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 open(folder.get_abs_path('metadata.json'),
'r',
encoding='utf8') as fhandle:
metadata = json.load(fhandle)
with 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(data['groups_uuid'].values()))
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
# batch size for bulk create operations
batch_size = get_config_option('db.batch_size')
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,
batch_size=batch_size)
else:
model.objects.bulk_create(objects_to_create,
batch_size=batch_size)
# 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
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,
batch_size=batch_size)
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 existing.values()
]
new = new_entries.get(NODE_ENTITY_NAME, {})
new_pk = [
foreign_ids_reverse_mappings[NODE_ENTITY_NAME][v['uuid']]
for v in new.values()
]
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 = ImportGroup(label=group_label).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('DONE.')
return ret_dict
def import_data_sqla(in_path,
group=None,
ignore_unknown_nodes=False,
extras_mode_existing='kcl',
extras_mode_new='import',
comment_mode='newest',
silent=False,
**kwargs):
"""Import exported AiiDA archive to the AiiDA database and repository.
Specific for the SQLAlchemy 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 progress bar and summary.
: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 aiida.backends.sqlalchemy.models.node import DbNode, DbLink
from aiida.backends.sqlalchemy.utils import flag_modified
# 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()
if silent:
logging.disable(level=logging.CRITICAL)
################
# 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,
**kwargs)
elif zipfile.is_zipfile(in_path):
extract_zip(in_path,
folder,
silent=silent,
nodes_export_subfolder=NODES_EXPORT_SUBFOLDER,
**kwargs)
else:
raise exceptions.ImportValidationError(
'Unable to detect the input file format, it is neither a '
'tar file, nor a (possibly compressed) zip file.')
if not folder.get_content_list():
raise exceptions.CorruptArchive(
'The provided file/folder ({}) is empty'.format(in_path))
try:
IMPORT_LOGGER.debug('CACHING metadata.json')
with open(folder.get_abs_path('metadata.json'),
encoding='utf8') as fhandle:
metadata = json.load(fhandle)
IMPORT_LOGGER.debug('CACHING data.json')
with open(folder.get_abs_path('data.json'),
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)
start_summary(in_path, comment_mode, extras_mode_new,
extras_mode_existing)
###################################################################
# CREATE UUID REVERSE TABLES AND CHECK IF #
# I HAVE ALL NODES FOR THE LINKS #
###################################################################
IMPORT_LOGGER.debug(
'CHECKING IF NODES FROM LINKS ARE IN DB OR ARCHIVE...')
linked_nodes = set(
chain.from_iterable(
(l['input'], l['output']) for l in data['links_uuid']))
group_nodes = set(chain.from_iterable(data['groups_uuid'].values()))
# Check that UUIDs are valid
linked_nodes = set(x for x in linked_nodes if validate_uuid(x))
group_nodes = set(x for x in group_nodes if validate_uuid(x))
import_nodes_uuid = set()
for value in data['export_data'].get(NODE_ENTITY_NAME, {}).values():
import_nodes_uuid.add(value['uuid'])
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.
entity_order = [
USER_ENTITY_NAME, COMPUTER_ENTITY_NAME, NODE_ENTITY_NAME,
GROUP_ENTITY_NAME, LOG_ENTITY_NAME, COMMENT_ENTITY_NAME
]
# I make a new list that contains the entity names:
# eg: ['User', 'Computer', 'Node', 'Group']
for import_field_name in metadata['all_fields_info']:
if import_field_name not in entity_order:
raise exceptions.ImportValidationError(
"You are trying to import an unknown model '{}'!".format(
import_field_name))
for idx, entity_name in enumerate(entity_order):
dependencies = []
# for every field, I checked the dependencies given as value for key requires
for field in metadata['all_fields_info'][entity_name].values():
try:
dependencies.append(field['requires'])
except KeyError:
# (No ForeignKey)
pass
for dependency in dependencies:
if dependency not in entity_order[:idx]:
raise exceptions.ArchiveImportError(
'Entity {} requires {} but would be loaded first; stopping...'
.format(entity_name, dependency))
###################################################
# CREATE IMPORT DATA DIRECT UNIQUE_FIELD MAPPINGS #
###################################################
# This is nested dictionary of entity_name:{id:uuid}
# to map one id (the pk) to a different one.
# One of the things to remove for v0.4
# {
# 'Node': {2362: '82a897b5-fb3a-47d7-8b22-c5fe1b4f2c14',
# 2363: 'ef04aa5d-99e7-4bfd-95ef-fe412a6a3524', 2364: '1dc59576-af21-4d71-81c2-bac1fc82a84a'},
# 'User': {1: 'aiida@localhost'}
# }
IMPORT_LOGGER.debug('CREATING PK-2-UUID/EMAIL MAPPING...')
import_unique_ids_mappings = {}
# Export data since v0.3 contains the keys entity_name
for entity_name, import_data in data['export_data'].items():
# Again I need the entity_name since that's what's being stored since 0.3
if entity_name in metadata['unique_identifiers']:
# I have to reconvert the pk to integer
import_unique_ids_mappings[entity_name] = {
int(k): v[metadata['unique_identifiers'][entity_name]]
for k, v in import_data.items()
}
###############
# IMPORT DATA #
###############
# DO ALL WITH A TRANSACTION
import aiida.backends.sqlalchemy
session = aiida.backends.sqlalchemy.get_scoped_session()
try:
foreign_ids_reverse_mappings = {}
new_entries = {}
existing_entries = {}
IMPORT_LOGGER.debug('GENERATING LIST OF DATA...')
# Instantiate progress bar
progress_bar = get_progress_bar(total=1,
leave=False,
disable=silent)
pbar_base_str = 'Generating list of data - '
# Get total entities from data.json
# To be used with progress bar
number_of_entities = 0
# I first generate the list of data
for entity_name in entity_order:
entity = entity_names_to_entities[entity_name]
# I get the unique identifier, since v0.3 stored under entity_name
unique_identifier = metadata['unique_identifiers'].get(
entity_name, None)
# so, new_entries. Also, since v0.3 it makes more sense to use the entity_name
new_entries[entity_name] = {}
existing_entries[entity_name] = {}
foreign_ids_reverse_mappings[entity_name] = {}
# Not necessarily all models are exported
if entity_name in data['export_data']:
IMPORT_LOGGER.debug(' %s...', entity_name)
progress_bar.set_description_str(pbar_base_str +
entity_name,
refresh=False)
number_of_entities += len(data['export_data'][entity_name])
if unique_identifier is not None:
import_unique_ids = set(
v[unique_identifier]
for v in data['export_data'][entity_name].values())
relevant_db_entries = {}
if import_unique_ids:
builder = QueryBuilder()
builder.append(entity,
filters={
unique_identifier: {
'in': import_unique_ids
}
},
project='*')
if builder.count():
progress_bar = get_progress_bar(
total=builder.count(), disable=silent)
for object_ in builder.iterall():
progress_bar.update()
relevant_db_entries.update({
getattr(object_[0], unique_identifier):
object_[0]
})
foreign_ids_reverse_mappings[entity_name] = {
k: v.pk
for k, v in relevant_db_entries.items()
}
IMPORT_LOGGER.debug(' GOING THROUGH ARCHIVE...')
imported_comp_names = set()
for key, value in data['export_data'][
entity_name].items():
if entity_name == GROUP_ENTITY_NAME:
# Check if there is already a group with the same name,
# and if so, recreate the name
orig_label = value['label']
dupl_counter = 0
while QueryBuilder().append(
entity,
filters={
'label': {
'==': value['label']
}
}).count():
# Rename the new group
value[
'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 entity_name == COMPUTER_ENTITY_NAME:
# The following is done for compatibility
# reasons in case the export file was generated
# with the Django export method. In Django the
# metadata and the transport parameters are
# stored as (unicode) strings of the serialized
# JSON objects and not as simple serialized
# JSON objects.
if isinstance(value['metadata'], (str, bytes)):
value['metadata'] = json.loads(
value['metadata'])
# Check if there is already a computer with the
# same name in the database
builder = QueryBuilder()
builder.append(
entity,
filters={'name': {
'==': value['name']
}},
project=['*'],
tag='res')
dupl = builder.count(
) or value['name'] in imported_comp_names
dupl_counter = 0
orig_name = value['name']
while dupl:
# Rename the new computer
value[
'name'] = orig_name + DUPL_SUFFIX.format(
dupl_counter)
builder = QueryBuilder()
builder.append(entity,
filters={
'name': {
'==': value['name']
}
},
project=['*'],
tag='res')
dupl = builder.count(
) or value['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(value['name'])
if value[unique_identifier] in relevant_db_entries:
# Already in DB
# again, switched to entity_name in v0.3
existing_entries[entity_name][key] = value
else:
# To be added
new_entries[entity_name][key] = value
else:
new_entries[entity_name] = data['export_data'][
entity_name]
# Progress bar - reset for import
progress_bar = get_progress_bar(total=number_of_entities,
disable=silent)
reset_progress_bar = {}
# I import data from the given model
for entity_name in entity_order:
entity = entity_names_to_entities[entity_name]
fields_info = metadata['all_fields_info'].get(entity_name, {})
unique_identifier = metadata['unique_identifiers'].get(
entity_name, '')
# Progress bar initialization - Model
if reset_progress_bar:
progress_bar = get_progress_bar(
total=reset_progress_bar['total'], disable=silent)
progress_bar.n = reset_progress_bar['n']
reset_progress_bar = {}
pbar_base_str = '{}s - '.format(entity_name)
progress_bar.set_description_str(pbar_base_str +
'Initializing',
refresh=True)
# EXISTING ENTRIES
if existing_entries[entity_name]:
# Progress bar update - Model
progress_bar.set_description_str(
pbar_base_str + '{} existing entries'.format(
len(existing_entries[entity_name])),
refresh=True)
for import_entry_pk, entry_data in existing_entries[
entity_name].items():
unique_id = entry_data[unique_identifier]
existing_entry_pk = foreign_ids_reverse_mappings[
entity_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 entity_name == COMMENT_ENTITY_NAME:
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[entity_name][
import_entry_pk] = entry_data
if entity_name not in ret_dict:
ret_dict[entity_name] = {'new': [], 'existing': []}
ret_dict[entity_name]['existing'].append(
(import_entry_pk, existing_entry_pk))
IMPORT_LOGGER.debug('Existing %s: %s (%s->%s)',
entity_name, unique_id,
import_entry_pk, existing_entry_pk)
# Store all objects for this model in a list, and store them
# all in once at the end.
objects_to_create = list()
# In the following list we add the objects to be updated
objects_to_update = list()
# This is needed later to associate the import entry with the new pk
import_new_entry_pks = dict()
# NEW ENTRIES
if new_entries[entity_name]:
# Progress bar update - Model
progress_bar.set_description_str(
pbar_base_str +
'{} new entries'.format(len(new_entries[entity_name])),
refresh=True)
for import_entry_pk, entry_data in new_entries[
entity_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())
# We convert the Django fields to SQLA. Note that some of
# the Django fields were converted to SQLA compatible
# fields by the deserialize_field method. This was done
# for optimization reasons in Django but makes them
# compatible with the SQLA schema and they don't need any
# further conversion.
if entity_name in file_fields_to_model_fields:
for file_fkey in file_fields_to_model_fields[
entity_name]:
# This is an exception because the DbLog model defines the `_metadata` column instead of the
# `metadata` column used in the Django model. This is because the SqlAlchemy model base
# class already has a metadata attribute that cannot be overridden. For consistency, the
# `DbLog` class however expects the `metadata` keyword in its constructor, so we should
# ignore the mapping here
if entity_name == LOG_ENTITY_NAME and file_fkey == 'metadata':
continue
model_fkey = file_fields_to_model_fields[
entity_name][file_fkey]
if model_fkey in import_data:
continue
import_data[model_fkey] = import_data[file_fkey]
import_data.pop(file_fkey, None)
db_entity = get_object_from_string(
entity_names_to_sqla_schema[entity_name])
objects_to_create.append(db_entity(**import_data))
import_new_entry_pks[unique_id] = import_entry_pk
if entity_name == NODE_ENTITY_NAME:
IMPORT_LOGGER.debug(
'STORING NEW NODE REPOSITORY FILES & ATTRIBUTES...')
# NEW NODES
for object_ in objects_to_create:
import_entry_uuid = object_.uuid
import_entry_pk = import_new_entry_pks[
import_entry_uuid]
# Progress bar initialization - Node
progress_bar.update()
pbar_node_base_str = pbar_base_str + 'UUID={} - '.format(
import_entry_uuid.split('-')[0])
# 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)
progress_bar.set_description_str(pbar_node_base_str +
'Repository',
refresh=True)
destdir.replace_with_folder(subfolder.abspath,
move=True,
overwrite=True)
# For Nodes, we also have to store Attributes!
IMPORT_LOGGER.debug('STORING NEW NODE ATTRIBUTES...')
progress_bar.set_description_str(pbar_node_base_str +
'Attributes',
refresh=True)
# 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 extras
if extras_mode_new == 'import':
IMPORT_LOGGER.debug('STORING NEW NODE EXTRAS...')
progress_bar.set_description_str(
pbar_node_base_str + 'Extras', refresh=True)
# 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':
IMPORT_LOGGER.debug('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)
IMPORT_LOGGER.debug('UPDATING EXISTING NODE EXTRAS...')
import_existing_entry_pks = {
entry_data[unique_identifier]: import_entry_pk
for import_entry_pk, entry_data in
existing_entries[entity_name].items()
}
for node in session.query(DbNode).filter(
DbNode.uuid.in_(import_existing_entry_pks)).all():
import_entry_uuid = str(node.uuid)
import_entry_pk = import_existing_entry_pks[
import_entry_uuid]
# Progress bar initialization - Node
pbar_node_base_str = pbar_base_str + 'UUID={} - '.format(
import_entry_uuid.split('-')[0])
progress_bar.set_description_str(pbar_node_base_str +
'Extras',
refresh=False)
progress_bar.update()
# 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))
old_extras = node.extras.copy()
# 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
new_extras = merge_extras(node.extras, extras,
extras_mode_existing)
if new_extras != old_extras:
node.extras = new_extras
flag_modified(node, 'extras')
objects_to_update.append(node)
else:
# Update progress bar with new non-Node entries
progress_bar.update(n=len(existing_entries[entity_name]) +
len(new_entries[entity_name]))
progress_bar.set_description_str(pbar_base_str + 'Storing',
refresh=True)
# Store them all in once; However, the PK are not set in this way...
if objects_to_create:
session.add_all(objects_to_create)
if objects_to_update:
session.add_all(objects_to_update)
session.flush()
just_saved = {}
if import_new_entry_pks.keys():
reset_progress_bar = {
'total': progress_bar.total,
'n': progress_bar.n
}
progress_bar = get_progress_bar(
total=len(import_new_entry_pks), disable=silent)
builder = QueryBuilder()
builder.append(entity,
filters={
unique_identifier: {
'in':
list(import_new_entry_pks.keys())
}
},
project=[unique_identifier, 'id'])
for entry in builder.iterall():
progress_bar.update()
just_saved.update({entry[0]: entry[1]})
progress_bar.set_description_str(pbar_base_str + 'Done!',
refresh=True)
# 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():
from uuid import UUID
if isinstance(unique_id, UUID):
unique_id = str(unique_id)
import_entry_pk = import_new_entry_pks[unique_id]
foreign_ids_reverse_mappings[entity_name][
unique_id] = new_pk
if entity_name not in ret_dict:
ret_dict[entity_name] = {'new': [], 'existing': []}
ret_dict[entity_name]['new'].append(
(import_entry_pk, new_pk))
IMPORT_LOGGER.debug('N %s: %s (%s->%s)', entity_name,
unique_id, import_entry_pk, new_pk)
IMPORT_LOGGER.debug('STORING NODE LINKS...')
import_links = data['links_uuid']
if import_links:
progress_bar = get_progress_bar(total=len(import_links),
disable=silent)
pbar_base_str = 'Links - '
for link in import_links:
# Check for dangling Links within the, supposed, self-consistent archive
progress_bar.set_description_str(
pbar_base_str + 'label={}'.format(link['label']),
refresh=False)
progress_bar.update()
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
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']))
# Since backend specific Links (DbLink) are not validated upon creation, we will now validate them.
source = QueryBuilder().append(Node,
filters={
'id': in_id
},
project='*').first()[0]
target = QueryBuilder().append(Node,
filters={
'id': out_id
},
project='*').first()[0]
link_type = LinkType(link['type'])
# Check for existence of a triple link, i.e. unique triple.
# If it exists, then the link already exists, continue to next link, otherwise, validate link.
if link_triple_exists(source, target, link_type,
link['label']):
continue
try:
validate_link(source, target, link_type, link['label'])
except ValueError as why:
raise exceptions.ImportValidationError(
'Error occurred during Link validation: {}'.format(
why))
# New link
session.add(
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))
IMPORT_LOGGER.debug(' (%d new links...)',
len(ret_dict.get('Link', {}).get('new', [])))
IMPORT_LOGGER.debug('STORING GROUP ELEMENTS...')
import_groups = data['groups_uuid']
if import_groups:
progress_bar = get_progress_bar(total=len(import_groups),
disable=silent)
pbar_base_str = 'Groups - '
for groupuuid, groupnodes in import_groups.items():
# # TODO: cache these to avoid too many queries
qb_group = QueryBuilder().append(
Group, filters={'uuid': {
'==': groupuuid
}})
group_ = qb_group.first()[0]
progress_bar.set_description_str(
pbar_base_str + 'label={}'.format(group_.label),
refresh=False)
progress_bar.update()
nodes_ids_to_add = [
foreign_ids_reverse_mappings[NODE_ENTITY_NAME][node_uuid]
for node_uuid in groupnodes
]
qb_nodes = QueryBuilder().append(
Node, filters={'id': {
'in': nodes_ids_to_add
}})
# Adding nodes to group avoiding the SQLA ORM to increase speed
nodes_to_add = [n[0].backend_entity for n in qb_nodes.all()]
group_.backend_entity.add_nodes(nodes_to_add, skip_orm=True)
######################################################
# 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 existing.values()
]
new = new_entries.get(NODE_ENTITY_NAME, {})
new_pk = [
foreign_ids_reverse_mappings[NODE_ENTITY_NAME][v['uuid']]
for v in new.values()
]
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:
from aiida.backends.sqlalchemy.models.group import DbGroup
# 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 session.query(DbGroup).filter(
DbGroup.label == group_label).count() > 0:
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 = ImportGroup(label=group_label)
session.add(group.backend_entity._dbmodel)
# Adding nodes to group avoiding the SQLA ORM to increase speed
builder = QueryBuilder().append(
Node, filters={'id': {
'in': pks_for_group
}})
progress_bar = get_progress_bar(total=len(pks_for_group),
disable=silent)
progress_bar.set_description_str(
'Creating import Group - Preprocessing', refresh=True)
first = True
nodes = []
for entry in builder.iterall():
if first:
progress_bar.set_description_str(
'Creating import Group', refresh=False)
first = False
progress_bar.update()
nodes.append(entry[0].backend_entity)
group.backend_entity.add_nodes(nodes, skip_orm=True)
progress_bar.set_description_str('Done (cleaning up)',
refresh=True)
else:
IMPORT_LOGGER.debug(
'No Nodes to import, so no Group created, if it did not already exist'
)
IMPORT_LOGGER.debug('COMMITTING EVERYTHING...')
session.commit()
# Finalize Progress bar
close_progress_bar(leave=False)
# Summarize import
result_summary(ret_dict, getattr(group, 'label', None))
except:
# Finalize Progress bar
close_progress_bar(leave=False)
result_summary({}, None)
IMPORT_LOGGER.debug('Rolling back')
session.rollback()
raise
# Reset logging level
if silent:
logging.disable(level=logging.NOTSET)
return ret_dict
def import_data_sqla(in_path: str,
group: Optional[Group] = None,
ignore_unknown_nodes: bool = False,
extras_mode_existing: str = 'kcl',
extras_mode_new: str = 'import',
comment_mode: str = 'newest',
silent: Optional[bool] = None,
**kwargs: Any): # pylint: disable=unused-argument
"""Import exported AiiDA archive to the AiiDA database and repository.
Specific for the SQLAlchemy 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 progress bar and summary.
: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.
"""
# Initial check(s)
if silent is not None:
warnings.warn(
'silent keyword is deprecated and will be removed in AiiDA v2.0.0, set the logger level explicitly instead',
AiidaDeprecationWarning) # pylint: disable=no-member
if extras_mode_new not in ['import', 'none']:
raise exceptions.ImportValidationError(
f"Unknown extras_mode_new value: {extras_mode_new}, should be either 'import' or 'none'"
)
reader_cls = get_reader(detect_archive_type(in_path))
# 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()
# The returned dictionary with new and existing nodes and links
# model_name -> new or existing -> list pk
ret_dict: Dict[str, dict] = {}
with reader_cls(in_path) as reader:
reader.check_version()
start_summary(in_path, comment_mode, extras_mode_new,
extras_mode_existing)
##########################################################################
# CREATE UUID REVERSE TABLES AND CHECK IF I HAVE ALL NODES FOR THE LINKS #
##########################################################################
IMPORT_LOGGER.debug(
'CHECKING IF NODES FROM LINKS ARE IN DB OR ARCHIVE...')
linked_nodes = set(
chain.from_iterable(
(l['input'], l['output']) for l in reader.iter_link_data()))
group_nodes = set(
chain.from_iterable(
(uuids for _, uuids in reader.iter_group_uuids())))
# Check that UUIDs are valid
linked_nodes = set(x for x in linked_nodes if validate_uuid(x))
group_nodes = set(x for x in group_nodes if validate_uuid(x))
import_nodes_uuid = set(v for v in reader.iter_node_uuids())
# 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.
entity_order = [
USER_ENTITY_NAME, COMPUTER_ENTITY_NAME, NODE_ENTITY_NAME,
GROUP_ENTITY_NAME, LOG_ENTITY_NAME, COMMENT_ENTITY_NAME
]
for entity_name in reader.entity_names:
if entity_name not in entity_order:
raise exceptions.ImportValidationError(
f"You are trying to import an unknown model '{entity_name}'!"
)
for idx, entity_name in enumerate(entity_order):
dependencies = []
# for every field, I checked the dependencies given as value for key requires
for field in reader.metadata.all_fields_info[entity_name].values():
try:
dependencies.append(field['requires'])
except KeyError:
# (No ForeignKey)
pass
for dependency in dependencies:
if dependency not in entity_order[:idx]:
raise exceptions.ArchiveImportError(
f'Entity {entity_name} requires {dependency} but would be loaded first; stopping...'
)
IMPORT_LOGGER.debug('CREATING PK-2-UUID/EMAIL MAPPING...')
# entity_name -> pk -> unique id
import_unique_ids_mappings: Dict[str, Dict[int, str]] = {}
for entity_name, identifier in reader.metadata.unique_identifiers.items(
):
import_unique_ids_mappings[entity_name] = {
int(k): f[identifier]
for k, f in reader.iter_entity_fields(entity_name,
fields=(identifier, ))
}
# count total number of entities to import
number_of_entities: int = sum(
reader.entity_count(entity_name) for entity_name in entity_order)
IMPORT_LOGGER.debug('Importing %s entities', number_of_entities)
###########################################
# IMPORT ALL DATA IN A SINGLE TRANSACTION #
###########################################
with sql_transaction() as session: # type: Session
# entity_name -> str(pk) -> fields
new_entries: Dict[str, Dict[str, dict]] = {}
existing_entries: Dict[str, Dict[str, dict]] = {}
# entity_name -> identifier -> pk
foreign_ids_reverse_mappings: Dict[str, Dict[str, int]] = {}
IMPORT_LOGGER.debug('ASSESSING IMPORT DATA...')
for entity_name in entity_order:
_select_entity_data(
entity_name=entity_name,
reader=reader,
new_entries=new_entries,
existing_entries=existing_entries,
foreign_ids_reverse_mappings=foreign_ids_reverse_mappings,
extras_mode_new=extras_mode_new,
)
IMPORT_LOGGER.debug('STORING ENTITIES...')
for entity_name in entity_order:
_store_entity_data(
reader=reader,
entity_name=entity_name,
comment_mode=comment_mode,
extras_mode_existing=extras_mode_existing,
new_entries=new_entries,
existing_entries=existing_entries,
foreign_ids_reverse_mappings=foreign_ids_reverse_mappings,
import_unique_ids_mappings=import_unique_ids_mappings,
ret_dict=ret_dict,
# batch_size=batch_size,
session=session)
# store all pks to add to import group
pks_for_group: List[int] = [
foreign_ids_reverse_mappings[NODE_ENTITY_NAME][v['uuid']]
for entries in [existing_entries, new_entries]
for v in entries.get(NODE_ENTITY_NAME, {}).values()
]
# now delete the entity data because we no longer need it
del existing_entries
del new_entries
IMPORT_LOGGER.debug('STORING NODE LINKS...')
_store_node_links(
reader=reader,
ignore_unknown_nodes=ignore_unknown_nodes,
foreign_ids_reverse_mappings=foreign_ids_reverse_mappings,
ret_dict=ret_dict,
# batch_size=batch_size,
session=session)
IMPORT_LOGGER.debug('STORING GROUP ELEMENTS...')
_add_nodes_to_groups(
group_count=reader.entity_count(GROUP_ENTITY_NAME),
group_uuids=reader.iter_group_uuids(),
foreign_ids_reverse_mappings=foreign_ids_reverse_mappings)
######################################
# Put everything in a specific group #
######################################
# Note this is done in a separate transaction
group = _make_import_group(group=group, node_pks=pks_for_group)
# Summarize import
result_summary(ret_dict, getattr(group, 'label', None))
return ret_dict