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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)
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