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#!/usr/bin/env python3
"""
Transform an DOAJ article dump (JSON) into ingest requests.
TODO: should we also attempt PDF ingest for HTML links? They seem to often be
landing pages. Or could have some pipeline that notices, eg, `citation_pdf_url`
in the HTML headers and adds an ingest request on that basis. Or even just run
the re-ingest in-process and publish a second result.
"""
import sys
import json
import argparse
import urlcanon
from typing import Optional, List
DOMAIN_BLOCKLIST = [
# large OA publishers (we get via DOI)
# large repos and aggregators (we crawl directly)
"://arxiv.org/",
"://europepmc.org/",
"ncbi.nlm.nih.gov/",
#"semanticscholar.org/",
"://doi.org/",
"zenodo.org/",
"figshare.com/",
"://archive.org/",
".archive.org/",
# large publishers/platforms; may remove in the future
#"://link.springer.com/",
#"://dergipark.gov.tr/",
#"frontiersin.org/",
#"scielo",
]
# these default to PDF; note that we also do pdf ingests for HTML pages
CONTENT_TYPE_MAP = {
"abstract": [],
"doc": [],
"": ["pdf"],
"doi": ["pdf"],
"url": ["pdf"],
"fulltext": ["pdf"],
"anySimpleType": ["pdf"],
"application/pdf": ["pdf"],
"html": ["html", "pdf"],
"text/html": ["html", "pdf"],
"xml": ["xml"],
}
def canon(s: str) -> str:
parsed = urlcanon.parse_url(s)
return str(urlcanon.whatwg(parsed))
def transform(obj: dict) -> List[dict]:
"""
Transforms from a single DOAJ object to zero or more ingest requests.
Returns a list of dicts.
"""
doaj_id = obj['id'].lower()
assert doaj_id
bibjson = obj['bibjson']
if not bibjson['link']:
return []
requests = []
doi: Optional[str] = None
for ident in (bibjson['identifier'] or []):
if ident['type'].lower() == "doi" and ident['id'].startswith('10.'):
doi = ident['id'].lower()
for link in (bibjson['link'] or []):
if link.get('type') != "fulltext" or not link.get('url'):
continue
ingest_types = CONTENT_TYPE_MAP.get((link.get('content_type') or '').lower())
if not ingest_types:
continue
skip = False
for domain in DOMAIN_BLOCKLIST:
if domain in link['url'].lower():
skip = True
if skip:
continue
try:
base_url = canon(link['url'])
except UnicodeEncodeError:
continue
for ingest_type in ingest_types:
request = {
'base_url': base_url,
'ingest_type': ingest_type,
'link_source': 'doaj',
'link_source_id': doaj_id,
'ingest_request_source': 'doaj',
'release_stage': 'published',
'rel': 'publisher',
'ext_ids': {
'doi': doi,
'doaj': doaj_id,
},
'edit_extra': {},
}
requests.append(request)
return requests
def run(args) -> None:
for l in args.json_file:
if not l.strip():
continue
row = json.loads(l)
requests = transform(row) or []
for r in requests:
print("{}".format(json.dumps(r, sort_keys=True)))
def main() -> None:
parser = argparse.ArgumentParser(
formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument('json_file',
help="DOAJ article dump file to use",
type=argparse.FileType('r'))
subparsers = parser.add_subparsers()
args = parser.parse_args()
run(args)
if __name__ == '__main__':
main()
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