[galaxy-commits] commit/galaxy-central: greg: Rename the Tool Shed's repository_maintenance_util module to be repository_util.

1 new commit in galaxy-central: https://bitbucket.org/galaxy/galaxy-central/commits/4ee9e584dbc0/ Changeset: 4ee9e584dbc0 User: greg Date: 2014-07-22 21:38:59 Summary: Rename the Tool Shed's repository_maintenance_util module to be repository_util. Affected #: 9 files diff -r 9cce4ead10795278446af4ab84eecfc4e2b26dce -r 4ee9e584dbc016727e4c90f73bbf53081f775c5a 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 @@ -16,7 +16,7 @@ from tool_shed.util import encoding_util from tool_shed.util import hg_util from tool_shed.util import readme_util -from tool_shed.util import repository_maintenance_util +from tool_shed.util import repository_util from tool_shed.util import shed_util_common as suc from tool_shed.util import tool_dependency_util from tool_shed.util import tool_util @@ -48,7 +48,7 @@ def activate_repository( self, trans, **kwd ): """Activate a repository that was deactivated but not uninstalled.""" repository_id = kwd[ 'id' ] - repository = repository_maintenance_util.get_installed_tool_shed_repository( trans.app, repository_id ) + repository = repository_util.get_installed_tool_shed_repository( trans.app, repository_id ) try: trans.app.installed_repository_manager.activate_repository( repository ) except Exception, e: @@ -74,7 +74,7 @@ def browse_repository( self, trans, **kwd ): message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) - repository = repository_maintenance_util.get_installed_tool_shed_repository( trans.app, kwd[ 'id' ] ) + repository = repository_util.get_installed_tool_shed_repository( trans.app, kwd[ 'id' ] ) return trans.fill_template( '/admin/tool_shed_repository/browse_repository.mako', repository=repository, message=message, @@ -107,7 +107,7 @@ action='purge_repository', **kwd ) ) if operation == "activate or reinstall": - repository = repository_maintenance_util.get_installed_tool_shed_repository( trans.app, kwd[ 'id' ] ) + repository = repository_util.get_installed_tool_shed_repository( trans.app, kwd[ 'id' ] ) if repository.uninstalled: # Since we're reinstalling the repository we need to find the latest changeset revision to which it can # be updated so that we can reset the metadata if necessary. This will ensure that information about @@ -208,7 +208,7 @@ def check_for_updates( self, trans, **kwd ): """Send a request to the relevant tool shed to see if there are any updates.""" repository_id = kwd.get( 'id', None ) - repository = repository_maintenance_util.get_installed_tool_shed_repository( trans.app, repository_id ) + repository = repository_util.get_installed_tool_shed_repository( trans.app, repository_id ) tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, str( repository.tool_shed ) ) params = '?galaxy_url=%s&name=%s&owner=%s&changeset_revision=%s' % \ ( web.url_for( '/', qualified=True ), @@ -234,7 +234,7 @@ status = kwd.get( 'status', 'done' ) remove_from_disk = kwd.get( 'remove_from_disk', '' ) remove_from_disk_checked = CheckboxField.is_checked( remove_from_disk ) - tool_shed_repository = repository_maintenance_util.get_installed_tool_shed_repository( trans.app, kwd[ 'id' ] ) + tool_shed_repository = repository_util.get_installed_tool_shed_repository( trans.app, kwd[ 'id' ] ) shed_tool_conf, tool_path, relative_install_dir = \ suc.get_tool_panel_config_tool_path_install_dir( trans.app, tool_shed_repository ) if relative_install_dir: @@ -397,7 +397,7 @@ of the installed tool shed repository in Galaxy. We need it so that we can derive the tool shed from which it was installed. """ - repository = repository_maintenance_util.get_installed_tool_shed_repository( trans.app, repository_id ) + repository = repository_util.get_installed_tool_shed_repository( trans.app, repository_id ) tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, str( repository.tool_shed ) ) if tool_shed_url is None or repository_name is None or repository_owner is None or changeset_revision is None: message = "Unable to retrieve tool dependencies from the Tool Shed because one or more of the following required " @@ -422,7 +422,7 @@ Send a request to the appropriate tool shed to retrieve the dictionary of information required to reinstall an updated revision of an uninstalled tool shed repository. """ - repository = repository_maintenance_util.get_installed_tool_shed_repository( trans.app, repository_id ) + repository = repository_util.get_installed_tool_shed_repository( trans.app, repository_id ) tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, str( repository.tool_shed ) ) if tool_shed_url is None or repository_name is None or repository_owner is None or changeset_revision is None: message = "Unable to retrieve updated repository information from the Tool Shed because one or more of the following " @@ -516,7 +516,7 @@ status = kwd.get( 'status', 'done' ) repository_id = kwd.get( 'id', None ) if repository_id is not None: - repository = repository_maintenance_util.get_installed_tool_shed_repository( trans.app, repository_id ) + repository = repository_util.get_installed_tool_shed_repository( trans.app, repository_id ) if repository is not None: tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, str( repository.tool_shed ) ) name = str( repository.name ) @@ -574,7 +574,7 @@ dependencies are included in the updated revision. """ updating_repository_id = kwd.get( 'updating_repository_id', None ) - repository = repository_maintenance_util.get_installed_tool_shed_repository( trans.app, updating_repository_id ) + repository = repository_util.get_installed_tool_shed_repository( trans.app, updating_repository_id ) # All received dependencies need to be installed - confirmed by the caller. encoded_tool_dependencies_dict = kwd.get( 'encoded_tool_dependencies_dict', None ) if encoded_tool_dependencies_dict is not None: @@ -750,7 +750,7 @@ if repository_id is None: return trans.show_error_message( 'Missing required encoded repository id.' ) operation = kwd.get( 'operation', None ) - repository = repository_maintenance_util.get_installed_tool_shed_repository( trans.app, repository_id ) + repository = repository_util.get_installed_tool_shed_repository( trans.app, repository_id ) if repository is None: return trans.show_error_message( 'Invalid repository specified.' ) tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, str( repository.tool_shed ) ) @@ -1279,7 +1279,7 @@ repository_id = kwd.get( 'id', None ) new_kwd = {} if repository_id is not None: - repository = repository_maintenance_util.get_installed_tool_shed_repository( trans.app, repository_id ) + repository = repository_util.get_installed_tool_shed_repository( trans.app, repository_id ) if repository: if repository.is_new: if kwd.get( 'purge_repository_button', False ): @@ -1317,7 +1317,7 @@ message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) repository_id = kwd[ 'id' ] - tool_shed_repository = repository_maintenance_util.get_installed_tool_shed_repository( trans.app, repository_id ) + tool_shed_repository = repository_util.get_installed_tool_shed_repository( trans.app, repository_id ) no_changes = kwd.get( 'no_changes', '' ) no_changes_checked = CheckboxField.is_checked( no_changes ) install_repository_dependencies = CheckboxField.is_checked( kwd.get( 'install_repository_dependencies', '' ) ) @@ -1387,14 +1387,14 @@ tool_dependencies = metadata.get( 'tool_dependencies', None ) else: tool_dependencies = None - repo_info_dict = repository_maintenance_util.create_repo_info_dict( trans.app, - repository_clone_url=repository_clone_url, - changeset_revision=tool_shed_repository.changeset_revision, - ctx_rev=ctx_rev, - repository_owner=tool_shed_repository.owner, - repository_name=tool_shed_repository.name, - tool_dependencies=tool_dependencies, - repository_dependencies=repository_dependencies ) + repo_info_dict = repository_util.create_repo_info_dict( trans.app, + repository_clone_url=repository_clone_url, + changeset_revision=tool_shed_repository.changeset_revision, + ctx_rev=ctx_rev, + repository_owner=tool_shed_repository.owner, + repository_name=tool_shed_repository.name, + tool_dependencies=tool_dependencies, + repository_dependencies=repository_dependencies ) if repo_info_dict not in repo_info_dicts: repo_info_dicts.append( repo_info_dict ) # Make sure all tool_shed_repository records exist. @@ -1460,7 +1460,7 @@ action='browse_repositories', message=message, status=status ) ) - tool_shed_repository = repository_maintenance_util.get_installed_tool_shed_repository( trans.app, repository_id ) + tool_shed_repository = repository_util.get_installed_tool_shed_repository( trans.app, repository_id ) rrm = RepairRepositoryManager( trans.app ) if kwd.get( 'repair_repository_button', False ): encoded_repair_dict = kwd.get( 'repair_dict', None ) @@ -1478,7 +1478,7 @@ repository = trans.install_model.context.query( trans.install_model.ToolShedRepository ).get( trans.security.decode_id( tsr_id ) ) repositories_for_repair.append( repository ) return self.repair_tool_shed_repositories( trans, rrm, repositories_for_repair, ordered_repo_info_dicts ) - tool_shed_repository = repository_maintenance_util.get_installed_tool_shed_repository( trans.app, repository_id ) + tool_shed_repository = repository_util.get_installed_tool_shed_repository( trans.app, repository_id ) repair_dict = rrm.get_repair_dict( tool_shed_repository ) encoded_repair_dict = encoding_util.tool_shed_encode( repair_dict ) ordered_tsr_ids = repair_dict.get( 'ordered_tsr_ids', [] ) @@ -1540,7 +1540,7 @@ repository_id = kwd.get( 'id', None ) latest_changeset_revision = kwd.get( 'latest_changeset_revision', None ) latest_ctx_rev = kwd.get( 'latest_ctx_rev', None ) - tool_shed_repository = repository_maintenance_util.get_installed_tool_shed_repository( trans.app, repository_id ) + tool_shed_repository = repository_util.get_installed_tool_shed_repository( trans.app, repository_id ) repository_clone_url = common_util.generate_clone_url_for_installed_repository( trans.app, tool_shed_repository ) metadata = tool_shed_repository.metadata tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, str( tool_shed_repository.tool_shed ) ) @@ -1600,14 +1600,14 @@ repository_dependencies = \ rdim.get_repository_dependencies_for_installed_tool_shed_repository( trans.app, tool_shed_repository ) - repo_info_dict = repository_maintenance_util.create_repo_info_dict( trans.app, - repository_clone_url=repository_clone_url, - changeset_revision=tool_shed_repository.installed_changeset_revision, - ctx_rev=tool_shed_repository.ctx_rev, - repository_owner=tool_shed_repository.owner, - repository_name=tool_shed_repository.name, - tool_dependencies=tool_dependencies, - repository_dependencies=repository_dependencies ) + repo_info_dict = repository_util.create_repo_info_dict( trans.app, + repository_clone_url=repository_clone_url, + changeset_revision=tool_shed_repository.installed_changeset_revision, + ctx_rev=tool_shed_repository.ctx_rev, + repository_owner=tool_shed_repository.owner, + repository_name=tool_shed_repository.name, + tool_dependencies=tool_dependencies, + repository_dependencies=repository_dependencies ) irm = trans.app.installed_repository_manager dependencies_for_repository_dict = irm.get_dependencies_for_repository( tool_shed_url, repo_info_dict, @@ -1727,7 +1727,7 @@ @web.require_admin def reset_repository_metadata( self, trans, id ): """Reset all metadata on a single installed tool shed repository.""" - repository = repository_maintenance_util.get_installed_tool_shed_repository( trans.app, id ) + repository = repository_util.get_installed_tool_shed_repository( trans.app, id ) repository_clone_url = common_util.generate_clone_url_for_installed_repository( trans.app, repository ) tool_path, relative_install_dir = repository.get_tool_relative_path( trans.app ) if relative_install_dir: @@ -1766,7 +1766,7 @@ @web.require_admin def reset_to_install( self, trans, **kwd ): """An error occurred while cloning the repository, so reset everything necessary to enable another attempt.""" - repository = repository_maintenance_util.get_installed_tool_shed_repository( trans.app, kwd[ 'id' ] ) + repository = repository_util.get_installed_tool_shed_repository( trans.app, kwd[ 'id' ] ) if kwd.get( 'reset_repository', False ): suc.set_repository_attributes( trans.app, repository, @@ -1792,7 +1792,7 @@ Get the tool_versions from the tool shed for each tool in the installed revision of a selected tool shed repository and update the metadata for the repository's revision in the Galaxy database. """ - repository = repository_maintenance_util.get_installed_tool_shed_repository( trans.app, kwd[ 'id' ] ) + repository = repository_util.get_installed_tool_shed_repository( trans.app, kwd[ 'id' ] ) tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, str( repository.tool_shed ) ) params = '?name=%s&owner=%s&changeset_revision=%s' % ( str( repository.name ), str( repository.owner ), @@ -2076,8 +2076,7 @@ for repository in trans.install_model.context.query( trans.install_model.ToolShedRepository ) \ .filter( trans.install_model.ToolShedRepository.table.c.deleted == False ): ok, updated = \ - repository_maintenance_util.check_or_update_tool_shed_status_for_installed_repository( trans.app, - repository ) + repository_util.check_or_update_tool_shed_status_for_installed_repository( trans.app, repository ) if ok: success_count += 1 else: @@ -2093,8 +2092,7 @@ repository_id = kwd.get( 'id', None ) repository = suc.get_tool_shed_repository_by_id( trans.app, repository_id ) ok, updated = \ - repository_maintenance_util.check_or_update_tool_shed_status_for_installed_repository( trans.app, - repository ) + repository_util.check_or_update_tool_shed_status_for_installed_repository( trans.app, repository ) if ok: if updated: message = "The tool shed status for repository <b>%s</b> has been updated." % str( repository.name ) @@ -2113,7 +2111,7 @@ def view_tool_metadata( self, trans, repository_id, tool_id, **kwd ): message = kwd.get( 'message', '' ) status = kwd.get( 'status', 'done' ) - repository = repository_maintenance_util.get_installed_tool_shed_repository( trans.app, repository_id ) + repository = repository_util.get_installed_tool_shed_repository( trans.app, repository_id ) repository_metadata = repository.metadata shed_config_dict = repository.get_shed_config_dict( trans.app ) tool_metadata = {} diff -r 9cce4ead10795278446af4ab84eecfc4e2b26dce -r 4ee9e584dbc016727e4c90f73bbf53081f775c5a lib/galaxy/webapps/tool_shed/api/repositories.py --- a/lib/galaxy/webapps/tool_shed/api/repositories.py +++ b/lib/galaxy/webapps/tool_shed/api/repositories.py @@ -19,7 +19,7 @@ from tool_shed.util import basic_util from tool_shed.util import encoding_util from tool_shed.util import hg_util -from tool_shed.util import repository_maintenance_util +from tool_shed.util import repository_util from tool_shed.util import shed_util_common as suc from tool_shed.util import tool_util @@ -194,10 +194,10 @@ includes_tools_for_display_in_tool_panel, \ has_repository_dependencies, \ has_repository_dependencies_only_if_compiling_contained_td = \ - repository_maintenance_util.get_repo_info_dict( trans.app, - trans.user, - encoded_repository_id, - changeset_revision ) + repository_util.get_repo_info_dict( trans.app, + trans.user, + encoded_repository_id, + changeset_revision ) return repository_dict, repository_metadata_dict, repo_info_dict else: log.debug( "Unable to locate repository_metadata record for repository id %s and changeset_revision %s" % \ diff -r 9cce4ead10795278446af4ab84eecfc4e2b26dce -r 4ee9e584dbc016727e4c90f73bbf53081f775c5a lib/galaxy/webapps/tool_shed/controllers/admin.py --- a/lib/galaxy/webapps/tool_shed/controllers/admin.py +++ b/lib/galaxy/webapps/tool_shed/controllers/admin.py @@ -11,7 +11,7 @@ from tool_shed.metadata import repository_metadata_manager from tool_shed.util import metadata_util -from tool_shed.util import repository_maintenance_util +from tool_shed.util import repository_util from tool_shed.util import shed_util_common as suc log = logging.getLogger( __name__ ) @@ -320,14 +320,14 @@ def manage_role_associations( self, trans, **kwd ): """Manage users, groups and repositories associated with a role.""" role_id = kwd.get( 'id', None ) - role = repository_maintenance_util.get_role_by_id( trans.app, role_id ) + role = repository_util.get_role_by_id( trans.app, role_id ) # We currently only have a single role associated with a repository, the repository admin role. repository_role_association = role.repositories[ 0 ] repository = repository_role_association.repository - associations_dict = repository_maintenance_util.handle_role_associations( trans.app, - role, - repository, - **kwd ) + associations_dict = repository_util.handle_role_associations( trans.app, + role, + repository, + **kwd ) in_users = associations_dict.get( 'in_users', [] ) out_users = associations_dict.get( 'out_users', [] ) in_groups = associations_dict.get( 'in_groups', [] ) diff -r 9cce4ead10795278446af4ab84eecfc4e2b26dce -r 4ee9e584dbc016727e4c90f73bbf53081f775c5a lib/galaxy/webapps/tool_shed/controllers/repository.py --- a/lib/galaxy/webapps/tool_shed/controllers/repository.py +++ b/lib/galaxy/webapps/tool_shed/controllers/repository.py @@ -31,7 +31,7 @@ from tool_shed.util import hg_util from tool_shed.util import metadata_util from tool_shed.util import readme_util -from tool_shed.util import repository_maintenance_util +from tool_shed.util import repository_util from tool_shed.util import search_util from tool_shed.util import shed_util_common as suc from tool_shed.util import tool_util @@ -1070,7 +1070,7 @@ repository_type = kwd.get( 'repository_type', rt_util.UNRESTRICTED ) if kwd.get( 'create_repository_button', False ): error = False - message = repository_maintenance_util.validate_repository_name( trans.app, name, trans.user ) + message = repository_util.validate_repository_name( trans.app, name, trans.user ) if message: error = True if not description: @@ -1079,13 +1079,13 @@ if error: status = 'error' else: - repository, message = repository_maintenance_util.create_repository( trans.app, - name, - repository_type, - description, - long_description, - user_id=trans.user.id, - category_ids=category_ids ) + repository, message = repository_util.create_repository( trans.app, + name, + repository_type, + description, + long_description, + user_id=trans.user.id, + category_ids=category_ids ) trans.response.send_redirect( web.url_for( controller='repository', action='manage_repository', message=message, @@ -1820,7 +1820,7 @@ repository_id, changeset_revision = tup repo_info_dict, cur_includes_tools, cur_includes_tool_dependencies, cur_includes_tools_for_display_in_tool_panel, \ cur_has_repository_dependencies, cur_has_repository_dependencies_only_if_compiling_contained_td = \ - repository_maintenance_util.get_repo_info_dict( trans.app, trans.user, repository_id, changeset_revision ) + repository_util.get_repo_info_dict( trans.app, trans.user, repository_id, changeset_revision ) if cur_has_repository_dependencies and not has_repository_dependencies: has_repository_dependencies = True if cur_has_repository_dependencies_only_if_compiling_contained_td and not has_repository_dependencies_only_if_compiling_contained_td: @@ -1951,16 +1951,16 @@ after_changeset_revision=changeset_revision ) repository_metadata = suc.get_repository_metadata_by_changeset_revision( trans.app, repository_id, changeset_revision ) ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision ) - repo_info_dict = repository_maintenance_util.create_repo_info_dict( app=trans.app, - repository_clone_url=repository_clone_url, - changeset_revision=changeset_revision, - ctx_rev=str( ctx.rev() ), - repository_owner=repository.user.username, - repository_name=repository.name, - repository=repository, - repository_metadata=repository_metadata, - tool_dependencies=None, - repository_dependencies=None ) + repo_info_dict = repository_util.create_repo_info_dict( app=trans.app, + repository_clone_url=repository_clone_url, + changeset_revision=changeset_revision, + ctx_rev=str( ctx.rev() ), + repository_owner=repository.user.username, + repository_name=repository.name, + repository=repository, + repository_metadata=repository_metadata, + tool_dependencies=None, + repository_dependencies=None ) includes_data_managers = False includes_datatypes = False includes_tools = False @@ -2274,7 +2274,7 @@ repository.long_description = long_description flush_needed = True if repository.times_downloaded == 0 and repo_name != repository.name: - message = repository_maintenance_util.validate_repository_name( trans.app, repo_name, user ) + message = repository_util.validate_repository_name( trans.app, repo_name, user ) if message: error = True else: @@ -2284,12 +2284,12 @@ trans.app.hgweb_config_manager.change_entry( old_lhs, new_lhs, repo_dir ) # Change the entry in the repository's hgrc file. hgrc_file = os.path.join( repo_dir, '.hg', 'hgrc' ) - repository_maintenance_util.change_repository_name_in_hgrc_file( hgrc_file, repo_name ) + repository_util.change_repository_name_in_hgrc_file( hgrc_file, repo_name ) # Rename the repository's admin role to match the new repository name. repository_admin_role = repository.admin_role repository_admin_role.name = \ - repository_maintenance_util.get_repository_admin_role_name( str( repo_name ), - str( repository.user.username ) ) + repository_util.get_repository_admin_role_name( str( repo_name ), + str( repository.user.username ) ) trans.sa_session.add( repository_admin_role ) repository.name = repo_name flush_needed = True @@ -2379,7 +2379,7 @@ current_allow_push_list = current_allow_push.split( ',' ) else: current_allow_push_list = [] - allow_push_select_field = repository_maintenance_util.build_allow_push_select_field( trans, current_allow_push_list ) + allow_push_select_field = repository_util.build_allow_push_select_field( trans, current_allow_push_list ) checked = alerts_checked or user.email in email_alerts alerts_check_box = CheckboxField( 'alerts', checked=checked ) changeset_revision_select_field = grids_util.build_changeset_revision_select_field( trans, @@ -2521,10 +2521,10 @@ if repository_metadata: metadata = repository_metadata.metadata role = repository.admin_role - associations_dict = repository_maintenance_util.handle_role_associations( trans.app, - role, - repository, - **kwd ) + associations_dict = repository_util.handle_role_associations( trans.app, + role, + repository, + **kwd ) in_users = associations_dict.get( 'in_users', [] ) out_users = associations_dict.get( 'out_users', [] ) in_groups = associations_dict.get( 'in_groups', [] ) diff -r 9cce4ead10795278446af4ab84eecfc4e2b26dce -r 4ee9e584dbc016727e4c90f73bbf53081f775c5a lib/tool_shed/capsule/capsule_manager.py --- a/lib/tool_shed/capsule/capsule_manager.py +++ b/lib/tool_shed/capsule/capsule_manager.py @@ -24,7 +24,7 @@ from tool_shed.util import common_util from tool_shed.util import encoding_util from tool_shed.util import hg_util -from tool_shed.util import repository_maintenance_util +from tool_shed.util import repository_util from tool_shed.util import shed_util_common as suc from tool_shed.util import xml_util @@ -462,13 +462,13 @@ else: category_ids.append( self.app.security.encode_id( category.id ) ) # Create the repository record in the database. - repository, create_message = repository_maintenance_util.create_repository( self.app, - name, - type, - description, - long_description, - user_id=user_id, - category_ids=category_ids ) + repository, create_message = repository_util.create_repository( self.app, + name, + type, + description, + long_description, + user_id=user_id, + category_ids=category_ids ) if create_message: results_message += create_message # Populate the new repository with the contents of exported repository archive. diff -r 9cce4ead10795278446af4ab84eecfc4e2b26dce -r 4ee9e584dbc016727e4c90f73bbf53081f775c5a lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py --- a/lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py +++ b/lib/tool_shed/galaxy_install/metadata/installed_repository_metadata_manager.py @@ -9,7 +9,7 @@ from tool_shed.metadata import metadata_generator from tool_shed.util import common_util -from tool_shed.util import repository_maintenance_util +from tool_shed.util import repository_util from tool_shed.util import shed_util_common as suc from tool_shed.util import tool_util from tool_shed.util import xml_util @@ -78,7 +78,7 @@ """Reset all metadata on a single tool shed repository installed into a Galaxy instance.""" invalid_file_tups = [] metadata_dict = {} - repository = repository_maintenance_util.get_installed_tool_shed_repository( self.app, id ) + repository = repository_util.get_installed_tool_shed_repository( self.app, id ) repository_clone_url = common_util.generate_clone_url_for_installed_repository( self.app, repository ) tool_path, relative_install_dir = repository.get_tool_relative_path( self.app ) if relative_install_dir: @@ -118,7 +118,7 @@ unsuccessful_count = 0 for repository_id in repository_ids: try: - repository = repository_maintenance_util.get_installed_tool_shed_repository( self.app, repository_id ) + repository = repository_util.get_installed_tool_shed_repository( self.app, repository_id ) owner = str( repository.owner ) invalid_file_tups, metadata_dict = \ self.reset_all_metadata_on_installed_repository( repository_id ) diff -r 9cce4ead10795278446af4ab84eecfc4e2b26dce -r 4ee9e584dbc016727e4c90f73bbf53081f775c5a lib/tool_shed/galaxy_install/repair_repository_manager.py --- a/lib/tool_shed/galaxy_install/repair_repository_manager.py +++ b/lib/tool_shed/galaxy_install/repair_repository_manager.py @@ -10,7 +10,7 @@ from tool_shed.util import common_util from tool_shed.util import container_util from tool_shed.util import shed_util_common as suc -from tool_shed.util import repository_maintenance_util +from tool_shed.util import repository_util from tool_shed.util import tool_dependency_util @@ -127,16 +127,16 @@ new_tool_panel_section_label=tool_panel_section_name ) else: tool_dependencies = None - repo_info_dict = repository_maintenance_util.create_repo_info_dict( app=self.app, - repository_clone_url=repository_clone_url, - changeset_revision=repository.changeset_revision, - ctx_rev=repository.ctx_rev, - repository_owner=repository.owner, - repository_name=repository.name, - repository=None, - repository_metadata=None, - tool_dependencies=tool_dependencies, - repository_dependencies=repository_dependencies ) + repo_info_dict = repository_util.create_repo_info_dict( app=self.app, + repository_clone_url=repository_clone_url, + changeset_revision=repository.changeset_revision, + ctx_rev=repository.ctx_rev, + repository_owner=repository.owner, + repository_name=repository.name, + repository=None, + repository_metadata=None, + tool_dependencies=tool_dependencies, + repository_dependencies=repository_dependencies ) return repo_info_dict, tool_panel_section_key def repair_tool_shed_repository( self, repository, repo_info_dict ): diff -r 9cce4ead10795278446af4ab84eecfc4e2b26dce -r 4ee9e584dbc016727e4c90f73bbf53081f775c5a lib/tool_shed/util/repository_maintenance_util.py --- a/lib/tool_shed/util/repository_maintenance_util.py +++ /dev/null @@ -1,330 +0,0 @@ -import ConfigParser -import logging -import os -import re - -from galaxy import util -from galaxy import web -from galaxy.web.form_builder import build_select_field -from galaxy.webapps.tool_shed.model import directory_hash_id - -from tool_shed.dependencies.repository import relation_builder - -from tool_shed.util import common_util -from tool_shed.util import hg_util -from tool_shed.util import shed_util_common as suc - -log = logging.getLogger( __name__ ) - -VALID_REPOSITORYNAME_RE = re.compile( "^[a-z0-9\_]+$" ) - -def build_allow_push_select_field( trans, current_push_list, selected_value='none' ): - options = [] - for user in trans.sa_session.query( trans.model.User ): - if user.username not in current_push_list: - options.append( user ) - return build_select_field( trans, - objs=options, - label_attr='username', - select_field_name='allow_push', - selected_value=selected_value, - refresh_on_change=False, - multiple=True ) - -def change_repository_name_in_hgrc_file( hgrc_file, new_name ): - config = ConfigParser.ConfigParser() - config.read( hgrc_file ) - config.read( hgrc_file ) - config.set( 'web', 'name', new_name ) - new_file = open( hgrc_file, 'wb' ) - config.write( new_file ) - new_file.close() - -def check_or_update_tool_shed_status_for_installed_repository( app, repository ): - updated = False - tool_shed_status_dict = suc.get_tool_shed_status_for_installed_repository( app, repository ) - if tool_shed_status_dict: - ok = True - if tool_shed_status_dict != repository.tool_shed_status: - repository.tool_shed_status = tool_shed_status_dict - app.install_model.context.add( repository ) - app.install_model.context.flush() - updated = True - else: - ok = False - return ok, updated - -def create_repo_info_dict( app, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_name=None, - repository=None, repository_metadata=None, tool_dependencies=None, repository_dependencies=None ): - """ - Return a dictionary that includes all of the information needed to install a repository into a local - Galaxy instance. The dictionary will also contain the recursive list of repository dependencies defined - for the repository, as well as the defined tool dependencies. - - This method is called from Galaxy under four scenarios: - 1. During the tool shed repository installation process via the tool shed's get_repository_information() - method. In this case both the received repository and repository_metadata will be objects, but - tool_dependencies and repository_dependencies will be None. - 2. When getting updates for an installed repository where the updates include newly defined repository - dependency definitions. This scenario is similar to 1. above. The tool shed's get_repository_information() - method is the caller, and both the received repository and repository_metadata will be objects, but - tool_dependencies and repository_dependencies will be None. - 3. When a tool shed repository that was uninstalled from a Galaxy instance is being reinstalled with no - updates available. In this case, both repository and repository_metadata will be None, but tool_dependencies - and repository_dependencies will be objects previously retrieved from the tool shed if the repository includes - definitions for them. - 4. When a tool shed repository that was uninstalled from a Galaxy instance is being reinstalled with updates - available. In this case, this method is reached via the tool shed's get_updated_repository_information() - method, and both repository and repository_metadata will be objects but tool_dependencies and - repository_dependencies will be None. - """ - repo_info_dict = {} - repository = suc.get_repository_by_name_and_owner( app, repository_name, repository_owner ) - if app.name == 'tool_shed': - # We're in the tool shed. - repository_metadata = suc.get_repository_metadata_by_changeset_revision( app, - app.security.encode_id( repository.id ), - changeset_revision ) - if repository_metadata: - metadata = repository_metadata.metadata - if metadata: - tool_shed_url = str( web.url_for( '/', qualified=True ) ).rstrip( '/' ) - rb = relation_builder.RelationBuilder( app, repository, repository_metadata, tool_shed_url ) - # Get a dictionary of all repositories upon which the contents of the received repository depends. - repository_dependencies = rb.get_repository_dependencies_for_changeset_revision() - tool_dependencies = metadata.get( 'tool_dependencies', {} ) - if tool_dependencies: - new_tool_dependencies = {} - for dependency_key, requirements_dict in tool_dependencies.items(): - if dependency_key in [ 'set_environment' ]: - new_set_environment_dict_list = [] - for set_environment_dict in requirements_dict: - set_environment_dict[ 'repository_name' ] = repository_name - set_environment_dict[ 'repository_owner' ] = repository_owner - set_environment_dict[ 'changeset_revision' ] = changeset_revision - new_set_environment_dict_list.append( set_environment_dict ) - new_tool_dependencies[ dependency_key ] = new_set_environment_dict_list - else: - requirements_dict[ 'repository_name' ] = repository_name - requirements_dict[ 'repository_owner' ] = repository_owner - requirements_dict[ 'changeset_revision' ] = changeset_revision - new_tool_dependencies[ dependency_key ] = requirements_dict - tool_dependencies = new_tool_dependencies - # Cast unicode to string, with the exception of description, since it is free text and can contain special characters. - repo_info_dict[ str( repository.name ) ] = ( repository.description, - str( repository_clone_url ), - str( changeset_revision ), - str( ctx_rev ), - str( repository_owner ), - repository_dependencies, - tool_dependencies ) - return repo_info_dict - -def create_repository( app, name, type, description, long_description, user_id, category_ids=[] ): - sa_session = app.model.context.current - # Add the repository record to the database. - repository = app.model.Repository( name=name, - type=type, - description=description, - long_description=long_description, - user_id=user_id ) - # Flush to get the id. - sa_session.add( repository ) - sa_session.flush() - # Create an admin role for the repository. - repository_admin_role = create_repository_admin_role( app, repository ) - # Determine the repository's repo_path on disk. - dir = os.path.join( app.config.file_path, *directory_hash_id( repository.id ) ) - # Create directory if it does not exist. - if not os.path.exists( dir ): - os.makedirs( dir ) - # Define repo name inside hashed directory. - repository_path = os.path.join( dir, "repo_%d" % repository.id ) - # Create local repository directory. - if not os.path.exists( repository_path ): - os.makedirs( repository_path ) - # Create the local repository. - repo = hg_util.get_repo_for_repository( app, repository=None, repo_path=repository_path, create=True ) - # Add an entry in the hgweb.config file for the local repository. - lhs = "repos/%s/%s" % ( repository.user.username, repository.name ) - app.hgweb_config_manager.add_entry( lhs, repository_path ) - # Create a .hg/hgrc file for the local repository. - hg_util.create_hgrc_file( app, repository ) - flush_needed = False - if category_ids: - # Create category associations - for category_id in category_ids: - category = sa_session.query( app.model.Category ) \ - .get( app.security.decode_id( category_id ) ) - rca = app.model.RepositoryCategoryAssociation( repository, category ) - sa_session.add( rca ) - flush_needed = True - if flush_needed: - sa_session.flush() - # Update the repository registry. - app.repository_registry.add_entry( repository ) - message = "Repository <b>%s</b> has been created." % str( repository.name ) - return repository, message - -def create_repository_admin_role( app, repository ): - """ - Create a new role with name-spaced name based on the repository name and its owner's public user - name. This will ensure that the tole name is unique. - """ - sa_session = app.model.context.current - name = get_repository_admin_role_name( str( repository.name ), str( repository.user.username ) ) - description = 'A user or group member with this role can administer this repository.' - role = app.model.Role( name=name, description=description, type=app.model.Role.types.SYSTEM ) - sa_session.add( role ) - sa_session.flush() - # Associate the role with the repository owner. - ura = app.model.UserRoleAssociation( repository.user, role ) - # Associate the role with the repository. - rra = app.model.RepositoryRoleAssociation( repository, role ) - sa_session.add( rra ) - sa_session.flush() - return role - -def get_installed_tool_shed_repository( app, id ): - """Get a tool shed repository record from the Galaxy database defined by the id.""" - return app.install_model.context.query( app.install_model.ToolShedRepository ) \ - .get( app.security.decode_id( id ) ) - -def get_repo_info_dict( app, user, repository_id, changeset_revision ): - repository = suc.get_repository_in_tool_shed( app, repository_id ) - repo = hg_util.get_repo_for_repository( app, repository=repository, repo_path=None, create=False ) - repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( user, repository ) - repository_metadata = suc.get_repository_metadata_by_changeset_revision( app, - repository_id, - changeset_revision ) - if not repository_metadata: - # The received changeset_revision is no longer installable, so get the next changeset_revision - # in the repository's changelog. This generally occurs only with repositories of type - # repository_suite_definition or tool_dependency_definition. - next_downloadable_changeset_revision = \ - suc.get_next_downloadable_changeset_revision( repository, repo, changeset_revision ) - if next_downloadable_changeset_revision: - repository_metadata = suc.get_repository_metadata_by_changeset_revision( app, - repository_id, - next_downloadable_changeset_revision ) - if repository_metadata: - # For now, we'll always assume that we'll get repository_metadata, but if we discover our assumption - # is not valid we'll have to enhance the callers to handle repository_metadata values of None in the - # returned repo_info_dict. - metadata = repository_metadata.metadata - if 'tools' in metadata: - includes_tools = True - else: - includes_tools = False - includes_tools_for_display_in_tool_panel = repository_metadata.includes_tools_for_display_in_tool_panel - repository_dependencies_dict = metadata.get( 'repository_dependencies', {} ) - repository_dependencies = repository_dependencies_dict.get( 'repository_dependencies', [] ) - has_repository_dependencies, has_repository_dependencies_only_if_compiling_contained_td = \ - suc.get_repository_dependency_types( repository_dependencies ) - if 'tool_dependencies' in metadata: - includes_tool_dependencies = True - else: - includes_tool_dependencies = False - else: - # Here's where we may have to handle enhancements to the callers. See above comment. - includes_tools = False - has_repository_dependencies = False - has_repository_dependencies_only_if_compiling_contained_td = False - includes_tool_dependencies = False - includes_tools_for_display_in_tool_panel = False - ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision ) - repo_info_dict = create_repo_info_dict( app=app, - repository_clone_url=repository_clone_url, - changeset_revision=changeset_revision, - ctx_rev=str( ctx.rev() ), - repository_owner=repository.user.username, - repository_name=repository.name, - repository=repository, - repository_metadata=repository_metadata, - tool_dependencies=None, - repository_dependencies=None ) - return repo_info_dict, includes_tools, includes_tool_dependencies, includes_tools_for_display_in_tool_panel, \ - has_repository_dependencies, has_repository_dependencies_only_if_compiling_contained_td - -def get_repository_admin_role_name( repository_name, repository_owner ): - return '%s_%s_admin' % ( str( repository_name ), str( repository_owner ) ) - -def get_role_by_id( app, role_id ): - """Get a Role from the database by id.""" - sa_session = app.model.context.current - return sa_session.query( app.model.Role ).get( app.security.decode_id( role_id ) ) - -def handle_role_associations( app, role, repository, **kwd ): - sa_session = app.model.context.current - message = kwd.get( 'message', '' ) - status = kwd.get( 'status', 'done' ) - repository_owner = repository.user - if kwd.get( 'manage_role_associations_button', False ): - in_users_list = util.listify( kwd.get( 'in_users', [] ) ) - in_users = [ sa_session.query( app.model.User ).get( x ) for x in in_users_list ] - # Make sure the repository owner is always associated with the repostory's admin role. - owner_associated = False - for user in in_users: - if user.id == repository_owner.id: - owner_associated = True - break - if not owner_associated: - in_users.append( repository_owner ) - message += "The repository owner must always be associated with the repository's administrator role. " - status = 'error' - in_groups_list = util.listify( kwd.get( 'in_groups', [] ) ) - in_groups = [ sa_session.query( app.model.Group ).get( x ) for x in in_groups_list ] - in_repositories = [ repository ] - app.security_agent.set_entity_role_associations( roles=[ role ], - users=in_users, - groups=in_groups, - repositories=in_repositories ) - sa_session.refresh( role ) - message += "Role <b>%s</b> has been associated with %d users, %d groups and %d repositories. " % \ - ( str( role.name ), len( in_users ), len( in_groups ), len( in_repositories ) ) - in_users = [] - out_users = [] - in_groups = [] - out_groups = [] - for user in sa_session.query( app.model.User ) \ - .filter( app.model.User.table.c.deleted==False ) \ - .order_by( app.model.User.table.c.email ): - if user in [ x.user for x in role.users ]: - in_users.append( ( user.id, user.email ) ) - else: - out_users.append( ( user.id, user.email ) ) - for group in sa_session.query( app.model.Group ) \ - .filter( app.model.Group.table.c.deleted==False ) \ - .order_by( app.model.Group.table.c.name ): - if group in [ x.group for x in role.groups ]: - in_groups.append( ( group.id, group.name ) ) - else: - out_groups.append( ( group.id, group.name ) ) - associations_dict = dict( in_users=in_users, - out_users=out_users, - in_groups=in_groups, - out_groups=out_groups, - message=message, - status=status ) - return associations_dict - -def validate_repository_name( app, name, user ): - # Repository names must be unique for each user, must be at least four characters - # in length and must contain only lower-case letters, numbers, and the '_' character. - if name in [ 'None', None, '' ]: - return 'Enter the required repository name.' - if name in [ 'repos' ]: - return "The term <b>%s</b> is a reserved word in the tool shed, so it cannot be used as a repository name." % name - check_existing = suc.get_repository_by_name_and_owner( app, name, user.username ) - if check_existing is not None: - if check_existing.deleted: - return 'You have a deleted repository named <b>%s</b>, so choose a different name.' % name - else: - return "You already have a repository named <b>%s</b>, so choose a different name." % name - if len( name ) < 4: - return "Repository names must be at least 4 characters in length." - if len( name ) > 80: - return "Repository names cannot be more than 80 characters in length." - if not( VALID_REPOSITORYNAME_RE.match( name ) ): - return "Repository names must contain only lower-case letters, numbers and underscore <b>_</b>." - return '' diff -r 9cce4ead10795278446af4ab84eecfc4e2b26dce -r 4ee9e584dbc016727e4c90f73bbf53081f775c5a lib/tool_shed/util/repository_util.py --- /dev/null +++ b/lib/tool_shed/util/repository_util.py @@ -0,0 +1,330 @@ +import ConfigParser +import logging +import os +import re + +from galaxy import util +from galaxy import web +from galaxy.web.form_builder import build_select_field +from galaxy.webapps.tool_shed.model import directory_hash_id + +from tool_shed.dependencies.repository import relation_builder + +from tool_shed.util import common_util +from tool_shed.util import hg_util +from tool_shed.util import shed_util_common as suc + +log = logging.getLogger( __name__ ) + +VALID_REPOSITORYNAME_RE = re.compile( "^[a-z0-9\_]+$" ) + +def build_allow_push_select_field( trans, current_push_list, selected_value='none' ): + options = [] + for user in trans.sa_session.query( trans.model.User ): + if user.username not in current_push_list: + options.append( user ) + return build_select_field( trans, + objs=options, + label_attr='username', + select_field_name='allow_push', + selected_value=selected_value, + refresh_on_change=False, + multiple=True ) + +def change_repository_name_in_hgrc_file( hgrc_file, new_name ): + config = ConfigParser.ConfigParser() + config.read( hgrc_file ) + config.read( hgrc_file ) + config.set( 'web', 'name', new_name ) + new_file = open( hgrc_file, 'wb' ) + config.write( new_file ) + new_file.close() + +def check_or_update_tool_shed_status_for_installed_repository( app, repository ): + updated = False + tool_shed_status_dict = suc.get_tool_shed_status_for_installed_repository( app, repository ) + if tool_shed_status_dict: + ok = True + if tool_shed_status_dict != repository.tool_shed_status: + repository.tool_shed_status = tool_shed_status_dict + app.install_model.context.add( repository ) + app.install_model.context.flush() + updated = True + else: + ok = False + return ok, updated + +def create_repo_info_dict( app, repository_clone_url, changeset_revision, ctx_rev, repository_owner, repository_name=None, + repository=None, repository_metadata=None, tool_dependencies=None, repository_dependencies=None ): + """ + Return a dictionary that includes all of the information needed to install a repository into a local + Galaxy instance. The dictionary will also contain the recursive list of repository dependencies defined + for the repository, as well as the defined tool dependencies. + + This method is called from Galaxy under four scenarios: + 1. During the tool shed repository installation process via the tool shed's get_repository_information() + method. In this case both the received repository and repository_metadata will be objects, but + tool_dependencies and repository_dependencies will be None. + 2. When getting updates for an installed repository where the updates include newly defined repository + dependency definitions. This scenario is similar to 1. above. The tool shed's get_repository_information() + method is the caller, and both the received repository and repository_metadata will be objects, but + tool_dependencies and repository_dependencies will be None. + 3. When a tool shed repository that was uninstalled from a Galaxy instance is being reinstalled with no + updates available. In this case, both repository and repository_metadata will be None, but tool_dependencies + and repository_dependencies will be objects previously retrieved from the tool shed if the repository includes + definitions for them. + 4. When a tool shed repository that was uninstalled from a Galaxy instance is being reinstalled with updates + available. In this case, this method is reached via the tool shed's get_updated_repository_information() + method, and both repository and repository_metadata will be objects but tool_dependencies and + repository_dependencies will be None. + """ + repo_info_dict = {} + repository = suc.get_repository_by_name_and_owner( app, repository_name, repository_owner ) + if app.name == 'tool_shed': + # We're in the tool shed. + repository_metadata = suc.get_repository_metadata_by_changeset_revision( app, + app.security.encode_id( repository.id ), + changeset_revision ) + if repository_metadata: + metadata = repository_metadata.metadata + if metadata: + tool_shed_url = str( web.url_for( '/', qualified=True ) ).rstrip( '/' ) + rb = relation_builder.RelationBuilder( app, repository, repository_metadata, tool_shed_url ) + # Get a dictionary of all repositories upon which the contents of the received repository depends. + repository_dependencies = rb.get_repository_dependencies_for_changeset_revision() + tool_dependencies = metadata.get( 'tool_dependencies', {} ) + if tool_dependencies: + new_tool_dependencies = {} + for dependency_key, requirements_dict in tool_dependencies.items(): + if dependency_key in [ 'set_environment' ]: + new_set_environment_dict_list = [] + for set_environment_dict in requirements_dict: + set_environment_dict[ 'repository_name' ] = repository_name + set_environment_dict[ 'repository_owner' ] = repository_owner + set_environment_dict[ 'changeset_revision' ] = changeset_revision + new_set_environment_dict_list.append( set_environment_dict ) + new_tool_dependencies[ dependency_key ] = new_set_environment_dict_list + else: + requirements_dict[ 'repository_name' ] = repository_name + requirements_dict[ 'repository_owner' ] = repository_owner + requirements_dict[ 'changeset_revision' ] = changeset_revision + new_tool_dependencies[ dependency_key ] = requirements_dict + tool_dependencies = new_tool_dependencies + # Cast unicode to string, with the exception of description, since it is free text and can contain special characters. + repo_info_dict[ str( repository.name ) ] = ( repository.description, + str( repository_clone_url ), + str( changeset_revision ), + str( ctx_rev ), + str( repository_owner ), + repository_dependencies, + tool_dependencies ) + return repo_info_dict + +def create_repository( app, name, type, description, long_description, user_id, category_ids=[] ): + sa_session = app.model.context.current + # Add the repository record to the database. + repository = app.model.Repository( name=name, + type=type, + description=description, + long_description=long_description, + user_id=user_id ) + # Flush to get the id. + sa_session.add( repository ) + sa_session.flush() + # Create an admin role for the repository. + repository_admin_role = create_repository_admin_role( app, repository ) + # Determine the repository's repo_path on disk. + dir = os.path.join( app.config.file_path, *directory_hash_id( repository.id ) ) + # Create directory if it does not exist. + if not os.path.exists( dir ): + os.makedirs( dir ) + # Define repo name inside hashed directory. + repository_path = os.path.join( dir, "repo_%d" % repository.id ) + # Create local repository directory. + if not os.path.exists( repository_path ): + os.makedirs( repository_path ) + # Create the local repository. + repo = hg_util.get_repo_for_repository( app, repository=None, repo_path=repository_path, create=True ) + # Add an entry in the hgweb.config file for the local repository. + lhs = "repos/%s/%s" % ( repository.user.username, repository.name ) + app.hgweb_config_manager.add_entry( lhs, repository_path ) + # Create a .hg/hgrc file for the local repository. + hg_util.create_hgrc_file( app, repository ) + flush_needed = False + if category_ids: + # Create category associations + for category_id in category_ids: + category = sa_session.query( app.model.Category ) \ + .get( app.security.decode_id( category_id ) ) + rca = app.model.RepositoryCategoryAssociation( repository, category ) + sa_session.add( rca ) + flush_needed = True + if flush_needed: + sa_session.flush() + # Update the repository registry. + app.repository_registry.add_entry( repository ) + message = "Repository <b>%s</b> has been created." % str( repository.name ) + return repository, message + +def create_repository_admin_role( app, repository ): + """ + Create a new role with name-spaced name based on the repository name and its owner's public user + name. This will ensure that the tole name is unique. + """ + sa_session = app.model.context.current + name = get_repository_admin_role_name( str( repository.name ), str( repository.user.username ) ) + description = 'A user or group member with this role can administer this repository.' + role = app.model.Role( name=name, description=description, type=app.model.Role.types.SYSTEM ) + sa_session.add( role ) + sa_session.flush() + # Associate the role with the repository owner. + ura = app.model.UserRoleAssociation( repository.user, role ) + # Associate the role with the repository. + rra = app.model.RepositoryRoleAssociation( repository, role ) + sa_session.add( rra ) + sa_session.flush() + return role + +def get_installed_tool_shed_repository( app, id ): + """Get a tool shed repository record from the Galaxy database defined by the id.""" + return app.install_model.context.query( app.install_model.ToolShedRepository ) \ + .get( app.security.decode_id( id ) ) + +def get_repo_info_dict( app, user, repository_id, changeset_revision ): + repository = suc.get_repository_in_tool_shed( app, repository_id ) + repo = hg_util.get_repo_for_repository( app, repository=repository, repo_path=None, create=False ) + repository_clone_url = common_util.generate_clone_url_for_repository_in_tool_shed( user, repository ) + repository_metadata = suc.get_repository_metadata_by_changeset_revision( app, + repository_id, + changeset_revision ) + if not repository_metadata: + # The received changeset_revision is no longer installable, so get the next changeset_revision + # in the repository's changelog. This generally occurs only with repositories of type + # repository_suite_definition or tool_dependency_definition. + next_downloadable_changeset_revision = \ + suc.get_next_downloadable_changeset_revision( repository, repo, changeset_revision ) + if next_downloadable_changeset_revision: + repository_metadata = suc.get_repository_metadata_by_changeset_revision( app, + repository_id, + next_downloadable_changeset_revision ) + if repository_metadata: + # For now, we'll always assume that we'll get repository_metadata, but if we discover our assumption + # is not valid we'll have to enhance the callers to handle repository_metadata values of None in the + # returned repo_info_dict. + metadata = repository_metadata.metadata + if 'tools' in metadata: + includes_tools = True + else: + includes_tools = False + includes_tools_for_display_in_tool_panel = repository_metadata.includes_tools_for_display_in_tool_panel + repository_dependencies_dict = metadata.get( 'repository_dependencies', {} ) + repository_dependencies = repository_dependencies_dict.get( 'repository_dependencies', [] ) + has_repository_dependencies, has_repository_dependencies_only_if_compiling_contained_td = \ + suc.get_repository_dependency_types( repository_dependencies ) + if 'tool_dependencies' in metadata: + includes_tool_dependencies = True + else: + includes_tool_dependencies = False + else: + # Here's where we may have to handle enhancements to the callers. See above comment. + includes_tools = False + has_repository_dependencies = False + has_repository_dependencies_only_if_compiling_contained_td = False + includes_tool_dependencies = False + includes_tools_for_display_in_tool_panel = False + ctx = hg_util.get_changectx_for_changeset( repo, changeset_revision ) + repo_info_dict = create_repo_info_dict( app=app, + repository_clone_url=repository_clone_url, + changeset_revision=changeset_revision, + ctx_rev=str( ctx.rev() ), + repository_owner=repository.user.username, + repository_name=repository.name, + repository=repository, + repository_metadata=repository_metadata, + tool_dependencies=None, + repository_dependencies=None ) + return repo_info_dict, includes_tools, includes_tool_dependencies, includes_tools_for_display_in_tool_panel, \ + has_repository_dependencies, has_repository_dependencies_only_if_compiling_contained_td + +def get_repository_admin_role_name( repository_name, repository_owner ): + return '%s_%s_admin' % ( str( repository_name ), str( repository_owner ) ) + +def get_role_by_id( app, role_id ): + """Get a Role from the database by id.""" + sa_session = app.model.context.current + return sa_session.query( app.model.Role ).get( app.security.decode_id( role_id ) ) + +def handle_role_associations( app, role, repository, **kwd ): + sa_session = app.model.context.current + message = kwd.get( 'message', '' ) + status = kwd.get( 'status', 'done' ) + repository_owner = repository.user + if kwd.get( 'manage_role_associations_button', False ): + in_users_list = util.listify( kwd.get( 'in_users', [] ) ) + in_users = [ sa_session.query( app.model.User ).get( x ) for x in in_users_list ] + # Make sure the repository owner is always associated with the repostory's admin role. + owner_associated = False + for user in in_users: + if user.id == repository_owner.id: + owner_associated = True + break + if not owner_associated: + in_users.append( repository_owner ) + message += "The repository owner must always be associated with the repository's administrator role. " + status = 'error' + in_groups_list = util.listify( kwd.get( 'in_groups', [] ) ) + in_groups = [ sa_session.query( app.model.Group ).get( x ) for x in in_groups_list ] + in_repositories = [ repository ] + app.security_agent.set_entity_role_associations( roles=[ role ], + users=in_users, + groups=in_groups, + repositories=in_repositories ) + sa_session.refresh( role ) + message += "Role <b>%s</b> has been associated with %d users, %d groups and %d repositories. " % \ + ( str( role.name ), len( in_users ), len( in_groups ), len( in_repositories ) ) + in_users = [] + out_users = [] + in_groups = [] + out_groups = [] + for user in sa_session.query( app.model.User ) \ + .filter( app.model.User.table.c.deleted==False ) \ + .order_by( app.model.User.table.c.email ): + if user in [ x.user for x in role.users ]: + in_users.append( ( user.id, user.email ) ) + else: + out_users.append( ( user.id, user.email ) ) + for group in sa_session.query( app.model.Group ) \ + .filter( app.model.Group.table.c.deleted==False ) \ + .order_by( app.model.Group.table.c.name ): + if group in [ x.group for x in role.groups ]: + in_groups.append( ( group.id, group.name ) ) + else: + out_groups.append( ( group.id, group.name ) ) + associations_dict = dict( in_users=in_users, + out_users=out_users, + in_groups=in_groups, + out_groups=out_groups, + message=message, + status=status ) + return associations_dict + +def validate_repository_name( app, name, user ): + # Repository names must be unique for each user, must be at least four characters + # in length and must contain only lower-case letters, numbers, and the '_' character. + if name in [ 'None', None, '' ]: + return 'Enter the required repository name.' + if name in [ 'repos' ]: + return "The term <b>%s</b> is a reserved word in the tool shed, so it cannot be used as a repository name." % name + check_existing = suc.get_repository_by_name_and_owner( app, name, user.username ) + if check_existing is not None: + if check_existing.deleted: + return 'You have a deleted repository named <b>%s</b>, so choose a different name.' % name + else: + return "You already have a repository named <b>%s</b>, so choose a different name." % name + if len( name ) < 4: + return "Repository names must be at least 4 characters in length." + if len( name ) > 80: + return "Repository names cannot be more than 80 characters in length." + if not( VALID_REPOSITORYNAME_RE.match( name ) ): + return "Repository names must contain only lower-case letters, numbers and underscore <b>_</b>." + return '' Repository URL: https://bitbucket.org/galaxy/galaxy-central/ -- This is a commit notification from bitbucket.org. 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