#!/usr/bin/env python3 """ fetch_parse.py — fetch & text-extract the CDS/ADS/EWDS deep documentation (Confluence wiki pages + PDFs + service webpages) so the non-marine stores get the same deep-doc RAG depth as CMEMS marine. Input : meta_harvest/deep_doc_plan.json dataset_id -> [{title,url,kind}] Output: deep_docs/parsed/.md cleaned text per unique URL deep_docs/manifest.jsonl one line per URL (checkpoint: resumable) No VLM needed: Confluence/webpages via requests+bs4+markdownify, PDFs via PyMuPDF. Env: SAMPLE_N= to only process the first n URLs (smoke test). """ import json import os import re import sys import hashlib import threading from concurrent.futures import ThreadPoolExecutor, as_completed from pathlib import Path import requests from bs4 import BeautifulSoup from markdownify import markdownify as mdify import fitz # PyMuPDF ROOT = Path(__file__).resolve().parent.parent PLAN = ROOT / "meta_harvest" / "deep_doc_plan.json" OUTDIR = ROOT / "deep_docs" / "parsed" MANIFEST = ROOT / "deep_docs" / "manifest.jsonl" UA = {"User-Agent": "Mozilla/5.0 (copernicus-rag deep-doc harvester; research use)"} def log(*a): print(*a, file=sys.stderr, flush=True) def uhash(url): return hashlib.md5(url.encode()).hexdigest()[:16] def clean_md(md: str) -> str: md = re.sub(r"\n{3,}", "\n\n", md) md = re.sub(r"[ \t]+\n", "\n", md) # drop obvious confluence chrome lines drop = ("Skip to", "Configure Space tools", "Space shortcuts", "Copyright ©", "Powered by Atlassian", "Evaluate Confluence", "You are viewing") lines = [ln for ln in md.splitlines() if not any(d in ln for d in drop)] return "\n".join(lines).strip() def parse_html(html: str) -> str: soup = BeautifulSoup(html, "html.parser") for t in soup(["script", "style", "nav", "header", "footer", "noscript", "form"]): t.decompose() node = (soup.select_one("#main-content") or soup.select_one(".wiki-content") or soup.select_one("div[role=main]") or soup.select_one("main") or soup.select_one("article") or soup.body or soup) md = mdify(str(node), heading_style="ATX", strip=["img"]) return clean_md(md) def parse_pdf(content: bytes) -> str: doc = fitz.open(stream=content, filetype="pdf") parts = [page.get_text("text") for page in doc] doc.close() return clean_md("\n\n".join(parts)) def fetch_one(url: str, kind: str) -> tuple[str, str]: """Return (markdown, status). status in {ok, empty, http_, error}.""" try: r = requests.get(url, headers=UA, timeout=40, allow_redirects=True) if r.status_code != 200: return "", f"http_{r.status_code}" ct = r.headers.get("content-type", "").lower() if kind == "pdf" or "application/pdf" in ct or url.lower().split("?")[0].endswith(".pdf"): md = parse_pdf(r.content) else: md = parse_html(r.text) return md, ("ok" if len(md) >= 200 else "empty") except Exception as e: return "", f"error:{type(e).__name__}" def main(): OUTDIR.mkdir(parents=True, exist_ok=True) plan = json.loads(PLAN.read_text()) # unique url -> {title, kind, datasets:[]} urls: dict[str, dict] = {} for dsid, docs in plan.items(): for d in docs: u = d["url"] e = urls.setdefault(u, {"title": d.get("title", ""), "kind": d.get("kind"), "datasets": []}) e["datasets"].append(dsid) done = set() if MANIFEST.exists(): for line in MANIFEST.read_text().splitlines(): if line.strip(): done.add(json.loads(line)["url"]) todo = [u for u in urls if u not in done] sample = int(os.environ.get("SAMPLE_N", "0")) if sample: todo = todo[:sample] log(f"unique urls={len(urls)} done={len(done)} todo={len(todo)}" + (f" (SAMPLE {sample})" if sample else "")) workers = int(os.environ.get("WORKERS", "10")) lock = threading.Lock() counts = {"ok": 0, "done": 0} mf = open(MANIFEST, "a", encoding="utf-8") def work(url): meta = urls[url] md, status = fetch_one(url, meta["kind"]) rec = {"url": url, "kind": meta["kind"], "title": meta["title"], "datasets": meta["datasets"], "status": status, "n_chars": len(md), "md_path": ""} if status == "ok": p = OUTDIR / f"{uhash(url)}.md" header = f"# {meta['title']}\n\n\n\n" p.write_text(header + md, encoding="utf-8") rec["md_path"] = str(p.relative_to(ROOT)) with lock: mf.write(json.dumps(rec, ensure_ascii=False) + "\n") mf.flush() counts["done"] += 1 counts["ok"] += status == "ok" if counts["done"] % 40 == 0: log(f" {counts['done']}/{len(todo)} ok={counts['ok']}") with ThreadPoolExecutor(max_workers=workers) as ex: list(as_completed(ex.submit(work, u) for u in todo)) mf.close() log(f"DONE todo={len(todo)} ok={counts['ok']}") if __name__ == "__main__": main()