diff --git a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py index 75bdf9b63e8..d8bd9f6fecd 100644 --- a/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py +++ b/lib/galaxy/webapps/galaxy/controllers/admin_toolshed.py @@ -228,94 +228,104 @@ class AdminToolshed( AdminGalaxy ): but we may choose to do so in the future if it becomes necessary. """ message = escape( kwd.get( 'message', '' ) ) + statuses = [ None, '' 'info', 'done', 'warning', 'error' ] status = kwd.get( 'status', 'done' ) + if status in statuses: + status = statuses.index( status ) + else: + status = 1 remove_from_disk = kwd.get( 'remove_from_disk', '' ) remove_from_disk_checked = CheckboxField.is_checked( remove_from_disk ) - 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: - if tool_path: - relative_install_dir = os.path.join( tool_path, relative_install_dir ) - repository_install_dir = os.path.abspath( relative_install_dir ) - else: - repository_install_dir = None - errors = '' - if kwd.get( 'deactivate_or_uninstall_repository_button', False ): - if tool_shed_repository.includes_tools_for_display_in_tool_panel: - # Handle tool panel alterations. - tpm = tool_panel_manager.ToolPanelManager( trans.app ) - tpm.remove_repository_contents( tool_shed_repository, - shed_tool_conf, - uninstall=remove_from_disk_checked ) - if tool_shed_repository.includes_data_managers: - dmh = data_manager.DataManagerHandler( trans.app ) - dmh.remove_from_data_manager( tool_shed_repository ) - if tool_shed_repository.includes_datatypes: - # Deactivate proprietary datatypes. - cdl = custom_datatype_manager.CustomDatatypeLoader( trans.app ) - installed_repository_dict = cdl.load_installed_datatypes( tool_shed_repository, - repository_install_dir, - deactivate=True ) - if installed_repository_dict: - converter_path = installed_repository_dict.get( 'converter_path' ) - if converter_path is not None: - cdl.load_installed_datatype_converters( installed_repository_dict, deactivate=True ) - display_path = installed_repository_dict.get( 'display_path' ) - if display_path is not None: - cdl.load_installed_display_applications( installed_repository_dict, deactivate=True ) - if remove_from_disk_checked: - try: - # Remove the repository from disk. - shutil.rmtree( repository_install_dir ) - log.debug( "Removed repository installation directory: %s" % str( repository_install_dir ) ) - removed = True - except Exception, e: - log.debug( "Error removing repository installation directory %s: %s" % ( str( repository_install_dir ), str( e ) ) ) - if isinstance( e, OSError ) and not os.path.exists( repository_install_dir ): + tool_shed_repositories = repository_util.get_installed_tool_shed_repository( trans.app, kwd[ 'id' ] ) + if not isinstance( tool_shed_repositories, list ): + tool_shed_repositories = [tool_shed_repositories] + for tool_shed_repository in tool_shed_repositories: + 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: + if tool_path: + relative_install_dir = os.path.join( tool_path, relative_install_dir ) + repository_install_dir = os.path.abspath( relative_install_dir ) + else: + repository_install_dir = None + errors = '' + if kwd.get( 'deactivate_or_uninstall_repository_button', False ): + if tool_shed_repository.includes_tools_for_display_in_tool_panel: + # Handle tool panel alterations. + tpm = tool_panel_manager.ToolPanelManager( trans.app ) + tpm.remove_repository_contents( tool_shed_repository, + shed_tool_conf, + uninstall=remove_from_disk_checked ) + if tool_shed_repository.includes_data_managers: + dmh = data_manager.DataManagerHandler( trans.app ) + dmh.remove_from_data_manager( tool_shed_repository ) + if tool_shed_repository.includes_datatypes: + # Deactivate proprietary datatypes. + cdl = custom_datatype_manager.CustomDatatypeLoader( trans.app ) + installed_repository_dict = cdl.load_installed_datatypes( tool_shed_repository, + repository_install_dir, + deactivate=True ) + if installed_repository_dict: + converter_path = installed_repository_dict.get( 'converter_path' ) + if converter_path is not None: + cdl.load_installed_datatype_converters( installed_repository_dict, deactivate=True ) + display_path = installed_repository_dict.get( 'display_path' ) + if display_path is not None: + cdl.load_installed_display_applications( installed_repository_dict, deactivate=True ) + if remove_from_disk_checked: + try: + # Remove the repository from disk. + shutil.rmtree( repository_install_dir ) + log.debug( "Removed repository installation directory: %s" % str( repository_install_dir ) ) removed = True - log.debug( "Repository directory does not exist on disk, marking as uninstalled." ) - else: - removed = False - if removed: - tool_shed_repository.uninstalled = True - # Remove all installed tool dependencies and tool dependencies stuck in the INSTALLING state, but don't touch any - # repository dependencies. - tool_dependencies_to_uninstall = tool_shed_repository.tool_dependencies_installed_or_in_error - tool_dependencies_to_uninstall.extend( tool_shed_repository.tool_dependencies_being_installed ) - for tool_dependency in tool_dependencies_to_uninstall: - uninstalled, error_message = tool_dependency_util.remove_tool_dependency( trans.app, tool_dependency ) - if error_message: - errors = '%s %s' % ( errors, error_message ) - tool_shed_repository.deleted = True - if remove_from_disk_checked: - tool_shed_repository.status = trans.install_model.ToolShedRepository.installation_status.UNINSTALLED - tool_shed_repository.error_message = None - if trans.app.config.manage_dependency_relationships: - # Remove the uninstalled repository and any tool dependencies from the in-memory dictionaries in the - # installed_repository_manager. - trans.app.installed_repository_manager.handle_repository_uninstall( tool_shed_repository ) - else: - tool_shed_repository.status = trans.install_model.ToolShedRepository.installation_status.DEACTIVATED - trans.install_model.context.add( tool_shed_repository ) - trans.install_model.context.flush() - if remove_from_disk_checked: - message = 'The repository named %s has been uninstalled. ' % escape( tool_shed_repository.name ) - if errors: - message += 'Attempting to uninstall tool dependencies resulted in errors: %s' % errors - status = 'error' + except Exception, e: + log.debug( "Error removing repository installation directory %s: %s" % ( str( repository_install_dir ), str( e ) ) ) + if isinstance( e, OSError ) and not os.path.exists( repository_install_dir ): + removed = True + log.debug( "Repository directory does not exist on disk, marking as uninstalled." ) + else: + removed = False + if removed: + tool_shed_repository.uninstalled = True + # Remove all installed tool dependencies and tool dependencies stuck in the INSTALLING state, but don't touch any + # repository dependencies. + tool_dependencies_to_uninstall = tool_shed_repository.tool_dependencies_installed_or_in_error + tool_dependencies_to_uninstall.extend( tool_shed_repository.tool_dependencies_being_installed ) + for tool_dependency in tool_dependencies_to_uninstall: + uninstalled, error_message = tool_dependency_util.remove_tool_dependency( trans.app, tool_dependency ) + if error_message: + errors = '%s %s' % ( errors, error_message ) + tool_shed_repository.deleted = True + if remove_from_disk_checked: + tool_shed_repository.status = trans.install_model.ToolShedRepository.installation_status.UNINSTALLED + tool_shed_repository.error_message = None + if trans.app.config.manage_dependency_relationships: + # Remove the uninstalled repository and any tool dependencies from the in-memory dictionaries in the + # installed_repository_manager. + trans.app.installed_repository_manager.handle_repository_uninstall( tool_shed_repository ) else: - status = 'done' - else: - message = 'The repository named %s has been deactivated. ' % escape( tool_shed_repository.name ) - status = 'done' + tool_shed_repository.status = trans.install_model.ToolShedRepository.installation_status.DEACTIVATED + trans.install_model.context.add( tool_shed_repository ) + trans.install_model.context.flush() + if remove_from_disk_checked: + message += 'The repository named %s has been uninstalled. ' % escape( tool_shed_repository.name ) + if errors: + message += 'Attempting to uninstall tool dependencies resulted in errors: %s' % errors + status = max( status, statuses.index( 'error' ) ) + else: + status = max( status, statuses.index( 'done' ) ) + else: + message = 'The repository named %s has been deactivated. ' % escape( tool_shed_repository.name ) + status = max( status, statuses.index( 'done' ) ) + status = statuses[ status ] + if kwd.get( 'deactivate_or_uninstall_repository_button', False ): return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='browse_repositories', message=message, status=status ) ) remove_from_disk_check_box = CheckboxField( 'remove_from_disk', checked=remove_from_disk_checked ) return trans.fill_template( '/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako', - repository=tool_shed_repository, + repository=tool_shed_repositories, remove_from_disk_check_box=remove_from_disk_check_box, message=message, status=status ) diff --git a/lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py b/lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py index 4f4982ea7dd..2218c8dd3d8 100644 --- a/lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py +++ b/lib/tool_shed/galaxy_install/grids/admin_toolshed_grids.py @@ -196,7 +196,7 @@ class InstalledRepositoryGrid( grids.Grid ): condition=( lambda item: not item.deleted and item.status != tool_shed_install.ToolShedRepository.installation_status.NEW ), - allow_multiple=False, + allow_multiple=True, url_args=dict( controller='admin_toolshed', action='browse_repositories', operation='deactivate or uninstall' ) ), diff --git a/lib/tool_shed/util/repository_util.py b/lib/tool_shed/util/repository_util.py index d3b43037692..990313dbef3 100644 --- a/lib/tool_shed/util/repository_util.py +++ b/lib/tool_shed/util/repository_util.py @@ -275,8 +275,17 @@ def create_repository_admin_role( app, repository ): 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 ) ) + rval = [] + if isinstance( id, list ): + return_list = True + else: + id = [ id ] + return_list = False + for i in id: + rval.append( app.install_model.context.query( app.install_model.ToolShedRepository ).get( app.security.decode_id( i ) ) ) + if return_list: + return rval + return rval[0] def get_repo_info_dict( app, user, repository_id, changeset_revision ): diff --git a/templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako b/templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako index a46be5012fc..8b1b3f7b863 100644 --- a/templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako +++ b/templates/admin/tool_shed_repository/deactivate_or_uninstall_repository.mako @@ -3,16 +3,28 @@ <%namespace file="/admin/tool_shed_repository/common.mako" import="*" /> <%namespace file="/admin/tool_shed_repository/repository_actions_menu.mako" import="*" /> -${render_galaxy_repository_actions( repository )} +<% +repository = context.get( 'repository', None ) +if isinstance( repository, list ): + repositories = repository +else: + repositories = [ repository ] +%> + +%if len( repositories ) == 1: + ${render_galaxy_repository_actions( repositories[0] )} +%endif %if message: ${render_msg( message, status )} %endif
+
+%for repository in repositories: +
${repository.name|h}
-
${repository.description|h} @@ -169,10 +181,12 @@ ${render_galaxy_repository_actions( repository )} %endif %endif
+
+%endfor
<% - can_deactivate_repository = repository.can_deactivate - can_uninstall_repository = repository.can_uninstall + can_deactivate_repository = True in map( lambda x: x.can_deactivate, repositories ) + can_uninstall_repository = True in map( lambda x: x.can_uninstall, repositories ) %> %if can_deactivate_repository and can_uninstall_repository: <% deactivate_uninstall_button_text = "Deactivate or Uninstall" %>