def copy_database (target_db, admin_user = None, admin_password = None, force = False):
""" Copy the current database to a new database name (see http://www.mongodb.org/display/DOCS/Clone+Database)
"""
with connection.protect():
# save the current connection
db_connection = connection.connection()
db_connection_ = connection.connection_information()
source_db = db_connection_["db"]
if (source_db == target_db):
logger.debug("Ignored request to copy '%s' into itself." % target_db)
return
# open a connection to the admin collection
admin_connection = connection.connect(db = "admin", user = admin_user, password = admin_password)
if (target_db in admin_connection.connection.database_names()):
if (force):
logger.debug("'%s' already exists and will be merged with content of '%s'." % (source_db, target_db))
else:
raise errors.DBOperationError("Unable to copy database '%s' to '%s': target already exists." % (source_db, target_db))
# copy the database
try:
admin_connection.connection.copy_database(source_db, target_db)
# restore the current connection
finally:
connection._connection = db_connection
connection._connection_information = db_connection_
logger.debug("Copy of '%s' into '%s' successful." % (source_db, target_db))
def drop_collection(collection):
""" Drop a collection
"""
with connection.protect():
connection.connection().drop_collection(collection)
logger.debug("Collection '%s' was dropped." % collection)
def remove (self):
""" Remove this object from the database.
.. note::
- Relationships from and to this object are removed as well.
- The object remains in memory, flagged as uncommitted.
.. seealso::
:meth:`~PersistentObject.remove_all`
"""
# remove all relationships with other objects
for collection_name in methods.list_collections():
if ("_id" in self._properties):
for object in self._in_vertices(collection_name):
object._disconnect_from(self, None)
for object in self._out_vertices(collection_name):
self._disconnect_from(object, None)
# if the object has been committed at least once,
if ("_id" in self._properties):
# remove the object from the database
with connection.protect():
methods.remove_object(self)
# and declare it has never having been committed
del self._properties["_id"]
self._committed = False
def drop_collection (collection):
""" Drop a collection
"""
with connection.protect():
connection.connection().drop_collection(collection)
logger.debug("Collection '%s' was dropped." % collection)
def remove(self):
""" Remove this object from the database.
.. note::
- Relationships from and to this object are removed as well.
- The object remains in memory, flagged as uncommitted.
.. seealso::
:meth:`~PersistentObject.remove_all`
"""
# remove all relationships with other objects
for collection_name in methods.list_collections():
if ("_id" in self._properties):
for object in self._in_vertices(collection_name):
object._disconnect_from(self, None)
for object in self._out_vertices(collection_name):
self._disconnect_from(object, None)
# if the object has been committed at least once,
if ("_id" in self._properties):
# remove the object from the database
with connection.protect():
methods.remove_object(self)
# and declare it has never having been committed
del self._properties["_id"]
self._committed = False
def commit(self):
""" Commit this object to the database.
.. note::
- The commit will not be performed if the object has already been
committed once and no modification (property manipulation) has
been performed since then.
- If an object already exists in the database with the same values
for properties flagged as unique a :class:`MetagenomeDB.errors.DuplicateObjectError`
exception is thrown.
.. seealso::
:meth:`~PersistentObject.is_committed`
"""
if (self._committed):
return
"""
# pre-flight: if some patch needs to be applied on the object's
# properties, we temporary store the old values
tmp = {}
for (key, value) in patch.iteritems():
assert (key != "_id") ###
tmp[key] = self._properties[key]
self._properties[key] = value
"""
with connection.protect():
methods._commit(self)
"""
# post-flight: we restore the object's properties, if needed
for (key, value) in tmp.iteritems():
self._properties[key] = value
"""
self._committed = True
def remove_object (object):
""" Remove an object from a collection
"""
collection_name = object.__class__.__name__
with connection.protect():
connection.connection()[collection_name].remove({"_id": object["_id"]})
del _cache[object["_id"]]
logger.debug("Object %s was removed from collection '%s'." % (object, collection_name))
def remove_object(object):
""" Remove an object from a collection
"""
collection_name = object.__class__.__name__
with connection.protect():
connection.connection()[collection_name].remove({"_id": object["_id"]})
del _cache[object["_id"]]
logger.debug("Object %s was removed from collection '%s'." %
(object, collection_name))
def list_collections (with_classes = False): """ Return a list of all existing collections in the database that can be mapped to an instance of a PersistentObject class or subclass. """ # list all collections in the database with connection.protect(): collection_names = connection.connection().collection_names() # return collections represented by PersistentObject subclasses collections = [] for collection_name in collection_names: if (collection_name in _classes): if (with_classes): collections.append((collection_name, _classes[collection_name])) else: collections.append(collection_name) return collections
def list_collections(with_classes=False):
""" Return a list of all existing collections in the database that can be
mapped to an instance of a PersistentObject class or subclass.
"""
# list all collections in the database
with connection.protect():
collection_names = connection.connection().collection_names()
# return collections represented by PersistentObject subclasses
collections = []
for collection_name in collection_names:
if (collection_name in _classes):
if (with_classes):
collections.append(
(collection_name, _classes[collection_name]))
else:
collections.append(collection_name)
return collections
def copy_database(target_db,
admin_user=None,
admin_password=None,
force=False):
""" Copy the current database to a new database name (see http://www.mongodb.org/display/DOCS/Clone+Database)
"""
with connection.protect():
# save the current connection
db_connection = connection.connection()
db_connection_ = connection.connection_information()
source_db = db_connection_["db"]
if (source_db == target_db):
logger.debug("Ignored request to copy '%s' into itself." %
target_db)
return
# open a connection to the admin collection
admin_connection = connection.connect(db="admin",
user=admin_user,
password=admin_password)
if (target_db in admin_connection.connection.database_names()):
if (force):
logger.debug(
"'%s' already exists and will be merged with content of '%s'."
% (source_db, target_db))
else:
raise errors.DBOperationError(
"Unable to copy database '%s' to '%s': target already exists."
% (source_db, target_db))
# copy the database
try:
admin_connection.connection.copy_database(source_db, target_db)
# restore the current connection
finally:
connection._connection = db_connection
connection._connection_information = db_connection_
logger.debug("Copy of '%s' into '%s' successful." % (source_db, target_db))
def commit (self):
""" Commit this object to the database.
.. note::
- The commit will not be performed if the object has already been
committed once and no modification (property manipulation) has
been performed since then.
- If an object already exists in the database with the same values
for properties flagged as unique a :class:`MetagenomeDB.errors.DuplicateObjectError`
exception is thrown.
.. seealso::
:meth:`~PersistentObject.is_committed`
"""
if (self._committed):
return
"""
# pre-flight: if some patch needs to be applied on the object's
# properties, we temporary store the old values
tmp = {}
for (key, value) in patch.iteritems():
assert (key != "_id") ###
tmp[key] = self._properties[key]
self._properties[key] = value
"""
with connection.protect():
methods._commit(self)
"""
# post-flight: we restore the object's properties, if needed
for (key, value) in tmp.iteritems():
self._properties[key] = value
"""
self._committed = True
