Added support for queries against Materials Project (#2097)

* Added suppert for queries against Materials Project

* Removed pagesize and structure methods and corrected spelling

* Moved license entry to DbEntry and replaced collection with properties

* Added a test and moved MPRester inside setup_db

* Changed naming scheme

* Added aiida.tools.dbimporters.plugins to the allowed test suite

* Added files

* Simplified code and added a way to disable the test

aiida/cmdline/commands/cmd_devel.py

@@ -48,6 +48,7 @@ def get_valid_test_paths():
         'aiida.cmdline.utils',
         'aiida.cmdline.params.types',
         'aiida.cmdline.params.options',
+        'aiida.tools.dbimporters.plugins',
     ]
 
     valid_test_paths = {}

aiida/tools/dbimporters/plugins/materialsproject.py

@@ -0,0 +1,202 @@
+# -*- 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               #
+###########################################################################
+"""Module that contains the class definitions necessary to offer support for
+queries to Materials Project."""
+
+from __future__ import absolute_import
+import os
+import datetime
+import requests
+from six import raise_from
+from pymatgen import MPRester
+from aiida.tools.dbimporters.baseclasses import CifEntry, DbImporter, DbSearchResults
+
+
+class MaterialsProjectImporter(DbImporter):
+    """
+    Database importer for the Materials Project.
+    """
+
+    _properties = 'structure'
+    _supported_keywords = None
+
+    def __init__(self, **kwargs):
+        """
+        Instantiate the MaterialsProjectImporter by setting up the Materials API (MAPI)
+        connection details.
+        """
+        self.setup_db(**kwargs)
+
+    def setup_db(self, **kwargs):
+        """
+        Setup the required parameters to the REST API
+        """
+        try:
+            api_key = kwargs['api_key']
+        except KeyError:
+            try:
+                api_key = os.environ['PMG_MAPI_KEY']
+            except KeyError as exc:
+                raise_from(
+                    KeyError('API key not supplied and PMG_MAPI_KEY environment '
+                             'variable not set. Either pass it when initializing the class, '
+                             'or set the environment variable PMG_MAPI_KEY to your API key.'), exc)
+            api_key = None
+
+        self._api_key = api_key
+        self._verify_api_key()
+        self._mpr = MPRester(self._api_key)
+
+    def _verify_api_key(self):
+        """
+        Verify the supplied API key by issuing a request to Materials Project.
+        """
+        response = requests.get(
+            'https://www.materialsproject.org/rest/v1/api_check', headers={'X-API-KEY': self._api_key})
+        response_content = response.json()  # a dict
+        if 'error' in response_content:
+            raise RuntimeError(response_content['error'])
+        if not response_content['valid_response']:
+            raise RuntimeError('Materials Project did not give a valid response for the API key check.')
+        if not response_content['api_key_valid']:
+            raise RuntimeError('Your API key for Materials Project is not valid.')
+
+    @property
+    def api_key(self):
+        """
+        Return the API key configured for the importer
+        """
+        return self._api_key
+
+    @property
+    def properties(self):
+        """
+        Return the properties that will be queried
+        """
+        return self._properties
+
+    @property
+    def get_supported_keywords(self):
+        """
+        Returns the list of all supported query keywords
+
+        :return: list of strings
+        """
+        return self._supported_keywords
+
+    def query(self, **kwargs):
+        """
+        Query the database with a given dictionary of query parameters for a given properties
+
+        :param query: a dictionary with the query parameters
+        :param properties: the properties to query
+        """
+        try:
+            query = kwargs['query']
+        except AttributeError:
+            raise AttributeError('Make sure the supplied dictionary has `query` as a key. This '
+                                 'should contain a dictionary with the right query needed.')
+        try:
+            properties = kwargs['properties']
+        except AttributeError:
+            raise AttributeError('Make sure the supplied dictionary has `properties` as a key.')
+
+        if not isinstance(query, dict):
+            raise TypeError('The query argument should be a dictionary')
+
+        if properties is None:
+            properties = self._properties
+
+        if properties != 'structure':
+            raise ValueError('Unsupported properties: {}'.format(properties))
+
+        results = []
+        properties_list = ['material_id', 'cif']
+        for entry in self._find(query, properties_list):
+            results.append(entry)
+        search_results = MaterialsProjectSearchResults(results, return_class=MaterialsProjectCifEntry)
+
+        return search_results
+
+    def _find(self, query, properties):
+        """
+        Query the database with a given dictionary of query parameters
+
+        :param query: a dictionary with the query parameters
+        """
+        for entry in self._mpr.query(criteria=query, properties=properties):
+            yield entry
+
+
+class MaterialsProjectCifEntry(CifEntry):  # pylint: disable=abstract-method
+    """
+    A Materials Project entry class which extends the DbEntry class with a CifEntry class.
+
+    """
+
+    _license = 'Materials Project'
+
+    def __init__(self, url, **kwargs):
+        """
+        The DbSearchResults base class instantiates a new DbEntry by explicitly passing the url
+        of the entry as an argument. In this case it is the same as the 'uri' value that is
+        already contained in the source dictionary so we just copy it
+        """
+        cif = kwargs.pop('cif', None)
+        kwargs['uri'] = url
+        super(MaterialsProjectCifEntry, self).__init__(**kwargs)
+
+        if cif is not None:
+            self.cif = cif
+
+
+class MaterialsProjectSearchResults(DbSearchResults):  # pylint: disable=abstract-method
+    """
+    A collection of MaterialsProjectEntry query result entries.
+
+    :param results: query result entry dictionary
+    :return_class: the class associated with each
+    """
+
+    _db_name = 'Materials Project'
+    _db_uri = 'https://materialsproject.org'
+    _material_base_url = 'https://materialsproject.org/materials/'
+    _version = str(datetime.datetime.now())
+
+    def __init__(self, results, return_class):
+        self._return_class = return_class
+        super(MaterialsProjectSearchResults, self).__init__(results)
+
+    def _get_source_dict(self, result_dict):
+        """
+        Return the source information dictionary of an Materials Project query result entry
+
+        :param result_dict: query result entry dictionary
+        """
+        source_dict = {
+            'db_name': self._db_name,
+            'db_uri': self._db_uri,
+            'id': result_dict['material_id'],
+            'uri': self._get_url(result_dict),
+            'version': self._version,
+        }
+
+        if 'cif' in result_dict:
+            source_dict['cif'] = result_dict['cif']
+
+        return source_dict
+
+    def _get_url(self, result_dict):
+        """
+        Return the permanent URI of the result entry
+
+        :param result_dict: query result entry dictionary
+        """
+        return self._material_base_url + result_dict['material_id'],

aiida/tools/dbimporters/plugins/mpds.py

@@ -117,7 +117,7 @@ def structures(self):
         return self._structures
 
     @property
-    def supported_keywords(self):
+    def get_supported_keywords(self):
         """
         Returns the list of all supported query keywords
 

aiida/tools/dbimporters/plugins/test_materialsproject.py

@@ -0,0 +1,44 @@
+# -*- 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               #
+###########################################################################
+"""
+Module that contains the class definitions necessary to offer support for
+queries to Materials Project.
+"""
+
+from __future__ import absolute_import
+import pytest
+from aiida.tools.dbimporters import DbImporterFactory
+from aiida.backends.testbase import AiidaTestCase
+
+
+def run_materialsproject_api_tests():
+    from aiida.settings import profile_conf
+    return profile_conf.get('run_materialsproject_api_tests', False)
+
+
+class TestMaterialsProject(AiidaTestCase):
+    """
+    Contains the tests to verify the functionality of the Materials Project importer
+    functions.
+    """
+
+    import unittest
+
+    @unittest.skipIf(not run_materialsproject_api_tests(), "MaterialsProject API tests not enabled")
+    def test_invalid_api_key(self):  # pylint: disable=no-self-use
+        """
+        Test if Materials Project rejects an invalid API key and that we catch the error.
+        Please enable the test in the profile configurator.
+        """
+        importer_class = DbImporterFactory('materialsproject')
+        importer_parameters = {'api_key': 'thisisawrongkey'}
+
+        with pytest.raises(Exception):
+            importer_class(**importer_parameters)

setup.py

@@ -143,6 +143,7 @@
                 'icsd = aiida.tools.dbimporters.plugins.icsd:IcsdDbImporter',
                 'mpod = aiida.tools.dbimporters.plugins.mpod:MpodDbImporter',
                 'mpds = aiida.tools.dbimporters.plugins.mpds:MpdsDbImporter',
+                'materialsproject = aiida.tools.dbimporters.plugins.materialsproject:MaterialsProjectImporter',
                 'nninc = aiida.tools.dbimporters.plugins.nninc:NnincDbImporter',
                 'oqmd = aiida.tools.dbimporters.plugins.oqmd:OqmdDbImporter',
                 'pcod = aiida.tools.dbimporters.plugins.pcod:PcodDbImporter',