def remove_all (cls):
""" Remove all objects of this type from the database.
.. note::
- Relationships from and to these objects are removed as well.
- Instanciated objects remain in memory, flagged as uncommitted.
.. seealso::
:meth:`~PersistentObject.remove`
"""
collection_name = cls.__name__
n_objects = methods.find(collection_name, None, count = True)
objects = methods.find(collection_name, None)
n = 0
for object in objects:
try:
object.remove()
n += 1
except:
continue
if (n < n_objects):
logger.warning("%s out of %s objects in collection '%s' were not removed." % (n_objects - n, n_objects, collection_name))
return
methods.drop_collection(cls.__name__)
def remove_all(cls):
""" Remove all objects of this type from the database.
.. note::
- Relationships from and to these objects are removed as well.
- Instanciated objects remain in memory, flagged as uncommitted.
.. seealso::
:meth:`~PersistentObject.remove`
"""
collection_name = cls.__name__
n_objects = methods.find(collection_name, None, count=True)
objects = methods.find(collection_name, None)
n = 0
for object in objects:
try:
object.remove()
n += 1
except:
continue
if (n < n_objects):
logger.warning(
"%s out of %s objects in collection '%s' were not removed." %
(n_objects - n, n_objects, collection_name))
return
methods.drop_collection(cls.__name__)
def _out_vertices (self, neighbor_collection, neighbor_filter = None, relationship_filter = None, count = False):
""" List (or count) all outgoing relationships between this object and others.
.. note::
- This method should not be called directly.
- If relationship_filter is not None, a query is performed in the
database; hence, the source object must be committed. If not a
:class:`MetagenomeDB.errors.UncommittedObjectError` exception is thrown.
"""
targets = self._properties["_relationship_with"]
if (len(targets) == 0):
if (count):
return 0
else:
return []
# consider neighbors regardless of their relationship
if (relationship_filter == None):
candidates = targets
# consider neighbors matching relationship_filter
else:
if (not self._committed):
raise errors.UncommittedObjectError("Cannot list relationships from %s to other objects: the source is not committed." % self)
candidates = []
for target_id in targets:
query = {
"_id": self._properties["_id"],
"_relationships.%s" % target_id: {"$elemMatch": utils.tree.flatten(relationship_filter)}
}
if (methods.find(self.__class__.__name__, query, count = True) == 0):
continue
candidates.append(target_id)
if (len(candidates) == 0):
if (count):
return 0
else:
return []
# select candidates matching neighbor_filter
query = {"_id": {"$in": [bson.objectid.ObjectId(id) for id in candidates]}}
if (neighbor_filter != None):
neighbor_filter = utils.tree.expand(neighbor_filter)
for key in neighbor_filter:
query[key] = neighbor_filter[key]
return methods.find(neighbor_collection, query, count = count)
def run(self, group = None, errors = None):
"""
Called by Synctrex to run the synchronisation. This function takes in
charge the preparation of the Sync, etc.
"""
if not self.synctrex.can_sync_run(self, group):
return
if not errors:
errors = []
errors += self.check()
if errors:
return errors
self.select_group(group or self.group)
main = self.dest if self.dest.is_remote() else self.source
method = methods.find(main, [self.method] if self.method else None)
event = events.Event(sync = self, method = method,
main = main) #, errors = errors)
self.trigger('pre_sync', event, True)
exit_code = method.run(self)
if exit_code:
self.trigger('fail', event, True)
# fixme: errors?
else:
self.trigger('success', event, True)
self.trigger('post_sync', event, True)
def _in_vertices (self, neighbor_collection, neighbor_filter = None, relationship_filter = None, count = False):
""" List (or count) all incoming relationships between objects and this object.
.. note::
This method should not be called directly.
"""
# if the present object has never been committed,
# no object can possibly be linked to it.
if (not "_id" in self._properties):
logger.debug("Attempt to list in-neighbors of %s while this object has never been committed." % self)
if (count):
return 0
else:
return []
object_id = str(self._properties["_id"])
query = {"_relationship_with": object_id}
if (relationship_filter != None):
query["_relationships.%s" % object_id] = {"$elemMatch": utils.tree.flatten(relationship_filter)}
if (neighbor_filter != None):
neighbor_filter = utils.tree.expand(neighbor_filter)
for key in neighbor_filter:
query[key] = neighbor_filter[key]
return methods.find(neighbor_collection, query, count = count)
def find_one (cls, filter): """ Find the first (or only) object of this type that match a query. Parameters: - **filter**: filter for the object to select; see :doc:`queries`. Return: An object, or None if no object found. .. seealso:: :meth:`~PersistentObject.find` """ return methods.find(cls.__name__, query = filter, find_one = True)
def find_one(cls, filter):
""" Find the first (or only) object of this type that match a query.
Parameters:
- **filter**: filter for the object to select; see :doc:`queries`.
Return:
An object, or None if no object found.
.. seealso::
:meth:`~PersistentObject.find`
"""
return methods.find(cls.__name__, query=filter, find_one=True)
def find (cls, filter = None): """ Find all objects of this type that match a query. Parameters: - **filter**: filter for the objects to select (optional); see :doc:`queries`. Return: A generator. .. seealso:: :meth:`~PersistentObject.count`, :meth:`~PersistentObject.find_one` """ return methods.find(cls.__name__, query = filter)
def find(cls, filter=None):
""" Find all objects of this type that match a query.
Parameters:
- **filter**: filter for the objects to select (optional); see
:doc:`queries`.
Return:
A generator.
.. seealso::
:meth:`~PersistentObject.count`, :meth:`~PersistentObject.find_one`
"""
return methods.find(cls.__name__, query=filter)
def _in_vertices(self,
neighbor_collection,
neighbor_filter=None,
relationship_filter=None,
count=False):
""" List (or count) all incoming relationships between objects and this object.
.. note::
This method should not be called directly.
"""
# if the present object has never been committed,
# no object can possibly be linked to it.
if (not "_id" in self._properties):
logger.debug(
"Attempt to list in-neighbors of %s while this object has never been committed."
% self)
if (count):
return 0
else:
return []
object_id = str(self._properties["_id"])
query = {"_relationship_with": object_id}
if (relationship_filter != None):
query["_relationships.%s" % object_id] = {
"$elemMatch": utils.tree.flatten(relationship_filter)
}
if (neighbor_filter != None):
neighbor_filter = utils.tree.expand(neighbor_filter)
for key in neighbor_filter:
query[key] = neighbor_filter[key]
return methods.find(neighbor_collection, query, count=count)
def _disconnect_from (self, target, relationship_filter):
""" Disconnect this object from another.
.. note::
- This method should not be called directly.
- The target MUST have been committed at least once. However, the
source (i.e., the present object) can exist in memory only.
- Throw a :class:`MetagenomeDB.errors.UncommittedObjectError` exception if the
target has never been committed, or if attempting to use
**relationship_filter** while the source is not committed.
- Throw a :class:`MetagenomeDB.errors.InvalidObjectOperationError` if the
source is not connected to the target.
"""
if (not "_id" in target._properties):
raise errors.UncommittedObjectError("Cannot disconnect %s from %s: target has never been committed." % target)
target_id = str(target._properties["_id"])
if (not target_id in self._properties["_relationships"]):
raise errors.InvalidObjectOperationError("%s is not connected to %s." % (self, target))
# case 1: we remove all relationships between the object and target
if (relationship_filter == None):
del self._properties["_relationships"][target_id]
self._properties["_relationship_with"].remove(target_id)
self._committed = False
logger.debug("Removed all relationships between %s and %s." % (self, target))
# case 2: we remove all relationships matching a criteria
else:
if (not self._committed):
raise errors.UncommittedObjectError("Cannot disconnect %s from %s: the source is not committed." % (self, target))
n_relationships = len(self._properties["_relationships"][target_id])
clazz = self.__class__.__name__
to_remove = []
for n in range(n_relationships):
query = {"_id": self._properties["_id"]}
for key, value in utils.tree.flatten(relationship_filter).iteritems():
query["_relationships.%s.%s.%s" % (target_id, n, key)] = value
if (methods.find(clazz, query, count = True) == 0):
continue
to_remove.append(n)
if (len(to_remove) == 0):
raise errors.InvalidObjectOperationError("%s is not connected to %s by any relationship matching %s." % (self, target, utils.tree.flatten(relationship_filter)))
for n in sorted(to_remove, reverse = True):
logger.debug("Removed relationship %s between %s and %s." % (self._properties["_relationships"][target_id][n], self, target))
del self._properties["_relationships"][target_id][n]
if (len(to_remove) == n_relationships):
del self._properties["_relationships"][target_id]
self._properties["_relationship_with"].remove(target_id)
self._committed = False
def _out_vertices(self,
neighbor_collection,
neighbor_filter=None,
relationship_filter=None,
count=False):
""" List (or count) all outgoing relationships between this object and others.
.. note::
- This method should not be called directly.
- If relationship_filter is not None, a query is performed in the
database; hence, the source object must be committed. If not a
:class:`MetagenomeDB.errors.UncommittedObjectError` exception is thrown.
"""
targets = self._properties["_relationship_with"]
if (len(targets) == 0):
if (count):
return 0
else:
return []
# consider neighbors regardless of their relationship
if (relationship_filter == None):
candidates = targets
# consider neighbors matching relationship_filter
else:
if (not self._committed):
raise errors.UncommittedObjectError(
"Cannot list relationships from %s to other objects: the source is not committed."
% self)
candidates = []
for target_id in targets:
query = {
"_id": self._properties["_id"],
"_relationships.%s" % target_id: {
"$elemMatch": utils.tree.flatten(relationship_filter)
}
}
if (methods.find(self.__class__.__name__, query,
count=True) == 0):
continue
candidates.append(target_id)
if (len(candidates) == 0):
if (count):
return 0
else:
return []
# select candidates matching neighbor_filter
query = {
"_id": {
"$in": [bson.objectid.ObjectId(id) for id in candidates]
}
}
if (neighbor_filter != None):
neighbor_filter = utils.tree.expand(neighbor_filter)
for key in neighbor_filter:
query[key] = neighbor_filter[key]
return methods.find(neighbor_collection, query, count=count)
def _disconnect_from(self, target, relationship_filter):
""" Disconnect this object from another.
.. note::
- This method should not be called directly.
- The target MUST have been committed at least once. However, the
source (i.e., the present object) can exist in memory only.
- Throw a :class:`MetagenomeDB.errors.UncommittedObjectError` exception if the
target has never been committed, or if attempting to use
**relationship_filter** while the source is not committed.
- Throw a :class:`MetagenomeDB.errors.InvalidObjectOperationError` if the
source is not connected to the target.
"""
if (not "_id" in target._properties):
raise errors.UncommittedObjectError(
"Cannot disconnect %s from %s: target has never been committed."
% target)
target_id = str(target._properties["_id"])
if (not target_id in self._properties["_relationships"]):
raise errors.InvalidObjectOperationError(
"%s is not connected to %s." % (self, target))
# case 1: we remove all relationships between the object and target
if (relationship_filter == None):
del self._properties["_relationships"][target_id]
self._properties["_relationship_with"].remove(target_id)
self._committed = False
logger.debug("Removed all relationships between %s and %s." %
(self, target))
# case 2: we remove all relationships matching a criteria
else:
if (not self._committed):
raise errors.UncommittedObjectError(
"Cannot disconnect %s from %s: the source is not committed."
% (self, target))
n_relationships = len(
self._properties["_relationships"][target_id])
clazz = self.__class__.__name__
to_remove = []
for n in range(n_relationships):
query = {"_id": self._properties["_id"]}
for key, value in utils.tree.flatten(
relationship_filter).iteritems():
query["_relationships.%s.%s.%s" %
(target_id, n, key)] = value
if (methods.find(clazz, query, count=True) == 0):
continue
to_remove.append(n)
if (len(to_remove) == 0):
raise errors.InvalidObjectOperationError(
"%s is not connected to %s by any relationship matching %s."
% (self, target, utils.tree.flatten(relationship_filter)))
for n in sorted(to_remove, reverse=True):
logger.debug("Removed relationship %s between %s and %s." %
(self._properties["_relationships"][target_id][n],
self, target))
del self._properties["_relationships"][target_id][n]
if (len(to_remove) == n_relationships):
del self._properties["_relationships"][target_id]
self._properties["_relationship_with"].remove(target_id)
self._committed = False
