def iter_node_repos(
self,
uuids: Iterable[str],
callback: Callable[[str, Any], None] = null_callback,
) -> Iterator[Folder]:
path_prefixes = [
os.path.join(self.REPO_FOLDER, export_shard_uuid(uuid))
for uuid in uuids
]
if not path_prefixes:
return
self.assert_within_context()
assert self._sandbox is not None # required by mypy
# unarchive the common folder if it does not exist
common_prefix = os.path.commonpath(path_prefixes)
if not self._sandbox.get_subfolder(common_prefix).exists():
self._extract(path_prefix=common_prefix, callback=callback)
callback(
'init', {
'total': len(path_prefixes),
'description': 'Iterating node repositories'
})
for uuid, path_prefix in zip(uuids, path_prefixes):
callback('update', 1)
subfolder = self._sandbox.get_subfolder(path_prefix)
if not subfolder.exists():
raise CorruptArchive(
f'Unable to find the repository folder for Node with UUID={uuid} in the exported file'
)
yield subfolder
def write_node_repo_folder(self,
uuid: str,
path: Union[str, Path],
overwrite: bool = True):
self.assert_within_context()
(self._archivepath / NODES_EXPORT_SUBFOLDER /
export_shard_uuid(uuid)).puttree(path, check_exists=not overwrite)
def test_missing_node_repo_folder_import(self, temp_dir):
"""
Make sure `~aiida.tools.importexport.common.exceptions.CorruptArchive` is raised during import when missing
Node repository folder.
Create and export a Node and manually remove its repository folder in the export file.
Attempt to import it and make sure `~aiida.tools.importexport.common.exceptions.CorruptArchive` is raised,
due to the missing folder.
"""
import tarfile
from aiida.common.folders import SandboxFolder
from aiida.tools.importexport.common.archive import extract_tar
from aiida.tools.importexport.common.config import NODES_EXPORT_SUBFOLDER
from aiida.tools.importexport.common.utils import export_shard_uuid
node = orm.CalculationNode().store()
node.seal()
node_uuid = node.uuid
node_repo = RepositoryFolder(section=Repository._section_name, uuid=node_uuid) # pylint: disable=protected-access
self.assertTrue(
node_repo.exists(), msg='Newly created and stored Node should have had an existing repository folder'
)
# Export and reset db
filename = os.path.join(temp_dir, 'export.aiida')
export([node], filename=filename, file_format='tar.gz', silent=True)
self.reset_database()
# Untar export file, remove repository folder, re-tar
node_shard_uuid = export_shard_uuid(node_uuid)
node_top_folder = node_shard_uuid.split('/')[0]
with SandboxFolder() as folder:
extract_tar(filename, folder, silent=True, nodes_export_subfolder=NODES_EXPORT_SUBFOLDER)
node_folder = folder.get_subfolder(os.path.join(NODES_EXPORT_SUBFOLDER, node_shard_uuid))
self.assertTrue(
node_folder.exists(), msg="The Node's repository folder should still exist in the export file"
)
# Removing the Node's repository folder from the export file
shutil.rmtree(
folder.get_subfolder(os.path.join(NODES_EXPORT_SUBFOLDER, node_top_folder)).abspath, ignore_errors=True
)
self.assertFalse(
node_folder.exists(),
msg="The Node's repository folder should now have been removed in the export file"
)
filename_corrupt = os.path.join(temp_dir, 'export_corrupt.aiida')
with tarfile.open(filename_corrupt, 'w:gz', format=tarfile.PAX_FORMAT, dereference=True) as tar:
tar.add(folder.abspath, arcname='')
# Try to import, check it raises and check the raise message
with self.assertRaises(exceptions.CorruptArchive) as exc:
import_data(filename_corrupt, silent=True)
self.assertIn(
'Unable to find the repository folder for Node with UUID={}'.format(node_uuid), str(exc.exception)
)
def write_node_repo_folder(self,
uuid: str,
path: Union[str, Path],
overwrite: bool = True):
self.assert_within_context()
repo_folder = self._folder.get_subfolder(
NODES_EXPORT_SUBFOLDER).get_subfolder(export_shard_uuid(uuid))
repo_folder.insert_path(src=os.path.abspath(path),
dest_name='.',
overwrite=overwrite)
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_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 export_tree(what,
folder,
allowed_licenses=None,
forbidden_licenses=None,
silent=False,
include_comments=True,
include_logs=True,
**kwargs):
"""Export the entries passed in the 'what' list to a file tree.
:param what: a list of entity instances; they can belong to different models/entities.
:type what: list
:param folder: a temporary folder to build the archive before compression.
:type folder: :py:class:`~aiida.common.folders.Folder`
:param allowed_licenses: List or function. If a list, then checks whether all licenses of Data nodes are in the
list. If a function, then calls function for licenses of Data nodes expecting True if license is allowed, False
otherwise.
:type allowed_licenses: list
:param forbidden_licenses: List or function. If a list, then checks whether all licenses of Data nodes are in the
list. If a function, then calls function for licenses of Data nodes expecting True if license is allowed, False
otherwise.
:type forbidden_licenses: list
:param silent: suppress prints.
:type silent: bool
:param include_comments: In-/exclude export of comments for given node(s) in ``what``.
Default: True, *include* comments in export (as well as relevant users).
:type include_comments: bool
:param include_logs: In-/exclude export of logs for given node(s) in ``what``.
Default: True, *include* logs in export.
:type include_logs: bool
:param kwargs: graph traversal rules. See :const:`aiida.common.links.GraphTraversalRules` what rule names
are toggleable and what the defaults are.
:raises `~aiida.tools.importexport.common.exceptions.ArchiveExportError`: if there are any internal errors when
exporting.
:raises `~aiida.common.exceptions.LicensingException`: if any node is licensed under forbidden license.
"""
from collections import defaultdict
if not silent:
print('STARTING EXPORT...')
all_fields_info, unique_identifiers = get_all_fields_info()
entities_starting_set = defaultdict(set)
# The set that contains the nodes ids of the nodes that should be exported
given_data_entry_ids = set()
given_calculation_entry_ids = set()
given_group_entry_ids = set()
given_computer_entry_ids = set()
given_groups = set()
given_log_entry_ids = set()
given_comment_entry_ids = set()
# I store a list of the actual dbnodes
for entry in what:
# This returns the class name (as in imports). E.g. for a model node:
# aiida.backends.djsite.db.models.DbNode
# entry_class_string = get_class_string(entry)
# Now a load the backend-independent name into entry_entity_name, e.g. Node!
# entry_entity_name = schema_to_entity_names(entry_class_string)
if issubclass(entry.__class__, orm.Group):
entities_starting_set[GROUP_ENTITY_NAME].add(entry.uuid)
given_group_entry_ids.add(entry.id)
given_groups.add(entry)
elif issubclass(entry.__class__, orm.Node):
entities_starting_set[NODE_ENTITY_NAME].add(entry.uuid)
if issubclass(entry.__class__, orm.Data):
given_data_entry_ids.add(entry.pk)
elif issubclass(entry.__class__, orm.ProcessNode):
given_calculation_entry_ids.add(entry.pk)
elif issubclass(entry.__class__, orm.Computer):
entities_starting_set[COMPUTER_ENTITY_NAME].add(entry.uuid)
given_computer_entry_ids.add(entry.pk)
else:
raise exceptions.ArchiveExportError(
'I was given {} ({}), which is not a Node, Computer, or Group instance'
.format(entry, type(entry)))
# Add all the nodes contained within the specified groups
for group in given_groups:
for entry in group.nodes:
entities_starting_set[NODE_ENTITY_NAME].add(entry.uuid)
if issubclass(entry.__class__, orm.Data):
given_data_entry_ids.add(entry.pk)
elif issubclass(entry.__class__, orm.ProcessNode):
given_calculation_entry_ids.add(entry.pk)
for entity, entity_set in entities_starting_set.items():
entities_starting_set[entity] = list(entity_set)
# We will iteratively explore the AiiDA graph to find further nodes that
# should also be exported.
# At the same time, we will create the links_uuid list of dicts to be exported
if not silent:
print('RETRIEVING LINKED NODES AND STORING LINKS...')
to_be_exported, links_uuid, graph_traversal_rules = retrieve_linked_nodes(
given_calculation_entry_ids, given_data_entry_ids, **kwargs)
## Universal "entities" attributed to all types of nodes
# Logs
if include_logs and to_be_exported:
# Get related log(s) - universal for all nodes
builder = orm.QueryBuilder()
builder.append(orm.Log,
filters={'dbnode_id': {
'in': to_be_exported
}},
project='id')
res = {_[0] for _ in builder.all()}
given_log_entry_ids.update(res)
# Comments
if include_comments and to_be_exported:
# Get related log(s) - universal for all nodes
builder = orm.QueryBuilder()
builder.append(orm.Comment,
filters={'dbnode_id': {
'in': to_be_exported
}},
project='id')
res = {_[0] for _ in builder.all()}
given_comment_entry_ids.update(res)
# Here we get all the columns that we plan to project per entity that we
# would like to extract
given_entities = list()
if given_group_entry_ids:
given_entities.append(GROUP_ENTITY_NAME)
if to_be_exported:
given_entities.append(NODE_ENTITY_NAME)
if given_computer_entry_ids:
given_entities.append(COMPUTER_ENTITY_NAME)
if given_log_entry_ids:
given_entities.append(LOG_ENTITY_NAME)
if given_comment_entry_ids:
given_entities.append(COMMENT_ENTITY_NAME)
entries_to_add = dict()
for given_entity in given_entities:
project_cols = ['id']
# The following gets a list of fields that we need,
# e.g. user, mtime, uuid, computer
entity_prop = all_fields_info[given_entity].keys()
# Here we do the necessary renaming of properties
for prop in entity_prop:
# nprop contains the list of projections
nprop = (file_fields_to_model_fields[given_entity][prop] if prop
in file_fields_to_model_fields[given_entity] else prop)
project_cols.append(nprop)
# Getting the ids that correspond to the right entity
if given_entity == GROUP_ENTITY_NAME:
entry_ids_to_add = given_group_entry_ids
elif given_entity == NODE_ENTITY_NAME:
entry_ids_to_add = to_be_exported
elif given_entity == COMPUTER_ENTITY_NAME:
entry_ids_to_add = given_computer_entry_ids
elif given_entity == LOG_ENTITY_NAME:
entry_ids_to_add = given_log_entry_ids
elif given_entity == COMMENT_ENTITY_NAME:
entry_ids_to_add = given_comment_entry_ids
builder = orm.QueryBuilder()
builder.append(entity_names_to_entities[given_entity],
filters={'id': {
'in': entry_ids_to_add
}},
project=project_cols,
tag=given_entity,
outerjoin=True)
entries_to_add[given_entity] = builder
# TODO (Spyros) To see better! Especially for functional licenses
# Check the licenses of exported data.
if allowed_licenses is not None or forbidden_licenses is not None:
builder = orm.QueryBuilder()
builder.append(orm.Node,
project=['id', 'attributes.source.license'],
filters={'id': {
'in': to_be_exported
}})
# Skip those nodes where the license is not set (this is the standard behavior with Django)
node_licenses = list(
(a, b) for [a, b] in builder.all() if b is not None)
check_licenses(node_licenses, allowed_licenses, forbidden_licenses)
############################################################
##### Start automatic recursive export data generation #####
############################################################
if not silent:
print('STORING DATABASE ENTRIES...')
export_data = dict()
entity_separator = '_'
for entity_name, partial_query in entries_to_add.items():
foreign_fields = {
k: v
for k, v in all_fields_info[entity_name].items()
# all_fields_info[model_name].items()
if 'requires' in v
}
for value in foreign_fields.values():
ref_model_name = value['requires']
fill_in_query(partial_query, entity_name, ref_model_name,
[entity_name], entity_separator)
for temp_d in partial_query.iterdict():
for k in temp_d.keys():
# Get current entity
current_entity = k.split(entity_separator)[-1]
# This is a empty result of an outer join.
# It should not be taken into account.
if temp_d[k]['id'] is None:
continue
temp_d2 = {
temp_d[k]['id']:
serialize_dict(temp_d[k],
remove_fields=['id'],
rename_fields=model_fields_to_file_fields[
current_entity])
}
try:
export_data[current_entity].update(temp_d2)
except KeyError:
export_data[current_entity] = temp_d2
#######################################
# Manually manage attributes and extras
#######################################
# I use .get because there may be no nodes to export
all_nodes_pk = list()
if NODE_ENTITY_NAME in export_data:
all_nodes_pk.extend(export_data.get(NODE_ENTITY_NAME).keys())
if sum(len(model_data) for model_data in export_data.values()) == 0:
if not silent:
print('No nodes to store, exiting...')
return
if not silent:
print('Exporting a total of {} db entries, of which {} nodes.'.format(
sum(len(model_data) for model_data in export_data.values()),
len(all_nodes_pk)))
# ATTRIBUTES and EXTRAS
if not silent:
print('STORING NODE ATTRIBUTES AND EXTRAS...')
node_attributes = {}
node_extras = {}
# A second QueryBuilder query to get the attributes and extras. See if this can be optimized
if all_nodes_pk:
all_nodes_query = orm.QueryBuilder()
all_nodes_query.append(orm.Node,
filters={'id': {
'in': all_nodes_pk
}},
project=['id', 'attributes', 'extras'])
for res_pk, res_attributes, res_extras in all_nodes_query.iterall():
node_attributes[str(res_pk)] = res_attributes
node_extras[str(res_pk)] = res_extras
if not silent:
print('STORING GROUP ELEMENTS...')
groups_uuid = dict()
# If a group is in the exported date, we export the group/node correlation
if GROUP_ENTITY_NAME in export_data:
for curr_group in export_data[GROUP_ENTITY_NAME]:
group_uuid_qb = orm.QueryBuilder()
group_uuid_qb.append(entity_names_to_entities[GROUP_ENTITY_NAME],
filters={'id': {
'==': curr_group
}},
project=['uuid'],
tag='group')
group_uuid_qb.append(entity_names_to_entities[NODE_ENTITY_NAME],
project=['uuid'],
with_group='group')
for res in group_uuid_qb.iterall():
if str(res[0]) in groups_uuid:
groups_uuid[str(res[0])].append(str(res[1]))
else:
groups_uuid[str(res[0])] = [str(res[1])]
#######################################
# Final check for unsealed ProcessNodes
#######################################
process_nodes = set()
for node_pk, content in export_data.get(NODE_ENTITY_NAME, {}).items():
if content['node_type'].startswith('process.'):
process_nodes.add(node_pk)
check_process_nodes_sealed(process_nodes)
######################################
# Now I store
######################################
# subfolder inside the export package
nodesubfolder = folder.get_subfolder(NODES_EXPORT_SUBFOLDER,
create=True,
reset_limit=True)
if not silent:
print('STORING DATA...')
data = {
'node_attributes': node_attributes,
'node_extras': node_extras,
'export_data': export_data,
'links_uuid': links_uuid,
'groups_uuid': groups_uuid
}
# N.B. We're really calling zipfolder.open (if exporting a zipfile)
with folder.open('data.json', mode='w') as fhandle:
# fhandle.write(json.dumps(data, cls=UUIDEncoder))
fhandle.write(json.dumps(data))
# Add proper signature to unique identifiers & all_fields_info
# Ignore if a key doesn't exist in any of the two dictionaries
metadata = {
'aiida_version': get_version(),
'export_version': EXPORT_VERSION,
'all_fields_info': all_fields_info,
'unique_identifiers': unique_identifiers,
'export_parameters': {
'graph_traversal_rules': graph_traversal_rules,
'entities_starting_set': entities_starting_set,
'include_comments': include_comments,
'include_logs': include_logs
}
}
with folder.open('metadata.json', 'w') as fhandle:
fhandle.write(json.dumps(metadata))
if silent is not True:
print('STORING REPOSITORY FILES...')
# If there are no nodes, there are no repository files to store
if all_nodes_pk:
# Large speed increase by not getting the node itself and looping in memory in python, but just getting the uuid
uuid_query = orm.QueryBuilder()
uuid_query.append(orm.Node,
filters={'id': {
'in': all_nodes_pk
}},
project=['uuid'])
for res in uuid_query.all():
uuid = str(res[0])
sharded_uuid = export_shard_uuid(uuid)
# Important to set create=False, otherwise creates twice a subfolder. Maybe this is a bug of insert_path?
thisnodefolder = nodesubfolder.get_subfolder(sharded_uuid,
create=False,
reset_limit=True)
# Make sure the node's repository folder was not deleted
src = RepositoryFolder(section=Repository._section_name, uuid=uuid) # pylint: disable=protected-access
if not src.exists():
raise exceptions.ArchiveExportError(
'Unable to find the repository folder for Node with UUID={} in the local repository'
.format(uuid))
# In this way, I copy the content of the folder, and not the folder itself
thisnodefolder.insert_path(src=src.abspath, dest_name='.')
def write_to_archive(
folder: Union[Folder, ZipFolder],
metadata: dict,
all_node_uuids: Set[str],
export_data: Dict[str, Dict[int, dict]],
node_attributes: Dict[str, dict],
node_extras: Dict[str, dict],
groups_uuid: Dict[str, List[str]],
links_uuid: List[dict],
silent: bool,
) -> None:
"""Store data to the archive."""
######################################
# Now collecting and storing
######################################
# subfolder inside the export package
nodesubfolder = folder.get_subfolder(NODES_EXPORT_SUBFOLDER,
create=True,
reset_limit=True)
EXPORT_LOGGER.debug("ADDING DATA TO EXPORT ARCHIVE...")
data = {
"node_attributes": node_attributes,
"node_extras": node_extras,
"export_data": export_data,
"links_uuid": links_uuid,
"groups_uuid": groups_uuid,
}
# N.B. We're really calling zipfolder.open (if exporting a zipfile)
with folder.open("data.json", mode="w") as fhandle:
# fhandle.write(json.dumps(data, cls=UUIDEncoder))
fhandle.write(json.dumps(data))
with folder.open("metadata.json", "w") as fhandle:
fhandle.write(json.dumps(metadata))
EXPORT_LOGGER.debug("ADDING REPOSITORY FILES TO EXPORT ARCHIVE...")
# If there are no nodes, there are no repository files to store
if all_node_uuids:
progress_bar = get_progress_bar(total=len(all_node_uuids),
disable=silent)
pbar_base_str = "Exporting repository - "
for uuid in all_node_uuids:
sharded_uuid = export_shard_uuid(uuid)
progress_bar.set_description_str(
f"{pbar_base_str}UUID={uuid.split('-')[0]}", refresh=False)
progress_bar.update()
# Important to set create=False, otherwise creates twice a subfolder.
# Maybe this is a bug of insert_path?
thisnodefolder = nodesubfolder.get_subfolder(sharded_uuid,
create=False,
reset_limit=True)
# Make sure the node's repository folder was not deleted
src = RepositoryFolder(section=Repository._section_name, uuid=uuid) # pylint: disable=protected-access
if not src.exists():
raise exceptions.ArchiveExportError(
f"Unable to find the repository folder for Node with UUID={uuid} "
"in the local repository")
# In this way, I copy the content of the folder, and not the folder itself
thisnodefolder.insert_path(src=src.abspath, dest_name=".")
def export_tree(entities=None,
folder=None,
allowed_licenses=None,
forbidden_licenses=None,
silent=False,
include_comments=True,
include_logs=True,
**kwargs):
"""Export the entries passed in the 'entities' list to a file tree.
.. deprecated:: 1.2.1
Support for the parameter `what` will be removed in `v2.0.0`. Please use `entities` instead.
:param entities: a list of entity instances; they can belong to different models/entities.
:type entities: list
:param folder: a temporary folder to build the archive before compression.
:type folder: :py:class:`~aiida.common.folders.Folder`
:param allowed_licenses: List or function. If a list, then checks whether all licenses of Data nodes are in the
list. If a function, then calls function for licenses of Data nodes expecting True if license is allowed, False
otherwise.
:type allowed_licenses: list
:param forbidden_licenses: List or function. If a list, then checks whether all licenses of Data nodes are in the
list. If a function, then calls function for licenses of Data nodes expecting True if license is allowed, False
otherwise.
:type forbidden_licenses: list
:param silent: suppress console prints and progress bar.
:type silent: bool
:param include_comments: In-/exclude export of comments for given node(s) in ``entities``.
Default: True, *include* comments in export (as well as relevant users).
:type include_comments: bool
:param include_logs: In-/exclude export of logs for given node(s) in ``entities``.
Default: True, *include* logs in export.
:type include_logs: bool
:param kwargs: graph traversal rules. See :const:`aiida.common.links.GraphTraversalRules` what rule names
are toggleable and what the defaults are.
:raises `~aiida.tools.importexport.common.exceptions.ArchiveExportError`: if there are any internal errors when
exporting.
:raises `~aiida.common.exceptions.LicensingException`: if any node is licensed under forbidden license.
"""
from collections import defaultdict
from aiida.tools.graph.graph_traversers import get_nodes_export
if silent:
logging.disable(level=logging.CRITICAL)
EXPORT_LOGGER.debug('STARTING EXPORT...')
# Backwards-compatibility
entities = deprecated_parameters(
old={
'name': 'what',
'value': kwargs.pop('what', None)
},
new={
'name': 'entities',
'value': entities
},
)
type_check(
entities, (list, tuple, set),
msg='`entities` must be specified and given as a list of AiiDA entities'
)
entities = list(entities)
type_check(
folder, (Folder, ZipFolder),
msg='`folder` must be specified and given as an AiiDA Folder entity')
all_fields_info, unique_identifiers = get_all_fields_info()
entities_starting_set = defaultdict(set)
# The set that contains the nodes ids of the nodes that should be exported
given_node_entry_ids = set()
given_log_entry_ids = set()
given_comment_entry_ids = set()
# Instantiate progress bar - go through list of `entities`
pbar_total = len(entities) + 1 if entities else 1
progress_bar = get_progress_bar(total=pbar_total,
leave=False,
disable=silent)
progress_bar.set_description_str('Collecting chosen entities',
refresh=False)
# I store a list of the actual dbnodes
for entry in entities:
progress_bar.update()
# This returns the class name (as in imports). E.g. for a model node:
# aiida.backends.djsite.db.models.DbNode
# entry_class_string = get_class_string(entry)
# Now a load the backend-independent name into entry_entity_name, e.g. Node!
# entry_entity_name = schema_to_entity_names(entry_class_string)
if issubclass(entry.__class__, orm.Group):
entities_starting_set[GROUP_ENTITY_NAME].add(entry.uuid)
elif issubclass(entry.__class__, orm.Node):
entities_starting_set[NODE_ENTITY_NAME].add(entry.uuid)
given_node_entry_ids.add(entry.pk)
elif issubclass(entry.__class__, orm.Computer):
entities_starting_set[COMPUTER_ENTITY_NAME].add(entry.uuid)
else:
raise exceptions.ArchiveExportError(
'I was given {} ({}), which is not a Node, Computer, or Group instance'
.format(entry, type(entry)))
# Add all the nodes contained within the specified groups
if GROUP_ENTITY_NAME in entities_starting_set:
progress_bar.set_description_str('Retrieving Nodes from Groups ...',
refresh=True)
# Use single query instead of given_group.nodes iterator for performance.
qh_groups = orm.QueryBuilder().append(
orm.Group,
filters={
'uuid': {
'in': entities_starting_set[GROUP_ENTITY_NAME]
}
},
tag='groups').queryhelp
# Delete this import once the dbexport.zip module has been renamed
from builtins import zip # pylint: disable=redefined-builtin
node_results = orm.QueryBuilder(**qh_groups).append(
orm.Node, project=['id', 'uuid'], with_group='groups').all()
if node_results:
pks, uuids = map(list, zip(*node_results))
entities_starting_set[NODE_ENTITY_NAME].update(uuids)
given_node_entry_ids.update(pks)
del node_results, pks, uuids
progress_bar.update()
# We will iteratively explore the AiiDA graph to find further nodes that should also be exported.
# At the same time, we will create the links_uuid list of dicts to be exported
progress_bar = get_progress_bar(total=1, disable=silent)
progress_bar.set_description_str(
'Getting provenance and storing links ...', refresh=True)
traverse_output = get_nodes_export(starting_pks=given_node_entry_ids,
get_links=True,
**kwargs)
node_ids_to_be_exported = traverse_output['nodes']
graph_traversal_rules = traverse_output['rules']
# A utility dictionary for mapping PK to UUID.
if node_ids_to_be_exported:
qbuilder = orm.QueryBuilder().append(
orm.Node,
project=('id', 'uuid'),
filters={'id': {
'in': node_ids_to_be_exported
}},
)
node_pk_2_uuid_mapping = dict(qbuilder.all())
else:
node_pk_2_uuid_mapping = {}
# The set of tuples now has to be transformed to a list of dicts
links_uuid = [{
'input': node_pk_2_uuid_mapping[link.source_id],
'output': node_pk_2_uuid_mapping[link.target_id],
'label': link.link_label,
'type': link.link_type
} for link in traverse_output['links']]
progress_bar.update()
# Progress bar initialization - Entities
progress_bar = get_progress_bar(total=1, disable=silent)
progress_bar.set_description_str('Initializing export of all entities',
refresh=True)
## Universal "entities" attributed to all types of nodes
# Logs
if include_logs and node_ids_to_be_exported:
# Get related log(s) - universal for all nodes
builder = orm.QueryBuilder()
builder.append(orm.Log,
filters={'dbnode_id': {
'in': node_ids_to_be_exported
}},
project='uuid')
res = set(builder.all(flat=True))
given_log_entry_ids.update(res)
# Comments
if include_comments and node_ids_to_be_exported:
# Get related log(s) - universal for all nodes
builder = orm.QueryBuilder()
builder.append(orm.Comment,
filters={'dbnode_id': {
'in': node_ids_to_be_exported
}},
project='uuid')
res = set(builder.all(flat=True))
given_comment_entry_ids.update(res)
# Here we get all the columns that we plan to project per entity that we would like to extract
given_entities = set(entities_starting_set.keys())
if node_ids_to_be_exported:
given_entities.add(NODE_ENTITY_NAME)
if given_log_entry_ids:
given_entities.add(LOG_ENTITY_NAME)
if given_comment_entry_ids:
given_entities.add(COMMENT_ENTITY_NAME)
progress_bar.update()
if given_entities:
progress_bar = get_progress_bar(total=len(given_entities),
disable=silent)
pbar_base_str = 'Preparing entities'
entries_to_add = dict()
for given_entity in given_entities:
progress_bar.set_description_str(pbar_base_str +
' - {}s'.format(given_entity),
refresh=False)
progress_bar.update()
project_cols = ['id']
# The following gets a list of fields that we need,
# e.g. user, mtime, uuid, computer
entity_prop = all_fields_info[given_entity].keys()
# Here we do the necessary renaming of properties
for prop in entity_prop:
# nprop contains the list of projections
nprop = (file_fields_to_model_fields[given_entity][prop] if prop
in file_fields_to_model_fields[given_entity] else prop)
project_cols.append(nprop)
# Getting the ids that correspond to the right entity
entry_uuids_to_add = entities_starting_set.get(given_entity, set())
if not entry_uuids_to_add:
if given_entity == LOG_ENTITY_NAME:
entry_uuids_to_add = given_log_entry_ids
elif given_entity == COMMENT_ENTITY_NAME:
entry_uuids_to_add = given_comment_entry_ids
elif given_entity == NODE_ENTITY_NAME:
entry_uuids_to_add.update(
{node_pk_2_uuid_mapping[_]
for _ in node_ids_to_be_exported})
builder = orm.QueryBuilder()
builder.append(entity_names_to_entities[given_entity],
filters={'uuid': {
'in': entry_uuids_to_add
}},
project=project_cols,
tag=given_entity,
outerjoin=True)
entries_to_add[given_entity] = builder
# TODO (Spyros) To see better! Especially for functional licenses
# Check the licenses of exported data.
if allowed_licenses is not None or forbidden_licenses is not None:
builder = orm.QueryBuilder()
builder.append(orm.Node,
project=['id', 'attributes.source.license'],
filters={'id': {
'in': node_ids_to_be_exported
}})
# Skip those nodes where the license is not set (this is the standard behavior with Django)
node_licenses = list(
(a, b) for [a, b] in builder.all() if b is not None)
check_licenses(node_licenses, allowed_licenses, forbidden_licenses)
############################################################
##### Start automatic recursive export data generation #####
############################################################
EXPORT_LOGGER.debug('GATHERING DATABASE ENTRIES...')
if entries_to_add:
progress_bar = get_progress_bar(total=len(entries_to_add),
disable=silent)
export_data = defaultdict(dict)
entity_separator = '_'
for entity_name, partial_query in entries_to_add.items():
progress_bar.set_description_str('Exporting {}s'.format(entity_name),
refresh=False)
progress_bar.update()
foreign_fields = {
k: v
for k, v in all_fields_info[entity_name].items() if 'requires' in v
}
for value in foreign_fields.values():
ref_model_name = value['requires']
fill_in_query(partial_query, entity_name, ref_model_name,
[entity_name], entity_separator)
for temp_d in partial_query.iterdict():
for key in temp_d:
# Get current entity
current_entity = key.split(entity_separator)[-1]
# This is a empty result of an outer join.
# It should not be taken into account.
if temp_d[key]['id'] is None:
continue
export_data[current_entity].update({
temp_d[key]['id']:
serialize_dict(temp_d[key],
remove_fields=['id'],
rename_fields=model_fields_to_file_fields[
current_entity])
})
# Close progress up until this point in order to print properly
close_progress_bar(leave=False)
#######################################
# Manually manage attributes and extras
#######################################
# Pointer. Renaming, since Nodes have now technically been retrieved and "stored"
all_node_pks = node_ids_to_be_exported
model_data = sum(len(model_data) for model_data in export_data.values())
if not model_data:
EXPORT_LOGGER.log(msg='Nothing to store, exiting...',
level=LOG_LEVEL_REPORT)
return
EXPORT_LOGGER.log(
msg='Exporting a total of {} database entries, of which {} are Nodes.'.
format(model_data, len(all_node_pks)),
level=LOG_LEVEL_REPORT)
# Instantiate new progress bar
progress_bar = get_progress_bar(total=1, leave=False, disable=silent)
# ATTRIBUTES and EXTRAS
EXPORT_LOGGER.debug('GATHERING NODE ATTRIBUTES AND EXTRAS...')
node_attributes = {}
node_extras = {}
# Another QueryBuilder query to get the attributes and extras. TODO: See if this can be optimized
if all_node_pks:
all_nodes_query = orm.QueryBuilder().append(
orm.Node,
filters={'id': {
'in': all_node_pks
}},
project=['id', 'attributes', 'extras'])
progress_bar = get_progress_bar(total=all_nodes_query.count(),
disable=silent)
progress_bar.set_description_str('Exporting Attributes and Extras',
refresh=False)
for node_pk, attributes, extras in all_nodes_query.iterall():
progress_bar.update()
node_attributes[str(node_pk)] = attributes
node_extras[str(node_pk)] = extras
EXPORT_LOGGER.debug('GATHERING GROUP ELEMENTS...')
groups_uuid = defaultdict(list)
# If a group is in the exported data, we export the group/node correlation
if GROUP_ENTITY_NAME in export_data:
group_uuids_with_node_uuids = orm.QueryBuilder().append(
orm.Group,
filters={
'id': {
'in': export_data[GROUP_ENTITY_NAME]
}
},
project='uuid',
tag='groups').append(orm.Node, project='uuid', with_group='groups')
# This part is _only_ for the progress bar
total_node_uuids_for_groups = group_uuids_with_node_uuids.count()
if total_node_uuids_for_groups:
progress_bar = get_progress_bar(total=total_node_uuids_for_groups,
disable=silent)
progress_bar.set_description_str('Exporting Groups ...',
refresh=False)
for group_uuid, node_uuid in group_uuids_with_node_uuids.iterall():
progress_bar.update()
groups_uuid[group_uuid].append(node_uuid)
#######################################
# Final check for unsealed ProcessNodes
#######################################
process_nodes = set()
for node_pk, content in export_data.get(NODE_ENTITY_NAME, {}).items():
if content['node_type'].startswith('process.'):
process_nodes.add(node_pk)
check_process_nodes_sealed(process_nodes)
######################################
# Now collecting and storing
######################################
# subfolder inside the export package
nodesubfolder = folder.get_subfolder(NODES_EXPORT_SUBFOLDER,
create=True,
reset_limit=True)
EXPORT_LOGGER.debug('ADDING DATA TO EXPORT ARCHIVE...')
data = {
'node_attributes': node_attributes,
'node_extras': node_extras,
'export_data': export_data,
'links_uuid': links_uuid,
'groups_uuid': groups_uuid
}
# N.B. We're really calling zipfolder.open (if exporting a zipfile)
with folder.open('data.json', mode='w') as fhandle:
# fhandle.write(json.dumps(data, cls=UUIDEncoder))
fhandle.write(json.dumps(data))
# Turn sets into lists to be able to export them as JSON metadata.
for entity, entity_set in entities_starting_set.items():
entities_starting_set[entity] = list(entity_set)
metadata = {
'aiida_version': get_version(),
'export_version': EXPORT_VERSION,
'all_fields_info': all_fields_info,
'unique_identifiers': unique_identifiers,
'export_parameters': {
'graph_traversal_rules': graph_traversal_rules,
'entities_starting_set': entities_starting_set,
'include_comments': include_comments,
'include_logs': include_logs
}
}
with folder.open('metadata.json', 'w') as fhandle:
fhandle.write(json.dumps(metadata))
EXPORT_LOGGER.debug('ADDING REPOSITORY FILES TO EXPORT ARCHIVE...')
# If there are no nodes, there are no repository files to store
if all_node_pks:
all_node_uuids = {node_pk_2_uuid_mapping[_] for _ in all_node_pks}
progress_bar = get_progress_bar(total=len(all_node_uuids),
disable=silent)
pbar_base_str = 'Exporting repository - '
for uuid in all_node_uuids:
sharded_uuid = export_shard_uuid(uuid)
progress_bar.set_description_str(
pbar_base_str + 'UUID={}'.format(uuid.split('-')[0]),
refresh=False)
progress_bar.update()
# Important to set create=False, otherwise creates twice a subfolder. Maybe this is a bug of insert_path?
thisnodefolder = nodesubfolder.get_subfolder(sharded_uuid,
create=False,
reset_limit=True)
# Make sure the node's repository folder was not deleted
src = RepositoryFolder(section=Repository._section_name, uuid=uuid) # pylint: disable=protected-access
if not src.exists():
raise exceptions.ArchiveExportError(
'Unable to find the repository folder for Node with UUID={} in the local repository'
.format(uuid))
# In this way, I copy the content of the folder, and not the folder itself
thisnodefolder.insert_path(src=src.abspath, dest_name='.')
close_progress_bar(leave=False)
# Reset logging level
if silent:
logging.disable(level=logging.NOTSET)
