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Source code for galaxy.webapps.galaxy.controllers.admin_toolshed

import json
import logging
import os
import shutil

from six import string_types
from sqlalchemy import or_

import tool_shed.repository_types.util as rt_util
from admin import AdminGalaxy
from galaxy import util, web
from galaxy.tools.deps import views
from galaxy.web.form_builder import CheckboxField
from tool_shed.galaxy_install import dependency_display
from tool_shed.galaxy_install import install_manager
from tool_shed.galaxy_install.datatypes import custom_datatype_manager
from tool_shed.galaxy_install.grids import admin_toolshed_grids
from tool_shed.galaxy_install.metadata.installed_repository_metadata_manager import InstalledRepositoryMetadataManager
from tool_shed.galaxy_install.repair_repository_manager import RepairRepositoryManager
from tool_shed.galaxy_install.repository_dependencies import repository_dependency_manager
from tool_shed.galaxy_install.tools import data_manager
from tool_shed.galaxy_install.tools import tool_panel_manager
from tool_shed.tools import tool_version_manager
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 readme_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
from tool_shed.util import workflow_util
from tool_shed.util.web_util import escape

log = logging.getLogger( __name__ )


[docs]class AdminToolshed( AdminGalaxy ): installed_repository_grid = admin_toolshed_grids.InstalledRepositoryGrid() repository_installation_grid = admin_toolshed_grids.RepositoryInstallationGrid() tool_dependency_grid = admin_toolshed_grids.ToolDependencyGrid()
[docs] @web.expose @web.require_admin def activate_repository( self, trans, **kwd ): """Activate a repository that was deactivated but not uninstalled.""" repository_id = kwd[ 'id' ] repository = repository_util.get_installed_tool_shed_repository( trans.app, repository_id ) try: trans.app.installed_repository_manager.activate_repository( repository ) except Exception as e: error_message = "Error activating repository %s: %s" % ( escape( repository.name ), str( e ) ) log.exception( error_message ) message = '%s.<br/>You may be able to resolve this by uninstalling and then reinstalling the repository. Click <a href="%s">here</a> to uninstall the repository.' \ % ( error_message, web.url_for( controller='admin_toolshed', action='deactivate_or_uninstall_repository', id=trans.security.encode_id( repository.id ) ) ) status = 'error' return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='manage_repository', id=repository_id, message=message, status=status ) ) message = 'The <b>%s</b> repository has been activated.' % escape( repository.name ) status = 'done' return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='browse_repositories', message=message, status=status ) )
[docs] @web.expose @web.require_admin def browse_repository( self, trans, **kwd ): message = escape( kwd.get( 'message', '' ) ) status = kwd.get( 'status', 'done' ) 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, status=status )
[docs] @web.expose @web.require_admin def browse_repositories( self, trans, **kwd ): if 'operation' in kwd: operation = kwd.pop( 'operation' ).lower() if operation == "manage_repository": return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='manage_repository', **kwd ) ) if operation == "get updates": return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='check_for_updates', **kwd ) ) if operation == "update tool shed status": return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='update_tool_shed_status_for_installed_repository', **kwd ) ) if operation == "reset to install": kwd[ 'reset_repository' ] = True return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='reset_to_install', **kwd ) ) if operation == "purge": return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='purge_repository', **kwd ) ) if operation == "activate or reinstall": 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 # repository dependencies and tool dependencies will be current. Only allow selecting a different section # in the tool panel if the repository was uninstalled and it contained tools that should be displayed in # the tool panel. changeset_revision_dict = \ trans.app.update_repository_manager.get_update_to_changeset_revision_and_ctx_rev( repository ) current_changeset_revision = changeset_revision_dict.get( 'changeset_revision', None ) current_ctx_rev = changeset_revision_dict.get( 'ctx_rev', None ) if current_changeset_revision and current_ctx_rev: if current_ctx_rev == repository.ctx_rev: # The uninstalled repository is current. return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='reselect_tool_panel_section', **kwd ) ) else: # The uninstalled repository has updates available in the tool shed. updated_repo_info_dict = \ self.get_updated_repository_information( trans=trans, repository_id=trans.security.encode_id( repository.id ), repository_name=repository.name, repository_owner=repository.owner, changeset_revision=current_changeset_revision ) json_repo_info_dict = json.dumps( updated_repo_info_dict ) encoded_repo_info_dict = encoding_util.tool_shed_encode( json_repo_info_dict ) kwd[ 'latest_changeset_revision' ] = current_changeset_revision kwd[ 'latest_ctx_rev' ] = current_ctx_rev kwd[ 'updated_repo_info_dict' ] = encoded_repo_info_dict return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='reselect_tool_panel_section', **kwd ) ) else: message = "Unable to get latest revision for repository <b>%s</b> from " % escape( str( repository.name ) ) message += "the Tool Shed, so repository re-installation is not possible at this time." status = "error" return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='browse_repositories', message=message, status=status ) ) else: return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='activate_repository', **kwd ) ) if operation == "deactivate or uninstall": return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='deactivate_or_uninstall_repository', **kwd ) ) if operation == "install latest revision": return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='install_latest_repository_revision', **kwd ) ) if operation == 'install': # The user is attempting to install a white ghost. kwd[ 'status' ] = 'error' kwd[ 'message' ] = 'It seems you are attempting to install a "white ghost", which should instead be purged.' return self.installed_repository_grid( trans, **kwd )
[docs] @web.expose @web.require_admin def browse_tool_dependency( self, trans, **kwd ): message = escape( kwd.get( 'message', '' ) ) status = kwd.get( 'status', 'done' ) tool_dependency_ids = tool_dependency_util.get_tool_dependency_ids( as_string=False, **kwd ) tool_dependency = tool_dependency_util.get_tool_dependency( trans.app, tool_dependency_ids[ 0 ] ) if tool_dependency.in_error_state: message = "This tool dependency is not installed correctly (see the <b>Tool dependency installation error</b> below). " message += "Choose <b>Uninstall this tool dependency</b> from the <b>Repository Actions</b> menu, correct problems " message += "if necessary, and try installing the dependency again." status = "error" repository = tool_dependency.tool_shed_repository return trans.fill_template( '/admin/tool_shed_repository/browse_tool_dependency.mako', repository=repository, tool_dependency=tool_dependency, message=message, status=status )
[docs] @web.expose @web.require_admin def browse_tool_shed( self, trans, **kwd ): tool_shed_url = kwd.get( 'tool_shed_url', '' ) tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, tool_shed_url ) params = dict( galaxy_url=web.url_for( '/', qualified=True ) ) url = util.build_url( tool_shed_url, pathspec=[ 'repository', 'browse_valid_categories' ], params=params ) return trans.response.send_redirect( url )
[docs] @web.expose @web.require_admin def browse_toolsheds( self, trans, **kwd ): message = escape( kwd.get( 'message', '' ) ) return trans.fill_template( '/admin/tool_shed_repository/browse_toolsheds.mako', message=message, status='error' )
[docs] @web.expose @web.require_admin def browse_tool_sheds( self, trans, **kwd ): message = escape( kwd.get( 'message', '' ) ) return trans.fill_template( '/webapps/galaxy/admin/tool_sheds.mako', message=message, status='error' )
[docs] @web.expose @web.require_admin 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_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 = dict( galaxy_url=web.url_for( '/', qualified=True ), name=str( repository.name ), owner=str( repository.owner ), changeset_revision=str( repository.changeset_revision ) ) pathspec = [ 'repository', 'check_for_updates' ] url = util.build_url( tool_shed_url, pathspec=pathspec, params=params ) return trans.response.send_redirect( url )
[docs] @web.expose @web.require_admin def deactivate_or_uninstall_repository( self, trans, **kwd ): """ Handle all changes when a tool shed repository is being deactivated or uninstalled. Notice that if the repository contents include a file named tool_data_table_conf.xml.sample, its entries are not removed from the defined config.shed_tool_data_table_config. This is because it becomes a bit complex to determine if other installed repositories include tools that require the same entry. For now we'll never delete entries from config.shed_tool_data_table_config, 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_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 except Exception as 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: tool_shed_repository.status = trans.install_model.ToolShedRepository.installation_status.DEACTIVATED trans.install_model.context.current.add( tool_shed_repository ) trans.install_model.context.current.flush() if remove_from_disk_checked: message += 'The repository named <b>%s</b> 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 <b>%s</b> 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_repositories, remove_from_disk_check_box=remove_from_disk_check_box, message=message, status=status )
[docs] @web.expose def display_image_in_repository( self, trans, **kwd ): """ Open an image file that is contained in an installed tool shed repository or that is referenced by a URL for display. The image can be defined in either a README.rst file contained in the repository or the help section of a Galaxy tool config that is contained in the repository. The following image definitions are all supported. The former $PATH_TO_IMAGES is no longer required, and is now ignored. .. image:: https://raw.github.com/galaxy/some_image.png .. image:: $PATH_TO_IMAGES/some_image.png .. image:: /static/images/some_image.gif .. image:: some_image.jpg .. image:: /deep/some_image.png """ repository_id = kwd.get( 'repository_id', None ) relative_path_to_image_file = kwd.get( 'image_file', None ) if repository_id and relative_path_to_image_file: repository = repository_util.get_tool_shed_repository_by_id( trans.app, repository_id ) if repository: repo_files_dir = repository.repo_files_directory( trans.app ) # The following line sometimes returns None. TODO: Figure out why. path_to_file = repository_util.get_absolute_path_to_file_in_repository( repo_files_dir, relative_path_to_image_file ) if path_to_file and os.path.exists( path_to_file ): file_name = os.path.basename( relative_path_to_image_file ) try: extension = file_name.split( '.' )[ -1 ] except Exception: extension = None if extension: mimetype = trans.app.datatypes_registry.get_mimetype_by_extension( extension ) if mimetype: trans.response.set_content_type( mimetype ) return open( path_to_file, 'r' ) return None
[docs] @web.expose @web.require_admin def find_tools_in_tool_shed( self, trans, **kwd ): tool_shed_url = kwd.get( 'tool_shed_url', '' ) tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, tool_shed_url ) params = dict( galaxy_url=web.url_for( '/', qualified=True ) ) url = util.build_url( tool_shed_url, pathspec=[ 'repository', 'find_tools' ], params=params ) return trans.response.send_redirect( url )
[docs] @web.expose @web.require_admin def find_workflows_in_tool_shed( self, trans, **kwd ): tool_shed_url = kwd.get( 'tool_shed_url', '' ) tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, tool_shed_url ) params = dict( galaxy_url=web.url_for( '/', qualified=True ) ) url = util.build_url( tool_shed_url, pathspec=[ 'repository', 'find_workflows' ], params=params ) return trans.response.send_redirect( url )
[docs] @web.expose @web.require_admin def generate_workflow_image( self, trans, workflow_name, repository_id=None ): """Return an svg image representation of a workflow dictionary created when the workflow was exported.""" return workflow_util.generate_workflow_image( trans, workflow_name, repository_metadata_id=None, repository_id=repository_id )
[docs] @web.json @web.require_admin def get_file_contents( self, trans, file_path, repository_id ): # Avoid caching trans.response.headers['Pragma'] = 'no-cache' trans.response.headers['Expires'] = '0' return suc.get_repository_file_contents( trans.app, file_path, repository_id, is_admin=True )
[docs] @web.expose @web.require_admin def get_tool_dependencies( self, trans, repository_id, repository_name, repository_owner, changeset_revision ): """ Send a request to the appropriate tool shed to retrieve the dictionary of tool dependencies defined for the received repository name, owner and changeset revision. The received repository_id is the encoded id 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_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 " message += "parameters is None: tool_shed_url: %s, repository_name: %s, repository_owner: %s, changeset_revision: %s " % \ ( str( tool_shed_url ), str( repository_name ), str( repository_owner ), str( changeset_revision ) ) raise Exception( message ) params = dict( name=repository_name, owner=repository_owner, changeset_revision=changeset_revision ) pathspec = [ 'repository', 'get_tool_dependencies' ] raw_text = util.url_get( tool_shed_url, password_mgr=self.app.tool_shed_registry.url_auth( tool_shed_url ), pathspec=pathspec, params=params ) if len( raw_text ) > 2: encoded_text = json.loads( raw_text ) text = encoding_util.tool_shed_decode( encoded_text ) else: text = '' return text
[docs] @web.expose @web.require_admin def get_updated_repository_information( self, trans, repository_id, repository_name, repository_owner, changeset_revision ): """ 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_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 " message += "required parameters is None: tool_shed_url: %s, repository_name: %s, repository_owner: %s, changeset_revision: %s " % \ ( str( tool_shed_url ), str( repository_name ), str( repository_owner ), str( changeset_revision ) ) raise Exception( message ) params = dict( name=str( repository_name ), owner=str( repository_owner ), changeset_revision=changeset_revision ) pathspec = [ 'repository', 'get_updated_repository_information' ] raw_text = util.url_get( tool_shed_url, password_mgr=self.app.tool_shed_registry.url_auth( tool_shed_url ), pathspec=pathspec, params=params ) repo_information_dict = json.loads( raw_text ) return repo_information_dict
[docs] @web.expose @web.require_admin def import_workflow( self, trans, workflow_name, repository_id, **kwd ): """Import a workflow contained in an installed tool shed repository into Galaxy.""" message = str( escape( kwd.get( 'message', '' ) ) ) status = kwd.get( 'status', 'done' ) if workflow_name: workflow_name = encoding_util.tool_shed_decode( workflow_name ) repository = repository_util.get_tool_shed_repository_by_id( trans.app, repository_id ) if repository: workflow, status, message = workflow_util.import_workflow( trans, repository, workflow_name ) if workflow: workflow_name = encoding_util.tool_shed_encode( str( workflow.name ) ) else: message += 'Unable to locate a workflow named <b>%s</b> within the installed tool shed repository named <b>%s</b>' % \ ( escape( str( workflow_name ) ), escape( str( repository.name ) ) ) status = 'error' else: message = 'Invalid repository id <b>%s</b> received.' % str( repository_id ) status = 'error' else: message = 'The value of workflow_name is required, but was not received.' status = 'error' return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='view_workflow', workflow_name=workflow_name, repository_id=repository_id, message=message, status=status ) )
[docs] @web.expose @web.require_admin def initiate_tool_dependency_installation( self, trans, tool_dependencies, **kwd ): """ Install specified dependencies for repository tools. The received list of tool_dependencies are the database records for those dependencies defined in the tool_dependencies.xml file (contained in the repository) that should be installed. This allows for filtering out dependencies that have not been checked for installation on the 'Manage tool dependencies' page for an installed tool shed repository. """ # Get the tool_shed_repository from one of the tool_dependencies. message = str( escape( kwd.get( 'message', '' ) ) ) status = kwd.get( 'status', 'done' ) err_msg = '' tool_shed_repository = tool_dependencies[ 0 ].tool_shed_repository # Get the tool_dependencies.xml file from the repository. tool_dependencies_config = hg_util.get_config_from_disk( rt_util.TOOL_DEPENDENCY_DEFINITION_FILENAME, tool_shed_repository.repo_path( trans.app ) ) itdm = install_manager.InstallToolDependencyManager( trans.app ) installed_tool_dependencies = itdm.install_specified_tool_dependencies( tool_shed_repository=tool_shed_repository, tool_dependencies_config=tool_dependencies_config, tool_dependencies=tool_dependencies, from_tool_migration_manager=False ) for installed_tool_dependency in installed_tool_dependencies: if installed_tool_dependency.status == trans.app.install_model.ToolDependency.installation_status.ERROR: text = util.unicodify( installed_tool_dependency.error_message ) if text is not None: err_msg += ' %s' % text if err_msg: message += err_msg status = 'error' message += "Installed tool dependencies: %s" % ', '.join( td.name for td in installed_tool_dependencies ) td_ids = [ trans.security.encode_id( td.id ) for td in tool_shed_repository.tool_dependencies ] return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='manage_tool_dependencies', tool_dependency_ids=td_ids, message=message, status=status ) )
[docs] @web.expose @web.require_admin def install_latest_repository_revision( self, trans, **kwd ): """Install the latest installable revision of a repository that has been previously installed.""" message = escape( kwd.get( 'message', '' ) ) status = kwd.get( 'status', 'done' ) repository_id = kwd.get( 'id', None ) if repository_id is not None: 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 ) owner = str( repository.owner ) params = dict( galaxy_url=web.url_for( '/', qualified=True ), name=name, owner=owner ) pathspec = [ 'repository', 'get_latest_downloadable_changeset_revision' ] raw_text = util.url_get( tool_shed_url, password_mgr=self.app.tool_shed_registry.url_auth( tool_shed_url ), pathspec=pathspec, params=params ) url = util.build_url( tool_shed_url, pathspec=pathspec, params=params ) latest_downloadable_revision = json.loads( raw_text ) if latest_downloadable_revision == hg_util.INITIAL_CHANGELOG_HASH: message = 'Error retrieving the latest downloadable revision for this repository via the url <b>%s</b>.' % url status = 'error' else: # Make sure the latest changeset_revision of the repository has not already been installed. # Updates to installed repository revisions may have occurred, so make sure to locate the # appropriate repository revision if one exists. We need to create a temporary repo_info_tuple # with the following entries to handle this. # ( description, clone_url, changeset_revision, ctx_rev, owner, repository_dependencies, tool_dependencies ) tmp_clone_url = util.build_url( tool_shed_url, pathspec=[ 'repos', owner, name ] ) tmp_repo_info_tuple = ( None, tmp_clone_url, latest_downloadable_revision, None, owner, None, None ) installed_repository, installed_changeset_revision = \ repository_util.repository_was_previously_installed( trans.app, tool_shed_url, name, tmp_repo_info_tuple, from_tip=False ) if installed_repository: current_changeset_revision = str( installed_repository.changeset_revision ) message = 'Revision <b>%s</b> of repository <b>%s</b> owned by <b>%s</b> has already been installed.' % \ ( latest_downloadable_revision, name, owner ) if current_changeset_revision != latest_downloadable_revision: message += ' The current changeset revision is <b>%s</b>.' % current_changeset_revision status = 'error' else: # Install the latest downloadable revision of the repository. params = dict( name=name, owner=owner, changeset_revisions=str( latest_downloadable_revision ), galaxy_url=web.url_for( '/', qualified=True ) ) pathspec = [ 'repository', 'install_repositories_by_revision' ] url = util.build_url( tool_shed_url, pathspec=pathspec, params=params ) return trans.response.send_redirect( url ) else: message = 'Cannot locate installed tool shed repository with encoded id <b>%s</b>.' % str( repository_id ) status = 'error' else: message = 'The request parameters did not include the required encoded <b>id</b> of installed repository.' status = 'error' return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='browse_repositories', message=message, status=status ) )
[docs] @web.expose @web.require_admin def install_tool_dependencies_with_update( self, trans, **kwd ): """ Updating an installed tool shed repository where new tool dependencies but no new repository dependencies are included in the updated revision. """ updating_repository_id = kwd.get( 'updating_repository_id', None ) 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: tool_dependencies_dict = encoding_util.tool_shed_decode( encoded_tool_dependencies_dict ) else: tool_dependencies_dict = {} encoded_relative_install_dir = kwd.get( 'encoded_relative_install_dir', None ) if encoded_relative_install_dir is not None: relative_install_dir = encoding_util.tool_shed_decode( encoded_relative_install_dir ) else: relative_install_dir = '' updating_to_changeset_revision = kwd.get( 'updating_to_changeset_revision', None ) updating_to_ctx_rev = kwd.get( 'updating_to_ctx_rev', None ) encoded_updated_metadata = kwd.get( 'encoded_updated_metadata', None ) message = escape( kwd.get( 'message', '' ) ) status = kwd.get( 'status', 'done' ) if 'install_tool_dependencies_with_update_button' in kwd: # Now that the user has chosen whether to install tool dependencies or not, we can # update the repository record with the changes in the updated revision. if encoded_updated_metadata: updated_metadata = encoding_util.tool_shed_decode( encoded_updated_metadata ) else: updated_metadata = None repository = trans.app.update_repository_manager.update_repository_record( repository=repository, updated_metadata_dict=updated_metadata, updated_changeset_revision=updating_to_changeset_revision, updated_ctx_rev=updating_to_ctx_rev ) if tool_dependencies_dict: tool_dependencies = tool_dependency_util.create_tool_dependency_objects( trans.app, repository, relative_install_dir, set_status=False ) message = "The installed repository named '%s' has been updated to change set revision '%s'. " % \ ( escape( str( repository.name ) ), updating_to_changeset_revision ) self.initiate_tool_dependency_installation( trans, tool_dependencies, message=message, status=status ) # Handle tool dependencies check box. if trans.app.config.tool_dependency_dir is None: if tool_dependencies_dict: message = ("Tool dependencies defined in this repository can be automatically installed if you set " "the value of your <b>tool_dependency_dir</b> setting in your Galaxy config file " "(galaxy.ini) and restart your Galaxy server.") status = "warning" install_tool_dependencies_check_box_checked = False else: install_tool_dependencies_check_box_checked = True install_tool_dependencies_check_box = CheckboxField( 'install_tool_dependencies', checked=install_tool_dependencies_check_box_checked ) view = views.DependencyResolversView(self.app) if view.installable_resolvers: install_resolver_dependencies_check_box = CheckboxField( 'install_resolver_dependencies', checked=True ) else: install_resolver_dependencies_check_box = None return trans.fill_template( '/admin/tool_shed_repository/install_tool_dependencies_with_update.mako', repository=repository, updating_repository_id=updating_repository_id, updating_to_ctx_rev=updating_to_ctx_rev, updating_to_changeset_revision=updating_to_changeset_revision, encoded_updated_metadata=encoded_updated_metadata, encoded_relative_install_dir=encoded_relative_install_dir, encoded_tool_dependencies_dict=encoded_tool_dependencies_dict, install_resolver_dependencies_check_box=install_resolver_dependencies_check_box, install_tool_dependencies_check_box=install_tool_dependencies_check_box, tool_dependencies_dict=tool_dependencies_dict, message=message, status=status )
[docs] @web.expose @web.require_admin def manage_repositories( self, trans, **kwd ): message = escape( kwd.get( 'message', '' ) ) api_installation = util.asbool( kwd.get( 'api', 'false' ) ) if api_installation: tsr_ids = json.loads( kwd.get( 'tool_shed_repository_ids', '[]' ) ) kwd[ 'tool_shed_repository_ids' ] = tsr_ids tsridslist = common_util.get_tool_shed_repository_ids( **kwd ) else: tsridslist = common_util.get_tool_shed_repository_ids( **kwd ) if 'operation' in kwd: operation = kwd[ 'operation' ].lower() if not tsridslist: message = 'Select at least 1 tool shed repository to %s.' % operation kwd[ 'message' ] = message kwd[ 'status' ] = 'error' del kwd[ 'operation' ] return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='manage_repositories', **kwd ) ) if operation == 'browse': return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='browse_repository', **kwd ) ) elif operation == 'uninstall': # TODO: I believe this block should be removed, but make sure.. repositories_for_uninstallation = [] for repository_id in tsridslist: repository = trans.install_model.context.query( trans.install_model.ToolShedRepository ) \ .get( trans.security.decode_id( repository_id ) ) if repository.status in [ trans.install_model.ToolShedRepository.installation_status.INSTALLED, trans.install_model.ToolShedRepository.installation_status.ERROR ]: repositories_for_uninstallation.append( repository ) if repositories_for_uninstallation: return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='uninstall_repositories', **kwd ) ) else: kwd[ 'message' ] = 'All selected tool shed repositories are already uninstalled.' kwd[ 'status' ] = 'error' elif operation == "install": irm = install_manager.InstallRepositoryManager( trans.app ) reinstalling = util.string_as_bool( kwd.get( 'reinstalling', False ) ) encoded_kwd = kwd[ 'encoded_kwd' ] decoded_kwd = encoding_util.tool_shed_decode( encoded_kwd ) install_resolver_dependencies = CheckboxField.is_checked( decoded_kwd.get( 'install_resolver_dependencies', '' ) ) install_tool_dependencies = CheckboxField.is_checked( decoded_kwd.get( 'install_tool_dependencies', '' ) ) tsr_ids = decoded_kwd[ 'tool_shed_repository_ids' ] decoded_kwd['install_resolver_dependencies'] = install_resolver_dependencies decoded_kwd['install_tool_dependencies'] = install_tool_dependencies try: tool_shed_repositories = irm.install_repositories( tsr_ids=tsr_ids, decoded_kwd=decoded_kwd, reinstalling=reinstalling, ) tsr_ids_for_monitoring = [ trans.security.encode_id( tsr.id ) for tsr in tool_shed_repositories ] if api_installation: return json.dumps( tsr_ids_for_monitoring ) else: trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='monitor_repository_installation', tool_shed_repository_ids=tsr_ids_for_monitoring ) ) except install_manager.RepositoriesInstalledException as e: kwd[ 'message' ] = e.message kwd[ 'status' ] = 'error' return self.repository_installation_grid( trans, **kwd )
[docs] @web.expose @web.require_admin def manage_repository( self, trans, **kwd ): message = escape( kwd.get( 'message', '' ) ) status = kwd.get( 'status', 'done' ) repository_id = kwd.get( 'id', None ) if repository_id is None: return trans.show_error_message( 'Missing required encoded repository id.' ) operation = kwd.get( 'operation', None ) 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 ) ) name = str( repository.name ) owner = str( repository.owner ) installed_changeset_revision = str( repository.installed_changeset_revision ) if repository.status in [ trans.install_model.ToolShedRepository.installation_status.CLONING ]: tool_shed_repository_ids = [ repository_id ] return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='monitor_repository_installation', tool_shed_repository_ids=tool_shed_repository_ids ) ) if repository.can_install and operation == 'install': # Send a request to the tool shed to install the repository. params = dict( name=name, owner=owner, changeset_revisions=installed_changeset_revision, galaxy_url=web.url_for( '/', qualified=True ) ) pathspec = [ 'repository', 'install_repositories_by_revision' ] url = util.build_url( tool_shed_url, pathspec=pathspec, params=params ) return trans.response.send_redirect( url ) description = kwd.get( 'description', repository.description ) shed_tool_conf, tool_path, relative_install_dir = suc.get_tool_panel_config_tool_path_install_dir( trans.app, repository ) if relative_install_dir: repo_files_dir = os.path.abspath( os.path.join( tool_path, relative_install_dir, name ) ) else: repo_files_dir = None if repository.in_error_state: message = "This repository is not installed correctly (see the <b>Repository installation error</b> below). Choose " message += "<b>Reset to install</b> from the <b>Repository Actions</b> menu, correct problems if necessary and try " message += "installing the repository again." status = "error" elif repository.can_install: message = "This repository is not installed. You can install it by choosing <b>Install</b> from the <b>Repository Actions</b> menu." status = "error" elif kwd.get( 'edit_repository_button', False ): if description != repository.description: repository.description = description trans.install_model.context.add( repository ) trans.install_model.context.flush() message = "The repository information has been updated." dd = dependency_display.DependencyDisplayer( trans.app ) containers_dict = dd.populate_containers_dict_from_repository_metadata( tool_shed_url=tool_shed_url, tool_path=tool_path, repository=repository, reinstalling=False, required_repo_info_dicts=None ) view = views.DependencyResolversView(self.app) tool_requirements_d = suc.get_requirements_from_repository(repository) requirements_status = view.get_requirements_status(tool_requirements_d, repository.installed_tool_dependencies) return trans.fill_template( '/admin/tool_shed_repository/manage_repository.mako', repository=repository, description=description, repo_files_dir=repo_files_dir, containers_dict=containers_dict, requirements_status=requirements_status, message=message, status=status )
[docs] @web.expose @web.require_admin def manage_repository_tool_dependencies( self, trans, **kwd ): message = escape( kwd.get( 'message', '' ) ) status = kwd.get( 'status', 'done' ) tool_dependency_ids = tool_dependency_util.get_tool_dependency_ids( as_string=False, **kwd ) if tool_dependency_ids: # We need a tool_shed_repository, so get it from one of the tool_dependencies. tool_dependency = tool_dependency_util.get_tool_dependency( trans.app, tool_dependency_ids[ 0 ] ) tool_shed_repository = tool_dependency.tool_shed_repository else: # The user must be on the manage_repository_tool_dependencies page and clicked the button to either install or uninstall a # tool dependency, but they didn't check any of the available tool dependencies on which to perform the action. repository_id = kwd.get( 'repository_id', None ) tool_shed_repository = repository_util.get_tool_shed_repository_by_id( trans.app, repository_id ) if 'operation' in kwd: operation = kwd[ 'operation' ].lower() if not tool_dependency_ids: message = 'Select at least 1 tool dependency to %s.' % operation kwd[ 'message' ] = message kwd[ 'status' ] = 'error' del kwd[ 'operation' ] return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='manage_repository_tool_dependencies', **kwd ) ) if operation == 'browse': return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='browse_tool_dependency', **kwd ) ) elif operation == 'uninstall': tool_dependencies_for_uninstallation = [] for tool_dependency_id in tool_dependency_ids: tool_dependency = tool_dependency_util.get_tool_dependency( trans.app, tool_dependency_id ) if tool_dependency.status in [ trans.install_model.ToolDependency.installation_status.INSTALLED, trans.install_model.ToolDependency.installation_status.ERROR ]: tool_dependencies_for_uninstallation.append( tool_dependency ) if tool_dependencies_for_uninstallation: return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='uninstall_tool_dependencies', **kwd ) ) else: message = 'No selected tool dependencies can be uninstalled, you may need to use the <b>Repair repository</b> feature.' status = 'error' elif operation == "install": if trans.app.config.tool_dependency_dir: tool_dependencies_for_installation = [] for tool_dependency_id in tool_dependency_ids: tool_dependency = tool_dependency_util.get_tool_dependency( trans.app, tool_dependency_id ) if tool_dependency.status in [ trans.install_model.ToolDependency.installation_status.NEVER_INSTALLED, trans.install_model.ToolDependency.installation_status.UNINSTALLED ]: tool_dependencies_for_installation.append( tool_dependency ) if tool_dependencies_for_installation: self.initiate_tool_dependency_installation( trans, tool_dependencies_for_installation, message=message, status=status ) else: message = 'All selected tool dependencies are already installed.' status = 'error' else: message = 'Set the value of your <b>tool_dependency_dir</b> setting in your Galaxy config file (galaxy.ini) ' message += ' and restart your Galaxy server to install tool dependencies.' status = 'error' installed_tool_dependencies_select_field = \ tool_dependency_util.build_tool_dependencies_select_field( trans.app, tool_shed_repository=tool_shed_repository, name='inst_td_ids', uninstalled_only=False ) uninstalled_tool_dependencies_select_field = \ tool_dependency_util.build_tool_dependencies_select_field( trans.app, tool_shed_repository=tool_shed_repository, name='uninstalled_tool_dependency_ids', uninstalled_only=True ) return trans.fill_template( '/admin/tool_shed_repository/manage_repository_tool_dependencies.mako', repository=tool_shed_repository, installed_tool_dependencies_select_field=installed_tool_dependencies_select_field, uninstalled_tool_dependencies_select_field=uninstalled_tool_dependencies_select_field, message=message, status=status )
[docs] @web.expose @web.require_admin def manage_tool_dependencies( self, trans, **kwd ): # This method is called when tool dependencies are being installed. See the related manage_repository_tool_dependencies # method for managing the tool dependencies for a specified installed tool shed repository. message = escape( kwd.get( 'message', '' ) ) status = kwd.get( 'status', 'done' ) tool_dependency_ids = tool_dependency_util.get_tool_dependency_ids( as_string=False, **kwd ) repository_id = kwd.get( 'repository_id', None ) if tool_dependency_ids: # We need a tool_shed_repository, so get it from one of the tool_dependencies. tool_dependency = tool_dependency_util.get_tool_dependency( trans.app, tool_dependency_ids[ 0 ] ) tool_shed_repository = tool_dependency.tool_shed_repository else: # The user must be on the manage_repository_tool_dependencies page and clicked the button to either install or uninstall a # tool dependency, but they didn't check any of the available tool dependencies on which to perform the action. tool_shed_repository = repository_util.get_tool_shed_repository_by_id( trans.app, repository_id ) self.tool_dependency_grid.title = "Tool shed repository '%s' tool dependencies" % escape( tool_shed_repository.name ) if 'operation' in kwd: operation = kwd[ 'operation' ].lower() if not tool_dependency_ids: message = 'Select at least 1 tool dependency to %s.' % operation kwd[ 'message' ] = message kwd[ 'status' ] = 'error' del kwd[ 'operation' ] return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='manage_tool_dependencies', **kwd ) ) if operation == 'browse': return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='browse_tool_dependency', **kwd ) ) elif operation == "install": if trans.app.config.tool_dependency_dir: tool_dependencies_for_installation = [] for tool_dependency_id in tool_dependency_ids: tool_dependency = tool_dependency_util.get_tool_dependency( trans.app, tool_dependency_id ) if tool_dependency.status in [ trans.install_model.ToolDependency.installation_status.NEVER_INSTALLED, trans.install_model.ToolDependency.installation_status.UNINSTALLED ]: tool_dependencies_for_installation.append( tool_dependency ) if tool_dependencies_for_installation: self.initiate_tool_dependency_installation( trans, tool_dependencies_for_installation, message=message, status=status ) else: kwd[ 'message' ] = 'All selected tool dependencies are already installed.' kwd[ 'status' ] = 'error' else: message = 'Set the value of your <b>tool_dependency_dir</b> setting in your Galaxy config file (galaxy.ini) ' message += ' and restart your Galaxy server to install tool dependencies.' kwd[ 'message' ] = message kwd[ 'status' ] = 'error' # Redirect if no tool dependencies are in the process of being installed. if tool_shed_repository.tool_dependencies_being_installed: return self.tool_dependency_grid( trans, **kwd ) return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='manage_repository_tool_dependencies', tool_dependency_ids=tool_dependency_ids, repository_id=repository_id, message=message, status=status ) )
[docs] @web.expose @web.require_admin def monitor_repository_installation( self, trans, **kwd ): tsridslist = common_util.get_tool_shed_repository_ids( **kwd ) if not tsridslist: tsridslist = repository_util.get_ids_of_tool_shed_repositories_being_installed( trans.app, as_string=False ) kwd[ 'tool_shed_repository_ids' ] = tsridslist return self.repository_installation_grid( trans, **kwd )
[docs] @web.json @web.require_admin def open_folder( self, trans, folder_path, repository_id ): # Avoid caching trans.response.headers['Pragma'] = 'no-cache' trans.response.headers['Expires'] = '0' return suc.open_repository_files_folder( trans.app, folder_path, repository_id, is_admin=True )
[docs] @web.expose @web.require_admin def prepare_for_install( self, trans, **kwd ): if not suc.have_shed_tool_conf_for_install( trans.app ): message = 'The <b>tool_config_file</b> setting in <b>galaxy.ini</b> must include at least one ' message += 'shed tool configuration file name with a <b>&lt;toolbox&gt;</b> tag that includes a <b>tool_path</b> ' message += 'attribute value which is a directory relative to the Galaxy installation directory in order ' message += 'to automatically install tools from a Galaxy Tool Shed (e.g., the file name <b>shed_tool_conf.xml</b> ' message += 'whose <b>&lt;toolbox&gt;</b> tag is <b>&lt;toolbox tool_path="../shed_tools"&gt;</b>).<p/>See the ' message += '<a href="https://galaxyproject.org/installing-repositories-to-galaxy/" target="_blank">Installation ' message += 'of Galaxy Tool Shed repository tools into a local Galaxy instance</a> section of the Galaxy Tool ' message += 'Shed wiki for all of the details.' return trans.show_error_message( message ) message = escape( kwd.get( 'message', '' ) ) status = kwd.get( 'status', 'done' ) shed_tool_conf = kwd.get( 'shed_tool_conf', None ) tool_shed_url = kwd.get( 'tool_shed_url', '' ) tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, tool_shed_url ) # Handle repository dependencies, which do not include those that are required only for compiling a dependent # repository's tool dependencies. 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_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 ) ) # Some tools should not be displayed in the tool panel (e.g., DataManager tools and datatype converters). includes_tools_for_display_in_tool_panel = util.string_as_bool( kwd.get( 'includes_tools_for_display_in_tool_panel', False ) ) includes_tool_dependencies = util.string_as_bool( kwd.get( 'includes_tool_dependencies', False ) ) install_resolver_dependencies = kwd.get( 'install_resolver_dependencies', '' ) install_tool_dependencies = kwd.get( 'install_tool_dependencies', '' ) # In addition to installing new repositories, this method is called when updating an installed repository # to a new changeset_revision where the update includes newly defined repository dependencies. updating = util.asbool( kwd.get( 'updating', False ) ) updating_repository_id = kwd.get( 'updating_repository_id', None ) updating_to_changeset_revision = kwd.get( 'updating_to_changeset_revision', None ) updating_to_ctx_rev = kwd.get( 'updating_to_ctx_rev', None ) encoded_updated_metadata = kwd.get( 'encoded_updated_metadata', None ) encoded_repo_info_dicts = kwd.get( 'encoded_repo_info_dicts', '' ) if encoded_repo_info_dicts: encoded_repo_info_dicts = encoded_repo_info_dicts.split( encoding_util.encoding_sep ) if not encoded_repo_info_dicts: # The request originated in the tool shed via a tool search or from this controller's # update_to_changeset_revision() method. repository_ids = kwd.get( 'repository_ids', None ) if updating: # We have updated an installed repository where the updates included newly defined repository # and possibly tool dependencies. We will have arrived here only if the updates include newly # defined repository dependencies. We're preparing to allow the user to elect to install these # dependencies. At this point, the repository has been updated to the latest changeset revision, # but the received repository id is from the Galaxy side (the caller is this controller's # update_to_changeset_revision() method. We need to get the id of the same repository from the # Tool Shed side. repository = repository_util.get_tool_shed_repository_by_id( trans.app, updating_repository_id ) # For backward compatibility to the 12/20/12 Galaxy release. try: params = dict( name=str( repository.name ), owner=str( repository.owner ) ) pathspec = [ 'repository', 'get_repository_id' ] repository_ids = util.url_get( tool_shed_url, password_mgr=self.app.tool_shed_registry.url_auth( tool_shed_url ), pathspec=pathspec, params=params ) except Exception as e: # The Tool Shed cannot handle the get_repository_id request, so the code must be older than the # 04/2014 Galaxy release when it was introduced. It will be safest to error out and let the # Tool Shed admin update the Tool Shed to a later release. message = 'The updates available for the repository <b>%s</b> ' % escape( str( repository.name ) ) message += 'include newly defined repository or tool dependency definitions, and attempting ' message += 'to update the repository resulted in the following error. Contact the Tool Shed ' message += 'administrator if necessary.<br/>%s' % str( e ) status = 'error' return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='browse_repositories', message=message, status=status ) ) changeset_revisions = updating_to_changeset_revision else: changeset_revisions = kwd.get( 'changeset_revisions', None ) # Get the information necessary to install each repository. params = dict( repository_ids=str( repository_ids ), changeset_revisions=str( changeset_revisions ) ) pathspec = [ 'repository', 'get_repository_information' ] raw_text = util.url_get( tool_shed_url, password_mgr=self.app.tool_shed_registry.url_auth( tool_shed_url ), pathspec=pathspec, params=params ) repo_information_dict = json.loads( raw_text ) for encoded_repo_info_dict in repo_information_dict.get( 'repo_info_dicts', [] ): decoded_repo_info_dict = encoding_util.tool_shed_decode( encoded_repo_info_dict ) if not includes_tools: includes_tools = util.string_as_bool( decoded_repo_info_dict.get( 'includes_tools', False ) ) if not includes_tools_for_display_in_tool_panel: includes_tools_for_display_in_tool_panel = \ util.string_as_bool( decoded_repo_info_dict.get( 'includes_tools_for_display_in_tool_panel', False ) ) if not has_repository_dependencies: has_repository_dependencies = util.string_as_bool( repo_information_dict.get( 'has_repository_dependencies', False ) ) if not includes_tool_dependencies: includes_tool_dependencies = util.string_as_bool( repo_information_dict.get( 'includes_tool_dependencies', False ) ) encoded_repo_info_dicts = util.listify( repo_information_dict.get( 'repo_info_dicts', [] ) ) repo_info_dicts = [ encoding_util.tool_shed_decode( encoded_repo_info_dict ) for encoded_repo_info_dict in encoded_repo_info_dicts ] dd = dependency_display.DependencyDisplayer( trans.app ) install_repository_manager = install_manager.InstallRepositoryManager( trans.app ) if kwd.get( 'select_tool_panel_section_button', False ): if updating: repository = repository_util.get_tool_shed_repository_by_id( trans.app, updating_repository_id ) decoded_updated_metadata = encoding_util.tool_shed_decode( encoded_updated_metadata ) # Now that the user has decided whether they will handle dependencies, we can update # the repository to the latest revision. repository = trans.app.update_repository_manager.update_repository_record( repository=repository, updated_metadata_dict=decoded_updated_metadata, updated_changeset_revision=updating_to_changeset_revision, updated_ctx_rev=updating_to_ctx_rev ) install_repository_dependencies = CheckboxField.is_checked( install_repository_dependencies ) if includes_tool_dependencies: install_tool_dependencies = CheckboxField.is_checked( install_tool_dependencies ) else: install_tool_dependencies = False install_resolver_dependencies = CheckboxField.is_checked( install_resolver_dependencies ) tool_path = suc.get_tool_path_by_shed_tool_conf_filename( trans.app, shed_tool_conf ) installation_dict = dict( install_repository_dependencies=install_repository_dependencies, new_tool_panel_section_label=new_tool_panel_section_label, no_changes_checked=False, repo_info_dicts=repo_info_dicts, 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 = \ install_repository_manager.handle_tool_shed_repositories( installation_dict ) if created_or_updated_tool_shed_repositories: installation_dict = dict( created_or_updated_tool_shed_repositories=created_or_updated_tool_shed_repositories, filtered_repo_info_dicts=filtered_repo_info_dicts, has_repository_dependencies=has_repository_dependencies, includes_tool_dependencies=includes_tool_dependencies, includes_tools=includes_tools, includes_tools_for_display_in_tool_panel=includes_tools_for_display_in_tool_panel, install_repository_dependencies=install_repository_dependencies, install_resolver_dependencies=install_resolver_dependencies, install_tool_dependencies=install_tool_dependencies, message=message, new_tool_panel_section_label=new_tool_panel_section_label, shed_tool_conf=shed_tool_conf, status=status, 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 ) encoded_kwd, query, tool_shed_repositories, encoded_repository_ids = \ install_repository_manager.initiate_repository_installation( installation_dict ) return trans.fill_template( 'admin/tool_shed_repository/initiate_repository_installation.mako', encoded_kwd=encoded_kwd, query=query, tool_shed_repositories=tool_shed_repositories, initiate_repository_installation_ids=encoded_repository_ids, reinstalling=False ) else: kwd[ 'message' ] = message kwd[ 'status' ] = status return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='manage_repositories', **kwd ) ) shed_tool_conf_select_field = tool_util.build_shed_tool_conf_select_field( trans.app ) tool_path = suc.get_tool_path_by_shed_tool_conf_filename( trans.app, shed_tool_conf ) tool_panel_section_select_field = tool_util.build_tool_panel_section_select_field( trans.app ) tool_requirements = suc.get_tool_shed_repo_requirements(app=trans.app, tool_shed_url=tool_shed_url, repo_info_dicts=repo_info_dicts) view = views.DependencyResolversView(self.app) requirements_status = view.get_requirements_status(tool_requirements) if len( repo_info_dicts ) == 1: # If we're installing or updating a single repository, see if it contains a readme or # dependencies that we can display. repo_info_dict = repo_info_dicts[ 0 ] dependencies_for_repository_dict = \ trans.app.installed_repository_manager.get_dependencies_for_repository( tool_shed_url, repo_info_dict, includes_tool_dependencies, updating=updating ) if not has_repository_dependencies: has_repository_dependencies = dependencies_for_repository_dict.get( 'has_repository_dependencies', False ) if not includes_tool_dependencies: includes_tool_dependencies = dependencies_for_repository_dict.get( 'includes_tool_dependencies', False ) if not includes_tools: includes_tools = dependencies_for_repository_dict.get( 'includes_tools', False ) if not includes_tools_for_display_in_tool_panel: includes_tools_for_display_in_tool_panel = \ dependencies_for_repository_dict.get( 'includes_tools_for_display_in_tool_panel', False ) installed_repository_dependencies = dependencies_for_repository_dict.get( 'installed_repository_dependencies', None ) installed_tool_dependencies = dependencies_for_repository_dict.get( 'installed_tool_dependencies', None ) missing_repository_dependencies = dependencies_for_repository_dict.get( 'missing_repository_dependencies', None ) missing_tool_dependencies = dependencies_for_repository_dict.get( 'missing_tool_dependencies', None ) readme_files_dict = readme_util.get_readme_files_dict_for_display( trans.app, tool_shed_url, repo_info_dict ) # We're handling 1 of 3 scenarios here: (1) we're installing a tool shed repository for the first time, so we've # retrieved the list of installed and missing repository dependencies from the database (2) we're handling the # scenario where an error occurred during the installation process, so we have a tool_shed_repository record in # the database with associated repository dependency records. Since we have the repository dependencies in both # of the above 2 cases, we'll merge the list of missing repository dependencies into the list of installed # repository dependencies since each displayed repository dependency will display a status, whether installed or # missing. The 3rd scenario is where we're updating an installed repository and the updates include newly # defined repository (and possibly tool) dependencies. In this case, merging will result in newly defined # dependencies to be lost. We pass the updating parameter to make sure merging occurs only when appropriate. containers_dict = \ dd.populate_containers_dict_for_new_install( tool_shed_url=tool_shed_url, tool_path=tool_path, readme_files_dict=readme_files_dict, installed_repository_dependencies=installed_repository_dependencies, missing_repository_dependencies=missing_repository_dependencies, installed_tool_dependencies=installed_tool_dependencies, missing_tool_dependencies=missing_tool_dependencies, updating=updating ) else: # We're installing a list of repositories, each of which may have tool dependencies or repository dependencies. containers_dicts = [] for repo_info_dict in repo_info_dicts: dependencies_for_repository_dict = \ trans.app.installed_repository_manager.get_dependencies_for_repository( tool_shed_url, repo_info_dict, includes_tool_dependencies, updating=updating ) if not has_repository_dependencies: has_repository_dependencies = dependencies_for_repository_dict.get( 'has_repository_dependencies', False ) if not includes_tool_dependencies: includes_tool_dependencies = dependencies_for_repository_dict.get( 'includes_tool_dependencies', False ) if not includes_tools: includes_tools = dependencies_for_repository_dict.get( 'includes_tools', False ) if not includes_tools_for_display_in_tool_panel: includes_tools_for_display_in_tool_panel = \ dependencies_for_repository_dict.get( 'includes_tools_for_display_in_tool_panel', False ) installed_repository_dependencies = dependencies_for_repository_dict.get( 'installed_repository_dependencies', None ) installed_tool_dependencies = dependencies_for_repository_dict.get( 'installed_tool_dependencies', None ) missing_repository_dependencies = dependencies_for_repository_dict.get( 'missing_repository_dependencies', None ) missing_tool_dependencies = dependencies_for_repository_dict.get( 'missing_tool_dependencies', None ) containers_dict = dd.populate_containers_dict_for_new_install( tool_shed_url=tool_shed_url, tool_path=tool_path, readme_files_dict=None, installed_repository_dependencies=installed_repository_dependencies, missing_repository_dependencies=missing_repository_dependencies, installed_tool_dependencies=installed_tool_dependencies, missing_tool_dependencies=missing_tool_dependencies, updating=updating ) containers_dicts.append( containers_dict ) # Merge all containers into a single container. containers_dict = dd.merge_containers_dicts_for_new_install( containers_dicts ) # Handle tool dependencies check box. if trans.app.config.tool_dependency_dir is None: if includes_tool_dependencies: message = "Tool dependencies defined in this repository can be automatically installed if you set " message += "the value of your <b>tool_dependency_dir</b> setting in your Galaxy config file " message += "(galaxy.ini) and restart your Galaxy server before installing the repository." status = "warning" install_tool_dependencies_check_box_checked = False else: install_tool_dependencies_check_box_checked = True install_tool_dependencies_check_box = CheckboxField( 'install_tool_dependencies', checked=install_tool_dependencies_check_box_checked ) # Handle repository dependencies check box. install_repository_dependencies_check_box = CheckboxField( 'install_repository_dependencies', checked=True ) view = views.DependencyResolversView(self.app) if view.installable_resolvers: install_resolver_dependencies_check_box = CheckboxField( 'install_resolver_dependencies', checked=True ) else: install_resolver_dependencies_check_box = None encoded_repo_info_dicts = encoding_util.encoding_sep.join( encoded_repo_info_dicts ) tool_shed_url = kwd[ 'tool_shed_url' ] return trans.fill_template( '/admin/tool_shed_repository/select_tool_panel_section.mako', encoded_repo_info_dicts=encoded_repo_info_dicts, updating=updating, updating_repository_id=updating_repository_id, updating_to_ctx_rev=updating_to_ctx_rev, updating_to_changeset_revision=updating_to_changeset_revision, encoded_updated_metadata=encoded_updated_metadata, includes_tools=includes_tools, includes_tools_for_display_in_tool_panel=includes_tools_for_display_in_tool_panel, includes_tool_dependencies=includes_tool_dependencies, install_tool_dependencies_check_box=install_tool_dependencies_check_box, install_resolver_dependencies_check_box=install_resolver_dependencies_check_box, has_repository_dependencies=has_repository_dependencies, install_repository_dependencies_check_box=install_repository_dependencies_check_box, 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, tool_panel_section_select_field=tool_panel_section_select_field, tool_shed_url=tool_shed_url, requirements_status=requirements_status, message=message, status=status )
[docs] @web.expose @web.require_admin def purge_repository( self, trans, **kwd ): """Purge a "white ghost" repository from the database.""" repository_id = kwd.get( 'id', None ) new_kwd = {} if repository_id is not None: 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 ): irm = trans.app.installed_repository_manager purge_status, purge_message = irm.purge_repository( repository ) if purge_status == 'ok': new_kwd[ 'status' ] = "done" else: new_kwd[ 'status' ] = 'error' new_kwd[ 'message' ] = purge_message else: return trans.fill_template( 'admin/tool_shed_repository/purge_repository_confirmation.mako', repository=repository ) else: new_kwd[ 'status' ] = 'error' new_kwd[ 'message' ] = 'Repositories must have a <b>New</b> status in order to be purged.' else: new_kwd[ 'status' ] = 'error' new_kwd[ 'message' ] = 'Cannot locate the database record for the repository with encoded id %s.' % str( repository_id ) else: new_kwd[ 'status' ] = 'error' new_kwd[ 'message' ] = 'Invalid repository id value "None" received for repository to be purged.' return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='browse_repositories', **new_kwd ) )
[docs] @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. """ rdim = repository_dependency_manager.RepositoryDependencyInstallManager( trans.app ) message = escape( kwd.get( 'message', '' ) ) status = kwd.get( 'status', 'done' ) repository_id = kwd[ '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', '' ) ) install_tool_dependencies = CheckboxField.is_checked( kwd.get( 'install_tool_dependencies', '' ) ) install_resolver_dependencies = CheckboxField.is_checked( kwd.get( 'install_resolver_dependencies', '' ) ) shed_tool_conf, tool_path, relative_install_dir = \ suc.get_tool_panel_config_tool_path_install_dir( trans.app, tool_shed_repository ) repository_clone_url = common_util.generate_clone_url_for_installed_repository( trans.app, tool_shed_repository ) tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, tool_shed_repository.tool_shed ) tool_section = None 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 # Keep track of tool dependencies defined for the current repository or those defined for any of # its repository dependencies. includes_tool_dependencies = tool_shed_repository.includes_tool_dependencies if tool_shed_repository.includes_tools_for_display_in_tool_panel: tpm = tool_panel_manager.ToolPanelManager( trans.app ) # Handle the selected tool panel location for loading tools included in the tool shed repository. tool_section, tool_panel_section_key = \ tpm.handle_tool_panel_selection( toolbox=trans.app.toolbox, 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: repository_type = suc.get_repository_type_from_tool_shed(trans.app, tool_shed_url, tool_shed_repository.name, tool_shed_repository.owner) if repository_type == rt_util.TOOL_DEPENDENCY_DEFINITION: # Repositories of type tool_dependency_definition must get the latest # metadata from the Tool Shed since they have only a single installable # revision. raw_text = suc.get_tool_dependency_definition_metadata_from_tool_shed(trans.app, tool_shed_url, tool_shed_repository.name, tool_shed_repository.owner) new_meta = json.loads(raw_text) # Clean up old repository dependency and tool dependency relationships. suc.clean_dependency_relationships(trans, new_meta, tool_shed_repository, tool_shed_url) # The repository's status must be updated from 'Uninstalled' to 'New' when initiating reinstall # so the repository_installation_updater will function. tool_shed_repository = repository_util.create_or_update_tool_shed_repository( trans.app, tool_shed_repository.name, tool_shed_repository.description, tool_shed_repository.installed_changeset_revision, tool_shed_repository.ctx_rev, repository_clone_url, metadata, trans.install_model.ToolShedRepository.installation_status.NEW, tool_shed_repository.changeset_revision, tool_shed_repository.owner, tool_shed_repository.dist_to_shed ) ctx_rev = suc.get_ctx_rev( trans.app, tool_shed_url, tool_shed_repository.name, tool_shed_repository.owner, tool_shed_repository.installed_changeset_revision ) repo_info_dicts = [] repo_info_dict = kwd.get( 'repo_info_dict', None ) if repo_info_dict: if isinstance( repo_info_dict, string_types ): repo_info_dict = encoding_util.tool_shed_decode( repo_info_dict ) else: # Entering this else block occurs only if the tool_shed_repository does not include any valid tools. if install_repository_dependencies: repository_dependencies = \ rdim.get_repository_dependencies_for_installed_tool_shed_repository( trans.app, tool_shed_repository ) else: repository_dependencies = None if metadata: tool_dependencies = metadata.get( 'tool_dependencies', None ) else: tool_dependencies = None 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. created_or_updated_tool_shed_repositories, tool_panel_section_keys, repo_info_dicts, filtered_repo_info_dicts = \ rdim.create_repository_dependency_objects( tool_path=tool_path, tool_shed_url=tool_shed_url, repo_info_dicts=repo_info_dicts, install_repository_dependencies=install_repository_dependencies, no_changes_checked=no_changes_checked, 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 re-installation. for index, tps_key in enumerate( tool_panel_section_keys ): if tps_key is None: tool_panel_section_keys[ index ] = tool_panel_section_key encoded_repository_ids = [ trans.security.encode_id( r.id ) for r in created_or_updated_tool_shed_repositories ] new_kwd = dict( includes_tool_dependencies=includes_tool_dependencies, includes_tools=tool_shed_repository.includes_tools, includes_tools_for_display_in_tool_panel=tool_shed_repository.includes_tools_for_display_in_tool_panel, install_tool_dependencies=install_tool_dependencies, install_resolver_dependencies=install_resolver_dependencies, repo_info_dicts=filtered_repo_info_dicts, message=message, new_tool_panel_section_label=new_tool_panel_section_label, shed_tool_conf=shed_tool_conf, status=status, 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, tool_shed_url=tool_shed_url ) encoded_kwd = encoding_util.tool_shed_encode( new_kwd ) tsr_ids = [ r.id for r in created_or_updated_tool_shed_repositories ] tool_shed_repositories = [] for tsr_id in tsr_ids: tsr = trans.install_model.context.query( trans.install_model.ToolShedRepository ).get( tsr_id ) tool_shed_repositories.append( tsr ) clause_list = [] for tsr_id in tsr_ids: clause_list.append( trans.install_model.ToolShedRepository.table.c.id == tsr_id ) query = trans.install_model.context.current.query( trans.install_model.ToolShedRepository ) \ .filter( or_( *clause_list ) ) return trans.fill_template( 'admin/tool_shed_repository/initiate_repository_installation.mako', encoded_kwd=encoded_kwd, query=query, tool_shed_repositories=tool_shed_repositories, initiate_repository_installation_ids=encoded_repository_ids, reinstalling=True )
[docs] @web.expose @web.require_admin def repair_repository( self, trans, **kwd ): """ Inspect the repository dependency hierarchy for a specified repository and attempt to make sure they are all properly installed as well as each repository's tool dependencies. """ message = escape( kwd.get( 'message', '' ) ) status = kwd.get( 'status', 'done' ) repository_id = kwd.get( 'id', None ) if not repository_id: message = 'Invalid installed tool shed repository id %s received.' % str( repository_id ) status = 'error' return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='browse_repositories', message=message, status=status ) ) 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 ) if encoded_repair_dict: repair_dict = encoding_util.tool_shed_decode( encoded_repair_dict ) else: repair_dict = None if not repair_dict: repair_dict = rrm.get_repair_dict( tool_shed_repository ) ordered_tsr_ids = repair_dict.get( 'ordered_tsr_ids', [] ) ordered_repo_info_dicts = repair_dict.get( 'ordered_repo_info_dicts', [] ) if ordered_tsr_ids and ordered_repo_info_dicts: repositories_for_repair = [] for tsr_id in ordered_tsr_ids: 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_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', [] ) ordered_repo_info_dicts = repair_dict.get( 'ordered_repo_info_dicts', [] ) return trans.fill_template( 'admin/tool_shed_repository/repair_repository.mako', repository=tool_shed_repository, encoded_repair_dict=encoded_repair_dict, repair_dict=repair_dict, message=message, status=status )
[docs] @web.expose @web.require_admin def repair_tool_shed_repositories( self, trans, repair_repository_manager, tool_shed_repositories, repo_info_dicts, **kwd ): """Repair specified tool shed repositories.""" # The received lists of tool_shed_repositories and repo_info_dicts are ordered. for index, tool_shed_repository in enumerate( tool_shed_repositories ): repo_info_dict = repo_info_dicts[ index ] repair_repository_manager.repair_tool_shed_repository( tool_shed_repository, encoding_util.tool_shed_encode( repo_info_dict ) ) tsr_ids_for_monitoring = [ trans.security.encode_id( tsr.id ) for tsr in tool_shed_repositories ] return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='monitor_repository_installation', tool_shed_repository_ids=tsr_ids_for_monitoring ) )
[docs] @web.json def repository_installation_status_updates( self, trans, ids=None, status_list=None ): # Avoid caching trans.response.headers[ 'Pragma' ] = 'no-cache' trans.response.headers[ 'Expires' ] = '0' # Create new HTML for any ToolShedRepository records whose status that has changed. rval = [] if ids is not None and status_list is not None: ids = util.listify( ids ) status_list = util.listify( status_list ) for tup in zip( ids, status_list ): id, status = tup repository = trans.install_model.context.query( trans.install_model.ToolShedRepository ).get( trans.security.decode_id( id ) ) if repository.status != status: rval.append( dict( id=id, status=repository.status, html_status=unicode( trans.fill_template( "admin/tool_shed_repository/repository_installation_status.mako", repository=repository ), 'utf-8' ) ) ) return rval
[docs] @web.expose @web.require_admin def reselect_tool_panel_section( self, trans, **kwd ): """ Select or change the tool panel section to contain the tools included in the tool shed repository being reinstalled. If there are updates available for the repository in the tool shed, the tool_dependencies and repository_dependencies associated with the updated changeset revision will have been retrieved from the tool shed and passed in the received kwd. In this case, the stored tool shed repository metadata from the Galaxy database will not be used since it is outdated. """ message = '' status = 'done' 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_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 ) ) tool_path = tool_shed_repository.get_tool_relative_path( trans.app )[0] if latest_changeset_revision and latest_ctx_rev: # There are updates available in the tool shed for the repository, so use the received # dependency information which was retrieved from the tool shed. encoded_updated_repo_info_dict = kwd.get( 'updated_repo_info_dict', None ) updated_repo_info_dict = encoding_util.tool_shed_decode( encoded_updated_repo_info_dict ) readme_files_dict = updated_repo_info_dict.get( 'readme_files_dict', None ) includes_data_managers = updated_repo_info_dict.get( 'includes_data_managers', False ) includes_datatypes = updated_repo_info_dict.get( 'includes_datatypes', False ) includes_workflows = updated_repo_info_dict.get( 'includes_workflows', False ) includes_tool_dependencies = updated_repo_info_dict.get( 'includes_tool_dependencies', False ) repo_info_dict = updated_repo_info_dict[ 'repo_info_dict' ] else: # There are no updates available from the tool shed for the repository, so use its locally stored metadata. includes_data_managers = False includes_datatypes = False includes_tool_dependencies = False includes_workflows = False readme_files_dict = None tool_dependencies = None if metadata: if 'data_manager' in metadata: includes_data_managers = True if 'datatypes' in metadata: includes_datatypes = True if 'tool_dependencies' in metadata: includes_tool_dependencies = True if 'workflows' in metadata: includes_workflows = True # Since we're reinstalling, we need to send a request to the tool shed to get the README files. params = dict( name=tool_shed_repository.name, owner=tool_shed_repository.owner, changeset_revision=tool_shed_repository.installed_changeset_revision ) pathspec = [ 'repository', 'get_readme_files' ] raw_text = util.url_get( tool_shed_url, password_mgr=self.app.tool_shed_registry.url_auth( tool_shed_url ), pathspec=pathspec, params=params ) readme_files_dict = json.loads( raw_text ) tool_dependencies = metadata.get( 'tool_dependencies', None ) rdim = repository_dependency_manager.RepositoryDependencyInstallManager( trans.app ) repository_dependencies = \ rdim.get_repository_dependencies_for_installed_tool_shed_repository( trans.app, tool_shed_repository ) 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, includes_tool_dependencies, updating=True ) includes_tool_dependencies = dependencies_for_repository_dict.get( 'includes_tool_dependencies', False ) includes_tools = dependencies_for_repository_dict.get( 'includes_tools', False ) includes_tools_for_display_in_tool_panel = dependencies_for_repository_dict.get( 'includes_tools_for_display_in_tool_panel', False ) installed_repository_dependencies = dependencies_for_repository_dict.get( 'installed_repository_dependencies', None ) installed_tool_dependencies = dependencies_for_repository_dict.get( 'installed_tool_dependencies', None ) missing_repository_dependencies = dependencies_for_repository_dict.get( 'missing_repository_dependencies', None ) missing_tool_dependencies = dependencies_for_repository_dict.get( 'missing_tool_dependencies', None ) if installed_repository_dependencies or missing_repository_dependencies: has_repository_dependencies = True else: has_repository_dependencies = False if includes_tools_for_display_in_tool_panel: # Get the location in the tool panel in which the tools were originally loaded. if 'tool_panel_section' in metadata: tool_panel_dict = metadata[ 'tool_panel_section' ] if tool_panel_dict: if tool_util.panel_entry_per_tool( tool_panel_dict ): # The following forces everything to be loaded into 1 section (or no section) in the tool panel. tool_section_dicts = tool_panel_dict[ tool_panel_dict.keys()[ 0 ] ] tool_section_dict = tool_section_dicts[ 0 ] original_section_name = tool_section_dict[ 'name' ] else: original_section_name = tool_panel_dict[ 'name' ] else: original_section_name = '' else: original_section_name = '' tool_panel_section_select_field = tool_util.build_tool_panel_section_select_field( trans.app ) no_changes_check_box = CheckboxField( 'no_changes', checked=True ) if original_section_name: message += "The tools contained in your <b>%s</b> repository were last loaded into the tool panel section <b>%s</b>. " \ % ( escape( tool_shed_repository.name ), original_section_name ) message += "Uncheck the <b>No changes</b> check box and select a different tool panel section to load the tools in a " message += "different section in the tool panel. " status = 'warning' else: message += "The tools contained in your <b>%s</b> repository were last loaded into the tool panel outside of any sections. " % escape( tool_shed_repository.name ) message += "Uncheck the <b>No changes</b> check box and select a tool panel section to load the tools into that section. " status = 'warning' else: no_changes_check_box = None original_section_name = '' tool_panel_section_select_field = None shed_tool_conf_select_field = tool_util.build_shed_tool_conf_select_field( trans.app ) dd = dependency_display.DependencyDisplayer( trans.app ) containers_dict = \ dd.populate_containers_dict_for_new_install( tool_shed_url=tool_shed_url, tool_path=tool_path, readme_files_dict=readme_files_dict, installed_repository_dependencies=installed_repository_dependencies, missing_repository_dependencies=missing_repository_dependencies, installed_tool_dependencies=installed_tool_dependencies, missing_tool_dependencies=missing_tool_dependencies, updating=False ) # Since we're reinstalling we'll merge the list of missing repository dependencies into the list of # installed repository dependencies since each displayed repository dependency will display a status, # whether installed or missing. containers_dict = dd.merge_missing_repository_dependencies_to_installed_container( containers_dict ) # Handle repository dependencies check box. install_repository_dependencies_check_box = CheckboxField( 'install_repository_dependencies', checked=True ) # Handle tool dependencies check box. if trans.app.config.tool_dependency_dir is None: if includes_tool_dependencies: message += "Tool dependencies defined in this repository can be automatically installed if you set the value of your <b>tool_dependency_dir</b> " message += "setting in your Galaxy config file (galaxy.ini) and restart your Galaxy server before installing the repository. " status = "warning" install_tool_dependencies_check_box_checked = False else: install_tool_dependencies_check_box_checked = True install_tool_dependencies_check_box = CheckboxField( 'install_tool_dependencies', checked=install_tool_dependencies_check_box_checked ) view = views.DependencyResolversView(self.app) if view.installable_resolvers: install_resolver_dependencies_check_box = CheckboxField( 'install_resolver_dependencies', checked=True ) else: install_resolver_dependencies_check_box = None return trans.fill_template( '/admin/tool_shed_repository/reselect_tool_panel_section.mako', repository=tool_shed_repository, no_changes_check_box=no_changes_check_box, original_section_name=original_section_name, includes_data_managers=includes_data_managers, includes_datatypes=includes_datatypes, includes_tools=includes_tools, includes_tools_for_display_in_tool_panel=includes_tools_for_display_in_tool_panel, includes_tool_dependencies=includes_tool_dependencies, includes_workflows=includes_workflows, has_repository_dependencies=has_repository_dependencies, install_repository_dependencies_check_box=install_repository_dependencies_check_box, install_tool_dependencies_check_box=install_tool_dependencies_check_box, install_resolver_dependencies_check_box=install_resolver_dependencies_check_box, containers_dict=containers_dict, tool_panel_section_select_field=tool_panel_section_select_field, shed_tool_conf_select_field=shed_tool_conf_select_field, encoded_repo_info_dict=encoding_util.tool_shed_encode( repo_info_dict ), repo_info_dict=repo_info_dict, message=message, status=status )
[docs] @web.expose @web.require_admin def reset_metadata_on_selected_installed_repositories( self, trans, **kwd ): irmm = InstalledRepositoryMetadataManager( trans.app ) if 'reset_metadata_on_selected_repositories_button' in kwd: message, status = irmm.reset_metadata_on_selected_repositories( trans.user, **kwd ) else: message = escape( kwd.get( 'message', '' ) ) status = kwd.get( 'status', 'done' ) repositories_select_field = irmm.build_repository_ids_select_field() return trans.fill_template( '/admin/tool_shed_repository/reset_metadata_on_selected_repositories.mako', repositories_select_field=repositories_select_field, message=message, status=status )
[docs] @web.expose @web.require_admin def reset_repository_metadata( self, trans, id ): """Reset all metadata on a single installed tool shed repository.""" 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: original_metadata_dict = repository.metadata irmm = InstalledRepositoryMetadataManager( app=trans.app, repository=repository, changeset_revision=repository.changeset_revision, repository_clone_url=repository_clone_url, shed_config_dict=repository.get_shed_config_dict( trans.app ), relative_install_dir=relative_install_dir, repository_files_dir=None, resetting_all_metadata_on_repository=False, updating_installed_repository=False, persist=False ) irmm.generate_metadata_for_changeset_revision() irmm_metadata_dict = irmm.get_metadata_dict() if irmm_metadata_dict != original_metadata_dict: repository.metadata = irmm_metadata_dict irmm.update_in_shed_tool_config() trans.install_model.context.add( repository ) trans.install_model.context.flush() message = 'Metadata has been reset on repository <b>%s</b>.' % escape( repository.name ) status = 'done' else: message = 'Metadata did not need to be reset on repository <b>%s</b>.' % escape( repository.name ) status = 'done' else: message = 'Error locating installation directory for repository <b>%s</b>.' % escape( repository.name ) status = 'error' return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='manage_repository', id=id, message=message, status=status ) )
[docs] @web.expose @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_util.get_installed_tool_shed_repository( trans.app, kwd[ 'id' ] ) if kwd.get( 'reset_repository', False ): repository_util.set_repository_attributes( trans.app, repository, status=trans.install_model.ToolShedRepository.installation_status.NEW, error_message=None, deleted=False, uninstalled=False, remove_from_disk=True ) new_kwd = {} new_kwd[ 'message' ] = "You can now attempt to install the repository named <b>%s</b> again." % escape( str( repository.name ) ) new_kwd[ 'status' ] = "done" return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='browse_repositories', **new_kwd ) ) return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='manage_repository', **kwd ) )
[docs] @web.expose @web.require_admin def set_tool_versions( self, trans, **kwd ): """ 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_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 = dict( name=repository.name, owner=repository.owner, changeset_revision=repository.changeset_revision ) pathspec = [ 'repository', 'get_tool_versions' ] text = util.url_get( tool_shed_url, password_mgr=self.app.tool_shed_registry.url_auth( tool_shed_url ), pathspec=pathspec, params=params ) if text: tool_version_dicts = json.loads( text ) tvm = tool_version_manager.ToolVersionManager( trans.app ) tvm.handle_tool_versions( tool_version_dicts, repository ) message = "Tool versions have been set for all included tools." status = 'done' else: message = ("Version information for the tools included in the <b>%s</b> repository is missing. " "Reset all of this reppository's metadata in the tool shed, then set the installed tool versions " "from the installed repository's <b>Repository Actions</b> menu. " % escape( repository.name )) status = 'error' shed_tool_conf, tool_path, relative_install_dir = suc.get_tool_panel_config_tool_path_install_dir( trans.app, repository ) repo_files_dir = os.path.abspath( os.path.join( relative_install_dir, repository.name ) ) dd = dependency_display.DependencyDisplayer( trans.app ) containers_dict = dd.populate_containers_dict_from_repository_metadata( tool_shed_url=tool_shed_url, tool_path=tool_path, repository=repository, reinstalling=False, required_repo_info_dicts=None ) return trans.fill_template( '/admin/tool_shed_repository/manage_repository.mako', repository=repository, description=repository.description, repo_files_dir=repo_files_dir, containers_dict=containers_dict, message=message, status=status )
[docs] @web.json def tool_dependency_status_updates( self, trans, ids=None, status_list=None ): # Avoid caching trans.response.headers[ 'Pragma' ] = 'no-cache' trans.response.headers[ 'Expires' ] = '0' # Create new HTML for any ToolDependency records whose status that has changed. rval = [] if ids is not None and status_list is not None: ids = util.listify( ids ) status_list = util.listify( status_list ) for tup in zip( ids, status_list ): id, status = tup tool_dependency = trans.install_model.context.query( trans.install_model.ToolDependency ).get( trans.security.decode_id( id ) ) if tool_dependency.status != status: rval.append( dict( id=id, status=tool_dependency.status, html_status=unicode( trans.fill_template( "admin/tool_shed_repository/tool_dependency_installation_status.mako", tool_dependency=tool_dependency ), 'utf-8' ) ) ) return rval
[docs] @web.expose @web.require_admin def uninstall_tool_dependencies( self, trans, **kwd ): message = escape( kwd.get( 'message', '' ) ) status = kwd.get( 'status', 'done' ) tool_dependency_ids = tool_dependency_util.get_tool_dependency_ids( as_string=False, **kwd ) if not tool_dependency_ids: tool_dependency_ids = util.listify( kwd.get( 'id', None ) ) tool_dependencies = [] for tool_dependency_id in tool_dependency_ids: tool_dependency = tool_dependency_util.get_tool_dependency( trans.app, tool_dependency_id ) tool_dependencies.append( tool_dependency ) tool_shed_repository = tool_dependencies[ 0 ].tool_shed_repository if kwd.get( 'uninstall_tool_dependencies_button', False ): errors = False # Filter tool dependencies to only those that are installed but in an error state. tool_dependencies_for_uninstallation = [] for tool_dependency in tool_dependencies: if tool_dependency.can_uninstall: tool_dependencies_for_uninstallation.append( tool_dependency ) for tool_dependency in tool_dependencies_for_uninstallation: uninstalled, error_message = tool_dependency_util.remove_tool_dependency( trans.app, tool_dependency ) if error_message: errors = True message = '%s %s' % ( message, error_message ) if errors: message = "Error attempting to uninstall tool dependencies: %s" % message status = 'error' else: message = "These tool dependencies have been uninstalled: %s" % \ ','.join( td.name for td in tool_dependencies_for_uninstallation ) td_ids = [ trans.security.encode_id( td.id ) for td in tool_shed_repository.tool_dependencies ] return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='manage_repository_tool_dependencies', tool_dependency_ids=td_ids, status=status, message=message ) ) return trans.fill_template( '/admin/tool_shed_repository/uninstall_tool_dependencies.mako', repository=tool_shed_repository, tool_dependency_ids=tool_dependency_ids, tool_dependencies=tool_dependencies, message=message, status=status )
[docs] @web.expose @web.require_admin def update_to_changeset_revision( self, trans, **kwd ): """Update a cloned repository to the latest revision possible.""" message = escape( kwd.get( 'message', '' ) ) status = kwd.get( 'status', 'done' ) tool_shed_url = kwd.get( 'tool_shed_url', '' ) # Handle protocol changes over time. tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( trans.app, tool_shed_url ) name = kwd.get( 'name', None ) owner = kwd.get( 'owner', None ) changeset_revision = kwd.get( 'changeset_revision', None ) latest_changeset_revision = kwd.get( 'latest_changeset_revision', None ) latest_ctx_rev = kwd.get( 'latest_ctx_rev', None ) repository = repository_util.get_installed_repository( trans.app, tool_shed=tool_shed_url, name=name, owner=owner, changeset_revision=changeset_revision ) original_metadata_dict = repository.metadata original_repository_dependencies_dict = original_metadata_dict.get( 'repository_dependencies', {} ) original_repository_dependencies = original_repository_dependencies_dict.get( 'repository_dependencies', [] ) original_tool_dependencies_dict = original_metadata_dict.get( 'tool_dependencies', {} ) if changeset_revision and latest_changeset_revision and latest_ctx_rev: if changeset_revision == latest_changeset_revision: message = "The installed repository named '%s' is current, there are no updates available. " % name else: shed_tool_conf, tool_path, relative_install_dir = suc.get_tool_panel_config_tool_path_install_dir( trans.app, repository ) if relative_install_dir: if tool_path: repo_files_dir = os.path.abspath( os.path.join( tool_path, relative_install_dir, name ) ) else: repo_files_dir = os.path.abspath( os.path.join( relative_install_dir, name ) ) repo = hg_util.get_repo_for_repository( trans.app, repository=None, repo_path=repo_files_dir, create=False ) repository_clone_url = os.path.join( tool_shed_url, 'repos', owner, name ) hg_util.pull_repository( repo, repository_clone_url, latest_ctx_rev ) hg_util.update_repository( repo, latest_ctx_rev ) # Remove old Data Manager entries if repository.includes_data_managers: dmh = data_manager.DataManagerHandler( trans.app ) dmh.remove_from_data_manager( repository ) # Update the repository metadata. tpm = tool_panel_manager.ToolPanelManager( trans.app ) irmm = InstalledRepositoryMetadataManager( app=trans.app, tpm=tpm, repository=repository, changeset_revision=latest_changeset_revision, repository_clone_url=repository_clone_url, shed_config_dict=repository.get_shed_config_dict( trans.app ), relative_install_dir=relative_install_dir, repository_files_dir=None, resetting_all_metadata_on_repository=False, updating_installed_repository=True, persist=True ) irmm.generate_metadata_for_changeset_revision() irmm_metadata_dict = irmm.get_metadata_dict() if 'tools' in irmm_metadata_dict: tool_panel_dict = irmm_metadata_dict.get( 'tool_panel_section', None ) if tool_panel_dict is None: tool_panel_dict = tpm.generate_tool_panel_dict_from_shed_tool_conf_entries( repository ) repository_tools_tups = irmm.get_repository_tools_tups() tpm.add_to_tool_panel( repository_name=str( repository.name ), repository_clone_url=repository_clone_url, changeset_revision=str( repository.installed_changeset_revision ), repository_tools_tups=repository_tools_tups, owner=str( repository.owner ), shed_tool_conf=shed_tool_conf, tool_panel_dict=tool_panel_dict, new_install=False ) # Add new Data Manager entries if 'data_manager' in irmm_metadata_dict: dmh = data_manager.DataManagerHandler( trans.app ) dmh.install_data_managers( trans.app.config.shed_data_manager_config_file, irmm_metadata_dict, repository.get_shed_config_dict( trans.app ), os.path.join( relative_install_dir, name ), repository, repository_tools_tups ) if 'repository_dependencies' in irmm_metadata_dict or 'tool_dependencies' in irmm_metadata_dict: new_repository_dependencies_dict = irmm_metadata_dict.get( 'repository_dependencies', {} ) new_repository_dependencies = new_repository_dependencies_dict.get( 'repository_dependencies', [] ) new_tool_dependencies_dict = irmm_metadata_dict.get( 'tool_dependencies', {} ) if new_repository_dependencies: # [[http://localhost:9009', package_picard_1_56_0', devteam', 910b0b056666', False', False']] proceed_to_install = False if new_repository_dependencies == original_repository_dependencies: for new_repository_tup in new_repository_dependencies: # Make sure all dependencies are installed. # TODO: Repository dependencies that are not installed should be displayed to the user, # giving them the option to install them or not. This is the same behavior as when initially # installing and when re-installing. new_tool_shed, new_name, new_owner, new_changeset_revision, new_pir, new_oicct = \ common_util.parse_repository_dependency_tuple( new_repository_tup ) # Mock up a repo_info_tupe that has the information needed to see if the repository dependency # was previously installed. repo_info_tuple = ( '', new_tool_shed, new_changeset_revision, '', new_owner, [], [] ) # Since the value of new_changeset_revision came from a repository dependency # definition, it may occur earlier in the Tool Shed's repository changelog than # the Galaxy tool_shed_repository.installed_changeset_revision record value, so # we set from_tip to True to make sure we get the entire set of changeset revisions # from the Tool Shed. new_repository_db_record, installed_changeset_revision = \ repository_util.repository_was_previously_installed( trans.app, tool_shed_url, new_name, repo_info_tuple, from_tip=True ) if new_repository_db_record: if new_repository_db_record.status in [ trans.install_model.ToolShedRepository.installation_status.ERROR, trans.install_model.ToolShedRepository.installation_status.NEW, trans.install_model.ToolShedRepository.installation_status.UNINSTALLED ]: proceed_to_install = True break else: proceed_to_install = True break if proceed_to_install: # Updates received include newly defined repository dependencies, so allow the user # the option of installting them. We cannot update the repository with the changes # until that happens, so we have to send them along. new_kwd = dict( tool_shed_url=tool_shed_url, updating_repository_id=trans.security.encode_id( repository.id ), updating_to_ctx_rev=latest_ctx_rev, updating_to_changeset_revision=latest_changeset_revision, encoded_updated_metadata=encoding_util.tool_shed_encode( irmm_metadata_dict ), updating=True ) return self.prepare_for_install( trans, **new_kwd ) # Updates received did not include any newly defined repository dependencies but did include # newly defined tool dependencies. If the newly defined tool dependencies are not the same # as the originally defined tool dependencies, we need to install them. proceed_to_install = False for new_key, new_val in new_tool_dependencies_dict.items(): if new_key not in original_tool_dependencies_dict: proceed_to_install = True break original_val = original_tool_dependencies_dict[ new_key ] if new_val != original_val: proceed_to_install = True break if proceed_to_install: encoded_tool_dependencies_dict = encoding_util.tool_shed_encode( irmm_metadata_dict.get( 'tool_dependencies', {} ) ) encoded_relative_install_dir = encoding_util.tool_shed_encode( relative_install_dir ) new_kwd = dict( updating_repository_id=trans.security.encode_id( repository.id ), updating_to_ctx_rev=latest_ctx_rev, updating_to_changeset_revision=latest_changeset_revision, encoded_updated_metadata=encoding_util.tool_shed_encode( irmm_metadata_dict ), encoded_relative_install_dir=encoded_relative_install_dir, encoded_tool_dependencies_dict=encoded_tool_dependencies_dict, message=message, status=status ) return self.install_tool_dependencies_with_update( trans, **new_kwd ) # Updates received did not include any newly defined repository dependencies or newly defined # tool dependencies that need to be installed. repository = trans.app.update_repository_manager.update_repository_record( repository=repository, updated_metadata_dict=irmm_metadata_dict, updated_changeset_revision=latest_changeset_revision, updated_ctx_rev=latest_ctx_rev ) message = "The installed repository named '%s' has been updated to change set revision '%s'. " % \ ( name, latest_changeset_revision ) else: message = "The directory containing the installed repository named '%s' cannot be found. " % name status = 'error' else: message = "The latest changeset revision could not be retrieved for the installed repository named '%s'. " % name status = 'error' return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='manage_repository', id=trans.security.encode_id( repository.id ), message=message, status=status ) )
[docs] @web.expose @web.require_admin def update_tool_shed_status_for_installed_repository( self, trans, **kwd ): message, status = repository_util.check_for_updates( trans.app, trans.install_model, kwd.get( 'id', None ) ) return trans.response.send_redirect( web.url_for( controller='admin_toolshed', action='browse_repositories', message=message, status=status ) )
[docs] @web.expose @web.require_admin def view_tool_metadata( self, trans, repository_id, tool_id, **kwd ): message = escape( kwd.get( 'message', '' ) ) status = kwd.get( 'status', 'done' ) 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 = {} tool_lineage = [] tool = None if 'tools' in repository_metadata: for tool_metadata_dict in repository_metadata[ 'tools' ]: if tool_metadata_dict[ 'id' ] == tool_id: tool_metadata = tool_metadata_dict tool_config = tool_metadata[ 'tool_config' ] if shed_config_dict and shed_config_dict.get( 'tool_path' ): tool_config = os.path.join( shed_config_dict.get( 'tool_path' ), tool_config ) tool = trans.app.toolbox.load_tool( os.path.abspath( tool_config ), guid=tool_metadata[ 'guid' ] ) if tool: tvm = tool_version_manager.ToolVersionManager( trans.app ) tool_version = tvm.get_tool_version( str( tool.id ) ) tool_lineage = tool_version.get_version_ids( trans.app, reverse=True ) break return trans.fill_template( "/admin/tool_shed_repository/view_tool_metadata.mako", repository=repository, repository_metadata=repository_metadata, tool=tool, tool_metadata=tool_metadata, tool_lineage=tool_lineage, message=message, status=status )
[docs] @web.expose @web.require_admin def view_workflow( self, trans, workflow_name=None, repository_id=None, **kwd ): """Retrieve necessary information about a workflow from the database so that it can be displayed in an svg image.""" message = escape( kwd.get( 'message', '' ) ) status = kwd.get( 'status', 'done' ) if workflow_name: workflow_name = encoding_util.tool_shed_decode( workflow_name ) repository = repository_util.get_tool_shed_repository_by_id( trans.app, repository_id ) changeset_revision = repository.changeset_revision metadata = repository.metadata return trans.fill_template( "/admin/tool_shed_repository/view_workflow.mako", repository=repository, changeset_revision=changeset_revision, repository_id=repository_id, workflow_name=workflow_name, metadata=metadata, message=message, status=status )