def create_core(args):
schema = args.name
config = args.config and load(args.config) or {}
db_config = Database()
LazyEntityMeta.attach(db_config, database='CGRdb_config')
db_config.bind('postgres', user=args.user, password=args.password, host=args.host, database=args.base,
port=args.port)
db_config.generate_mapping()
db = Database()
LazyEntityMeta.attach(db, schema, 'CGRdb')
db.bind('postgres', user=args.user, password=args.password, host=args.host, database=args.base, port=args.port)
db.generate_mapping(create_tables=True)
with db_session:
db.execute('CREATE EXTENSION IF NOT EXISTS smlar')
db.execute('CREATE EXTENSION IF NOT EXISTS intarray')
db.execute('CREATE EXTENSION IF NOT EXISTS pg_cron')
with db_session:
db.execute(f'CREATE INDEX idx_smlar_molecule_structure ON "{schema}"."MoleculeStructure" USING '
'GIST (bit_array _int4_sml_ops)')
db.execute(f'CREATE INDEX idx_smlar_reaction_index ON "{schema}"."ReactionIndex" USING '
'GIST (bit_array _int4_sml_ops)')
db.execute(f'CREATE INDEX idx_subst_molecule_structure ON "{schema}"."MoleculeStructure" USING '
'GIN (bit_array gin__int_ops)')
db.execute(f'CREATE INDEX idx_subst_reaction_index ON "{schema}"."ReactionIndex" USING '
'GIN (bit_array gin__int_ops)')
db.execute(f"SELECT cron.schedule('0 3 * * *', $$$$\n"
f'DELETE FROM "{schema}"."MoleculeSearchCache"'
" WHERE date < CURRENT_TIMESTAMP - INTERVAL '1 day' $$$$)")
db.execute(f"SELECT cron.schedule('0 3 * * *', $$$$\n"
f'DELETE FROM "{schema}"."ReactionSearchCache"'
" WHERE date < CURRENT_TIMESTAMP - INTERVAL '1 day' $$$$)")
with db_session:
db_config.Config(name=schema, config=config, version=major_version)
def create_core(args):
major_version = '.'.join(get_distribution('CGRdb').version.split('.')[:-1])
schema = args.name
config = args.config and load(args.config) or {}
if 'packages' not in config:
config['packages'] = []
for p in config['packages']:
try:
p = get_distribution(p)
import_module(p.project_name)
except (DistributionNotFound, VersionConflict):
raise ImportError(
f'packages not installed or has invalid versions: {p}')
db_config = Database()
LazyEntityMeta.attach(db_config, database='CGRdb_config')
db_config.bind('postgres',
user=args.user,
password=args.password,
host=args.host,
database=args.base,
port=args.port)
db_config.generate_mapping()
with db_session:
if db_config.Config.exists(name=schema):
raise KeyError('schema already exists')
db = Database()
LazyEntityMeta.attach(db, schema, 'CGRdb')
db.bind('postgres',
user=args.user,
password=args.password,
host=args.host,
database=args.base,
port=args.port)
db.generate_mapping(create_tables=True)
with db_session:
db.execute(f'ALTER TABLE "{schema}"."Reaction" DROP COLUMN structure')
db.execute(
f'ALTER TABLE "{schema}"."Reaction" RENAME TO "ReactionRecord"')
db.execute(
f'CREATE VIEW "{schema}"."Reaction" AS SELECT id, NULL::bytea as structure '
f'FROM "{schema}"."ReactionRecord"')
db.execute(init_session.replace('{schema}', schema))
db.execute(merge_molecules.replace('{schema}', schema))
db.execute(insert_molecule.replace('{schema}', schema))
db.execute(insert_molecule_trigger.replace('{schema}', schema))
db.execute(after_insert_molecule.replace('{schema}', schema))
db.execute(after_insert_molecule_trigger.replace('{schema}', schema))
db.execute(delete_molecule.replace('{schema}', schema))
db.execute(delete_molecule_trigger.replace('{schema}', schema))
db.execute(insert_reaction.replace('{schema}', schema))
db.execute(insert_reaction_trigger.replace('{schema}', schema))
db.execute(search_similar_molecules.replace('{schema}', schema))
db.execute(search_substructure_molecule.replace('{schema}', schema))
db.execute(search_similar_reactions.replace('{schema}', schema))
db.execute(search_substructure_reaction.replace('{schema}', schema))
db.execute(
search_substructure_fingerprint_molecule.replace(
'{schema}', schema))
db.execute(
search_similar_fingerprint_molecule.replace('{schema}', schema))
db.execute(search_reactions_by_molecule.replace('{schema}', schema))
db.execute(search_mappingless_reaction.replace('{schema}', schema))
if args.indexed:
with db_session:
db.execute(
f'CREATE INDEX idx_moleculestructure__smlar ON "{schema}"."MoleculeStructure" USING '
'GIST (fingerprint _int4_sml_ops)')
db.execute(
f'CREATE INDEX idx_moleculestructure__subst ON "{schema}"."MoleculeStructure" USING '
'GIN (fingerprint gin__int_ops)')
db.execute(
f'CREATE INDEX idx_reactionindex__smlar ON "{schema}"."ReactionIndex" USING '
'GIST (fingerprint _int4_sml_ops)')
db.execute(
f'CREATE INDEX idx_reactionindex__subst ON "{schema}"."ReactionIndex" USING '
'GIN (fingerprint gin__int_ops)')
with db_session:
db_config.Config(name=schema, config=config, version=major_version)
def create_core(args):
major_version = '.'.join(get_distribution('CGRdb').version.split('.')[:-1])
schema = args.name
config = args.config and load(args.config) or {}
if 'packages' not in config:
config['packages'] = []
for p in config['packages']:
try:
p = get_distribution(p)
import_module(p.project_name)
except (DistributionNotFound, VersionConflict):
raise ImportError(
f'packages not installed or has invalid versions: {p}')
db_config = Database()
LazyEntityMeta.attach(db_config, database='CGRdb_config')
db_config.bind('postgres', **args.connection)
db_config.generate_mapping()
with db_session:
if db_config.Config.exists(name=schema):
raise KeyError('schema already exists')
with db_session:
db_config.execute(f'DROP SCHEMA IF EXISTS {schema} CASCADE')
db_config.execute(f'CREATE SCHEMA {schema}')
db = Database()
LazyEntityMeta.attach(db, schema, 'CGRdb')
db.bind('postgres', **args.connection)
db.generate_mapping(create_tables=True)
with db_session:
db.execute(f'ALTER TABLE "{schema}"."Reaction" DROP COLUMN structure')
db.execute(
f'ALTER TABLE "{schema}"."Reaction" RENAME TO "ReactionRecord"')
db.execute(
f'CREATE VIEW "{schema}"."Reaction" AS SELECT id, NULL::bytea as structure '
f'FROM "{schema}"."ReactionRecord"')
with db_session:
db.execute(init_session.replace('{schema}', schema))
db.execute(insert_molecule.replace('{schema}', schema))
db.execute(after_insert_molecule.replace('{schema}', schema))
db.execute(delete_molecule.replace('{schema}', schema))
db.execute(insert_reaction.replace('{schema}', schema))
db.execute(merge_molecules.replace('{schema}', schema))
db.execute(insert_molecule_trigger.replace('{schema}', schema))
db.execute(after_insert_molecule_trigger.replace('{schema}', schema))
db.execute(delete_molecule_trigger.replace('{schema}', schema))
db.execute(insert_reaction_trigger.replace('{schema}', schema))
db.execute(search_structure_molecule.replace('{schema}', schema))
db.execute(search_structure_reaction.replace('{schema}', schema))
db.execute(search_similar_molecules.replace('{schema}', schema))
db.execute(search_substructure_molecule.replace('{schema}', schema))
db.execute(search_similar_reactions.replace('{schema}', schema))
db.execute(search_substructure_reaction.replace('{schema}', schema))
db.execute(search_reactions_by_molecule.replace('{schema}', schema))
db.execute(search_mappingless_reaction.replace('{schema}', schema))
with db_session:
db_config.Config(name=schema, config=config, version=major_version)