[massive store] ensure the cwmassive_initialized table is deleted if needed
This may be necessary if a previous import did badly crached, leaving the
cwmassive_initialized behind.
# coding: utf-8
# copyright 2015-2016 LOGILAB S.A. (Paris, FRANCE), all rights reserved.
# contact http://www.logilab.fr/ -- mailto:contact@logilab.fr
#
# This file is part of CubicWeb.
#
# CubicWeb is free software: you can redistribute it and/or modify it under the
# terms of the GNU Lesser General Public License as published by the Free
# Software Foundation, either version 2.1 of the License, or (at your option)
# any later version.
#
# CubicWeb is distributed in the hope that it will be useful, but WITHOUT ANY
# WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR
# A PARTICULAR PURPOSE. See the GNU Lesser General Public License for more
# details.
#
# You should have received a copy of the GNU Lesser General Public License along
# with CubicWeb. If not, see <http://www.gnu.org/licenses/>.
from collections import defaultdict
from itertools import chain
import logging
from uuid import uuid4
from six import text_type
from six.moves import range
from cubicweb.dataimport import stores, pgstore
from cubicweb.server.schema2sql import eschema_sql_def
class MassiveObjectStore(stores.RQLObjectStore):
"""Store for massive import of data, with delayed insertion of meta data.
WARNINGS:
- This store may only be used with PostgreSQL for now, as it relies
on the COPY FROM method, and on specific PostgreSQL tables to get all
the indexes.
- This store can only insert relations that are not inlined (i.e.,
which do *not* have inlined=True in their definition in the schema),
unless they are specified as entity attributes.
It should be used as follows:
store = MassiveObjectStore(cnx)
eid_p = store.prepare_insert_entity('Person',
cwuri=u'http://dbpedia.org/toto',
name=u'Toto')
eid_loc = store.prepare_insert_entity('Location',
cwuri=u'http://geonames.org/11111',
name=u'Somewhere')
store.prepare_insert_relation(eid_p, 'lives_in', eid_loc)
store.flush()
...
store.commit()
store.finish()
Full-text indexation is not handled, you'll have to reindex the proper entity types by yourself
if desired.
"""
def __init__(self, cnx, slave_mode=False, eids_seq_range=10000, metagen=None):
"""Create a MassiveObject store, with the following arguments:
- `cnx`, a connection to the repository
- `metagen`, optional :class:`MetadataGenerator` instance
- `eids_seq_range`: size of eid range reserved by the store for each batch
"""
super(MassiveObjectStore, self).__init__(cnx)
self.uuid = text_type(uuid4()).replace('-', '')
self.slave_mode = slave_mode
if metagen is None:
metagen = stores.MetadataGenerator(cnx)
self.metagen = metagen
self.logger = logging.getLogger('dataimport.massive_store')
self.sql = cnx.system_sql
self.schema = cnx.vreg.schema
self.default_values = get_default_values(self.schema)
self.get_next_eid = lambda g=self._get_eid_gen(eids_seq_range): next(g)
self._source_dbhelper = cnx.repo.system_source.dbhelper
self._dbh = PGHelper(cnx)
self._data_entities = defaultdict(list)
self._data_relations = defaultdict(list)
self._initialized = {}
def _get_eid_gen(self, eids_seq_range):
""" Function getting the next eid. This is done by preselecting
a given number of eids from the 'entities_id_seq', and then
storing them"""
while True:
last_eid = self._cnx.repo.system_source.create_eid(self._cnx, eids_seq_range)
for eid in range(last_eid - eids_seq_range + 1, last_eid + 1):
yield eid
# master/slaves specific API
def master_init(self, commit=True):
"""Initialize database for massive insertion.
This is expected to be called once, by the master store in master/slaves configuration.
"""
assert not self.slave_mode
if self not in self._initialized:
self.sql('DROP TABLE IF EXISTS cwmassive_initialized')
self.sql('CREATE TABLE cwmassive_initialized'
'(retype text, type varchar(128), uuid varchar(32))')
self._initialized[self] = None
if commit:
self.commit()
# SQL utilities #########################################################
def _drop_metadata_constraints(self):
"""Drop constraints and indexes for the metadata tables.
They will be recreated by the `finish` method.
"""
rtypes = [rtype for rtype in self.metagen.meta_relations
if not self.schema.rschema(rtype).final]
rtypes += ('is_instance_of', 'is', 'cw_source')
for rtype in rtypes:
self._dbh.drop_constraints(rtype + '_relation')
self._dbh.drop_indexes(rtype + '_relation')
# don't drop constraints for the entities table, the only one is the primary key's index on
# eid and we want to keep it
self._dbh.drop_indexes('entities')
def restart_eid_sequence(self, start_eid):
self.sql(self._cnx.repo.system_source.dbhelper.sql_restart_numrange(
'entities_id_seq', initial_value=start_eid))
self._cnx.commit()
# store api ################################################################
def prepare_insert_entity(self, etype, **data):
"""Given an entity type, attributes and inlined relations, returns the inserted entity's
eid.
"""
if etype not in self._initialized:
if not self.slave_mode:
self.master_init(commit=False)
tablename = 'cw_%s' % etype.lower()
tmp_tablename = '%s_%s' % (tablename, self.uuid)
self.sql("INSERT INTO cwmassive_initialized VALUES (%(e)s, 'etype', %(uuid)s)",
{'e': etype, 'uuid': self.uuid})
attr_defs = eschema_sql_def(self._source_dbhelper, self.schema[etype])
self.sql('CREATE TABLE %s(%s);' % (tmp_tablename,
', '.join('cw_%s %s' % (column, sqltype)
for column, sqltype in attr_defs)))
self._initialized[etype] = [attr for attr, _ in attr_defs]
if 'eid' not in data:
# If eid is not given and the eids sequence is set, use the value from the sequence
eid = self.get_next_eid()
data['eid'] = eid
self._data_entities[etype].append(data)
return data['eid']
def prepare_insert_relation(self, eid_from, rtype, eid_to, **kwargs):
"""Insert into the database a relation ``rtype`` between entities with eids ``eid_from``
and ``eid_to``.
Relation must not be inlined.
"""
if rtype not in self._initialized:
if not self.slave_mode:
self.master_init(commit=False)
assert not self._cnx.vreg.schema.rschema(rtype).inlined
self._initialized[rtype] = None
tablename = '%s_relation' % rtype.lower()
tmp_tablename = '%s_%s' % (tablename, self.uuid)
self.sql("INSERT INTO cwmassive_initialized VALUES (%(r)s, 'rtype', %(uuid)s)",
{'r': rtype, 'uuid': self.uuid})
self.sql('CREATE TABLE %s(eid_from integer, eid_to integer)' % tmp_tablename)
self._data_relations[rtype].append({'eid_from': eid_from, 'eid_to': eid_to})
def flush(self):
"""Flush the data"""
self.flush_entities()
self.flush_relations()
def finish(self):
"""Remove temporary tables and columns."""
assert not self.slave_mode, 'finish method should only be called by the master store'
self.logger.info("Start cleaning")
# Get all the initialized etypes/rtypes
if self._dbh.table_exists('cwmassive_initialized'):
cu = self.sql('SELECT retype, type, uuid FROM cwmassive_initialized')
entities = defaultdict(list)
relations = defaultdict(list)
for retype, _type, uuid in cu.fetchall():
if _type == 'rtype':
relations[retype].append(uuid)
else: # _type = 'etype'
entities[retype].append(uuid)
# if there is some entities to insert, delete constraint on metadata tables once for all
if entities:
self._drop_metadata_constraints()
# get back entity data from the temporary tables
for etype, uuids in entities.items():
tablename = 'cw_%s' % etype.lower()
attr_defs = eschema_sql_def(self._source_dbhelper, self.schema[etype])
columns = ','.join('cw_%s' % attr for attr, _ in attr_defs)
self._dbh.drop_constraints(tablename)
self._dbh.drop_indexes(tablename)
for uuid in uuids:
tmp_tablename = '%s_%s' % (tablename, uuid)
self.sql('INSERT INTO %(table)s(%(columns)s) '
'SELECT %(columns)s FROM %(tmp_table)s'
% {'table': tablename, 'tmp_table': tmp_tablename,
'columns': columns})
self._insert_etype_metadata(etype, tmp_tablename)
self._tmp_data_cleanup(tmp_tablename, etype, uuid)
# get back relation data from the temporary tables
for rtype, uuids in relations.items():
tablename = '%s_relation' % rtype.lower()
self._dbh.drop_constraints(tablename)
self._dbh.drop_indexes(tablename)
for uuid in uuids:
tmp_tablename = '%s_%s' % (tablename, uuid)
self.fill_relation_table(tablename, tmp_tablename)
self._tmp_data_cleanup(tmp_tablename, rtype, uuid)
# restore all deleted indexes and constraints
self._dbh.restore_indexes_and_constraints()
# delete the meta data table
self.sql('DROP TABLE IF EXISTS cwmassive_initialized')
self.commit()
def _insert_etype_metadata(self, etype, tmp_tablename):
"""Massive insertion of meta data for `etype`, with new entities in `tmp_tablename`.
"""
# insert standard metadata relations
for rtype, eid in self.metagen.base_etype_rels(etype).items():
self.fill_meta_relation_table(tmp_tablename, rtype, eid)
# insert cw_source, is and is_instance_of relations (normally handled by the system source)
self.fill_meta_relation_table(tmp_tablename, 'cw_source', self.metagen.source.eid)
eschema = self.schema[etype]
self.fill_meta_relation_table(tmp_tablename, 'is', eschema.eid)
for parent_eschema in chain(eschema.ancestors(), [eschema]):
self.fill_meta_relation_table(tmp_tablename, 'is_instance_of', parent_eschema.eid)
self.fill_entities_table(etype, tmp_tablename)
def fill_entities_table(self, etype, tmp_tablename):
# finally insert records into the entities table
self.sql("INSERT INTO entities(eid, type) "
"SELECT cw_eid, '%s' FROM %s "
"WHERE NOT EXISTS (SELECT 1 FROM entities WHERE eid=cw_eid)"
% (etype, tmp_tablename))
def fill_relation_table(self, tablename, tmp_tablename):
# XXX no index on the original relation table, EXISTS subquery may be sloooow
self.sql('INSERT INTO %(table)s(eid_from, eid_to) SELECT DISTINCT '
'T.eid_from, T.eid_to FROM %(tmp_table)s AS T '
'WHERE NOT EXISTS (SELECT 1 FROM %(table)s AS TT WHERE '
'TT.eid_from=T.eid_from AND TT.eid_to=T.eid_to);'
% {'table': tablename, 'tmp_table': tmp_tablename})
def fill_meta_relation_table(self, tmp_tablename, rtype, eid_to):
self.sql("INSERT INTO %s_relation(eid_from, eid_to) SELECT cw_eid, %s FROM %s "
"WHERE NOT EXISTS (SELECT 1 FROM entities WHERE eid=cw_eid)"
% (rtype, eid_to, tmp_tablename))
def _tmp_data_cleanup(self, tmp_tablename, ertype, uuid):
"""Drop temporary relation table and record from cwmassive_initialized."""
self.sql('DROP TABLE %(tmp_table)s' % {'tmp_table': tmp_tablename})
self.sql('DELETE FROM cwmassive_initialized '
'WHERE retype = %(rtype)s AND uuid = %(uuid)s',
{'rtype': ertype, 'uuid': uuid})
# FLUSH #################################################################
def flush_relations(self):
"""Flush the relations data from in-memory structures to a temporary table."""
for rtype, data in self._data_relations.items():
if not data:
# There is no data for these etype for this flush round.
continue
buf = pgstore._create_copyfrom_buffer(data, ('eid_from', 'eid_to'))
cursor = self._cnx.cnxset.cu
tablename = '%s_relation' % rtype.lower()
tmp_tablename = '%s_%s' % (tablename, self.uuid)
cursor.copy_from(buf, tmp_tablename, null='NULL', columns=('eid_from', 'eid_to'))
# Clear data cache
self._data_relations[rtype] = []
def flush_entities(self):
"""Flush the entities data from in-memory structures to a temporary table."""
metagen = self.metagen
for etype, data in self._data_entities.items():
if not data:
# There is no data for these etype for this flush round.
continue
attrs = self._initialized[etype]
_base_data = dict.fromkeys(attrs)
_base_data.update(self.default_values[etype])
_base_data.update(metagen.base_etype_attrs(etype))
_data = []
for d in data:
# do this first on `d`, because it won't fill keys associated to None as provided by
# `_base_data`
metagen.init_entity_attrs(etype, d['eid'], d)
# XXX warn/raise if there is some key not in attrs?
_d = _base_data.copy()
_d.update(d)
_data.append(_d)
buf = pgstore._create_copyfrom_buffer(_data, attrs)
tablename = 'cw_%s' % etype.lower()
tmp_tablename = '%s_%s' % (tablename, self.uuid)
columns = ['cw_%s' % attr for attr in attrs]
cursor = self._cnx.cnxset.cu
cursor.copy_from(buf, tmp_tablename, null='NULL', columns=columns)
# Clear data cache
self._data_entities[etype] = []
def get_default_values(schema):
"""analyzes yams ``schema`` and returns the list of default values.
The returned value is a dictionary mapping entity types to a
sub-dictionnaries mapping attribute names -> default values.
"""
default_values = {}
# iterates on all entity types
for eschema in schema.entities():
# for each entity type, iterates on attribute definitions
default_values[eschema.type] = eschema_constraints = {}
for rschema, _ in eschema.attribute_definitions():
# for each attribute, if a size constraint is found,
# append it to the size constraint list
if eschema.default(rschema.type) is not None:
eschema_constraints[rschema.type] = eschema.default(rschema.type)
return default_values
class PGHelper(object):
"""This class provides some helper methods to manipulate a postgres database metadata (index and
constraints).
"""
def __init__(self, cnx):
self.sql = cnx.system_sql
# Deals with pg schema, see #3216686
pg_schema = cnx.repo.config.system_source_config.get('db-namespace') or 'public'
self.pg_schema = pg_schema
def drop_indexes(self, tablename):
"""Drop indexes and constraints, storing them in a table for later restore."""
# Create a table to save the constraints, it allows reloading even after crash
self.sql('CREATE TABLE IF NOT EXISTS cwmassive_constraints(sql TEXT, insert_order SERIAL)')
indexes = self.table_indexes(tablename)
for name, query in indexes.items():
self.sql('INSERT INTO cwmassive_constraints(sql) VALUES (%(sql)s)', {'sql': query})
self.sql('DROP INDEX %s' % name)
def drop_constraints(self, tablename):
self.sql('CREATE TABLE IF NOT EXISTS cwmassive_constraints(sql TEXT, insert_order SERIAL)')
constraints = self.table_constraints(tablename)
for name, query in constraints.items():
self.sql('INSERT INTO cwmassive_constraints(sql) VALUES (%(sql)s)', {'sql': query})
self.sql('ALTER TABLE %s DROP CONSTRAINT %s' % (tablename, name))
def restore_indexes_and_constraints(self):
"""Restore indexes and constraints."""
if not self.table_exists('cwmassive_constraints'):
return
cu = self.sql('SELECT sql, insert_order FROM cwmassive_constraints '
'ORDER BY insert_order DESC')
for query, order in cu.fetchall():
self.sql(query)
self.sql('DELETE FROM cwmassive_constraints WHERE insert_order=%(order)s',
{'order': order})
self.sql('DROP TABLE cwmassive_constraints')
def table_exists(self, tablename):
"""Return True if the given table already exists in the database."""
cu = self.sql('SELECT 1 from information_schema.tables '
'WHERE table_name=%(t)s AND table_schema=%(s)s',
{'t': tablename, 's': self.pg_schema})
return bool(cu.fetchone())
def table_indexes(self, tablename):
"""Return a dictionary of indexes {index name: index sql}, constraints included."""
indexes = {}
for name in self._index_names(tablename):
indexes[name] = self._index_sql(name)
return indexes
def table_constraints(self, tablename):
"""Return a dictionary of constraints {constraint name: constraint sql}."""
constraints = {}
for name in self._constraint_names(tablename):
query = self._constraint_sql(name)
constraints[name] = 'ALTER TABLE %s ADD CONSTRAINT %s %s' % (tablename, name, query)
return constraints
def _index_names(self, tablename):
"""Return the names of all indexes in the given table (including constraints.)"""
cu = self.sql("SELECT c.relname FROM pg_catalog.pg_class c "
"JOIN pg_catalog.pg_index i ON i.indexrelid = c.oid "
"JOIN pg_catalog.pg_class c2 ON i.indrelid = c2.oid "
"LEFT JOIN pg_catalog.pg_user u ON u.usesysid = c.relowner "
"LEFT JOIN pg_catalog.pg_namespace n ON n.oid = c.relnamespace "
"WHERE c.relkind IN ('i','') "
" AND c2.relname = %(t)s "
" AND i.indisprimary = FALSE "
" AND n.nspname NOT IN ('pg_catalog', 'pg_toast') "
" AND pg_catalog.pg_table_is_visible(c.oid);", {'t': tablename})
return [name for name, in cu.fetchall()]
def _constraint_names(self, tablename):
"""Return the names of all constraints in the given table."""
cu = self.sql("SELECT i.conname FROM pg_catalog.pg_class c "
"JOIN pg_catalog.pg_constraint i ON i.conrelid = c.oid "
"JOIN pg_catalog.pg_class c2 ON i.conrelid=c2.oid "
"LEFT JOIN pg_catalog.pg_user u ON u.usesysid = c.relowner "
"LEFT JOIN pg_catalog.pg_namespace n ON n.oid = c.relnamespace "
"WHERE c2.relname = %(t)s "
"AND n.nspname NOT IN ('pg_catalog', 'pg_toast') "
"AND pg_catalog.pg_table_is_visible(c.oid)", {'t': tablename})
return [name for name, in cu.fetchall()]
def _index_sql(self, name):
"""Return the SQL to be used to recreate the index of the given name."""
return self.sql('SELECT pg_get_indexdef(c.oid) FROM pg_catalog.pg_class c '
'LEFT JOIN pg_catalog.pg_namespace n ON n.oid = c.relnamespace '
'WHERE c.relname = %(r)s AND n.nspname=%(n)s',
{'r': name, 'n': self.pg_schema}).fetchone()[0]
def _constraint_sql(self, name):
"""Return the SQL to be used to recreate the constraint."""
return self.sql('SELECT pg_get_constraintdef(c.oid) FROM pg_catalog.pg_constraint c '
'LEFT JOIN pg_catalog.pg_namespace n ON n.oid = c.connamespace '
'WHERE c.conname = %(r)s AND n.nspname=%(n)s',
{'r': name, 'n': self.pg_schema}).fetchone()[0]