# -*- coding: utf-8 -*-
###########################################################################
# 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 #
###########################################################################
""""Implementation of `DbImporter` for the PCOD database."""
from aiida.tools.dbimporters.plugins.cod import CodDbImporter, CodEntry, CodSearchResults
[docs]class PcodDbImporter(CodDbImporter):
"""
Database importer for Predicted Crystallography Open Database.
"""
_keywords = {
'id': ['file', CodDbImporter._int_clause],
'element': ['element', CodDbImporter._composition_clause],
'number_of_elements': ['nel', CodDbImporter._int_clause],
'formula': ['formula', CodDbImporter._formula_clause],
'volume': ['vol', CodDbImporter._volume_clause],
'spacegroup': ['sg', CodDbImporter._str_exact_clause],
'a': ['a', CodDbImporter._length_clause],
'b': ['b', CodDbImporter._length_clause],
'c': ['c', CodDbImporter._length_clause],
'alpha': ['alpha', CodDbImporter._angle_clause],
'beta': ['beta', CodDbImporter._angle_clause],
'gamma': ['gamma', CodDbImporter._angle_clause],
'text': ['text', CodDbImporter._str_fuzzy_clause]
}
[docs] def __init__(self, **kwargs):
super().__init__(**kwargs)
self._db_parameters = {'host': 'www.crystallography.net', 'user': 'pcod_reader', 'passwd': '', 'db': 'pcod'}
self.setup_db(**kwargs)
[docs] def query_sql(self, **kwargs):
"""
Forms a SQL query for querying the PCOD database using
``keyword = value`` pairs, specified in ``kwargs``.
:return: string containing a SQL statement.
"""
sql_parts = []
for key, value in self._keywords.items():
if key in kwargs:
values = kwargs.pop(key)
if not isinstance(values, list):
values = [values]
sql_parts.append(f'({value[1](self, value[0], key, values)})')
if kwargs:
raise NotImplementedError(f"following keyword(s) are not implemented: {', '.join(kwargs.keys())}")
return f"SELECT file FROM data WHERE {' AND '.join(sql_parts)}"
[docs] def query(self, **kwargs):
"""
Performs a query on the PCOD database using ``keyword = value`` pairs,
specified in ``kwargs``.
:return: an instance of
:py:class:`aiida.tools.dbimporters.plugins.pcod.PcodSearchResults`.
"""
query_statement = self.query_sql(**kwargs)
self._connect_db()
results = []
try:
self._cursor.execute(query_statement)
self._db.commit()
for row in self._cursor.fetchall():
results.append({'id': str(row[0])})
finally:
self._disconnect_db()
return PcodSearchResults(results)
[docs]class PcodSearchResults(CodSearchResults): # pylint: disable=abstract-method
"""
Results of the search, performed on PCOD.
"""
_base_url = 'http://www.crystallography.net/pcod/cif/'
[docs] def __init__(self, results):
super().__init__(results)
self._return_class = PcodEntry
[docs] def _get_url(self, result_dict):
"""
Returns an URL of an entry CIF file.
:param result_dict: dictionary, describing an entry in the results.
"""
return f"{self._base_url + result_dict['id'][0]}/{result_dict['id'][0:3]}/{result_dict['id']}.cif"
[docs]class PcodEntry(CodEntry): # pylint: disable=abstract-method
"""
Represents an entry from PCOD.
"""
_license = 'CC0'
[docs] def __init__(
self,
uri,
db_name='Predicted Crystallography Open Database',
db_uri='http://www.crystallography.net/pcod',
**kwargs
):
"""
Creates an instance of
:py:class:`aiida.tools.dbimporters.plugins.pcod.PcodEntry`, related
to the supplied URI.
"""
super().__init__(db_name=db_name, db_uri=db_uri, uri=uri, **kwargs)