# # 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