Added first implementation for dcat api.

nomad/app/__init__.py

@@ -17,8 +17,8 @@
 #
 
 '''
-This module comprises the nomad@FAIRDI APIs. Currently there is NOMAD's official api, and
-we will soon at the optimade api. The app module also servers documentation, gui, and
+This module comprises the nomad@FAIRDI APIs. Currently there is NOMAD's official api, optimade api,
+and dcat api. The app module also servers documentation, gui, and
 alive.
 '''
 from flask import Flask, Blueprint, jsonify, url_for, abort, request, make_response
@@ -37,6 +37,7 @@ from nomad import config, utils as nomad_utils
 
 from .api import blueprint as api_blueprint, api
 from .optimade import blueprint as optimade_blueprint, api as optimade
+from .dcat import blueprint as dcat_blueprint
 from .docs import blueprint as docs_blueprint
 from .dist import blueprint as dist_blueprint
 from .gui import blueprint as gui_blueprint
@@ -112,6 +113,7 @@ CORS(app)
 
 app.register_blueprint(api_blueprint, url_prefix='/api')
 app.register_blueprint(optimade_blueprint, url_prefix='/optimade')
+app.register_blueprint(dcat_blueprint, url_prefix='/dcat')
 app.register_blueprint(docs_blueprint, url_prefix='/docs')
 app.register_blueprint(dist_blueprint, url_prefix='/dist')
 app.register_blueprint(gui_blueprint, url_prefix='/gui')

nomad/app/dcat/__init__.py

+# Copyright 2018 Markus Scheidgen
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#   http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an"AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+'''
+The optimade implementation of NOMAD.
+'''
+
+from flask import Blueprint
+from flask_restplus import Api
+
+from .api import blueprint, api
+from .datasets import Dataset

nomad/app/dcat/api.py

+# Copyright 2018 Markus Scheidgen
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#   http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an"AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from flask import Blueprint
+from flask_restplus import Api
+import urllib.parse
+
+from nomad import config
+
+blueprint = Blueprint('dcat', __name__)
+
+base_url = 'https://%s/%s/dcat' % (
+    config.services.api_host.strip('/'),
+    config.services.api_base_path.strip('/'))
+
+
+def url(*args, **kwargs):
+    ''' Returns the full dcat api url for the given path (args) and query (kwargs) parameters. '''
+    url = base_url + '/' + '/'.join(args)
+
+    if len(kwargs) > 0:
+        return '%s?%s' % (url, urllib.parse.urlencode(kwargs))
+    else:
+        return url
+
+
+api = Api(
+    blueprint,
+    version='1.0', title='NOMAD\'s API for servicing dcat resources',
+    description='NOMAD\'s API for serving dcat resources',
+    validate=True)
+
+
+# For some unknown reason it is necessary for each fr api to have a handler.
+# Otherwise the global app error handler won't be called.
+@api.errorhandler(Exception)
+def errorhandler(error):
+    '''When an internal server error is caused by an unexpected exception.'''
+    return str(error)

nomad/app/dcat/datasets.py

+# Copyright 2018 Markus Scheidgen
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#   http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an"AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from flask_restplus import Resource, abort, reqparse
+from flask import Response
+from elasticsearch.exceptions import NotFoundError
+
+from nomad import search
+
+from .api import api
+from .mapping import Mapping
+
+ns = api.namespace('datasets', description='The API for DCAT datasets.')
+
+
+arg_parser = reqparse.RequestParser()
+arg_parser.add_argument('format', type=str, choices=[
+    'xml',
+    'n3',
+    'turtle',
+    'nt',
+    'pretty-xml',
+    'trig'])
+
+
+@ns.route('/<string:entry_id>')
+class Dataset(Resource):
+    @api.doc('get_dcat_dataset')
+    @api.expect(arg_parser)
+    @api.produces(['application/xml'])
+    @api.response(404, 'There is no entry with the given id.')
+    @api.response(401, 'This entry is not publically accessible.')
+    @api.response(200, 'Data send', headers={'Content-Type': 'application/xml'})
+    def get(self, entry_id):
+        ''' Returns a DCAT dataset for a given NOMAD entry id. '''
+
+        format_ = arg_parser.parse_args().get('format')
+        if format_ is None:
+            format_ = 'xml'
+
+        try:
+            entry = search.entry_document.get(entry_id)
+        except NotFoundError:
+            abort(404, message='There is no calculation with id %s' % entry_id)
+
+        if entry.with_embargo or not entry.published:
+            abort(401, message='Not authorized to access %s' % entry_id)
+
+        mapping = Mapping()
+        mapping.map_entry(entry)
+        return Response(
+            mapping.g.serialize(format=format_).decode('utf-8'), 200,
+            {'Content-Type': 'application/xml'})

nomad/app/dcat/mapping.py

+# Copyright 2020 Markus Scheidgen
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#   http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an"AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+from rdflib import Graph, Literal, RDF, URIRef, BNode
+from rdflib.namespace import Namespace, DCAT, DCTERMS as DCT
+
+from nomad import config
+from nomad.datamodel import User
+
+from nomad.datamodel import EntryMetadata, User
+
+from .api import url
+
+
+VCARD = Namespace('http://www.w3.org/2006/vcard/ns#')
+
+
+class Mapping():
+    def __init__(self):
+        self.g = Graph()
+        self.g.namespace_manager.bind('dcat', DCAT)
+        self.g.namespace_manager.bind('dct', DCT)
+        self.g.namespace_manager.bind('vcard', VCARD)
+
+        self.vcards = {}
+
+    def map_entry(self, entry: EntryMetadata):
+        dataset = URIRef(url('datasets', entry.calc_id))
+
+        self.g.add((dataset, RDF.type, DCAT.Dataset))
+        self.g.add((dataset, DCT.identifier, Literal(entry.calc_id)))
+        self.g.add((dataset, DCT.issued, Literal(entry.upload_time)))
+        self.g.add((dataset, DCT.modified, Literal(entry.last_processing)))
+        self.g.add((dataset, DCAT.landing_page, URIRef('%s/entry/id/%s/%s' % (
+            config.gui_url(), entry.upload_id, entry.calc_id))))
+        self.g.add((dataset, DCT.title, Literal('unavailbale' if entry.formula is None else entry.formula)))
+        self.g.add((dataset, DCT.description, Literal('unavailbale' if entry.comment is None else entry.comment)))
+
+        self.g.add((dataset, DCT.publisher, self.map_user(entry.uploader)))
+        for author in entry.authors:
+            self.g.add((dataset, DCT.creator, self.map_user(author)))
+
+        return dataset
+
+    def map_user(self, user: User):
+        vcard = self.vcards.get(user.user_id)
+        if vcard is not None:
+            return vcard
+
+        user = User.get(user.user_id)
+        vcard = BNode()
+        self.g.add((vcard, RDF.type, VCARD.Individual))
+        self.g.add((vcard, VCARD.givenName, Literal(user.first_name)))
+        self.g.add((vcard, VCARD.familyName, Literal(user.last_name)))
+        self.g.add((vcard, VCARD.nickName, Literal(user.username)))
+        self.g.add((vcard, VCARD.hasEmail, Literal(user.email)))
+
+        self.vcards[user.user_id] = vcard
+
+        return vcard

requirements.txt

@@ -75,6 +75,7 @@ unidecode
 python-json-logger
 recommonmark
 jinja2
+rdflib
 
 # [dev]
 setuptools

tests/app/test_dcat.py

+# Copyright 2018 Markus Scheidgen
+#
+# Licensed under the Apache License, Version 2.0 (the "License");
+# you may not use this file except in compliance with the License.
+# You may obtain a copy of the License at
+#
+#   http://www.apache.org/licenses/LICENSE-2.0
+#
+# Unless required by applicable law or agreed to in writing, software
+# distributed under the License is distributed on an"AS IS" BASIS,
+# WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
+# See the License for the specific language governing permissions and
+# limitations under the License.
+
+import json
+import pytest
+from datetime import datetime
+
+from nomad.datamodel import EntryMetadata
+
+from tests.conftest import clear_elastic
+from tests.app.test_app import BlueprintClient
+
+
+@pytest.fixture(scope='session')
+def api(session_client):
+    return BlueprintClient(session_client, '/dcat')
+
+
+@pytest.fixture(scope='module')
+def example_entry(elastic_infra, test_user, other_test_user):
+    clear_elastic(elastic_infra)
+
+    entry = EntryMetadata(
+        calc_id='test-id',
+        upload_id='upload-id',
+        upload_time=datetime.now(),
+        last_processing=datetime.now(),
+        uploader=test_user,
+        coauthors=[other_test_user],
+        comment='this is a calculation comment',
+        formula='H20',
+        published=True)
+
+    entry.a_elastic.index()
+    yield
+    clear_elastic(elastic_infra)
+
+
+def test_get_dataset(api, example_entry):
+    calc_id = 'test-id'
+    rv = api.get('/datasets/%s' % calc_id)
+    assert rv.status_code == 200