import sys import json import sqlite3 import datetime import itertools import subprocess import fatcat_client from .common import FatcatImporter # The docs/guide should be the cannonical home for these mappings; update there # first CROSSREF_TYPE_MAP = { 'book': 'book', 'book-chapter': 'chapter', 'book-part': 'chapter', 'book-section': 'chapter', 'component': None, 'dataset': 'dataset', 'dissertation': 'thesis', 'edited-book': 'book', 'journal-article': 'article-journal', 'monograph': 'book', 'other': None, 'peer-review': 'peer_review', 'posted-content': 'post', 'proceedings-article': 'paper-conference', 'reference-book': 'book', 'reference-entry': 'entry', 'report': 'report', 'standard': 'standard', } class CrossrefImporter(FatcatImporter): """ Importer for Crossref metadata. Can use a local sqlite3 file for faster "external identifier" lookups See https://github.com/CrossRef/rest-api-doc for JSON schema notes """ def __init__(self, api, issn_map_file, **kwargs): eg_desc = kwargs.get('editgroup_description', "Automated import of Crossref DOI metadata, harvested from REST API") eg_extra = kwargs.get('editgroup_extra', dict()) eg_extra['agent'] = eg_extra.get('agent', 'fatcat_tools.CrossrefImporter') super().__init__(api, issn_map_file=issn_map_file, editgroup_description=eg_desc, editgroup_extra=eg_extra) extid_map_file = kwargs.get('extid_map_file') create_containers = kwargs.get('create_containers') check_existing = kwargs.get('check_existing') self.extid_map_db = None if extid_map_file: db_uri = "file:{}?mode=ro".format(extid_map_file) print("Using external ID map: {}".format(db_uri)) self.extid_map_db = sqlite3.connect(db_uri, uri=True) else: print("Not using external ID map") self.create_containers = create_containers self.check_existing = check_existing def lookup_ext_ids(self, doi): if self.extid_map_db is None: return dict(core_id=None, pmid=None, pmcid=None, wikidata_qid=None) row = self.extid_map_db.execute("SELECT core, pmid, pmcid, wikidata FROM ids WHERE doi=? LIMIT 1", [doi.lower()]).fetchone() if row is None: return dict(core_id=None, pmid=None, pmcid=None, wikidata_qid=None) row = [str(cell or '') or None for cell in row] return dict( core_id=row[0], pmid=row[1], pmcid=row[2], wikidata_qid=row[3]) def map_release_type(self, crossref_type): return CROSSREF_TYPE_MAP.get(crossref_type) def parse_crossref_dict(self, obj): """ obj is a python dict (parsed from json). returns a ReleaseEntity """ # Do require the 'title' keys to exsit, as release entities do if (not 'title' in obj) or (not obj['title']): return None # Ways to be out of scope (provisionally) # journal-issue and journal-volume map to None, but allowed for now if obj.get('type') in (None, 'journal', 'proceedings', 'standard-series', 'report-series', 'book-series', 'book-set', 'book-track', 'proceedings-series'): return None # lookup existing DOI existing_release = None if self.check_existing: try: existing_release = self.api.lookup_release(doi=obj['DOI'].lower()) except fatcat_client.rest.ApiException as err: if err.status != 404: raise err # eventually we'll want to support "updates", but for now just skip if # entity already exists if existing_release: return None # contribs def do_contribs(obj_list, ctype): contribs = [] for i, am in enumerate(obj_list): creator_id = None if 'ORCID' in am.keys(): creator_id = self.lookup_orcid(am['ORCID'].split('/')[-1]) # Sorry humans :( if am.get('given') and am.get('family'): raw_name = "{} {}".format(am['given'], am['family']) elif am.get('family'): raw_name = am['family'] else: # TODO: defaults back to a pseudo-null value raw_name = am.get('given', '<blank>') extra = dict() if ctype == "author": index = i else: index = None if am.get('affiliation'): # note: affiliation => affiliations extra['affiliations'] = am.get('affiliation') if am.get('sequence') and am.get('sequence') != "additional": extra['sequence'] = am.get('sequence') if not extra: extra = None assert ctype in ("author", "editor", "translator") contribs.append(fatcat_client.ReleaseContrib( creator_id=creator_id, index=index, raw_name=raw_name, role=ctype, extra=extra)) return contribs contribs = do_contribs(obj.get('author', []), "author") contribs.extend(do_contribs(obj.get('editor', []), "editor")) contribs.extend(do_contribs(obj.get('translator', []), "translator")) # container issn = obj.get('ISSN', [None])[0] issnl = self.issn2issnl(issn) container_id = None if issnl: container_id = self.lookup_issnl(issnl) publisher = obj.get('publisher') ce = None if (container_id is None and self.create_containers and (issnl is not None) and obj.get('container-title') and len(obj['container-title']) > 0): ce = fatcat_client.ContainerEntity( issnl=issnl, publisher=publisher, name=obj['container-title'][0]) # references refs = [] for i, rm in enumerate(obj.get('reference', [])): try: year = int(rm.get('year')) # NOTE: will need to update/config in the future! # NOTE: are there crossref works with year < 100? if year > 2025 or year < 100: year = None except: year = None extra = rm.copy() if rm.get('DOI'): extra['doi'] = rm.get('DOI').lower() key = rm.get('key') if key and key.startswith(obj['DOI'].upper()): key = key.replace(obj['DOI'].upper() + "-", '') key = key.replace(obj['DOI'].upper(), '') container_name = rm.get('volume-title') if not container_name: container_name = rm.get('journal-title') extra.pop('DOI', None) extra.pop('key', None) extra.pop('year', None) extra.pop('volume-name', None) extra.pop('journal-title', None) extra.pop('title', None) extra.pop('first-page', None) extra.pop('doi-asserted-by', None) if extra: extra = dict(crossref=extra) else: extra = None refs.append(fatcat_client.ReleaseRef( index=i, # doing lookups would be a second import pass target_release_id=None, key=key, year=year, container_name=container_name, title=rm.get('title'), locator=rm.get('first-page'), # TODO: just dump JSON somewhere here? extra=extra)) # abstracts abstracts = [] if obj.get('abstract') != None: abstracts.append(fatcat_client.ReleaseEntityAbstracts( mimetype="application/xml+jats", content=obj.get('abstract'))) # extra fields extra = dict() for key in ('subject', 'type', 'license', 'alternative-id', 'container-title', 'original-title', 'subtitle', 'archive', 'funder', 'group-title'): # TODO: unpack "container-title" array val = obj.get(key) if val: extra[key] = val if 'license' in extra and extra['license']: for i in range(len(extra['license'])): if 'start' in extra['license'][i]: extra['license'][i]['start'] = extra['license'][i]['start']['date-time'] if len(obj['title']) > 1: extra['other-titles'] = obj['title'][1:] # TODO: this should be top-level extra['is_kept'] = len(obj.get('archive', [])) > 0 # ISBN isbn13 = None for raw in obj.get('ISBN', []): # TODO: convert if not ISBN-13 format if len(raw) == 17: isbn13 = raw break # release status if obj['type'] in ('journal-article', 'conference-proceeding', 'book', 'dissertation', 'book-chapter'): release_status = "published" else: # unknown release_status = None # external identifiers extids = self.lookup_ext_ids(doi=obj['DOI'].lower()) # TODO: filter out huge releases; we'll get them later (and fix bug in # fatcatd) if max(len(contribs), len(refs), len(abstracts)) > 750: return None # release date parsing is amazingly complex raw_date = obj['issued']['date-parts'][0] if not raw_date or not raw_date[0]: # got some NoneType, even though at least year is supposed to be set release_year = None release_date = None elif len(raw_date) == 3: release_year = raw_date[0] release_date = datetime.date(year=raw_date[0], month=raw_date[1], day=raw_date[2]) else: # sometimes only the year is included, not the full date release_year = raw_date[0] release_date = None re = fatcat_client.ReleaseEntity( work_id=None, title=obj.get('title', [None])[0], contribs=contribs, refs=refs, container_id=container_id, publisher=publisher, release_type=self.map_release_type(obj['type']), release_status=release_status, doi=obj['DOI'].lower(), isbn13=isbn13, core_id=extids['core_id'], pmid=extids['pmid'], pmcid=extids['pmcid'], wikidata_qid=extids['wikidata_qid'], release_date=release_date, release_year=release_year, issue=obj.get('issue'), volume=obj.get('volume'), pages=obj.get('page'), abstracts=abstracts, extra=dict(crossref=extra)) return (re, ce) def create_row(self, row, editgroup_id=None): if row is None: return obj = json.loads(row) entities = self.parse_crossref_dict(obj) if entities is not None: (re, ce) = entities if ce is not None: container = self.api.create_container(ce, editgroup_id=editgroup_id) re.container_id = container.ident self._issnl_id_map[ce.issnl] = container.ident self.api.create_release(re, editgroup_id=editgroup_id) self.counts['insert'] += 1 def create_batch(self, batch, editgroup_id=None): """Current work/release pairing disallows batch creation of releases. Could do batch work creation and then match against releases, but meh.""" release_batch = [] for row in batch: if row is None: continue obj = json.loads(row) entities = self.parse_crossref_dict(obj) if entities is not None: (re, ce) = entities if ce is not None: ce_eg = self.api.create_editgroup(fatcat_client.Editgroup()) container = self.api.create_container(ce, editgroup_id=ce_eg.editgroup_id) self.api.accept_editgroup(ce_eg.editgroup_id) re.container_id = container.ident self._issnl_id_map[ce.issnl] = container.ident release_batch.append(re) self.api.create_release_batch(release_batch, autoaccept="true", editgroup_id=editgroup_id) self.counts['insert'] += len(release_batch)