def setUpClass(cls):
from aiida.orm.user import User
from aiida.orm.computer import Computer
from aiida.common.utils import get_configured_user_email
# I create the user only once:
# We create the user only once:
# Otherwise, get_automatic_user() will fail when the
# user is recreated because it caches the user!
# In any case, store it in cls.user though
# Other possibility: flush the user cache on delete
users = User.search_for_users(email=get_configured_user_email())
assert (len(users) <= 1)
if users:
cls.user = users[0]
else:
cls.user = User(get_configured_user_email())
cls.user.password = '******'
cls.user.save()
try:
cls.computer = Computer.get('test_comp')
except NotExistent:
cls.computer = Computer(name='test_comp',
hostname='localhost',
transport_type='local',
scheduler_type='pbspro',
workdir='/tmp/aiida')
cls.computer.store()
def get_schema(self):
# Construct the full class string
class_string = 'aiida.orm.' + self._aiida_type
# Load correspondent orm class
orm_class = get_object_from_string(class_string)
# Construct the json object to be returned
basic_schema = orm_class.get_schema()
schema = {}
ordering = []
# get addional info and column order from translator class
# and combine it with basic schema
if len(self._schema_projections["column_order"]) > 0:
for field in self._schema_projections["column_order"]:
# basic schema
if field in basic_schema.keys():
schema[field] = basic_schema[field]
else:
## Note: if column name starts with user_* get the schema information from
# user class. It is added mainly to handle user_email case.
# TODO need to improve
field_parts = field.split("_")
if field_parts[0] == "user" and field != "user_id" and len(
field_parts) > 1:
from aiida.orm.user import User
user_schema = User.get_schema()
if field_parts[1] in user_schema.keys():
schema[field] = user_schema[field_parts[1]]
else:
raise KeyError(
"{} is not present in user schema".format(
field))
else:
raise KeyError(
"{} is not present in ORM basic schema".format(
field))
# additional info defined in translator class
if field in self._schema_projections["additional_info"]:
schema[field].update(
self._schema_projections["additional_info"][field])
else:
raise KeyError(
"{} is not present in default projection additional info"
.format(field))
# order
ordering = self._schema_projections["column_order"]
else:
raise ConfigurationError(
"Define column order to get schema for {}".format(
self._aiida_type))
return dict(fields=schema, ordering=ordering)
def test_session_update_and_expiration_2(self):
"""
expire_on_commit=True & committing computer and code objects with
their built-in store function.
"""
from aiida.backends.sqlalchemy.models.user import DbUser
from aiida.orm.computer import Computer
from aiida.orm.code import Code
from aiida.orm.user import User
session = aiida.backends.sqlalchemy.get_scoped_session()
self.set_connection(expire_on_commit=True)
user = User(email=get_configured_user_email())
session.add(user._dbuser)
session.commit()
defaults = dict(name='localhost',
hostname='localhost',
transport_type='local',
scheduler_type='pbspro',
workdir='/tmp/aiida')
computer = Computer(**defaults)
computer.store()
code = Code()
code.set_remote_computer_exec((computer, '/x.x'))
code.store()
self.drop_connection()
def test_session_update_and_expiration_3(self):
"""
expire_on_commit=False & adding manually and committing
computer and code objects.
"""
from aiida.orm.computer import Computer
from aiida.orm.code import Code
from aiida.orm.user import User
self.set_connection(expire_on_commit=False)
session = aiida.backends.sqlalchemy.get_scoped_session()
user = User(email=get_configured_user_email())
session.add(user._dbuser)
session.commit()
defaults = dict(name='localhost',
hostname='localhost',
transport_type='local',
scheduler_type='pbspro',
workdir='/tmp/aiida')
computer = Computer(**defaults)
session.add(computer._dbcomputer)
session.commit()
code = Code()
code.set_remote_computer_exec((computer, '/x.x'))
session.add(code.dbnode)
session.commit()
self.drop_connection()
def setUpClass(cls, *args, **kwargs):
"""
Create some data needed for the tests
"""
super(TestVerdiDataCommands, cls).setUpClass()
from aiida.orm.user import User
from aiida.orm.group import Group
# Create a secondary user
new_email = "[email protected]"
new_user = User(email=new_email)
new_user.force_save()
# Create a group to add specific data inside
g1 = Group(name=cls.group_name)
g1.store()
cls.group_id = g1.id
cls.create_bands_data(cls.cmd_to_nodeid_map,
cls.cmd_to_nodeid_map_for_groups,
cls.cmd_to_nodeid_map_for_nuser, g1, new_user)
cls.create_structure_data(cls.cmd_to_nodeid_map,
cls.cmd_to_nodeid_map_for_groups,
cls.cmd_to_nodeid_map_for_nuser, g1,
new_user)
cls.create_cif_data(cls.cmd_to_nodeid_map,
cls.cmd_to_nodeid_map_for_groups,
cls.cmd_to_nodeid_map_for_nuser, g1, new_user)
cls.create_trajectory_data(cls.cmd_to_nodeid_map,
cls.cmd_to_nodeid_map_for_groups,
cls.cmd_to_nodeid_map_for_nuser, g1,
new_user)
def computer_enable(self, *args):
"""
Enable a computer.
"""
if not is_dbenv_loaded():
load_dbenv()
import argparse
from django.core.exceptions import ObjectDoesNotExist
from aiida.common.exceptions import NotExistent
from aiida.orm.implementation import User
parser = argparse.ArgumentParser(prog=self.get_full_command_name(),
description='Enable a computer')
# The default states are those that are shown if no option is given
parser.add_argument(
'-u',
'--only-for-user',
type=str,
metavar='EMAIL',
dest='user_email',
help="Enable a computer only for the given user. "
"If not specified, enables the computer "
"globally.",
)
parser.add_argument('computer',
type=str,
help="The name of the computer that you "
"want to enable")
parsed_args = parser.parse_args(args)
user_email = parsed_args.user_email
computername = parsed_args.computer
try:
computer = self.get_computer(name=computername)
except NotExistent:
print >> sys.stderr, "No computer exists with name '{}'".format(
computername)
sys.exit(1)
if user_email is None:
if computer.is_enabled():
print "Computer '{}' already enabled.".format(computername)
else:
computer.set_enabled_state(True)
print "Computer '{}' enabled.".format(computername)
else:
user_list = User.search_for_users(email=user_email)
if user_list is None or len(user_list) == 0:
print >> sys.stderr, ("No user with email '{}' in the "
"database.".format(user_email))
sys.exit(1)
user = user_list[0]
try:
dbauthinfo = computer.get_dbauthinfo(user._dbuser)
if not dbauthinfo.enabled:
dbauthinfo.enabled = True
dbauthinfo.save()
print "Computer '{}' enabled for user {}.".format(
computername, user.get_full_name())
else:
print "Computer '{}' was already enabled for user {} {}.".format(
computername, user.first_name, user.last_name)
except NotExistent:
print >> sys.stderr, ("User with email '{}' is not configured "
"for computer '{}' yet.".format(
user_email, computername))
sys.exit(1)
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."
def computer_disable(self, *args):
"""
Disable a computer.
If a computer is disabled, AiiDA does not try to connect to it to
submit new calculations or check for the state of existing calculations.
Useful, for instance, if you know that a computer is under maintenance.
"""
if not is_dbenv_loaded():
load_dbenv()
import argparse
from aiida.common.exceptions import NotExistent
parser = argparse.ArgumentParser(prog=self.get_full_command_name(),
description='Disable a computer')
# The default states are those that are shown if no option is given
parser.add_argument(
'-u',
'--only-for-user',
type=str,
metavar='EMAIL',
dest='user_email',
help="Disable a computer only for the given user. "
"If not specified, disables the computer "
"globally.",
)
parser.add_argument('computer',
type=str,
help="The name of the computer that you "
"want to disable")
parsed_args = parser.parse_args(args)
user_email = parsed_args.user_email
computername = parsed_args.computer
try:
computer = self.get_computer(name=computername)
except NotExistent:
print >> sys.stderr, "No computer exists with name '{}'".format(
computername)
sys.exit(1)
if user_email is None:
if not computer.is_enabled():
print "Computer '{}' already disabled.".format(computername)
else:
computer.set_enabled_state(False)
print "Computer '{}' disabled.".format(computername)
else:
user_list = User.search_for_users(email=user_email)
if user_list is None or len(user_list) == 0:
print >> sys.stderr, ("No user with email '{}' in the "
"database.".format(user_email))
sys.exit(1)
user = user_list[0]
try:
dbauthinfo = computer.get_dbauthinfo(user)
if dbauthinfo.enabled:
dbauthinfo.enabled = False
dbauthinfo.save()
print "Computer '{}' disabled for user {}.".format(
computername, user.get_full_name())
else:
print("Computer '{}' was already disabled for user {} {}.".
format(computername, user.first_name,
user.last_name))
except NotExistent:
print >> sys.stderr, ("User with email '{}' is not configured "
"for computer '{}' yet.".format(
user_email, computername))
def computer_test(self, *args):
"""
Test the connection to a computer.
It tries to connect, to get the list of calculations on the queue and
to perform other tests.
"""
import argparse
import traceback
if not is_dbenv_loaded():
load_dbenv()
from django.core.exceptions import ObjectDoesNotExist
from aiida.common.exceptions import NotExistent
from aiida.orm.user import User
from aiida.backends.utils import get_automatic_user
from aiida.orm.computer import Computer as OrmComputer
parser = argparse.ArgumentParser(prog=self.get_full_command_name(),
description='Test a remote computer')
# The default states are those that are shown if no option is given
parser.add_argument(
'-u',
'--user',
type=str,
metavar='EMAIL',
dest='user_email',
help="Test the connection for a given AiiDA user."
"If not specified, uses the current "
"default user.",
)
parser.add_argument(
'-t',
'--traceback',
action='store_true',
help="Print the full traceback in case an exception "
"is raised",
)
parser.add_argument('computer',
type=str,
help="The name of the computer that you "
"want to test")
parsed_args = parser.parse_args(args)
user_email = parsed_args.user_email
computername = parsed_args.computer
print_traceback = parsed_args.traceback
try:
computer = self.get_computer(name=computername)
except NotExistent:
print >> sys.stderr, "No computer exists with name '{}'".format(
computername)
sys.exit(1)
if user_email is None:
user = User(dbuser=get_automatic_user())
else:
user_list = User.search_for_users(email=user_email)
# If no user is found
if not user_list:
print >> sys.stderr, ("No user with email '{}' in the "
"database.".format(user_email))
sys.exit(1)
user = user_list[0]
print "Testing computer '{}' for user {}...".format(
computername, user.email)
try:
dbauthinfo = computer.get_dbauthinfo(user._dbuser)
except NotExistent:
print >> sys.stderr, ("User with email '{}' is not yet configured "
"for computer '{}' yet.".format(
user.email, computername))
sys.exit(1)
warning_string = None
if not dbauthinfo.enabled:
warning_string = (
"** NOTE! Computer is disabled for the "
"specified user!\n Do you really want to test it? [y/N] ")
if not computer.is_enabled():
warning_string = ("** NOTE! Computer is disabled!\n"
" Do you really want to test it? [y/N] ")
if warning_string:
answer = raw_input(warning_string)
if not (answer == 'y' or answer == 'Y'):
sys.exit(0)
s = OrmComputer(dbcomputer=dbauthinfo.dbcomputer).get_scheduler()
t = dbauthinfo.get_transport()
## STARTING TESTS HERE
num_failures = 0
num_tests = 0
try:
print "> Testing connection..."
with t:
s.set_transport(t)
num_tests += 1
for test in [
self._computer_test_get_jobs,
self._computer_create_temp_file
]:
num_tests += 1
try:
succeeded = test(transport=t,
scheduler=s,
dbauthinfo=dbauthinfo)
except Exception as e:
print "* The test raised an exception!"
if print_traceback:
print "** Full traceback:"
# Indent
print "\n".join([
" {}".format(l)
for l in traceback.format_exc().splitlines()
])
else:
print "** {}: {}".format(e.__class__.__name__,
e.message)
print(
"** (use the --traceback option to see the "
"full traceback)")
succeeded = False
if not succeeded:
num_failures += 1
if num_failures:
print "Some tests failed! ({} out of {} failed)".format(
num_failures, num_tests)
else:
print "Test completed (all {} tests succeeded)".format(
num_tests)
except Exception as e:
print "** Error while trying to connect to the computer! I cannot "
print " perform following tests, so I stop."
if print_traceback:
print "** Full traceback:"
# Indent
print "\n".join([
" {}".format(l)
for l in traceback.format_exc().splitlines()
])
else:
print "{}: {}".format(e.__class__.__name__, e.message)
print(
"(use the --traceback option to see the "
"full traceback)")
succeeded = False
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
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:
click.echo(
"--non-interactive requires all values to be given on the commandline! Missing argument: {}"
.format(e.message),
err=True)
sys.exit(1)
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
from aiida.backends import settings
from aiida.backends.sqlalchemy.utils import (
_load_dbenv_noschemacheck, check_schema_version)
from aiida.backends.profile import load_profile
# We avoid calling load_dbenv since we want to force the schema
# migration
if not is_dbenv_loaded():
settings.LOAD_DBENV_CALLED = True
# This is going to set global variables in settings, including
# settings.BACKEND
load_profile()
_load_dbenv_noschemacheck()
# Perform the needed migration quietly
check_schema_version(force_migration=True)
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
aiida.cmdline.commands.user.do_configure(
email=kwargs['email'],
first_name=kwargs.get('first_name'),
last_name=kwargs.get('last_name'),
institution=kwargs.get('institution'),
no_password=True,
non_interactive=non_interactive,
force=True)
print "Setup finished."
def get_bands_and_parents_structure(self, args):
"""
Search for bands and return bands and the closest structure that is a parent of the instance.
This is the backend independent way, can be overriden for performance reason
:returns:
A list of sublists, each latter containing (in order):
pk as string, formula as string, creation date, bandsdata-label
"""
import datetime
from aiida.utils import timezone
from aiida.orm.querybuilder import QueryBuilder
from aiida.backends.utils import get_automatic_user
from aiida.orm.implementation import User
from aiida.orm.implementation import Group
from aiida.orm.data.structure import (get_formula, get_symbols_string)
from aiida.orm.data.array.bands import BandsData
from aiida.orm.data.structure import StructureData
qb = QueryBuilder()
if args.all_users is False:
au = get_automatic_user()
user = User(dbuser=au)
qb.append(User, tag="creator", filters={"email": user.email})
else:
qb.append(User, tag="creator")
bdata_filters = {}
if args.past_days is not None:
now = timezone.now()
n_days_ago = now - datetime.timedelta(days=args.past_days)
bdata_filters.update({"ctime": {'>=': n_days_ago}})
qb.append(BandsData,
tag="bdata",
created_by="creator",
filters=bdata_filters,
project=["id", "label", "ctime"])
group_filters = {}
if args.group_name is not None:
group_filters.update({"name": {"in": args.group_name}})
if args.group_pk is not None:
group_filters.update({"id": {"in": args.group_pk}})
if group_filters:
qb.append(Group,
tag="group",
filters=group_filters,
group_of="bdata")
qb.append(
StructureData,
tag="sdata",
ancestor_of="bdata",
# We don't care about the creator of StructureData
project=["id", "attributes.kinds", "attributes.sites"])
qb.order_by({StructureData: {'ctime': 'desc'}})
list_data = qb.distinct()
entry_list = []
already_visited_bdata = set()
for [bid, blabel, bdate, sid, akinds, asites] in list_data.all():
# We process only one StructureData per BandsData.
# We want to process the closest StructureData to
# every BandsData.
# We hope that the StructureData with the latest
# creation time is the closest one.
# This will be updated when the QueryBuilder supports
# order_by by the distance of two nodes.
if already_visited_bdata.__contains__(bid):
continue
already_visited_bdata.add(bid)
if args.element is not None:
all_symbols = [_["symbols"][0] for _ in akinds]
if not any([s in args.element for s in all_symbols]):
continue
if args.element_only is not None:
all_symbols = [_["symbols"][0] for _ in akinds]
if not all([s in all_symbols for s in args.element_only]):
continue
# We want only the StructureData that have attributes
if akinds is None or asites is None:
continue
symbol_dict = {}
for k in akinds:
symbols = k['symbols']
weights = k['weights']
symbol_dict[k['name']] = get_symbols_string(symbols, weights)
try:
symbol_list = []
for s in asites:
symbol_list.append(symbol_dict[s['kind_name']])
formula = get_formula(symbol_list, mode=args.formulamode)
# If for some reason there is no kind with the name
# referenced by the site
except KeyError:
formula = "<<UNKNOWN>>"
entry_list.append(
[str(bid),
str(formula),
bdate.strftime('%d %b %Y'), blabel])
return entry_list
def code_list(self, *args):
"""
List available codes
"""
import argparse
parser = argparse.ArgumentParser(
prog=self.get_full_command_name(),
description='List the codes in the database.')
# The default states are those that are shown if no option is given
parser.add_argument(
'-c',
'--computer',
help="Filter only codes on a given computer",
)
parser.add_argument(
'-p',
'--plugin',
help="Filter only calculation with a given plugin",
)
parser.add_argument(
'-A',
'--all-users',
dest='all_users',
action='store_true',
help="Show codes of all users",
)
parser.add_argument(
'-o',
'--show-owner',
dest='show_owner',
action='store_true',
help="Show also the owner of the code",
)
parser.add_argument(
'-a',
'--all-codes',
action='store_true',
help="Show also hidden codes",
)
parser.set_defaults(all_users=False, hidden=False)
parsed_args = parser.parse_args(args)
computer_filter = parsed_args.computer
plugin_filter = parsed_args.plugin
all_users = parsed_args.all_users
show_owner = parsed_args.show_owner
reveal_filter = parsed_args.all_codes
from aiida.orm.querybuilder import QueryBuilder
from aiida.orm.code import Code
from aiida.orm.computer import Computer
from aiida.orm.user import User
from aiida.backends.utils import get_automatic_user
qb_user_filters = dict()
if not all_users:
user = User(dbuser=get_automatic_user())
qb_user_filters['email'] = user.email
qb_computer_filters = dict()
if computer_filter is not None:
qb_computer_filters['name'] = computer_filter
qb_code_filters = dict()
if plugin_filter is not None:
qb_code_filters['attributes.input_plugin'] = plugin_filter
if not reveal_filter:
qb_code_filters['attributes.hidden'] = {"~==": True}
qb = QueryBuilder()
qb.append(Code,
tag="code",
filters=qb_code_filters,
project=["id", "label"])
qb.append(Computer,
computer_of="code",
project=["name"],
filters=qb_computer_filters)
qb.append(User,
creator_of="code",
project=["email"],
filters=qb_user_filters)
print "# List of configured codes:"
print "# (use 'verdi code show CODEID' to see the details)"
if qb.count > 0:
for pk, label, computername, useremail in qb.iterall():
if show_owner:
owner_string = " ({})".format(useremail)
else:
owner_string = ""
if computername is None:
computernamestring = ""
else:
computernamestring = "@{}".format(computername)
print "* pk {} - {}{}{}".format(pk, label, computernamestring,
owner_string)
else:
print "# No codes found matching the specified criteria."
def code_list(self, *args):
"""
List available codes
"""
import argparse
parser = argparse.ArgumentParser(
prog=self.get_full_command_name(),
description='List the codes in the database.')
# The default states are those that are shown if no option is given
parser.add_argument(
'-c',
'--computer',
help="Filter only codes on a given computer",
)
parser.add_argument(
'-p',
'--plugin',
help="Filter only calculation with a given plugin",
)
parser.add_argument(
'-A',
'--all-users',
dest='all_users',
action='store_true',
help="Show codes of all users",
)
parser.add_argument(
'-o',
'--show-owner',
dest='show_owner',
action='store_true',
help="Show also the owner of the code",
)
parser.add_argument(
'-a',
'--all-codes',
action='store_true',
help="Show also hidden codes",
)
parser.set_defaults(all_users=False, hidden=False)
parsed_args = parser.parse_args(args)
computer_filter = parsed_args.computer
plugin_filter = parsed_args.plugin
all_users = parsed_args.all_users
show_owner = parsed_args.show_owner
reveal_filter = parsed_args.all_codes
from aiida.orm.querybuilder import QueryBuilder
from aiida.orm.code import Code
from aiida.orm.computer import Computer
from aiida.orm.user import User
from aiida.backends.utils import get_automatic_user
qb_user_filters = dict()
if not all_users:
user = User(dbuser=get_automatic_user())
qb_user_filters['email'] = user.email
qb_computer_filters = dict()
if computer_filter is not None:
qb_computer_filters['name'] = computer_filter
qb_code_filters = dict()
if plugin_filter is not None:
qb_code_filters['attributes.input_plugin'] = plugin_filter
if not reveal_filter:
qb_code_filters['attributes.hidden'] = {"~==": True}
print "# List of configured codes:"
print "# (use 'verdi code show CODEID' to see the details)"
if computer_filter is not None:
qb = QueryBuilder()
qb.append(Code,
tag="code",
filters=qb_code_filters,
project=["id", "label"])
# We have a user assigned to the code so we can ask for the
# presence of a user even if there is no user filter
qb.append(User,
creator_of="code",
project=["email"],
filters=qb_user_filters)
# We also add the filter on computer. This will automatically
# return codes that have a computer (and of course satisfy the
# other filters). The codes that have a computer attached are the
# remote codes.
qb.append(Computer,
computer_of="code",
project=["name"],
filters=qb_computer_filters)
self.print_list_res(qb, show_owner)
# If there is no filter on computers
else:
# Print all codes that have a computer assigned to them
# (these are the remote codes)
qb = QueryBuilder()
qb.append(Code,
tag="code",
filters=qb_code_filters,
project=["id", "label"])
# We have a user assigned to the code so we can ask for the
# presence of a user even if there is no user filter
qb.append(User,
creator_of="code",
project=["email"],
filters=qb_user_filters)
qb.append(Computer, computer_of="code", project=["name"])
self.print_list_res(qb, show_owner)
# Now print all the local codes. To get the local codes we ask
# the dbcomputer_id variable to be None.
qb = QueryBuilder()
comp_non_existence = {"dbcomputer_id": {"==": None}}
if not qb_code_filters:
qb_code_filters = comp_non_existence
else:
new_qb_code_filters = {
"and": [qb_code_filters, comp_non_existence]
}
qb_code_filters = new_qb_code_filters
qb.append(Code,
tag="code",
filters=qb_code_filters,
project=["id", "label"])
# We have a user assigned to the code so we can ask for the
# presence of a user even if there is no user filter
qb.append(User,
creator_of="code",
project=["email"],
filters=qb_user_filters)
self.print_list_res(qb, show_owner)
def test_configure_from_file(configure):
from aiida.orm.user import User
user = User.get_all_users()[0]
assert user.first_name == 'AiiDA'
def test_6(self):
"""
This test checks that nodes belonging to user A (which is not the
default user) can be correctly exported, imported, enriched with nodes
from the default user, re-exported & re-imported and that in the end
all the nodes that have been finally imported belonging to the right
users.
"""
import os
import shutil
import tempfile
from aiida.orm import load_node
from aiida.orm.calculation.job import JobCalculation
from aiida.orm.data.structure import StructureData
from aiida.orm.importexport import export
from aiida.common.datastructures import calc_states
from aiida.common.links import LinkType
from aiida.common.utils import get_configured_user_email
from aiida.orm.user import User
# Creating a folder for the import/export files
temp_folder = tempfile.mkdtemp()
try:
# Create another user
new_email = "[email protected]"
user = User(email=new_email)
user.force_save()
# Create a structure data node that has a calculation as output
sd1 = StructureData()
sd1.dbnode.user = user._dbuser
sd1.label = 'sd1'
sd1.store()
jc1 = JobCalculation()
jc1.set_computer(self.computer)
jc1.set_resources({"num_machines": 1, "num_mpiprocs_per_machine": 1})
jc1.dbnode.user = user._dbuser
jc1.label = 'jc1'
jc1.store()
jc1.add_link_from(sd1)
jc1._set_state(calc_states.PARSING)
# Create some nodes from a different user
sd2 = StructureData()
sd2.dbnode.user = user._dbuser
sd2.label = 'sd2'
sd2.store()
sd2.add_link_from(jc1, label='l1', link_type=LinkType.RETURN)
# Set the jc1 to FINISHED
jc1._set_state(calc_states.FINISHED)
# At this point we export the generated data
filename1 = os.path.join(temp_folder, "export1.tar.gz")
export([sd2.dbnode], outfile=filename1, silent=True)
uuids1 = [sd1.uuid, jc1.uuid, sd2.uuid]
self.clean_db()
self.insert_data()
import_data(filename1, silent=True)
# Check that the imported nodes are correctly imported and that
# the user assigned to the nodes is the right one
for uuid in uuids1:
self.assertEquals(load_node(uuid).get_user().email, new_email)
# Now we continue to generate more data based on the imported
# data
sd2_imp = load_node(sd2.uuid)
jc2 = JobCalculation()
jc2.set_computer(self.computer)
jc2.set_resources({"num_machines": 1, "num_mpiprocs_per_machine": 1})
jc2.label = 'jc2'
jc2.store()
jc2.add_link_from(sd2_imp, label='l2')
jc2._set_state(calc_states.PARSING)
sd3 = StructureData()
sd3.label = 'sd3'
sd3.store()
sd3.add_link_from(jc2, label='l3', link_type=LinkType.RETURN)
# Set the jc2 to FINISHED
jc2._set_state(calc_states.FINISHED)
# Store the UUIDs of the nodes that should be checked
# if they can be imported correctly.
uuids2 = [jc2.uuid, sd3.uuid]
filename2 = os.path.join(temp_folder, "export2.tar.gz")
export([sd3.dbnode], outfile=filename2, silent=True)
self.clean_db()
self.insert_data()
import_data(filename2, silent=True)
# Check that the imported nodes are correctly imported and that
# the user assigned to the nodes is the right one
for uuid in uuids1:
self.assertEquals(load_node(uuid).get_user().email, new_email)
for uuid in uuids2:
self.assertEquals(load_node(uuid).get_user().email,
get_configured_user_email())
finally:
# Deleting the created temporary folder
shutil.rmtree(temp_folder, ignore_errors=True)
def test_5(self):
"""
This test checks that nodes belonging to different users are correctly
exported & imported.
"""
import os
import shutil
import tempfile
from aiida.orm import load_node
from aiida.orm.calculation.job import JobCalculation
from aiida.orm.data.structure import StructureData
from aiida.orm.importexport import export
from aiida.common.datastructures import calc_states
from aiida.common.links import LinkType
from aiida.orm.user import User
from aiida.common.utils import get_configured_user_email
# Creating a folder for the import/export files
temp_folder = tempfile.mkdtemp()
try:
# Create another user
new_email = "[email protected]"
user = User(email=new_email)
user.force_save()
# Create a structure data node that has a calculation as output
sd1 = StructureData()
sd1.dbnode.user = user._dbuser
sd1.label = 'sd1'
sd1.store()
jc1 = JobCalculation()
jc1.set_computer(self.computer)
jc1.set_resources({"num_machines": 1, "num_mpiprocs_per_machine": 1})
jc1.dbnode.user = user._dbuser
jc1.label = 'jc1'
jc1.store()
jc1.add_link_from(sd1)
jc1._set_state(calc_states.PARSING)
# Create some nodes from a different user
sd2 = StructureData()
sd2.dbnode.user = user._dbuser
sd2.label = 'sd2'
sd2.store()
sd2.add_link_from(jc1, label='l1', link_type=LinkType.RETURN)
jc2 = JobCalculation()
jc2.set_computer(self.computer)
jc2.set_resources({"num_machines": 1, "num_mpiprocs_per_machine": 1})
jc2.label = 'jc2'
jc2.store()
jc2.add_link_from(sd2, label='l2')
jc2._set_state(calc_states.PARSING)
sd3 = StructureData()
sd3.label = 'sd3'
sd3.store()
sd3.add_link_from(jc2, label='l3', link_type=LinkType.RETURN)
uuids_u1 = [sd1.uuid, jc1.uuid, sd2.uuid]
uuids_u2 = [jc2.uuid, sd3.uuid]
filename = os.path.join(temp_folder, "export.tar.gz")
export([sd3.dbnode], outfile=filename, silent=True)
self.clean_db()
import_data(filename, silent=True)
# Check that the imported nodes are correctly imported and that
# the user assigned to the nodes is the right one
for uuid in uuids_u1:
self.assertEquals(load_node(uuid).get_user().email, new_email)
for uuid in uuids_u2:
self.assertEquals(load_node(uuid).get_user().email,
get_configured_user_email())
finally:
# Deleting the created temporary folder
shutil.rmtree(temp_folder, ignore_errors=True)
def configure_user(self, *args):
"""
Configure the user that can run the daemon.
"""
if not is_dbenv_loaded():
from aiida.backends.utils import load_dbenv
load_dbenv(process='daemon')
if args:
print >> sys.stderr, (
"No arguments allowed for the '{}' command.".format(
self.get_full_command_name()))
sys.exit(1)
from aiida.utils import timezone
from aiida.backends.utils import get_daemon_user, set_daemon_user
from aiida.common.utils import (get_configured_user_email,
query_yes_no, query_string)
from aiida.daemon.timestamps import get_most_recent_daemon_timestamp
from aiida.common.utils import str_timedelta
from aiida.orm.user import User
old_daemon_user = get_daemon_user()
this_user = get_configured_user_email()
print("> Current default user: {}".format(this_user))
print("> Currently configured user who can run the daemon: {}".format(
old_daemon_user))
if old_daemon_user == this_user:
print(
" (therefore, at the moment you are the user who can run "
"the daemon)")
pid = self.get_daemon_pid()
if pid is not None:
print("The daemon is running! I will not proceed.")
sys.exit(1)
else:
print(" (therefore, you cannot run the daemon, at the moment)")
most_recent_timestamp = get_most_recent_daemon_timestamp()
print "*" * 76
print "* {:72s} *".format("WARNING! Change this setting only if you "
"are sure of what you are doing.")
print "* {:72s} *".format("Moreover, make sure that the "
"daemon is stopped.")
if most_recent_timestamp is not None:
timestamp_delta = timezone.now() - most_recent_timestamp
last_check_string = (
"[The most recent timestamp from the daemon was {}]".format(
str_timedelta(timestamp_delta)))
print "* {:72s} *".format(last_check_string)
print "*" * 76
answer = query_yes_no(
"Are you really sure that you want to change "
"the daemon user?",
default="no")
if not answer:
sys.exit(0)
print ""
print "Enter below the email of the new user who can run the daemon."
new_daemon_user_email = query_string("New daemon user: "******"ERROR! The user you specified ({}) does "
"not exist in the database!!".format(new_daemon_user_email))
print("The available users are {}".format(
[_.email for _ in User.search_for_users()]))
sys.exit(1)
set_daemon_user(new_daemon_user_email)
print "The new user that can run the daemon is now {} {}.".format(
found_users[0].first_name, found_users[0].last_name)
def get_aiida_class(self):
from aiida.orm.user import User
return User(dbuser=self)