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Source code for tool_shed.galaxy_install.update_repository_manager

"""
Determine if installed tool shed repositories have updates available in their respective tool sheds.
"""
import logging
import threading

from sqlalchemy import false

import tool_shed.util.shed_util_common as suc
from galaxy import util
from tool_shed.util import common_util
from tool_shed.util import encoding_util
from tool_shed.util import repository_util

log = logging.getLogger( __name__ )


[docs]class UpdateRepositoryManager( object ):
[docs] def __init__( self, app ): self.app = app self.context = self.app.install_model.context # Ideally only one Galaxy server process should be able to check for repository updates. if self.app.config.enable_tool_shed_check: self.running = True self.sleeper = Sleeper() self.restarter = threading.Thread( target=self.__restarter ) self.restarter.daemon = True self.app.application_stack.register_postfork_function(self.restarter.start) self.seconds_to_sleep = int( app.config.hours_between_check * 3600 )
[docs] def get_update_to_changeset_revision_and_ctx_rev( self, repository ): """Return the changeset revision hash to which the repository can be updated.""" changeset_revision_dict = {} tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( self.app, str( repository.tool_shed ) ) params = dict( name=str( repository.name ), owner=str( repository.owner ), changeset_revision=str( repository.installed_changeset_revision ) ) pathspec = [ 'repository', 'get_changeset_revision_and_ctx_rev' ] try: encoded_update_dict = util.url_get( tool_shed_url, password_mgr=self.app.tool_shed_registry.url_auth( tool_shed_url ), pathspec=pathspec, params=params ) if encoded_update_dict: update_dict = encoding_util.tool_shed_decode( encoded_update_dict ) includes_data_managers = update_dict.get( 'includes_data_managers', False ) includes_datatypes = update_dict.get( 'includes_datatypes', False ) includes_tools = update_dict.get( 'includes_tools', False ) includes_tools_for_display_in_tool_panel = update_dict.get( 'includes_tools_for_display_in_tool_panel', False ) includes_tool_dependencies = update_dict.get( 'includes_tool_dependencies', False ) includes_workflows = update_dict.get( 'includes_workflows', False ) has_repository_dependencies = update_dict.get( 'has_repository_dependencies', False ) has_repository_dependencies_only_if_compiling_contained_td = update_dict.get( 'has_repository_dependencies_only_if_compiling_contained_td', False ) changeset_revision = update_dict.get( 'changeset_revision', None ) ctx_rev = update_dict.get( 'ctx_rev', None ) changeset_revision_dict[ 'includes_data_managers' ] = includes_data_managers changeset_revision_dict[ 'includes_datatypes' ] = includes_datatypes changeset_revision_dict[ 'includes_tools' ] = includes_tools changeset_revision_dict[ 'includes_tools_for_display_in_tool_panel' ] = includes_tools_for_display_in_tool_panel changeset_revision_dict[ 'includes_tool_dependencies' ] = includes_tool_dependencies changeset_revision_dict[ 'includes_workflows' ] = includes_workflows changeset_revision_dict[ 'has_repository_dependencies' ] = has_repository_dependencies changeset_revision_dict[ 'has_repository_dependencies_only_if_compiling_contained_td' ] = has_repository_dependencies_only_if_compiling_contained_td changeset_revision_dict[ 'changeset_revision' ] = changeset_revision changeset_revision_dict[ 'ctx_rev' ] = ctx_rev except Exception as e: log.debug( "Error getting change set revision for update from the tool shed for repository '%s': %s" % ( repository.name, str( e ) ) ) changeset_revision_dict[ 'includes_data_managers' ] = False changeset_revision_dict[ 'includes_datatypes' ] = False changeset_revision_dict[ 'includes_tools' ] = False changeset_revision_dict[ 'includes_tools_for_display_in_tool_panel' ] = False changeset_revision_dict[ 'includes_tool_dependencies' ] = False changeset_revision_dict[ 'includes_workflows' ] = False changeset_revision_dict[ 'has_repository_dependencies' ] = False changeset_revision_dict[ 'has_repository_dependencies_only_if_compiling_contained_td' ] = False changeset_revision_dict[ 'changeset_revision' ] = None changeset_revision_dict[ 'ctx_rev' ] = None return changeset_revision_dict
def __restarter( self ): log.info( 'Update repository manager restarter starting up...' ) while self.running: # Make a call to the Tool Shed for each installed repository to get the latest # status information in the Tool Shed for the repository. This information includes # items like newer installable repository revisions, current revision updates, whether # the repository revision is the latest installable revision, and whether the repository # has been deprecated in the Tool Shed. for repository in self.context.query( self.app.install_model.ToolShedRepository ) \ .filter( self.app.install_model.ToolShedRepository.table.c.deleted == false() ): tool_shed_status_dict = repository_util.get_tool_shed_status_for_installed_repository( self.app, repository ) if tool_shed_status_dict: if tool_shed_status_dict != repository.tool_shed_status: repository.tool_shed_status = tool_shed_status_dict self.context.flush() else: # The received tool_shed_status_dict is an empty dictionary, so coerce to None. tool_shed_status_dict = None if tool_shed_status_dict != repository.tool_shed_status: repository.tool_shed_status = tool_shed_status_dict self.context.flush() self.sleeper.sleep( self.seconds_to_sleep ) log.info( 'Update repository manager restarter shutting down...' )
[docs] def shutdown( self ): if self.app.config.enable_tool_shed_check: self.running = False self.sleeper.wake()
[docs] def update_repository_record( self, repository, updated_metadata_dict, updated_changeset_revision, updated_ctx_rev ): """ Update a tool_shed_repository database record with new information retrieved from the Tool Shed. This happens when updating an installed repository to a new changeset revision. """ repository.metadata = updated_metadata_dict tool_shed_url = common_util.get_tool_shed_url_from_tool_shed_registry( self.app, repository.tool_shed ) suc.clean_dependency_relationships(self.app, updated_metadata_dict, repository, tool_shed_url) # Update the repository.changeset_revision column in the database. repository.changeset_revision = updated_changeset_revision repository.ctx_rev = updated_ctx_rev # Update the repository.tool_shed_status column in the database. tool_shed_status_dict = repository_util.get_tool_shed_status_for_installed_repository( self.app, repository ) if tool_shed_status_dict: repository.tool_shed_status = tool_shed_status_dict else: repository.tool_shed_status = None self.app.install_model.context.add( repository ) self.app.install_model.context.flush() self.app.install_model.context.refresh( repository ) return repository
[docs]class Sleeper( object ): """ Provides a 'sleep' method that sleeps for a number of seconds *unless* the notify method is called (from a different thread). """
[docs] def __init__( self ): self.condition = threading.Condition()
[docs] def sleep( self, seconds ): self.condition.acquire() self.condition.wait( seconds ) self.condition.release()
[docs] def wake( self ): self.condition.acquire() self.condition.notify() self.condition.release()