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Backfill collaboration + citation data for existing items from OpenAlex.
Re-fetches each item's OpenAlex record (batched 50 DOIs per request to
conserve API quota) and populates:
- item_affiliations rows (institution / ROR / country per authorship)
- items.coauthor_countries / african_country_count / is_intra_african
- items.openalex_id / cited_by_count / counts_by_year
Usage:
python scripts/backfill_collaboration_data.py # DRY RUN
python scripts/backfill_collaboration_data.py --apply
python scripts/backfill_collaboration_data.py --apply --limit 500
python scripts/backfill_collaboration_data.py --apply --force # redo enriched rows
Idempotent: items that already have affiliation rows are skipped unless
--force. Respects ~1 req/sec. Set OPENALEX_API_KEY in the environment.
"""
import argparse
import json
import os
import sys
import time
sys.path.insert(0, os.path.dirname(os.path.dirname(os.path.abspath(__file__))))
from uraas.config.african_countries import african_countries_in
from uraas.database import Item, ItemAffiliation, SessionLocal
from uraas.utils.analytics_cache import analytics_cache
from uraas.utils.openalex_client import oa_get
BATCH = 50
SELECT = "id,doi,authorships,cited_by_count,counts_by_year"
def _norm_doi(doi: str) -> str:
return (
(doi or "")
.replace("https://doi.org/", "")
.replace("http://dx.doi.org/", "")
.strip()
.lower()
)
def fetch_batch_by_doi(dois):
"""One OpenAlex call for up to 50 DOIs. Returns {normalized_doi: work}.
DOIs are pipe-joined raw — requests URL-encodes the whole filter param;
pre-quoting each DOI double-encodes and matches nothing."""
flt = "doi:" + "|".join(dois)
data = oa_get("/works", {"filter": flt, "select": SELECT, "per-page": BATCH})
out = {}
for work in (data or {}).get("results", []):
nd = _norm_doi(work.get("doi", ""))
if nd:
out[nd] = work
return out
def fetch_batch_by_openalex_id(ids):
"""One OpenAlex call for up to 50 OpenAlex work IDs."""
flt = "openalex_id:" + "|".join(ids)
data = oa_get("/works", {"filter": flt, "select": SELECT, "per-page": BATCH})
out = {}
for work in (data or {}).get("results", []):
wid = work.get("id", "").replace("https://openalex.org/", "")
if wid:
out[wid] = work
return out
def extract_affiliations(work):
"""(ror_short, name) -> {ror, name, country_code, author_count}."""
rows = {}
for authorship in work.get("authorships", []):
for inst in authorship.get("institutions", []):
name = inst.get("display_name", "") or ""
ror = (inst.get("ror") or "").replace("https://ror.org/", "")
cc = (inst.get("country_code") or "").upper()
if not (name or ror):
continue
row = rows.setdefault(
(ror, name),
{"ror": ror, "name": name, "country_code": cc, "author_count": 0},
)
row["author_count"] += 1
if cc and not row["country_code"]:
row["country_code"] = cc
return list(rows.values())
def apply_work(session, item, work):
"""Write affiliation rows + collaboration/citation columns for one item."""
affs = extract_affiliations(work)
# Idempotency: replace any existing affiliation rows for this item.
session.query(ItemAffiliation).filter_by(item_id=item.id).delete()
for aff in affs:
session.add(
ItemAffiliation(
item_id=item.id,
ror=(aff["ror"] or "")[:128] or None,
institution_name=(aff["name"] or "")[:255] or None,
country_code=(aff["country_code"] or "")[:2] or None,
author_count=aff["author_count"],
)
)
african = african_countries_in(a["country_code"] for a in affs)
item.coauthor_countries = ",".join(african) or None
item.african_country_count = len(african)
item.is_intra_african = len(african) >= 2
item.openalex_id = work.get("id", "").replace("https://openalex.org/", "") or None
item.cited_by_count = work.get("cited_by_count", 0) or 0
cby = work.get("counts_by_year") or []
item.counts_by_year = json.dumps(cby) if cby else None
return len(affs), item.is_intra_african
def main():
parser = argparse.ArgumentParser(description=__doc__)
parser.add_argument("--apply", action="store_true", help="Write changes (default: dry run)")
parser.add_argument("--limit", type=int, default=0, help="Max items to process (0 = all)")
parser.add_argument(
"--force", action="store_true", help="Re-fetch items that already have affiliation data"
)
args = parser.parse_args()
session = SessionLocal()
try:
q = session.query(Item)
if not args.force:
enriched = {i for (i,) in session.query(ItemAffiliation.item_id).distinct()}
else:
enriched = set()
items = [
it
for it in q.all()
if it.id not in enriched and (it.doi or "openalex.org" in (it.url or ""))
]
skipped_no_id = q.count() - len(items) - len(enriched & {it.id for it in q})
if args.limit:
items = items[: args.limit]
print("=" * 64)
print(f"Items to enrich: {len(items)} (already enriched, skipped: {len(enriched)})")
print("=" * 64)
if not args.apply:
print("[DRY RUN] No API calls or writes. Re-run with --apply.")
return 0
by_doi = [it for it in items if it.doi]
by_oaid = [
it for it in items if not it.doi and "openalex.org" in (it.url or "")
]
updated = intra = not_found = 0
# ── DOI batches ──────────────────────────────────────────────────
doi_map = {_norm_doi(it.doi): it for it in by_doi}
doi_keys = list(doi_map)
for start in range(0, len(doi_keys), BATCH):
chunk = doi_keys[start : start + BATCH]
works = fetch_batch_by_doi(chunk)
for nd in chunk:
it = doi_map[nd]
work = works.get(nd)
if not work:
not_found += 1
continue
_, is_ia = apply_work(session, it, work)
updated += 1
intra += int(is_ia)
session.commit()
print(
f" [doi {start + len(chunk)}/{len(doi_keys)}] "
f"updated={updated} intra_african={intra} not_found={not_found}"
)
time.sleep(1.0)
# ── OpenAlex-ID batches (items without DOI) ──────────────────────
oaid_map = {}
for it in by_oaid:
wid = (it.url or "").rstrip("/").split("/")[-1]
if wid.startswith("W"):
oaid_map[wid] = it
oaid_keys = list(oaid_map)
for start in range(0, len(oaid_keys), BATCH):
chunk = oaid_keys[start : start + BATCH]
works = fetch_batch_by_openalex_id(chunk)
for wid in chunk:
it = oaid_map[wid]
work = works.get(wid)
if not work:
not_found += 1
continue
_, is_ia = apply_work(session, it, work)
updated += 1
intra += int(is_ia)
session.commit()
print(
f" [oaid {start + len(chunk)}/{len(oaid_keys)}] "
f"updated={updated} intra_african={intra} not_found={not_found}"
)
time.sleep(1.0)
analytics_cache.invalidate_all()
total_ia = session.query(Item).filter(Item.is_intra_african.is_(True)).count()
total = session.query(Item).count()
print("\n" + "=" * 64)
print(f"DONE. updated={updated} not_found={not_found}")
print(
f"Repository intra-African collaboration: {total_ia}/{total} "
f"({(total_ia / total * 100) if total else 0:.1f}%) — continental baseline ~8.4%"
)
print("=" * 64)
return 0
finally:
session.close()
if __name__ == "__main__":
sys.exit(main())
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