###########################################################################
# Copyright (c), The AiiDA team. All rights reserved. #
# This file is part of the AiiDA code. #
# #
# The code is hosted on GitHub at https://github.com/aiidateam/aiida-core #
# For further information on the license, see the LICENSE.txt file #
# For further information please visit http://www.aiida.net #
###########################################################################
"""Module of `Data` sub class to represent a pseudopotential single file in UPF format and related utilities."""
import json
import re
from upf_to_json import upf_to_json
from aiida.common.warnings import warn_deprecation
from .singlefile import SinglefileData
__all__ = ('UpfData',)
[docs]
def emit_deprecation():
warn_deprecation(
'The `aiida.orm.nodes.data.upf` module is deprecated. For details how to replace it, please see '
'https://aiida-pseudo.readthedocs.io/en/latest/howto.html#migrate-from-legacy-upfdata-from-aiida-core.',
version=3,
)
REGEX_UPF_VERSION = re.compile(
r"""
\s*<UPF\s+version\s*="
(?P<version>.*)">
""",
re.VERBOSE,
)
REGEX_ELEMENT_V1 = re.compile(
r"""
(?P<element_name>[a-zA-Z]{1,2})
\s+
Element
""",
re.VERBOSE,
)
REGEX_ELEMENT_V2 = re.compile(
r"""
\s*
element\s*=\s*(?P<quote_symbol>['"])\s*
(?P<element_name>[a-zA-Z]{1,2})\s*
(?P=quote_symbol)
""",
re.VERBOSE,
)
[docs]
def get_pseudos_from_structure(structure, family_name):
"""Return a dictionary mapping each kind name of the structure to corresponding `UpfData` from given family.
:param structure: a `StructureData`
:param family_name: the name of a UPF family group
:return: dictionary mapping each structure kind name onto `UpfData` of corresponding element
:raise aiida.common.MultipleObjectsError: if more than one UPF for the same element is found in the group.
:raise aiida.common.NotExistent: if no UPF for an element in the group is found in the group.
"""
from aiida.common.exceptions import MultipleObjectsError, NotExistent
emit_deprecation()
pseudo_list = {}
family_pseudos = {}
family = UpfData.get_upf_group(family_name)
for node in family.nodes:
if isinstance(node, UpfData):
if node.element in family_pseudos:
raise MultipleObjectsError(
f'More than one UPF for element {node.element} found in family {family_name}'
)
family_pseudos[node.element] = node
for kind in structure.kinds:
try:
pseudo_list[kind.name] = family_pseudos[kind.symbol]
except KeyError:
raise NotExistent(f'No UPF for element {kind.symbol} found in family {family_name}')
return pseudo_list
[docs]
def upload_upf_family(folder, group_label, group_description, stop_if_existing=True, backend=None):
"""Upload a set of UPF files in a given group.
:param folder: a path containing all UPF files to be added.
Only files ending in .UPF (case-insensitive) are considered.
:param group_label: the name of the group to create. If it exists and is non-empty, a UniquenessError is raised.
:param group_description: string to be set as the group description. Overwrites previous descriptions.
:param stop_if_existing: if True, check for the md5 of the files and, if the file already exists in the DB, raises a
MultipleObjectsError. If False, simply adds the existing UPFData node to the group.
"""
import os
from aiida import orm
from aiida.common import AIIDA_LOGGER
from aiida.common.exceptions import UniquenessError
from aiida.common.files import md5_file
emit_deprecation()
if not os.path.isdir(folder):
raise ValueError('folder must be a directory')
# only files, and only those ending with .upf or .UPF;
# go to the real file if it is a symlink
filenames = [
os.path.realpath(os.path.join(folder, i))
for i in os.listdir(folder)
if os.path.isfile(os.path.join(folder, i)) and i.lower().endswith('.upf')
]
nfiles = len(filenames)
if backend:
default_user = orm.User.get_collection(backend).get_default()
group, group_created = orm.UpfFamily.get_collection(backend).get_or_create(label=group_label, user=default_user)
else:
default_user = orm.User.collection.get_default()
group, group_created = orm.UpfFamily.collection.get_or_create(label=group_label, user=default_user)
if group.user.email != default_user.email:
raise UniquenessError(
'There is already a UpfFamily group with label {}'
', but it belongs to user {}, therefore you '
'cannot modify it'.format(group_label, group.user.email)
)
# Always update description, even if the group already existed
group.description = group_description
# NOTE: GROUP SAVED ONLY AFTER CHECKS OF UNICITY
pseudo_and_created = []
for filename in filenames:
md5sum = md5_file(filename)
builder = orm.QueryBuilder(backend=backend)
builder.append(UpfData, filters={'attributes.md5': {'==': md5sum}})
existing_upf = builder.first(flat=True)
if existing_upf is None:
# return the upfdata instances, not stored
pseudo, created = UpfData.get_or_create(filename, use_first=True, store_upf=False, backend=backend)
# to check whether only one upf per element exists
# NOTE: actually, created has the meaning of "to_be_created"
pseudo_and_created.append((pseudo, created))
else:
if stop_if_existing:
raise ValueError(f'A UPF with identical MD5 to {filename} cannot be added with stop_if_existing')
pseudo_and_created.append((existing_upf, False))
# check whether pseudo are unique per element
elements = [(i[0].element, i[0].md5sum) for i in pseudo_and_created]
# If group already exists, check also that I am not inserting more than
# once the same element
if not group_created:
for aiida_n in group.nodes:
# Skip non-pseudos
if not isinstance(aiida_n, UpfData):
continue
elements.append((aiida_n.element, aiida_n.md5sum))
elements = set(elements) # Discard elements with the same MD5, that would
# not be stored twice
elements_names = [e[0] for e in elements]
if not len(elements_names) == len(set(elements_names)):
duplicates = {x for x in elements_names if elements_names.count(x) > 1}
duplicates_string = ', '.join(i for i in duplicates)
raise UniquenessError(f'More than one UPF found for the elements: {duplicates_string}.')
# At this point, save the group, if still unstored
if group_created:
group.store()
# save the upf in the database, and add them to group
for pseudo, created in pseudo_and_created:
if created:
pseudo.store()
AIIDA_LOGGER.debug(f'New node {pseudo.uuid} created for file {pseudo.filename}')
else:
AIIDA_LOGGER.debug(f'Reusing node {pseudo.uuid} for file {pseudo.filename}')
# Add elements to the group all togetehr
group.add_nodes([pseudo for pseudo, created in pseudo_and_created])
nuploaded = len([_ for _, created in pseudo_and_created if created])
return nfiles, nuploaded
[docs]
def parse_upf(fname, check_filename=True, encoding='utf-8'):
"""Try to get relevant information from the UPF. For the moment, only the
element name. Note that even UPF v.2 cannot be parsed with the XML minidom!
(e.g. due to the & characters in the human-readable section).
If check_filename is True, raise a ParsingError exception if the filename
does not start with the element name.
"""
import os
from aiida.common import AIIDA_LOGGER
from aiida.common.exceptions import ParsingError
from aiida.orm.nodes.data.structure import _valid_symbols
emit_deprecation()
parsed_data = {}
try:
upf_contents = fname.read()
except AttributeError:
with open(fname, encoding=encoding) as handle:
upf_contents = handle.read()
else:
if check_filename:
raise ValueError('cannot use filelike objects when `check_filename=True`, use a filepath instead.')
fname = 'file.txt'
match = REGEX_UPF_VERSION.search(upf_contents)
if match:
version = match.group('version')
AIIDA_LOGGER.debug(f'Version found: {version} for file {fname}')
else:
AIIDA_LOGGER.debug(f'Assuming version 1 for file {fname}')
version = '1'
parsed_data['version'] = version
try:
version_major = int(version.partition('.')[0])
except ValueError:
# If the version string does not contain a dot, fallback
# to version 1
AIIDA_LOGGER.debug(f'Falling back to version 1 for file {fname} version string {version} unrecognized')
version_major = 1
element = None
if version_major == 1:
match = REGEX_ELEMENT_V1.search(upf_contents)
if match:
element = match.group('element_name')
else: # all versions > 1
match = REGEX_ELEMENT_V2.search(upf_contents)
if match:
element = match.group('element_name')
if element is None:
raise ParsingError(f'Unable to find the element of UPF {fname}')
element = element.capitalize()
if element not in _valid_symbols:
raise ParsingError(f'Unknown element symbol {element} for file {fname}')
if check_filename:
if not os.path.basename(fname).lower().startswith(element.lower()):
raise ParsingError(
'Filename {0} was recognized for element ' '{1}, but the filename does not start ' 'with {1}'.format(
fname, element
)
)
parsed_data['element'] = element
return parsed_data
[docs]
class UpfData(SinglefileData):
"""`Data` sub class to represent a pseudopotential single file in UPF format."""
[docs]
@classmethod
def get_or_create(cls, filepath, use_first=False, store_upf=True, backend=None):
"""Get the `UpfData` with the same md5 of the given file, or create it if it does not yet exist.
:param filepath: an absolute filepath on disk
:param use_first: if False (default), raise an exception if more than one potential is found.
If it is True, instead, use the first available pseudopotential.
:param store_upf: boolean, if false, the `UpfData` if created will not be stored.
:return: tuple of `UpfData` and boolean indicating whether it was created.
"""
import os
from aiida.common.files import md5_file
emit_deprecation()
if not os.path.isabs(filepath):
raise ValueError('filepath must be an absolute path')
pseudos = cls.from_md5(md5_file(filepath), backend=backend)
if not pseudos:
instance = cls(file=filepath, backend=backend)
if store_upf:
instance.store()
return (instance, True)
if len(pseudos) > 1:
if use_first:
return (pseudos[0], False)
raise ValueError(
'More than one copy of a pseudopotential with the same MD5 has been found in the DB. pks={}'.format(
','.join([str(i.pk) for i in pseudos])
)
)
return (pseudos[0], False)
[docs]
def __init__(self, *args, **kwargs):
emit_deprecation()
super().__init__(*args, **kwargs)
[docs]
def store(self, *args, **kwargs):
"""Store the node, reparsing the file so that the md5 and the element are correctly reset."""
from aiida.common.exceptions import ParsingError
from aiida.common.files import md5_from_filelike
if self.is_stored:
return self
# Do not check the filename because it will fail since we are passing in a handle, which doesn't have a filename
# and so `parse_upf` will raise. The reason we have to pass in a handle is because this is the repository does
# not allow to get an absolute filepath. Anyway, the filename was already checked in `set_file` when the file
# was set for the first time. All the logic in this method is duplicated in `store` and `_validate` and badly
# needs to be refactored, but that is for another time.
with self.open(mode='r') as handle:
parsed_data = parse_upf(handle, check_filename=False)
# Open in binary mode which is required for generating the md5 checksum
with self.open(mode='rb') as handle:
md5 = md5_from_filelike(handle)
try:
element = parsed_data['element']
except KeyError:
raise ParsingError(f'Could not parse the element from the UPF file {self.filename}')
self.base.attributes.set('element', str(element))
self.base.attributes.set('md5', md5)
return super().store(*args, **kwargs)
[docs]
@classmethod
def from_md5(cls, md5, backend=None):
"""Return a list of all `UpfData` that match the given md5 hash.
.. note:: assumes hash of stored `UpfData` nodes is stored in the `md5` attribute
:param md5: the file hash
:return: list of existing `UpfData` nodes that have the same md5 hash
"""
from aiida.orm.querybuilder import QueryBuilder
builder = QueryBuilder(backend=backend)
builder.append(cls, filters={'attributes.md5': {'==': md5}})
return builder.all(flat=True)
[docs]
def set_file(self, file, filename=None):
"""Store the file in the repository and parse it to set the `element` and `md5` attributes.
:param file: filepath or filelike object of the UPF potential file to store.
Hint: Pass io.BytesIO(b"my string") to construct the file directly from a string.
:param filename: specify filename to use (defaults to name of provided file).
"""
from aiida.common.exceptions import ParsingError
from aiida.common.files import md5_file, md5_from_filelike
parsed_data = parse_upf(file)
try:
md5sum = md5_file(file)
except TypeError:
md5sum = md5_from_filelike(file)
try:
element = parsed_data['element']
except KeyError:
raise ParsingError(f"No 'element' parsed in the UPF file {self.filename}; unable to store")
super().set_file(file, filename=filename)
self.base.attributes.set('element', str(element))
self.base.attributes.set('md5', md5sum)
[docs]
def get_upf_family_names(self):
"""Get the list of all upf family names to which the pseudo belongs."""
from aiida.orm import QueryBuilder, UpfFamily
query = QueryBuilder(backend=self.backend)
query.append(UpfFamily, tag='group', project='label')
query.append(UpfData, filters={'id': {'==': self.pk}}, with_group='group')
return query.all(flat=True)
@property
def element(self):
"""Return the element of the UPF pseudopotential.
:return: the element
"""
return self.base.attributes.get('element', None)
@property
def md5sum(self):
"""Return the md5 checksum of the UPF pseudopotential file.
:return: the md5 checksum
"""
return self.base.attributes.get('md5', None)
[docs]
def _validate(self):
"""Validate the UPF potential file stored for this node."""
from aiida.common.exceptions import ValidationError
from aiida.common.files import md5_from_filelike
super()._validate()
# Do not check the filename because it will fail since we are passing in a handle, which doesn't have a filename
# and so `parse_upf` will raise. The reason we have to pass in a handle is because this is the repository does
# not allow to get an absolute filepath. Anyway, the filename was already checked in `set_file` when the file
# was set for the first time. All the logic in this method is duplicated in `store` and `_validate` and badly
# needs to be refactored, but that is for another time.
with self.open(mode='r') as handle:
parsed_data = parse_upf(handle, check_filename=False)
# Open in binary mode which is required for generating the md5 checksum
with self.open(mode='rb') as handle:
md5 = md5_from_filelike(handle)
try:
element = parsed_data['element']
except KeyError:
raise ValidationError(f"No 'element' could be parsed in the UPF {self.filename}")
try:
attr_element = self.base.attributes.get('element')
except AttributeError:
raise ValidationError("attribute 'element' not set.")
try:
attr_md5 = self.base.attributes.get('md5')
except AttributeError:
raise ValidationError("attribute 'md5' not set.")
if attr_element != element:
raise ValidationError(f"Attribute 'element' says '{attr_element}' but '{element}' was parsed instead.")
if attr_md5 != md5:
raise ValidationError(f"Attribute 'md5' says '{attr_md5}' but '{md5}' was parsed instead.")
[docs]
def _prepare_upf(self, main_file_name=''):
"""Return UPF content."""
return_string = self.get_content()
return return_string.encode('utf-8'), {}
[docs]
@classmethod
def get_upf_group(cls, group_label):
"""Return the UPF family group with the given label.
:param group_label: the family group label
:return: the `Group` with the given label, if it exists
"""
from aiida.orm import UpfFamily
return UpfFamily.get(label=group_label)
[docs]
@classmethod
def get_upf_groups(cls, filter_elements=None, user=None, backend=None):
"""Return all names of groups of type UpfFamily, possibly with some filters.
:param filter_elements: A string or a list of strings.
If present, returns only the groups that contains one UPF for every element present in the list. The default
is `None`, meaning that all families are returned.
:param user: if None (default), return the groups for all users.
If defined, it should be either a `User` instance or the user email.
:return: list of `Group` entities of type UPF.
"""
from aiida.orm import QueryBuilder, UpfFamily, User
builder = QueryBuilder(backend=backend)
builder.append(UpfFamily, tag='group', project='*')
if user:
builder.append(User, filters={'email': {'==': user}}, with_group='group')
if isinstance(filter_elements, str):
filter_elements = [filter_elements]
if filter_elements is not None:
builder.append(UpfData, filters={'attributes.element': {'in': filter_elements}}, with_group='group')
builder.order_by({UpfFamily: {'id': 'asc'}})
return builder.all(flat=True)
[docs]
def _prepare_json(self, main_file_name=''):
"""Returns UPF PP in json format."""
with self.open() as file_handle:
upf_json = upf_to_json(file_handle.read(), fname=self.filename)
return json.dumps(upf_json).encode('utf-8'), {}
