scripts/pubs_rag/load_pubs_qdrant.py

#!/usr/bin/env python3
"""
load_pubs_qdrant.py — stream the ALREADY-EMBEDDED Copernicus publications corpus
(out/chunks_embedded.jsonl, 768-dim gemini-embedding-2-preview, L2-norm)
into a fresh embedded Qdrant at pubs_rag/qdrant_db, collection `publications`.

NO re-embedding: dense vectors are read straight from the archive.
Sparse BM25 (FastEmbed Qdrant/bm25, IDF modifier) is computed from text_raw
during load. Join metadata (canonical DOI, domains, has_local_md, registry
orphan/linked_products) comes from pubs_join.build_paper_index.

Payload: chunk_id, paper_id, doi (CANONICAL), title, journal, year, domains[],
section, chunk_type, text_raw (<=2500), orphan, linked_products[], has_local_md.
Indexes: doi, paper_id, journal, year, domains, orphan, linked_products,
chunk_type.

Single clean run (embedded Qdrant = single-process lock). ~20-60 min.
"""
import argparse
import json
import shutil
import time
import uuid
from pathlib import Path

from qdrant_client import QdrantClient, models
from fastembed import SparseTextEmbedding

import pubs_join

ROOT = Path(__file__).resolve().parent
OUT = ROOT / "out"
LOG = OUT / "load_archive.log"
COLLECTION = "publications"
DENSE_DIM = 768
LOCAL_DB = ROOT / "qdrant_db"
ARCHIVE = pubs_join.ARCHIVE
BATCH = 400

_bm25 = SparseTextEmbedding(model_name="Qdrant/bm25")
_logf = None


def log(msg: str):
    line = f"[{time.strftime('%H:%M:%S')}] {msg}"
    print(line, flush=True)
    if _logf:
        _logf.write(line + "\n")
        _logf.flush()


def create_collection(client: QdrantClient):
    names = [c.name for c in client.get_collections().collections]
    if COLLECTION in names:
        client.delete_collection(COLLECTION)
    client.create_collection(
        collection_name=COLLECTION,
        vectors_config={"dense": models.VectorParams(size=DENSE_DIM, distance=models.Distance.COSINE)},
        sparse_vectors_config={"sparse": models.SparseVectorParams(modifier=models.Modifier.IDF)},
    )
    for field, schema in [
        ("doi", models.PayloadSchemaType.KEYWORD),
        ("paper_id", models.PayloadSchemaType.KEYWORD),
        ("journal", models.PayloadSchemaType.KEYWORD),
        ("year", models.PayloadSchemaType.INTEGER),
        ("domains", models.PayloadSchemaType.KEYWORD),
        ("orphan", models.PayloadSchemaType.BOOL),
        ("linked_products", models.PayloadSchemaType.KEYWORD),
        ("chunk_type", models.PayloadSchemaType.KEYWORD),
    ]:
        client.create_payload_index(collection_name=COLLECTION, field_name=field, field_schema=schema)
    log(f"created '{COLLECTION}' (dense 768 cosine + sparse bm25, 8 payload indexes)")


def sparse_batch(texts):
    return list(_bm25.embed(texts))


def flush(client, buf_pts, buf_txt):
    sparses = sparse_batch(buf_txt)
    for pt, sp in zip(buf_pts, sparses):
        pt.vector["sparse"] = models.SparseVector(
            indices=sp.indices.tolist(), values=sp.values.tolist())
    client.upsert(collection_name=COLLECTION, points=buf_pts)


def load(client, index, limit=None):
    buf_pts, buf_txt = [], []
    total = skipped = 0
    t0 = time.time()
    with open(ARCHIVE, encoding="utf-8") as f:
        for i, line in enumerate(f):
            if limit and i >= limit:
                break
            c = json.loads(line)
            emb = c.get("embedding")
            if not emb:
                skipped += 1
                continue
            pid = c["paper_id"]
            m = index[pid]
            raw = c.get("text_raw") or c.get("text_with_prefix", "")
            year = c.get("year")
            try:
                year = int(year)
            except (TypeError, ValueError):
                year = None
            section = c.get("section") or c.get("section_path") or c.get("section_name") or ""
            pt = models.PointStruct(
                id=str(uuid.uuid5(uuid.NAMESPACE_DNS, c["chunk_id"])),
                vector={"dense": emb},  # sparse filled in flush()
                payload={
                    "chunk_id": c["chunk_id"],
                    "paper_id": pid,
                    "doi": m["doi"],
                    "title": c.get("title", ""),
                    "journal": c.get("journal", ""),
                    "year": year,
                    "domains": m["domains"],
                    "section": section,
                    "chunk_type": c.get("chunk_type", "text"),
                    "text_raw": raw[:2500],
                    "orphan": m["orphan"],
                    "linked_products": m["linked_products"],
                    "has_local_md": m["has_local_md"],
                },
            )
            buf_pts.append(pt)
            buf_txt.append(raw)
            if len(buf_pts) >= BATCH:
                flush(client, buf_pts, buf_txt)
                total += len(buf_pts)
                buf_pts, buf_txt = [], []
                if total % 5000 < BATCH:
                    rate = total / (time.time() - t0)
                    log(f"  loaded {total:,} chunks  {rate:.0f}/s  "
                        f"eta {(430066 - total) / max(rate, 1) / 60:.1f} min")
    if buf_pts:
        flush(client, buf_pts, buf_txt)
        total += len(buf_pts)
    dur = time.time() - t0
    pc = client.get_collection(COLLECTION).points_count
    log(f"DONE: loaded {total:,} chunks (skipped {skipped}) in {dur/60:.1f} min "
        f"({total/dur:.0f}/s); collection points_count={pc:,}")
    return total, dur


def main():
    global _logf
    ap = argparse.ArgumentParser()
    ap.add_argument("--limit", type=int, default=None)
    ap.add_argument("--fresh", action="store_true", help="rm qdrant_db dir first")
    a = ap.parse_args()

    OUT.mkdir(exist_ok=True)
    _logf = open(LOG, "a", encoding="utf-8")
    log("=== load_pubs_qdrant start ===")

    free_gb = shutil.disk_usage(str(ROOT)).free / 1e9
    log(f"disk free: {free_gb:.1f} GB")
    if free_gb < 4:
        raise SystemExit("need ~4GB free")

    log("building paper join index (one pass over archive headers)...")
    index, stats = pubs_join.build_paper_index(log=log)
    pubs_join.print_report(stats)

    if a.fresh and LOCAL_DB.exists():
        shutil.rmtree(LOCAL_DB)
        log(f"removed {LOCAL_DB}")

    client = QdrantClient(path=str(LOCAL_DB))
    log(f"Qdrant: local {LOCAL_DB}")
    create_collection(client)
    total, dur = load(client, index, a.limit)
    client.close()
    log("client closed")


if __name__ == "__main__":
    main()