def add_to_group(node):
try:
g = Group.get_from_string('examples')
except NotExistent:
g = Group(name='examples')
g.store()
g.add_nodes(node)
def import_data_dj(
in_path,
group=None,
ignore_unknown_nodes=False,
extras_mode_existing='kcl',
extras_mode_new='import',
comment_mode='newest',
silent=False
):
"""Import exported AiiDA archive to the AiiDA database and repository.
Specific for the Django backend.
If ``in_path`` is a folder, calls extract_tree; otherwise, tries to detect the compression format
(zip, tar.gz, tar.bz2, ...) and calls the correct function.
:param in_path: the path to a file or folder that can be imported in AiiDA.
:type in_path: str
:param group: Group wherein all imported Nodes will be placed.
:type group: :py:class:`~aiida.orm.groups.Group`
:param extras_mode_existing: 3 letter code that will identify what to do with the extras import.
The first letter acts on extras that are present in the original node and not present in the imported node.
Can be either:
'k' (keep it) or
'n' (do not keep it).
The second letter acts on the imported extras that are not present in the original node.
Can be either:
'c' (create it) or
'n' (do not create it).
The third letter defines what to do in case of a name collision.
Can be either:
'l' (leave the old value),
'u' (update with a new value),
'd' (delete the extra), or
'a' (ask what to do if the content is different).
:type extras_mode_existing: str
:param extras_mode_new: 'import' to import extras of new nodes or 'none' to ignore them.
:type extras_mode_new: str
:param comment_mode: Comment import modes (when same UUIDs are found).
Can be either:
'newest' (will keep the Comment with the most recent modification time (mtime)) or
'overwrite' (will overwrite existing Comments with the ones from the import file).
:type comment_mode: str
:param silent: suppress prints.
:type silent: bool
:return: New and existing Nodes and Links.
:rtype: dict
:raises `~aiida.tools.importexport.common.exceptions.ImportValidationError`: if parameters or the contents of
`metadata.json` or `data.json` can not be validated.
:raises `~aiida.tools.importexport.common.exceptions.CorruptArchive`: if the provided archive at ``in_path`` is
corrupted.
:raises `~aiida.tools.importexport.common.exceptions.IncompatibleArchiveVersionError`: if the provided archive's
export version is not equal to the export version of AiiDA at the moment of import.
:raises `~aiida.tools.importexport.common.exceptions.ArchiveImportError`: if there are any internal errors when
importing.
:raises `~aiida.tools.importexport.common.exceptions.ImportUniquenessError`: if a new unique entity can not be
created.
"""
from django.db import transaction # pylint: disable=import-error,no-name-in-module
from aiida.backends.djsite.db import models
# This is the export version expected by this function
expected_export_version = StrictVersion(EXPORT_VERSION)
# The returned dictionary with new and existing nodes and links
ret_dict = {}
# Initial check(s)
if group:
if not isinstance(group, Group):
raise exceptions.ImportValidationError('group must be a Group entity')
elif not group.is_stored:
group.store()
################
# EXTRACT DATA #
################
# The sandbox has to remain open until the end
with SandboxFolder() as folder:
if os.path.isdir(in_path):
extract_tree(in_path, folder)
else:
if tarfile.is_tarfile(in_path):
extract_tar(in_path, folder, silent=silent, nodes_export_subfolder=NODES_EXPORT_SUBFOLDER)
elif zipfile.is_zipfile(in_path):
try:
extract_zip(in_path, folder, silent=silent, nodes_export_subfolder=NODES_EXPORT_SUBFOLDER)
except ValueError as exc:
print('The following problem occured while processing the provided file: {}'.format(exc))
return
else:
raise exceptions.ImportValidationError(
'Unable to detect the input file format, it is neither a '
'(possibly compressed) tar file, nor a zip file.'
)
if not folder.get_content_list():
raise exceptions.CorruptArchive('The provided file/folder ({}) is empty'.format(in_path))
try:
with io.open(folder.get_abs_path('metadata.json'), 'r', encoding='utf8') as fhandle:
metadata = json.load(fhandle)
with io.open(folder.get_abs_path('data.json'), 'r', encoding='utf8') as fhandle:
data = json.load(fhandle)
except IOError as error:
raise exceptions.CorruptArchive(
'Unable to find the file {} in the import file or folder'.format(error.filename)
)
######################
# PRELIMINARY CHECKS #
######################
export_version = StrictVersion(str(metadata['export_version']))
if export_version != expected_export_version:
msg = 'Export file version is {}, can import only version {}'\
.format(metadata['export_version'], expected_export_version)
if export_version < expected_export_version:
msg += "\nUse 'verdi export migrate' to update this export file."
else:
msg += '\nUpdate your AiiDA version in order to import this file.'
raise exceptions.IncompatibleArchiveVersionError(msg)
##########################################################################
# CREATE UUID REVERSE TABLES AND CHECK IF I HAVE ALL NODES FOR THE LINKS #
##########################################################################
linked_nodes = set(chain.from_iterable((l['input'], l['output']) for l in data['links_uuid']))
group_nodes = set(chain.from_iterable(six.itervalues(data['groups_uuid'])))
if NODE_ENTITY_NAME in data['export_data']:
import_nodes_uuid = set(v['uuid'] for v in data['export_data'][NODE_ENTITY_NAME].values())
else:
import_nodes_uuid = set()
# the combined set of linked_nodes and group_nodes was obtained from looking at all the links
# the set of import_nodes_uuid was received from the stuff actually referred to in export_data
unknown_nodes = linked_nodes.union(group_nodes) - import_nodes_uuid
if unknown_nodes and not ignore_unknown_nodes:
raise exceptions.DanglingLinkError(
'The import file refers to {} nodes with unknown UUID, therefore it cannot be imported. Either first '
'import the unknown nodes, or export also the parents when exporting. The unknown UUIDs are:\n'
''.format(len(unknown_nodes)) + '\n'.join('* {}'.format(uuid) for uuid in unknown_nodes)
)
###################################
# DOUBLE-CHECK MODEL DEPENDENCIES #
###################################
# The entity import order. It is defined by the database model relationships.
model_order = (
USER_ENTITY_NAME, COMPUTER_ENTITY_NAME, NODE_ENTITY_NAME, GROUP_ENTITY_NAME, LOG_ENTITY_NAME,
COMMENT_ENTITY_NAME
)
for import_field_name in metadata['all_fields_info']:
if import_field_name not in model_order:
raise exceptions.ImportValidationError(
"You are trying to import an unknown model '{}'!".format(import_field_name)
)
for idx, model_name in enumerate(model_order):
dependencies = []
for field in metadata['all_fields_info'][model_name].values():
try:
dependencies.append(field['requires'])
except KeyError:
# (No ForeignKey)
pass
for dependency in dependencies:
if dependency not in model_order[:idx]:
raise exceptions.ArchiveImportError(
'Model {} requires {} but would be loaded first; stopping...'.format(model_name, dependency)
)
###################################################
# CREATE IMPORT DATA DIRECT UNIQUE_FIELD MAPPINGS #
###################################################
import_unique_ids_mappings = {}
for model_name, import_data in data['export_data'].items():
if model_name in metadata['unique_identifiers']:
# I have to reconvert the pk to integer
import_unique_ids_mappings[model_name] = {
int(k): v[metadata['unique_identifiers'][model_name]] for k, v in import_data.items()
}
###############
# IMPORT DATA #
###############
# DO ALL WITH A TRANSACTION
with transaction.atomic():
foreign_ids_reverse_mappings = {}
new_entries = {}
existing_entries = {}
# I first generate the list of data
for model_name in model_order:
cls_signature = entity_names_to_signatures[model_name]
model = get_object_from_string(cls_signature)
fields_info = metadata['all_fields_info'].get(model_name, {})
unique_identifier = metadata['unique_identifiers'].get(model_name, None)
new_entries[model_name] = {}
existing_entries[model_name] = {}
foreign_ids_reverse_mappings[model_name] = {}
# Not necessarily all models are exported
if model_name in data['export_data']:
# skip nodes that are already present in the DB
if unique_identifier is not None:
import_unique_ids = set(v[unique_identifier] for v in data['export_data'][model_name].values())
relevant_db_entries_result = model.objects.filter(
**{'{}__in'.format(unique_identifier): import_unique_ids}
)
# Note: uuids need to be converted to strings
relevant_db_entries = {
str(getattr(n, unique_identifier)): n for n in relevant_db_entries_result
}
foreign_ids_reverse_mappings[model_name] = {k: v.pk for k, v in relevant_db_entries.items()}
for key, value in data['export_data'][model_name].items():
if value[unique_identifier] in relevant_db_entries.keys():
# Already in DB
existing_entries[model_name][key] = value
else:
# To be added
new_entries[model_name][key] = value
else:
new_entries[model_name] = data['export_data'][model_name].copy()
# Show Comment mode if not silent
if not silent:
print('Comment mode: {}'.format(comment_mode))
# I import data from the given model
for model_name in model_order:
cls_signature = entity_names_to_signatures[model_name]
model = get_object_from_string(cls_signature)
fields_info = metadata['all_fields_info'].get(model_name, {})
unique_identifier = metadata['unique_identifiers'].get(model_name, None)
# EXISTING ENTRIES
for import_entry_pk, entry_data in existing_entries[model_name].items():
unique_id = entry_data[unique_identifier]
existing_entry_id = foreign_ids_reverse_mappings[model_name][unique_id]
import_data = dict(
deserialize_field(
k,
v,
fields_info=fields_info,
import_unique_ids_mappings=import_unique_ids_mappings,
foreign_ids_reverse_mappings=foreign_ids_reverse_mappings
) for k, v in entry_data.items()
)
# TODO COMPARE, AND COMPARE ATTRIBUTES
if model is models.DbComment:
new_entry_uuid = merge_comment(import_data, comment_mode)
if new_entry_uuid is not None:
entry_data[unique_identifier] = new_entry_uuid
new_entries[model_name][import_entry_pk] = entry_data
if model_name not in ret_dict:
ret_dict[model_name] = {'new': [], 'existing': []}
ret_dict[model_name]['existing'].append((import_entry_pk, existing_entry_id))
if not silent:
print('existing %s: %s (%s->%s)' % (model_name, unique_id, import_entry_pk, existing_entry_id))
# print(" `-> WARNING: NO DUPLICITY CHECK DONE!")
# CHECK ALSO FILES!
# Store all objects for this model in a list, and store them all in once at the end.
objects_to_create = []
# This is needed later to associate the import entry with the new pk
import_new_entry_pks = {}
imported_comp_names = set()
# NEW ENTRIES
for import_entry_pk, entry_data in new_entries[model_name].items():
unique_id = entry_data[unique_identifier]
import_data = dict(
deserialize_field(
k,
v,
fields_info=fields_info,
import_unique_ids_mappings=import_unique_ids_mappings,
foreign_ids_reverse_mappings=foreign_ids_reverse_mappings
) for k, v in entry_data.items()
)
if model is models.DbGroup:
# Check if there is already a group with the same name
dupl_counter = 0
orig_label = import_data['label']
while model.objects.filter(label=import_data['label']):
import_data['label'] = orig_label + DUPL_SUFFIX.format(dupl_counter)
dupl_counter += 1
if dupl_counter == 100:
raise exceptions.ImportUniquenessError(
'A group of that label ( {} ) already exists and I could not create a new one'
''.format(orig_label)
)
elif model is models.DbComputer:
# Check if there is already a computer with the same name in the database
dupl = (
model.objects.filter(name=import_data['name']) or import_data['name'] in imported_comp_names
)
orig_name = import_data['name']
dupl_counter = 0
while dupl:
# Rename the new computer
import_data['name'] = (orig_name + DUPL_SUFFIX.format(dupl_counter))
dupl = (
model.objects.filter(name=import_data['name']) or
import_data['name'] in imported_comp_names
)
dupl_counter += 1
if dupl_counter == 100:
raise exceptions.ImportUniquenessError(
'A computer of that name ( {} ) already exists and I could not create a new one'
''.format(orig_name)
)
imported_comp_names.add(import_data['name'])
objects_to_create.append(model(**import_data))
import_new_entry_pks[unique_id] = import_entry_pk
if model_name == NODE_ENTITY_NAME:
if not silent:
print('STORING NEW NODE REPOSITORY FILES...')
# NEW NODES
for object_ in objects_to_create:
import_entry_uuid = object_.uuid
import_entry_pk = import_new_entry_pks[import_entry_uuid]
# Before storing entries in the DB, I store the files (if these are nodes).
# Note: only for new entries!
subfolder = folder.get_subfolder(
os.path.join(NODES_EXPORT_SUBFOLDER, export_shard_uuid(import_entry_uuid))
)
if not subfolder.exists():
raise exceptions.CorruptArchive(
'Unable to find the repository folder for Node with UUID={} in the exported '
'file'.format(import_entry_uuid)
)
destdir = RepositoryFolder(section=Repository._section_name, uuid=import_entry_uuid)
# Replace the folder, possibly destroying existing previous folders, and move the files
# (faster if we are on the same filesystem, and in any case the source is a SandboxFolder)
destdir.replace_with_folder(subfolder.abspath, move=True, overwrite=True)
# For DbNodes, we also have to store its attributes
if not silent:
print('STORING NEW NODE ATTRIBUTES...')
# Get attributes from import file
try:
object_.attributes = data['node_attributes'][str(import_entry_pk)]
except KeyError:
raise exceptions.CorruptArchive(
'Unable to find attribute info for Node with UUID={}'.format(import_entry_uuid)
)
# For DbNodes, we also have to store its extras
if extras_mode_new == 'import':
if not silent:
print('STORING NEW NODE EXTRAS...')
# Get extras from import file
try:
extras = data['node_extras'][str(import_entry_pk)]
except KeyError:
raise exceptions.CorruptArchive(
'Unable to find extra info for Node with UUID={}'.format(import_entry_uuid)
)
# TODO: remove when aiida extras will be moved somewhere else
# from here
extras = {key: value for key, value in extras.items() if not key.startswith('_aiida_')}
if object_.node_type.endswith('code.Code.'):
extras = {key: value for key, value in extras.items() if not key == 'hidden'}
# till here
object_.extras = extras
elif extras_mode_new == 'none':
if not silent:
print('SKIPPING NEW NODE EXTRAS...')
else:
raise exceptions.ImportValidationError(
"Unknown extras_mode_new value: {}, should be either 'import' or 'none'"
''.format(extras_mode_new)
)
# EXISTING NODES (Extras)
# For the existing nodes that are also in the imported list we also update their extras if necessary
if not silent:
print('UPDATING EXISTING NODE EXTRAS (mode: {})'.format(extras_mode_existing))
import_existing_entry_pks = {
entry_data[unique_identifier]: import_entry_pk
for import_entry_pk, entry_data in existing_entries[model_name].items()
}
for node in models.DbNode.objects.filter(uuid__in=import_existing_entry_pks).all(): # pylint: disable=no-member
import_entry_uuid = str(node.uuid)
import_entry_pk = import_existing_entry_pks[import_entry_uuid]
# Get extras from import file
try:
extras = data['node_extras'][str(import_entry_pk)]
except KeyError:
raise exceptions.CorruptArchive(
'Unable to find extra info for ode with UUID={}'.format(import_entry_uuid)
)
# TODO: remove when aiida extras will be moved somewhere else
# from here
extras = {key: value for key, value in extras.items() if not key.startswith('_aiida_')}
if node.node_type.endswith('code.Code.'):
extras = {key: value for key, value in extras.items() if not key == 'hidden'}
# till here
node.extras = merge_extras(node.extras, extras, extras_mode_existing)
# Already saving existing node here to update its extras
node.save()
# If there is an mtime in the field, disable the automatic update
# to keep the mtime that we have set here
if 'mtime' in [field.name for field in model._meta.local_fields]:
with models.suppress_auto_now([(model, ['mtime'])]):
# Store them all in once; however, the PK are not set in this way...
model.objects.bulk_create(objects_to_create)
else:
model.objects.bulk_create(objects_to_create)
# Get back the just-saved entries
just_saved_queryset = model.objects.filter(
**{
'{}__in'.format(unique_identifier): import_new_entry_pks.keys()
}
).values_list(unique_identifier, 'pk')
# note: convert uuids from type UUID to strings
just_saved = {str(key): value for key, value in just_saved_queryset}
# Now I have the PKs, print the info
# Moreover, add newly created Nodes to foreign_ids_reverse_mappings
for unique_id, new_pk in just_saved.items():
import_entry_pk = import_new_entry_pks[unique_id]
foreign_ids_reverse_mappings[model_name][unique_id] = new_pk
if model_name not in ret_dict:
ret_dict[model_name] = {'new': [], 'existing': []}
ret_dict[model_name]['new'].append((import_entry_pk, new_pk))
if not silent:
print('NEW %s: %s (%s->%s)' % (model_name, unique_id, import_entry_pk, new_pk))
if not silent:
print('STORING NODE LINKS...')
import_links = data['links_uuid']
links_to_store = []
# Needed, since QueryBuilder does not yet work for recently saved Nodes
existing_links_raw = models.DbLink.objects.all().values_list('input', 'output', 'label', 'type')
existing_links = {(l[0], l[1], l[2], l[3]) for l in existing_links_raw}
existing_outgoing_unique = {(l[0], l[3]) for l in existing_links_raw}
existing_outgoing_unique_pair = {(l[0], l[2], l[3]) for l in existing_links_raw}
existing_incoming_unique = {(l[1], l[3]) for l in existing_links_raw}
existing_incoming_unique_pair = {(l[1], l[2], l[3]) for l in existing_links_raw}
calculation_node_types = 'process.calculation.'
workflow_node_types = 'process.workflow.'
data_node_types = 'data.'
link_mapping = {
LinkType.CALL_CALC: (workflow_node_types, calculation_node_types, 'unique_triple', 'unique'),
LinkType.CALL_WORK: (workflow_node_types, workflow_node_types, 'unique_triple', 'unique'),
LinkType.CREATE: (calculation_node_types, data_node_types, 'unique_pair', 'unique'),
LinkType.INPUT_CALC: (data_node_types, calculation_node_types, 'unique_triple', 'unique_pair'),
LinkType.INPUT_WORK: (data_node_types, workflow_node_types, 'unique_triple', 'unique_pair'),
LinkType.RETURN: (workflow_node_types, data_node_types, 'unique_pair', 'unique_triple'),
}
for link in import_links:
# Check for dangling Links within the, supposed, self-consistent archive
try:
in_id = foreign_ids_reverse_mappings[NODE_ENTITY_NAME][link['input']]
out_id = foreign_ids_reverse_mappings[NODE_ENTITY_NAME][link['output']]
except KeyError:
if ignore_unknown_nodes:
continue
else:
raise exceptions.ImportValidationError(
'Trying to create a link with one or both unknown nodes, stopping (in_uuid={}, '
'out_uuid={}, label={}, type={})'.format(
link['input'], link['output'], link['label'], link['type']
)
)
# Check if link already exists, skip if it does
# This is equivalent to an existing triple link (i.e. unique_triple from below)
if (in_id, out_id, link['label'], link['type']) in existing_links:
continue
# Since backend specific Links (DbLink) are not validated upon creation, we will now validate them.
try:
validate_link_label(link['label'])
except ValueError as why:
raise exceptions.ImportValidationError('Error during Link label validation: {}'.format(why))
source = models.DbNode.objects.get(id=in_id)
target = models.DbNode.objects.get(id=out_id)
if source.uuid == target.uuid:
raise exceptions.ImportValidationError('Cannot add a link to oneself')
link_type = LinkType(link['type'])
type_source, type_target, outdegree, indegree = link_mapping[link_type]
# Check if source Node is a valid type
if not source.node_type.startswith(type_source):
raise exceptions.ImportValidationError(
'Cannot add a {} link from {} to {}'.format(link_type, source.node_type, target.node_type)
)
# Check if target Node is a valid type
if not target.node_type.startswith(type_target):
raise exceptions.ImportValidationError(
'Cannot add a {} link from {} to {}'.format(link_type, source.node_type, target.node_type)
)
# If the outdegree is `unique` there cannot already be any other outgoing link of that type,
# i.e., the source Node may not have a LinkType of current LinkType, going out, existing already.
if outdegree == 'unique' and (in_id, link['type']) in existing_outgoing_unique:
raise exceptions.ImportValidationError(
'Node<{}> already has an outgoing {} link'.format(source.uuid, link_type)
)
# If the outdegree is `unique_pair`,
# then the link labels for outgoing links of this type should be unique,
# i.e., the source Node may not have a LinkType of current LinkType, going out,
# that also has the current Link label, existing already.
elif outdegree == 'unique_pair' and \
(in_id, link['label'], link['type']) in existing_outgoing_unique_pair:
raise exceptions.ImportValidationError(
'Node<{}> already has an outgoing {} link with label "{}"'.format(
source.uuid, link_type, link['label']
)
)
# If the indegree is `unique` there cannot already be any other incoming links of that type,
# i.e., the target Node may not have a LinkType of current LinkType, coming in, existing already.
if indegree == 'unique' and (out_id, link['type']) in existing_incoming_unique:
raise exceptions.ImportValidationError(
'Node<{}> already has an incoming {} link'.format(target.uuid, link_type)
)
# If the indegree is `unique_pair`,
# then the link labels for incoming links of this type should be unique,
# i.e., the target Node may not have a LinkType of current LinkType, coming in
# that also has the current Link label, existing already.
elif indegree == 'unique_pair' and \
(out_id, link['label'], link['type']) in existing_incoming_unique_pair:
raise exceptions.ImportValidationError(
'Node<{}> already has an incoming {} link with label "{}"'.format(
target.uuid, link_type, link['label']
)
)
# New link
links_to_store.append(
models.DbLink(input_id=in_id, output_id=out_id, label=link['label'], type=link['type'])
)
if 'Link' not in ret_dict:
ret_dict['Link'] = {'new': []}
ret_dict['Link']['new'].append((in_id, out_id))
# Add new Link to sets of existing Links 'input PK', 'output PK', 'label', 'type'
existing_links.add((in_id, out_id, link['label'], link['type']))
existing_outgoing_unique.add((in_id, link['type']))
existing_outgoing_unique_pair.add((in_id, link['label'], link['type']))
existing_incoming_unique.add((out_id, link['type']))
existing_incoming_unique_pair.add((out_id, link['label'], link['type']))
# Store new links
if links_to_store:
if not silent:
print(' ({} new links...)'.format(len(links_to_store)))
models.DbLink.objects.bulk_create(links_to_store)
else:
if not silent:
print(' (0 new links...)')
if not silent:
print('STORING GROUP ELEMENTS...')
import_groups = data['groups_uuid']
for groupuuid, groupnodes in import_groups.items():
# TODO: cache these to avoid too many queries
group_ = models.DbGroup.objects.get(uuid=groupuuid)
nodes_to_store = [foreign_ids_reverse_mappings[NODE_ENTITY_NAME][node_uuid] for node_uuid in groupnodes]
if nodes_to_store:
group_.dbnodes.add(*nodes_to_store)
######################################################
# Put everything in a specific group
######################################################
existing = existing_entries.get(NODE_ENTITY_NAME, {})
existing_pk = [foreign_ids_reverse_mappings[NODE_ENTITY_NAME][v['uuid']] for v in six.itervalues(existing)]
new = new_entries.get(NODE_ENTITY_NAME, {})
new_pk = [foreign_ids_reverse_mappings[NODE_ENTITY_NAME][v['uuid']] for v in six.itervalues(new)]
pks_for_group = existing_pk + new_pk
# So that we do not create empty groups
if pks_for_group:
# If user specified a group, import all things into it
if not group:
# Get an unique name for the import group, based on the current (local) time
basename = timezone.localtime(timezone.now()).strftime('%Y%m%d-%H%M%S')
counter = 0
group_label = basename
while Group.objects.find(filters={'label': group_label}):
counter += 1
group_label = '{}_{}'.format(basename, counter)
if counter == 100:
raise exceptions.ImportUniquenessError(
"Overflow of import groups (more than 100 import groups exists with basename '{}')"
''.format(basename)
)
group = Group(label=group_label, type_string=IMPORTGROUP_TYPE).store()
# Add all the nodes to the new group
# TODO: decide if we want to return the group label
nodes = [entry[0] for entry in QueryBuilder().append(Node, filters={'id': {'in': pks_for_group}}).all()]
group.add_nodes(nodes)
if not silent:
print("IMPORTED NODES ARE GROUPED IN THE IMPORT GROUP LABELED '{}'".format(group.label))
else:
if not silent:
print('NO NODES TO IMPORT, SO NO GROUP CREATED, IF IT DID NOT ALREADY EXIST')
if not silent:
print('*** WARNING: MISSING EXISTING UUID CHECKS!!')
print('*** WARNING: TODO: UPDATE IMPORT_DATA WITH DEFAULT VALUES! (e.g. calc status, user pwd, ...)')
print('DONE.')
return ret_dict
# Create groups for each and fill them with desired nodes
print("Creating discovery groups, with tagged nodes:", dis_nodes)
all_dis_groups = []
for full_group in all_groups:
mat_id = full_group.label.split("_")[1]
dis_group = Group(label=GROUP_DIR + mat_id).store()
all_dis_groups.append(dis_group)
left_nodes = dis_nodes.copy()
for node in full_group.nodes:
if TAG_KEY not in node.extras:
sys.exit("WARNING: node <{}> has no extra '{}'".format(
node.id, TAG_KEY))
if node.extras[TAG_KEY] in left_nodes:
dis_group.add_nodes(node)
left_nodes.remove(node.extras[TAG_KEY])
if node.extras[
TAG_KEY] == 'orig_cif': #to change at a certain point!
dis_group.set_extra('mat_id', mat_id)
for extra_key in [
'doi_ref', 'workflow_version', 'name_conventional',
'class_material'
]:
extra_val = node.extras[extra_key]
dis_group.set_extra(extra_key, extra_val)
print(mat_id, "missing nodes for discovery: ", left_nodes)
# Export these groups
if EXPORT:
[
alat,
0.,
0.,
],
[
0.,
alat,
0.,
],
[
0.,
0.,
alat,
],
]
# BaTiO3 cubic structure
s = StructureData(cell=cell)
s.append_atom(position=(0., 0., 0.), symbols=['Ba'])
s.append_atom(position=(alat / 2., alat / 2., alat / 2.), symbols=['Ti'])
s.append_atom(position=(alat / 2., alat / 2., 0.), symbols=['O'])
s.append_atom(position=(alat / 2., 0., alat / 2.), symbols=['O'])
s.append_atom(position=(0., alat / 2., alat / 2.), symbols=['O'])
g = Group(name="input_group").store()
g.add_nodes(s.store())
w = TestWorkChain
run(w, structure=s.store(), code=code)
