first iteration of oai2ingestrequest script

1 files changed, 137 insertions, 0 deletions

diff --git a/python/scripts/oai2ingestrequest.py b/python/scripts/oai2ingestrequest.py
new file mode 100755
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+++ b/python/scripts/oai2ingestrequest.py
@@ -0,0 +1,137 @@
+#!/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()