[galaxy-dev] [hg] galaxy 3015: Fix most of the db flushes to be compatibel wi...

details: http://www.bx.psu.edu/hg/galaxy/rev/b33b8f5e03b8 changeset: 3015:b33b8f5e03b8 user: Greg Von Kuster <greg@bx.psu.edu> date: Wed Nov 11 15:59:41 2009 -0500 description: Fix most of the db flushes to be compatibel with sqlalchemy 05. Add the _monkeypatch_query_method() back into assignmapper due to a single object.get() method in the MetadataCollection class since Metadata has no current hook into mapping.context ( the sqlalchemy session ). There a 4 flushes in metadata,py and 20 flushes in model.__init__.py that still use the _monkeypatch_session_method in assignmapper due to the same issue, but all other flushes are fixed. diffstat: lib/galaxy/datatypes/metadata.py | 6 +- lib/galaxy/jobs/__init__.py | 25 +- lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py | 39 +- lib/galaxy/model/orm/ext/assignmapper.py | 15 +- lib/galaxy/security/__init__.py | 1255 +++++---- lib/galaxy/tools/__init__.py | 40 +- lib/galaxy/tools/actions/__init__.py | 15 +- lib/galaxy/tools/actions/upload.py | 2 +- lib/galaxy/tools/actions/upload_common.py | 41 +- lib/galaxy/tools/parameters/basic.py | 4 +- lib/galaxy/web/controllers/admin.py | 72 +- lib/galaxy/web/controllers/async.py | 3 +- lib/galaxy/web/controllers/dataset.py | 3 +- lib/galaxy/web/controllers/forms.py | 6 +- lib/galaxy/web/controllers/history.py | 30 +- lib/galaxy/web/controllers/library.py | 19 +- lib/galaxy/web/controllers/library_admin.py | 53 +- lib/galaxy/web/controllers/library_common.py | 23 +- lib/galaxy/web/controllers/requests.py | 34 +- lib/galaxy/web/controllers/requests_admin.py | 71 +- lib/galaxy/web/controllers/root.py | 18 +- lib/galaxy/web/controllers/tracks.py | 6 +- lib/galaxy/web/controllers/user.py | 42 +- lib/galaxy/web/controllers/workflow.py | 8 +- lib/galaxy/web/framework/__init__.py | 12 +- scripts/cleanup_datasets/cleanup_datasets.py | 29 +- scripts/cleanup_datasets/update_metadata.py | 3 +- scripts/update_database/update_database_with_security_libraries.py | 229 - scripts/update_database/update_database_with_security_libraries.sh | 9 - test/functional/test_DNAse_flanked_genes.py | 6 +- test/functional/test_history_functions.py | 5 +- test/functional/test_metadata_editing.py | 2 +- test/functional/test_security_and_libraries.py | 10 +- test/functional/test_user_info.py | 6 +- tools/data_source/hbvar_filter.py | 3 +- tools/data_source/microbial_import_code.py | 11 +- tools/emboss_5/emboss_format_corrector.py | 9 +- tools/filters/axt_to_lav_code.py | 3 +- tools/filters/lav_to_bed_code.py | 3 +- tools/maf/maf_to_bed_code.py | 15 +- tools/visualization/LAJ_code.py | 3 +- 41 files changed, 1065 insertions(+), 1123 deletions(-) diffs (truncated from 3757 to 3000 lines): diff -r 0edb42925161 -r b33b8f5e03b8 lib/galaxy/datatypes/metadata.py --- a/lib/galaxy/datatypes/metadata.py Wed Nov 11 15:13:12 2009 -0500 +++ b/lib/galaxy/datatypes/metadata.py Wed Nov 11 15:59:41 2009 -0500 @@ -391,9 +391,9 @@ return value if DATABASE_CONNECTION_AVAILABLE: try: - # FIXME: GVK ( 10/23/09 ) Can we get a valid db session without this import? - from galaxy.model.mapping import context as sa_session - return sa_session.query( galaxy.model.MetadataFile ).get( value ) + # FIXME: GVK ( 11/11/09 ) had to add the monkey patch back into assignmapper for the get + # method for this since Metadata has no hook into mapping.context ( the salalchemy session ). + return galaxy.model.MetadataFile.get( value ) except: #value was not a valid id return None diff -r 0edb42925161 -r b33b8f5e03b8 lib/galaxy/jobs/__init__.py --- a/lib/galaxy/jobs/__init__.py Wed Nov 11 15:13:12 2009 -0500 +++ b/lib/galaxy/jobs/__init__.py Wed Nov 11 15:59:41 2009 -0500 @@ -390,7 +390,8 @@ # We need command_line persisted to the db in order for Galaxy to re-queue the job # if the server was stopped and restarted before the job finished job.command_line = self.command_line - job.flush() + self.sa_session.add( job ) + self.sa_session.flush() # Return list of all extra files extra_filenames = config_filenames if param_filename is not None: @@ -435,11 +436,13 @@ dataset.set_size() if dataset.ext == 'auto': dataset.extension = 'data' - dataset.flush() + self.sa_session.add( dataset ) + self.sa_session.flush() job.state = model.Job.states.ERROR job.command_line = self.command_line job.info = message - job.flush() + self.sa_session.add( job ) + self.sa_session.flush() # If the job was deleted, just clean up self.cleanup() @@ -452,11 +455,13 @@ dataset.state = state if info: dataset.info = info - dataset.flush() + self.sa_session.add( dataset ) + self.sa_session.flush() if info: job.info = info job.state = state - job.flush() + self.sa_session.add( job ) + self.sa_session.flush() def get_state( self ): job = self.sa_session.query( model.Job ).get( self.job_id ) @@ -468,7 +473,8 @@ self.sa_session.refresh( job ) job.job_runner_name = runner_url job.job_runner_external_id = external_id - job.flush() + self.sa_session.add( job ) + self.sa_session.flush() def finish( self, stdout, stderr ): """ @@ -554,7 +560,8 @@ dataset.blurb = "empty" if dataset.ext == 'auto': dataset.extension = 'txt' - dataset.flush() + self.sa_session.add( dataset ) + self.sa_session.flush() if context['stderr']: dataset_assoc.dataset.dataset.state = model.Dataset.states.ERROR else: @@ -566,7 +573,6 @@ # panel stops checking for updates. So allow the # self.sa_session.flush() at the bottom of this method set # the state instead. - #dataset_assoc.dataset.dataset.flush() # Save stdout and stderr if len( stdout ) > 32768: @@ -839,7 +845,8 @@ job.info = error_msg else: job.state = job.states.DELETED - job.flush() + self.sa_session.add( job ) + self.sa_session.flush() # if job is in JobQueue or FooJobRunner's put method, # job_runner_name will be unset and the job will be dequeued due to # state change above diff -r 0edb42925161 -r b33b8f5e03b8 lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py --- a/lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py Wed Nov 11 15:13:12 2009 -0500 +++ b/lib/galaxy/model/migrate/versions/0005_cleanup_datasets_fix.py Wed Nov 11 15:59:41 2009 -0500 @@ -155,7 +155,8 @@ # Relationships if not dataset and create_dataset: dataset = Dataset( state=Dataset.states.NEW ) - dataset.flush() + context.add( dataset ) + context.flush() self.dataset = dataset self.parent_id = parent_id self.validation_errors = validation_errors @@ -166,7 +167,8 @@ return self.dataset.state def set_dataset_state ( self, state ): self.dataset.state = state - self.dataset.flush() #flush here, because hda.flush() won't flush the Dataset object + context.add( self.dataset ) + context.flush() #flush here, because hda.flush() won't flush the Dataset object state = property( get_dataset_state, set_dataset_state ) def get_file_name( self ): return self.dataset.get_file_name() @@ -327,7 +329,8 @@ parent_id=parent_id, copied_from_history_dataset_association=self, history = target_history ) - hda.flush() + context.add( hda ) + context.flush() hda.set_size() # Need to set after flushed, as MetadataFiles require dataset.id hda.metadata = self.metadata @@ -337,7 +340,7 @@ if not self.datatype.copy_safe_peek: # In some instances peek relies on dataset_id, i.e. gmaj.zip for viewing MAFs hda.set_peek() - hda.flush() + context.flush() return hda def to_library_dataset_dataset_association( self, target_folder, replace_dataset=None, parent_id=None ): if replace_dataset: @@ -347,7 +350,8 @@ # If replace_dataset is None, the Library level permissions will be taken from the folder and applied to the new # LibraryDataset, and the current user's DefaultUserPermissions will be applied to the associated Dataset. library_dataset = LibraryDataset( folder=target_folder, name=self.name, info=self.info ) - library_dataset.flush() + context.add( library_dataset ) + context.flush() ldda = LibraryDatasetDatasetAssociation( name=self.name, info=self.info, blurb=self.blurb, @@ -361,21 +365,24 @@ parent_id=parent_id, copied_from_history_dataset_association=self, user=self.history.user ) - ldda.flush() + context.add( ldda ) + context.flush() # Permissions must be the same on the LibraryDatasetDatasetAssociation and the associated LibraryDataset # Must set metadata after ldda flushed, as MetadataFiles require ldda.id ldda.metadata = self.metadata if not replace_dataset: target_folder.add_library_dataset( library_dataset, genome_build=ldda.dbkey ) - target_folder.flush() + context.add( target_folder ) + context.flush() library_dataset.library_dataset_dataset_association_id = ldda.id - library_dataset.flush() + context.add( library_dataset ) + context.flush() for child in self.children: child_copy = child.to_library_dataset_dataset_association( target_folder=target_folder, replace_dataset=replace_dataset, parent_id=ldda.id ) if not self.datatype.copy_safe_peek: # In some instances peek relies on dataset_id, i.e. gmaj.zip for viewing MAFs ldda.set_peek() - ldda.flush() + context.flush() return ldda def clear_associated_files( self, metadata_safe = False, purge = False ): # metadata_safe = True means to only clear when assoc.metadata_safe == False @@ -412,13 +419,14 @@ copied_from_library_dataset_dataset_association=self, history=target_history, hid=hid ) - hda.flush() + context.flush() hda.metadata = self.metadata #need to set after flushed, as MetadataFiles require dataset.id for child in self.children: child_copy = child.to_history_dataset_association( target_history=target_history, parent_id=hda.id ) if not self.datatype.copy_safe_peek: hda.set_peek() #in some instances peek relies on dataset_id, i.e. gmaj.zip for viewing MAFs - hda.flush() + context.add( hda ) + context.flush() return hda def copy( self, copy_children = False, parent_id = None, target_folder = None ): ldda = LibraryDatasetDatasetAssociation( name=self.name, @@ -433,7 +441,8 @@ parent_id=parent_id, copied_from_library_dataset_dataset_association=self, folder=target_folder ) - ldda.flush() + context.add( ldda ) + context.flush() # Need to set after flushed, as MetadataFiles require dataset.id ldda.metadata = self.metadata if copy_children: @@ -442,7 +451,7 @@ if not self.datatype.copy_safe_peek: # In some instances peek relies on dataset_id, i.e. gmaj.zip for viewing MAFs ldda.set_peek() - ldda.flush() + context.flush() return ldda def clear_associated_files( self, metadata_safe = False, purge = False ): return @@ -466,8 +475,8 @@ def set_library_dataset_dataset_association( self, ldda ): self.library_dataset_dataset_association = ldda ldda.library_dataset = self - ldda.flush() - self.flush() + context.add_all( ( self, ldda ) ) + context.flush() def get_info( self ): if self.library_dataset_dataset_association: return self.library_dataset_dataset_association.info diff -r 0edb42925161 -r b33b8f5e03b8 lib/galaxy/model/orm/ext/assignmapper.py --- a/lib/galaxy/model/orm/ext/assignmapper.py Wed Nov 11 15:13:12 2009 -0500 +++ b/lib/galaxy/model/orm/ext/assignmapper.py Wed Nov 11 15:59:41 2009 -0500 @@ -18,8 +18,20 @@ from sqlalchemy.orm import Query from sqlalchemy.orm import mapper as sqla_mapper +def _monkeypatch_query_method( name, session, class_ ): + # TODO: eliminate this method by fixing the single query in ~/datatypes/metadata.py ( line 396 ) + def do(self, *args, **kwargs): + return getattr( class_.query, name)(*args, **kwargs) + try: + do.__name__ = name + except: + pass + if not hasattr(class_, name): + setattr(class_, name, classmethod(do)) def _monkeypatch_session_method( name, session, class_ ): - # TODO: eliminate this method by fixing the session flushes + # TODO: eliminate this method by fixing the session flushes in ~/model/__init__.py ( 20 of them ) + # and ~/datatypes/metadata.py ( 4 of them ). The affected objects have no known hook into mapping.context + # ( i.e., sqlalchemy session ). def do( self, *args, **kwargs ): if self not in session.deleted: session.add( self ) @@ -42,6 +54,7 @@ setattr( self, key, value ) cls.__init__ = __init__ cls.query = scoped_session.query_property() + _monkeypatch_query_method( 'get', scoped_session, cls ) _monkeypatch_session_method( 'flush', scoped_session, cls ) return sqla_mapper( cls, *arg, **kw ) return mapper( class_, *args, **kwargs ) diff -r 0edb42925161 -r b33b8f5e03b8 lib/galaxy/security/__init__.py --- a/lib/galaxy/security/__init__.py Wed Nov 11 15:13:12 2009 -0500 +++ b/lib/galaxy/security/__init__.py Wed Nov 11 15:59:41 2009 -0500 @@ -1,625 +1,630 @@ -""" -Galaxy Security - -""" -import logging, socket -from datetime import datetime, timedelta -from galaxy.util.bunch import Bunch -from galaxy.model.orm import * - -log = logging.getLogger(__name__) - -class Action( object ): - def __init__( self, action, description, model ): - self.action = action - self.description = description - self.model = model - -class RBACAgent: - """Class that handles galaxy security""" - permitted_actions = Bunch( - DATASET_MANAGE_PERMISSIONS = Action( "manage permissions", "Role members can manage the roles associated with this dataset", "grant" ), - DATASET_ACCESS = Action( "access", "Role members can import this dataset into their history for analysis", "restrict" ), - LIBRARY_ADD = Action( "add library item", "Role members can add library items to this library item", "grant" ), - LIBRARY_MODIFY = Action( "modify library item", "Role members can modify this library item", "grant" ), - LIBRARY_MANAGE = Action( "manage library permissions", "Role members can manage roles associated with this library item", "grant" ) - ) - def get_action( self, name, default=None ): - """Get a permitted action by its dict key or action name""" - for k, v in self.permitted_actions.items(): - if k == name or v.action == name: - return v - return default - def get_actions( self ): - """Get all permitted actions as a list of Action objects""" - return self.permitted_actions.__dict__.values() - def get_item_actions( self, action, item ): - raise 'No valid method of retrieving action (%s) for item %s.' % ( action, item ) - def guess_derived_permissions_for_datasets( self, datasets = [] ): - raise "Unimplemented Method" - def can_access_dataset( self, roles, dataset ): - raise "Unimplemented Method" - def can_manage_dataset( self, roles, dataset ): - raise "Unimplemented Method" - def can_add_library_item( self, user, roles, item ): - raise "Unimplemented Method" - def can_modify_library_item( self, user, roles, item ): - raise "Unimplemented Method" - def can_manage_library_item( self, user, roles, item ): - raise "Unimplemented Method" - def associate_components( self, **kwd ): - raise 'No valid method of associating provided components: %s' % kwd - def create_private_user_role( self, user ): - raise "Unimplemented Method" - def get_private_user_role( self, user ): - raise "Unimplemented Method" - def user_set_default_permissions( self, user, permissions={}, history=False, dataset=False ): - raise "Unimplemented Method" - def history_set_default_permissions( self, history, permissions=None, dataset=False, bypass_manage_permission=False ): - raise "Unimplemented Method" - def set_all_dataset_permissions( self, dataset, permissions ): - raise "Unimplemented Method" - def set_dataset_permission( self, dataset, permission ): - raise "Unimplemented Method" - def set_all_library_permissions( self, dataset, permissions ): - raise "Unimplemented Method" - def dataset_is_public( self, dataset ): - raise "Unimplemented Method" - def make_dataset_public( self, dataset ): - raise "Unimplemented Method" - def get_component_associations( self, **kwd ): - raise "Unimplemented Method" - def components_are_associated( self, **kwd ): - return bool( self.get_component_associations( **kwd ) ) - def convert_permitted_action_strings( self, permitted_action_strings ): - """ - When getting permitted actions from an untrusted source like a - form, ensure that they match our actual permitted actions. - """ - return filter( lambda x: x is not None, [ self.permitted_actions.get( action_string ) for action_string in permitted_action_strings ] ) - -class GalaxyRBACAgent( RBACAgent ): - def __init__( self, model, permitted_actions=None ): - self.model = model - if permitted_actions: - self.permitted_actions = permitted_actions - # List of "library_item" objects and their associated permissions and info template objects - self.library_item_assocs = ( - ( self.model.Library, self.model.LibraryPermissions ), - ( self.model.LibraryFolder, self.model.LibraryFolderPermissions ), - ( self.model.LibraryDataset, self.model.LibraryDatasetPermissions ), - ( self.model.LibraryDatasetDatasetAssociation, self.model.LibraryDatasetDatasetAssociationPermissions ) ) - @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.model.context.current - def allow_dataset_action( self, roles, action, dataset ): - """ - Returns true when user has permission to perform an action on an - instance of Dataset. - """ - dataset_actions = self.get_item_actions( action, dataset ) - if not dataset_actions: - return action.model == 'restrict' - ret_val = False - for dataset_action in dataset_actions: - if dataset_action.role in roles: - ret_val = True - break - return ret_val - def can_access_dataset( self, roles, dataset ): - return self.allow_dataset_action( roles, self.permitted_actions.DATASET_ACCESS, dataset ) - def can_manage_dataset( self, roles, dataset ): - return self.allow_dataset_action( roles, self.permitted_actions.DATASET_MANAGE_PERMISSIONS, dataset ) - def allow_library_item_action( self, user, roles, action, item ): - """ - Method for checking a permission for the current user to perform a - specific library action on a library item, which must be one of: - Library, LibraryFolder, LibraryDataset, LibraryDatasetDatasetAssociation - """ - if user is None: - # All permissions are granted, so non-users cannot have permissions - return False - # Check to see if user has access to any of the roles associated with action - item_actions = self.get_item_actions( action, item ) - if not item_actions: - # All permissions are granted, so item must have action - return False - ret_val = False - for item_action in item_actions: - if item_action.role in roles: - ret_val = True - break - return ret_val - def can_add_library_item( self, user, roles, item ): - return self.allow_library_item_action( user, roles, self.permitted_actions.LIBRARY_ADD, item ) - def can_modify_library_item( self, user, roles, item ): - return self.allow_library_item_action( user, roles, self.permitted_actions.LIBRARY_MODIFY, item ) - def can_manage_library_item( self, user, roles, item ): - return self.allow_library_item_action( user, roles, self.permitted_actions.LIBRARY_MANAGE, item ) - def get_item_actions( self, action, item ): - # item must be one of: Dataset, Library, LibraryFolder, LibraryDataset, LibraryDatasetDatasetAssociation - return [ permission for permission in item.actions if permission.action == action.action ] - def guess_derived_permissions_for_datasets( self, datasets=[] ): - """Returns a dict of { action : [ role, role, ... ] } for the output dataset based upon provided datasets""" - perms = {} - for dataset in datasets: - if not isinstance( dataset, self.model.Dataset ): - dataset = dataset.dataset - these_perms = {} - # initialize blank perms - for action in self.get_actions(): - these_perms[ action ] = [] - # collect this dataset's perms - these_perms = self.get_dataset_permissions( dataset ) - # join or intersect this dataset's permissions with others - for action, roles in these_perms.items(): - if action not in perms.keys(): - perms[ action ] = roles - else: - if action.model == 'grant': - # intersect existing roles with new roles - perms[ action ] = filter( lambda x: x in perms[ action ], roles ) - elif action.model == 'restrict': - # join existing roles with new roles - perms[ action ].extend( filter( lambda x: x not in perms[ action ], roles ) ) - return perms - def associate_components( self, **kwd ): - if 'user' in kwd: - if 'group' in kwd: - return self.associate_user_group( kwd['user'], kwd['group'] ) - elif 'role' in kwd: - return self.associate_user_role( kwd['user'], kwd['role'] ) - elif 'role' in kwd: - if 'group' in kwd: - return self.associate_group_role( kwd['group'], kwd['role'] ) - if 'action' in kwd: - if 'dataset' in kwd and 'role' in kwd: - return self.associate_action_dataset_role( kwd['action'], kwd['dataset'], kwd['role'] ) - raise 'No valid method of associating provided components: %s' % kwd - def associate_user_group( self, user, group ): - assoc = self.model.UserGroupAssociation( user, group ) - assoc.flush() - return assoc - def associate_user_role( self, user, role ): - assoc = self.model.UserRoleAssociation( user, role ) - assoc.flush() - return assoc - def associate_group_role( self, group, role ): - assoc = self.model.GroupRoleAssociation( group, role ) - assoc.flush() - return assoc - def associate_action_dataset_role( self, action, dataset, role ): - assoc = self.model.DatasetPermissions( action, dataset, role ) - assoc.flush() - return assoc - def create_private_user_role( self, user ): - # Create private role - role = self.model.Role( name=user.email, description='Private Role for ' + user.email, type=self.model.Role.types.PRIVATE ) - role.flush() - # Add user to role - self.associate_components( role=role, user=user ) - return role - def get_private_user_role( self, user, auto_create=False ): - role = self.sa_session.query( self.model.Role ) \ - .filter( and_( self.model.Role.table.c.name == user.email, - self.model.Role.table.c.type == self.model.Role.types.PRIVATE ) ) \ - .first() - if not role: - if auto_create: - return self.create_private_user_role( user ) - else: - return None - return role - def user_set_default_permissions( self, user, permissions={}, history=False, dataset=False, bypass_manage_permission=False, default_access_private = False ): - # bypass_manage_permission is used to change permissions of datasets in a userless history when logging in - if user is None: - return None - if not permissions: - #default permissions - permissions = { self.permitted_actions.DATASET_MANAGE_PERMISSIONS : [ self.get_private_user_role( user, auto_create=True ) ] } - #new_user_dataset_access_role_default_private is set as True in config file - if default_access_private: - permissions[ self.permitted_actions.DATASET_ACCESS ] = permissions.values()[ 0 ] - # Delete all of the current default permissions for the user - for dup in user.default_permissions: - self.sa_session.delete( dup ) - dup.flush() - # Add the new default permissions for the user - for action, roles in permissions.items(): - if isinstance( action, Action ): - action = action.action - for dup in [ self.model.DefaultUserPermissions( user, action, role ) for role in roles ]: - dup.flush() - if history: - for history in user.active_histories: - self.history_set_default_permissions( history, permissions=permissions, dataset=dataset, bypass_manage_permission=bypass_manage_permission ) - def user_get_default_permissions( self, user ): - permissions = {} - for dup in user.default_permissions: - action = self.get_action( dup.action ) - if action in permissions: - permissions[ action ].append( dup.role ) - else: - permissions[ action ] = [ dup.role ] - return permissions - def history_set_default_permissions( self, history, permissions={}, dataset=False, bypass_manage_permission=False ): - # bypass_manage_permission is used to change permissions of datasets in a user-less history when logging in - user = history.user - if not user: - # default permissions on a user-less history are None - return None - if not permissions: - permissions = self.user_get_default_permissions( user ) - # Delete all of the current default permission for the history - for dhp in history.default_permissions: - self.sa_session.delete( dhp ) - dhp.flush() - # Add the new default permissions for the history - for action, roles in permissions.items(): - if isinstance( action, Action ): - action = action.action - for dhp in [ self.model.DefaultHistoryPermissions( history, action, role ) for role in roles ]: - dhp.flush() - if dataset: - # Only deal with datasets that are not purged - for hda in history.activatable_datasets: - dataset = hda.dataset - if dataset.library_associations: - # Don't change permissions on a dataset associated with a library - continue - if [ assoc for assoc in dataset.history_associations if assoc.history not in user.histories ]: - # Don't change permissions on a dataset associated with a history not owned by the user - continue - if bypass_manage_permission or self.can_manage_dataset( user.all_roles(), dataset ): - self.set_all_dataset_permissions( dataset, permissions ) - def history_get_default_permissions( self, history ): - permissions = {} - for dhp in history.default_permissions: - action = self.get_action( dhp.action ) - if action in permissions: - permissions[ action ].append( dhp.role ) - else: - permissions[ action ] = [ dhp.role ] - return permissions - def set_all_dataset_permissions( self, dataset, permissions={} ): - """ - Set new permissions on a dataset, eliminating all current permissions - permissions looks like: { Action : [ Role, Role ] } - """ - # Delete all of the current permissions on the dataset - # TODO: If setting ACCESS permission, at least 1 user must have every role associated with this dataset, - # or the dataset is inaccessible. See admin/library_dataset_dataset_association() - for dp in dataset.actions: - self.sa_session.delete( dp ) - dp.flush() - # Add the new permissions on the dataset - for action, roles in permissions.items(): - if isinstance( action, Action ): - action = action.action - for dp in [ self.model.DatasetPermissions( action, dataset, role ) for role in roles ]: - dp.flush() - def set_dataset_permission( self, dataset, permission={} ): - """ - Set a specific permission on a dataset, leaving all other current permissions on the dataset alone - permissions looks like: { Action : [ Role, Role ] } - """ - # TODO: If setting ACCESS permission, at least 1 user must have every role associated with this dataset, - # or the dataset is inaccessible. See admin/library_dataset_dataset_association() - for action, roles in permission.items(): - if isinstance( action, Action ): - action = action.action - # Delete the current specific permission on the dataset if one exists - for dp in dataset.actions: - if dp.action == action: - self.sa_session.delete( dp ) - dp.flush() - # Add the new specific permission on the dataset - for dp in [ self.model.DatasetPermissions( action, dataset, role ) for role in roles ]: - dp.flush() - def dataset_is_public( self, dataset ): - # A dataset is considered public if there are no "access" actions associated with it. Any - # other actions ( 'manage permissions', 'edit metadata' ) are irrelevant. - return self.permitted_actions.DATASET_ACCESS.action not in [ a.action for a in dataset.actions ] - def make_dataset_public( self, dataset ): - # A dataset is considered public if there are no "access" actions associated with it. Any - # other actions ( 'manage permissions', 'edit metadata' ) are irrelevant. - for dp in dataset.actions: - if dp.action == self.permitted_actions.DATASET_ACCESS.action: - self.sa_session.delete( dp ) - dp.flush() - def get_dataset_permissions( self, dataset ): - """ - Return a dictionary containing the actions and associated roles on dataset. - The dictionary looks like: { Action : [ Role, Role ] } - dataset must be an instance of Dataset() - """ - permissions = {} - for dp in dataset.actions: - action = self.get_action( dp.action ) - if action in permissions: - permissions[ action ].append( dp.role ) - else: - permissions[ action ] = [ dp.role ] - return permissions - def copy_dataset_permissions( self, src, dst ): - if not isinstance( src, self.model.Dataset ): - src = src.dataset - if not isinstance( dst, self.model.Dataset ): - dst = dst.dataset - self.set_all_dataset_permissions( dst, self.get_dataset_permissions( src ) ) - def privately_share_dataset( self, dataset, users = [] ): - intersect = None - for user in users: - roles = [ ura.role for ura in user.roles if ura.role.type == self.model.Role.types.SHARING ] - if intersect is None: - intersect = roles - else: - new_intersect = [] - for role in roles: - if role in intersect: - new_intersect.append( role ) - intersect = new_intersect - sharing_role = None - if intersect: - for role in intersect: - if not filter( lambda x: x not in users, [ ura.user for ura in role.users ] ): - # only use a role if it contains ONLY the users we're sharing with - sharing_role = role - break - if sharing_role is None: - sharing_role = self.model.Role( name = "Sharing role for: " + ", ".join( [ u.email for u in users ] ), - type = self.model.Role.types.SHARING ) - sharing_role.flush() - for user in users: - self.associate_components( user=user, role=sharing_role ) - self.set_dataset_permission( dataset, { self.permitted_actions.DATASET_ACCESS : [ sharing_role ] } ) - def set_all_library_permissions( self, library_item, permissions={} ): - # Set new permissions on library_item, eliminating all current permissions - for role_assoc in library_item.actions: - self.sa_session.delete( role_assoc ) - role_assoc.flush() - # Add the new permissions on library_item - for item_class, permission_class in self.library_item_assocs: - if isinstance( library_item, item_class ): - for action, roles in permissions.items(): - if isinstance( action, Action ): - action = action.action - for role_assoc in [ permission_class( action, library_item, role ) for role in roles ]: - role_assoc.flush() - def get_library_dataset_permissions( self, library_dataset ): - # Permissions will always be the same for LibraryDatasets and associated - # LibraryDatasetDatasetAssociations - if isinstance( library_dataset, self.model.LibraryDatasetDatasetAssociation ): - library_dataset = library_dataset.library_dataset - permissions = {} - for library_dataset_permission in library_dataset.actions: - action = self.get_action( library_dataset_permission.action ) - if action in permissions: - permissions[ action ].append( library_dataset_permission.role ) - else: - permissions[ action ] = [ library_dataset_permission.role ] - return permissions - def copy_library_permissions( self, source_library_item, target_library_item, user=None ): - # Copy all permissions from source - permissions = {} - for role_assoc in source_library_item.actions: - if role_assoc.action in permissions: - permissions[role_assoc.action].append( role_assoc.role ) - else: - permissions[role_assoc.action] = [ role_assoc.role ] - self.set_all_library_permissions( target_library_item, permissions ) - if user: - item_class = None - for item_class, permission_class in self.library_item_assocs: - if isinstance( target_library_item, item_class ): - break - if item_class: - # Make sure user's private role is included - private_role = self.model.security_agent.get_private_user_role( user ) - for name, action in self.permitted_actions.items(): - if not permission_class.filter_by( role_id = private_role.id, action = action.action ).first(): - lp = permission_class( action.action, target_library_item, private_role ) - lp.flush() - else: - raise 'Invalid class (%s) specified for target_library_item (%s)' % \ - ( target_library_item.__class__, target_library_item.__class__.__name__ ) - def show_library_item( self, user, roles, library_item, actions_to_check, hidden_folder_ids='' ): - """ - This method must be sent an instance of Library() or LibraryFolder(). Recursive execution produces a - comma-separated string of folder ids whose folders do NOT meet the criteria for showing. Along with - the string, True is returned if the current user has permission to perform any 1 of actions_to_check - on library_item. Otherwise, cycle through all sub-folders in library_item until one is found that meets - this criteria, if it exists. This method does not necessarily scan the entire library as it returns - when it finds the first library_item that allows user to perform any one action in actions_to_check. - """ - for action in actions_to_check: - if self.allow_library_item_action( user, roles, action, library_item ): - return True, hidden_folder_ids - if isinstance( library_item, self.model.Library ): - return self.show_library_item( user, roles, library_item.root_folder, actions_to_check, hidden_folder_ids='' ) - if isinstance( library_item, self.model.LibraryFolder ): - for folder in library_item.active_folders: - can_show, hidden_folder_ids = self.show_library_item( user, roles, folder, actions_to_check, hidden_folder_ids=hidden_folder_ids ) - if can_show: - return True, hidden_folder_ids - if hidden_folder_ids: - hidden_folder_ids = '%s,%d' % ( hidden_folder_ids, folder.id ) - else: - hidden_folder_ids = '%d' % folder.id - return False, hidden_folder_ids - def get_showable_folders( self, user, roles, library_item, actions_to_check, hidden_folder_ids=[], showable_folders=[] ): - """ - This method must be sent an instance of Library(), all the folders of which are scanned to determine if - user is allowed to perform any action in actions_to_check. The param hidden_folder_ids, if passed, should - contain a list of folder IDs which was generated when the library was previously scanned - using the same actions_to_check. A list of showable folders is generated. This method scans the entire library. - """ - if isinstance( library_item, self.model.Library ): - return self.get_showable_folders( user, roles, library_item.root_folder, actions_to_check, showable_folders=[] ) - if isinstance( library_item, self.model.LibraryFolder ): - if library_item.id not in hidden_folder_ids: - for action in actions_to_check: - if self.allow_library_item_action( user, roles, action, library_item ): - showable_folders.append( library_item ) - break - for folder in library_item.active_folders: - self.get_showable_folders( user, roles, folder, actions_to_check, showable_folders=showable_folders ) - return showable_folders - def set_entity_user_associations( self, users=[], roles=[], groups=[], delete_existing_assocs=True ): - for user in users: - if delete_existing_assocs: - for a in user.non_private_roles + user.groups: - self.sa_session.delete( a ) - a.flush() - self.sa_session.refresh( user ) - for role in roles: - # Make sure we are not creating an additional association with a PRIVATE role - if role not in user.roles: - self.associate_components( user=user, role=role ) - for group in groups: - self.associate_components( user=user, group=group ) - def set_entity_group_associations( self, groups=[], users=[], roles=[], delete_existing_assocs=True ): - for group in groups: - if delete_existing_assocs: - for a in group.roles + group.users: - self.sa_session.delete( a ) - a.flush() - for role in roles: - self.associate_components( group=group, role=role ) - for user in users: - self.associate_components( group=group, user=user ) - def set_entity_role_associations( self, roles=[], users=[], groups=[], delete_existing_assocs=True ): - for role in roles: - if delete_existing_assocs: - for a in role.users + role.groups: - self.sa_session.delete( a ) - a.flush() - for user in users: - self.associate_components( user=user, role=role ) - for group in groups: - self.associate_components( group=group, role=role ) - def get_component_associations( self, **kwd ): - assert len( kwd ) == 2, 'You must specify exactly 2 Galaxy security components to check for associations.' - if 'dataset' in kwd: - if 'action' in kwd: - return self.sa_session.query( self.model.DatasetPermissions ).filter_by( action = kwd['action'].action, dataset_id = kwd['dataset'].id ).first() - elif 'user' in kwd: - if 'group' in kwd: - return self.sa_session.query( self.model.UserGroupAssociation ).filter_by( group_id = kwd['group'].id, user_id = kwd['user'].id ).first() - elif 'role' in kwd: - return self.sa_session.query( self.model.UserRoleAssociation ).filter_by( role_id = kwd['role'].id, user_id = kwd['user'].id ).first() - elif 'group' in kwd: - if 'role' in kwd: - return self.sa_session.query( self.model.GroupRoleAssociation ).filter_by( role_id = kwd['role'].id, group_id = kwd['group'].id ).first() - raise 'No valid method of associating provided components: %s' % kwd - def check_folder_contents( self, user, roles, folder, hidden_folder_ids='' ): - """ - This method must always be sent an instance of LibraryFolder(). Recursive execution produces a - comma-separated string of folder ids whose folders do NOT meet the criteria for showing. Along - with the string, True is returned if the current user has permission to access folder. Otherwise, - cycle through all sub-folders in folder until one is found that meets this criteria, if it exists. - This method does not necessarily scan the entire library as it returns when it finds the first - folder that is accessible to user. - """ - action = self.permitted_actions.DATASET_ACCESS - lddas = self.sa_session.query( self.model.LibraryDatasetDatasetAssociation ) \ - .join( "library_dataset" ) \ - .filter( self.model.LibraryDataset.folder == folder ) \ - .join( "dataset" ) \ - .options( eagerload_all( "dataset.actions" ) ) \ - .all() - for ldda in lddas: - ldda_access_permissions = self.get_item_actions( action, ldda.dataset ) - if not ldda_access_permissions: - # Dataset is public - return True, hidden_folder_ids - for ldda_access_permission in ldda_access_permissions: - if ldda_access_permission.role in roles: - # The current user has access permission on the dataset - return True, hidden_folder_ids - for sub_folder in folder.active_folders: - can_access, hidden_folder_ids = self.check_folder_contents( user, roles, sub_folder, hidden_folder_ids=hidden_folder_ids ) - if can_access: - return True, hidden_folder_ids - if hidden_folder_ids: - hidden_folder_ids = '%s,%d' % ( hidden_folder_ids, sub_folder.id ) - else: - hidden_folder_ids = '%d' % sub_folder.id - return False, hidden_folder_ids - -class HostAgent( RBACAgent ): - """ - A simple security agent which allows access to datasets based on host. - This exists so that externals sites such as UCSC can gain access to - datasets which have permissions which would normally prevent such access. - """ - # TODO: Make sites user configurable - sites = Bunch( - ucsc_main = ( 'hgw1.cse.ucsc.edu', 'hgw2.cse.ucsc.edu', 'hgw3.cse.ucsc.edu', 'hgw4.cse.ucsc.edu', - 'hgw5.cse.ucsc.edu', 'hgw6.cse.ucsc.edu', 'hgw7.cse.ucsc.edu', 'hgw8.cse.ucsc.edu' ), - ucsc_test = ( 'hgwdev.cse.ucsc.edu', ), - ucsc_archaea = ( 'lowepub.cse.ucsc.edu', ) - ) - def __init__( self, model, permitted_actions=None ): - self.model = model - if permitted_actions: - self.permitted_actions = permitted_actions - @property - def sa_session( self ): - return self.model.context.current - def allow_action( self, addr, action, **kwd ): - if 'dataset' in kwd and action == self.permitted_actions.DATASET_ACCESS: - hda = kwd['dataset'] - if action == self.permitted_actions.DATASET_ACCESS and action.action not in [ dp.action for dp in hda.dataset.actions ]: - log.debug( 'Allowing access to public dataset with hda: %i.' % hda.id ) - return True # dataset has no roles associated with the access permission, thus is already public - hdadaa = self.sa_session.query( self.model.HistoryDatasetAssociationDisplayAtAuthorization ) \ - .filter_by( history_dataset_association_id = hda.id ).first() - if not hdadaa: - log.debug( 'Denying access to private dataset with hda: %i. No hdadaa record for this dataset.' % hda.id ) - return False # no auth - # We could just look up the reverse of addr, but then we'd also - # have to verify it with the forward address and special case any - # IPs (instead of hosts) in the server list. - # - # This would be improved by caching, but that's what the OS's name - # service cache daemon is for (you ARE running nscd, right?). - for server in HostAgent.sites.get( hdadaa.site, [] ): - # We're going to search in order, but if the remote site is load - # balancing their connections (as UCSC does), this is okay. - try: - if socket.gethostbyname( server ) == addr: - break # remote host is in the server list - except ( socket.error, socket.gaierror ): - pass # can't resolve, try next - else: - log.debug( 'Denying access to private dataset with hda: %i. Remote addr is not a valid server for site: %s.' % ( hda.id, hdadaa.site ) ) - return False # remote addr is not in the server list - if ( datetime.utcnow() - hdadaa.update_time ) > timedelta( seconds=60 ): - log.debug( 'Denying access to private dataset with hda: %i. Authorization was granted, but has expired.' % hda.id ) - return False # not authz'd in the last 60 seconds - log.debug( 'Allowing access to private dataset with hda: %i. Remote server is: %s.' % ( hda.id, server ) ) - return True - else: - raise 'The dataset access permission is the only valid permission in the host security agent.' - def set_dataset_permissions( self, hda, user, site ): - hdadaa = self.sa_session.query( self.model.HistoryDatasetAssociationDisplayAtAuthorization ) \ - .filter_by( history_dataset_association_id = hda.id ).first() - if hdadaa: - hdadaa.update_time = datetime.utcnow() - else: - hdadaa = self.model.HistoryDatasetAssociationDisplayAtAuthorization( hda=hda, user=user, site=site ) - hdadaa.flush() - -def get_permitted_actions( filter=None ): - '''Utility method to return a subset of RBACAgent's permitted actions''' - if filter is None: - return RBACAgent.permitted_actions - tmp_bunch = Bunch() - [ tmp_bunch.__dict__.__setitem__(k, v) for k, v in RBACAgent.permitted_actions.items() if k.startswith( filter ) ] - return tmp_bunch +""" +Galaxy Security + +""" +import logging, socket +from datetime import datetime, timedelta +from galaxy.util.bunch import Bunch +from galaxy.model.orm import * + +log = logging.getLogger(__name__) + +class Action( object ): + def __init__( self, action, description, model ): + self.action = action + self.description = description + self.model = model + +class RBACAgent: + """Class that handles galaxy security""" + permitted_actions = Bunch( + DATASET_MANAGE_PERMISSIONS = Action( "manage permissions", "Role members can manage the roles associated with this dataset", "grant" ), + DATASET_ACCESS = Action( "access", "Role members can import this dataset into their history for analysis", "restrict" ), + LIBRARY_ADD = Action( "add library item", "Role members can add library items to this library item", "grant" ), + LIBRARY_MODIFY = Action( "modify library item", "Role members can modify this library item", "grant" ), + LIBRARY_MANAGE = Action( "manage library permissions", "Role members can manage roles associated with this library item", "grant" ) + ) + def get_action( self, name, default=None ): + """Get a permitted action by its dict key or action name""" + for k, v in self.permitted_actions.items(): + if k == name or v.action == name: + return v + return default + def get_actions( self ): + """Get all permitted actions as a list of Action objects""" + return self.permitted_actions.__dict__.values() + def get_item_actions( self, action, item ): + raise 'No valid method of retrieving action (%s) for item %s.' % ( action, item ) + def guess_derived_permissions_for_datasets( self, datasets = [] ): + raise "Unimplemented Method" + def can_access_dataset( self, roles, dataset ): + raise "Unimplemented Method" + def can_manage_dataset( self, roles, dataset ): + raise "Unimplemented Method" + def can_add_library_item( self, user, roles, item ): + raise "Unimplemented Method" + def can_modify_library_item( self, user, roles, item ): + raise "Unimplemented Method" + def can_manage_library_item( self, user, roles, item ): + raise "Unimplemented Method" + def associate_components( self, **kwd ): + raise 'No valid method of associating provided components: %s' % kwd + def create_private_user_role( self, user ): + raise "Unimplemented Method" + def get_private_user_role( self, user ): + raise "Unimplemented Method" + def user_set_default_permissions( self, user, permissions={}, history=False, dataset=False ): + raise "Unimplemented Method" + def history_set_default_permissions( self, history, permissions=None, dataset=False, bypass_manage_permission=False ): + raise "Unimplemented Method" + def set_all_dataset_permissions( self, dataset, permissions ): + raise "Unimplemented Method" + def set_dataset_permission( self, dataset, permission ): + raise "Unimplemented Method" + def set_all_library_permissions( self, dataset, permissions ): + raise "Unimplemented Method" + def dataset_is_public( self, dataset ): + raise "Unimplemented Method" + def make_dataset_public( self, dataset ): + raise "Unimplemented Method" + def get_component_associations( self, **kwd ): + raise "Unimplemented Method" + def components_are_associated( self, **kwd ): + return bool( self.get_component_associations( **kwd ) ) + def convert_permitted_action_strings( self, permitted_action_strings ): + """ + When getting permitted actions from an untrusted source like a + form, ensure that they match our actual permitted actions. + """ + return filter( lambda x: x is not None, [ self.permitted_actions.get( action_string ) for action_string in permitted_action_strings ] ) + +class GalaxyRBACAgent( RBACAgent ): + def __init__( self, model, permitted_actions=None ): + self.model = model + if permitted_actions: + self.permitted_actions = permitted_actions + # List of "library_item" objects and their associated permissions and info template objects + self.library_item_assocs = ( + ( self.model.Library, self.model.LibraryPermissions ), + ( self.model.LibraryFolder, self.model.LibraryFolderPermissions ), + ( self.model.LibraryDataset, self.model.LibraryDatasetPermissions ), + ( self.model.LibraryDatasetDatasetAssociation, self.model.LibraryDatasetDatasetAssociationPermissions ) ) + @property + def sa_session( self ): + """Returns a SQLAlchemy session""" + return self.model.context + def allow_dataset_action( self, roles, action, dataset ): + """ + Returns true when user has permission to perform an action on an + instance of Dataset. + """ + dataset_actions = self.get_item_actions( action, dataset ) + if not dataset_actions: + return action.model == 'restrict' + ret_val = False + for dataset_action in dataset_actions: + if dataset_action.role in roles: + ret_val = True + break + return ret_val + def can_access_dataset( self, roles, dataset ): + return self.allow_dataset_action( roles, self.permitted_actions.DATASET_ACCESS, dataset ) + def can_manage_dataset( self, roles, dataset ): + return self.allow_dataset_action( roles, self.permitted_actions.DATASET_MANAGE_PERMISSIONS, dataset ) + def allow_library_item_action( self, user, roles, action, item ): + """ + Method for checking a permission for the current user to perform a + specific library action on a library item, which must be one of: + Library, LibraryFolder, LibraryDataset, LibraryDatasetDatasetAssociation + """ + if user is None: + # All permissions are granted, so non-users cannot have permissions + return False + # Check to see if user has access to any of the roles associated with action + item_actions = self.get_item_actions( action, item ) + if not item_actions: + # All permissions are granted, so item must have action + return False + ret_val = False + for item_action in item_actions: + if item_action.role in roles: + ret_val = True + break + return ret_val + def can_add_library_item( self, user, roles, item ): + return self.allow_library_item_action( user, roles, self.permitted_actions.LIBRARY_ADD, item ) + def can_modify_library_item( self, user, roles, item ): + return self.allow_library_item_action( user, roles, self.permitted_actions.LIBRARY_MODIFY, item ) + def can_manage_library_item( self, user, roles, item ): + return self.allow_library_item_action( user, roles, self.permitted_actions.LIBRARY_MANAGE, item ) + def get_item_actions( self, action, item ): + # item must be one of: Dataset, Library, LibraryFolder, LibraryDataset, LibraryDatasetDatasetAssociation + return [ permission for permission in item.actions if permission.action == action.action ] + def guess_derived_permissions_for_datasets( self, datasets=[] ): + """Returns a dict of { action : [ role, role, ... ] } for the output dataset based upon provided datasets""" + perms = {} + for dataset in datasets: + if not isinstance( dataset, self.model.Dataset ): + dataset = dataset.dataset + these_perms = {} + # initialize blank perms + for action in self.get_actions(): + these_perms[ action ] = [] + # collect this dataset's perms + these_perms = self.get_dataset_permissions( dataset ) + # join or intersect this dataset's permissions with others + for action, roles in these_perms.items(): + if action not in perms.keys(): + perms[ action ] = roles + else: + if action.model == 'grant': + # intersect existing roles with new roles + perms[ action ] = filter( lambda x: x in perms[ action ], roles ) + elif action.model == 'restrict': + # join existing roles with new roles + perms[ action ].extend( filter( lambda x: x not in perms[ action ], roles ) ) + return perms + def associate_components( self, **kwd ): + if 'user' in kwd: + if 'group' in kwd: + return self.associate_user_group( kwd['user'], kwd['group'] ) + elif 'role' in kwd: + return self.associate_user_role( kwd['user'], kwd['role'] ) + elif 'role' in kwd: + if 'group' in kwd: + return self.associate_group_role( kwd['group'], kwd['role'] ) + if 'action' in kwd: + if 'dataset' in kwd and 'role' in kwd: + return self.associate_action_dataset_role( kwd['action'], kwd['dataset'], kwd['role'] ) + raise 'No valid method of associating provided components: %s' % kwd + def associate_user_group( self, user, group ): + assoc = self.model.UserGroupAssociation( user, group ) + self.sa_session.add( assoc ) + self.sa_session.flush() + return assoc + def associate_user_role( self, user, role ): + assoc = self.model.UserRoleAssociation( user, role ) + self.sa_session.add( assoc ) + self.sa_session.flush() + return assoc + def associate_group_role( self, group, role ): + assoc = self.model.GroupRoleAssociation( group, role ) + self.sa_session.add( assoc ) + self.sa_session.flush() + return assoc + def associate_action_dataset_role( self, action, dataset, role ): + assoc = self.model.DatasetPermissions( action, dataset, role ) + self.sa_session.add( assoc ) + self.sa_session.flush() + return assoc + def create_private_user_role( self, user ): + # Create private role + role = self.model.Role( name=user.email, description='Private Role for ' + user.email, type=self.model.Role.types.PRIVATE ) + self.sa_session.add( role ) + self.sa_session.flush() + # Add user to role + self.associate_components( role=role, user=user ) + return role + def get_private_user_role( self, user, auto_create=False ): + role = self.sa_session.query( self.model.Role ) \ + .filter( and_( self.model.Role.table.c.name == user.email, + self.model.Role.table.c.type == self.model.Role.types.PRIVATE ) ) \ + .first() + if not role: + if auto_create: + return self.create_private_user_role( user ) + else: + return None + return role + def user_set_default_permissions( self, user, permissions={}, history=False, dataset=False, bypass_manage_permission=False, default_access_private = False ): + # bypass_manage_permission is used to change permissions of datasets in a userless history when logging in + if user is None: + return None + if not permissions: + #default permissions + permissions = { self.permitted_actions.DATASET_MANAGE_PERMISSIONS : [ self.get_private_user_role( user, auto_create=True ) ] } + #new_user_dataset_access_role_default_private is set as True in config file + if default_access_private: + permissions[ self.permitted_actions.DATASET_ACCESS ] = permissions.values()[ 0 ] + # Delete all of the current default permissions for the user + for dup in user.default_permissions: + self.sa_session.delete( dup ) + # Add the new default permissions for the user + for action, roles in permissions.items(): + if isinstance( action, Action ): + action = action.action + for dup in [ self.model.DefaultUserPermissions( user, action, role ) for role in roles ]: + self.sa_session.add( dup ) + self.sa_session.flush() + if history: + for history in user.active_histories: + self.history_set_default_permissions( history, permissions=permissions, dataset=dataset, bypass_manage_permission=bypass_manage_permission ) + def user_get_default_permissions( self, user ): + permissions = {} + for dup in user.default_permissions: + action = self.get_action( dup.action ) + if action in permissions: + permissions[ action ].append( dup.role ) + else: + permissions[ action ] = [ dup.role ] + return permissions + def history_set_default_permissions( self, history, permissions={}, dataset=False, bypass_manage_permission=False ): + # bypass_manage_permission is used to change permissions of datasets in a user-less history when logging in + user = history.user + if not user: + # default permissions on a user-less history are None + return None + if not permissions: + permissions = self.user_get_default_permissions( user ) + # Delete all of the current default permission for the history + for dhp in history.default_permissions: + self.sa_session.delete( dhp ) + # Add the new default permissions for the history + for action, roles in permissions.items(): + if isinstance( action, Action ): + action = action.action + for dhp in [ self.model.DefaultHistoryPermissions( history, action, role ) for role in roles ]: + self.sa_session.add( dhp ) + self.sa_session.flush() + if dataset: + # Only deal with datasets that are not purged + for hda in history.activatable_datasets: + dataset = hda.dataset + if dataset.library_associations: + # Don't change permissions on a dataset associated with a library + continue + if [ assoc for assoc in dataset.history_associations if assoc.history not in user.histories ]: + # Don't change permissions on a dataset associated with a history not owned by the user + continue + if bypass_manage_permission or self.can_manage_dataset( user.all_roles(), dataset ): + self.set_all_dataset_permissions( dataset, permissions ) + def history_get_default_permissions( self, history ): + permissions = {} + for dhp in history.default_permissions: + action = self.get_action( dhp.action ) + if action in permissions: + permissions[ action ].append( dhp.role ) + else: + permissions[ action ] = [ dhp.role ] + return permissions + def set_all_dataset_permissions( self, dataset, permissions={} ): + """ + Set new permissions on a dataset, eliminating all current permissions + permissions looks like: { Action : [ Role, Role ] } + """ + # Delete all of the current permissions on the dataset + # TODO: If setting ACCESS permission, at least 1 user must have every role associated with this dataset, + # or the dataset is inaccessible. See admin/library_dataset_dataset_association() + for dp in dataset.actions: + self.sa_session.delete( dp ) + # Add the new permissions on the dataset + for action, roles in permissions.items(): + if isinstance( action, Action ): + action = action.action + for dp in [ self.model.DatasetPermissions( action, dataset, role ) for role in roles ]: + self.sa_session.add( dp ) + self.sa_session.flush() + def set_dataset_permission( self, dataset, permission={} ): + """ + Set a specific permission on a dataset, leaving all other current permissions on the dataset alone + permissions looks like: { Action : [ Role, Role ] } + """ + # TODO: If setting ACCESS permission, at least 1 user must have every role associated with this dataset, + # or the dataset is inaccessible. See admin/library_dataset_dataset_association() + for action, roles in permission.items(): + if isinstance( action, Action ): + action = action.action + # Delete the current specific permission on the dataset if one exists + for dp in dataset.actions: + if dp.action == action: + self.sa_session.delete( dp ) + # Add the new specific permission on the dataset + for dp in [ self.model.DatasetPermissions( action, dataset, role ) for role in roles ]: + self.sa_session.add( dp ) + self.sa_session.flush() + def dataset_is_public( self, dataset ): + # A dataset is considered public if there are no "access" actions associated with it. Any + # other actions ( 'manage permissions', 'edit metadata' ) are irrelevant. + return self.permitted_actions.DATASET_ACCESS.action not in [ a.action for a in dataset.actions ] + def make_dataset_public( self, dataset ): + # A dataset is considered public if there are no "access" actions associated with it. Any + # other actions ( 'manage permissions', 'edit metadata' ) are irrelevant. + for dp in dataset.actions: + if dp.action == self.permitted_actions.DATASET_ACCESS.action: + self.sa_session.delete( dp ) + self.sa_session.flush() + def get_dataset_permissions( self, dataset ): + """ + Return a dictionary containing the actions and associated roles on dataset. + The dictionary looks like: { Action : [ Role, Role ] } + dataset must be an instance of Dataset() + """ + permissions = {} + for dp in dataset.actions: + action = self.get_action( dp.action ) + if action in permissions: + permissions[ action ].append( dp.role ) + else: + permissions[ action ] = [ dp.role ] + return permissions + def copy_dataset_permissions( self, src, dst ): + if not isinstance( src, self.model.Dataset ): + src = src.dataset + if not isinstance( dst, self.model.Dataset ): + dst = dst.dataset + self.set_all_dataset_permissions( dst, self.get_dataset_permissions( src ) ) + def privately_share_dataset( self, dataset, users = [] ): + intersect = None + for user in users: + roles = [ ura.role for ura in user.roles if ura.role.type == self.model.Role.types.SHARING ] + if intersect is None: + intersect = roles + else: + new_intersect = [] + for role in roles: + if role in intersect: + new_intersect.append( role ) + intersect = new_intersect + sharing_role = None + if intersect: + for role in intersect: + if not filter( lambda x: x not in users, [ ura.user for ura in role.users ] ): + # only use a role if it contains ONLY the users we're sharing with + sharing_role = role + break + if sharing_role is None: + sharing_role = self.model.Role( name = "Sharing role for: " + ", ".join( [ u.email for u in users ] ), + type = self.model.Role.types.SHARING ) + self.sa_session.add( sharing_role ) + self.sa_session.flush() + for user in users: + self.associate_components( user=user, role=sharing_role ) + self.set_dataset_permission( dataset, { self.permitted_actions.DATASET_ACCESS : [ sharing_role ] } ) + def set_all_library_permissions( self, library_item, permissions={} ): + # Set new permissions on library_item, eliminating all current permissions + for role_assoc in library_item.actions: + self.sa_session.delete( role_assoc ) + # Add the new permissions on library_item + for item_class, permission_class in self.library_item_assocs: + if isinstance( library_item, item_class ): + for action, roles in permissions.items(): + if isinstance( action, Action ): + action = action.action + for role_assoc in [ permission_class( action, library_item, role ) for role in roles ]: + self.sa_session.add( role_assoc ) + self.sa_session.flush() + def get_library_dataset_permissions( self, library_dataset ): + # Permissions will always be the same for LibraryDatasets and associated + # LibraryDatasetDatasetAssociations + if isinstance( library_dataset, self.model.LibraryDatasetDatasetAssociation ): + library_dataset = library_dataset.library_dataset + permissions = {} + for library_dataset_permission in library_dataset.actions: + action = self.get_action( library_dataset_permission.action ) + if action in permissions: + permissions[ action ].append( library_dataset_permission.role ) + else: + permissions[ action ] = [ library_dataset_permission.role ] + return permissions + def copy_library_permissions( self, source_library_item, target_library_item, user=None ): + # Copy all permissions from source + permissions = {} + for role_assoc in source_library_item.actions: + if role_assoc.action in permissions: + permissions[role_assoc.action].append( role_assoc.role ) + else: + permissions[role_assoc.action] = [ role_assoc.role ] + self.set_all_library_permissions( target_library_item, permissions ) + if user: + item_class = None + for item_class, permission_class in self.library_item_assocs: + if isinstance( target_library_item, item_class ): + break + if item_class: + # Make sure user's private role is included + private_role = self.model.security_agent.get_private_user_role( user ) + for name, action in self.permitted_actions.items(): + if not permission_class.filter_by( role_id = private_role.id, action = action.action ).first(): + lp = permission_class( action.action, target_library_item, private_role ) + self.sa_session.add( lp ) + self.sa_session.flush() + else: + raise 'Invalid class (%s) specified for target_library_item (%s)' % \ + ( target_library_item.__class__, target_library_item.__class__.__name__ ) + def show_library_item( self, user, roles, library_item, actions_to_check, hidden_folder_ids='' ): + """ + This method must be sent an instance of Library() or LibraryFolder(). Recursive execution produces a + comma-separated string of folder ids whose folders do NOT meet the criteria for showing. Along with + the string, True is returned if the current user has permission to perform any 1 of actions_to_check + on library_item. Otherwise, cycle through all sub-folders in library_item until one is found that meets + this criteria, if it exists. This method does not necessarily scan the entire library as it returns + when it finds the first library_item that allows user to perform any one action in actions_to_check. + """ + for action in actions_to_check: + if self.allow_library_item_action( user, roles, action, library_item ): + return True, hidden_folder_ids + if isinstance( library_item, self.model.Library ): + return self.show_library_item( user, roles, library_item.root_folder, actions_to_check, hidden_folder_ids='' ) + if isinstance( library_item, self.model.LibraryFolder ): + for folder in library_item.active_folders: + can_show, hidden_folder_ids = self.show_library_item( user, roles, folder, actions_to_check, hidden_folder_ids=hidden_folder_ids ) + if can_show: + return True, hidden_folder_ids + if hidden_folder_ids: + hidden_folder_ids = '%s,%d' % ( hidden_folder_ids, folder.id ) + else: + hidden_folder_ids = '%d' % folder.id + return False, hidden_folder_ids + def get_showable_folders( self, user, roles, library_item, actions_to_check, hidden_folder_ids=[], showable_folders=[] ): + """ + This method must be sent an instance of Library(), all the folders of which are scanned to determine if + user is allowed to perform any action in actions_to_check. The param hidden_folder_ids, if passed, should + contain a list of folder IDs which was generated when the library was previously scanned + using the same actions_to_check. A list of showable folders is generated. This method scans the entire library. + """ + if isinstance( library_item, self.model.Library ): + return self.get_showable_folders( user, roles, library_item.root_folder, actions_to_check, showable_folders=[] ) + if isinstance( library_item, self.model.LibraryFolder ): + if library_item.id not in hidden_folder_ids: + for action in actions_to_check: + if self.allow_library_item_action( user, roles, action, library_item ): + showable_folders.append( library_item ) + break + for folder in library_item.active_folders: + self.get_showable_folders( user, roles, folder, actions_to_check, showable_folders=showable_folders ) + return showable_folders + def set_entity_user_associations( self, users=[], roles=[], groups=[], delete_existing_assocs=True ): + for user in users: + if delete_existing_assocs: + for a in user.non_private_roles + user.groups: + self.sa_session.delete( a ) + self.sa_session.flush() + self.sa_session.refresh( user ) + for role in roles: + # Make sure we are not creating an additional association with a PRIVATE role + if role not in user.roles: + self.associate_components( user=user, role=role ) + for group in groups: + self.associate_components( user=user, group=group ) + def set_entity_group_associations( self, groups=[], users=[], roles=[], delete_existing_assocs=True ): + for group in groups: + if delete_existing_assocs: + for a in group.roles + group.users: + self.sa_session.delete( a ) + self.sa_session.flush() + for role in roles: + self.associate_components( group=group, role=role ) + for user in users: + self.associate_components( group=group, user=user ) + def set_entity_role_associations( self, roles=[], users=[], groups=[], delete_existing_assocs=True ): + for role in roles: + if delete_existing_assocs: + for a in role.users + role.groups: + self.sa_session.delete( a ) + self.sa_session.flush() + for user in users: + self.associate_components( user=user, role=role ) + for group in groups: + self.associate_components( group=group, role=role ) + def get_component_associations( self, **kwd ): + assert len( kwd ) == 2, 'You must specify exactly 2 Galaxy security components to check for associations.' + if 'dataset' in kwd: + if 'action' in kwd: + return self.sa_session.query( self.model.DatasetPermissions ).filter_by( action = kwd['action'].action, dataset_id = kwd['dataset'].id ).first() + elif 'user' in kwd: + if 'group' in kwd: + return self.sa_session.query( self.model.UserGroupAssociation ).filter_by( group_id = kwd['group'].id, user_id = kwd['user'].id ).first() + elif 'role' in kwd: + return self.sa_session.query( self.model.UserRoleAssociation ).filter_by( role_id = kwd['role'].id, user_id = kwd['user'].id ).first() + elif 'group' in kwd: + if 'role' in kwd: + return self.sa_session.query( self.model.GroupRoleAssociation ).filter_by( role_id = kwd['role'].id, group_id = kwd['group'].id ).first() + raise 'No valid method of associating provided components: %s' % kwd + def check_folder_contents( self, user, roles, folder, hidden_folder_ids='' ): + """ + This method must always be sent an instance of LibraryFolder(). Recursive execution produces a + comma-separated string of folder ids whose folders do NOT meet the criteria for showing. Along + with the string, True is returned if the current user has permission to access folder. Otherwise, + cycle through all sub-folders in folder until one is found that meets this criteria, if it exists. + This method does not necessarily scan the entire library as it returns when it finds the first + folder that is accessible to user. + """ + action = self.permitted_actions.DATASET_ACCESS + lddas = self.sa_session.query( self.model.LibraryDatasetDatasetAssociation ) \ + .join( "library_dataset" ) \ + .filter( self.model.LibraryDataset.folder == folder ) \ + .join( "dataset" ) \ + .options( eagerload_all( "dataset.actions" ) ) \ + .all() + for ldda in lddas: + ldda_access_permissions = self.get_item_actions( action, ldda.dataset ) + if not ldda_access_permissions: + # Dataset is public + return True, hidden_folder_ids + for ldda_access_permission in ldda_access_permissions: + if ldda_access_permission.role in roles: + # The current user has access permission on the dataset + return True, hidden_folder_ids + for sub_folder in folder.active_folders: + can_access, hidden_folder_ids = self.check_folder_contents( user, roles, sub_folder, hidden_folder_ids=hidden_folder_ids ) + if can_access: + return True, hidden_folder_ids + if hidden_folder_ids: + hidden_folder_ids = '%s,%d' % ( hidden_folder_ids, sub_folder.id ) + else: + hidden_folder_ids = '%d' % sub_folder.id + return False, hidden_folder_ids + +class HostAgent( RBACAgent ): + """ + A simple security agent which allows access to datasets based on host. + This exists so that externals sites such as UCSC can gain access to + datasets which have permissions which would normally prevent such access. + """ + # TODO: Make sites user configurable + sites = Bunch( + ucsc_main = ( 'hgw1.cse.ucsc.edu', 'hgw2.cse.ucsc.edu', 'hgw3.cse.ucsc.edu', 'hgw4.cse.ucsc.edu', + 'hgw5.cse.ucsc.edu', 'hgw6.cse.ucsc.edu', 'hgw7.cse.ucsc.edu', 'hgw8.cse.ucsc.edu' ), + ucsc_test = ( 'hgwdev.cse.ucsc.edu', ), + ucsc_archaea = ( 'lowepub.cse.ucsc.edu', ) + ) + def __init__( self, model, permitted_actions=None ): + self.model = model + if permitted_actions: + self.permitted_actions = permitted_actions + @property + def sa_session( self ): + """Returns a SQLAlchemy session""" + return self.model.context + def allow_action( self, addr, action, **kwd ): + if 'dataset' in kwd and action == self.permitted_actions.DATASET_ACCESS: + hda = kwd['dataset'] + if action == self.permitted_actions.DATASET_ACCESS and action.action not in [ dp.action for dp in hda.dataset.actions ]: + log.debug( 'Allowing access to public dataset with hda: %i.' % hda.id ) + return True # dataset has no roles associated with the access permission, thus is already public + hdadaa = self.sa_session.query( self.model.HistoryDatasetAssociationDisplayAtAuthorization ) \ + .filter_by( history_dataset_association_id = hda.id ).first() + if not hdadaa: + log.debug( 'Denying access to private dataset with hda: %i. No hdadaa record for this dataset.' % hda.id ) + return False # no auth + # We could just look up the reverse of addr, but then we'd also + # have to verify it with the forward address and special case any + # IPs (instead of hosts) in the server list. + # + # This would be improved by caching, but that's what the OS's name + # service cache daemon is for (you ARE running nscd, right?). + for server in HostAgent.sites.get( hdadaa.site, [] ): + # We're going to search in order, but if the remote site is load + # balancing their connections (as UCSC does), this is okay. + try: + if socket.gethostbyname( server ) == addr: + break # remote host is in the server list + except ( socket.error, socket.gaierror ): + pass # can't resolve, try next + else: + log.debug( 'Denying access to private dataset with hda: %i. Remote addr is not a valid server for site: %s.' % ( hda.id, hdadaa.site ) ) + return False # remote addr is not in the server list + if ( datetime.utcnow() - hdadaa.update_time ) > timedelta( seconds=60 ): + log.debug( 'Denying access to private dataset with hda: %i. Authorization was granted, but has expired.' % hda.id ) + return False # not authz'd in the last 60 seconds + log.debug( 'Allowing access to private dataset with hda: %i. Remote server is: %s.' % ( hda.id, server ) ) + return True + else: + raise 'The dataset access permission is the only valid permission in the host security agent.' + def set_dataset_permissions( self, hda, user, site ): + hdadaa = self.sa_session.query( self.model.HistoryDatasetAssociationDisplayAtAuthorization ) \ + .filter_by( history_dataset_association_id = hda.id ).first() + if hdadaa: + hdadaa.update_time = datetime.utcnow() + else: + hdadaa = self.model.HistoryDatasetAssociationDisplayAtAuthorization( hda=hda, user=user, site=site ) + self.sa_session.add( hdadaa ) + self.sa_session.flush() + +def get_permitted_actions( filter=None ): + '''Utility method to return a subset of RBACAgent's permitted actions''' + if filter is None: + return RBACAgent.permitted_actions + tmp_bunch = Bunch() + [ tmp_bunch.__dict__.__setitem__(k, v) for k, v in RBACAgent.permitted_actions.items() if k.startswith( filter ) ] + return tmp_bunch diff -r 0edb42925161 -r b33b8f5e03b8 lib/galaxy/tools/__init__.py --- a/lib/galaxy/tools/__init__.py Wed Nov 11 15:13:12 2009 -0500 +++ b/lib/galaxy/tools/__init__.py Wed Nov 11 15:59:41 2009 -0500 @@ -272,7 +272,10 @@ self.app = app # Parse XML element containing configuration self.parse( root ) - + @property + def sa_session( self ): + """Returns a SQLAlchemy session""" + return self.app.model.context def parse( self, root ): """ Read tool configuration from the element `root` and fill in `self`. @@ -863,7 +866,7 @@ if 'async_datasets' in inputs and inputs['async_datasets'] not in [ 'None', '', None ]: for id in inputs['async_datasets'].split(','): try: - data = trans.sa_session.query( trans.model.HistoryDatasetAssociation ).get( int( id ) ) + data = self.sa_session.query( trans.model.HistoryDatasetAssociation ).get( int( id ) ) except: log.exception( 'Unable to load precreated dataset (%s) sent in upload form' % id ) continue @@ -874,7 +877,8 @@ else: data.state = data.states.ERROR data.info = 'Upload of this dataset was interrupted. Please try uploading again or' - data.flush() + self.sa_session.add( data ) + self.sa_session.flush() # It's unlikely the user will ever see this. return 'message.mako', dict( message_type='error', message='Your upload was interrupted. If this was uninentional, please retry it.', refresh_frames=[], cont=None ) @@ -1454,7 +1458,8 @@ if data.missing_meta(): data = app.datatypes_registry.change_datatype( data, 'tabular' ) data.set_peek() - data.flush() + self.sa_session.add( data ) + self.sa_session.flush() def collect_associated_files( self, output, job_working_directory ): for name, hda in output.items(): @@ -1493,7 +1498,8 @@ self.app.security_agent.copy_dataset_permissions( outdata.dataset, child_dataset.dataset ) # Move data from temp location to dataset location shutil.move( filename, child_dataset.file_name ) - child_dataset.flush() + self.sa_session.add( child_dataset ) + self.sa_session.flush() child_dataset.set_size() child_dataset.name = "Secondary Dataset (%s)" % ( designation ) child_dataset.init_meta() @@ -1507,16 +1513,19 @@ if job: assoc = self.app.model.JobToOutputDatasetAssociation( '__new_child_file_%s|%s__' % ( name, designation ), child_dataset ) assoc.job = job - assoc.flush() + self.sa_session.add( assoc ) + self.sa_session.flush() child_dataset.state = outdata.state - child_dataset.flush() + self.sa_session.add( child_dataset ) + self.sa_session.flush() # Add child to return dict children[name][designation] = child_dataset for dataset in outdata.dataset.history_associations: #need to update all associated output hdas, i.e. history was shared with job running if outdata == dataset: continue # Create new child dataset child_data = child_dataset.copy( parent_id = dataset.id ) - child_data.flush() + self.sa_session.add( child_dataset ) + self.sa_session.flush() return children def collect_primary_datasets( self, output): @@ -1540,7 +1549,8 @@ # Create new primary dataset primary_data = self.app.model.HistoryDatasetAssociation( extension=ext, designation=designation, visible=visible, dbkey=dbkey, create_dataset=True ) self.app.security_agent.copy_dataset_permissions( outdata.dataset, primary_data.dataset ) - primary_data.flush() + self.sa_session.add( primary_data ) + self.sa_session.flush() # Move data from temp location to dataset location shutil.move( filename, primary_data.file_name ) primary_data.set_size() @@ -1558,9 +1568,11 @@ if job: assoc = self.app.model.JobToOutputDatasetAssociation( '__new_primary_file_%s|%s__' % ( name, designation ), primary_data ) assoc.job = job - assoc.flush() + self.sa_session.add( assoc ) + self.sa_session.flush() primary_data.state = outdata.state - primary_data.flush() + self.sa_session.add( primary_data ) + self.sa_session.flush() outdata.history.add_dataset( primary_data ) # Add dataset to return dict primary_datasets[name][designation] = primary_data @@ -1568,7 +1580,8 @@ if outdata == dataset: continue new_data = primary_data.copy() dataset.history.add( new_data ) - new_data.flush() + self.sa_session.add( new_data ) + self.sa_session.flush() return primary_datasets class SetMetadataTool( Tool ): @@ -1581,7 +1594,8 @@ # For now, we'll leave the default metadata and set the state back to its original. dataset.datatype.after_edit( dataset ) dataset.state = param_dict.get( '__ORIGINAL_DATASET_STATE__' ) - dataset.flush() + self.sa_session.add( dataset ) + self.sa_session.flush() # ---- Utility classes to be factored out ----------------------------------- diff -r 0edb42925161 -r b33b8f5e03b8 lib/galaxy/tools/actions/__init__.py --- a/lib/galaxy/tools/actions/__init__.py Wed Nov 11 15:13:12 2009 -0500 +++ b/lib/galaxy/tools/actions/__init__.py Wed Nov 11 15:59:41 2009 -0500 @@ -44,9 +44,11 @@ new_data = data.datatype.convert_dataset( trans, data, target_ext, return_output = True, visible = False ).values()[0] new_data.hid = data.hid new_data.name = data.name - new_data.flush() + trans.sa_session.add( new_data ) + trans.sa_session.flush() assoc.dataset = new_data - assoc.flush() + trans.sa_session.add( assoc ) + trans.sa_session.flush() data = new_data user, roles = trans.get_user_and_roles() if data and not trans.app.security_agent.can_access_dataset( roles, data.dataset ): @@ -198,7 +200,8 @@ ext = when_elem.get( 'format', ext ) data = trans.app.model.HistoryDatasetAssociation( extension=ext, create_dataset=True ) # Commit the dataset immediately so it gets database assigned unique id - data.flush() + trans.sa_session.add( data ) + trans.sa_session.flush() trans.app.security_agent.set_all_dataset_permissions( data.dataset, output_permissions ) # Create an empty file immediately open( data.file_name, "w" ).close() @@ -241,7 +244,8 @@ if name not in child_dataset_names and name not in incoming: #don't add children; or already existing datasets, i.e. async created data = out_data[ name ] trans.history.add_dataset( data, set_hid = set_output_hid ) - data.flush() + trans.sa_session.add( data ) + trans.sa_session.flush() # Add all the children to their parents for parent_name, child_name in parent_to_child_pairs: parent_dataset = out_data[ parent_name ] @@ -293,7 +297,8 @@ # Job should not be queued, so set state to ok job.state = JOB_OK job.info = "Redirected to: %s" % redirect_url - job.flush() + trans.sa_session.add( job ) + trans.sa_session.flush() trans.response.send_redirect( url_for( controller='tool_runner', action='redirect', redirect_url=redirect_url ) ) else: # Queue the job for execution diff -r 0edb42925161 -r b33b8f5e03b8 lib/galaxy/tools/actions/upload.py --- a/lib/galaxy/tools/actions/upload.py Wed Nov 11 15:13:12 2009 -0500 +++ b/lib/galaxy/tools/actions/upload.py Wed Nov 11 15:59:41 2009 -0500 @@ -21,6 +21,6 @@ if not uploaded_datasets: return 'No data was entered in the upload form, please go back and choose data to upload.' - json_file_path = upload_common.create_paramfile( uploaded_datasets ) + json_file_path = upload_common.create_paramfile( trans, uploaded_datasets ) data_list = [ ud.data for ud in uploaded_datasets ] return upload_common.create_job( trans, incoming, tool, json_file_path, data_list ) diff -r 0edb42925161 -r b33b8f5e03b8 lib/galaxy/tools/actions/upload_common.py --- a/lib/galaxy/tools/actions/upload_common.py Wed Nov 11 15:13:12 2009 -0500 +++ b/lib/galaxy/tools/actions/upload_common.py Wed Nov 11 15:59:41 2009 -0500 @@ -117,7 +117,8 @@ hda.state = state else: hda.state = hda.states.QUEUED - hda.flush() + trans.sa_session.add( hda ) + trans.sa_session.flush() trans.history.add_dataset( hda, genome_build = uploaded_dataset.dbkey ) permissions = trans.app.security_agent.history_get_default_permissions( trans.history ) trans.app.security_agent.set_all_dataset_permissions( hda.dataset, permissions ) @@ -142,14 +143,16 @@ new_folder = trans.app.model.LibraryFolder( name=name, description='Automatically created by upload tool' ) new_folder.genome_build = util.dbnames.default_value folder.add_folder( new_folder ) - new_folder.flush() + trans.sa_session.add( new_folder ) + trans.sa_session.flush() trans.app.security_agent.copy_library_permissions( folder, new_folder ) folder = new_folder if library_bunch.replace_dataset: ld = library_bunch.replace_dataset else: ld = trans.app.model.LibraryDataset( folder=folder, name=uploaded_dataset.name ) - ld.flush() + trans.sa_session.add( ld ) + trans.sa_session.flush() trans.app.security_agent.copy_library_permissions( folder, ld ) ldda = trans.app.model.LibraryDatasetDatasetAssociation( name = uploaded_dataset.name, extension = uploaded_dataset.file_type, @@ -162,7 +165,8 @@ else: ldda.state = ldda.states.QUEUED ldda.message = library_bunch.message - ldda.flush() + trans.sa_session.add( ldda ) + trans.sa_session.flush() # Permissions must be the same on the LibraryDatasetDatasetAssociation and the associated LibraryDataset trans.app.security_agent.copy_library_permissions( ld, ldda ) if library_bunch.replace_dataset: @@ -172,9 +176,11 @@ # Copy the current user's DefaultUserPermissions to the new LibraryDatasetDatasetAssociation.dataset trans.app.security_agent.set_all_dataset_permissions( ldda.dataset, trans.app.security_agent.user_get_default_permissions( trans.user ) ) folder.add_library_dataset( ld, genome_build=uploaded_dataset.dbkey ) - folder.flush() + trans.sa_session.add( folder ) + trans.sa_session.flush() ld.library_dataset_dataset_association_id = ldda.id - ld.flush() + trans.sa_session.add( ld ) + trans.sa_session.flush() # Handle template included in the upload form, if any if library_bunch.template and library_bunch.template_field_contents: # Since information templates are inherited, the template fields can be displayed on the upload form. @@ -182,15 +188,18 @@ # for the new library_dataset_dataset_association object. # Create a new FormValues object, using the template we previously retrieved form_values = trans.app.model.FormValues( library_bunch.template, library_bunch.template_field_contents ) - form_values.flush() + trans.sa_session.add( form_values ) + trans.sa_session.flush() # Create a new info_association between the current ldda and form_values info_association = trans.app.model.LibraryDatasetDatasetInfoAssociation( ldda, library_bunch.template, form_values ) - info_association.flush() + trans.sa_session.add( info_association ) + trans.sa_session.flush() # If roles were selected upon upload, restrict access to the Dataset to those roles if library_bunch.roles: for role in library_bunch.roles: dp = trans.app.model.DatasetPermissions( trans.app.security_agent.permitted_actions.DATASET_ACCESS.action, ldda.dataset, role ) - dp.flush() + trans.sa_session.add( dp ) + trans.sa_session.flush() return ldda def new_upload( trans, uploaded_dataset, library_bunch=None, state=None ): @@ -210,16 +219,18 @@ else: data.extension = uploaded_dataset.file_type data.dbkey = uploaded_dataset.dbkey - data.flush() + trans.sa_session.add( data ) + trans.sa_session.flush() if library_bunch: library_bunch.folder.genome_build = uploaded_dataset.dbkey - library_bunch.folder.flush() + trans.sa_session.add( library_bunch.folder ) + trans.sa_session.flush() else: trans.history.genome_build = uploaded_dataset.dbkey uploaded_dataset.data = data return uploaded_datasets -def create_paramfile( uploaded_datasets ): +def create_paramfile( trans, uploaded_datasets ): """ Create the upload tool's JSON "param" file. """ @@ -233,7 +244,8 @@ data.init_meta() for meta_name, meta_value in uploaded_dataset.metadata.iteritems(): setattr( data.metadata, meta_name, meta_value ) - data.flush() + trans.sa_session.add( data ) + trans.sa_session.flush() json = dict( file_type = uploaded_dataset.file_type, dataset_id = data.dataset.id, dbkey = uploaded_dataset.dbkey, @@ -278,7 +290,8 @@ job.tool_id = tool.id job.tool_version = tool.version job.state = job.states.UPLOAD - job.flush() + trans.sa_session.add( job ) + trans.sa_session.flush() log.info( 'tool %s created job id %d' % ( tool.id, job.id ) ) trans.log_event( 'created job id %d' % job.id, tool_id=tool.id ) diff -r 0edb42925161 -r b33b8f5e03b8 lib/galaxy/tools/parameters/basic.py --- a/lib/galaxy/tools/parameters/basic.py Wed Nov 11 15:13:12 2009 -0500 +++ b/lib/galaxy/tools/parameters/basic.py Wed Nov 11 15:59:41 2009 -0500 @@ -726,8 +726,10 @@ >>> # Mock up a history (not connected to database) >>> from galaxy.model import History, HistoryDatasetAssociation >>> from galaxy.util.bunch import Bunch + >>> from galaxy.model.mapping import context as sa_session >>> hist = History() - >>> hist.flush() + >>> sa_session.add( hist ) + >>> sa_session.flush() >>> hist.add_dataset( HistoryDatasetAssociation( id=1, extension='interval', create_dataset=True ) ) >>> dtp = DataToolParameter( None, XML( '<param name="blah" type="data" format="interval"/>' ) ) >>> print dtp.name diff -r 0edb42925161 -r b33b8f5e03b8 lib/galaxy/web/controllers/admin.py --- a/lib/galaxy/web/controllers/admin.py Wed Nov 11 15:13:12 2009 -0500 +++ b/lib/galaxy/web/controllers/admin.py Wed Nov 11 15:59:41 2009 -0500 @@ -350,23 +350,24 @@ else: # Create the role role = trans.app.model.Role( name=name, description=description, type=trans.app.model.Role.types.ADMIN ) - role.flush() + trans.sa_session.add( role ) # Create the UserRoleAssociations for user in [ trans.sa_session.query( trans.app.model.User ).get( x ) for x in in_users ]: ura = trans.app.model.UserRoleAssociation( user, role ) - ura.flush() + trans.sa_session.add( ura ) # Create the GroupRoleAssociations for group in [ trans.sa_session.query( trans.app.model.Group ).get( x ) for x in in_groups ]: gra = trans.app.model.GroupRoleAssociation( group, role ) - gra.flush() + trans.sa_session.add( gra ) if create_group_for_role == 'yes': # Create the group group = trans.app.model.Group( name=name ) - group.flush() + trans.sa_session.add( group ) msg = "Group '%s' has been created, and role '%s' has been created with %d associated users and %d associated groups" % \ ( group.name, role.name, len( in_users ), len( in_groups ) ) else: msg = "Role '%s' has been created with %d associated users and %d associated groups" % ( role.name, len( in_users ), len( in_groups ) ) + trans.sa_session.flush() trans.response.send_redirect( web.url_for( controller='admin', action='roles', message=util.sanitize_text( msg ), status='done' ) ) trans.response.send_redirect( web.url_for( controller='admin', action='create_role', msg=util.sanitize_text( msg ), messagetype='error' ) ) out_users = [] @@ -402,13 +403,12 @@ for dup in user.default_permissions: if role == dup.role: trans.sa_session.delete( dup ) - dup.flush() # Delete DefaultHistoryPermissions for previously associated users that have been removed from the role for history in user.histories: for dhp in history.default_permissions: if role == dhp.role: trans.sa_session.delete( dhp ) - dhp.flush() + trans.sa_session.flush() in_groups = [ trans.sa_session.query( trans.app.model.Group ).get( x ) for x in util.listify( params.in_groups ) ] trans.app.security_agent.set_entity_role_associations( roles=[ role ], users=in_users, groups=in_groups ) trans.sa_session.refresh( role ) @@ -428,7 +428,8 @@ else: role.name = new_name role.description = new_description - role.flush() + trans.sa_session.add( role ) + trans.sa_session.flush() msg = "Role '%s' has been renamed to '%s'" % ( old_name, new_name ) return trans.response.send_redirect( web.url_for( action='roles', message=util.sanitize_text( msg ), status='done' ) ) return trans.fill_template( '/admin/dataset_security/role/role_rename.mako', role=role, msg=msg, messagetype=messagetype ) @@ -491,7 +492,8 @@ params = util.Params( kwd ) role = get_role( trans, params.id ) role.deleted = True - role.flush() + trans.sa_session.add( role ) + trans.sa_session.flush() message = "Role '%s' has been marked as deleted." % role.name trans.response.send_redirect( web.url_for( action='roles', message=util.sanitize_text( message ), status='done' ) ) @web.expose @@ -500,7 +502,8 @@ params = util.Params( kwd ) role = get_role( trans, params.id ) role.deleted = False - role.flush() + trans.sa_session.add( role ) + trans.sa_session.flush() message = "Role '%s' has been marked as not deleted." % role.name trans.response.send_redirect( web.url_for( action='roles', message=util.sanitize_text( message ), status='done' ) ) @web.expose @@ -525,23 +528,19 @@ for dup in user.default_permissions: if role == dup.role: trans.sa_session.delete( dup ) - dup.flush() # Delete DefaultHistoryPermissions for associated users for history in user.histories: for dhp in history.default_permissions: if role == dhp.role: trans.sa_session.delete( dhp ) - dhp.flush() trans.sa_session.delete( ura ) - ura.flush() # Delete GroupRoleAssociations for gra in role.groups: trans.sa_session.delete( gra ) - gra.flush() # Delete DatasetPermissionss for dp in role.dataset_actions: trans.sa_session.delete( dp ) - dp.flush() + trans.sa_session.flush() message = "The following have been purged from the database for role '%s': " % role.name message += "DefaultUserPermissions, DefaultHistoryPermissions, UserRoleAssociations, GroupRoleAssociations, DatasetPermissionss." trans.response.send_redirect( web.url_for( action='roles', message=util.sanitize_text( message ), status='done' ) ) @@ -592,7 +591,8 @@ return trans.fill_template( '/admin/dataset_security/group/group_rename.mako', group=group, msg=msg, messagetype='error' ) else: group.name = new_name - group.flush() + trans.sa_session.add( group ) + trans.sa_session.flush() msg = "Group '%s' has been renamed to '%s'" % ( old_name, new_name ) return trans.response.send_redirect( web.url_for( action='groups', msg=util.sanitize_text( msg ), messagetype='done' ) ) return trans.fill_template( '/admin/dataset_security/group/group_rename.mako', group=group, msg=msg, messagetype=messagetype ) @@ -640,15 +640,18 @@ else: # Create the group group = trans.app.model.Group( name=name ) - group.flush() + trans.sa_session.add( group ) + trans.sa_session.flush() # Create the UserRoleAssociations for user in [ trans.sa_session.query( trans.app.model.User ).get( x ) for x in in_users ]: uga = trans.app.model.UserGroupAssociation( user, group ) - uga.flush() + trans.sa_session.add( uga ) + trans.sa_session.flush() # Create the GroupRoleAssociations for role in [ trans.sa_session.query( trans.app.model.Role ).get( x ) for x in in_roles ]: gra = trans.app.model.GroupRoleAssociation( group, role ) - gra.flush() + trans.sa_session.add( gra ) + trans.sa_session.flush() msg = "Group '%s' has been created with %d associated users and %d associated roles" % ( name, len( in_users ), len( in_roles ) ) trans.response.send_redirect( web.url_for( controller='admin', action='groups', message=util.sanitize_text( msg ), status='done' ) ) trans.response.send_redirect( web.url_for( controller='admin', action='create_group', msg=util.sanitize_text( msg ), messagetype='error' ) ) @@ -675,7 +678,8 @@ params = util.Params( kwd ) group = get_group( trans, params.id ) group.deleted = True - group.flush() + trans.sa_session.add( group ) + trans.sa_session.flush() msg = "Group '%s' has been marked as deleted." % group.name trans.response.send_redirect( web.url_for( action='groups', message=util.sanitize_text( msg ), status='done' ) ) @web.expose @@ -684,7 +688,8 @@ params = util.Params( kwd ) group = get_group( trans, params.id ) group.deleted = False - group.flush() + trans.sa_session.add( group ) + trans.sa_session.flush() msg = "Group '%s' has been marked as not deleted." % group.name trans.response.send_redirect( web.url_for( action='groups', message=util.sanitize_text( msg ), status='done' ) ) @web.expose @@ -701,12 +706,10 @@ # Delete UserGroupAssociations for uga in group.users: trans.sa_session.delete( uga ) - uga.flush() # Delete GroupRoleAssociations for gra in group.roles: trans.sa_session.delete( gra ) - gra.flush() - # Delete the Group + trans.sa_session.flush() message = "The following have been purged from the database for group '%s': UserGroupAssociations, GroupRoleAssociations." % group.name trans.response.send_redirect( web.url_for( action='groups', message=util.sanitize_text( message ), status='done' ) ) @@ -756,7 +759,8 @@ user.set_password_cleartext( password ) if trans.app.config.use_remote_user: user.external = True - user.flush() + trans.sa_session.add( user ) + trans.sa_session.flush() trans.app.security_agent.create_private_user_role( user ) trans.app.security_agent.user_set_default_permissions( user, history=False, dataset=False ) message = 'Created new user account (%s)' % user.email @@ -804,7 +808,8 @@ break else: user.set_password_cleartext( password ) - user.flush() + trans.sa_session.add( user ) + trans.sa_session.flush() if not message and not status: message = "Passwords reset for %d users" % len( ids ) status = 'done' @@ -831,7 +836,8 @@ for user_id in ids: user = get_user( trans, user_id ) user.deleted = True - user.flush() + trans.sa_session.add( user ) + trans.sa_session.flush() message += " %s " % user.email trans.response.send_redirect( web.url_for( action='users', message=util.sanitize_text( message ), status='done' ) ) @web.expose @@ -848,7 +854,8 @@ user = get_user( trans, user_id ) if user.deleted: user.deleted = False - user.flush() + trans.sa_session.add( user ) + trans.sa_session.flush() count += 1 undeleted_users += " %s" % user.email message = "Undeleted %d users: %s" % ( count, undeleted_users ) @@ -895,23 +902,22 @@ # Delete Dataset if not d.deleted: d.deleted = True - d.flush() + trans.sa_session.add( d ) hda.deleted = True - hda.flush() + trans.sa_session.add( hda ) h.deleted = True - h.flush() + trans.sa_session.add( h ) # Delete UserGroupAssociations for uga in user.groups: trans.sa_session.delete( uga ) - uga.flush() # Delete UserRoleAssociations EXCEPT FOR THE PRIVATE ROLE for ura in user.roles: if ura.role_id != private_role.id: trans.sa_session.delete( ura ) - ura.flush() # Purge the user user.purged = True - user.flush() + trans.sa_session.add( user ) + trans.sa_session.flush() message += "%s " % user.email trans.response.send_redirect( web.url_for( controller='admin', action='users', diff -r 0edb42925161 -r b33b8f5e03b8 lib/galaxy/web/controllers/async.py --- a/lib/galaxy/web/controllers/async.py Wed Nov 11 15:13:12 2009 -0500 +++ b/lib/galaxy/web/controllers/async.py Wed Nov 11 15:59:41 2009 -0500 @@ -109,9 +109,10 @@ data.dbkey = GALAXY_BUILD data.info = GALAXY_INFO data.state = data.states.NEW - data.flush() + trans.sa_session.add( data ) open( data.file_name, 'wb' ).close() #create the file trans.history.add_dataset( data, genome_build=GALAXY_BUILD ) + trans.sa_session.add( trans.history ) trans.sa_session.flush() trans.log_event( "Added dataset %d to history %d" %(data.id, trans.history.id ), tool_id=tool_id ) diff -r 0edb42925161 -r b33b8f5e03b8 lib/galaxy/web/controllers/dataset.py --- a/lib/galaxy/web/controllers/dataset.py Wed Nov 11 15:13:12 2009 -0500 +++ b/lib/galaxy/web/controllers/dataset.py Wed Nov 11 15:59:41 2009 -0500 @@ -356,7 +356,8 @@ if new_history_name: new_history.name = new_history_name new_history.user = user - new_history.flush() + trans.sa_session.add( new_history ) + trans.sa_session.flush() target_history_ids.append( new_history.id ) if user: target_histories = [ hist for hist in map( trans.sa_session.query( trans.app.model.History ).get, target_history_ids ) if ( hist is not None and hist.user == user )] diff -r 0edb42925161 -r b33b8f5e03b8 lib/galaxy/web/controllers/forms.py --- a/lib/galaxy/web/controllers/forms.py Wed Nov 11 15:13:12 2009 -0500 +++ b/lib/galaxy/web/controllers/forms.py Wed Nov 11 15:59:41 2009 -0500 @@ -113,7 +113,8 @@ messagetype = params.get( 'messagetype', 'done' ) fd = trans.sa_session.query( trans.app.model.FormDefinition ).get( int( util.restore_text( params.form_id ) ) ) fd.form_definition_current.deleted = True - fd.form_definition_current.flush() + trans.sa_session.add( fd.form_definition_current ) + trans.sa_session.flush() return self._show_forms_list(trans, msg='The form definition named %s is deleted.' % fd.name, messagetype='done') @@ -125,7 +126,8 @@ messagetype = params.get( 'messagetype', 'done' ) fd = trans.sa_session.query( trans.app.model.FormDefinition ).get( int( util.restore_text( params.form_id ) ) ) fd.form_definition_current.deleted = False - fd.form_definition_current.flush() + trans.sa_session.add( fd.form_definition_current ) + trans.sa_session.flush() return self._show_forms_list(trans, msg='The form definition named %s is undeleted.' % fd.name, messagetype='done') diff -r 0edb42925161 -r b33b8f5e03b8 lib/galaxy/web/controllers/history.py --- a/lib/galaxy/web/controllers/history.py Wed Nov 11 15:13:12 2009 -0500 +++ b/lib/galaxy/web/controllers/history.py Wed Nov 11 15:59:41 2009 -0500 @@ -306,7 +306,8 @@ except: association = None new_history.add_galaxy_session( galaxy_session, association=association ) - new_history.flush() + trans.sa_session.add( new_history ) + trans.sa_session.flush() trans.set_history( new_history ) # No message return None, None @@ -335,7 +336,7 @@ # Current user is the user with which the histories were shared association = trans.sa_session.query( trans.app.model.HistoryUserShareAssociation ).filter_by( user=trans.user, history=history ).one() trans.sa_session.delete( association ) - association.flush() + trans.sa_session.flush() message = "Unshared %d shared histories" % len( ids ) status = 'done' # Render the list view @@ -348,7 +349,8 @@ return trans.show_error_message( "History (%s) has been shared with others, unshare it before deleting it. " % history.name ) if not history.deleted: history.deleted = True - history.flush() + trans.sa_session.add( history ) + trans.sa_session.flush() trans.log_event( "History id %d marked as deleted" % history.id ) # Regardless of whether it was previously deleted, we make a new history active trans.new_history() @@ -365,6 +367,7 @@ assert history.user == trans.user # Rename history.name = new_name + trans.sa_session.add( history ) trans.sa_session.flush() @web.expose @@ -406,7 +409,8 @@ except: association = None new_history.add_galaxy_session( galaxy_session, association=association ) - new_history.flush() + trans.sa_session.add( new_history ) + trans.sa_session.flush() if not user_history.datasets: trans.set_history( new_history ) return trans.show_ok_message( """ @@ -424,7 +428,8 @@ except: association = None new_history.add_galaxy_session( galaxy_session, association=association ) - new_history.flush() + trans.sa_session.add( new_history ) + trans.sa_session.flush() trans.set_history( new_history ) return trans.show_ok_message( """ History "%s" has been imported. Click <a href="%s">here</a> @@ -731,9 +736,8 @@ share = trans.app.model.HistoryUserShareAssociation() share.history = history share.user = send_to_user - session = trans.sa_session - session.add( share ) - session.flush() + trans.sa_session.add( share ) + trans.sa_session.flush() if history not in shared_histories: shared_histories.append( history ) if send_to_err: @@ -752,12 +756,13 @@ if ids: histories = [ get_history( trans, history_id ) for history_id in ids ] for history in histories: + trans.sa_session.add( history ) if params.get( 'enable_import_via_link', False ): history.importable = True - history.flush() + trans.sa_session.flush() elif params.get( 'disable_import_via_link', False ): history.importable = False - history.flush() + trans.sa_session.flush() elif params.get( 'unshare_user', False ): user = trans.sa_session.query( trans.app.model.User ).get( trans.security.decode_id( kwd[ 'unshare_user' ] ) ) if not user: @@ -767,7 +772,7 @@ if husas: for husa in husas: trans.sa_session.delete( husa ) - husa.flush() + trans.sa_session.flush() histories = [] # Get all histories that have been shared with others husas = trans.sa_session.query( trans.app.model.HistoryUserShareAssociation ) \ @@ -818,7 +823,8 @@ elif name[i] not in [None,'',' ']: name[i] = escape(name[i]) histories[i].name = name[i] - histories[i].flush() + trans.sa_session.add( histories[i] ) + trans.sa_session.flush() change_msg = change_msg + "<p>History: "+cur_names[i]+" renamed to: "+name[i]+"</p>" trans.log_event( "History renamed: id: %s, renamed to: '%s'" % (str(histories[i].id), name[i] ) ) else: diff -r 0edb42925161 -r b33b8f5e03b8 lib/galaxy/web/controllers/library.py --- a/lib/galaxy/web/controllers/library.py Wed Nov 11 15:13:12 2009 -0500 +++ b/lib/galaxy/web/controllers/library.py Wed Nov 11 15:59:41 2009 -0500 @@ -169,11 +169,11 @@ else: library.name = new_name library.description = new_description - library.flush() # Rename the root_folder library.root_folder.name = new_name library.root_folder.description = new_description - library.root_folder.flush() + trans.sa_session.add_all( ( library, library.root_folder ) ) + trans.sa_session.flush() msg = "Library '%s' has been renamed to '%s'" % ( old_name, new_name ) return trans.response.send_redirect( web.url_for( controller='library', action='library', @@ -240,7 +240,8 @@ # ? unspecified (?) new_folder.genome_build = util.dbnames.default_value folder.add_folder( new_folder ) - new_folder.flush() + trans.sa_session.add( new_folder ) + trans.sa_session.flush() # New folders default to having the same permissions as their parent folder trans.app.security_agent.copy_library_permissions( folder, new_folder ) msg = "New folder named '%s' has been added to the library" % new_folder.name @@ -273,7 +274,8 @@ else: folder.name = new_name folder.description = new_description - folder.flush() + trans.sa_session.add( folder ) + trans.sa_session.flush() msg = "Folder '%s' has been renamed to '%s'" % ( old_name, new_name ) return trans.response.send_redirect( web.url_for( controller='library', action='folder', @@ -359,7 +361,8 @@ else: library_dataset.name = new_name library_dataset.info = new_info - library_dataset.flush() + trans.sa_session.add( library_dataset ) + trans.sa_session.flush() msg = "Dataset '%s' has been renamed to '%s'" % ( old_name, new_name ) messagetype = 'done' else: @@ -502,7 +505,8 @@ elif params.get( 'delete', False ): if trans.app.security_agent.can_modify_library_item( user, roles, folder ): ldda.deleted = True - ldda.flush() + trans.sa_session.add( ldda ) + trans.sa_session.flush() msg = 'Dataset %s has been removed from this data library' % ldda.name messagetype = 'done' else: @@ -894,7 +898,8 @@ for ldda_id in ldda_ids: ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( ldda_id ) hda = ldda.to_history_dataset_association( target_history=history, add_to_history = True ) - history.flush() + trans.sa_session.add( history ) + trans.sa_session.flush() msg = "%i dataset(s) have been imported into your history" % len( ldda_ids ) return trans.response.send_redirect( web.url_for( controller='library', action='browse_library', diff -r 0edb42925161 -r b33b8f5e03b8 lib/galaxy/web/controllers/library_admin.py --- a/lib/galaxy/web/controllers/library_admin.py Wed Nov 11 15:13:12 2009 -0500 +++ b/lib/galaxy/web/controllers/library_admin.py Wed Nov 11 15:59:41 2009 -0500 @@ -89,9 +89,9 @@ library = trans.app.model.Library( name = util.restore_text( params.name ), description = util.restore_text( params.description ) ) root_folder = trans.app.model.LibraryFolder( name = util.restore_text( params.name ), description = "" ) - root_folder.flush() library.root_folder = root_folder - library.flush() + trans.sa_session.add_all( ( library, root_folder ) ) + trans.sa_session.flush() msg = "The new library named '%s' has been created" % library.name return trans.response.send_redirect( web.url_for( controller='library_admin', action='browse_library', @@ -116,11 +116,11 @@ else: library.name = new_name library.description = new_description - library.flush() # Rename the root_folder library.root_folder.name = new_name library.root_folder.description = new_description - library.root_folder.flush() + trans.sa_session.add_all( ( library, library.root_folder ) ) + trans.sa_session.flush() msg = "Library '%s' has been renamed to '%s'" % ( old_name, new_name ) return trans.response.send_redirect( web.url_for( controller='library_admin', action='library', @@ -148,15 +148,17 @@ # to deleted. This allows for the library to be undeleted ( before it is purged ), # restoring all of its contents. ldda.deleted = True - ldda.flush() + trans.sa_session.add( ldda ) library_dataset.deleted = True - library_dataset.flush() + trans.sa_session.add( library_dataset ) library_folder.deleted = True - library_folder.flush() + trans.sa_session.add( library_folder ) + trans.sa_session.flush() trans.sa_session.refresh( library ) delete_folder( library.root_folder ) library.deleted = True - library.flush() + trans.sa_session.add( library ) + trans.sa_session.flush() msg = "Library '%s' and all of its contents have been marked deleted" % library.name return trans.response.send_redirect( web.url_for( action='browse_libraries', msg=util.sanitize_text( msg ), messagetype='done' ) ) elif action == 'permissions': @@ -218,14 +220,14 @@ # us, as well as removing the file from disk. #if not dataset.deleted and len( dataset.active_library_associations ) <= 1: # This is our current ldda dataset.deleted = True - dataset.flush() ldda.deleted = True - ldda.flush() + trans.sa_session.add_all( ( dataset, ldda ) ) library_dataset.deleted = True - library_dataset.flush() + trans.sa_session.add( library_dataset ) library_folder.deleted = True library_folder.purged = True - library_folder.flush() + trans.sa_session.add( library_folder ) + trans.sa_session.flush() if not library.deleted: msg = "Library '%s' has not been marked deleted, so it cannot be purged" % ( library.name ) return trans.response.send_redirect( web.url_for( controller='library_admin', @@ -235,7 +237,8 @@ else: purge_folder( library.root_folder ) library.purged = True - library.flush() + trans.sa_session.add( library ) + trans.sa_session.flush() msg = "Library '%s' and all of its contents have been purged, datasets will be removed from disk via the cleanup_datasets script" % library.name return trans.response.send_redirect( web.url_for( controller='library_admin', action='deleted_libraries', @@ -273,7 +276,8 @@ # ? unspecified (?) new_folder.genome_build = util.dbnames.default_value folder.add_folder( new_folder ) - new_folder.flush() + trans.sa_session.add( new_folder ) + trans.sa_session.flush() # New folders default to having the same permissions as their parent folder trans.app.security_agent.copy_library_permissions( folder, new_folder ) msg = "New folder named '%s' has been added to the library" % new_folder.name @@ -305,7 +309,8 @@ else: folder.name = new_name folder.description = new_description - folder.flush() + trans.sa_session.add( folder ) + trans.sa_session.flush() msg = "Folder '%s' has been renamed to '%s'" % ( old_name, new_name ) return trans.response.send_redirect( web.url_for( controller='library_admin', action='folder', @@ -322,7 +327,8 @@ messagetype=messagetype ) elif action == 'delete': folder.deleted = True - folder.flush() + trans.sa_session.add( folder ) + trans.sa_session.flush() msg = "Folder '%s' and all of its contents have been marked deleted" % folder.name return trans.response.send_redirect( web.url_for( action='browse_library', obj_id=library_id, @@ -379,7 +385,8 @@ else: library_dataset.name = new_name library_dataset.info = new_info - library_dataset.flush() + trans.sa_session.add( library_dataset ) + trans.sa_session.flush() msg = "Dataset '%s' has been renamed to '%s'" % ( old_name, new_name ) messagetype = 'done' return trans.fill_template( '/admin/library/library_dataset_info.mako', @@ -499,7 +506,8 @@ messagetype=messagetype ) elif params.get( 'delete', False ): ldda.deleted = True - ldda.flush() + trans.sa_session.add( ldda ) + trans.sa_session.flush() msg = 'Dataset %s has been removed from this data library' % ldda.name return trans.fill_template( "/admin/library/ldda_edit_info.mako", ldda=ldda, @@ -893,7 +901,8 @@ for ldda_id in ldda_ids: ldda = trans.sa_session.query( trans.app.model.LibraryDatasetDatasetAssociation ).get( ldda_id ) ldda.deleted = True - ldda.flush() + trans.sa_session.add( ldda ) + trans.sa_session.flush() msg = "The selected datasets have been removed from this data library" trans.response.send_redirect( web.url_for( controller='library_admin', action='browse_library', @@ -930,7 +939,8 @@ library_item_desc = library_item_type.capitalize() library_item = trans.sa_session.query( library_item_types[ library_item_type ] ).get( int( library_item_id ) ) library_item.deleted = True - library_item.flush() + trans.sa_session.add( library_item ) + trans.sa_session.flush() msg = util.sanitize_text( "%s '%s' has been marked deleted" % ( library_item_desc, library_item.name ) ) messagetype = 'done' if library_item_type == 'library': @@ -961,7 +971,8 @@ messagetype = 'error' else: library_item.deleted = False - library_item.flush() + trans.sa_session.add( library_item ) + trans.sa_session.flush() msg = util.sanitize_text( "%s '%s' has been marked undeleted" % ( library_item_desc, library_item.name ) ) messagetype = 'done' if library_item_type == 'library': diff -r 0edb42925161 -r b33b8f5e03b8 lib/galaxy/web/controllers/library_common.py --- a/lib/galaxy/web/controllers/library_common.py Wed Nov 11 15:13:12 2009 -0500 +++ b/lib/galaxy/web/controllers/library_common.py Wed Nov 11 15:59:41 2009 -0500 @@ -97,7 +97,7 @@ upload_option=upload_option, msg=util.sanitize_text( msg ), messagetype='error' ) ) - json_file_path = upload_common.create_paramfile( uploaded_datasets ) + json_file_path = upload_common.create_paramfile( trans, uploaded_datasets ) data_list = [ ud.data for ud in uploaded_datasets ] return upload_common.create_job( trans, tool_params, tool, json_file_path, data_list, folder=library_bunch.folder ) def make_library_uploaded_dataset( self, trans, params, name, path, type, library_bunch, in_folder=None ): @@ -116,7 +116,8 @@ if params.get( 'link_data_only', False ): uploaded_dataset.link_data_only = True uploaded_dataset.data.file_name = os.path.abspath( path ) - uploaded_dataset.data.flush() + trans.sa_session.add( uploaded_dataset.data ) + trans.sa_session.data.flush() return uploaded_dataset def get_server_dir_uploaded_datasets( self, trans, params, full_dir, import_dir_desc, library_bunch, err_redirect, msg ): files = [] @@ -248,14 +249,16 @@ form = trans.sa_session.query( trans.app.model.FormDefinition ).get( int( kwd[ 'form_id' ] ) ) #fields = list( copy.deepcopy( form.fields ) ) form_values = trans.app.model.FormValues( form, [] ) - form_values.flush() + trans.sa_session.add( form_values ) + trans.sa_session.flush() if folder_id: assoc = trans.app.model.LibraryFolderInfoAssociation( library_item, form, form_values ) elif ldda_id: assoc = trans.app.model.LibraryDatasetDatasetInfoAssociation( library_item, form, form_values ) else: assoc = trans.app.model.LibraryInfoAssociation( library_item, form, form_values ) - assoc.flush() + trans.sa_session.add( assoc ) + trans.sa_session.flush() msg = 'An information template based on the form "%s" has been added to this %s.' % ( form.name, library_item_desc ) trans.response.send_redirect( web.url_for( controller=cntrller, action=response_action, @@ -315,21 +318,25 @@ # Update existing content only if it has changed if form_values.content != field_contents: form_values.content = field_contents - form_values.flush() + trans.sa_session.add( form_values ) + trans.sa_session.flush() else: # Inherit the next available info_association so we can get the template info_association, inherited = library_item.get_info_association() template = info_association.template # Create a new FormValues object form_values = trans.app.model.FormValues( template, field_contents ) - form_values.flush() + trans.sa_session.add( form_values ) + trans.sa_session.flush() # Create a new info_association between the current library item and form_values if library_item_type == 'folder': info_association = trans.app.model.LibraryFolderInfoAssociation( library_item, template, form_values ) - info_association.flush() + trans.sa_session.add( info_association ) + trans.sa_session.flush() elif library_item_type == 'library_dataset_dataset_association': info_association = trans.app.model.LibraryDatasetDatasetInfoAssociation( library_item, template, form_values ) - info_association.flush() + trans.sa_session.add( info_association ) + trans.sa_session.flush() msg = 'The information has been updated.' return trans.response.send_redirect( web.url_for( controller=cntrller, action=response_action, diff -r 0edb42925161 -r b33b8f5e03b8 lib/galaxy/web/controllers/requests.py --- a/lib/galaxy/web/controllers/requests.py Wed Nov 11 15:13:12 2009 -0500 +++ b/lib/galaxy/web/controllers/requests.py Wed Nov 11 15:59:41 2009 -0500 @@ -300,9 +300,11 @@ for field_index in range(len(request.type.sample_form.fields)): sample_values.append(util.restore_text( params.get( 'sample_%i_field_%i' % (sample_index, field_index), '' ) )) form_values = trans.app.model.FormValues(request.type.sample_form, sample_values) - form_values.flush() + trans.sa_session.add( form_values ) + trans.sa_session.flush() s = trans.app.model.Sample(sample_name, '', request, form_values) - s.flush() + trans.sa_session.add( s ) + trans.sa_session.flush() else: for sample_index in range(len(current_samples)): sample_name = current_samples[sample_index][0] @@ -314,9 +316,9 @@ if sample: form_values = trans.sa_session.query( trans.app.model.FormValues ).get( sample.values.id ) form_values.content = sample_values - form_values.flush() sample.name = new_sample_name - sample.flush() + trans.sa_session.add( sample ) + trans.sa_session.flush() return trans.response.send_redirect( web.url_for( controller='requests', action='list', operation='show_request', @@ -350,8 +352,7 @@ s = request.has_sample(sample_name) if s: trans.sa_session.delete( s ) - s.flush() - request.flush() + trans.sa_session.flush() del current_samples[sample_index] return trans.fill_template( '/requests/show_request.mako', request=request, @@ -635,7 +636,8 @@ user_address.postal_code = util.restore_text(params.get('field_%i_postal_code' % index, '')) user_address.country = util.restore_text(params.get('field_%i_country' % index, '')) user_address.phone = util.restore_text(params.get('field_%i_phone' % index, '')) - user_address.flush() + trans.sa_session.add( user_address ) + trans.sa_session.flush() trans.sa_session.refresh( trans.user ) values.append(int(user_address.id)) elif value == unicode('none'): @@ -647,13 +649,15 @@ else: values.append(util.restore_text(params.get('field_%i' % index, ''))) form_values = trans.app.model.FormValues(request_type.request_form, values) - form_values.flush() + trans.sa_session.add( form_values ) + trans.sa_session.flush() if not request: request = trans.app.model.Request(name, desc, request_type, trans.user, form_values, library=library, folder=folder, state=trans.app.model.Request.states.UNSUBMITTED) - request.flush() + trans.sa_session.add( request ) + trans.sa_session.flush() else: request.name = name request.desc = desc @@ -772,7 +776,8 @@ message='This request cannot be deleted as it is already been submitted', **kwd) ) request.deleted = True - request.flush() + trans.sa_session.add( request ) + trans.sa_session.flush() kwd = {} kwd['id'] = trans.security.encode_id(request.id) return trans.response.send_redirect( web.url_for( controller='requests', @@ -793,7 +798,8 @@ **kwd) ) # change request's submitted field request.deleted = False - request.flush() + trans.sa_session.add( request ) + trans.sa_session.flush() kwd = {} kwd['id'] = trans.security.encode_id(request.id) return trans.response.send_redirect( web.url_for( controller='requests', @@ -824,10 +830,12 @@ new_state = request.type.states[0] for s in request.samples: event = trans.app.model.SampleEvent(s, new_state, 'Samples submitted to the system') - event.flush() + trans.sa_session.add( event ) + trans.sa_session.flush() # change request's submitted field request.state = request.states.SUBMITTED - request.flush() + trans.sa_session.add( request ) + trans.sa_session.flush() kwd = {} kwd['id'] = trans.security.encode_id(request.id) kwd['status'] = 'done' diff -r 0edb42925161 -r b33b8f5e03b8 lib/galaxy/web/controllers/requests_admin.py --- a/lib/galaxy/web/controllers/requests_admin.py Wed Nov 11 15:13:12 2009 -0500 +++ b/lib/galaxy/web/controllers/requests_admin.py Wed Nov 11 15:59:41 2009 -0500 @@ -199,7 +199,8 @@ message='This request cannot be deleted as it is already been submitted', **kwd) ) request.deleted = True - request.flush() + trans.sa_session.add( request ) + trans.sa_session.flush() kwd = {} kwd['id'] = trans.security.encode_id(request.id) return trans.response.send_redirect( web.url_for( controller='requests_admin', @@ -221,7 +222,8 @@ **kwd) ) # change request's submitted field request.deleted = False - request.flush() + trans.sa_session.add( request ) + trans.sa_session.flush() kwd = {} kwd['id'] = trans.security.encode_id(request.id) return trans.response.send_redirect( web.url_for( controller='requests_admin', @@ -253,10 +255,11 @@ new_state = request.type.states[0] for s in request.samples: event = trans.app.model.SampleEvent(s, new_state, 'Samples submitted to the system') - event.flush() + trans.sa_session.add( event ) # change request's submitted field request.state = request.states.SUBMITTED - request.flush() + trans.sa_session.add( request ) + trans.sa_session.flush() kwd = {} kwd['id'] = trans.security.encode_id(request.id) kwd['status'] = 'done' @@ -579,7 +582,8 @@ user_address.postal_code = util.restore_text(params.get('field_%i_postal_code' % index, '')) user_address.country = util.restore_text(params.get('field_%i_country' % index, '')) user_address.phone = util.restore_text(params.get('field_%i_phone' % index, '')) - user_address.flush() + trans.sa_session.add( user_address ) + trans.sa_session.flush() trans.sa_session.refresh( trans.user ) values.append(int(user_address.id)) elif value == unicode('none'): @@ -591,13 +595,14 @@ else: values.append(util.restore_text(params.get('field_%i' % index, ''))) form_values = trans.app.model.FormValues(request_type.request_form, values) - form_values.flush() + trans.sa_session.add( form_values ) + trans.sa_session.flush() if not request: request = trans.app.model.Request(name, desc, request_type, user, form_values, library=library, folder=folder, state=trans.app.model.Request.states.UNSUBMITTED) - request.flush() + trans.sa_session.add( request ) else: request.name = name request.desc = desc @@ -606,7 +611,8 @@ request.values = form_values request.library = library request.folder = folder - request.flush() + trans.sa_session.add( request ) + trans.sa_session.flush() return request @@ -671,7 +677,8 @@ **kwd) ) # change request's submitted field request.state = request.states.UNSUBMITTED - request.flush() + trans.sa_session.add( request ) + trans.sa_session.flush() kwd = {} kwd['id'] = trans.security.encode_id(request.id) kwd['status'] = 'done' @@ -797,9 +804,11 @@ for field_index in range(len(request.type.sample_form.fields)): sample_values.append(util.restore_text( params.get( 'sample_%i_field_%i' % (sample_index, field_index), '' ) )) form_values = trans.app.model.FormValues(request.type.sample_form, sample_values) - form_values.flush() + trans.sa_session.add( form_values ) + trans.sa_session.flush() s = trans.app.model.Sample(sample_name, '', request, form_values) - s.flush() + trans.sa_session.add( s ) + trans.sa_session.flush() else: for index in range(len(current_samples)): sample_index = index @@ -812,9 +821,11 @@ if sample: form_values = trans.sa_session.query( trans.app.model.FormValues ).get( sample.values.id ) form_values.content = sample_values - form_values.flush() + trans.sa_session.add( form_values ) + trans.sa_session.flush() sample.name = new_sample_name - sample.flush() + trans.sa_session.add( sample ) + trans.sa_session.flush() return trans.response.send_redirect( web.url_for( controller='requests_admin', action='list', operation='show_request', @@ -848,8 +859,7 @@ s = request.has_sample(sample_name) if s: trans.sa_session.delete( s ) - s.flush() - request.flush() + trans.sa_session.flush() del current_samples[sample_index] return trans.fill_template( '/admin/requests/show_request.mako', request=request, @@ -1026,21 +1036,22 @@ for index, sample in enumerate(request.samples): bar_code = util.restore_text(params.get('sample_%i_bar_code' % index, '')) sample.bar_code = bar_code - sample.flush() + trans.sa_session.add( sample ) + trans.sa_session.flush() # change the state of all the samples to the next state # get the new state new_state = request.type.states[1] for s in request.samples: event = trans.app.model.SampleEvent(s, new_state, 'Bar code added to this sample') - event.flush() + trans.sa_session.add( event ) + trans.sa_session.flush() return trans.response.send_redirect( web.url_for( controller='requests_admin', action='list', operation='show_request', id=trans.security.encode_id(request.id), message='Bar codes have been saved for this request', status='done')) - - def __set_request_state(self, request): + def __set_request_state( self, trans, request ): # check if all the samples of the current request are in the final state complete = True for s in request.samples: @@ -1050,9 +1061,8 @@ request.state = request.states.COMPLETE else: request.state = request.states.SUBMITTED - request.flush() - - + trans.sa_session.add( request ) + trans.sa_session.flush() def change_state(self, trans, sample): possible_states = sample.request.type.states curr_state = sample.current_state() @@ -1089,8 +1099,9 @@ trans.app.model.SampleState.table.c.id == selected_state ) ) \ .first() event = trans.app.model.SampleEvent(sample, new_state, comments) - event.flush() - self.__set_request_state(sample.request) + trans.sa_session.add( event ) + trans.sa_session.flush() + self.__set_request_state( trans, sample.request ) return trans.response.send_redirect( web.url_for( controller='requests_admin', action='show_events', sample_id=sample.id)) @@ -1208,17 +1219,19 @@ rt.desc = util.restore_text( params.description ) or "" rt.request_form = trans.sa_session.query( trans.app.model.FormDefinition ).get( int( params.request_form_id ) ) rt.sample_form = trans.sa_session.query( trans.app.model.FormDefinition ).get( int( params.sample_form_id ) ) - rt.flush() + trans.sa_session.add( rt ) + trans.sa_session.flush() # set sample states ss_list = trans.sa_session.query( trans.app.model.SampleState ).filter( trans.app.model.SampleState.table.c.request_type_id == rt.id ) for ss in ss_list: trans.sa_session.delete( ss ) - ss.flush() + trans.sa_session.flush() for i in range( num_states ): name = util.restore_text( params.get( 'state_name_%i' % i, None )) desc = util.restore_text( params.get( 'state_desc_%i' % i, None )) ss = trans.app.model.SampleState(name, desc, rt) - ss.flush() + trans.sa_session.add( ss ) + trans.sa_session.flush() msg = "The new request type named '%s' with %s state(s) has been created" % (rt.name, num_states) return rt, msg @web.expose @@ -1229,7 +1242,7 @@ messagetype = params.get( 'messagetype', 'done' ) rt = trans.sa_session.query( trans.app.model.RequestType ).get( int( util.restore_text( params.request_type_id ) ) ) rt.deleted = True - rt.flush() + trans.sa_session.flush() return trans.response.send_redirect( web.url_for( controller='requests_admin', action='manage_request_types', msg='Request type <b>%s</b> has been deleted' % rt.name, @@ -1242,7 +1255,7 @@ messagetype = params.get( 'messagetype', 'done' ) rt = trans.sa_session.query( trans.app.model.RequestType ).get( int( util.restore_text( params.request_type_id ) ) ) rt.deleted = False - rt.flush() + trans.sa_session.flush() return trans.response.send_redirect( web.url_for( controller='requests_admin', action='manage_request_types', msg='Request type <b>%s</b> has been undeleted' % rt.name, diff -r 0edb42925161 -r b33b8f5e03b8 lib/galaxy/web/controllers/root.py --- a/lib/galaxy/web/controllers/root.py Wed Nov 11 15:13:12 2009 -0500 +++ b/lib/galaxy/web/controllers/root.py Wed Nov 11 15:59:41 2009 -0500 @@ -460,7 +460,8 @@ except: association = None new_history.add_galaxy_session( galaxy_session, association=association ) - new_history.flush() + trans.sa_session.add( new_history ) + trans.sa_session.flush() if not user_history.datasets: trans.set_history( new_history ) trans.log_event( "History imported, id: %s, name: '%s': " % (str(new_history.id) , new_history.name ) ) @@ -479,7 +480,8 @@ except: association = None new_history.add_galaxy_session( galaxy_session, association=association ) - new_history.flush() + trans.sa_session.add( new_history ) + trans.sa_session.flush() trans.set_history( new_history ) trans.log_event( "History imported, id: %s, name: '%s': " % (str(new_history.id) , new_history.name ) ) return trans.show_ok_message( """ @@ -506,7 +508,8 @@ else: permissions = trans.app.security_agent.history_get_default_permissions( history ) trans.app.security_agent.set_all_dataset_permissions( data.dataset, permissions ) - data.flush() + trans.sa_session.add( data ) + trans.sa_session.flush() data_file = open( data.file_name, "wb" ) file_data.file.seek( 0 ) data_file.write( file_data.file.read() ) @@ -515,11 +518,11 @@ data.set_size() data.init_meta() data.set_meta() - data.flush() + trans.sa_session.flush() history.add_dataset( data ) - history.flush() + trans.sa_session.flush() data.set_peek() - data.flush() + trans.sa_session.flush() trans.log_event("Added dataset %d to history %d" %(data.id, trans.history.id)) return trans.show_ok_message("Dataset "+str(data.hid)+" added to history "+str(history_id)+".") except Exception, e: @@ -567,7 +570,8 @@ ## history = trans.app.model.History.get( old_data.history_id ) history = trans.get_history() history.add_dataset(new_data) - new_data.flush() + trans.sa_session.add( new_data ) + trans.sa_session.flush() return trans.show_message( "<p>Secondary dataset has been made primary.</p>", refresh_frames=['history'] ) except: return trans.show_error_message( "<p>Failed to make secondary dataset primary.</p>" ) diff -r 0edb42925161 -r b33b8f5e03b8 lib/galaxy/web/controllers/tracks.py --- a/lib/galaxy/web/controllers/tracks.py Wed Nov 11 15:13:12 2009 -0500 +++ b/lib/galaxy/web/controllers/tracks.py Wed Nov 11 15:59:41 2009 -0500 @@ -250,7 +250,9 @@ new_dataset = dataset.datatype.convert_dataset( trans, dataset, type, return_output = True, visible = False ).values()[0] new_dataset.hid = dataset.hid # Hrrmmm.... new_dataset.name = dataset.name - new_dataset.flush() + trans.sa_session.add( new_dataset ) + trans.sa_session.flush() assoc.dataset = new_dataset - assoc.flush() + trans.sa_session.add( assoc ) + trans.sa_session.flush() return new_dataset diff -r 0edb42925161 -r b33b8f5e03b8 lib/galaxy/web/controllers/user.py --- a/lib/galaxy/web/controllers/user.py Wed Nov 11 15:13:12 2009 -0500 +++ b/lib/galaxy/web/controllers/user.py Wed Nov 11 15:59:41 2009 -0500 @@ -46,7 +46,8 @@ conf_pass_err = "New passwords do not match." else: user.set_password_cleartext( new_pass ) - user.flush() + trans.sa_session.add( user ) + trans.sa_session.flush() trans.log_event( "User change password" ) return trans.show_ok_message( "Password has been changed for " + user.email) # Generate input form @@ -74,7 +75,8 @@ conf_email_err = "Email addresses do not match." else: user.email = email - user.flush() + trans.sa_session.add( user ) + trans.sa_session.flush() trans.log_event( "User change email" ) return trans.show_ok_message( "Email has been changed to: " + user.email, refresh_frames=['masthead', 'history'] ) return trans.show_form( @@ -99,7 +101,8 @@ username_err = "This username is not available" else: user.username = username - user.flush() + trans.sa_session.add( user ) + trans.sa_session.flush() trans.log_event( "User change username" ) return trans.show_ok_message( "Username been set to: " + user.username ) else: @@ -195,7 +198,8 @@ user = trans.app.model.User( email=email ) user.set_password_cleartext( password ) user.username = username - user.flush() + trans.sa_session.add( user ) + trans.sa_session.flush() trans.app.security_agent.create_private_user_role( user ) # We set default user permissions, before we log in and set the default history permissions trans.app.security_agent.user_set_default_permissions( user, default_access_private = trans.app.config.new_user_dataset_access_role_default_private ) @@ -289,7 +293,8 @@ user_address.postal_code = util.restore_text(params.get('field_%i_postal_code' % index, '')) user_address.country = util.restore_text(params.get('field_%i_country' % index, '')) user_address.phone = util.restore_text(params.get('field_%i_phone' % index, '')) - user_address.flush() + trans.sa_session.add( user_address ) + trans.sa_session.flush() trans.sa_session.refresh( user ) values.append(int(user_address.id)) elif value == unicode('none'): @@ -303,13 +308,15 @@ if new_user or not user.values: # new user or existing form_values = trans.app.model.FormValues(user_info_form, values) - form_values.flush() + trans.sa_session.add( form_values ) + trans.sa_session.flush() user.values = form_values elif user.values: # editing the user info of an existing user with existing user info user.values.content = values - user.values.flush() - user.flush() + trans.sa_session.add( user.values ) + trans.sa_session.add( user ) + trans.sa_session.flush() def __validate_email(self, trans, params, email, user=None): error = None if user: @@ -489,7 +496,8 @@ # the new email & username user.email = email user.username = username - user.flush() + trans.sa_session.add( user ) + trans.sa_session.flush() msg = 'The login information has been updated with the changes' if params.get('admin_view', 'False') == 'True': return trans.response.send_redirect( web.url_for( controller='user', @@ -532,7 +540,8 @@ messagetype='error') ) # save new password