diff options
Diffstat (limited to 'python/fatcat_tools/importers/crossref.py')
| -rw-r--r-- | python/fatcat_tools/importers/crossref.py | 272 |
1 files changed, 272 insertions, 0 deletions
diff --git a/python/fatcat_tools/importers/crossref.py b/python/fatcat_tools/importers/crossref.py new file mode 100644 index 00000000..dddb58d1 --- /dev/null +++ b/python/fatcat_tools/importers/crossref.py @@ -0,0 +1,272 @@ + +import sys +import json +import sqlite3 +import datetime +import itertools +import fatcat_client +from fatcat_tools.importers.common import FatcatImporter + + +class FatcatCrossrefImporter(FatcatImporter): + + def __init__(self, host_url, issn_map_file, extid_map_file=None, create_containers=True): + super().__init__(host_url, issn_map_file) + 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 + + 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 parse_crossref_dict(self, obj): + """ + obj is a python dict (parsed from json). + returns a ReleaseEntity + """ + + # This work is out of scope if it doesn't have authors and a title + if (not 'author' in obj) or (not 'title' in obj): + return None + + # Other ways to be out of scope (provisionally) + if (not 'type' in obj): + 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 + 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['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 != 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 + release_date = obj['issued']['date-parts'][0] + if not release_date or not release_date[0]: + # got some NoneType, even though at least year is supposed to be set + release_date = None + elif len(release_date) == 3: + release_date = datetime.datetime(year=release_date[0], month=release_date[1], day=release_date[2]) + else: + # only the year is actually required; mangle to first day for date + # (TODO: something better?) + release_date = datetime.datetime(year=release_date[0], month=1, day=1) + # convert to string ISO datetime format (if not null) + if release_date: + release_date = release_date.isoformat() + "Z" + + re = fatcat_client.ReleaseEntity( + work_id=None, + title=obj['title'][0], + contribs=contribs, + refs=refs, + container_id=container_id, + publisher=publisher, + 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, + 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=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=editgroup) + re.container_id = container.ident + self._issnl_id_map[ce.issnl] = container.ident + self.api.create_release(re, editgroup=editgroup) + self.insert_count = self.insert_count + 1 + + def create_batch(self, batch, editgroup=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(editor_id='aaaaaaaaaaaabkvkaaaaaaaaae')) + container = self.api.create_container(ce, editgroup=ce_eg.id) + self.api.accept_editgroup(ce_eg.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=editgroup) + self.insert_count = self.insert_count + len(release_batch) |