository_dependencies_check_box=install_repository_dependencies_check_box, - new_tool_panel_section=new_tool_panel_section, + new_tool_panel_section_label=new_tool_panel_section_label, containers_dict=containers_dict, shed_tool_conf=shed_tool_conf, shed_tool_conf_select_field=shed_tool_conf_select_field, @@ -1024,7 +1027,10 @@ @web.expose @web.require_admin def reinstall_repository( self, trans, **kwd ): - """Reinstall a tool shed repository that has been previously uninstalled, making sure to handle all repository and tool dependencies of the repository.""" + """ + Reinstall a tool shed repository that has been previously uninstalled, making sure to handle all repository + and tool dependencies of the repository. + """ message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) repository_id = kwd[ 'id' ] @@ -1040,8 +1046,8 @@ relative_install_dir = os.path.join( clone_dir, tool_shed_repository.name ) tool_shed_url = suc.get_url_from_tool_shed( trans.app, tool_shed_repository.tool_shed ) tool_section = None - tool_panel_section = kwd.get( 'tool_panel_section', '' ) - new_tool_panel_section = kwd.get( 'new_tool_panel_section', '' ) + tool_panel_section_id = kwd.get( 'tool_panel_section_id', '' ) + new_tool_panel_section_label = kwd.get( 'new_tool_panel_section_label', '' ) tool_panel_section_key = None tool_panel_section_keys = [] metadata = tool_shed_repository.metadata @@ -1049,11 +1055,15 @@ includes_tool_dependencies = tool_shed_repository.includes_tool_dependencies if tool_shed_repository.includes_tools_for_display_in_tool_panel: # Handle the selected tool panel location for loading tools included in the tool shed repository. - tool_section, new_tool_panel_section, tool_panel_section_key = tool_util.handle_tool_panel_selection( trans=trans, - metadata=metadata, - no_changes_checked=no_changes_checked, - tool_panel_section=tool_panel_section, - new_tool_panel_section=new_tool_panel_section ) + tool_section, tool_panel_section_key = \ + tool_util.handle_tool_panel_selection( trans=trans, + metadata=metadata, + no_changes_checked=no_changes_checked, + tool_panel_section_id=tool_panel_section_id, + new_tool_panel_section_label=new_tool_panel_section_label ) + if tool_section is not None: + # Just in case the tool_section.id differs from tool_panel_section_id, which it shouldn't... + tool_panel_section_id = str( tool_section.id ) if tool_shed_repository.status == trans.install_model.ToolShedRepository.installation_status.UNINSTALLED: # The repository's status must be updated from 'Uninstalled' to 'New' when initiating reinstall so the repository_installation_updater will function. tool_shed_repository = suc.create_or_update_tool_shed_repository( trans.app, @@ -1080,7 +1090,8 @@ else: # Entering this else block occurs only if the tool_shed_repository does not include any valid tools. if install_repository_dependencies: - repository_dependencies = repository_dependency_util.get_repository_dependencies_for_installed_tool_shed_repository( trans, tool_shed_repository ) + repository_dependencies = \ + repository_dependency_util.get_repository_dependencies_for_installed_tool_shed_repository( trans, tool_shed_repository ) else: repository_dependencies = None if metadata: @@ -1107,8 +1118,7 @@ repo_info_dicts=repo_info_dicts, install_repository_dependencies=install_repository_dependencies, no_changes_checked=no_changes_checked, - tool_panel_section=tool_panel_section, - new_tool_panel_section=new_tool_panel_section ) + tool_panel_section_id=tool_panel_section_id ) # Default the selected tool panel location for loading tools included in each newly installed required tool shed repository to the location # selected for the repository selected for reinstallation. for index, tps_key in enumerate( tool_panel_section_keys ): @@ -1121,10 +1131,10 @@ install_tool_dependencies=install_tool_dependencies, repo_info_dicts=filtered_repo_info_dicts, message=message, - new_tool_panel_section=new_tool_panel_section, + new_tool_panel_section_label=new_tool_panel_section_label, shed_tool_conf=shed_tool_conf, status=status, - tool_panel_section=tool_panel_section, + tool_panel_section_id=tool_panel_section_id, tool_path=tool_path, tool_panel_section_keys=tool_panel_section_keys, tool_shed_repository_ids=encoded_repository_ids, diff -r 6be4eb823a7ea30f35411251900487ee92734b7e -r a29d54619813d5da992b897557162a360b8d610c 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 @@ -244,9 +244,10 @@ 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_key, tool_panel_section = \ + tool_util.get_or_create_tool_section( trans, + tool_panel_section_id=tool_panel_section_id, + new_tool_panel_section_label=tool_panel_section_name ) else: tool_dependencies = None repo_info_dict = create_repo_info_dict( trans=trans, @@ -432,10 +433,10 @@ def handle_tool_shed_repositories( trans, installation_dict, using_api=False ): # The following installation_dict entries are all required. install_repository_dependencies = installation_dict[ 'install_repository_dependencies' ] - new_tool_panel_section = installation_dict[ 'new_tool_panel_section' ] + new_tool_panel_section_label = installation_dict[ 'new_tool_panel_section_label' ] no_changes_checked = installation_dict[ 'no_changes_checked' ] repo_info_dicts = installation_dict[ 'repo_info_dicts' ] - tool_panel_section = installation_dict[ 'tool_panel_section' ] + tool_panel_section_id = installation_dict[ 'tool_panel_section_id' ] tool_path = installation_dict[ 'tool_path' ] tool_shed_url = installation_dict[ 'tool_shed_url' ] created_or_updated_tool_shed_repositories, tool_panel_section_keys, repo_info_dicts, filtered_repo_info_dicts = \ @@ -445,8 +446,8 @@ repo_info_dicts=repo_info_dicts, install_repository_dependencies=install_repository_dependencies, no_changes_checked=no_changes_checked, - tool_panel_section=tool_panel_section, - new_tool_panel_section=new_tool_panel_section ) + tool_panel_section_id=tool_panel_section_id, + new_tool_panel_section_label=new_tool_panel_section_label ) return created_or_updated_tool_shed_repositories, tool_panel_section_keys, repo_info_dicts, filtered_repo_info_dicts def initiate_repository_installation( trans, installation_dict ): @@ -460,18 +461,19 @@ install_repository_dependencies = installation_dict[ 'install_repository_dependencies' ] install_tool_dependencies = installation_dict[ 'install_tool_dependencies' ] message = installation_dict[ 'message' ] - new_tool_panel_section = installation_dict[ 'new_tool_panel_section' ] + new_tool_panel_section_label = installation_dict[ 'new_tool_panel_section_label' ] shed_tool_conf = installation_dict[ 'shed_tool_conf' ] status = installation_dict[ 'status' ] - tool_panel_section = installation_dict[ 'tool_panel_section' ] + tool_panel_section_id = installation_dict[ 'tool_panel_section_id' ] tool_panel_section_keys = installation_dict[ 'tool_panel_section_keys' ] tool_path = installation_dict[ 'tool_path' ] tool_shed_url = installation_dict[ 'tool_shed_url' ] # Handle contained tools. - if includes_tools_for_display_in_tool_panel and ( new_tool_panel_section or tool_panel_section ): - tool_panel_section_key, tool_section = tool_util.handle_tool_panel_section( trans, - tool_panel_section=tool_panel_section, - new_tool_panel_section=new_tool_panel_section ) + if includes_tools_for_display_in_tool_panel and ( new_tool_panel_section_label or tool_panel_section_id ): + tool_panel_section_key, tool_section = \ + tool_util.handle_tool_panel_section( trans, + tool_panel_section_id=tool_panel_section_id, + new_tool_panel_section_label=new_tool_panel_section_label ) else: tool_panel_section_key = None tool_section = None @@ -667,16 +669,19 @@ 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 - contained in the list of repositories about to be installed, then they are not considered. Repository dependency definitions that contain circular dependencies - should not result in an infinite loop, but obviously prior installation will not be handled for one or more of the repositories that require prior installation. + 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 contained in the list of repositories about + to be installed, then they are not considered. Repository dependency definitions that contain circular dependencies + should not result in an infinite loop, but obviously prior installation will not be handled for one or more of the + repositories that require prior installation. """ ordered_tsr_ids = [] ordered_repo_info_dicts = [] ordered_tool_panel_section_keys = [] - # Create a dictionary whose keys are the received tsr_ids and whose values are a list of tsr_ids, each of which is contained in the received list of tsr_ids - # and whose associated repository must be installed prior to the repository associated with the tsr_id key. + # Create a dictionary whose keys are the received tsr_ids and whose values are a list of tsr_ids, each of which is + # contained in the received list of tsr_ids and whose associated repository must be installed prior to the repository + # associated with the tsr_id key. prior_install_required_dict = suc.get_prior_import_or_install_required_dict( trans, tsr_ids, repo_info_dicts ) processed_tsr_ids = [] while len( processed_tsr_ids ) != len( prior_install_required_dict.keys() ): @@ -688,17 +693,19 @@ for prior_install_required_id in prior_install_required_ids: if prior_install_required_id not in ordered_tsr_ids: # Install the associated repository dependency first. - prior_repo_info_dict, prior_tool_panel_section_key = get_repository_components_for_installation( prior_install_required_id, - tsr_ids, - repo_info_dicts, - tool_panel_section_keys=tool_panel_section_keys ) + prior_repo_info_dict, prior_tool_panel_section_key = \ + get_repository_components_for_installation( prior_install_required_id, + tsr_ids, + repo_info_dicts, + 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 ) 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 ) + 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 ) ordered_tool_panel_section_keys.append( tool_panel_section_key ) @@ -763,11 +770,12 @@ 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_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 ) + tool_section, tool_panel_section_key = \ + tool_util.handle_tool_panel_selection( trans, + metadata, + no_changes_checked=True, + tool_panel_section_id=None, + new_tool_panel_section_label=None ) else: # The tools will be loaded outside of any sections in the tool panel. tool_panel_section_key = None diff -r 6be4eb823a7ea30f35411251900487ee92734b7e -r a29d54619813d5da992b897557162a360b8d610c lib/tool_shed/util/repository_dependency_util.py --- a/lib/tool_shed/util/repository_dependency_util.py +++ b/lib/tool_shed/util/repository_dependency_util.py @@ -96,7 +96,7 @@ return True def create_repository_dependency_objects( trans, tool_path, tool_shed_url, repo_info_dicts, install_repository_dependencies=False, - no_changes_checked=False, tool_panel_section=None, new_tool_panel_section=None ): + no_changes_checked=False, tool_panel_section_id=None, new_tool_panel_section_label=None ): """ Discover all repository dependencies and make sure all tool_shed_repository and associated repository_dependency records exist as well as the dependency relationships between installed repositories. This method is called when uninstalled repositories are being reinstalled. @@ -174,28 +174,30 @@ # The database record for the tool shed repository currently being processed can be updated. Get the repository metadata # to see where it was previously located in the tool panel. if repository_db_record and repository_db_record.metadata: - tool_section, new_tool_panel_section, tool_panel_section_key = \ + tool_section, tool_panel_section_key = \ tool_util.handle_tool_panel_selection( trans=trans, metadata=repository_db_record.metadata, no_changes_checked=no_changes_checked, - tool_panel_section=tool_panel_section, - new_tool_panel_section=new_tool_panel_section ) + tool_panel_section_id=tool_panel_section_id, + new_tool_panel_section_label=new_tool_panel_section_label ) else: # We're installing a new tool shed repository that does not yet have a database record. - tool_panel_section_key, tool_section = tool_util.handle_tool_panel_section( trans, - tool_panel_section=tool_panel_section, - new_tool_panel_section=new_tool_panel_section ) - tool_shed_repository = suc.create_or_update_tool_shed_repository( app=trans.app, - name=name, - description=description, - installed_changeset_revision=changeset_revision, - ctx_rev=ctx_rev, - repository_clone_url=repository_clone_url, - metadata_dict={}, - status=trans.install_model.ToolShedRepository.installation_status.NEW, - current_changeset_revision=changeset_revision, - owner=repository_owner, - dist_to_shed=False ) + tool_panel_section_key, tool_section = \ + tool_util.handle_tool_panel_section( trans, + tool_panel_section_id=tool_panel_section_id, + new_tool_panel_section_label=new_tool_panel_section_label ) + tool_shed_repository = \ + suc.create_or_update_tool_shed_repository( app=trans.app, + name=name, + description=description, + installed_changeset_revision=changeset_revision, + ctx_rev=ctx_rev, + repository_clone_url=repository_clone_url, + metadata_dict={}, + status=trans.install_model.ToolShedRepository.installation_status.NEW, + current_changeset_revision=changeset_revision, + owner=repository_owner, + dist_to_shed=False ) if tool_shed_repository not in all_created_or_updated_tool_shed_repositories: 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. @@ -459,9 +461,10 @@ common_util.parse_repository_dependency_tuple( repository_dependency ) if suc.tool_shed_is_this_tool_shed( toolshed ): required_repository = suc.get_repository_by_name_and_owner( trans.app, name, owner ) - required_repository_metadata = metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans, - trans.security.encode_id( required_repository.id ), - changeset_revision ) + required_repository_metadata = \ + metadata_util.get_repository_metadata_by_repository_id_changeset_revision( trans, + trans.security.encode_id( required_repository.id ), + changeset_revision ) if required_repository_metadata: # The required_repository_metadata changeset_revision is installable. required_metadata = required_repository_metadata.metadata diff -r 6be4eb823a7ea30f35411251900487ee92734b7e -r a29d54619813d5da992b897557162a360b8d610c lib/tool_shed/util/tool_util.py --- a/lib/tool_shed/util/tool_util.py +++ b/lib/tool_shed/util/tool_util.py @@ -108,7 +108,7 @@ for k, v in trans.app.toolbox.tool_panel.items(): if isinstance( v, galaxy.tools.ToolSection ): options.append( ( v.name, v.id ) ) - select_field = SelectField( name='tool_panel_section', display='radio' ) + select_field = SelectField( name='tool_panel_section_id', display='radio' ) for option_tup in options: select_field.add_option( option_tup[ 0 ], option_tup[ 1 ] ) return select_field @@ -461,29 +461,28 @@ fh.close() return sample_files, deleted_sample_files -def get_or_create_tool_section( trans, tool_panel_section_id, new_tool_panel_section=None ): - tool_panel_section_key = 'section_%s' % str( tool_panel_section_id ) +def get_or_create_tool_section( trans, tool_panel_section_id, new_tool_panel_section_label=None ): + if tool_panel_section_id.startswith( 'section_' ): + tool_panel_section_key = tool_panel_section_id + tool_panel_section_id.lstrip( 'section_' ) + else: + tool_panel_section_key = 'section_%s' % str( tool_panel_section_id ) if tool_panel_section_key in trans.app.toolbox.tool_panel: # Appending a tool to an existing section in trans.app.toolbox.tool_panel tool_section = trans.app.toolbox.tool_panel[ tool_panel_section_key ] log.debug( "Appending to tool panel section: %s" % str( tool_section.name ) ) else: # Appending a new section to trans.app.toolbox.tool_panel - try: - new_tool_panel_section_name = new_tool_panel_section.name - except: - new_tool_panel_section_name = new_tool_panel_section - if new_tool_panel_section_name: - elem = XmlET.Element( 'section' ) - elem.attrib[ 'name' ] = new_tool_panel_section_name - elem.attrib[ 'id' ] = tool_panel_section_id - elem.attrib[ 'version' ] = '' - tool_section = galaxy.tools.ToolSection( elem ) - trans.app.toolbox.tool_panel[ tool_panel_section_key ] = tool_section - log.debug( "Loading new tool panel section: %s" % str( tool_section.name ) ) - else: - log.debug( "Unable to create new tool pane section using received new_tool_panel_section: %s" % str( new_tool_panel_section )) - return None, None + if new_tool_panel_section_label is None: + # This might add an ugly section label to the tool panel, but, oh well... + new_tool_panel_section_label = tool_panel_section_id + elem = XmlET.Element( 'section' ) + elem.attrib[ 'name' ] = new_tool_panel_section_label + elem.attrib[ 'id' ] = tool_panel_section_id + elem.attrib[ 'version' ] = '' + tool_section = galaxy.tools.ToolSection( elem ) + trans.app.toolbox.tool_panel[ tool_panel_section_key ] = tool_section + log.debug( "Loading new tool panel section: %s" % str( tool_section.name ) ) return tool_panel_section_key, tool_section def get_tool_path_install_dir( partial_install_dir, shed_tool_conf_dict, tool_dict, config_elems ): @@ -633,16 +632,20 @@ error = True return error, message -def handle_tool_panel_selection( trans, metadata, no_changes_checked, tool_panel_section, new_tool_panel_section ): - """Handle the selected tool panel location for loading tools included in tool shed repositories when installing or reinstalling them.""" +def handle_tool_panel_selection( trans, metadata, no_changes_checked, tool_panel_section_id, new_tool_panel_section_label ): + """ + Handle the selected tool panel location for loading tools included in tool shed repositories when installing + or reinstalling them. + """ # Get the location in the tool panel in which each tool was originally loaded. tool_section = None tool_panel_section_key = None 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. - new_tool_panel_section = None + # Make sure the no_changes check box overrides the new_tool_panel_section_label if the user checked the check + # box and entered something into the field. + new_tool_panel_section_label = None if 'tool_panel_section' in metadata: tool_panel_dict = metadata[ 'tool_panel_section' ] if not tool_panel_dict: @@ -656,24 +659,33 @@ original_section_id = tool_section_dict[ 'id' ] original_section_name = tool_section_dict[ 'name' ] if original_section_id: - tool_panel_section_key, tool_section = get_or_create_tool_section( trans, - tool_panel_section_id=original_section_id, - new_tool_panel_section=new_tool_panel_section ) + tool_panel_section_key, tool_section = \ + get_or_create_tool_section( trans, + tool_panel_section_id=original_section_id, + new_tool_panel_section_label=new_tool_panel_section_label ) else: # The user elected to change the tool panel section to contain the tools. tool_panel_section_key, tool_section = handle_tool_panel_section( trans, - tool_panel_section=tool_panel_section, - new_tool_panel_section=new_tool_panel_section ) - return tool_section, new_tool_panel_section, tool_panel_section_key + tool_panel_section_id=tool_panel_section_id, + new_tool_panel_section_label=new_tool_panel_section_label ) + return tool_section, tool_panel_section_key -def handle_tool_panel_section( trans, tool_panel_section=None, new_tool_panel_section=None ): - if new_tool_panel_section: - section_id = new_tool_panel_section.lower().replace( ' ', '_' ) - tool_panel_section_key, tool_section = get_or_create_tool_section( trans, - tool_panel_section_id=section_id, - new_tool_panel_section=new_tool_panel_section ) - elif tool_panel_section: - tool_panel_section_key = 'section_%s' % str( tool_panel_section ) +def handle_tool_panel_section( trans, tool_panel_section_id=None, new_tool_panel_section_label=None ): + """Return a ToolSection object retrieved from the current in-memory tool_panel.""" + # If tool_panel_section_id is received, the section exists in the tool panel. In this case, the value of the + # received tool_panel_section_id must be the id retrieved from a tool panel config (e.g., tool_conf.xml, which + # may have getext). If new_tool_panel_section_label is received, a new section will be added to the tool panel. + if new_tool_panel_section_label: + section_id = 'section_%s' % str( new_tool_panel_section_label.lower().replace( ' ', '_' ) ) + tool_panel_section_key, tool_section = \ + get_or_create_tool_section( trans, + tool_panel_section_id=section_id, + new_tool_panel_section_label=new_tool_panel_section_label ) + elif tool_panel_section_id: + if tool_panel_section_id.startswith( 'section_' ): + tool_panel_section_key = str( tool_panel_section_id ) + else: + tool_panel_section_key = 'section_%s' % str( tool_panel_section_id ) tool_section = trans.app.toolbox.tool_panel[ tool_panel_section_key ] else: return None, None diff -r 6be4eb823a7ea30f35411251900487ee92734b7e -r a29d54619813d5da992b897557162a360b8d610c templates/admin/tool_shed_repository/reselect_tool_panel_section.mako --- a/templates/admin/tool_shed_repository/reselect_tool_panel_section.mako +++ b/templates/admin/tool_shed_repository/reselect_tool_panel_section.mako @@ -80,7 +80,7 @@ </div><div class="form-row"><label>Add new tool panel section:</label> - <input name="new_tool_panel_section" type="textfield" value="" size="40"/> + <input name="new_tool_panel_section_label" type="textfield" value="" size="40"/><div class="toolParamHelp" style="clear: both;"> Add a new tool panel section to contain the installed tools (optional). </div> diff -r 6be4eb823a7ea30f35411251900487ee92734b7e -r a29d54619813d5da992b897557162a360b8d610c templates/admin/tool_shed_repository/select_tool_panel_section.mako --- a/templates/admin/tool_shed_repository/select_tool_panel_section.mako +++ b/templates/admin/tool_shed_repository/select_tool_panel_section.mako @@ -115,7 +115,7 @@ %endif <div class="form-row"><label>Add new tool panel section:</label> - <input name="new_tool_panel_section" type="textfield" value="${new_tool_panel_section}" size="40"/> + <input name="new_tool_panel_section_label" type="textfield" value="${new_tool_panel_section_label}" size="40"/><div class="toolParamHelp" style="clear: both;"> Add a new tool panel section to contain the installed tools (optional). </div> diff -r 6be4eb823a7ea30f35411251900487ee92734b7e -r a29d54619813d5da992b897557162a360b8d610c test/install_and_test_tool_shed_repositories/base/twilltestcase.py --- a/test/install_and_test_tool_shed_repositories/base/twilltestcase.py +++ b/test/install_and_test_tool_shed_repositories/base/twilltestcase.py @@ -47,7 +47,7 @@ install_tool_dependencies=False, install_repository_dependencies=True, no_changes=True, - new_tool_panel_section=None ): + new_tool_panel_section_label=None ): html = self.last_page() # Since the installation process is by necessity asynchronous, we have to get the parameters to 'manually' initiate the # installation process. This regex will return the tool shed repository IDs in group(1), the encoded_kwd parameter in @@ -71,7 +71,7 @@ def install_repository( self, repository_info_dict, install_tool_dependencies=True, install_repository_dependencies=True, strings_displayed=[], strings_not_displayed=[], preview_strings_displayed=[], - post_submit_strings_displayed=[], new_tool_panel_section=None, **kwd ): + post_submit_strings_displayed=[], new_tool_panel_section_label=None, **kwd ): name = repository_info_dict[ 'name' ] owner = repository_info_dict[ 'owner' ] changeset_revision = repository_info_dict[ 'changeset_revision' ] @@ -103,13 +103,13 @@ kwd = self.set_form_value( form, kwd, 'install_tool_dependencies', install_tool_dependencies ) kwd = self.set_form_value( form, kwd, 'install_repository_dependencies', install_repository_dependencies ) kwd = self.set_form_value( form, kwd, 'shed_tool_conf', self.shed_tool_conf ) - if new_tool_panel_section is not None: - kwd = self.set_form_value( form, kwd, 'new_tool_panel_section', new_tool_panel_section ) + if new_tool_panel_section_label is not None: + kwd = self.set_form_value( form, kwd, 'new_tool_panel_section_label', new_tool_panel_section_label ) submit_button_control = form.find_control( type='submit' ) assert submit_button_control is not None, 'No submit button found for form %s.' % form.attrs.get( 'id' ) self.submit_form( form.attrs.get( 'id' ), str( submit_button_control.name ), **kwd ) self.check_for_strings( post_submit_strings_displayed, strings_not_displayed ) - repository_ids = self.initiate_installation_process( new_tool_panel_section=new_tool_panel_section ) + repository_ids = self.initiate_installation_process( new_tool_panel_section_label=new_tool_panel_section_label ) log.debug( 'Waiting for the installation of repository IDs: %s' % str( repository_ids ) ) self.wait_for_repository_installation( repository_ids ) diff -r 6be4eb823a7ea30f35411251900487ee92734b7e -r a29d54619813d5da992b897557162a360b8d610c test/tool_shed/base/twilltestcase.py --- a/test/tool_shed/base/twilltestcase.py +++ b/test/tool_shed/base/twilltestcase.py @@ -804,7 +804,7 @@ install_tool_dependencies=False, install_repository_dependencies=True, no_changes=True, - new_tool_panel_section=None ): + new_tool_panel_section_label=None ): html = self.last_page() # Since the installation process is by necessity asynchronous, we have to get the parameters to 'manually' initiate the # installation process. This regex will return the tool shed repository IDs in group(1), the encoded_kwd parameter in @@ -855,7 +855,7 @@ def install_repository( self, name, owner, category_name, install_tool_dependencies=False, install_repository_dependencies=True, changeset_revision=None, strings_displayed=[], strings_not_displayed=[], preview_strings_displayed=[], - post_submit_strings_displayed=[], new_tool_panel_section=None, includes_tools_for_display_in_tool_panel=True, + post_submit_strings_displayed=[], new_tool_panel_section_label=None, includes_tools_for_display_in_tool_panel=True, **kwd ): self.browse_tool_shed( url=self.url ) self.browse_category( test_db_util.get_category_by_name( category_name ) ) @@ -877,13 +877,13 @@ kwd = self.set_form_value( form, kwd, 'install_tool_dependencies', install_tool_dependencies ) kwd = self.set_form_value( form, kwd, 'install_repository_dependencies', install_repository_dependencies ) kwd = self.set_form_value( form, kwd, 'shed_tool_conf', self.shed_tool_conf ) - if new_tool_panel_section is not None: - kwd = self.set_form_value( form, kwd, 'new_tool_panel_section', new_tool_panel_section ) + if new_tool_panel_section_label is not None: + kwd = self.set_form_value( form, kwd, 'new_tool_panel_section_label', new_tool_panel_section_label ) submit_button_control = form.find_control( type='submit' ) assert submit_button_control is not None, 'No submit button found for form %s.' % form.attrs.get( 'id' ) self.submit_form( form.attrs.get( 'id' ), str( submit_button_control.name ), **kwd ) self.check_for_strings( post_submit_strings_displayed, strings_not_displayed ) - repository_ids = self.initiate_installation_process( new_tool_panel_section=new_tool_panel_section ) + repository_ids = self.initiate_installation_process( new_tool_panel_section_label=new_tool_panel_section_label ) log.debug( 'Waiting for the installation of repository IDs: %s' % str( repository_ids ) ) self.wait_for_repository_installation( repository_ids ) @@ -1000,7 +1000,7 @@ install_repository_dependencies=True, install_tool_dependencies=False, no_changes=True, - new_tool_panel_section='', + new_tool_panel_section_label='', strings_displayed=[], strings_not_displayed=[] ): url = '/admin_toolshed/reselect_tool_panel_section?id=%s' % self.security.encode_id( installed_repository.id ) @@ -1011,15 +1011,15 @@ repo_dependencies = self.create_checkbox_query_string( field_name='install_repository_dependencies', value=install_repository_dependencies ) tool_dependencies = self.create_checkbox_query_string( field_name='install_tool_dependencies', value=install_tool_dependencies ) encoded_repository_id = self.security.encode_id( installed_repository.id ) - url = '/admin_toolshed/reinstall_repository?id=%s&%s&%s&no_changes=%s&new_tool_panel_section=%s' % \ - ( encoded_repository_id, repo_dependencies, tool_dependencies, str( no_changes ), new_tool_panel_section ) + url = '/admin_toolshed/reinstall_repository?id=%s&%s&%s&no_changes=%s&new_tool_panel_section_label=%s' % \ + ( encoded_repository_id, repo_dependencies, tool_dependencies, str( no_changes ), new_tool_panel_section_label ) self.visit_galaxy_url( url ) # Manually initiate the install process, as with installing a repository. See comments in the # initiate_installation_process method for details. repository_ids = self.initiate_installation_process( install_tool_dependencies, install_repository_dependencies, no_changes, - new_tool_panel_section ) + new_tool_panel_section_label ) # Finally, wait until all repositories are in a final state (either Error or Installed) before returning. self.wait_for_repository_installation( repository_ids ) diff -r 6be4eb823a7ea30f35411251900487ee92734b7e -r a29d54619813d5da992b897557162a360b8d610c test/tool_shed/functional/test_1000_install_basic_repository.py --- a/test/tool_shed/functional/test_1000_install_basic_repository.py +++ b/test/tool_shed/functional/test_1000_install_basic_repository.py @@ -93,7 +93,7 @@ self.install_repository( 'filtering_0000', common.test_user_1_name, 'Test 0000 Basic Repository Features 1', - new_tool_panel_section='test_1000' ) + new_tool_panel_section_label='test_1000' ) installed_repository = test_db_util.get_installed_repository_by_name_owner( 'filtering_0000', common.test_user_1_name ) strings_displayed = [ 'filtering_0000', "Galaxy's filtering tool", diff -r 6be4eb823a7ea30f35411251900487ee92734b7e -r a29d54619813d5da992b897557162a360b8d610c test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py --- a/test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py +++ b/test/tool_shed/functional/test_1010_install_repository_with_tool_dependencies.py @@ -109,7 +109,7 @@ category_name, strings_displayed=strings_displayed, install_tool_dependencies=False, - new_tool_panel_section='test_1010' ) + new_tool_panel_section_label='test_1010' ) installed_repository = test_db_util.get_installed_repository_by_name_owner( repository_name, common.test_user_1_name ) strings_displayed = [ 'freebayes_0010', "Galaxy's freebayes tool", diff -r 6be4eb823a7ea30f35411251900487ee92734b7e -r a29d54619813d5da992b897557162a360b8d610c test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py --- a/test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py +++ b/test/tool_shed/functional/test_1020_install_repository_with_repository_dependencies.py @@ -97,7 +97,7 @@ 'Test 0020 Basic Repository Dependencies', strings_displayed=strings_displayed, install_tool_dependencies=False, - new_tool_panel_section='test_1020' ) + new_tool_panel_section_label='test_1020' ) installed_repository = test_db_util.get_installed_repository_by_name_owner( 'emboss_0020', common.test_user_1_name ) strings_displayed = [ 'emboss_0020', 'Galaxy wrappers for Emboss version 5.0.0 tools for test 0020', diff -r 6be4eb823a7ea30f35411251900487ee92734b7e -r a29d54619813d5da992b897557162a360b8d610c test/tool_shed/functional/test_1030_install_repository_with_dependency_revisions.py --- a/test/tool_shed/functional/test_1030_install_repository_with_dependency_revisions.py +++ b/test/tool_shed/functional/test_1030_install_repository_with_dependency_revisions.py @@ -140,7 +140,7 @@ 'Test 0030 Repository Dependency Revisions', strings_displayed=strings_displayed, install_tool_dependencies=False, - new_tool_panel_section='test_1030' ) + new_tool_panel_section_label='test_1030' ) installed_repository = test_db_util.get_installed_repository_by_name_owner( 'emboss_0030', common.test_user_1_name ) strings_displayed = [ 'emboss_0030', 'Galaxy wrappers for Emboss version 5.0.0 tools for test 0030', diff -r 6be4eb823a7ea30f35411251900487ee92734b7e -r a29d54619813d5da992b897557162a360b8d610c test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py --- a/test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py +++ b/test/tool_shed/functional/test_1040_install_repository_basic_circular_dependencies.py @@ -126,7 +126,7 @@ self.reinstall_repository( installed_freebayes_repository, install_tool_dependencies=False, install_repository_dependencies=True, - new_tool_panel_section='freebayes', + new_tool_panel_section_label='freebayes', no_changes=False ) def test_0040_uninstall_filtering_repository( self ): diff -r 6be4eb823a7ea30f35411251900487ee92734b7e -r a29d54619813d5da992b897557162a360b8d610c test/tool_shed/functional/test_1050_circular_dependencies_4_levels.py --- a/test/tool_shed/functional/test_1050_circular_dependencies_4_levels.py +++ b/test/tool_shed/functional/test_1050_circular_dependencies_4_levels.py @@ -282,7 +282,7 @@ category_name, install_tool_dependencies=False, install_repository_dependencies=True, - new_tool_panel_section='column_maker' ) + new_tool_panel_section_label='column_maker' ) # This should result in column_maker and convert_chars being installed, and the rest never installed. installed_repositories = [ ( column_repository_name, common.test_user_1_name ), ( convert_repository_name, common.test_user_1_name ) ] @@ -300,7 +300,7 @@ category_name, install_tool_dependencies=False, install_repository_dependencies=True, - new_tool_panel_section='emboss_5_0050' ) + new_tool_panel_section_label='emboss_5_0050' ) if running_standalone: assert original_datatypes < self.get_datatypes_count(), 'Installing a repository that depends on emboss_datatypes did not add datatypes.' # Now we have emboss_datatypes, emboss, bismark, column_maker, and convert_chars installed, filtering and freebayes never installed. @@ -358,7 +358,7 @@ strings_displayed=strings_displayed, install_tool_dependencies=False, install_repository_dependencies=True, - new_tool_panel_section='freebayes' ) + new_tool_panel_section_label='freebayes' ) assert original_datatypes < self.get_datatypes_count(), 'Installing a repository that depends on emboss_datatypes did not add datatypes.' emboss_repository = test_db_util.get_installed_repository_by_name_owner( emboss_repository_name, common.test_user_1_name ) datatypes_repository = test_db_util.get_installed_repository_by_name_owner( emboss_datatypes_repository_name, common.test_user_1_name ) diff -r 6be4eb823a7ea30f35411251900487ee92734b7e -r a29d54619813d5da992b897557162a360b8d610c test/tool_shed/functional/test_1060_install_repository_with_workflow.py --- a/test/tool_shed/functional/test_1060_install_repository_with_workflow.py +++ b/test/tool_shed/functional/test_1060_install_repository_with_workflow.py @@ -82,7 +82,7 @@ common.test_user_1_name, 'Test 0060 Workflow Features', install_tool_dependencies=False, - new_tool_panel_section='test_1060' ) + new_tool_panel_section_label='test_1060' ) def test_0015_import_workflow_from_installed_repository( self ): '''Import the workflow from the installed repository and verify that it appears in the list of all workflows.''' installed_repository = test_db_util.get_installed_repository_by_name_owner( repository_name, common.test_user_1_name ) diff -r 6be4eb823a7ea30f35411251900487ee92734b7e -r a29d54619813d5da992b897557162a360b8d610c test/tool_shed/functional/test_1070_invalid_tool.py --- a/test/tool_shed/functional/test_1070_invalid_tool.py +++ b/test/tool_shed/functional/test_1070_invalid_tool.py @@ -71,7 +71,7 @@ common.test_user_1_name, category_name, install_tool_dependencies=False, - new_tool_panel_section='test_1070' ) + new_tool_panel_section_label='test_1070' ) installed_repository = test_db_util.get_installed_repository_by_name_owner( repository_name, common.test_user_1_name ) strings_displayed = [ 'bismark_0070', "Galaxy's bismark wrapper", diff -r 6be4eb823a7ea30f35411251900487ee92734b7e -r a29d54619813d5da992b897557162a360b8d610c test/tool_shed/functional/test_1080_advanced_circular_dependency_installation.py --- a/test/tool_shed/functional/test_1080_advanced_circular_dependency_installation.py +++ b/test/tool_shed/functional/test_1080_advanced_circular_dependency_installation.py @@ -109,7 +109,7 @@ category_name, install_tool_dependencies=False, install_repository_dependencies=False, - new_tool_panel_section='convert_chars' ) + new_tool_panel_section_label='convert_chars' ) installed_convert_repository = test_db_util.get_installed_repository_by_name_owner( convert_repository_name, common.test_user_1_name ) installed_column_repository = test_db_util.get_installed_repository_by_name_owner( column_repository_name, @@ -135,7 +135,7 @@ common.test_user_1_name, category_name, install_repository_dependencies=True, - new_tool_panel_section='column_maker', + new_tool_panel_section_label='column_maker', strings_displayed=[ 'install_repository_dependencies' ] ) installed_convert_repository = test_db_util.get_installed_repository_by_name_owner( convert_repository_name, common.test_user_1_name ) @@ -363,7 +363,7 @@ self.reinstall_repository( installed_convert_repository, install_repository_dependencies=True, no_changes=False, - new_tool_panel_section='convert_maker' ) + new_tool_panel_section_label='convert_maker' ) strings_displayed = [ 'column_maker_0080', 'Add column', self.url.replace( 'http://', '' ), diff -r 6be4eb823a7ea30f35411251900487ee92734b7e -r a29d54619813d5da992b897557162a360b8d610c test/tool_shed/functional/test_1085_repository_dependency_handling.py --- a/test/tool_shed/functional/test_1085_repository_dependency_handling.py +++ b/test/tool_shed/functional/test_1085_repository_dependency_handling.py @@ -99,7 +99,7 @@ category_name, install_tool_dependencies=False, install_repository_dependencies=True, - new_tool_panel_section='column_maker', + new_tool_panel_section_label='column_maker', strings_displayed=[ 'install_repository_dependencies' ] ) installed_convert_repository = test_db_util.get_installed_repository_by_name_owner( convert_repository_name, common.test_user_1_name ) @@ -145,7 +145,7 @@ self.reinstall_repository( installed_column_repository, install_tool_dependencies=False, install_repository_dependencies=False, - new_tool_panel_section='new_column_maker', + new_tool_panel_section_label='new_column_maker', no_changes=False ) strings_displayed = [ 'column_maker_1085', 'Add column', @@ -161,7 +161,7 @@ self.reinstall_repository( installed_convert_repository, install_tool_dependencies=False, install_repository_dependencies=False, - new_tool_panel_section='new_convert_chars', + new_tool_panel_section_label='new_convert_chars', no_changes=False ) strings_displayed = [ 'convert_chars_1085', 'Convert delimiters', diff -r 6be4eb823a7ea30f35411251900487ee92734b7e -r a29d54619813d5da992b897557162a360b8d610c test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py --- a/test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py +++ b/test/tool_shed/functional/test_1087_install_updated_repository_dependencies.py @@ -89,7 +89,7 @@ category_name, install_tool_dependencies=False, install_repository_dependencies=True, - new_tool_panel_section='column_maker', + new_tool_panel_section_label='column_maker', strings_not_displayed=[ 'install_repository_dependencies' ] ) installed_column_repository = test_db_util.get_installed_repository_by_name_owner( column_repository_name, common.test_user_1_name ) self.uninstall_repository( installed_column_repository, remove_from_disk=True ) diff -r 6be4eb823a7ea30f35411251900487ee92734b7e -r a29d54619813d5da992b897557162a360b8d610c test/tool_shed/functional/test_1090_install_tool_from_tool_search.py --- a/test/tool_shed/functional/test_1090_install_tool_from_tool_search.py +++ b/test/tool_shed/functional/test_1090_install_tool_from_tool_search.py @@ -226,7 +226,7 @@ category_name, install_tool_dependencies=False, install_repository_dependencies=False, - new_tool_panel_section='freebayes_1090' ) + new_tool_panel_section_label='freebayes_1090' ) installed_repositories = [ ( freebayes_repository_name, common.test_user_1_name ) ] strings_displayed = [ 'freebayes_0090' ] strings_not_displayed = [ 'filtering_0090', 'emboss_0090', 'emboss_datatypes_0090', 'bwa_color_0090', 'bwa_base_0090' ] @@ -246,7 +246,7 @@ category_name, install_tool_dependencies=False, install_repository_dependencies=False, - new_tool_panel_section='filtering_1090' ) + new_tool_panel_section_label='filtering_1090' ) installed_repositories = [ ( filtering_repository_name, common.test_user_1_name ), ( freebayes_repository_name, common.test_user_1_name ) ] strings_displayed = [ 'filtering_0090', 'freebayes_0090' ] @@ -307,7 +307,7 @@ self.install_repositories_from_search_results( repositories_to_install, install_repository_dependencies='True', install_tool_dependencies=False, - new_tool_panel_section='bwa_1090', + new_tool_panel_section_label='bwa_1090', strings_displayed=strings_displayed ) installed_repositories = [ ( emboss_repository_name, common.test_user_1_name ), diff -r 6be4eb823a7ea30f35411251900487ee92734b7e -r a29d54619813d5da992b897557162a360b8d610c test/tool_shed/functional/test_1120_simple_repository_dependency_multiple_owners.py --- a/test/tool_shed/functional/test_1120_simple_repository_dependency_multiple_owners.py +++ b/test/tool_shed/functional/test_1120_simple_repository_dependency_multiple_owners.py @@ -175,7 +175,7 @@ category_name='Test 0120', install_repository_dependencies=True, post_submit_strings_displayed=post_submit_strings_displayed, - new_tool_panel_section='Test 0120' ) + new_tool_panel_section_label='Test 0120' ) def test_0050_verify_repository_installation( self ): '''Verify installation of blastxml_to_top_descr_0120 and blast_datatypes_0120.''' diff -r 6be4eb823a7ea30f35411251900487ee92734b7e -r a29d54619813d5da992b897557162a360b8d610c test/tool_shed/functional/test_1200_uninstall_and_reinstall_basic_repository.py --- a/test/tool_shed/functional/test_1200_uninstall_and_reinstall_basic_repository.py +++ b/test/tool_shed/functional/test_1200_uninstall_and_reinstall_basic_repository.py @@ -75,7 +75,7 @@ self.install_repository( 'filtering_0000', common.test_user_1_name, 'Test 0000 Basic Repository Features 1', - new_tool_panel_section='test_1000' ) + new_tool_panel_section_label='test_1000' ) installed_repository = test_db_util.get_installed_repository_by_name_owner( 'filtering_0000', common.test_user_1_name ) strings_displayed = [ 'filtering_0000', "Galaxy's filtering tool for test 0000", diff -r 6be4eb823a7ea30f35411251900487ee92734b7e -r a29d54619813d5da992b897557162a360b8d610c test/tool_shed/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py --- a/test/tool_shed/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py +++ b/test/tool_shed/functional/test_1210_uninstall_reinstall_repository_with_tool_dependencies.py @@ -94,7 +94,7 @@ common.test_user_1_name, 'Test 0010 Repository With Tool Dependencies', strings_displayed=strings_displayed, - new_tool_panel_section='test_1210' ) + new_tool_panel_section_label='test_1210' ) installed_repository = test_db_util.get_installed_repository_by_name_owner( 'freebayes_0010', common.test_user_1_name ) strings_displayed = [ 'freebayes_0010', "Galaxy's freebayes tool", diff -r 6be4eb823a7ea30f35411251900487ee92734b7e -r a29d54619813d5da992b897557162a360b8d610c test/tool_shed/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py --- a/test/tool_shed/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py +++ b/test/tool_shed/functional/test_1220_uninstall_reinstall_repository_with_repository_dependencies.py @@ -91,7 +91,7 @@ common.test_user_1_name, 'Test 0020 Basic Repository Dependencies', strings_displayed=strings_displayed, - new_tool_panel_section='test_1210' ) + new_tool_panel_section_label='test_1210' ) installed_repository = test_db_util.get_installed_repository_by_name_owner( emboss_repository_name, common.test_user_1_name ) strings_displayed = [ 'emboss_0020', 'Galaxy wrappers for Emboss version 5.0.0 tools', diff -r 6be4eb823a7ea30f35411251900487ee92734b7e -r a29d54619813d5da992b897557162a360b8d610c test/tool_shed/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py --- a/test/tool_shed/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py +++ b/test/tool_shed/functional/test_1230_uninstall_reinstall_repository_with_dependency_revisions.py @@ -123,7 +123,7 @@ common.test_user_1_name, 'Test 0030 Repository Dependency Revisions', strings_displayed=strings_displayed, - new_tool_panel_section='test_1210' ) + new_tool_panel_section_label='test_1210' ) installed_repository = test_db_util.get_installed_repository_by_name_owner( emboss_repository_name, common.test_user_1_name ) strings_displayed = [ 'emboss_0030', 'Galaxy wrappers for Emboss version 5.0.0 tools', diff -r 6be4eb823a7ea30f35411251900487ee92734b7e -r a29d54619813d5da992b897557162a360b8d610c test/tool_shed/functional/test_1410_update_manager.py --- a/test/tool_shed/functional/test_1410_update_manager.py +++ b/test/tool_shed/functional/test_1410_update_manager.py @@ -78,7 +78,7 @@ self.install_repository( 'filtering_1410', common.test_user_1_name, category_name, - new_tool_panel_section='test_1410' ) + new_tool_panel_section_label='test_1410' ) installed_repository = test_db_util.get_installed_repository_by_name_owner( 'filtering_1410', common.test_user_1_name ) strings_displayed = [ 'filtering_1410', "Galaxy's filtering tool", diff -r 6be4eb823a7ea30f35411251900487ee92734b7e -r a29d54619813d5da992b897557162a360b8d610c test/tool_shed/functional/test_1430_repair_installed_repository.py --- a/test/tool_shed/functional/test_1430_repair_installed_repository.py +++ b/test/tool_shed/functional/test_1430_repair_installed_repository.py @@ -133,7 +133,7 @@ self.install_repository( 'column_1430', common.test_user_1_name, category_name, - new_tool_panel_section='repair', + new_tool_panel_section_label='repair', post_submit_strings_displayed=post_submit_strings_displayed, install_tool_dependencies=False, install_repository_dependencies=True ) diff -r 6be4eb823a7ea30f35411251900487ee92734b7e -r a29d54619813d5da992b897557162a360b8d610c test/tool_shed/functional/test_1450_installing_datatypes_sniffers.py --- a/test/tool_shed/functional/test_1450_installing_datatypes_sniffers.py +++ b/test/tool_shed/functional/test_1450_installing_datatypes_sniffers.py @@ -90,7 +90,7 @@ common.test_user_1_name, category_name, strings_displayed=strings_displayed, - new_tool_panel_section='test_1450' ) + new_tool_panel_section_label='test_1450' ) installed_repository = test_db_util.get_installed_repository_by_name_owner( 'proteomics_datatypes_1450', common.test_user_1_name ) strings_displayed = [ 'user1', self.url.replace( 'http://', '' ), Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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