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#!/usr/bin/env python3
"""
Transform an OAI-PMH bulk dump (JSON) into ingest requests.
Eg: https://archive.org/details/oai_harvest_20200215
"""
import argparse
import json
import sys
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/",
"://127.0.0.1/",
"://www.kb.dk/",
"://kb-images.kb.dk/",
"://mdz-nbn-resolving.de/",
"://aggr.ukm.um.si/",
"://edoc.mpg.de/",
"doaj.org/",
"orcid.org/",
"://gateway.isiknowledge.com/",
# OAI specific additions
"://hdl.handle.net/",
]
# OAI identifier prefixes for repositories that we want to skip (for various reasons)
OAI_BLOCKLIST = [
"oai:kb.dk:",
"oai:bdr.oai.bsb-muenchen.de:",
"oai:hispana.mcu.es:",
"oai:bnf.fr:",
"oai:ukm.si:",
"oai:biodiversitylibrary.org:",
"oai:hsp.org:",
"oai:repec:",
"oai:n/a:",
"oai:quod.lib.umich.edu:",
"oai:americanae.aecid.es:",
"oai:www.irgrid.ac.cn:",
"oai:espace.library.uq.edu:",
"oai:edoc.mpg.de:",
"oai:bibliotecadigital.jcyl.es:",
"oai:repository.erciyes.edu.tr:",
"oai:krm.or.kr:",
"oai:hypotheses.org:%",
]
RELEASE_STAGE_MAP = {
"info:eu-repo/semantics/draftVersion": "draft",
"info:eu-repo/semantics/submittedVersion": "submitted",
"info:eu-repo/semantics/acceptedVersion": "accepted",
"info:eu-repo/semantics/publishedVersion": "published",
"info:eu-repo/semantics/updatedVersion": "updated",
}
def canon(s):
parsed = urlcanon.parse_url(s)
return str(urlcanon.whatwg(parsed))
def transform(obj):
"""
Transforms from a single OAI-PMH object to zero or more ingest requests.
Returns a list of dicts.
"""
requests = []
if not obj.get("oai") or not obj["oai"].startswith("oai:"):
return []
if not obj.get("urls"):
return []
oai_id = obj["oai"].lower()
for prefix in OAI_BLOCKLIST:
if oai_id.startswith(prefix):
return []
# look in obj['formats'] for PDF?
if obj.get("formats"):
# if there is a list of formats, and it does not contain PDF, then
# skip. Note that we will continue if there is no formats list.
has_pdf = False
for f in obj["formats"]:
if "pdf" in f.lower():
has_pdf = True
if not has_pdf:
return []
doi = None
if obj.get("doi"):
doi = obj["doi"][0].lower().strip()
if not doi.startswith("10."):
doi = None
# infer release stage and/or type from obj['types']
release_stage = None
for t in obj.get("types", []):
if t in RELEASE_STAGE_MAP:
release_stage = RELEASE_STAGE_MAP[t]
# TODO: infer rel somehow? Eg, repository vs. OJS publisher
rel = None
for url in obj["urls"]:
skip = False
for domain in DOMAIN_BLOCKLIST:
if domain in url:
skip = True
if skip:
continue
try:
base_url = canon(url)
except UnicodeEncodeError:
continue
request = {
"base_url": base_url,
"ingest_type": "pdf",
"link_source": "oai",
"link_source_id": oai_id,
"ingest_request_source": "metha-bulk",
"release_stage": release_stage,
"rel": rel,
"ext_ids": {
"oai": obj["oai"].lower(),
},
"edit_extra": {},
}
if doi:
request["ext_ids"]["doi"] = doi
requests.append(request)
return requests
def run(args):
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():
parser = argparse.ArgumentParser(formatter_class=argparse.ArgumentDefaultsHelpFormatter)
parser.add_argument(
"json_file",
help="OAI-PMH dump file to use (usually stdin)",
type=argparse.FileType("r"),
)
subparsers = parser.add_subparsers()
args = parser.parse_args()
run(args)
if __name__ == "__main__":
main()
|
