#!/usr/bin/env python3 """ embed.py — Embed marine doc chunks with Gemini Embedding 2 (locked model). Model: gemini-embedding-2-preview (768-dim, L2-normalized, RETRIEVAL_DOCUMENT). No substitutes. Reranker is handled separately in search.py (Google Vertex Rank API). Key resolution order: 1. env GOOGLE_API_KEY 2. env GEMINI_API_KEY 3. vertex_api_key=... in /Users/dmpantiu/cmip6/cmip6_gpt/.env Modes: realtime — streaming API, resumable (default) batch — submit Batch API job (50% cost), then `status` / `download` status --resume download --resume Usage: python embed.py --mode realtime python embed.py --mode realtime --limit 20 # smoke test """ import argparse import json import math import os import sys import time from pathlib import Path import numpy as np import net_ipv4 # noqa: F401 — force IPv4 egress (VPN), must precede genai client ROOT = Path(__file__).resolve().parent OUT = ROOT / "out" IN_JSONL = OUT / "chunks.jsonl" OUT_JSONL = OUT / "chunks_embedded.jsonl" BATCH_INPUT = OUT / "batch_embed_input.jsonl" MODEL = "gemini-embedding-2-preview" TASK_TYPE = "RETRIEVAL_DOCUMENT" OUTPUT_DIM = 768 # AQ express key on gemini-embedding-2-preview is quota-capped at ~5 req/min. # Big batches (100 contents/req) + ~13s spacing keep us under the cap. RT_BATCH = 100 RT_SLEEP = 13.0 def resolve_key() -> str: for var in ("GOOGLE_API_KEY", "GEMINI_API_KEY"): if os.environ.get(var): return os.environ[var] # new key lives in copernicus_mcp/.env (field may be misspelled 'veretex_api_key') for env in (Path("/Users/dmpantiu/copernicus_mcp/.env"), Path("/Users/dmpantiu/cmip6/cmip6_gpt/.env")): if env.exists(): for line in env.read_text().splitlines(): line = line.strip() if "api_key" in line.lower() and "=" in line and not line.startswith("#"): return line.split("=", 1)[1].strip().strip('"').strip("'") raise SystemExit("No Gemini API key found (GOOGLE_API_KEY / vertex_api_key).") def get_client(): from google import genai return genai.Client(api_key=resolve_key()) def l2(vec): a = np.array(vec, dtype=np.float32) n = np.linalg.norm(a) return (a / n).tolist() if n > 0 else a.tolist() def load_chunks(limit=None): rows = [] with open(IN_JSONL) as f: for i, line in enumerate(f): if limit and i >= limit: break rows.append(json.loads(line)) return rows def embed_realtime(chunks): from google.genai import types client = get_client() done = set() if OUT_JSONL.exists(): for line in open(OUT_JSONL): try: done.add(json.loads(line)["chunk_id"]) except Exception: pass print(f"resume: {len(done)} already embedded") todo = [c for c in chunks if c["chunk_id"] not in done] print(f"to embed: {len(todo)} / {len(chunks)}") n = 0 with open(OUT_JSONL, "a", encoding="utf-8") as fout: for b in range(0, len(todo), RT_BATCH): batch = todo[b:b + RT_BATCH] texts = [c["text_with_prefix"] for c in batch] for attempt in range(6): try: # genai 1.64 can raise "client has been closed" — recreate on retry if attempt > 0: client = get_client() r = client.models.embed_content( model=MODEL, contents=texts, config=types.EmbedContentConfig( task_type=TASK_TYPE, output_dimensionality=OUTPUT_DIM), ) for c, e in zip(batch, r.embeddings): c["embedding"] = l2(e.values) fout.write(json.dumps(c, ensure_ascii=False) + "\n") n += 1 fout.flush() break except Exception as e: es = str(e) if "IP address restriction" in es: raise SystemExit( "BLOCKED: Gemini key has IP restriction. Whitelist this host's " "IP in Google Cloud Console (API key settings) and re-run.") if any(k in es for k in ("429", "RESOURCE_EXHAUSTED", "Quota exceeded")): wait = 35 # ~5 RPM quota — wait out the minute window elif "client has been closed" in es: wait = 2 # flaky genai transport; client recreated on retry else: wait = min(8 * (2 ** attempt), 60) print(f" retry {attempt+1}/8 in {wait}s: {repr(e)[:120]}", file=sys.stderr) time.sleep(wait) else: print(f" FATAL skip {len(batch)}", file=sys.stderr) if n % 400 == 0: print(f" [{n}/{len(todo)}]") time.sleep(RT_SLEEP) print(f"DONE: {n} embedded → {OUT_JSONL}") JOB_FILE = OUT / "batch_job.txt" def prepare_batch(chunks): # Correct batch schema: request.content (singular) + flat task_type/output_dimensionality. with open(BATCH_INPUT, "w", encoding="utf-8") as f: for c in chunks: f.write(json.dumps({ "key": c["chunk_id"], "request": { "content": {"parts": [{"text": c["text_with_prefix"]}]}, "task_type": TASK_TYPE, "output_dimensionality": OUTPUT_DIM, }, }, ensure_ascii=False) + "\n") print(f"batch input: {BATCH_INPUT} ({BATCH_INPUT.stat().st_size/1e6:.1f} MB, {len(chunks)} reqs)") def submit_batch(): client = get_client() up = client.files.upload(file=str(BATCH_INPUT), config={"display_name": "marine_embed_input", "mime_type": "jsonl"}) job = client.batches.create_embeddings( model=MODEL, src={"file_name": up.name}, config={"display_name": "marine_docs_embeddings"}) JOB_FILE.write_text(job.name) print(f"job: {job.name} state: {job.state} (saved to {JOB_FILE})") return job.name def _extract_values(resp: dict): """Pull the embedding vector out of a batch result line, shape-tolerant.""" for path in (("response", "embeddings"), ("response", "embedding"), ("embeddings",), ("embedding",)): node = resp ok = True for k in path: if isinstance(node, dict) and k in node: node = node[k] else: ok = False break if not ok: continue if isinstance(node, list) and node and isinstance(node[0], dict) and "values" in node[0]: return node[0]["values"] if isinstance(node, dict) and "values" in node: return node["values"] return None def poll_and_download(chunks, wait=True): client = get_client() name = JOB_FILE.read_text().strip() while True: job = client.batches.get(name=name) state = str(job.state) print(f" job {name}: {state}") if "SUCCEEDED" in state or "FAILED" in state or "CANCELLED" in state or "EXPIRED" in state: break if not wait: return False time.sleep(30) if "SUCCEEDED" not in state: print(f"job not successful: {state}") return False by_key = {c["chunk_id"]: c for c in chunks} dest = getattr(job, "dest", None) fn = getattr(dest, "file_name", None) if dest else None lines = [] if fn: lines = client.files.download(file=fn).decode("utf-8").strip().split("\n") elif dest and getattr(dest, "inlined_responses", None): lines = [json.dumps(r) for r in dest.inlined_responses] n = 0 with open(OUT_JSONL, "w", encoding="utf-8") as fout: for line in lines: if not line.strip(): continue r = json.loads(line) k = r.get("key") or r.get("custom_metadata") or r.get("custom_id") vals = _extract_values(r) if k in by_key and vals: c = dict(by_key[k]) c["embedding"] = l2(vals) fout.write(json.dumps(c, ensure_ascii=False) + "\n") n += 1 print(f"DOWNLOADED: {n}/{len(chunks)} embeddings → {OUT_JSONL}") return n >= len(chunks) * 0.99 def main(): ap = argparse.ArgumentParser() ap.add_argument("--mode", choices=["realtime", "batch", "submit", "poll", "status", "download"], default="realtime") ap.add_argument("--limit", type=int, default=None) ap.add_argument("--resume", type=str, default=None) a = ap.parse_args() chunks = load_chunks(a.limit) toks = sum(c["token_count"] for c in chunks) print(f"chunks={len(chunks):,} tokens={toks:,} " f"est realtime=${toks/1e6*0.25:.2f} batch=${toks/1e6*0.125:.2f}") if a.mode == "realtime": embed_realtime(chunks) elif a.mode in ("batch", "submit"): prepare_batch(chunks) submit_batch() if a.mode == "batch": poll_and_download(chunks, wait=True) elif a.mode == "poll": poll_and_download(chunks, wait=True) elif a.mode in ("status", "download"): client = get_client() name = a.resume or JOB_FILE.read_text().strip() job = client.batches.get(name=name) print(f"state: {job.state}") if a.mode == "download": poll_and_download(chunks, wait=False) if __name__ == "__main__": main()