def get_aiida_class(self):
"""
Return the corresponding aiida instance of class aiida.orm.Node or a
appropriate subclass.
"""
from aiida.common.pluginloader import from_type_to_pluginclassname
from aiida.orm.node import Node
try:
pluginclassname = from_type_to_pluginclassname(self.type)
except DbContentError:
raise DbContentError("The type name of node with pk= {} is "
"not valid: '{}'".format(self.pk, self.type))
try:
PluginClass = load_plugin(Node, 'aiida.orm', pluginclassname)
except MissingPluginError:
aiidalogger.error("Unable to find plugin for type '{}' (node= {}), "
"will use base Node class".format(self.type, self.pk))
PluginClass = Node
return PluginClass(dbnode=self)
def group_show(self, *args):
"""
Show information on a given group. Pass the PK as a parameter.
"""
if not is_dbenv_loaded():
load_dbenv()
import argparse
from aiida.common.exceptions import NotExistent
from aiida.orm import Group as G
from aiida.common.utils import str_timedelta
from aiida.utils import timezone
from aiida.common.pluginloader import from_type_to_pluginclassname
from tabulate import tabulate
parser = argparse.ArgumentParser(
prog=self.get_full_command_name(),
description='Information on a given AiiDA group.')
parser.add_argument('-r', '--raw',
dest='raw', action='store_true',
help="Show only a space-separated list of PKs of "
"the calculations in the group")
parser.add_argument('-u', '--uuid',
dest='uuid', action='store_true',
help="Show UUIDs together with PKs. Note: if the "
"--raw option is also passed, PKs are not "
"printed, but oly UUIDs.")
parser.add_argument('GROUP', help="The PK of the group to show")
parser.set_defaults(raw=False)
parser.set_defaults(uuid=False)
args = list(args)
parsed_args = parser.parse_args(args)
group = parsed_args.GROUP
try:
group_pk = int(group)
except ValueError:
group_pk = None
group_name = group
if group_pk is not None:
try:
group = G(dbgroup=group_pk)
except NotExistent as e:
print >> sys.stderr, "Error: {}.".format(e.message)
sys.exit(1)
else:
try:
group = G.get_from_string(group_name)
except NotExistent as e:
print >> sys.stderr, "Error: {}.".format(e.message)
sys.exit(1)
group_pk = group.pk
group_name = group.name
if parsed_args.raw:
if parsed_args.uuid:
print " ".join(str(_.uuid) for _ in group.nodes)
else:
print " ".join(str(_.pk) for _ in group.nodes)
else:
type_string = group.type_string
desc = group.description
now = timezone.now()
table = []
table.append(["Group name", group.name])
table.append(["Group type",
type_string if type_string else "<user-defined>"])
table.append(["Group description",
desc if desc else "<no description>"])
print(tabulate(table))
table = []
header = []
if parsed_args.uuid:
header.append('UUID')
header.extend(['PK', 'Type', 'Created'])
print "# Nodes:"
for n in group.nodes:
row = []
if parsed_args.uuid:
row.append(n.uuid)
row.append(n.pk)
row.append(from_type_to_pluginclassname(n.dbnode.type).
rsplit(".", 1)[1])
row.append(str_timedelta(now - n.ctime, short=True,
negative_to_zero=True))
table.append(row)
print(tabulate(table, headers=header))
def _list_calculations_old(cls,
states=None,
past_days=None,
group=None,
group_pk=None,
all_users=False,
pks=[],
relative_ctime=True):
"""
Return a string with a description of the AiiDA calculations.
.. todo:: does not support the query for the IMPORTED state (since it
checks the state in the Attributes, not in the DbCalcState table).
Decide which is the correct logi and implement the correct query.
:param states: a list of string with states. If set, print only the
calculations in the states "states", otherwise shows all.
Default = None.
:param past_days: If specified, show only calculations that were
created in the given number of past days.
:param group: If specified, show only calculations belonging to a
user-defined group with the given name.
Can use colons to separate the group name from the type,
as specified in :py:meth:`aiida.orm.group.Group.get_from_string`
method.
:param group_pk: If specified, show only calculations belonging to a
user-defined group with the given PK.
:param pks: if specified, must be a list of integers, and only
calculations within that list are shown. Otherwise, all
calculations are shown.
If specified, sets state to None and ignores the
value of the ``past_days`` option.")
:param relative_ctime: if true, prints the creation time relative from now.
(like 2days ago). Default = True
:param all_users: if True, list calculation belonging to all users.
Default = False
:return: a string with description of calculations.
"""
# I assume that calc_states are strings. If this changes in the future,
# update the filter below from dbattributes__tval to the correct field.
from aiida.backends.djsite.db.models import DbAuthInfo, DbAttribute
from aiida.daemon.timestamps import get_last_daemon_timestamp
if states:
for state in states:
if state not in calc_states:
return "Invalid state provided: {}.".format(state)
warnings_list = []
now = timezone.now()
if pks:
q_object = Q(pk__in=pks)
else:
q_object = Q()
if group is not None:
g_pk = Group.get_from_string(group).pk
q_object.add(Q(dbgroups__pk=g_pk), Q.AND)
if group_pk is not None:
q_object.add(Q(dbgroups__pk=group_pk), Q.AND)
if not all_users:
q_object.add(Q(user=get_automatic_user()), Q.AND)
if states is not None:
q_object.add(
Q(
dbattributes__key='state',
dbattributes__tval__in=states,
), Q.AND)
if past_days is not None:
now = timezone.now()
n_days_ago = now - datetime.timedelta(days=past_days)
q_object.add(Q(ctime__gte=n_days_ago), Q.AND)
calc_list_pk = list(
cls.query(q_object).distinct().values_list('pk', flat=True))
calc_list = cls.query(pk__in=calc_list_pk).order_by('ctime')
scheduler_states = dict(
DbAttribute.objects.filter(dbnode__pk__in=calc_list_pk,
key='scheduler_state').values_list(
'dbnode__pk', 'tval'))
# I do the query now, so that the list of pks gets cached
calc_list_data = list(
calc_list.filter(
# dbcomputer__dbauthinfo__aiidauser=F('user')
).distinct().order_by('ctime').values('pk', 'dbcomputer__name',
'ctime', 'type',
'dbcomputer__enabled',
'dbcomputer__pk',
'user__pk'))
list_comp_pk = [i['dbcomputer__pk'] for i in calc_list_data]
list_aiduser_pk = [i['user__pk'] for i in calc_list_data]
enabled_data = DbAuthInfo.objects.filter(
dbcomputer__pk__in=list_comp_pk,
aiidauser__pk__in=list_aiduser_pk).values_list(
'dbcomputer__pk', 'aiidauser__pk', 'enabled')
enabled_auth_dict = {(i[0], i[1]): i[2] for i in enabled_data}
states = {c.pk: c._get_state_string() for c in calc_list}
scheduler_lastcheck = dict(
DbAttribute.objects.filter(
dbnode__in=calc_list,
key='scheduler_lastchecktime').values_list(
'dbnode__pk', 'dval'))
## Get the last daemon check
try:
last_daemon_check = get_last_daemon_timestamp('updater',
when='stop')
except ValueError:
last_check_string = ("# Last daemon state_updater check: "
"(Error while retrieving the information)")
else:
if last_daemon_check is None:
last_check_string = "# Last daemon state_updater check: (Never)"
else:
last_check_string = ("# Last daemon state_updater check: "
"{} ({})".format(
str_timedelta(now - last_daemon_check,
negative_to_zero=True),
timezone.localtime(last_daemon_check).
strftime("at %H:%M:%S on %Y-%m-%d")))
disabled_ignorant_states = [
None, calc_states.FINISHED, calc_states.SUBMISSIONFAILED,
calc_states.RETRIEVALFAILED, calc_states.PARSINGFAILED,
calc_states.FAILED
]
if not calc_list:
return last_check_string
else:
# first save a matrix of results to be printed
res_str_list = [last_check_string]
str_matrix = []
title = [
'# Pk', 'State', 'Creation', 'Sched. state', 'Computer', 'Type'
]
str_matrix.append(title)
len_title = [len(i) for i in title]
for calcdata in calc_list_data:
remote_state = "None"
calc_state = states[calcdata['pk']]
remote_computer = calcdata['dbcomputer__name']
try:
sched_state = scheduler_states.get(calcdata['pk'], None)
if sched_state is None:
remote_state = "(unknown)"
else:
remote_state = '{}'.format(sched_state)
if calc_state == calc_states.WITHSCHEDULER:
last_check = scheduler_lastcheck.get(
calcdata['pk'], None)
if last_check is not None:
when_string = " {}".format(
str_timedelta(now - last_check,
short=True,
negative_to_zero=True))
verb_string = "was "
else:
when_string = ""
verb_string = ""
remote_state = "{}{}{}".format(
verb_string, sched_state, when_string)
except ValueError:
raise
calc_module = \
from_type_to_pluginclassname(calcdata['type']).rsplit(".", 1)[0]
prefix = 'calculation.job.'
prefix_len = len(prefix)
if calc_module.startswith(prefix):
calc_module = calc_module[prefix_len:].strip()
if relative_ctime:
calc_ctime = str_timedelta(now - calcdata['ctime'],
negative_to_zero=True,
max_num_fields=1)
else:
calc_ctime = " ".join([
timezone.localtime(
calcdata['ctime']).isoformat().split('T')[0],
timezone.localtime(
calcdata['ctime']).isoformat().split('T')[1].split(
'.')[0].rsplit(":", 1)[0]
])
the_state = states[calcdata['pk']]
# decide if it is needed to print enabled/disabled information
# By default, if the computer is not configured for the
# given user, assume it is user_enabled
user_enabled = enabled_auth_dict.get(
(calcdata['dbcomputer__pk'], calcdata['user__pk']), True)
global_enabled = calcdata["dbcomputer__enabled"]
enabled = "" if (user_enabled and global_enabled
or the_state in disabled_ignorant_states
) else " [Disabled]"
str_matrix.append([
calcdata['pk'], the_state, calc_ctime, remote_state,
remote_computer + "{}".format(enabled), calc_module
])
# prepare a formatted text of minimal row length (to fit in terminals!)
rows = []
for j in range(len(str_matrix[0])):
rows.append([len(str(i[j])) for i in str_matrix])
line_lengths = [
str(max(max(rows[i]), len_title[i])) for i in range(len(rows))
]
fmt_string = "{:<" + "}|{:<".join(line_lengths) + "}"
for row in str_matrix:
res_str_list.append(fmt_string.format(*[str(i) for i in row]))
res_str_list += ["# {}".format(_) for _ in warnings_list]
return "\n".join(res_str_list)
def get_ormclass(self, cls, ormclasstype):
"""
Return the valid ormclass for the connections
"""
# Checks whether valid cls and ormclasstype are done before
# If it is a class:
if cls:
# Nodes:
if issubclass(cls, self.Node):
# If something pass an ormclass node
# Users wouldn't do that, by why not...
ormclasstype = self.AiidaNode._plugin_type_string
query_type_string = self.AiidaNode._query_type_string
ormclass = cls
elif issubclass(cls, self.AiidaNode):
ormclasstype = cls._plugin_type_string
query_type_string = cls._query_type_string
ormclass = self.Node
# Groups:
elif issubclass(cls, self.Group):
ormclasstype = 'group'
query_type_string = None
ormclass = cls
elif issubclass(cls, self.AiidaGroup):
ormclasstype = 'group'
query_type_string = None
ormclass = self.Group
# Computers:
elif issubclass(cls, self.Computer):
ormclasstype = 'computer'
query_type_string = None
ormclass = cls
elif issubclass(cls, self.AiidaComputer):
ormclasstype = 'computer'
query_type_string = None
ormclass = self.Computer
# Users
elif issubclass(cls, self.User):
ormclasstype = 'user'
query_type_string = None
ormclass = cls
elif issubclass(cls, self.AiidaUser):
ormclasstype = 'user'
query_type_string = None
ormclass = self.User
else:
raise InputValidationError("\n\n\n"
"I do not know what to do with {}"
"\n\n\n".format(cls))
# If it is not a class
else:
if ormclasstype.lower() == 'group':
ormclasstype = ormclasstype.lower()
query_type_string = None
ormclass = self.Group
elif ormclasstype.lower() == 'computer':
ormclasstype = ormclasstype.lower()
query_type_string = None
ormclass = self.Computer
elif ormclasstype.lower() == 'user':
ormclasstype = ormclasstype.lower()
query_type_string = None
ormclass = self.User
else:
# At this point, it has to be a node.
# The only valid string at this point is a string
# that matches exactly the _plugin_type_string
# of a node class
from aiida.common.pluginloader import (
from_type_to_pluginclassname, load_plugin)
ormclass = self.Node
try:
pluginclassname = from_type_to_pluginclassname(
ormclasstype)
# I want to check at this point if that is a valid class,
# so I use the load_plugin to load the plugin class
# and use the classes _plugin_type_string attribute
# In the future, assuming the user knows what he or she is doing
# we could remove that check
# The query_type_string we can get from
# the aiida.common.pluginloader function get_query_type_string
PluginClass = load_plugin(self.AiidaNode, 'aiida.orm',
pluginclassname)
except (DbContentError, MissingPluginError) as e:
raise InputValidationError(
"\nYou provide a vertice of the path with\n"
"type={}\n"
"But that string is not a valid type string\n"
"Exception raise during check\n"
"{}".format(ormclasstype, e))
ormclasstype = PluginClass._plugin_type_string
query_type_string = PluginClass._query_type_string
return ormclass, ormclasstype, query_type_string