# -*- coding: utf-8 -*-
###########################################################################
# Copyright (c), The AiiDA team. All rights reserved. #
# This file is part of the AiiDA code. #
# #
# The code is hosted on GitHub at https://github.com/aiidateam/aiida_core #
# For further information on the license, see the LICENSE.txt file #
# For further information please visit http://www.aiida.net #
###########################################################################
import copy
from django.core.exceptions import ObjectDoesNotExist
from django.db import IntegrityError, transaction
from django.db.models import F
from aiida.backends.djsite.db.models import DbLink
from aiida.backends.djsite.utils import get_automatic_user
from aiida.common.exceptions import (InternalError, ModificationNotAllowed,
NotExistent, UniquenessError)
from aiida.common.folders import RepositoryFolder
from aiida.common.links import LinkType
from aiida.common.utils import get_new_uuid
from aiida.orm.implementation.general.node import AbstractNode, _NO_DEFAULT, _HASH_EXTRA_KEY
from aiida.orm.implementation.django.computer import Computer
from aiida.orm.mixins import Sealable
# from aiida.orm.implementation.django.utils import get_db_columns
from aiida.orm.implementation.general.utils import get_db_columns
[docs]class Node(AbstractNode):
[docs] @classmethod
def get_subclass_from_uuid(cls, uuid):
from aiida.backends.djsite.db.models import DbNode
try:
node = DbNode.objects.get(uuid=uuid).get_aiida_class()
except ObjectDoesNotExist:
raise NotExistent("No entry with UUID={} found".format(uuid))
if not isinstance(node, cls):
raise NotExistent("UUID={} is not an instance of {}".format(
uuid, cls.__name__))
return node
[docs] @classmethod
def get_subclass_from_pk(cls, pk):
from aiida.backends.djsite.db.models import DbNode
try:
node = DbNode.objects.get(pk=pk).get_aiida_class()
except ObjectDoesNotExist:
raise NotExistent("No entry with pk= {} found".format(pk))
if not isinstance(node, cls):
raise NotExistent("pk= {} is not an instance of {}".format(
pk, cls.__name__))
return node
[docs] @classmethod
def query(cls, *args, **kwargs):
from aiida.backends.djsite.db.models import DbNode
if cls._plugin_type_string:
if not cls._plugin_type_string.endswith('.'):
raise InternalError("The plugin type string does not "
"finish with a dot??")
# If it is 'calculation.Calculation.', we want to filter
# for things that start with 'calculation.' and so on
plug_type = cls._plugin_type_string
# Remove the implementation.django or sqla part.
if plug_type.startswith('implementation.'):
plug_type = '.'.join(plug_type.split('.')[2:])
pre, sep, _ = plug_type[:-1].rpartition('.')
superclass_string = "".join([pre, sep])
return DbNode.aiidaobjects.filter(
*args, type__startswith=superclass_string, **kwargs)
else:
# Base Node class, with empty string
return DbNode.aiidaobjects.filter(*args, **kwargs)
[docs] def __init__(self, **kwargs):
from aiida.backends.djsite.db.models import DbNode
super(Node, self).__init__()
self._temp_folder = None
dbnode = kwargs.pop('dbnode', None)
# Set the internal parameters
# Can be redefined in the subclasses
self._init_internal_params()
if dbnode is not None:
if not isinstance(dbnode, DbNode):
raise TypeError("dbnode is not a DbNode instance")
if dbnode.pk is None:
raise ValueError("If cannot load an aiida.orm.Node instance "
"from an unsaved Django DbNode object.")
if kwargs:
raise ValueError("If you pass a dbnode, you cannot pass any "
"further parameter")
# If I am loading, I cannot modify it
self._to_be_stored = False
self._dbnode = dbnode
# If this is changed, fix also the importer
self._repo_folder = RepositoryFolder(section=self._section_name,
uuid=self.uuid)
# NO VALIDATION ON __init__ BY DEFAULT, IT IS TOO SLOW SINCE IT OFTEN
# REQUIRES MULTIPLE DB HITS
# try:
# # Note: the validation often requires to load at least one
# # attribute, and therefore it will take a lot of time
# # because it has to cache every attribute.
# self._validate()
# except ValidationError as e:
# raise DbContentError("The data in the DB with UUID={} is not "
# "valid for class {}: {}".format(
# uuid, self.__class__.__name__, e.message))
else:
# TODO: allow to get the user from the parameters
user = get_automatic_user()
self._dbnode = DbNode(user=user,
uuid=get_new_uuid(),
type=self._plugin_type_string)
self._to_be_stored = True
# As creating the temp folder may require some time on slow
# filesystems, we defer its creation
self._temp_folder = None
# Used only before the first save
self._attrs_cache = {}
# If this is changed, fix also the importer
self._repo_folder = RepositoryFolder(section=self._section_name,
uuid=self.uuid)
# Automatically set all *other* attributes, if possible, otherwise
# stop
self._set_with_defaults(**kwargs)
@property
def type(self):
return self._dbnode.type
@property
def ctime(self):
return self._dbnode.ctime
@property
def mtime(self):
return self._dbnode.mtime
[docs] def _get_db_label_field(self):
return self._dbnode.label
[docs] def _update_db_label_field(self, field_value):
self._dbnode.label = field_value
if not self._to_be_stored:
with transaction.atomic():
self._dbnode.save()
self._increment_version_number_db()
[docs] def _get_db_description_field(self):
return self._dbnode.description
[docs] def _update_db_description_field(self, field_value):
self._dbnode.description = field_value
if not self._to_be_stored:
with transaction.atomic():
self._dbnode.save()
self._increment_version_number_db()
[docs] def _replace_dblink_from(self, src, label, link_type):
try:
self._add_dblink_from(src, label, link_type)
except UniquenessError:
# I have to replace the link; I do it within a transaction
with transaction.atomic():
self._remove_dblink_from(label)
self._add_dblink_from(src, label, link_type)
[docs] def _remove_dblink_from(self, label):
DbLink.objects.filter(output=self._dbnode, label=label).delete()
[docs] def _add_dblink_from(self, src, label=None, link_type=LinkType.UNSPECIFIED):
from aiida.orm.querybuilder import QueryBuilder
if not isinstance(src, Node):
raise ValueError("src must be a Node instance")
if self.uuid == src.uuid:
raise ValueError("Cannot link to itself")
if self._to_be_stored:
raise ModificationNotAllowed(
"Cannot call the internal _add_dblink_from if the "
"destination node is not stored")
if src._to_be_stored:
raise ModificationNotAllowed(
"Cannot call the internal _add_dblink_from if the "
"source node is not stored")
if link_type is LinkType.CREATE or link_type is LinkType.INPUT:
# Check for cycles. This works if the transitive closure is enabled; if it
# isn't, this test will never fail, but then having a circular link is not
# meaningful but does not pose a huge threat
#
# I am linking src->self; a loop would be created if a DbPath exists already
# in the TC table from self to src
if QueryBuilder().append(
Node, filters={'id': self.pk}, tag='parent').append(
Node, filters={'id': src.pk}, tag='child', descendant_of='parent').count() > 0:
raise ValueError(
"The link you are attempting to create would generate a loop")
if label is None:
autolabel_idx = 1
existing_from_autolabels = list(DbLink.objects.filter(
output=self._dbnode,
label__startswith="link_").values_list('label', flat=True))
while "link_{}".format(autolabel_idx) in existing_from_autolabels:
autolabel_idx += 1
safety_counter = 0
while True:
safety_counter += 1
if safety_counter > 100:
# Well, if you have more than 100 concurrent addings
# to the same node, you are clearly doing something wrong...
raise InternalError("Hey! We found more than 100 concurrent"
" adds of links "
"to the same nodes! Are you really doing that??")
try:
self._do_create_link(src, "link_{}".format(autolabel_idx), link_type)
break
except UniquenessError:
# Retry loop until you find a new loop
autolabel_idx += 1
else:
self._do_create_link(src, label, link_type)
[docs] def _do_create_link(self, src, label, link_type):
sid = None
try:
# transactions are needed here for Postgresql:
# https://docs.djangoproject.com/en/1.5/topics/db/transactions/#handling-exceptions-within-postgresql-transactions
sid = transaction.savepoint()
DbLink.objects.create(input=src._dbnode, output=self._dbnode,
label=label, type=link_type.value)
transaction.savepoint_commit(sid)
except IntegrityError as e:
transaction.savepoint_rollback(sid)
raise UniquenessError("There is already a link with the same "
"name (raw message was {})"
"".format(e.message))
[docs] def _get_db_output_links(self, link_type):
from aiida.backends.djsite.db.models import DbLink
link_filter = {'input': self._dbnode}
if link_type is not None:
link_filter['type'] = link_type.value
return ((i.label, i.output.get_aiida_class()) for i in
DbLink.objects.filter(**link_filter).distinct())
[docs] def get_computer(self):
"""
Get the computer associated to the node.
:return: the Computer object or None.
"""
if self._dbnode.dbcomputer is None:
return None
else:
return Computer(dbcomputer=self._dbnode.dbcomputer)
[docs] def _set_db_computer(self, computer):
from aiida.backends.djsite.db.models import DbComputer
self._dbnode.dbcomputer = DbComputer.get_dbcomputer(computer)
[docs] def _set_db_attr(self, key, value):
"""
Set the value directly in the DB, without checking if it is stored, or
using the cache.
DO NOT USE DIRECTLY.
:param str key: key name
:param value: its value
"""
from aiida.backends.djsite.db.models import DbAttribute
DbAttribute.set_value_for_node(self._dbnode, key, value)
self._increment_version_number_db()
[docs] def _del_db_attr(self, key):
from aiida.backends.djsite.db.models import DbAttribute
if not DbAttribute.has_key(self._dbnode, key):
raise AttributeError("DbAttribute {} does not exist".format(
key))
DbAttribute.del_value_for_node(self._dbnode, key)
self._increment_version_number_db()
[docs] def _get_db_attr(self, key):
from aiida.backends.djsite.db.models import DbAttribute
return DbAttribute.get_value_for_node(
dbnode=self._dbnode, key=key)
[docs] def _db_iterattrs(self):
from aiida.backends.djsite.db.models import DbAttribute
all_attrs = DbAttribute.get_all_values_for_node(self._dbnode)
for attr in all_attrs:
yield (attr, all_attrs[attr])
[docs] def _db_attrs(self):
# Note: I "duplicate" the code from iterattrs and reimplement it
# here, rather than
# calling iterattrs from here, because iterattrs is slow on each call
# since it has to call .getvalue(). To improve!
from aiida.backends.djsite.db.models import DbAttribute
attrlist = DbAttribute.list_all_node_elements(self._dbnode)
for attr in attrlist:
yield attr.key
[docs] def _increment_version_number_db(self):
from aiida.backends.djsite.db.models import DbNode
# I increment the node number using a filter
self._dbnode.nodeversion = F('nodeversion') + 1
self._dbnode.save()
# This reload internally the node of self._dbnode
# Note: I have to reload the object (to have the right values in memory,
# otherwise I only get the Django Field F object as a result!
self._dbnode = DbNode.objects.get(pk=self._dbnode.pk)
[docs] def copy(self, **kwargs):
newobject = self.__class__()
newobject._dbnode.type = self._dbnode.type # Inherit type
newobject.label = self.label # Inherit label
# TODO: add to the description the fact that this was a copy?
newobject.description = self.description # Inherit description
newobject._dbnode.dbcomputer = self._dbnode.dbcomputer # Inherit computer
for k, v in self.iterattrs():
if k != Sealable.SEALED_KEY:
newobject._set_attr(k, v)
for path in self.get_folder_list():
newobject.add_path(self.get_abs_path(path), path)
return newobject
@property
def uuid(self):
return unicode(self._dbnode.uuid)
@property
def id(self):
return self._dbnode.id
@property
def dbnode(self):
# I also update the internal _dbnode variable, if it was saved
# from aiida.backends.djsite.db.models import DbNode
# if not self._to_be_stored:
# self._dbnode = DbNode.objects.get(pk=self._dbnode.pk)
return self._dbnode
[docs] def _db_store_all(self, with_transaction=True, use_cache=None):
"""
Store the node, together with all input links, if cached, and also the
linked nodes, if they were not stored yet.
:parameter with_transaction: if False, no transaction is used. This
is meant to be used ONLY if the outer calling function has already
a transaction open!
"""
from django.db import transaction
from aiida.common.utils import EmptyContextManager
if with_transaction:
context_man = transaction.atomic()
else:
context_man = EmptyContextManager()
with context_man:
# Always without transaction: either it is the context_man here,
# or it is managed outside
self._store_input_nodes()
self.store(with_transaction=False, use_cache=use_cache)
self._store_cached_input_links(with_transaction=False)
return self
[docs] def get_user(self):
return self._dbnode.user
[docs] def _db_store(self, with_transaction=True):
"""
Store a new node in the DB, also saving its repository directory
and attributes.
After being called attributes cannot be
changed anymore! Instead, extras can be changed only AFTER calling
this store() function.
:note: After successful storage, those links that are in the cache, and
for which also the parent node is already stored, will be
automatically stored. The others will remain unstored.
:parameter with_transaction: if False, no transaction is used. This
is meant to be used ONLY if the outer calling function has already
a transaction open!
:param bool use_cache: Whether I attempt to find an equal node in the DB.
"""
# TODO: This needs to be generalized, allowing for flexible methods
# for storing data and its attributes.
from django.db import transaction
from aiida.common.utils import EmptyContextManager
from aiida.common.exceptions import ValidationError
from aiida.backends.djsite.db.models import DbAttribute
import aiida.orm.autogroup
if with_transaction:
context_man = transaction.atomic()
else:
context_man = EmptyContextManager()
# I save the corresponding django entry
# I set the folder
# NOTE: I first store the files, then only if this is successful,
# I store the DB entry. In this way,
# I assume that if a node exists in the DB, its folder is in place.
# On the other hand, periodically the user might need to run some
# bookkeeping utility to check for lone folders.
self._repository_folder.replace_with_folder(
self._get_temp_folder().abspath, move=True, overwrite=True)
# I do the transaction only during storage on DB to avoid timeout
# problems, especially with SQLite
try:
with context_man:
# Save the row
self._dbnode.save()
# Save its attributes 'manually' without incrementing
# the version for each add.
DbAttribute.reset_values_for_node(self._dbnode,
attributes=self._attrs_cache,
with_transaction=False)
# This should not be used anymore: I delete it to
# possibly free memory
del self._attrs_cache
self._temp_folder = None
self._to_be_stored = False
# Here, I store those links that were in the cache and
# that are between stored nodes.
self._store_cached_input_links()
# This is one of the few cases where it is ok to do a 'global'
# except, also because I am re-raising the exception
except:
# I put back the files in the sandbox folder since the
# transaction did not succeed
self._get_temp_folder().replace_with_folder(
self._repository_folder.abspath, move=True, overwrite=True)
raise
from aiida.backends.djsite.db.models import DbExtra
# I store the hash without cleaning and without incrementing the nodeversion number
DbExtra.set_value_for_node(self._dbnode, _HASH_EXTRA_KEY, self.get_hash())
return self