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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 sys
import json
import argparse
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/",
# OAI specific additions
"://hdl.handle.net/",
]
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 []
# 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': obj['oai'].lower(),
'ingest_request_source': 'metha-bulk',
'release_stage': release_stage,
'rel': rel,
'ext_ids': {
'doi': doi,
'oai': obj['oai'].lower(),
},
'edit_extra': {},
}
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()
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