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authorBryan Newbold <bnewbold@archive.org>2020-11-08 21:52:47 -0800
committerBryan Newbold <bnewbold@archive.org>2020-11-08 21:52:47 -0800
commit6a701f966b8bc760bf904c0569562b0159e13559 (patch)
treed440b3a9379b716de8aca3f9543249c240016ae0
parentecd36863e607e3c9e71fd91ece44a422f88dbe2e (diff)
downloadsandcrawler-6a701f966b8bc760bf904c0569562b0159e13559.tar.gz
sandcrawler-6a701f966b8bc760bf904c0569562b0159e13559.zip
basic DOAJ ingest request conversion script
-rwxr-xr-xpython/scripts/doaj2ingestrequest.py139
1 files changed, 139 insertions, 0 deletions
diff --git a/python/scripts/doaj2ingestrequest.py b/python/scripts/doaj2ingestrequest.py
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+++ b/python/scripts/doaj2ingestrequest.py
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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()