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import sys
import json
import sqlite3
import itertools
import fatcat_client
from fatcat.importer_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) or (not 'container-title' in obj) or
len(obj['container-title']) < 1):
return None
# contribs
contribs = []
for i, am in enumerate(obj['author']):
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>')
contribs.append(fatcat_client.ReleaseContrib(
creator_id=creator_id,
index=i+1,
raw_name=raw_name,
role="author"))
# 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:
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 = dict(crossref=rm)
if rm.get('DOI') != None:
extra['doi'] = rm.get('DOI').lower()
refs.append(fatcat_client.ReleaseRef(
index=i+1,
# doing lookups would be a second import pass
target_release_id=None,
# unreliable for crossref: key=rm['key'].split('|')[-1],
year=year,
container_title=rm.get('volume-title'),
title=rm.get('title'),
locator=rm.get('first-page'),
# TODO: just dump JSON somewhere here?
extra=dict(crossref=rm)))
# abstracts
abstracts = []
if obj.get('abstract') != None:
abstracts.append(fatcat_client.ReleaseEntityAbstracts(
mimetype="application/xml+jats",
content=obj.get('abstract')))
# release
extra = dict(crossref={
# TODO: if exsits: group_title, subtitle, isPreprintOf
'links': obj.get('link', []),
'subject': obj.get('subject'),
'type': obj['type'],
'license': obj.get('license', [dict(URL=None)])[0]['URL'] or None,
'alternative-id': obj.get('alternative-id', [])})
# external identifiers
extids = self.lookup_ext_ids(doi=obj['DOI'].lower())
re = fatcat_client.ReleaseEntity(
work_id=None,
title=obj['title'][0],
contribs=contribs,
refs=refs,
container_id=container_id,
release_type=obj['type'],
doi=obj['DOI'].lower(),
core_id=extids['core_id'],
pmid=extids['pmid'],
pmcid=extids['pmcid'],
wikidata_qid=extids['wikidata_qid'],
release_date=obj['created']['date-time'],
issue=obj.get('issue'),
volume=obj.get('volume'),
pages=obj.get('page'),
abstracts=abstracts,
extra=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:
container = self.api.create_container(ce, editgroup=editgroup)
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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