def get_code_helper(cls, label, machinename=None):
"""
:param label: the code label identifying the code to load
:param machinename: the machine name where code is setup
:raise aiida.common.NotExistent: if no code identified by the given string is found
:raise aiida.common.MultipleObjectsError: if the string cannot identify uniquely
a code
"""
from aiida.common.exceptions import NotExistent, MultipleObjectsError
from aiida.orm.querybuilder import QueryBuilder
from aiida.orm.computers import Computer
qb = QueryBuilder()
qb.append(cls, filters={'label': {'==': label}}, project=['*'], tag='code')
if machinename:
qb.append(Computer, filters={'name': {'==': machinename}}, with_node='code')
if qb.count() == 0:
raise NotExistent("'{}' is not a valid code name.".format(label))
elif qb.count() > 1:
codes = qb.all(flat=True)
retstr = ("There are multiple codes with label '{}', having IDs: ".format(label))
retstr += ', '.join(sorted([str(c.pk) for c in codes])) + '.\n'
retstr += ('Relabel them (using their ID), or refer to them with their ID.')
raise MultipleObjectsError(retstr)
else:
return qb.first()[0]
def get_subclass_from_pk(cls, pk):
from aiida.orm.querybuilder import QueryBuilder
from sqlalchemy.exc import DatabaseError
# If it is not an int make a final attempt
# to convert to an integer. If you fail,
# raise an exception.
try:
pk = int(pk)
except:
raise ValueError("Incorrect type for int")
try:
qb = QueryBuilder()
qb.append(cls, filters={'id': {'==': pk}})
if qb.count() == 0:
raise NotExistent("No entry with pk= {} found".format(pk))
node = qb.first()[0]
if not isinstance(node, cls):
raise NotExistent("pk= {} is not an instance of {}".format(
pk, cls.__name__))
return node
except DatabaseError as de:
raise ValueError(de.message)
def get_calc_by_label(workcalc, label):
qb = QueryBuilder()
qb.append(WorkChainNode, filters={'uuid':workcalc.uuid})
qb.append(CalcJob, with_incoming=WorkChainNode, filters={'label':label})
assert qb.count() == 1
calc = qb.first()[0]
assert(calc.is_finished_ok)
return calc
def get_calc_by_label(workcalc, label):
qb = QueryBuilder()
qb.append(WorkCalculation, filters={'uuid': workcalc.uuid})
qb.append(JobCalculation,
output_of=WorkCalculation,
filters={'label': label})
assert qb.count() == 1
calc = qb.first()[0]
assert (calc.get_state() == 'FINISHED')
return calc
def node(self, info, uuid: strawberry.ID) -> typing.Optional[Node]:
q = QueryBuilder()
q.append(orm.Node, filters={"uuid": {"==": uuid}}, project=["*"])
entry = q.first()
if entry:
# TODO: call function to return proper type depending AiiDA node_type, e.g. the generic version of:
# if entry[0].node_type == "data.gaussian.basisset.BasisSet.":
# return GaussianBasisset.from_orm(entry)
return BareNode.from_orm(entry)
return None
def computer(self, info, uuid: strawberry.ID) -> typing.Optional[Computer]:
try:
UUID(uuid)
except ValueError:
raise ValueError("invalid value passed for uuid"
) from None # mask original exception completely
q = QueryBuilder()
q.append(orm.Computer, filters={"uuid": {"==": uuid}}, project=["*"])
entry = q.first()
if entry:
return Computer.from_orm(entry)
return None
def get_subclass_from_uuid(cls, uuid):
from aiida.orm.querybuilder import QueryBuilder
from sqlalchemy.exc import DatabaseError
try:
qb = QueryBuilder()
qb.append(cls, filters={'uuid': {'==': str(uuid)}})
if qb.count() == 0:
raise NotExistent("No entry with UUID={} found".format(uuid))
node = qb.first()[0]
if not isinstance(node, cls):
raise NotExistent("UUID={} is not an instance of {}".format(
uuid, cls.__name__))
return node
except DatabaseError as de:
raise ValueError(de.message)
def _retrieve_basis_sets(files, stop_if_existing):
""" get existing basis sets or create if not
:param files: list of basis set file paths
:param stop_if_existing: if True, check for the md5 of the files and,
if the file already exists in the DB, raises a MultipleObjectsError.
If False, simply adds the existing BasisSetData node to the group.
:return:
"""
from aiida.orm.querybuilder import QueryBuilder
basis_and_created = []
for f in files:
_, content = parse_basis(f)
md5sum = md5_from_string(content)
qb = QueryBuilder()
qb.append(BasisSetData, filters={'attributes.md5': {'==': md5sum}})
existing_basis = qb.first()
if existing_basis is None:
# return the basis set data instances, not stored
basisset, created = BasisSetData.get_or_create(f,
use_first=True,
store_basis=False)
# to check whether only one basis set per element exists
# NOTE: actually, created has the meaning of "to_be_created"
basis_and_created.append((basisset, created))
else:
if stop_if_existing:
raise ValueError("A Basis Set with identical MD5 to "
" {} cannot be added with stop_if_existing"
"".format(f))
existing_basis = existing_basis[0]
basis_and_created.append((existing_basis, False))
return basis_and_created
def get_io_tree(self, uuid_pattern, tree_in_limit, tree_out_limit):
# pylint: disable=too-many-statements,too-many-locals
"""
json data to display nodes in tree format
:param uuid_pattern: main node uuid
:return: json data to display node tree
"""
from aiida.orm.querybuilder import QueryBuilder
from aiida.orm import Node
def get_node_description(node):
"""
Get the description of the node.
CalcJobNodes migrated from AiiDA < 1.0.0 do not have a valid CalcJobState,
in this case the function returns as description the type of the node (CalcJobNode)
:param node: node object
:return: description of the node
"""
try:
description = node.get_description()
except ValueError:
description = node.node_type.split('.')[-2]
return description
# Check whether uuid_pattern identifies a unique node
self._check_id_validity(uuid_pattern)
qb_obj = QueryBuilder()
qb_obj.append(Node, tag='main', project=['*'], filters=self._id_filter)
nodes = []
if qb_obj.count() > 0:
main_node = qb_obj.first()[0]
pk = main_node.pk
uuid = main_node.uuid
nodetype = main_node.node_type
nodelabel = main_node.label
description = get_node_description(main_node)
ctime = main_node.ctime
mtime = main_node.mtime
nodes.append({
'ctime': ctime,
'mtime': mtime,
'id': pk,
'uuid': uuid,
'node_type': nodetype,
'node_label': nodelabel,
'description': description,
'incoming': [],
'outgoing': []
})
# get all incoming
qb_obj = QueryBuilder()
qb_obj.append(Node, tag='main', project=['*'], filters=self._id_filter)
qb_obj.append(Node,
tag='in',
project=['*'],
edge_project=['label', 'type'],
with_outgoing='main').order_by(
{'in': [{
'id': {
'order': 'asc'
}
}]})
if tree_in_limit is not None:
qb_obj.limit(tree_in_limit)
sent_no_of_incomings = qb_obj.count()
if sent_no_of_incomings > 0:
for node_input in qb_obj.iterdict():
node = node_input['in']['*']
pk = node.pk
linklabel = node_input['main--in']['label']
linktype = node_input['main--in']['type']
uuid = node.uuid
nodetype = node.node_type
nodelabel = node.label
description = get_node_description(node)
node_ctime = node.ctime
node_mtime = node.mtime
nodes[0]['incoming'].append({
'ctime': node_ctime,
'mtime': node_mtime,
'id': pk,
'uuid': uuid,
'node_type': nodetype,
'node_label': nodelabel,
'description': description,
'link_label': linklabel,
'link_type': linktype
})
# get all outgoing
qb_obj = QueryBuilder()
qb_obj.append(Node, tag='main', project=['*'], filters=self._id_filter)
qb_obj.append(Node,
tag='out',
project=['*'],
edge_project=['label', 'type'],
with_incoming='main').order_by(
{'out': [{
'id': {
'order': 'asc'
}
}]})
if tree_out_limit is not None:
qb_obj.limit(tree_out_limit)
sent_no_of_outgoings = qb_obj.count()
if sent_no_of_outgoings > 0:
for output in qb_obj.iterdict():
node = output['out']['*']
pk = node.pk
linklabel = output['main--out']['label']
linktype = output['main--out']['type']
uuid = node.uuid
nodetype = node.node_type
nodelabel = node.label
description = get_node_description(node)
node_ctime = node.ctime
node_mtime = node.mtime
nodes[0]['outgoing'].append({
'ctime': node_ctime,
'mtime': node_mtime,
'id': pk,
'uuid': uuid,
'node_type': nodetype,
'node_label': nodelabel,
'description': description,
'link_label': linklabel,
'link_type': linktype
})
# count total no of nodes
builder = QueryBuilder()
builder.append(Node,
tag='main',
project=['id'],
filters=self._id_filter)
builder.append(Node, tag='in', project=['id'], with_outgoing='main')
total_no_of_incomings = builder.count()
builder = QueryBuilder()
builder.append(Node,
tag='main',
project=['id'],
filters=self._id_filter)
builder.append(Node, tag='out', project=['id'], with_incoming='main')
total_no_of_outgoings = builder.count()
metadata = [{
'total_no_of_incomings': total_no_of_incomings,
'total_no_of_outgoings': total_no_of_outgoings,
'sent_no_of_incomings': sent_no_of_incomings,
'sent_no_of_outgoings': sent_no_of_outgoings
}]
return {'nodes': nodes, 'metadata': metadata}
def upload_usp_family(folder,
group_label,
group_description,
stop_if_existing=True):
"""
Upload a set of usp/recpot files in a give group
:param folder: a path containing all UPF files to be added.
Only files ending in .usp/.recpot are considered.
:param group_label: the name of the group to create. If it exists and is
non-empty, a UniquenessError is raised.
:param group_description: a string to be set as the group description.
Overwrites previous descriptions, if the group was existing.
:param stop_if_existing: if True, check for the md5 of the files and,
if the file already exists in the DB, raises a MultipleObjectsError.
If False, simply adds the existing UPFData node to the group.
"""
import os
import aiida.common
#from aiida.common import aiidalogger
from aiida.common import UniquenessError, NotExistent
from aiida.orm.querybuilder import QueryBuilder
from .otfg import OTFGGroup
files = [
os.path.realpath(os.path.join(folder, i)) for i in os.listdir(folder)
if os.path.isfile(os.path.join(folder, i)) and (
i.lower().endswith('.usp') or i.lower().endswith('recpot')
or i.lower().endswith('.uspcc'))
]
nfiles = len(files)
try:
group = OTFGGroup.get(label=group_label)
group_created = False
except NotExistent:
group = OTFGGroup(label=group_label, )
group_created = True
# Update the descript even if the group already existed
group.description = group_description
pseudo_and_created = [] # A list of records (UspData, created)
for f in files:
md5sum = md5_file(f)
qb = QueryBuilder()
qb.append(UspData, filters={'attributes.md5': {'==': md5sum}})
existing_usp = qb.first()
# Add the file if it is in the database
if existing_usp is None:
pseudo, created = UspData.get_or_create(f,
use_first=True,
store_usp=False)
pseudo_and_created.append((pseudo, created))
# The same file is there already
else:
if stop_if_existing:
raise ValueError("A usp/recpot with identical MD5 to"
" {} cannot be added with stop_if_existing"
"".format(f))
existing_usp = existing_usp[0]
pseudo_and_created.append((existing_usp, False))
# Check for unique per element
elements = [(i[0].element, i[0].md5sum) for i in pseudo_and_created]
# Check if we will duplicate after insertion
if not group_created:
for aiida_n in group.nodes:
if not isinstance(aiida_n, UspData):
continue
elements.append((aiida_n.element, aiida_n.md5sum))
# Discard duplicated pairs
elements = set(elements)
elements_names = [e[0] for e in elements]
# Check the uniqueness of the complete group
if not len(elements_names) == len(set(elements_names)):
duplicates = set(
[x for x in elements_names if elements_names.count(x) > 1])
dup_string = ", ".join(duplicates)
raise UniquenessError(
"More than one usp/recpot found for the elements: " + dup_string +
".")
if group_created:
group.store()
# Save the usp in the database if necessary and add them to the group
for pseudo, created in pseudo_and_created:
if created:
pseudo.store()
#aiidalogger.debug("New node {} created for file {}".format(
# pseudo.uuid, pseudo.filename))
else:
#aiidalogger.debug("Reusing node {} for file {}".format(
# pseudo.uuid, pseudo.filename))
pass
nodes_new = [
pseduo for pseduo, created in pseudo_and_created if created is True
]
nodes_add = [pseduo for pseduo, created in pseudo_and_created]
group.add_nodes(nodes_add)
return nfiles, len(nodes_new)
def upload_psml_family(folder,
group_label,
group_description,
stop_if_existing=True):
"""
Upload a set of PSML files in a given group.
:param folder: a path containing all PSML files to be added.
Only files ending in .psml (case sensitive) are considered.
:param group_label: the name of the group to create. If it exists and is
non-empty, a UniquenessError is raised.
:param group_description: a string to be set as the group description.
Overwrites previous descriptions, if the group was existing.
:param stop_if_existing: if True, check for the md5 of the files and,
if the file already exists in the DB, raises a MultipleObjectsError.
If False, simply adds the existing PsmlData node to the group.
"""
import os
from aiida import orm
from aiida.common import AIIDA_LOGGER as aiidalogger
from aiida.common.exceptions import UniquenessError
from aiida.orm.querybuilder import QueryBuilder
from aiida_siesta.groups.pseudos import PsmlFamily
message = ( #pylint: disable=invalid-name
'This function has been deprecated and will be removed in `v2.0.0`. ' +
'`upload_psml_family` is substitued by `fam.create_from_folder` ' +
'where `fam` is an instance of the families classes in `aiida_pseudo.groups.family`.'
)
warnings.warn(message, AiidaSiestaDeprecationWarning)
if not os.path.isdir(folder):
raise ValueError("folder must be a directory")
# only files, and only those ending with .psml;
# go to the real file if it is a symlink
files = [
os.path.realpath(os.path.join(folder, i)) for i in os.listdir(folder)
if os.path.isfile(os.path.join(folder, i)) and i.endswith('.psml')
]
nfiles = len(files)
automatic_user = orm.User.objects.get_default()
#group, group_created = orm.Group.objects.get_or_create(
# label=group_label, type_string=PSMLGROUP_TYPE, user=automatic_user
#)
group, group_created = PsmlFamily.objects.get_or_create(
label=group_label, user=automatic_user)
if group.user.email != automatic_user.email:
raise UniquenessError(
"There is already a PsmlFamily group with name {}"
", but it belongs to user {}, therefore you "
"cannot modify it".format(group_label, group.user.email))
# Always update description, even if the group already existed
group.description = group_description
# NOTE: GROUP SAVED ONLY AFTER CHECKS OF UNICITY
pseudo_and_created = []
for afile in files:
md5sum = md5_file(afile)
qb = QueryBuilder()
qb.append(PsmlData, filters={'attributes.md5': {'==': md5sum}})
existing_psml = qb.first()
#existing_psml = PsmlData.query(dbattributes__key="md5",
# dbattributes__tval = md5sum)
if existing_psml is None:
# return the psmldata instances, not stored
pseudo, created = PsmlData.get_or_create(afile,
use_first=True,
store_psml=False)
# to check whether only one psml per element exists
# NOTE: actually, created has the meaning of "to_be_created"
pseudo_and_created.append((pseudo, created))
else:
if stop_if_existing:
raise ValueError("A PSML with identical MD5 to "
" {} cannot be added with stop_if_existing"
"".format(afile))
existing_psml = existing_psml[0]
pseudo_and_created.append((existing_psml, False))
# check whether pseudo are unique per element
elements = [(i[0].element, i[0].md5sum) for i in pseudo_and_created]
# If group already exists, check also that I am not inserting more than
# once the same element
if not group_created:
for aiida_n in group.nodes:
# Skip non-pseudos
if not isinstance(aiida_n, PsmlData):
continue
elements.append((aiida_n.element, aiida_n.md5sum))
elements = set(elements) # Discard elements with the same MD5, that would
# not be stored twice
elements_names = [e[0] for e in elements]
if not len(elements_names) == len(set(elements_names)):
duplicates = {x for x in elements_names if elements_names.count(x) > 1}
duplicates_string = ", ".join(i for i in duplicates)
raise UniquenessError("More than one PSML found for the elements: " +
duplicates_string + ".")
# At this point, save the group, if still unstored
if group_created:
group.store()
# save the psml in the database, and add them to group
for pseudo, created in pseudo_and_created:
if created:
pseudo.store()
aiidalogger.debug("New node {} created for file {}".format(
pseudo.uuid, pseudo.filename))
else:
aiidalogger.debug("Reusing node {} for file {}".format(
pseudo.uuid, pseudo.filename))
# Add elements to the group all togetehr
group.add_nodes([pseudo for pseudo, created in pseudo_and_created])
nuploaded = len([_ for _, created in pseudo_and_created if created])
return nfiles, nuploaded
def upload_psf_family(folder,
group_name,
group_description,
stop_if_existing=True):
"""
Upload a set of PSF files in a given group.
:param folder: a path containing all PSF files to be added.
Only files ending in .PSF (case-insensitive) are considered.
:param group_name: the name of the group to create. If it exists and is
non-empty, a UniquenessError is raised.
:param group_description: a string to be set as the group description.
Overwrites previous descriptions, if the group was existing.
:param stop_if_existing: if True, check for the md5 of the files and,
if the file already exists in the DB, raises a MultipleObjectsError.
If False, simply adds the existing PsfData node to the group.
"""
import os
import aiida.common
from aiida.common import aiidalogger
from aiida.orm import Group
from aiida.common.exceptions import UniquenessError, NotExistent
from aiida.backends.utils import get_automatic_user
from aiida.orm.querybuilder import QueryBuilder
if not os.path.isdir(folder):
raise ValueError("folder must be a directory")
# only files, and only those ending with .psf or .PSF;
# go to the real file if it is a symlink
files = [
os.path.realpath(os.path.join(folder, i)) for i in os.listdir(folder)
if os.path.isfile(os.path.join(folder, i))
and i.lower().endswith('.psf')
]
nfiles = len(files)
try:
group = Group.get(name=group_name, type_string=PSFGROUP_TYPE)
group_created = False
except NotExistent:
group = Group(name=group_name,
type_string=PSFGROUP_TYPE,
user=get_automatic_user())
group_created = True
if group.user != get_automatic_user():
raise UniquenessError("There is already a PsfFamily group with name {}"
", but it belongs to user {}, therefore you "
"cannot modify it".format(
group_name, group.user.email))
# Always update description, even if the group already existed
group.description = group_description
# NOTE: GROUP SAVED ONLY AFTER CHECKS OF UNICITY
pseudo_and_created = []
for f in files:
md5sum = aiida.common.utils.md5_file(f)
qb = QueryBuilder()
qb.append(PsfData, filters={'attributes.md5': {'==': md5sum}})
existing_psf = qb.first()
#existing_psf = PsfData.query(dbattributes__key="md5",
# dbattributes__tval = md5sum)
if existing_psf is None:
# return the psfdata instances, not stored
pseudo, created = PsfData.get_or_create(f,
use_first=True,
store_psf=False)
# to check whether only one psf per element exists
# NOTE: actually, created has the meaning of "to_be_created"
pseudo_and_created.append((pseudo, created))
else:
if stop_if_existing:
raise ValueError("A PSF with identical MD5 to "
" {} cannot be added with stop_if_existing"
"".format(f))
existing_psf = existing_psf[0]
pseudo_and_created.append((existing_psf, False))
# check whether pseudo are unique per element
elements = [(i[0].element, i[0].md5sum) for i in pseudo_and_created]
# If group already exists, check also that I am not inserting more than
# once the same element
if not group_created:
for aiida_n in group.nodes:
# Skip non-pseudos
if not isinstance(aiida_n, PsfData):
continue
elements.append((aiida_n.element, aiida_n.md5sum))
elements = set(elements) # Discard elements with the same MD5, that would
# not be stored twice
elements_names = [e[0] for e in elements]
if not len(elements_names) == len(set(elements_names)):
duplicates = set(
[x for x in elements_names if elements_names.count(x) > 1])
duplicates_string = ", ".join(i for i in duplicates)
raise UniquenessError("More than one PSF found for the elements: " +
duplicates_string + ".")
# At this point, save the group, if still unstored
if group_created:
group.store()
# save the psf in the database, and add them to group
for pseudo, created in pseudo_and_created:
if created:
pseudo.store()
aiidalogger.debug("New node {} created for file {}".format(
pseudo.uuid, pseudo.filename))
else:
aiidalogger.debug("Reusing node {} for file {}".format(
pseudo.uuid, pseudo.filename))
# Add elements to the group all togetehr
group.add_nodes(pseudo for pseudo, created in pseudo_and_created)
nuploaded = len([_ for _, created in pseudo_and_created if created])
return nfiles, nuploaded
def test_same_computer_different_name_import(self):
"""
This test checks that if the computer is re-imported with a different
name to the same database, then the original computer will not be
renamed. It also checks that the names were correctly imported (without
any change since there is no computer name collision)
"""
import os
import shutil
import tempfile
from aiida.orm.importexport import export
from aiida.orm.querybuilder import QueryBuilder
from aiida.orm.computer import Computer
from aiida.orm.calculation.job import JobCalculation
# Creating a folder for the import/export files
export_file_tmp_folder = tempfile.mkdtemp()
unpack_tmp_folder = tempfile.mkdtemp()
try:
# Store a calculation
calc1_label = "calc1"
calc1 = JobCalculation()
calc1.set_computer(self.computer)
calc1.set_resources({
"num_machines": 1,
"num_mpiprocs_per_machine": 1
})
calc1.label = calc1_label
calc1.store()
calc1._set_state(u'RETRIEVING')
# Store locally the computer name
comp1_name = unicode(self.computer.name)
# Export the first job calculation
filename1 = os.path.join(export_file_tmp_folder, "export1.tar.gz")
export([calc1.dbnode], outfile=filename1, silent=True)
# Rename the computer
self.computer.set_name(comp1_name + "_updated")
# Store a second calculation
calc2_label = "calc2"
calc2 = JobCalculation()
calc2.set_computer(self.computer)
calc2.set_resources({
"num_machines": 2,
"num_mpiprocs_per_machine": 2
})
calc2.label = calc2_label
calc2.store()
calc2._set_state(u'RETRIEVING')
# Export the second job calculation
filename2 = os.path.join(export_file_tmp_folder, "export2.tar.gz")
export([calc2.dbnode], outfile=filename2, silent=True)
# Clean the local database
self.clean_db()
# Check that there are no computers
qb = QueryBuilder()
qb.append(Computer, project=['*'])
self.assertEqual(
qb.count(), 0, "There should not be any computers"
"in the database at this point.")
# Check that there are no calculations
qb = QueryBuilder()
qb.append(JobCalculation, project=['*'])
self.assertEqual(
qb.count(), 0, "There should not be any "
"calculations in the database at "
"this point.")
# Import the first calculation
import_data(filename1, silent=True)
# Check that the calculation computer is imported correctly.
qb = QueryBuilder()
qb.append(JobCalculation, project=['label'])
self.assertEqual(qb.count(), 1, "Only one calculation should be "
"found.")
self.assertEqual(unicode(qb.first()[0]), calc1_label,
"The calculation label is not correct.")
# Check that the referenced computer is imported correctly.
qb = QueryBuilder()
qb.append(Computer, project=['name', 'uuid', 'id'])
self.assertEqual(qb.count(), 1, "Only one computer should be "
"found.")
self.assertEqual(unicode(qb.first()[0]), comp1_name,
"The computer name is not correct.")
# Import the second calculation
import_data(filename2, silent=True)
# Check that the number of computers remains the same and its data
# did not change.
qb = QueryBuilder()
qb.append(Computer, project=['name'])
self.assertEqual(qb.count(), 1, "Only one computer should be "
"found.")
self.assertEqual(unicode(qb.first()[0]), comp1_name,
"The computer name is not correct.")
finally:
# Deleting the created temporary folders
shutil.rmtree(export_file_tmp_folder, ignore_errors=True)
shutil.rmtree(unpack_tmp_folder, ignore_errors=True)
def get_io_tree(self, nodeId, maxDepth=None):
from aiida.orm.querybuilder import QueryBuilder
from aiida.orm.node import Node
def addNodes(nodeId, maxDepth, nodes, addedNodes, addedEdges,
edgeType):
qb = QueryBuilder()
qb.append(Node, tag="main", filters={"id": {"==": nodeId}})
if edgeType == "ancestors":
qb.append(Node,
tag=edgeType,
project=['id', 'type'],
edge_project=['path', 'depth'],
ancestor_of_beta='main',
edge_filters={'depth': {
'<=': maxDepth
}})
elif edgeType == "desc":
qb.append(Node,
tag=edgeType,
project=['id', 'type'],
edge_project=['path', 'depth'],
descendant_of_beta='main',
edge_filters={'depth': {
'<=': maxDepth
}})
if (qb.count() > 0):
qbResults = qb.get_results_dict()
for resultDict in qbResults:
if resultDict[edgeType]["id"] not in addedNodes:
nodes.append({
"id":
len(addedNodes),
"nodeid":
resultDict[edgeType]["id"],
"nodetype":
resultDict[edgeType]["type"],
"group":
edgeType + "-" +
str(resultDict["main--" + edgeType]["depth"])
})
addedNodes.append(resultDict[edgeType]["id"])
path = resultDict["main--" + edgeType]["path"]
if edgeType == "ancestors":
startEdge = path[0]
endEdge = path[1]
elif edgeType == "desc":
startEdge = path[-2]
endEdge = path[-1]
if startEdge not in addedEdges.keys():
addedEdges[startEdge] = [endEdge]
elif endEdge not in addedEdges[startEdge]:
addedEdges[startEdge].append(endEdge)
return nodes, addedNodes, addedEdges
def addEdges(edges, addedNodes, addedEdges):
for fromNodeId in addedEdges.keys():
fromNodeIdIndex = addedNodes.index(fromNodeId)
for toNodeId in addedEdges[fromNodeId]:
toNodeIdIndex = addedNodes.index(toNodeId)
edges.append({
"from": fromNodeIdIndex,
"to": toNodeIdIndex,
"arrows": "to",
"color": {
"inherit": 'from'
}
})
return edges
nodes = []
edges = []
addedNodes = []
addedEdges = {}
if maxDepth is None:
from aiida.restapi.common.config import MAX_TREE_DEPTH
maxDepth = MAX_TREE_DEPTH
qb = QueryBuilder()
qb.append(Node,
tag="main",
project=["id", "type"],
filters={"id": {
"==": nodeId
}})
if qb.count() > 0:
mainNode = qb.first()
nodes.append({
"id": 0,
"nodeid": mainNode[0],
"nodetype": mainNode[1],
"group": "mainNode"
})
addedNodes.append(mainNode[0])
# get all descendents
nodes, addedNodes, addedEdges = addNodes(nodeId, maxDepth, nodes,
addedNodes, addedEdges,
"ancestors")
nodes, addedNodes, addedEdges = addNodes(nodeId, maxDepth, nodes,
addedNodes, addedEdges,
"desc")
edges = addEdges(edges, addedNodes, addedEdges)
return {"nodes": nodes, "edges": edges}
def get_io_tree(self, uuid_pattern, tree_in_limit, tree_out_limit):
from aiida.orm.querybuilder import QueryBuilder
from aiida.orm.node import Node
def get_node_shape(ntype):
type = ntype.split(".")[0]
# default and data node shape
shape = "dot"
if type == "calculation":
shape = "square"
elif type == "code":
shape = "triangle"
return shape
# Check whether uuid_pattern identifies a unique node
self._check_id_validity(uuid_pattern)
qb = QueryBuilder()
qb.append(Node, tag="main", project=["*"], filters=self._id_filter)
nodes = []
edges = []
nodeCount = 0
if qb.count() > 0:
mainNode = qb.first()[0]
pk = mainNode.pk
uuid = mainNode.uuid
nodetype = mainNode.type
nodelabel = mainNode.label
display_type = nodetype.split('.')[-2]
description = mainNode.get_desc()
if description == '':
description = mainNode.type.split('.')[-2]
nodes.append({
"id": nodeCount,
"nodeid": pk,
"nodeuuid": uuid,
"nodetype": nodetype,
"nodelabel": nodelabel,
"displaytype": display_type,
"group": "mainNode",
"description": description,
"shape": get_node_shape(nodetype)
})
nodeCount += 1
# get all inputs
qb = QueryBuilder()
qb.append(Node, tag="main", project=['*'], filters=self._id_filter)
qb.append(Node,
tag="in",
project=['*'],
edge_project=['label', 'type'],
input_of='main')
if tree_in_limit is not None:
qb.limit(tree_in_limit)
input_node_pks = {}
sent_no_of_incomings = qb.count()
if sent_no_of_incomings > 0:
for input in qb.iterdict():
node = input['in']['*']
pk = node.pk
linklabel = input['main--in']['label']
linktype = input['main--in']['type']
# add node if it is not present
if pk not in input_node_pks.keys():
input_node_pks[pk] = nodeCount
uuid = node.uuid
nodetype = node.type
nodelabel = node.label
display_type = nodetype.split('.')[-2]
description = node.get_desc()
if description == '':
description = node.type.split('.')[-2]
nodes.append({
"id": nodeCount,
"nodeid": pk,
"nodeuuid": uuid,
"nodetype": nodetype,
"nodelabel": nodelabel,
"displaytype": display_type,
"group": "inputs",
"description": description,
"linklabel": linklabel,
"linktype": linktype,
"shape": get_node_shape(nodetype)
})
nodeCount += 1
from_edge = input_node_pks[pk]
edges.append({
"from": from_edge,
"to": 0,
"arrows": "to",
"color": {
"inherit": 'from'
},
"label": linktype,
})
# get all outputs
qb = QueryBuilder()
qb.append(Node, tag="main", project=['*'], filters=self._id_filter)
qb.append(Node,
tag="out",
project=['*'],
edge_project=['label', 'type'],
output_of='main')
if tree_out_limit is not None:
qb.limit(tree_out_limit)
output_node_pks = {}
sent_no_of_outgoings = qb.count()
if sent_no_of_outgoings > 0:
for output in qb.iterdict():
node = output['out']['*']
pk = node.pk
linklabel = output['main--out']['label']
linktype = output['main--out']['type']
# add node if it is not present
if pk not in output_node_pks.keys():
output_node_pks[pk] = nodeCount
uuid = node.uuid
nodetype = node.type
nodelabel = node.label
display_type = nodetype.split('.')[-2]
description = node.get_desc()
if description == '':
description = node.type.split('.')[-2]
nodes.append({
"id": nodeCount,
"nodeid": pk,
"nodeuuid": uuid,
"nodetype": nodetype,
"nodelabel": nodelabel,
"displaytype": display_type,
"group": "outputs",
"description": description,
"linklabel": linklabel,
"linktype": linktype,
"shape": get_node_shape(nodetype)
})
nodeCount += 1
to_edge = output_node_pks[pk]
edges.append({
"from": 0,
"to": to_edge,
"arrows": "to",
"color": {
"inherit": 'to'
},
"label": linktype
})
# count total no of nodes
qb = QueryBuilder()
qb.append(Node, tag="main", project=['id'], filters=self._id_filter)
qb.append(Node, tag="in", project=['id'], input_of='main')
total_no_of_incomings = qb.count()
qb = QueryBuilder()
qb.append(Node, tag="main", project=['id'], filters=self._id_filter)
qb.append(Node, tag="out", project=['id'], output_of='main')
total_no_of_outgoings = qb.count()
return {
"nodes": nodes,
"edges": edges,
"total_no_of_incomings": total_no_of_incomings,
"total_no_of_outgoings": total_no_of_outgoings,
"sent_no_of_incomings": sent_no_of_incomings,
"sent_no_of_outgoings": sent_no_of_outgoings
}
def get_io_tree(self, uuid_pattern):
from aiida.orm.querybuilder import QueryBuilder
from aiida.orm.node import Node
def get_node_shape(ntype):
type = ntype.split(".")[0]
# default and data node shape
shape = "dot"
if type == "calculation":
shape = "square"
elif type == "code":
shape = "triangle"
return shape
# Check whether uuid_pattern identifies a unique node
self._check_id_validity(uuid_pattern)
qb = QueryBuilder()
qb.append(Node, tag="main", project=["*"],
filters=self._id_filter)
nodes = []
edges = []
nodeCount = 0
if qb.count() > 0:
mainNode = qb.first()[0]
pk = mainNode.pk
uuid = mainNode.uuid
nodetype = mainNode.type
display_type = nodetype.split('.')[-2]
description = mainNode.get_desc()
if description == '':
description = mainNode.type.split('.')[-2]
nodes.append({
"id": nodeCount,
"nodeid": pk,
"nodeuuid": uuid,
"nodetype": nodetype,
"displaytype": display_type,
"group": "mainNode",
"description": description,
"shape": get_node_shape(nodetype)
})
nodeCount += 1
# get all inputs
qb = QueryBuilder()
qb.append(Node, tag="main", project=['*'],
filters=self._id_filter)
qb.append(Node, tag="in", project=['*'], edge_project=['label'],
input_of='main')
if qb.count() > 0:
for input in qb.iterdict():
node = input['in']['*']
linktype = input['main--in']['label']
pk = node.pk
uuid = node.uuid
nodetype = node.type
display_type = nodetype.split('.')[-2]
description = node.get_desc()
if description == '':
description = node.type.split('.')[-2]
nodes.append({
"id": nodeCount,
"nodeid": pk,
"nodeuuid": uuid,
"nodetype": nodetype,
"displaytype": display_type,
"group": "inputs",
"description": description,
"linktype": linktype,
"shape": get_node_shape(nodetype)
})
edges.append({
"from": nodeCount,
"to": 0,
"arrows": "to",
"color": {"inherit": 'from'},
"linktype": linktype,
})
nodeCount += 1
# get all outputs
qb = QueryBuilder()
qb.append(Node, tag="main", project=['*'],
filters=self._id_filter)
qb.append(Node, tag="out", project=['*'], edge_project=['label'],
output_of='main')
if qb.count() > 0:
for output in qb.iterdict():
node = output['out']['*']
linktype = output['main--out']['label']
pk = node.pk
uuid = node.uuid
nodetype = node.type
display_type = nodetype.split('.')[-2]
description = node.get_desc()
if description == '':
description = node.type.split('.')[-2]
nodes.append({
"id": nodeCount,
"nodeid": pk,
"nodeuuid": uuid,
"nodetype": nodetype,
"displaytype": display_type,
"group": "outputs",
"description": description,
"linktype": linktype,
"shape": get_node_shape(nodetype)
})
edges.append({
"from": 0,
"to": nodeCount,
"arrows": "to",
"color": {"inherit": 'to'},
"linktype": linktype
})
nodeCount += 1
return {"nodes": nodes, "edges": edges}
def configure_computer_v012(computer, user_email=None, authparams=None):
"""Configure the authentication information for a given computer
adapted from aiida-core v0.12.2:
aiida_core.aiida.cmdline.commands.computer.Computer.computer_configure
:param computer: the computer to authenticate against
:param user_email: the user email (otherwise use default)
:param authparams: a dictionary of additional authorisation parameters to use (in string format)
:return:
"""
from aiida.common.exceptions import ValidationError
from aiida.backends.utils import get_automatic_user
# aiida-core v1
# from aiida.orm.backend import construct_backend
# backend = construct_backend()
# get_automatic_user = backend.users.get_automatic_user
authparams = {} if authparams is None else authparams
transport = computer.get_transport_class()
valid_keys = transport.get_valid_auth_params()
if user_email is None:
user = get_automatic_user()
else:
from aiida.orm.querybuilder import QueryBuilder
qb = QueryBuilder()
qb.append(type="user", filters={'email': user_email})
user = qb.first()
if not user:
raise ValueError("user email not found: {}".format(user_email))
user = user[0]._dbuser # for Django, the wrong user class is returned
authinfo, old_authparams = _get_auth_info(computer, user)
# print ("Configuring computer '{}' for the AiiDA user '{}'".format(
# computername, user.email))
#
# print "Computer {} has transport of type {}".format(computername,
# computer.get_transport_type())
# from aiida.common.utils import get_configured_user_email
# if user.email != get_configured_user_email():
# print "*" * 72
# print "** {:66s} **".format("WARNING!")
# print "** {:66s} **".format(
# " You are configuring a different user.")
# print "** {:66s} **".format(
# " Note that the default suggestions are taken from your")
# print "** {:66s} **".format(
# " local configuration files, so they may be incorrect.")
# print "*" * 72
default_authparams = {}
for k in valid_keys:
if k in old_authparams:
default_authparams[k] = old_authparams.pop(k)
if k not in authparams:
authparams[k] = default_authparams[k]
if old_authparams:
print("WARNING: the following keys were previously in the "
"authorization parameters, but have not been recognized "
"and have been deleted: {}".format(", ".join(
old_authparams.keys())))
if set(authparams.keys()) != set(valid_keys):
raise ValueError(
"new_authparams should contain only the keys: {}".format(
valid_keys))
# convert keys from strings
transport_members = dict(inspect.getmembers(transport))
for k, txtval in authparams.items():
converter_name = '_convert_{}_fromstring'.format(k)
suggester_name = '_get_{}_suggestion_string'.format(k)
if converter_name not in transport_members:
raise ValueError("No {} defined in Transport {}".format(
converter_name, computer.get_transport_type()))
converter = transport_members[converter_name]
suggestion = ""
if k in default_authparams:
suggestion = default_authparams[k]
elif suggester_name in transport_members:
suggestion = transport_members[suggester_name](computer)
try:
authparams[k] = converter(txtval)
except ValidationError, err:
raise ValueError("error in the authparam "
"{0}: {1}, suggested value: {2}".format(
k, err, suggestion))
def get_from_string(cls, code_string):
"""
Get a Computer object with given identifier string, that can either be
the numeric ID (pk), or the label (if unique); the label can either
be simply the label, or in the format label@machinename. See the note
below for details on the string detection algorithm.
.. note:: If a string that can be converted to an integer is given,
the numeric ID is verified first (therefore, is a code A with a
label equal to the ID of another code B is present, code A cannot
be referenced by label). Similarly, the (leftmost) '@' symbol is
always used to split code and computername. Therefore do not use
'@' in the code name if you want to use this function
('@' in the computer name are instead valid).
:param code_string: the code string identifying the code to load
:raise NotExistent: if no code identified by the given string is found
:raise MultipleObjectsError: if the string cannot identify uniquely
a code
"""
from aiida.common.exceptions import NotExistent, MultipleObjectsError
from aiida.orm.querybuilder import QueryBuilder
from aiida.orm.computer import Computer
from aiida.orm.code import Code
try:
code_int = int(code_string)
try:
return cls.get_subclass_from_pk(code_int)
except NotExistent:
raise ValueError() # Jump to the following section
# to check if a code with the given
# label exists.
except MultipleObjectsError:
raise MultipleObjectsError("More than one code in the DB "
"with pk='{}'!".format(code_string))
except ValueError:
# Before dying, try to see if the user passed a (unique) label.
# split with the leftmost '@' symbol (i.e. code names cannot
# contain '@' symbols, computer names can)
qb = QueryBuilder()
codename, sep, computername = code_string.partition('@')
qb.append(cls,
filters={'label': {
'==': codename
}},
project=['*'],
tag='code')
if sep:
qb.append(Computer,
filters={'name': {
'==': computername
}},
computer_of='code')
if qb.count() == 0:
raise NotExistent("'{}' is not a valid code "
"ID or label.".format(code_string))
elif qb.count() > 1:
codes = [_ for [_] in qb.all()]
retstr = ("There are multiple codes with label '{}', "
"having IDs: ".format(code_string))
retstr += ", ".join(sorted([str(c.pk) for c in codes])) + ".\n"
retstr += ("Relabel them (using their ID), or refer to them "
"with their ID.")
raise MultipleObjectsError(retstr)
else:
return qb.first()[0]
def computer_configure(self, *args):
"""
Configure the authentication information for a given computer
"""
if not is_dbenv_loaded():
load_dbenv()
import readline
import inspect
from django.core.exceptions import ObjectDoesNotExist
from aiida.common.exceptions import (NotExistent, ValidationError)
from aiida.backends.utils import get_automatic_user
from aiida.common.utils import get_configured_user_email
from aiida.backends.settings import BACKEND
from aiida.backends.profile import BACKEND_SQLA, BACKEND_DJANGO
import argparse
parser = argparse.ArgumentParser(
prog=self.get_full_command_name(),
description='Configure a computer for a given AiiDA user.')
# The default states are those that are shown if no option is given
parser.add_argument(
'-u',
'--user',
type=str,
metavar='EMAIL',
help=
"Configure the computer for the given AiiDA user (otherwise, configure the current default user)",
)
parser.add_argument(
'computer',
type=str,
help="The name of the computer that you want to configure")
parsed_args = parser.parse_args(args)
user_email = parsed_args.user
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:
user = get_automatic_user()
else:
from aiida.orm.querybuilder import QueryBuilder
qb = QueryBuilder()
qb.append(type="user", filters={'email': user_email})
user = qb.first()
if user is None:
print >> sys.stderr, ("No user with email '{}' in the "
"database.".format(user_email))
sys.exit(1)
if BACKEND == BACKEND_DJANGO:
from aiida.backends.djsite.db.models import DbAuthInfo
try:
authinfo = DbAuthInfo.objects.get(
dbcomputer=computer.dbcomputer, aiidauser=user)
old_authparams = authinfo.get_auth_params()
except ObjectDoesNotExist:
authinfo = DbAuthInfo(dbcomputer=computer.dbcomputer,
aiidauser=user)
old_authparams = {}
elif BACKEND == BACKEND_SQLA:
from aiida.backends.sqlalchemy.models.authinfo import DbAuthInfo
from aiida.backends.sqlalchemy import session
authinfo = session.query(DbAuthInfo).filter(
DbAuthInfo.dbcomputer == computer.dbcomputer).filter(
DbAuthInfo.aiidauser == user).first()
if authinfo is None:
authinfo = DbAuthInfo(dbcomputer=computer.dbcomputer,
aiidauser=user)
old_authparams = {}
else:
old_authparams = authinfo.get_auth_params()
else:
raise Exception("Unknown backend {}".format(BACKEND))
Transport = computer.get_transport_class()
print("Configuring computer '{}' for the AiiDA user '{}'".format(
computername, user.email))
print "Computer {} has transport of type {}".format(
computername, computer.get_transport_type())
if user.email != get_configured_user_email():
print "*" * 72
print "** {:66s} **".format("WARNING!")
print "** {:66s} **".format(
" You are configuring a different user.")
print "** {:66s} **".format(
" Note that the default suggestions are taken from your")
print "** {:66s} **".format(
" local configuration files, so they may be incorrect.")
print "*" * 72
valid_keys = Transport.get_valid_auth_params()
default_authparams = {}
for k in valid_keys:
if k in old_authparams:
default_authparams[k] = old_authparams.pop(k)
if old_authparams:
print(
"WARNING: the following keys were previously in the "
"authorization parameters,")
print "but have not been recognized and have been deleted:"
print ", ".join(old_authparams.keys())
if not valid_keys:
print "There are no special keys to be configured. Configuration completed."
authinfo.set_auth_params({})
authinfo.save()
return
print ""
print "Note: to leave a field unconfigured, leave it empty and press [Enter]"
# I strip out the old auth_params that are not among the valid keys
new_authparams = {}
for k in valid_keys:
key_set = False
while not key_set:
try:
converter_name = '_convert_{}_fromstring'.format(k)
try:
converter = dict(
inspect.getmembers(Transport))[converter_name]
except KeyError:
print >> sys.stderr, (
"Internal error! "
"No {} defined in Transport {}".format(
converter_name, computer.get_transport_type()))
sys.exit(1)
if k in default_authparams:
readline.set_startup_hook(lambda: readline.insert_text(
str(default_authparams[k])))
else:
# Use suggestion only if parameters were not already set
suggester_name = '_get_{}_suggestion_string'.format(k)
try:
suggester = dict(
inspect.getmembers(Transport))[suggester_name]
suggestion = suggester(computer)
readline.set_startup_hook(
lambda: readline.insert_text(suggestion))
except KeyError:
readline.set_startup_hook()
txtval = raw_input("=> {} = ".format(k))
if txtval:
new_authparams[k] = converter(txtval)
key_set = True
except ValidationError as e:
print "Error in the inserted value: {}".format(e.message)
authinfo.set_auth_params(new_authparams)
authinfo.save()
print "Configuration stored for your user on computer '{}'.".format(
computername)
def test_same_computer_import(self):
"""
Test that you can import nodes in steps without any problems. In this
test we will import a first calculation and then a second one. The
import should work as expected and have in the end two job
calculations.
Each calculation is related to the same computer. In the end we should
have only one computer
"""
import os
import shutil
import tempfile
from aiida.orm.importexport import export
from aiida.orm.querybuilder import QueryBuilder
from aiida.orm.computer import Computer
from aiida.orm.calculation.job import JobCalculation
# Creating a folder for the import/export files
export_file_tmp_folder = tempfile.mkdtemp()
unpack_tmp_folder = tempfile.mkdtemp()
try:
# Store two job calculation related to the same computer
calc1_label = "calc1"
calc1 = JobCalculation()
calc1.set_computer(self.computer)
calc1.set_resources({
"num_machines": 1,
"num_mpiprocs_per_machine": 1
})
calc1.label = calc1_label
calc1.store()
calc1._set_state(u'RETRIEVING')
calc2_label = "calc2"
calc2 = JobCalculation()
calc2.set_computer(self.computer)
calc2.set_resources({
"num_machines": 2,
"num_mpiprocs_per_machine": 2
})
calc2.label = calc2_label
calc2.store()
calc2._set_state(u'RETRIEVING')
# Store locally the computer name
comp_name = unicode(self.computer.name)
comp_uuid = unicode(self.computer.uuid)
# Export the first job calculation
filename1 = os.path.join(export_file_tmp_folder, "export1.tar.gz")
export([calc1.dbnode], outfile=filename1, silent=True)
# Export the second job calculation
filename2 = os.path.join(export_file_tmp_folder, "export2.tar.gz")
export([calc2.dbnode], outfile=filename2, silent=True)
# Clean the local database
self.clean_db()
# Check that there are no computers
qb = QueryBuilder()
qb.append(Computer, project=['*'])
self.assertEqual(
qb.count(), 0, "There should not be any computers"
"in the database at this point.")
# Check that there are no calculations
qb = QueryBuilder()
qb.append(JobCalculation, project=['*'])
self.assertEqual(
qb.count(), 0, "There should not be any "
"calculations in the database at "
"this point.")
# Import the first calculation
import_data(filename1, silent=True)
# Check that the calculation computer is imported correctly.
qb = QueryBuilder()
qb.append(JobCalculation, project=['label'])
self.assertEqual(qb.count(), 1, "Only one calculation should be "
"found.")
self.assertEqual(unicode(qb.first()[0]), calc1_label,
"The calculation label is not correct.")
# Check that the referenced computer is imported correctly.
qb = QueryBuilder()
qb.append(Computer, project=['name', 'uuid', 'id'])
self.assertEqual(qb.count(), 1, "Only one computer should be "
"found.")
self.assertEqual(unicode(qb.first()[0]), comp_name,
"The computer name is not correct.")
self.assertEqual(unicode(qb.first()[1]), comp_uuid,
"The computer uuid is not correct.")
# Store the id of the computer
comp_id = qb.first()[2]
# Import the second calculation
import_data(filename2, silent=True)
# Check that the number of computers remains the same and its data
# did not change.
qb = QueryBuilder()
qb.append(Computer, project=['name', 'uuid', 'id'])
self.assertEqual(qb.count(), 1, "Only one computer should be "
"found.")
self.assertEqual(unicode(qb.first()[0]), comp_name,
"The computer name is not correct.")
self.assertEqual(unicode(qb.first()[1]), comp_uuid,
"The computer uuid is not correct.")
self.assertEqual(qb.first()[2], comp_id,
"The computer id is not correct.")
# Check that now you have two calculations attached to the same
# computer.
qb = QueryBuilder()
qb.append(Computer, tag='comp')
qb.append(JobCalculation, has_computer='comp', project=['label'])
self.assertEqual(qb.count(), 2, "Two calculations should be "
"found.")
ret_labels = set(_ for [_] in qb.all())
self.assertEqual(
ret_labels, set([calc1_label, calc2_label]),
"The labels of the calculations are not correct.")
finally:
# Deleting the created temporary folders
shutil.rmtree(export_file_tmp_folder, ignore_errors=True)
shutil.rmtree(unpack_tmp_folder, ignore_errors=True)
