File size: 4,003 Bytes
0ec8fd6 | 1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 22 23 24 25 26 27 28 29 30 31 32 33 34 35 36 37 38 39 40 41 42 43 44 45 46 47 48 49 50 51 52 53 54 55 56 57 58 59 60 61 62 63 64 65 66 67 68 69 70 71 72 73 74 75 76 77 78 79 80 81 82 83 84 85 86 87 88 89 90 91 92 93 94 95 96 97 98 99 100 101 102 103 104 105 106 107 108 109 110 111 112 113 114 115 116 117 118 119 120 | #!/usr/bin/env python
"""Resolve unique DOIs via Crossref REST API.
Resumable: results are appended to registry/crossref_resolved.jsonl as they
arrive; on rerun, DOIs already present there are skipped.
"""
import json
import re
import sys
import time
from pathlib import Path
from urllib.parse import quote
import httpx
REG = Path("/Users/dmpantiu/copernicus_mcp/publications/registry")
IN_FILE = REG / "unique_dois.jsonl"
OUT_FILE = REG / "crossref_resolved.jsonl"
UA = ("copernicus-rag-registry/1.0 "
"(https://marine.copernicus.eu EQC reference registry; "
"mailto:delon.riina@gmail.com)")
RATE_DELAY = 0.5 # ~2 req/s
MAX_RETRIES = 4
JATS_TAG_RE = re.compile(r"<[^>]+>")
def parse_message(msg: dict) -> dict:
title = (msg.get("title") or [None])[0]
journal = (msg.get("container-title") or [None])[0]
year = None
for k in ("issued", "published-print", "published-online", "created"):
dp = (msg.get(k) or {}).get("date-parts") or []
if dp and dp[0] and dp[0][0]:
year = dp[0][0]
break
authors = []
for a in (msg.get("author") or [])[:6]:
fam = a.get("family") or a.get("name")
if fam:
authors.append(fam)
abstract = msg.get("abstract")
if abstract:
abstract = JATS_TAG_RE.sub(" ", abstract)
abstract = " ".join(abstract.split())
return {
"title": title,
"journal": journal,
"year": year,
"authors": authors,
"abstract": abstract,
"type": msg.get("type"),
"is_referenced_by_count": msg.get("is-referenced-by-count"),
}
def main():
dois = [json.loads(l)["doi"] for l in open(IN_FILE)]
done = set()
if OUT_FILE.exists():
for l in open(OUT_FILE):
try:
done.add(json.loads(l)["doi"])
except (json.JSONDecodeError, KeyError):
pass
todo = [d for d in dois if d not in done]
print(f"{len(dois)} DOIs total, {len(done)} already resolved, {len(todo)} to do",
flush=True)
client = httpx.Client(
headers={"User-Agent": UA},
timeout=30.0,
follow_redirects=True,
)
n_ok = n_fail = 0
with open(OUT_FILE, "a") as out:
for i, doi in enumerate(todo):
url = f"https://api.crossref.org/works/{quote(doi, safe='')}"
rec = {"doi": doi, "resolved": False}
for attempt in range(MAX_RETRIES):
try:
r = client.get(url)
except httpx.HTTPError as e:
if attempt == MAX_RETRIES - 1:
rec["error"] = f"network:{type(e).__name__}"
time.sleep(2 * (attempt + 1))
continue
if r.status_code == 200:
try:
msg = r.json()["message"]
rec.update(parse_message(msg))
rec["resolved"] = True
except (ValueError, KeyError):
rec["error"] = "bad_json"
break
if r.status_code == 404:
rec["error"] = "not_found"
break
if r.status_code in (429, 500, 502, 503, 504):
wait = float(r.headers.get("Retry-After", 2 * (attempt + 1)))
time.sleep(min(wait, 30))
continue
rec["error"] = f"http_{r.status_code}"
break
out.write(json.dumps(rec, ensure_ascii=False) + "\n")
out.flush()
if rec["resolved"]:
n_ok += 1
else:
n_fail += 1
if (i + 1) % 50 == 0:
print(f" {i+1}/{len(todo)} done (ok={n_ok} fail={n_fail})",
flush=True)
time.sleep(RATE_DELAY)
print(f"finished: ok={n_ok} fail={n_fail}", flush=True)
if __name__ == "__main__":
sys.exit(main())
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