###########################################################################
# 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 #
###########################################################################
"""Module to manage nodes for the SQLA backend."""
from sqlalchemy.dialects.postgresql import JSONB, UUID
from sqlalchemy.orm import backref, relationship
from sqlalchemy.schema import Column
from sqlalchemy.sql.schema import ForeignKey, Index
from sqlalchemy.types import DateTime, Integer, String, Text
from aiida.common import timezone
from aiida.common.utils import get_new_uuid
from aiida.storage.psql_dos.models.base import Base
[docs]
class DbNode(Base):
"""Database model to store data for :py:class:`aiida.orm.Node`.
Each node can be categorized according to its ``node_type``,
which indicates what kind of data or process node it is.
Additionally, process nodes also have a ``process_type`` that further indicates what is the specific plugin it uses.
Nodes can also store two kind of properties:
- ``attributes`` are determined by the ``node_type``,
and are set before storing the node and can't be modified afterwards.
- ``extras``, on the other hand,
can be added and removed after the node has been stored and are usually set by the user.
"""
__tablename__ = 'db_dbnode'
id = Column(Integer, primary_key=True)
uuid = Column(UUID(as_uuid=True), default=get_new_uuid, nullable=False, unique=True)
node_type = Column(String(255), default='', nullable=False, index=True)
process_type = Column(String(255), index=True)
label = Column(String(255), nullable=False, default='', index=True)
description = Column(Text(), nullable=False, default='')
ctime = Column(DateTime(timezone=True), default=timezone.now, nullable=False, index=True)
mtime = Column(DateTime(timezone=True), default=timezone.now, onupdate=timezone.now, nullable=False, index=True)
attributes = Column(JSONB, default=dict)
extras = Column(JSONB, default=dict)
repository_metadata = Column(JSONB, nullable=False, default=dict)
dbcomputer_id = Column(
Integer,
ForeignKey('db_dbcomputer.id', deferrable=True, initially='DEFERRED', ondelete='RESTRICT'),
nullable=True,
index=True,
)
user_id = Column(
Integer,
ForeignKey('db_dbuser.id', deferrable=True, initially='DEFERRED', ondelete='RESTRICT'),
nullable=False,
index=True,
)
# TODO SP: The 'passive_deletes=all' argument here means that SQLAlchemy
# won't take care of automatic deleting in the DbLink table. This still
# isn't exactly the same behaviour than with Django. The solution to
# this is probably a ON DELETE inside the DB. On removing node with id=x,
# we would remove all link with x as an output.
dbcomputer = relationship('DbComputer', backref=backref('dbnodes', passive_deletes='all', cascade='merge'))
user = relationship(
'DbUser',
backref=backref(
'dbnodes',
passive_deletes='all',
cascade='merge',
),
)
# outputs via db_dblink table
outputs_q = relationship(
'DbNode',
secondary='db_dblink',
primaryjoin='DbNode.id == DbLink.input_id',
secondaryjoin='DbNode.id == DbLink.output_id',
backref=backref('inputs_q', passive_deletes=True, lazy='dynamic'),
lazy='dynamic',
passive_deletes=True,
)
__table_args__ = (
Index(
'ix_pat_db_dbnode_label', label, postgresql_using='btree', postgresql_ops={'label': 'varchar_pattern_ops'}
),
Index(
'ix_pat_db_dbnode_node_type',
node_type,
postgresql_using='btree',
postgresql_ops={'node_type': 'varchar_pattern_ops'},
),
Index(
'ix_pat_db_dbnode_process_type',
process_type,
postgresql_using='btree',
postgresql_ops={'process_type': 'varchar_pattern_ops'},
),
)
@property
def outputs(self):
return self.outputs_q.all()
@property
def inputs(self):
return self.inputs_q.all()
[docs]
def get_simple_name(self, invalid_result=None):
"""Return a string with the last part of the type name.
If the type is empty, use 'Node'.
If the type is invalid, return the content of the input variable
``invalid_result``.
:param invalid_result: The value to be returned if the node type is
not recognized.
"""
thistype = self.node_type
# Fix for base class
if thistype == '':
thistype = 'node.Node.'
if not thistype.endswith('.'):
return invalid_result
thistype = thistype[:-1] # Strip final dot
return thistype.rpartition('.')[2]
@property
def pk(self):
return self.id
[docs]
def __str__(self):
"""Get string object out of DbNode object."""
simplename = self.get_simple_name(invalid_result='Unknown')
# node pk + type
if self.label:
return f'{simplename} node [{self.pk}]: {self.label}'
return f'{simplename} node [{self.pk}]'
[docs]
class DbLink(Base):
"""Database model to store links between :py:class:`aiida.orm.Node`.
Each entry in this table contains not only the ``id`` information of the two nodes that are linked,
but also some extra properties of the link themselves.
This includes the ``type`` of the link (see the :ref:`topics:provenance:concepts` section for all possible types)
as well as a ``label`` which is more specific and typically determined by
the procedure generating the process node that links the data nodes.
"""
__tablename__ = 'db_dblink'
id = Column(Integer, primary_key=True)
input_id = Column(
Integer, ForeignKey('db_dbnode.id', deferrable=True, initially='DEFERRED'), nullable=False, index=True
)
output_id = Column(
Integer,
ForeignKey('db_dbnode.id', ondelete='CASCADE', deferrable=True, initially='DEFERRED'),
nullable=False,
index=True,
)
# https://docs.sqlalchemy.org/en/14/errors.html#relationship-x-will-copy-column-q-to-column-p-which-conflicts-with-relationship-s-y
input = relationship('DbNode', primaryjoin='DbLink.input_id == DbNode.id', overlaps='inputs_q,outputs_q')
output = relationship('DbNode', primaryjoin='DbLink.output_id == DbNode.id', overlaps='inputs_q,outputs_q')
label = Column(String(255), nullable=False, index=True)
type = Column(String(255), nullable=False, index=True)
# A calculation can have both a 'return' and a 'create' link to
# a single data output node, which would violate the unique constraint
# defined below, since the difference in link type is not considered.
# The distinction between the type of a 'create' and a 'return' link is not
# implemented at the moment, so the unique constraint is disabled.
__table_args__ = (
# I cannot add twice the same link
# I want unique labels among all inputs of a node
# UniqueConstraint('output_id', 'label'),
Index(
'ix_pat_db_dblink_label', label, postgresql_using='btree', postgresql_ops={'label': 'varchar_pattern_ops'}
),
Index('ix_pat_db_dblink_type', type, postgresql_using='btree', postgresql_ops={'type': 'varchar_pattern_ops'}),
)
[docs]
def __str__(self):
return '{} ({}) --> {} ({})'.format(
self.input.get_simple_name(invalid_result='Unknown node'),
self.input.pk,
self.output.get_simple_name(invalid_result='Unknown node'),
self.output.pk,
)
