def connect(name,
type='extract_from_name',
create_indices=True,
use_lock_file=False):
if type == 'extract_from_name':
if name is None:
type = None
elif name.startswith('postgres://'):
type = 'postgres'
else:
type = os.path.splitext(name)[1][1:]
if type is None:
return NoDatabase()
if type == 'json':
from ase.db.json import JSONDatabase
return JSONDatabase(name, use_lock_file=use_lock_file)
if type == 'db':
from ase.db.sqlite import SQLite3Database
return SQLite3Database(name, create_indices, use_lock_file)
if type == 'postgres':
from ase.db.postgresql import PostgreSQLDatabase as DB
return PostgreSQLDatabase(name, create_indices)
raise ValueError('Unknown database type: ' + type)
def connect(name,
type='extract_from_name',
create_indices=True,
use_lock_file=True,
append=True,
serial=False):
"""Create connection to database.
name: str
Filename or address of database.
type: str
One of 'json', 'db', 'postgresql',
(JSON, SQLite, PostgreSQL).
Default is 'extract_from_name', which will guess the type
from the name.
use_lock_file: bool
You can turn this off if you know what you are doing ...
append: bool
Use append=False to start a new database.
"""
if isinstance(name, PurePath):
name = str(name)
if type == 'extract_from_name':
if name is None:
type = None
elif not isinstance(name, basestring):
type = 'json'
elif (name.startswith('postgresql://')
or name.startswith('postgres://')):
type = 'postgresql'
else:
type = os.path.splitext(name)[1][1:]
if type == '':
raise ValueError('No file extension or database type given')
if type is None:
return Database()
if not append and world.rank == 0:
if isinstance(name, str) and os.path.isfile(name):
os.remove(name)
if type != 'postgresql' and isinstance(name, basestring):
name = os.path.abspath(name)
if type == 'json':
from ase.db.jsondb import JSONDatabase
return JSONDatabase(name, use_lock_file=use_lock_file, serial=serial)
if type == 'db':
from ase.db.sqlite import SQLite3Database
return SQLite3Database(name,
create_indices,
use_lock_file,
serial=serial)
if type == 'postgresql':
from ase.db.postgresql import PostgreSQLDatabase
return PostgreSQLDatabase(name)
raise ValueError('Unknown database type: ' + type)
def _initialize(self, con):
if self.initialized:
return
import ase
from ase.db.sqlite import SQLite3Database
SQLite3Database()._initialize(con)
self._metadata = {}
cur = con.execute(
'SELECT COUNT(*) FROM sqlite_master WHERE name="catapp"')
if cur.fetchone()[0] > 0:
self.update_names(con)
cur = con.execute(
'SELECT COUNT(*) FROM sqlite_master WHERE name="reaction"')
if cur.fetchone()[0] == 0:
for init_command in init_commands:
con.execute(init_command)
self.id = 1
self.pid = 1
con.commit()
self.initialized = True
def _initialize(self, con):
"""Set up tables in SQL"""
if self.initialized:
return
SQLite3Database()._initialize(con) # ASE db initialization
cur = con.execute(
'SELECT COUNT(*) FROM sqlite_master WHERE name="reaction"')
if cur.fetchone()[0] == 0: # no reaction table
for init_command in init_commands:
con.execute(init_command) # Create tables
con.commit()
self.initialized = True
def connect(name,
type='extract_from_name',
create_indices=True,
use_lock_file=True):
"""Create connection to database.
name: str
Filename or address of database.
type: str
One of 'json', 'db', 'postgresql', 'mysql'
(JSON, SQLite, PostgreSQL, MySQL/MariaDB).
Default is 'extract_from_name', which will ... guess the type
from the name.
use_lock_file: bool
You can turn this off if you know what you are doing ...
"""
if type == 'extract_from_name':
if name is None:
type = None
elif name.startswith('postgresql://'):
type = 'postgresql'
elif name.startswith('mysql://'):
type = 'mysql'
else:
type = os.path.splitext(name)[1][1:]
if type is None:
return Database()
if type == 'json':
from ase.db.jsondb import JSONDatabase
return JSONDatabase(name, use_lock_file=use_lock_file)
if type == 'db':
from ase.db.sqlite import SQLite3Database
return SQLite3Database(name, create_indices, use_lock_file)
if type == 'postgresql':
from ase.db.postgresql import PostgreSQLDatabase
return PostgreSQLDatabase(name[5:])
if type == 'mysql':
from ase.db.mysql import MySQLDatabase
return MySQLDatabase(name[5:])
raise ValueError('Unknown database type: ' + type)
def _initialize(self, con):
if self.initialized:
return
SQLite3Database()._initialize(con)
self._metadata = {}
cur = con.execute(
'SELECT COUNT(*) FROM sqlite_master WHERE name="reaction"')
if cur.fetchone()[0] == 0:
for init_command in init_commands:
con.execute(init_command)
self.id = 1
self.pid = 1
con.commit()
if self.id is None:
self.id = self.get_last_id(cur) + 1
self.pid = self.get_last_pub_id(cur) + 1
self.initialized = True