def setUpClass_method(self):
from aiida.backends.sqlalchemy import get_scoped_session
if self.test_session is None:
# Should we use reset_session?
self.test_session = get_scoped_session()
if self.drop_all:
Base.metadata.drop_all(self.test_session.connection)
Base.metadata.create_all(self.test_session.connection)
install_tc(self.test_session.connection)
else:
self.clean_db()
self.insert_data()
def setUpClass_method(self):
if self.test_session is None:
if self.connection is None:
config = get_profile_config(AIIDADB_PROFILE)
engine = get_engine(config)
self.test_session = get_session(engine=engine)
self.connection = engine.connect()
self.test_session = Session(bind=self.connection)
aiida.backends.sqlalchemy.session = self.test_session
if self.drop_all:
Base.metadata.drop_all(self.connection)
Base.metadata.create_all(self.connection)
install_tc(self.connection)
else:
self.clean_db()
self.insert_data()
def downgrade():
"""Migrations for the downgrade."""
op.create_table(
'db_dbpath', sa.Column('id', sa.INTEGER(), nullable=False),
sa.Column('parent_id',
sa.INTEGER(),
autoincrement=False,
nullable=True),
sa.Column('child_id', sa.INTEGER(), autoincrement=False,
nullable=True),
sa.Column('depth', sa.INTEGER(), autoincrement=False, nullable=True),
sa.Column('entry_edge_id',
sa.INTEGER(),
autoincrement=False,
nullable=True),
sa.Column('direct_edge_id',
sa.INTEGER(),
autoincrement=False,
nullable=True),
sa.Column('exit_edge_id',
sa.INTEGER(),
autoincrement=False,
nullable=True),
sa.ForeignKeyConstraint(['child_id'], ['db_dbnode.id'],
name='db_dbpath_child_id_fkey',
initially='DEFERRED',
deferrable=True),
sa.ForeignKeyConstraint(['parent_id'], ['db_dbnode.id'],
name='db_dbpath_parent_id_fkey',
initially='DEFERRED',
deferrable=True),
sa.PrimaryKeyConstraint('id', name='db_dbpath_pkey'))
# I get the session using the alembic connection
# (Keep in mind that alembic uses the AiiDA SQLA
# session)
session = Session(bind=op.get_bind())
install_tc(session)
def setUpClass(cls):
config = get_profile_config("tests")
engine_url = ("postgresql://{AIIDADB_USER}:{AIIDADB_PASS}@"
"{AIIDADB_HOST}:{AIIDADB_PORT}/{AIIDADB_NAME}").format(
**config)
engine = create_engine(engine_url,
json_serializer=dumps_json,
json_deserializer=loads_json)
cls.connection = engine.connect()
session = Session(bind=cls.connection)
sa.session = session
if cls.drop_all:
Base.metadata.drop_all(cls.connection)
Base.metadata.create_all(cls.connection)
install_tc(cls.connection)
email = get_configured_user_email()
has_user = DbUser.query.filter(DbUser.email == email).first()
if not has_user:
user = DbUser(email, "foo", "bar", "tests")
sa.session.add(user)
sa.session.commit()
sa.session.expire_all()
has_computer = DbComputer.query.filter(
DbComputer.hostname == 'localhost').first()
if not has_computer:
computer = SqlAlchemyTests._create_computer()
computer.store()
session.close()
def setup(profile, only_config, non_interactive=False, **kwargs):
'''
setup an aiida profile and aiida user (and the aiida default user).
:param profile: Profile name
:param only_config: do not create a new user
:param non_interactive: do not prompt for configuration values, fail if not all values are given as kwargs.
:param backend: one of 'django', 'sqlalchemy'
:param email: valid email address for the user
:param db_host: hostname for the database
:param db_port: port to connect to the database
:param db_user: name of the db user
:param db_pass: password of the db user
'''
from aiida.common.setup import (create_base_dirs, create_configuration,
set_default_profile, DEFAULT_UMASK,
create_config_noninteractive)
from aiida.backends.profile import BACKEND_SQLA, BACKEND_DJANGO
from aiida.backends.utils import set_backend_type, get_backend_type
from aiida.common.exceptions import InvalidOperation
# ~ cmdline_args = list(args)
# ~ only_user_config = False
# ~ try:
# ~ cmdline_args.remove('--only-config')
# ~ only_user_config = True
# ~ except ValueError:
# ~ # Parameter not provided
# ~ pass
only_user_config = only_config
# ~ if cmdline_args:
# ~ print >> sys.stderr, "Unknown parameters on the command line: "
# ~ print >> sys.stderr, ", ".join(cmdline_args)
# ~ sys.exit(1)
# create the directories to store the configuration files
create_base_dirs()
# gprofile = 'default' if profile is None else profile
# ~ gprofile = profile if settings_profile.AIIDADB_PROFILE is None \
# ~ else settings_profile.AIIDADB_PROFILE
if settings_profile.AIIDADB_PROFILE and profile:
sys.exit(
'the profile argument cannot be used if verdi is called with -p option: {} and {}'
.format(settings_profile.AIIDADB_PROFILE, profile))
gprofile = settings_profile.AIIDADB_PROFILE or profile
if gprofile == profile:
settings_profile.AIIDADB_PROFILE = profile
if not settings_profile.AIIDADB_PROFILE:
settings_profile.AIIDADB_PROFILE = 'default'
# used internally later
gprofile = settings_profile.AIIDADB_PROFILE
created_conf = None
# ask and store the configuration of the DB
if non_interactive:
try:
created_conf = create_config_noninteractive(
profile=gprofile,
backend=kwargs['backend'],
email=kwargs['email'],
db_host=kwargs['db_host'],
db_port=kwargs['db_port'],
db_name=kwargs['db_name'],
db_user=kwargs['db_user'],
db_pass=kwargs.get('db_pass', ''),
repo=kwargs['repo'],
force_overwrite=kwargs.get('force_overwrite', False))
except ValueError as e:
click.echo("Error during configuation: {}".format(e.message),
err=True)
sys.exit(1)
except KeyError as e:
sys.exit(
"--non-interactive requires all values to be given on the commandline! {}"
.format(e.message),
err=True)
else:
try:
created_conf = create_configuration(profile=gprofile)
except ValueError as e:
print >> sys.stderr, "Error during configuration: {}".format(
e.message)
sys.exit(1)
# set default DB profiles
set_default_profile('verdi', gprofile, force_rewrite=False)
set_default_profile('daemon', gprofile, force_rewrite=False)
if only_user_config:
print(
"Only user configuration requested, "
"skipping the migrate command")
else:
print "Executing now a migrate command..."
backend_choice = created_conf['AIIDADB_BACKEND']
if backend_choice == BACKEND_DJANGO:
print("...for Django backend")
# The correct profile is selected within load_dbenv.
# Setting os.umask here since sqlite database gets created in
# this step.
old_umask = os.umask(DEFAULT_UMASK)
# This check should be done more properly
# try:
# backend_type = get_backend_type()
# except KeyError:
# backend_type = None
#
# if backend_type is not None and backend_type != BACKEND_DJANGO:
# raise InvalidOperation("An already existing database found"
# "and a different than the selected"
# "backend was used for its "
# "management.")
try:
pass_to_django_manage([execname, 'migrate'], profile=gprofile)
finally:
os.umask(old_umask)
set_backend_type(BACKEND_DJANGO)
elif backend_choice == BACKEND_SQLA:
print("...for SQLAlchemy backend")
from aiida import is_dbenv_loaded, load_dbenv
if not is_dbenv_loaded():
load_dbenv()
from aiida.backends.sqlalchemy.models.base import Base
from aiida.backends.sqlalchemy.utils import install_tc, reset_session
from aiida.common.setup import get_profile_config
# This check should be done more properly
# try:
# backend_type = get_backend_type()
# except KeyError:
# backend_type = None
#
# if backend_type is not None and backend_type != BACKEND_SQLA:
# raise InvalidOperation("An already existing database found"
# "and a different than the selected"
# "backend was used for its "
# "management.")
# Those import are necessary for SQLAlchemy to correctly create
# the needed database tables.
from aiida.backends.sqlalchemy.models.authinfo import (DbAuthInfo)
from aiida.backends.sqlalchemy.models.comment import DbComment
from aiida.backends.sqlalchemy.models.computer import (DbComputer)
from aiida.backends.sqlalchemy.models.group import (
DbGroup, table_groups_nodes)
from aiida.backends.sqlalchemy.models.lock import DbLock
from aiida.backends.sqlalchemy.models.log import DbLog
from aiida.backends.sqlalchemy.models.node import (DbLink, DbNode,
DbPath,
DbCalcState)
from aiida.backends.sqlalchemy.models.user import DbUser
from aiida.backends.sqlalchemy.models.workflow import (
DbWorkflow, DbWorkflowData, DbWorkflowStep)
from aiida.backends.sqlalchemy.models.settings import DbSetting
reset_session(get_profile_config(gprofile))
from aiida.backends.sqlalchemy import get_scoped_session
connection = get_scoped_session().connection()
Base.metadata.create_all(connection)
install_tc(connection)
set_backend_type(BACKEND_SQLA)
else:
raise InvalidOperation("Not supported backend selected.")
print "Database was created successfully"
# I create here the default user
print "Loading new environment..."
if only_user_config:
from aiida.backends.utils import load_dbenv, is_dbenv_loaded
# db environment has not been loaded in this case
if not is_dbenv_loaded():
load_dbenv()
from aiida.common.setup import DEFAULT_AIIDA_USER
from aiida.orm.user import User as AiiDAUser
if not AiiDAUser.search_for_users(email=DEFAULT_AIIDA_USER):
print "Installing default AiiDA user..."
nuser = AiiDAUser(email=DEFAULT_AIIDA_USER)
nuser.first_name = "AiiDA"
nuser.last_name = "Daemon"
nuser.is_staff = True
nuser.is_active = True
nuser.is_superuser = True
nuser.force_save()
from aiida.common.utils import get_configured_user_email
email = get_configured_user_email()
print "Starting user configuration for {}...".format(email)
if email == DEFAULT_AIIDA_USER:
print "You set up AiiDA using the default Daemon email ({}),".format(
email)
print "therefore no further user configuration will be asked."
else:
# Ask to configure the new user
if not non_interactive:
user.configure.main(args=[email])
else:
# or don't ask
user.do_configure(kwargs['email'], kwargs.get('first_name'),
kwargs.get('last_name'),
kwargs.get('institution'), True)
print "Setup finished."
def upgrade():
op.create_table('db_dbuser',
sa.Column('id', sa.INTEGER(), nullable=False),
sa.Column('email', sa.VARCHAR(length=254), autoincrement=False, nullable=True),
sa.Column('password', sa.VARCHAR(length=128), autoincrement=False, nullable=True),
sa.Column('is_superuser', sa.BOOLEAN(), autoincrement=False, nullable=False),
sa.Column('first_name', sa.VARCHAR(length=254), autoincrement=False, nullable=True),
sa.Column('last_name', sa.VARCHAR(length=254), autoincrement=False, nullable=True),
sa.Column('institution', sa.VARCHAR(length=254), autoincrement=False, nullable=True),
sa.Column('is_staff', sa.BOOLEAN(), autoincrement=False, nullable=True),
sa.Column('is_active', sa.BOOLEAN(), autoincrement=False, nullable=True),
sa.Column('last_login', postgresql.TIMESTAMP(timezone=True), autoincrement=False, nullable=True),
sa.Column('date_joined', postgresql.TIMESTAMP(timezone=True), autoincrement=False, nullable=True),
sa.PrimaryKeyConstraint('id', name=u'db_dbuser_pkey'),
postgresql_ignore_search_path=False
)
op.create_index('ix_db_dbuser_email', 'db_dbuser', ['email'], unique=True)
op.create_table('db_dbworkflow',
sa.Column('id', sa.INTEGER(), nullable=False),
sa.Column('uuid', postgresql.UUID(), autoincrement=False, nullable=True),
sa.Column('ctime', postgresql.TIMESTAMP(timezone=True), autoincrement=False, nullable=True),
sa.Column('mtime', postgresql.TIMESTAMP(timezone=True), autoincrement=False, nullable=True),
sa.Column('user_id', sa.INTEGER(), autoincrement=False, nullable=True),
sa.Column('label', sa.VARCHAR(length=255), autoincrement=False, nullable=True),
sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True),
sa.Column('nodeversion', sa.INTEGER(), autoincrement=False, nullable=True),
sa.Column('lastsyncedversion', sa.INTEGER(), autoincrement=False, nullable=True),
sa.Column('state', sa.VARCHAR(length=255), autoincrement=False, nullable=True),
sa.Column('report', sa.TEXT(), autoincrement=False, nullable=True),
sa.Column('module', sa.TEXT(), autoincrement=False, nullable=True),
sa.Column('module_class', sa.TEXT(), autoincrement=False, nullable=True),
sa.Column('script_path', sa.TEXT(), autoincrement=False, nullable=True),
sa.Column('script_md5', sa.VARCHAR(length=255), autoincrement=False, nullable=True),
sa.ForeignKeyConstraint(['user_id'], [u'db_dbuser.id'], name=u'db_dbworkflow_user_id_fkey'),
sa.PrimaryKeyConstraint('id', name=u'db_dbworkflow_pkey'),
postgresql_ignore_search_path=False
)
op.create_index('ix_db_dbworkflow_label', 'db_dbworkflow', ['label'])
op.create_table('db_dbworkflowstep',
sa.Column('id', sa.INTEGER(), nullable=False),
sa.Column('parent_id', sa.INTEGER(), autoincrement=False, nullable=True),
sa.Column('user_id', sa.INTEGER(), autoincrement=False, nullable=True),
sa.Column('name', sa.VARCHAR(length=255), autoincrement=False, nullable=True),
sa.Column('time', postgresql.TIMESTAMP(timezone=True), autoincrement=False, nullable=True),
sa.Column('nextcall', sa.VARCHAR(length=255), autoincrement=False, nullable=True),
sa.Column('state', sa.VARCHAR(length=255), autoincrement=False, nullable=True),
sa.ForeignKeyConstraint(['parent_id'], [u'db_dbworkflow.id'], name=u'db_dbworkflowstep_parent_id_fkey'),
sa.ForeignKeyConstraint(['user_id'], [u'db_dbuser.id'], name=u'db_dbworkflowstep_user_id_fkey'),
sa.PrimaryKeyConstraint('id', name=u'db_dbworkflowstep_pkey'),
sa.UniqueConstraint('parent_id', 'name', name=u'db_dbworkflowstep_parent_id_name_key'),
postgresql_ignore_search_path=False
)
op.create_table('db_dbcomputer',
sa.Column('id', sa.INTEGER(), nullable=False),
sa.Column('uuid', postgresql.UUID(), autoincrement=False, nullable=True),
sa.Column('name', sa.VARCHAR(length=255), autoincrement=False, nullable=False),
sa.Column('hostname', sa.VARCHAR(length=255), autoincrement=False, nullable=True),
sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True),
sa.Column('enabled', sa.BOOLEAN(), autoincrement=False, nullable=True),
sa.Column('transport_type', sa.VARCHAR(length=255), autoincrement=False, nullable=True),
sa.Column('scheduler_type', sa.VARCHAR(length=255), autoincrement=False, nullable=True),
sa.Column('transport_params', postgresql.JSONB(), autoincrement=False, nullable=True),
sa.Column('metadata', postgresql.JSONB(), autoincrement=False, nullable=True),
sa.PrimaryKeyConstraint('id', name=u'db_dbcomputer_pkey'),
sa.UniqueConstraint('name', name=u'db_dbcomputer_name_key')
)
op.create_table('db_dbauthinfo',
sa.Column('id', sa.INTEGER(), nullable=False),
sa.Column('aiidauser_id', sa.INTEGER(), autoincrement=False, nullable=True),
sa.Column('dbcomputer_id', sa.INTEGER(), autoincrement=False, nullable=True),
sa.Column('metadata', postgresql.JSONB(), autoincrement=False, nullable=True),
sa.Column('auth_params', postgresql.JSONB(), autoincrement=False, nullable=True),
sa.Column('enabled', sa.BOOLEAN(), autoincrement=False, nullable=True),
sa.ForeignKeyConstraint(['aiidauser_id'], [u'db_dbuser.id'], name=u'db_dbauthinfo_aiidauser_id_fkey', ondelete=u'CASCADE', initially=u'DEFERRED', deferrable=True),
sa.ForeignKeyConstraint(['dbcomputer_id'], [u'db_dbcomputer.id'], name=u'db_dbauthinfo_dbcomputer_id_fkey', ondelete=u'CASCADE', initially=u'DEFERRED', deferrable=True),
sa.PrimaryKeyConstraint('id', name=u'db_dbauthinfo_pkey'),
sa.UniqueConstraint('aiidauser_id', 'dbcomputer_id', name=u'db_dbauthinfo_aiidauser_id_dbcomputer_id_key')
)
op.create_table('db_dbgroup',
sa.Column('id', sa.INTEGER(), nullable=False),
sa.Column('uuid', postgresql.UUID(), autoincrement=False, nullable=True),
sa.Column('name', sa.VARCHAR(length=255), autoincrement=False, nullable=True),
sa.Column('type', sa.VARCHAR(length=255), autoincrement=False, nullable=True),
sa.Column('time', postgresql.TIMESTAMP(timezone=True), autoincrement=False, nullable=True),
sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True),
sa.Column('user_id', sa.INTEGER(), autoincrement=False, nullable=True),
sa.ForeignKeyConstraint(['user_id'], [u'db_dbuser.id'], name=u'db_dbgroup_user_id_fkey', ondelete=u'CASCADE', initially=u'DEFERRED', deferrable=True),
sa.PrimaryKeyConstraint('id', name=u'db_dbgroup_pkey'),
sa.UniqueConstraint('name', 'type', name=u'db_dbgroup_name_type_key')
)
op.create_index('ix_db_dbgroup_name', 'db_dbgroup', ['name'])
op.create_index('ix_db_dbgroup_type', 'db_dbgroup', ['type'])
op.create_table('db_dbnode',
sa.Column('id', sa.INTEGER(), nullable=False),
sa.Column('uuid', postgresql.UUID(), autoincrement=False, nullable=True),
sa.Column('type', sa.VARCHAR(length=255), autoincrement=False, nullable=True),
sa.Column('label', sa.VARCHAR(length=255), autoincrement=False, nullable=True),
sa.Column('description', sa.TEXT(), autoincrement=False, nullable=True),
sa.Column('ctime', postgresql.TIMESTAMP(timezone=True), autoincrement=False, nullable=True),
sa.Column('mtime', postgresql.TIMESTAMP(timezone=True), autoincrement=False, nullable=True),
sa.Column('nodeversion', sa.INTEGER(), autoincrement=False, nullable=True),
sa.Column('public', sa.BOOLEAN(), autoincrement=False, nullable=True),
sa.Column('attributes', postgresql.JSONB(), autoincrement=False, nullable=True),
sa.Column('extras', postgresql.JSONB(), autoincrement=False, nullable=True),
sa.Column('dbcomputer_id', sa.INTEGER(), autoincrement=False, nullable=True),
sa.Column('user_id', sa.INTEGER(), autoincrement=False, nullable=False),
sa.ForeignKeyConstraint(['dbcomputer_id'], [u'db_dbcomputer.id'], name=u'db_dbnode_dbcomputer_id_fkey', ondelete=u'RESTRICT', initially=u'DEFERRED', deferrable=True),
sa.ForeignKeyConstraint(['user_id'], [u'db_dbuser.id'], name=u'db_dbnode_user_id_fkey', ondelete=u'RESTRICT', initially=u'DEFERRED', deferrable=True),
sa.PrimaryKeyConstraint('id', name=u'db_dbnode_pkey'),postgresql_ignore_search_path=False
)
op.create_index('ix_db_dbnode_label', 'db_dbnode', ['label'])
op.create_index('ix_db_dbnode_type', 'db_dbnode', ['type'])
op.create_table('db_dbgroup_dbnodes',
sa.Column('id', sa.INTEGER(), nullable=False),
sa.Column('dbnode_id', sa.INTEGER(), autoincrement=False, nullable=True),
sa.Column('dbgroup_id', sa.INTEGER(), autoincrement=False, nullable=True),
sa.ForeignKeyConstraint(['dbgroup_id'], [u'db_dbgroup.id'], name=u'db_dbgroup_dbnodes_dbgroup_id_fkey', initially=u'DEFERRED', deferrable=True),
sa.ForeignKeyConstraint(['dbnode_id'], [u'db_dbnode.id'], name=u'db_dbgroup_dbnodes_dbnode_id_fkey', initially=u'DEFERRED', deferrable=True),
sa.PrimaryKeyConstraint('id', name=u'db_dbgroup_dbnodes_pkey')
)
op.create_table('db_dblock',
sa.Column('key', sa.VARCHAR(length=255), autoincrement=False, nullable=False),
sa.Column('creation', postgresql.TIMESTAMP(timezone=True), autoincrement=False, nullable=True),
sa.Column('timeout', sa.INTEGER(), autoincrement=False, nullable=True),
sa.Column('owner', sa.VARCHAR(length=255), autoincrement=False, nullable=True),
sa.PrimaryKeyConstraint('key', name=u'db_dblock_pkey')
)
op.create_table('db_dbworkflowdata',
sa.Column('id', sa.INTEGER(), nullable=False),
sa.Column('parent_id', sa.INTEGER(), autoincrement=False, nullable=True),
sa.Column('name', sa.VARCHAR(length=255), autoincrement=False, nullable=True),
sa.Column('time', postgresql.TIMESTAMP(timezone=True), autoincrement=False, nullable=True),
sa.Column('data_type', sa.VARCHAR(length=255), autoincrement=False, nullable=True),
sa.Column('value_type', sa.VARCHAR(length=255), autoincrement=False, nullable=True),
sa.Column('json_value', sa.TEXT(), autoincrement=False, nullable=True),
sa.Column('aiida_obj_id', sa.INTEGER(), autoincrement=False, nullable=True),
sa.ForeignKeyConstraint(['aiida_obj_id'], [u'db_dbnode.id'], name=u'db_dbworkflowdata_aiida_obj_id_fkey'),
sa.ForeignKeyConstraint(['parent_id'], [u'db_dbworkflow.id'], name=u'db_dbworkflowdata_parent_id_fkey'),
sa.PrimaryKeyConstraint('id', name=u'db_dbworkflowdata_pkey'),
sa.UniqueConstraint('parent_id', 'name', 'data_type', name=u'db_dbworkflowdata_parent_id_name_data_type_key')
)
op.create_table('db_dblink',
sa.Column('id', sa.INTEGER(), nullable=False),
sa.Column('input_id', sa.INTEGER(), autoincrement=False, nullable=True),
sa.Column('output_id', sa.INTEGER(), autoincrement=False, nullable=True),
sa.Column('label', sa.VARCHAR(length=255), autoincrement=False, nullable=False),
sa.Column('type', sa.VARCHAR(length=255), autoincrement=False, nullable=True),
sa.ForeignKeyConstraint(['input_id'], [u'db_dbnode.id'], name=u'db_dblink_input_id_fkey', initially=u'DEFERRED', deferrable=True),
sa.ForeignKeyConstraint(['output_id'], [u'db_dbnode.id'], name=u'db_dblink_output_id_fkey', ondelete=u'CASCADE', initially=u'DEFERRED', deferrable=True),
sa.PrimaryKeyConstraint('id', name=u'db_dblink_pkey'),
)
op.create_index('ix_db_dblink_label', 'db_dblink', ['label'])
op.create_table('db_dbworkflowstep_calculations',
sa.Column('id', sa.INTEGER(), nullable=False),
sa.Column('dbworkflowstep_id', sa.INTEGER(), autoincrement=False, nullable=True),
sa.Column('dbnode_id', sa.INTEGER(), autoincrement=False, nullable=True),
sa.ForeignKeyConstraint(['dbnode_id'], [u'db_dbnode.id'], name=u'db_dbworkflowstep_calculations_dbnode_id_fkey'),
sa.ForeignKeyConstraint(['dbworkflowstep_id'], [u'db_dbworkflowstep.id'], name=u'db_dbworkflowstep_calculations_dbworkflowstep_id_fkey'),
sa.PrimaryKeyConstraint('id', name=u'db_dbworkflowstep_calculations_pkey'),
sa.UniqueConstraint('dbworkflowstep_id', 'dbnode_id', name=u'db_dbworkflowstep_calculations_id_dbnode_id_key')
)
op.create_table('db_dbpath',
sa.Column('id', sa.INTEGER(), nullable=False),
sa.Column('parent_id', sa.INTEGER(), autoincrement=False, nullable=True),
sa.Column('child_id', sa.INTEGER(), autoincrement=False, nullable=True),
sa.Column('depth', sa.INTEGER(), autoincrement=False, nullable=True),
sa.Column('entry_edge_id', sa.INTEGER(), autoincrement=False, nullable=True),
sa.Column('direct_edge_id', sa.INTEGER(), autoincrement=False, nullable=True),
sa.Column('exit_edge_id', sa.INTEGER(), autoincrement=False, nullable=True),
sa.ForeignKeyConstraint(['child_id'], [u'db_dbnode.id'], name=u'db_dbpath_child_id_fkey', initially=u'DEFERRED', deferrable=True),
sa.ForeignKeyConstraint(['parent_id'], [u'db_dbnode.id'], name=u'db_dbpath_parent_id_fkey', initially=u'DEFERRED', deferrable=True),
sa.PrimaryKeyConstraint('id', name=u'db_dbpath_pkey')
)
op.create_table('db_dbcalcstate',
sa.Column('id', sa.INTEGER(), nullable=False),
sa.Column('dbnode_id', sa.INTEGER(), autoincrement=False, nullable=True),
sa.Column('state', sa.VARCHAR(length=255), autoincrement=False, nullable=True),
sa.Column('time', postgresql.TIMESTAMP(timezone=True), autoincrement=False, nullable=True),
sa.ForeignKeyConstraint(['dbnode_id'], [u'db_dbnode.id'], name=u'db_dbcalcstate_dbnode_id_fkey', ondelete=u'CASCADE', initially=u'DEFERRED', deferrable=True),
sa.PrimaryKeyConstraint('id', name=u'db_dbcalcstate_pkey'),
sa.UniqueConstraint('dbnode_id', 'state', name=u'db_dbcalcstate_dbnode_id_state_key')
)
op.create_index('ix_db_dbcalcstate_state', 'db_dbcalcstate', ['state'])
op.create_table('db_dbsetting',
sa.Column('id', sa.INTEGER(), nullable=False),
sa.Column('key', sa.VARCHAR(length=255), autoincrement=False, nullable=False),
sa.Column('val', postgresql.JSONB(), autoincrement=False, nullable=True),
sa.Column('description', sa.VARCHAR(length=255), autoincrement=False, nullable=False),
sa.Column('time', postgresql.TIMESTAMP(timezone=True), autoincrement=False, nullable=True),
sa.PrimaryKeyConstraint('id', name=u'db_dbsetting_pkey'),
sa.UniqueConstraint('key', name=u'db_dbsetting_key_key')
)
op.create_index('ix_db_dbsetting_key', 'db_dbsetting', ['key'])
op.create_table('db_dbcomment',
sa.Column('id', sa.INTEGER(), nullable=False),
sa.Column('uuid', postgresql.UUID(), autoincrement=False, nullable=True),
sa.Column('dbnode_id', sa.INTEGER(), autoincrement=False, nullable=True),
sa.Column('ctime', postgresql.TIMESTAMP(timezone=True), autoincrement=False, nullable=True),
sa.Column('mtime', postgresql.TIMESTAMP(timezone=True), autoincrement=False, nullable=True),
sa.Column('user_id', sa.INTEGER(), autoincrement=False, nullable=True),
sa.Column('content', sa.TEXT(), autoincrement=False, nullable=True),
sa.ForeignKeyConstraint(['dbnode_id'], [u'db_dbnode.id'], name=u'db_dbcomment_dbnode_id_fkey', ondelete=u'CASCADE', initially=u'DEFERRED', deferrable=True),
sa.ForeignKeyConstraint(['user_id'], [u'db_dbuser.id'], name=u'db_dbcomment_user_id_fkey', ondelete=u'CASCADE', initially=u'DEFERRED', deferrable=True),
sa.PrimaryKeyConstraint('id', name=u'db_dbcomment_pkey')
)
op.create_table('db_dblog',
sa.Column('id', sa.INTEGER(), nullable=False),
sa.Column('time', postgresql.TIMESTAMP(timezone=True), autoincrement=False, nullable=True),
sa.Column('loggername', sa.VARCHAR(length=255), autoincrement=False, nullable=True),
sa.Column('levelname', sa.VARCHAR(length=255), autoincrement=False, nullable=True),
sa.Column('objname', sa.VARCHAR(length=255), autoincrement=False, nullable=True),
sa.Column('objpk', sa.INTEGER(), autoincrement=False, nullable=True),
sa.Column('message', sa.TEXT(), autoincrement=False, nullable=True),
sa.Column('metadata', postgresql.JSONB(), autoincrement=False, nullable=True),
sa.PrimaryKeyConstraint('id', name=u'db_dblog_pkey')
)
op.create_index('ix_db_dblog_levelname', 'db_dblog', ['levelname'])
op.create_index('ix_db_dblog_loggername', 'db_dblog', ['loggername'])
op.create_index('ix_db_dblog_objname', 'db_dblog', ['objname'])
op.create_index('ix_db_dblog_objpk', 'db_dblog', ['objpk'])
op.create_table('db_dbworkflowstep_sub_workflows',
sa.Column('id', sa.INTEGER(), nullable=False),
sa.Column('dbworkflowstep_id', sa.INTEGER(), autoincrement=False, nullable=True),
sa.Column('dbworkflow_id', sa.INTEGER(), autoincrement=False, nullable=True),
sa.ForeignKeyConstraint(['dbworkflow_id'], [u'db_dbworkflow.id'], name=u'db_dbworkflowstep_sub_workflows_dbworkflow_id_fkey'),
sa.ForeignKeyConstraint(['dbworkflowstep_id'], [u'db_dbworkflowstep.id'], name=u'db_dbworkflowstep_sub_workflows_dbworkflowstep_id_fkey'),
sa.PrimaryKeyConstraint('id', name=u'db_dbworkflowstep_sub_workflows_pkey'),
sa.UniqueConstraint('dbworkflowstep_id', 'dbworkflow_id', name=u'db_dbworkflowstep_sub_workflows_id_dbworkflow__key')
)
# I get the session using the alembic connection
# (Keep in mind that alembic uses the AiiDA SQLA
# session)
session = Session(bind=op.get_bind())
install_tc(session)
def run(self, *args):
from aiida.common.setup import (create_base_dirs, create_configuration,
set_default_profile, DEFAULT_UMASK)
from aiida.backends.profile import BACKEND_SQLA, BACKEND_DJANGO
from aiida.backends.utils import set_backend_type, get_backend_type
from aiida.common.exceptions import InvalidOperation
cmdline_args = list(args)
only_user_config = False
try:
cmdline_args.remove('--only-config')
only_user_config = True
except ValueError:
# Parameter not provided
pass
if cmdline_args:
print >> sys.stderr, "Unknown parameters on the command line: "
print >> sys.stderr, ", ".join(cmdline_args)
sys.exit(1)
# create the directories to store the configuration files
create_base_dirs()
# gprofile = 'default' if profile is None else profile
gprofile = 'default' if settings_profile.AIIDADB_PROFILE is None \
else settings_profile.AIIDADB_PROFILE
created_conf = None
# ask and store the configuration of the DB
try:
created_conf = create_configuration(profile=gprofile)
except ValueError as e:
print >> sys.stderr, "Error during configuration: {}".format(
e.message)
sys.exit(1)
# set default DB profiles
set_default_profile('verdi', gprofile, force_rewrite=False)
set_default_profile('daemon', gprofile, force_rewrite=False)
if only_user_config:
print(
"Only user configuration requested, "
"skipping the migrate command")
else:
print "Executing now a migrate command..."
backend_choice = created_conf['AIIDADB_BACKEND']
if backend_choice == BACKEND_DJANGO:
print("...for Django backend")
# The correct profile is selected within load_dbenv.
# Setting os.umask here since sqlite database gets created in
# this step.
old_umask = os.umask(DEFAULT_UMASK)
# This check should be done more properly
# try:
# backend_type = get_backend_type()
# except KeyError:
# backend_type = None
#
# if backend_type is not None and backend_type != BACKEND_DJANGO:
# raise InvalidOperation("An already existing database found"
# "and a different than the selected"
# "backend was used for its "
# "management.")
try:
pass_to_django_manage([execname, 'migrate'],
profile=gprofile)
finally:
os.umask(old_umask)
set_backend_type(BACKEND_DJANGO)
elif backend_choice == BACKEND_SQLA:
print("...for SQLAlchemy backend")
from aiida.backends.sqlalchemy.models.base import Base
from aiida.backends.sqlalchemy.utils import (get_engine,
install_tc)
from aiida.common.setup import get_profile_config
from aiida import is_dbenv_loaded, load_dbenv
if not is_dbenv_loaded():
load_dbenv()
# This check should be done more properly
# try:
# backend_type = get_backend_type()
# except KeyError:
# backend_type = None
#
# if backend_type is not None and backend_type != BACKEND_SQLA:
# raise InvalidOperation("An already existing database found"
# "and a different than the selected"
# "backend was used for its "
# "management.")
# Those import are necessary for SQLAlchemy to correctly create
# the needed database tables.
from aiida.backends.sqlalchemy.models.authinfo import (
DbAuthInfo)
from aiida.backends.sqlalchemy.models.comment import DbComment
from aiida.backends.sqlalchemy.models.computer import (
DbComputer)
from aiida.backends.sqlalchemy.models.group import (
DbGroup, table_groups_nodes)
from aiida.backends.sqlalchemy.models.lock import DbLock
from aiida.backends.sqlalchemy.models.log import DbLog
from aiida.backends.sqlalchemy.models.node import (DbLink,
DbNode,
DbPath,
DbCalcState)
from aiida.backends.sqlalchemy.models.user import DbUser
from aiida.backends.sqlalchemy.models.workflow import (
DbWorkflow, DbWorkflowData, DbWorkflowStep)
from aiida.backends.sqlalchemy.models.settings import DbSetting
connection = get_engine(get_profile_config(gprofile))
Base.metadata.create_all(connection)
install_tc(connection)
set_backend_type(BACKEND_SQLA)
else:
raise InvalidOperation("Not supported backend selected.")
print "Database was created successfully"
# I create here the default user
print "Loading new environment..."
if only_user_config:
from aiida.backends.utils import load_dbenv, is_dbenv_loaded
# db environment has not been loaded in this case
if not is_dbenv_loaded():
load_dbenv()
from aiida.common.setup import DEFAULT_AIIDA_USER
from aiida.orm.user import User as AiiDAUser
if not AiiDAUser.search_for_users(email=DEFAULT_AIIDA_USER):
print "Installing default AiiDA user..."
nuser = AiiDAUser(email=DEFAULT_AIIDA_USER)
nuser.first_name = "AiiDA"
nuser.last_name = "Daemon"
nuser.is_staff = True
nuser.is_active = True
nuser.is_superuser = True
nuser.force_save()
from aiida.common.utils import get_configured_user_email
email = get_configured_user_email()
print "Starting user configuration for {}...".format(email)
if email == DEFAULT_AIIDA_USER:
print "You set up AiiDA using the default Daemon email ({}),".format(
email)
print "therefore no further user configuration will be asked."
else:
# Ask to configure the new user
User().user_configure(email)
print "Install finished."
