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Source code for galaxy.managers.context

"""
Mixins for transaction-like objects.
"""
import string
from json import dumps

from six import text_type

from galaxy.util import bunch


[docs]class ProvidesAppContext( object ): """ For transaction-like objects to provide Galaxy convience layer for database and event handling. Mixed in class must provide `app` property. """
[docs] def log_action( self, user=None, action=None, context=None, params=None): """ Application-level logging of user actions. """ if self.app.config.log_actions: action = self.app.model.UserAction(action=action, context=context, params=text_type( dumps( params ) ) ) try: if user: action.user = user else: action.user = self.user except: action.user = None try: action.session_id = self.galaxy_session.id except: action.session_id = None self.sa_session.add( action ) self.sa_session.flush()
[docs] def log_event( self, message, tool_id=None, **kwargs ): """ Application level logging. Still needs fleshing out (log levels and such) Logging events is a config setting - if False, do not log. """ if self.app.config.log_events: event = self.app.model.Event() event.tool_id = tool_id try: event.message = message % kwargs except: event.message = message try: event.history = self.get_history() except: event.history = None try: event.history_id = self.history.id except: event.history_id = None try: event.user = self.user except: event.user = None try: event.session_id = self.galaxy_session.id except: event.session_id = None self.sa_session.add( event ) self.sa_session.flush()
@property def sa_session( self ): """ Returns a SQLAlchemy session -- currently just gets the current session from the threadlocal session context, but this is provided to allow migration toward a more SQLAlchemy 0.4 style of use. """ return self.app.model.context.current
[docs] def expunge_all( self ): app = self.app context = app.model.context context.expunge_all() # This is a bit hacky, should refctor this. Maybe refactor to app -> expunge_all() if hasattr(app, 'install_model'): install_model = app.install_model if install_model != app.model: install_model.context.expunge_all()
[docs] def get_toolbox(self): """Returns the application toolbox""" return self.app.toolbox
@property def model( self ): return self.app.model @property def install_model( self ): return self.app.install_model
[docs] def request_types(self): if self.sa_session.query( self.app.model.RequestType ).filter_by( deleted=False ).count() > 0: return True return False
[docs]class ProvidesUserContext( object ): """ For transaction-like objects to provide Galaxy convience layer for reasoning about users. Mixed in class must provide `user`, `api_inherit_admin`, and `app` properties. """ @property def anonymous( self ): return self.user is None and not self.api_inherit_admin
[docs] def get_current_user_roles( self ): user = self.user if user: roles = user.all_roles() else: roles = [] return roles
[docs] def user_is_admin( self ): if self.api_inherit_admin: return True return self.user and self.user.email in self.app.config.admin_users_list
[docs] def user_can_do_run_as( self ): run_as_users = [ user for user in self.app.config.get( "api_allow_run_as", "" ).split( "," ) if user ] if not run_as_users: return False user_in_run_as_users = self.user and self.user.email in run_as_users # Can do if explicitly in list or master_api_key supplied. can_do_run_as = user_in_run_as_users or self.api_inherit_admin return can_do_run_as
@property def user_ftp_dir( self ): base_dir = self.app.config.ftp_upload_dir if base_dir is None: return None else: # e.g. 'email' or 'username' identifier_attr = self.app.config.ftp_upload_dir_identifier identifier_value = getattr(self.user, identifier_attr) template = self.app.config.ftp_upload_dir_template path = string.Template(template).safe_substitute(dict( ftp_upload_dir=base_dir, ftp_upload_dir_identifier=identifier_value, )) return path
[docs]class ProvidesHistoryContext( object ): """ For transaction-like objects to provide Galaxy convience layer for reasoning about histories. Mixed in class must provide `user`, `history`, and `app` properties. """
[docs] def db_dataset_for( self, dbkey ): """ Returns the db_file dataset associated/needed by `dataset`, or `None`. """ # If no history, return None. if self.history is None: return None # TODO: when does this happen? is it Bunch or util.bunch.Bunch? if isinstance( self.history, bunch.Bunch ): # The API presents a Bunch for a history. Until the API is # more fully featured for handling this, also return None. return None datasets = self.sa_session.query( self.app.model.HistoryDatasetAssociation ) \ .filter_by( deleted=False, history_id=self.history.id, extension="len" ) for ds in datasets: if dbkey == ds.dbkey: return ds return None
@property def db_builds( self ): """ Returns the builds defined by galaxy and the builds defined by the user (chromInfo in history). """ # FIXME: This method should be removed return self.app.genome_builds.get_genome_build_names( trans=self )