# -*- 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 #
###########################################################################
"""Sqla query builder implementation"""
from __future__ import division
from __future__ import print_function
from __future__ import absolute_import
from datetime import datetime
import uuid
import six
# pylint: disable=no-name-in-module, import-error
from sqlalchemy_utils.types.choice import Choice
from sqlalchemy import and_, or_, not_
from sqlalchemy.types import Integer, Float, Boolean, DateTime
from sqlalchemy.dialects.postgresql import JSONB
from sqlalchemy.sql.expression import case, FunctionElement
from sqlalchemy.ext.compiler import compiles
import aiida.backends.sqlalchemy
from aiida.common.exceptions import InputValidationError
from aiida.orm.implementation.querybuilder import BackendQueryBuilder
[docs]class jsonb_array_length(FunctionElement): # pylint: disable=invalid-name
# pylint: disable=too-few-public-methods
name = 'jsonb_array_len'
@compiles(jsonb_array_length)
def compile(element, compiler, **_kw): # pylint: disable=function-redefined, redefined-builtin
"""
Get length of array defined in a JSONB column
"""
return "jsonb_array_length(%s)" % compiler.process(element.clauses)
[docs]class array_length(FunctionElement): # pylint: disable=invalid-name
# pylint: disable=too-few-public-methods
name = 'array_len'
@compiles(array_length)
def compile(element, compiler, **_kw): # pylint: disable=function-redefined
"""
Get length of array defined in a JSONB column
"""
return "array_length(%s)" % compiler.process(element.clauses)
[docs]class jsonb_typeof(FunctionElement): # pylint: disable=invalid-name
# pylint: disable=too-few-public-methods
name = 'jsonb_typeof'
[docs]@compiles(jsonb_typeof)
def compile(element, compiler, **_kw): # pylint: disable=function-redefined
"""
Get length of array defined in a JSONB column
"""
return "jsonb_typeof(%s)" % compiler.process(element.clauses)
[docs]class SqlaQueryBuilder(BackendQueryBuilder):
"""
QueryBuilder to use with SQLAlchemy-backend and
schema defined in backends.sqlalchemy.models
"""
# pylint: disable=redefined-outer-name, too-many-public-methods
@property
def Node(self):
import aiida.backends.sqlalchemy.models.node
return aiida.backends.sqlalchemy.models.node.DbNode
@property
def Link(self):
import aiida.backends.sqlalchemy.models.node
return aiida.backends.sqlalchemy.models.node.DbLink
@property
def Computer(self):
import aiida.backends.sqlalchemy.models.computer
return aiida.backends.sqlalchemy.models.computer.DbComputer
@property
def User(self):
import aiida.backends.sqlalchemy.models.user
return aiida.backends.sqlalchemy.models.user.DbUser
@property
def Group(self):
import aiida.backends.sqlalchemy.models.group
return aiida.backends.sqlalchemy.models.group.DbGroup
@property
def AuthInfo(self):
import aiida.backends.sqlalchemy.models.authinfo
return aiida.backends.sqlalchemy.models.authinfo.DbAuthInfo
@property
def Comment(self):
import aiida.backends.sqlalchemy.models.comment
return aiida.backends.sqlalchemy.models.comment.DbComment
@property
def Log(self):
import aiida.backends.sqlalchemy.models.log
return aiida.backends.sqlalchemy.models.log.DbLog
@property
def table_groups_nodes(self):
import aiida.backends.sqlalchemy.models.group
return aiida.backends.sqlalchemy.models.group.table_groups_nodes
[docs] def get_session(self):
return aiida.backends.sqlalchemy.get_scoped_session()
[docs] def modify_expansions(self, alias, expansions):
"""
For sqlalchemy, there are no additional expansions for now, so
I am returning an empty list
"""
# pylint: disable=protected-access
if issubclass(alias._sa_class_manager.class_, self.Computer) or \
issubclass(alias._sa_class_manager.class_, self.Log):
try:
expansions.remove('metadata')
expansions.append('_metadata')
except KeyError:
pass
return expansions
[docs] def get_filter_expr(self, operator, value, attr_key, is_attribute, alias=None, column=None, column_name=None):
"""
Applies a filter on the alias given.
Expects the alias of the ORM-class on which to filter, and filter_spec.
Filter_spec contains the specification on the filter.
Expects:
:param operator: The operator to apply, see below for further details
:param value:
The value for the right side of the expression,
the value you want to compare with.
:param path: The path leading to the value
:param attr_key: Boolean, whether the value is in a json-column,
or in an attribute like table.
Implemented and valid operators:
* for any type:
* == (compare single value, eg: '==':5.0)
* in (compare whether in list, eg: 'in':[5, 6, 34]
* for floats and integers:
* >
* <
* <=
* >=
* for strings:
* like (case - sensitive), for example
'like':'node.calc.%' will match node.calc.relax and
node.calc.RELAX and node.calc. but
not node.CALC.relax
* ilike (case - unsensitive)
will also match node.CaLc.relax in the above example
.. note::
The character % is a reserved special character in SQL,
and acts as a wildcard. If you specifically
want to capture a ``%`` in the string, use: ``_%``
* for arrays and dictionaries (only for the
SQLAlchemy implementation):
* contains: pass a list with all the items that
the array should contain, or that should be among
the keys, eg: 'contains': ['N', 'H'])
* has_key: pass an element that the list has to contain
or that has to be a key, eg: 'has_key':'N')
* for arrays only (SQLAlchemy version):
* of_length
* longer
* shorter
All the above filters invoke a negation of the
expression if preceded by **~**::
# first example:
filter_spec = {
'name' : {
'~in':[
'halle',
'lujah'
]
} # Name not 'halle' or 'lujah'
}
# second example:
filter_spec = {
'id' : {
'~==': 2
}
} # id is not 2
"""
# pylint: disable=too-many-arguments, too-many-branches
expr = None
if operator.startswith('~'):
negation = True
operator = operator.lstrip('~')
elif operator.startswith('!'):
negation = True
operator = operator.lstrip('!')
else:
negation = False
if operator in ('longer', 'shorter', 'of_length'):
if not isinstance(value, int):
raise InputValidationError("You have to give an integer when comparing to a length")
elif operator in ('like', 'ilike'):
if not isinstance(value, six.string_types):
raise InputValidationError("Value for operator {} has to be a string (you gave {})"
"".format(operator, value))
elif operator == 'in':
value_type_set = set(type(i) for i in value)
if len(value_type_set) > 1:
raise InputValidationError('{} contains more than one type'.format(value))
elif not value_type_set:
raise InputValidationError('{} contains is an empty list'.format(value))
elif operator in ('and', 'or'):
expressions_for_this_path = []
for filter_operation_dict in value:
for newoperator, newvalue in filter_operation_dict.items():
expressions_for_this_path.append(
self.get_filter_expr(
newoperator,
newvalue,
attr_key=attr_key,
is_attribute=is_attribute,
alias=alias,
column=column,
column_name=column_name))
if operator == 'and':
expr = and_(*expressions_for_this_path)
elif operator == 'or':
expr = or_(*expressions_for_this_path)
if expr is None:
if is_attribute:
expr = self.get_filter_expr_from_attributes(
operator, value, attr_key, column=column, column_name=column_name, alias=alias)
else:
if column is None:
if (alias is None) and (column_name is None):
raise RuntimeError("I need to get the column but do not know the alias and the column name")
column = self.get_column(column_name, alias)
expr = self.get_filter_expr_from_column(operator, value, column)
if negation:
return not_(expr)
return expr
[docs] def get_filter_expr_from_attributes(self, operator, value, attr_key, column=None, column_name=None, alias=None):
# Too many everything!
# pylint: disable=too-many-branches, too-many-arguments, too-many-statements
def cast_according_to_type(path_in_json, value):
"""Cast the value according to the type"""
if isinstance(value, bool):
type_filter = jsonb_typeof(path_in_json) == 'boolean'
casted_entity = path_in_json.astext.cast(Boolean)
elif isinstance(value, (int, float)):
type_filter = jsonb_typeof(path_in_json) == 'number'
casted_entity = path_in_json.astext.cast(Float)
elif isinstance(value, dict) or value is None:
type_filter = jsonb_typeof(path_in_json) == 'object'
casted_entity = path_in_json.astext.cast(JSONB) # BOOLEANS?
elif isinstance(value, dict):
type_filter = jsonb_typeof(path_in_json) == 'array'
casted_entity = path_in_json.astext.cast(JSONB) # BOOLEANS?
elif isinstance(value, six.string_types):
type_filter = jsonb_typeof(path_in_json) == 'string'
casted_entity = path_in_json.astext
elif value is None:
type_filter = jsonb_typeof(path_in_json) == 'null'
casted_entity = path_in_json.astext.cast(JSONB) # BOOLEANS?
elif isinstance(value, datetime):
# type filter here is filter whether this attributes stores
# a string and a filter whether this string
# is compatible with a datetime (using a regex)
# - What about historical values (BC, or before 1000AD)??
# - Different ways to represent the timezone
type_filter = jsonb_typeof(path_in_json) == 'string'
regex_filter = path_in_json.astext.op("SIMILAR TO")(
"\d\d\d\d-[0-1]\d-[0-3]\dT[0-2]\d:[0-5]\d:\d\d\.\d+((\+|\-)\d\d:\d\d)?") # pylint: disable=anomalous-backslash-in-string
type_filter = and_(type_filter, regex_filter)
casted_entity = path_in_json.cast(DateTime)
else:
raise TypeError('Unknown type {}'.format(type(value)))
return type_filter, casted_entity
if column is None:
column = self.get_column(column_name, alias)
database_entity = column[tuple(attr_key)]
if operator == '==':
type_filter, casted_entity = cast_according_to_type(database_entity, value)
expr = case([(type_filter, casted_entity == value)], else_=False)
elif operator == '>':
type_filter, casted_entity = cast_according_to_type(database_entity, value)
expr = case([(type_filter, casted_entity > value)], else_=False)
elif operator == '<':
type_filter, casted_entity = cast_according_to_type(database_entity, value)
expr = case([(type_filter, casted_entity < value)], else_=False)
elif operator in ('>=', '=>'):
type_filter, casted_entity = cast_according_to_type(database_entity, value)
expr = case([(type_filter, casted_entity >= value)], else_=False)
elif operator in ('<=', '=<'):
type_filter, casted_entity = cast_according_to_type(database_entity, value)
expr = case([(type_filter, casted_entity <= value)], else_=False)
elif operator == 'of_type':
# http://www.postgresql.org/docs/9.5/static/functions-json.html
# Possible types are object, array, string, number, boolean, and null.
valid_types = ('object', 'array', 'string', 'number', 'boolean', 'null')
if value not in valid_types:
raise InputValidationError("value {} for of_type is not among valid types\n"
"{}".format(value, valid_types))
expr = jsonb_typeof(database_entity) == value
elif operator == 'like':
type_filter, casted_entity = cast_according_to_type(database_entity, value)
expr = case([(type_filter, casted_entity.like(value))], else_=False)
elif operator == 'ilike':
type_filter, casted_entity = cast_according_to_type(database_entity, value)
expr = case([(type_filter, casted_entity.ilike(value))], else_=False)
elif operator == 'in':
type_filter, casted_entity = cast_according_to_type(database_entity, value[0])
expr = case([(type_filter, casted_entity.in_(value))], else_=False)
elif operator == 'contains':
expr = database_entity.cast(JSONB).contains(value)
elif operator == 'has_key':
expr = database_entity.cast(JSONB).has_key(value) # noqa
elif operator == 'of_length':
expr = case(
[(jsonb_typeof(database_entity) == 'array', jsonb_array_length(database_entity.cast(JSONB)) == value)],
else_=False)
elif operator == 'longer':
expr = case(
[(jsonb_typeof(database_entity) == 'array', jsonb_array_length(database_entity.cast(JSONB)) > value)],
else_=False)
elif operator == 'shorter':
expr = case(
[(jsonb_typeof(database_entity) == 'array', jsonb_array_length(database_entity.cast(JSONB)) < value)],
else_=False)
else:
raise InputValidationError("Unknown operator {} for filters in JSON field".format(operator))
return expr
[docs] def get_projectable_attribute(self, alias, column_name, attrpath, cast=None, **kwargs):
"""
:returns: An attribute store in a JSON field of the give column
"""
entity = self.get_column(column_name, alias)[attrpath]
if cast is None:
entity = entity
elif cast == 'f':
entity = entity.astext.cast(Float)
elif cast == 'i':
entity = entity.astext.cast(Integer)
elif cast == 'b':
entity = entity.astext.cast(Boolean)
elif cast == 't':
entity = entity.astext
elif cast == 'j':
entity = entity.astext.cast(JSONB)
elif cast == 'd':
entity = entity.astext.cast(DateTime)
else:
raise InputValidationError("Unkown casting key {}".format(cast))
return entity
[docs] def get_aiida_res(self, key, res):
"""
Some instance returned by ORM (django or SA) need to be converted
to Aiida instances (eg nodes). Choice (sqlalchemy_utils)
will return their value
:param key: The key
:param res: the result returned by the query
:returns: an aiida-compatible instance
"""
if isinstance(res, Choice):
returnval = res.value
elif isinstance(res, uuid.UUID):
returnval = six.text_type(res)
else:
try:
returnval = self._backend.get_backend_entity(res)
except TypeError:
returnval = res
return returnval
[docs] def yield_per(self, query, batch_size):
"""
:param count: Number of rows to yield per step
Yields *count* rows at a time
:returns: a generator
"""
try:
return query.yield_per(batch_size)
except Exception:
# exception was raised. Rollback the session
self.get_session().rollback()
raise
[docs] def count(self, query):
try:
return query.count()
except Exception:
# exception was raised. Rollback the session
self.get_session().rollback()
raise
[docs] def first(self, query):
"""
Executes query in the backend asking for one instance.
:returns: One row of aiida results
"""
try:
return query.first()
except Exception:
# exception was raised. Rollback the session
self.get_session().rollback()
raise
[docs] def iterall(self, query, batch_size, tag_to_index_dict):
if not tag_to_index_dict:
raise Exception("Got an empty dictionary: {}".format(tag_to_index_dict))
try:
results = query.yield_per(batch_size)
if len(tag_to_index_dict) == 1:
# Sqlalchemy, for some strange reason, does not return a list of lsits
# if you have provided an ormclass
if list(tag_to_index_dict.values()) == ['*']:
for rowitem in results:
yield [self.get_aiida_res(tag_to_index_dict[0], rowitem)]
else:
for rowitem, in results:
yield [self.get_aiida_res(tag_to_index_dict[0], rowitem)]
elif len(tag_to_index_dict) > 1:
for resultrow in results:
yield [
self.get_aiida_res(tag_to_index_dict[colindex], rowitem)
for colindex, rowitem in enumerate(resultrow)
]
else:
raise ValueError("Got an empty dictionary")
except Exception:
self.get_session().rollback()
raise
[docs] def iterdict(self, query, batch_size, tag_to_projected_entity_dict):
nr_items = sum(len(v) for v in tag_to_projected_entity_dict.values())
if not nr_items:
raise ValueError("Got an empty dictionary")
# Wrapping everything in an atomic transaction:
try:
results = query.yield_per(batch_size)
if nr_items > 1:
for this_result in results:
yield {
tag: {
attrkey: self.get_aiida_res(attrkey, this_result[index_in_sql_result])
for attrkey, index_in_sql_result in projected_entities_dict.items()
} for tag, projected_entities_dict in tag_to_projected_entity_dict.items()
}
elif nr_items == 1:
# I this case, sql returns a list, where each listitem is the result
# for one row. Here I am converting it to a list of lists (of length 1)
if [v for entityd in tag_to_projected_entity_dict.values() for v in entityd.keys()] == ['*']:
for this_result in results:
yield {
tag: {
attrkey: self.get_aiida_res(attrkey, this_result)
for attrkey, position in projected_entities_dict.items()
} for tag, projected_entities_dict in tag_to_projected_entity_dict.items()
}
else:
for this_result, in results:
yield {
tag: {
attrkey: self.get_aiida_res(attrkey, this_result)
for attrkey, position in projected_entities_dict.items()
} for tag, projected_entities_dict in tag_to_projected_entity_dict.items()
}
else:
raise ValueError("Got an empty dictionary")
except Exception:
self.get_session().rollback()
raise