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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 argparse
import json
import sys
from typing import List, Optional
import urlcanon
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/",
"://dx.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.get("id") 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"].strip())
except UnicodeEncodeError:
continue
if not base_url or len(base_url) > 1000:
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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