# -*- coding: utf-8 -*-
from aiida.tools.dbimporters.baseclasses \
import DbImporter, DbSearchResults, CifEntry
__copyright__ = u"Copyright (c), 2015, ECOLE POLYTECHNIQUE FEDERALE DE LAUSANNE (Theory and Simulation of Materials (THEOS) and National Centre for Computational Design and Discovery of Novel Materials (NCCR MARVEL)), Switzerland and ROBERT BOSCH LLC, USA. All rights reserved."
__license__ = "MIT license, see LICENSE.txt file"
__version__ = "0.5.0"
__contributors__ = "Andrea Cepellotti, Andrius Merkys, Giovanni Pizzi, Martin Uhrin"
[docs]class MpodDbImporter(DbImporter):
"""
Database importer for Material Properties Open Database.
"""
def _str_clause(self, key, alias, values):
"""
Returns part of HTTP GET query for querying string fields.
"""
if not isinstance(values, basestring) and not isinstance(values, int):
raise ValueError("incorrect value for keyword '" + alias + \
"' -- only strings and integers are accepted")
return "{}={}".format(key, values)
_keywords = {'phase_name': ['phase_name', _str_clause],
'formula': ['formula', _str_clause],
'element': ['element', None],
'cod_id': ['cod_code', _str_clause],
'authors': ['publ_author', _str_clause]}
def __init__(self, **kwargs):
self._query_url = "http://mpod.cimav.edu.mx/data/search/"
self.setup_db(**kwargs)
[docs] def query_get(self, **kwargs):
"""
Forms a HTTP GET query for querying the MPOD database.
May return more than one query in case an intersection is needed.
:return: a list containing strings for HTTP GET statement.
"""
if 'formula' in kwargs.keys() and 'element' in kwargs.keys():
raise ValueError("can not query both formula and elements "
"in MPOD")
elements = []
if 'element' in kwargs.keys():
elements = kwargs.pop('element')
if not isinstance(elements, list):
elements = [elements]
get_parts = []
for key in self._keywords.keys():
if key in kwargs.keys():
values = kwargs.pop(key)
get_parts.append(
self._keywords[key][1](self,
self._keywords[key][0],
key,
values))
if kwargs.keys():
raise NotImplementedError("search keyword(s) '"
"', '".join(kwargs.keys()) + "' "
"is(are) not implemented for MPOD")
queries = []
for e in elements:
queries.append(self._query_url + '?' +
"&".join(get_parts +
[self._str_clause('formula', 'element', e)]))
if not queries:
queries.append(self._query_url + '?' + "&".join(get_parts))
return queries
[docs] def query(self, **kwargs):
"""
Performs a query on the MPOD database using ``keyword = value`` pairs,
specified in ``kwargs``.
:return: an instance of
:py:class:`aiida.tools.dbimporters.plugins.mpod.MpodSearchResults`.
"""
import urllib2
import re
query_statements = self.query_get(**kwargs)
results = None
for query in query_statements:
response = urllib2.urlopen(query).read()
this_results = re.findall("/datafiles/(\d+)\.mpod", response)
if results is None:
results = this_results
else:
results = filter(set(results).__contains__, this_results)
return MpodSearchResults([{"id": x} for x in results])
[docs] def setup_db(self, query_url=None, **kwargs):
"""
Changes the database connection details.
"""
if query_url:
self._query_url = query_url
if kwargs.keys():
raise NotImplementedError( \
"unknown database connection parameter(s): '" + \
"', '".join(kwargs.keys()) + \
"', available parameters: 'query_url'")
[docs] def get_supported_keywords(self):
"""
Returns the list of all supported query keywords.
:return: list of strings
"""
return self._keywords.keys()
[docs]class MpodSearchResults(DbSearchResults):
"""
Results of the search, performed on MPOD.
"""
_base_url = "http://mpod.cimav.edu.mx/datafiles/"
def __init__(self, results):
super(MpodSearchResults, self).__init__(results)
self._return_class = MpodEntry
def __len__(self):
return len(self._results)
def _get_source_dict(self, result_dict):
"""
Returns a dictionary, which is passed as kwargs to the created
DbEntry instance, describing the source of the entry.
:param result_dict: dictionary, describing an entry in the results.
"""
return {'id': result_dict['id']}
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 self._base_url + result_dict['id'] + ".mpod"
[docs]class MpodEntry(CifEntry):
"""
Represents an entry from MPOD.
"""
def __init__(self, uri, **kwargs):
"""
Creates an instance of
:py:class:`aiida.tools.dbimporters.plugins.mpod.MpodEntry`, related
to the supplied URI.
"""
super(MpodEntry, self).__init__(db_name='Material Properties Open Database',
db_uri='http://mpod.cimav.edu.mx',
uri=uri,
**kwargs)