mapping.py

#
# Copyright The NOMAD Authors.
#
# This file is part of NOMAD. See https://nomad-lab.eu for further info.
#
# 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, FOAF, RDF

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#')
HYDRA = Namespace('http://www.w3.org/ns/hydra/core#')


def get_optional_entry_prop(entry, name):
    try:
        return entry[name]
    except KeyError:
        return 'unavailable'


class Mapping():
    def __init__(self):
        self.g = Graph()
        self.g.namespace_manager.bind('rdf', RDF)
        self.g.namespace_manager.bind('dcat', DCAT)
        self.g.namespace_manager.bind('dct', DCT)
        self.g.namespace_manager.bind('vcard', VCARD)
        self.g.namespace_manager.bind('foaf', FOAF)
        self.g.namespace_manager.bind('hydra', HYDRA)

        self.persons = {}

    def map_catalog(self, entries, after: str, modified_since):
        def uri_ref(after):
            kwargs = dict()
            if after is not None:
                kwargs['after'] = after
            if modified_since is not None:
                kwargs['modified_since'] = modified_since.strftime('%Y-%m-%d')
            return URIRef(url('catalog', **kwargs))

        after = after.strip()

        catalog = uri_ref(after=None)
        self.g.add((catalog, RDF.type, DCAT.Catalog))
        last_entry = None
        for entry in entries:
            self.g.add((catalog, DCT.dataset, self.map_entry(entry, slim=True)))
            last_entry = entry

        hydra_collection = uri_ref(after)
        self.g.add((hydra_collection, RDF.type, HYDRA.Collection))
        self.g.add((hydra_collection, HYDRA.totalItems, Literal(entries.total)))
        self.g.add((hydra_collection, HYDRA.first, uri_ref('')))
        if last_entry is not None:
            self.g.add((hydra_collection, HYDRA.next, uri_ref(last_entry.calc_id)))

        self.g.add((hydra_collection, RDF.type, HYDRA.collection))

    def map_entry(self, entry: EntryMetadata, slim=False):
        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, DCT.title, Literal(get_optional_entry_prop(entry, 'formula'))))
        self.g.add((dataset, DCT.description, Literal(get_optional_entry_prop(entry, 'comment'))))

        if slim:
            return dataset

        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.license, URIRef('https://creativecommons.org/licenses/by/4.0/legalcode')))
        self.g.add((dataset, DCT.language, URIRef('http://id.loc.gov/vocabulary/iso639-1/en')))

        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)))
        self.g.add((dataset, DCAT.contactPoint, self.map_contact(entry.uploader)))

        self.g.add((dataset, DCAT.distribution, self.map_distribution(entry, 'api')))
        self.g.add((dataset, DCAT.distribution, self.map_distribution(entry, 'json')))
        self.g.add((dataset, DCAT.distribution, self.map_distribution(entry, 'raw')))

        return dataset

    def map_user(self, user: User):
        person = self.persons.get(user.user_id)
        if person is not None:
            return person

        user = User.get(user.user_id)
        person = BNode()

        self.g.add((person, RDF.type, FOAF.Person))
        self.g.add((person, FOAF.givenName, Literal(user.first_name)))
        self.g.add((person, FOAF.familyName, Literal(user.last_name)))
        self.g.add((person, FOAF.nick, Literal(user.username)))
        self.g.add((person, FOAF.mbox, URIRef('mailto:%s' % (user.email))))

        self.persons[user.user_id] = person

        return person

    def map_contact(self, user: User):
        person = self.persons.get(user.user_id)
        if person is None:
            person = self.map_user(user)

        user = User.get(user.user_id)
        self.g.add((person, RDF.type, VCARD.Individual))
        self.g.add((person, VCARD.givenName, Literal(user.first_name)))
        self.g.add((person, VCARD.familyName, Literal(user.last_name)))
        self.g.add((person, VCARD.nickName, Literal(user.username)))
        self.g.add((person, VCARD.hasEmail, Literal(user.email)))
        self.g.add((person, VCARD.organizationName, Literal('unavailable' if user.affiliation is None else user.affiliation)))
        # address = BNode()
        # self.g.add((address, RDF.type, VCARD.Address))
        # self.g.add((address, VCARD.street_address, )) # affiliation_address?
        # self.g.add((address, VCARD.postal_code, )) # affiliation_address?
        # self.g.add((address, VCARD.country_name, )) # affiliation_address?
        # self.g.add((address, VCARD.locality, )) # affiliation_address?
        # self.g.add((address, VCARD.region, )) # affiliation_address?
        # self.g.add((person, VCARD.hasAddress, address))

        return person

    def map_distribution(self, entry, dist_kind):
        if dist_kind == 'api':
            # DataService: API
            service = BNode()
            self.g.add((service, RDF.type, DCAT.DataService))
            self.g.add((service, DCT.title, Literal('NOMAD API')))  # How to include terms from swagger document here?
            self.g.add((service, DCT.description, Literal('Official NOMAD API')))  # same question
            self.g.add((service, DCAT.endpointURL, URIRef('https://nomad-lab.eu/prod/rae/api/')))  # config.api_url() ?
            # not sure if the following needs to be dataset specific:
            self.g.add((service, DCAT.endpointDescription, URIRef('https://nomad-lab.eu/prod/rae/api/swagger.json')))

            # Distribution over API
            dist = BNode()
            self.g.add((dist, DCT.title, Literal('unavailable' if entry.formula is None else entry.formula + '_api')))
            self.g.add((dist, RDF.type, DCAT.Distribution))
            self.g.add((dist, DCAT.accessService, service))
        elif dist_kind == 'json':
            # Distribution as JSON
            dist = BNode()
            self.g.add((dist, RDF.type, DCAT.Distribution))
            self.g.add((dist, DCT.title, Literal(get_optional_entry_prop(entry, 'formula') + '_json')))
            self.g.add((dist, DCAT.mediaType, URIRef('https://www.iana.org/assignments/media-types/application/json')))
            self.g.add((dist, DCAT.packageFormat, URIRef('https://www.iana.org/assignments/media-types/application/zip')))
            self.g.add((dist, DCAT.downloadURL, URIRef(
                'http://nomad-lab.eu/prod/rae/api/archive/download?upload_id=%s&calc_id=%s' % (entry.upload_id, entry.calc_id))))
            self.g.add((dist, DCAT.accessURL, URIRef('%s/entry/id/%s/%s' % (
                config.gui_url(), entry.upload_id, entry.calc_id))))
        elif dist_kind == 'raw':
            # Distribution of the raw data
            dist = BNode()
            self.g.add((dist, RDF.type, DCAT.Distribution))
            self.g.add((dist, DCT.title, Literal(get_optional_entry_prop(entry, 'formula') + '_raw')))
            self.g.add((dist, DCAT.accessURL, URIRef('https://nomad-lab.eu/prod/rae/api/raw/calc/%s/%s' % (
                entry.upload_id, entry.calc_id))))
            self.g.add((dist, DCAT.packageFormat, URIRef('https://www.iana.org/assignments/media-types/application/zip')))

        return dist