scripts/marine_rag/rag_server.py

#!/usr/bin/env python3
"""
rag_server.py — `copernicus-rag` MCP server: RAG discovery + documentation layer
for Copernicus data, companion to the `copernicus` MCP server (which does the
actual subsetting/downloading).

Two-level flow:
  L0  search_datasets      — find datasets by meaning across ALL 4 stores
                             (CMEMS 1251 + CDS 136 + ADS 16 + EWDS 12 cards)
  L1  get_dataset_docs     — quality/EQC documentation (PUM/QUID/SQO) chunks
                             for a CMEMS product, semantically filtered
      search_docs          — same 29k doc chunks, searched globally
      list_dataset_documents / read_document — pull full doc markdown

Retrieval: Qdrant (embedded, out/qdrant_db) hybrid dense+BM25 with RRF fusion.
Dense query vector = gemini-embedding-2-preview (768-dim); if the embed call
fails (quota/net), we degrade to sparse-only BM25 and say so in the response.
Optional Google semantic-ranker rerank when GCP_PROJECT + ADC are set.

Invariants (mirrors copernicus-mcp): text/descriptors only — no raw scientific
bytes; logging to stderr only; tools never raise — they return {"ok": false}.
"""
from __future__ import annotations

import json
import logging
import os
import sys
import threading
from functools import lru_cache
from pathlib import Path

# stdio transport: stdout is the JSON-RPC channel — pin ALL logging to stderr
# before any library gets a chance to install a stdout handler.
logging.basicConfig(level=logging.WARNING, stream=sys.stderr, force=True)
for _name in ("httpx", "httpcore", "google", "google_genai", "fastembed", "qdrant_client"):
    logging.getLogger(_name).setLevel(logging.WARNING)

ROOT = Path(__file__).resolve().parent
sys.path.insert(0, str(ROOT))

import net_ipv4  # noqa: F401  — force IPv4 egress (VPN) before any genai call

from mcp.server.fastmcp import FastMCP
from qdrant_client import QdrantClient, models

import search as S  # embed_query, sparse_query, rerank_google, LOCAL_DB

OUT = ROOT / "out"
CARDS_COLLECTION = "copernicus_docs"   # 1 card per dataset, all 4 stores
DOCS_COLLECTION = "marine_docs"        # PUM/QUID/SQO chunks, CMEMS only
STORES = ("CMEMS", "CDS", "ADS", "EWDS")
DOC_TYPES = ("PUM", "QUID", "SQO", "CARD")
MAX_TEXT = 1600          # per-chunk text cap in tool output
READ_DEFAULT = 20_000    # default read_document window

PUBS_DB = ROOT.parent / "pubs_rag" / "qdrant_db"
PUBS_COLLECTION = "publications"
REGISTRY = ROOT.parent / "publications" / "registry" / "publications.jsonl"
PAPERS = ROOT.parent / "pubs_rag" / "out" / "papers.jsonl"
LINKS_SIDECAR = ROOT.parent / "pubs_rag" / "out" / "links_by_dataset.json"
PUB_DOMAINS = ("ocean/marine", "atmosphere", "cryosphere", "land",
               "climate-modeling", "climate-general", "emergency")

EQC_QA_DB = ROOT.parent / "eqc_qa" / "qdrant_db"
EQC_QA_COLLECTION = "eqc_qa"

# Deep documentation for the non-marine stores (CDS/ADS/EWDS): Confluence user
# guides / ATBDs / PDFs, chunked like marine_docs. Separate DB (own lock).
DEEP_DB = ROOT.parent / "deep_docs" / "qdrant_db"
DEEP_COLLECTION = "cds_docs"

# Notebook code layer: runnable example-notebook code ATTACHED to datasets
# (serve-time join by dataset id — NOT embedded/searched on its own).
NOTEBOOKS_SIDECAR = ROOT.parent / "eqc_qa" / "notebooks_by_dataset.json"

_lock = threading.Lock()
_client: QdrantClient | None = None
_pubs_client: QdrantClient | None = None
_eqc_client: QdrantClient | None = None
_deep_client: QdrantClient | None = None


def _log(msg: str) -> None:
    print(f"[copernicus-rag] {msg}", file=sys.stderr, flush=True)


# ── Qdrant SERVER fast path ─────────────────────────────────────────────────
# If a Qdrant server (server/docker-compose.yml) is reachable and carries the
# needed collection, use it instead of the embedded files: HNSW + payload
# indexes make publications queries ~30 ms vs minutes, and there is no
# single-process lock. Falls back to embedded silently when the server is
# down or lacks the collection. Disable with QDRANT_URL="".
QDRANT_URL = os.environ.get("QDRANT_URL", "http://localhost:6333")
_server_client: QdrantClient | None = None
_server_collections: frozenset | None = None


def _server() -> QdrantClient | None:
    global _server_client, _server_collections
    with _lock:
        if _server_collections is None:
            if not QDRANT_URL:
                _server_collections = frozenset()
                return None
            try:
                cl = QdrantClient(url=QDRANT_URL, timeout=30,
                                  check_compatibility=False)
                _server_collections = frozenset(
                    c.name for c in cl.get_collections().collections)
                _server_client = cl
                _log(f"qdrant SERVER at {QDRANT_URL}: "
                     f"{sorted(_server_collections)}")
            except Exception as e:
                _server_collections = frozenset()
                _log(f"qdrant server unreachable ({repr(e)[:60]}) — "
                     "using embedded indexes")
        return _server_client


def _via_server(collection: str) -> QdrantClient | None:
    cl = _server()
    if cl is not None and collection in (_server_collections or ()):
        return cl
    return None


def _qdrant() -> QdrantClient:
    srv = _via_server("marine_docs")
    if srv is not None and _via_server("copernicus_docs") is not None:
        return srv
    global _client
    with _lock:
        if _client is None:
            _log(f"opening embedded Qdrant at {S.LOCAL_DB}")
            try:
                _client = QdrantClient(path=str(S.LOCAL_DB))
            except Exception as e:
                raise RuntimeError(
                    "cannot open marine index (locked by a load script or another "
                    f"server instance? retry when it finishes): {repr(e)[:120]}") from e
        return _client


@lru_cache(maxsize=1)
def _catalog():
    """CMEMS product catalog: by product_id + dataset_id -> product_id map."""
    cat = json.loads((OUT / "catalog.json").read_text())
    by_pid = {c["product_id"]: c for c in cat}
    ds_to_pid = {}
    for c in cat:
        for ds in c.get("dataset_ids", []):
            ds_to_pid[ds.lower()] = c["product_id"]
    return by_pid, ds_to_pid


def resolve_product(any_id: str) -> str | None:
    """Exact product/dataset id, else UNIQUE prefix, else UNIQUE substring.

    Ambiguous fragments (e.g. "006" is contained in 13 product ids) return
    None instead of silently picking an arbitrary product.
    """
    by_pid, ds_to_pid = _catalog()
    if any_id in by_pid:
        return any_id
    low = any_id.lower()
    if not low:
        return None
    if low in ds_to_pid:
        return ds_to_pid[low]
    exact = [pid for pid in by_pid if pid.lower() == low]
    if exact:
        return exact[0]
    starts = [pid for pid in by_pid if pid.lower().startswith(low)]
    if len(starts) == 1:
        return starts[0]
    contains = starts or [pid for pid in by_pid if low in pid.lower()]
    return contains[0] if len(contains) == 1 else None


def _pubs_qdrant() -> QdrantClient | None:
    """Client for the separate publications DB; None until the index is built."""
    srv = _via_server(PUBS_COLLECTION)
    if srv is not None:
        return srv
    global _pubs_client
    with _lock:
        if _pubs_client is None:
            if not PUBS_DB.exists():
                return None
            _log(f"opening embedded Qdrant at {PUBS_DB}")
            try:
                _pubs_client = QdrantClient(path=str(PUBS_DB))
            except Exception as e:
                raise RuntimeError(
                    "cannot open publications index (locked by load_pubs_qdrant.py "
                    f"or another server instance? retry when it finishes): {repr(e)[:120]}") from e
        return _pubs_client


def _pubs_status() -> str:
    """Human-readable build status of the publications index."""
    return ("publications index not on disk yet — PDFs are being downloaded "
            "and VLM-parsed; the collection grows as parses land")


def _eqc_qdrant() -> QdrantClient | None:
    """Client for the CDS/C3S EQC quality-assessment DB; None until built."""
    srv = _via_server(EQC_QA_COLLECTION)
    if srv is not None:
        return srv
    global _eqc_client
    with _lock:
        if _eqc_client is None:
            if not EQC_QA_DB.exists():
                return None
            _log(f"opening embedded Qdrant at {EQC_QA_DB}")
            try:
                _eqc_client = QdrantClient(path=str(EQC_QA_DB))
            except Exception as e:
                raise RuntimeError(
                    "cannot open EQC-QA index (locked by load_eqc_qa.py or another "
                    f"server instance? retry when it finishes): {repr(e)[:120]}") from e
        return _eqc_client


def _deep_qdrant() -> QdrantClient | None:
    """Client for the CDS/ADS/EWDS deep-docs DB; None until built."""
    srv = _via_server(DEEP_COLLECTION)
    if srv is not None:
        return srv
    global _deep_client
    with _lock:
        if _deep_client is None:
            if not DEEP_DB.exists():
                return None
            _log(f"opening embedded Qdrant at {DEEP_DB}")
            try:
                _deep_client = QdrantClient(path=str(DEEP_DB))
            except Exception as e:
                raise RuntimeError(
                    "cannot open deep-docs index (locked by embed_load.py or another "
                    f"server instance? retry when it finishes): {repr(e)[:120]}") from e
        return _deep_client


@lru_cache(maxsize=1)
def _notebooks() -> tuple[dict, dict, dict]:
    """Notebook code recipes attached to datasets (serve-time join, no re-index).

    Returns (by_dataset_id -> [records], by_notebook_id -> record,
    generic_by_store -> [store-level how-to records]). Cached for process
    lifetime: restart the server to pick up newly attached notebooks.
    """
    by_ds: dict = {}
    by_id: dict = {}
    generic: dict = {}
    if NOTEBOOKS_SIDECAR.exists():
        data = json.loads(NOTEBOOKS_SIDECAR.read_text())
        by_ds = data.get("by_dataset", {})
        generic = data.get("generic_by_store", {})
        for recs in by_ds.values():
            for r in recs:
                by_id[r["notebook_id"]] = r
        for recs in generic.values():
            for r in recs:
                by_id.setdefault(r["notebook_id"], r)
    return by_ds, by_id, generic


def _nb_refs(dataset_id: str | None, product_id: str | None = None,
             kind: str | None = None) -> list[dict]:
    """Compact notebook refs attached to a dataset/collection id (for list views)."""
    by_ds, _, _ = _notebooks()
    recs = by_ds.get(dataset_id or "") or by_ds.get(product_id or "") or []
    out = []
    for r in recs:
        if kind and kind not in (r.get("recipe_kinds") or []):
            continue
        out.append({"notebook_id": r["notebook_id"], "title": r.get("title"),
                    "recipe_kinds": r.get("recipe_kinds"),
                    "n_code_lines": r.get("n_code_lines"),
                    "source_repo": r.get("source_repo")})
    return out


_dim_cache: dict[tuple[int, str], int | None] = {}


def _dense_dim_ok(client: QdrantClient, collection: str, qdim: int) -> bool:
    """Guard: the query embedder must match the collection's dense dim.

    A local EMBED_MODEL (e.g. 384-d bge-small) against the gemini-768 corpus
    would silently return garbage — degrade to BM25-only and say why once.
    """
    key = (id(client), collection)
    if key not in _dim_cache:
        try:
            vecs = client.get_collection(collection).config.params.vectors
            _dim_cache[key] = getattr(vecs.get("dense"), "size", None) \
                if isinstance(vecs, dict) else getattr(vecs, "size", None)
        except Exception:
            _dim_cache[key] = None
    cdim = _dim_cache[key]
    if cdim is None or cdim == qdim:
        return True
    _log(f"EMBED_MODEL dim {qdim} != '{collection}' dense dim {cdim} — "
         "BM25-only (re-embed the corpus with this model, or unset EMBED_MODEL)")
    return False


def _query(collection: str, query: str, flt: models.Filter | None,
           top_k: int, prefetch: int = 50, client: QdrantClient | None = None):
    """Hybrid dense+sparse RRF; degrades to sparse-only if dense embed fails.

    Only the embed call may trigger the fallback (SystemExit included: a
    missing API key must not kill the server); Qdrant errors propagate to
    the caller so they are reported as what they are.

    Returns (points, retrieval_mode).
    """
    client = client or _qdrant()
    sparse_vec = S.sparse_query(query)
    dense_vec = None
    try:
        dense_vec = S.embed_query(query)
    except (Exception, SystemExit) as e:
        _log(f"dense embed unavailable ({repr(e)[:120]}); sparse-only fallback")
    if dense_vec is not None and not _dense_dim_ok(client, collection, len(dense_vec)):
        dense_vec = None  # wrong embedder for this corpus — sparse-only
    if dense_vec is not None:
        res = client.query_points(
            collection_name=collection,
            prefetch=[
                models.Prefetch(query=dense_vec, using="dense", limit=prefetch, filter=flt),
                models.Prefetch(query=sparse_vec, using="sparse", limit=prefetch, filter=flt),
            ],
            query=models.FusionQuery(fusion=models.Fusion.RRF),
            limit=top_k, with_payload=True,
        )
        return res.points, "hybrid(dense+bm25)"
    res = client.query_points(
        collection_name=collection, query=sparse_vec, using="sparse",
        limit=top_k, with_payload=True, query_filter=flt,
    )
    return res.points, "bm25-only (dense embed unavailable)"


def _maybe_rerank(query: str, points, top_k: int, rerank: bool):
    if not rerank or not points:
        return points, False
    rr = S.rerank_google(query, points, top_k)
    return (rr, True) if rr is not None else (points, False)


def _err(msg: str, **extra) -> dict:
    return {"ok": False, "error": msg, **extra}


mcp = FastMCP("copernicus-rag")


@mcp.tool()
def search_datasets(query: str, store: str | None = None, top_k: int = 10,
                    rerank: bool = True) -> dict:
    """Semantic (RAG) search for Copernicus datasets by description, across all
    four data stores: CMEMS (marine), CDS (climate/ERA5), ADS (atmosphere),
    EWDS (emergency/flood/fire). One card per dataset (~1415 total).

    Use this FIRST to discover which dataset to work with. Then, for CMEMS
    results, call get_dataset_docs(product_id) to read its quality (EQC)
    documentation before analyzing data.

    Args:
        query: natural-language description of the data you need
               (e.g. "daily arctic sea ice concentration satellite").
        store: optional filter — one of CMEMS, CDS, ADS, EWDS.
        top_k: number of datasets to return (default 10).
        rerank: also rerank with Google semantic-ranker (needs GCP ADC).
    """
    try:
        if store:
            store = store.upper()
            if store not in STORES:
                return _err(f"unknown store '{store}'", valid_stores=list(STORES))
        top_k = max(1, min(int(top_k), 30))
        flt = models.Filter(must=[models.FieldCondition(
            key="store", match=models.MatchValue(value=store))]) if store else None
        points, mode = _query(CARDS_COLLECTION, query, flt, max(top_k, 20))
        points, reranked = _maybe_rerank(query, points, top_k, rerank)
        by_pid, _ = _catalog()
        results = []
        for p in points[:top_k]:
            pl = p.payload
            pid = pl.get("product_id", "")
            has_docs = bool(by_pid.get(pid, {}).get("has_docs"))
            results.append({
                "store": pl.get("store"),
                "dataset_id": pl.get("dataset_id"),
                "product_id": pid,
                "title": pl.get("product_title"),
                "description": (pl.get("text_raw") or "")[:MAX_TEXT],
                "has_eqc_docs": has_docs,
                "notebooks": _nb_refs(pl.get("dataset_id"), pid),
                "score": getattr(p, "score", None),
            })
        return {"ok": True, "query": query, "store": store or "ALL",
                "retrieval": mode, "reranked": reranked,
                "n_results": len(results), "results": results,
                "next_step": ("for CMEMS hits call get_dataset_docs(product_id) "
                              "to read quality docs; where a hit has notebooks[], "
                              "call get_dataset_code(dataset_id) for runnable code")}
    except Exception as e:
        _log(f"search_datasets failed: {repr(e)}")
        return _err(f"search failed: {repr(e)[:200]}")


def _deep_dataset_docs(dataset_id: str, question: str | None,
                       top_k: int, rerank: bool) -> dict | None:
    """Deep CDS/ADS/EWDS documentation (cds_docs) for a collection id.
    Returns a result dict, or None if the deep index is unavailable / has no
    match for this id (so the caller can fall through to 'unknown id')."""
    client = _deep_qdrant()
    if client is None:
        return None
    top_k = max(1, min(int(top_k), 20))
    q = question or (f"{dataset_id} documentation: variables, methodology, accuracy, "
                     "validation, how to use and interpret this dataset")
    must = [models.FieldCondition(key="dataset_ids", match=models.MatchValue(value=dataset_id))]
    points, mode = _query(DEEP_COLLECTION, q, models.Filter(must=must),
                          max(top_k, 20), prefetch=40, client=client)
    if not points:
        return None
    points, reranked = _maybe_rerank(q, points, top_k, rerank)
    results = [{
        "store": p.payload.get("store"),
        "doc_title": p.payload.get("doc_title"),
        "doc_url": p.payload.get("doc_url"),
        "section": p.payload.get("section"),
        "text": (p.payload.get("text_raw") or "")[:MAX_TEXT],
        "score": getattr(p, "score", None),
    } for p in points[:top_k]]
    return {"ok": True, "dataset_id": dataset_id, "layer": "deep_docs (CDS/ADS/EWDS)",
            "query": q, "retrieval": mode, "reranked": reranked,
            "n_results": len(results), "results": results,
            "notebooks": _nb_refs(dataset_id, dataset_id),
            "next_step": ("get_eqc_quality_report(dataset_id) for quality assessment; "
                          "get_dataset_code(dataset_id) for runnable code")}


@mcp.tool()
def get_dataset_docs(dataset_or_product_id: str, question: str | None = None,
                     doc_type: str | None = None, top_k: int = 8,
                     rerank: bool = True) -> dict:
    """Level-2 EQC lookup: retrieve the quality/usage documentation chunks
    (PUM = Product User Manual, QUID = Quality Information Document,
    SQO = Scientific Quality Overview) for one CMEMS product or dataset.

    Call this AFTER search_datasets, BEFORE analyzing data: it tells you the
    variables, units, spatial/temporal coverage, accuracy, validation results
    and known caveats — i.e. how to interpret the numbers you will pull.

    Args:
        dataset_or_product_id: CMEMS product_id or dataset_id
            (e.g. "MEDSEA_ANALYSISFORECAST_PHY_006_013" or a dataset id).
        question: optional focus (e.g. "salinity validation accuracy");
            default surfaces the how-to-analyze essentials.
        doc_type: optional filter — PUM, QUID or SQO.
        top_k: number of doc chunks to return (default 8).
        rerank: also rerank with Google semantic-ranker (needs GCP ADC).
    """
    try:
        pid = resolve_product(dataset_or_product_id)
        if not pid:
            deep = _deep_dataset_docs(dataset_or_product_id, question, top_k, rerank)
            if deep is not None:
                return deep
            return _err(f"unknown dataset/product id: {dataset_or_product_id}",
                        hint="use an id returned by search_datasets")
        by_pid, _ = _catalog()
        prod = by_pid[pid]
        if doc_type:
            doc_type = doc_type.upper()
            if doc_type not in DOC_TYPES:
                return _err(f"unknown doc_type '{doc_type}'", valid=list(DOC_TYPES))
        top_k = max(1, min(int(top_k), 20))
        q = question or (f"{prod['product_title']} variables, spatial and temporal "
                         "coverage, accuracy, validation, how to use and interpret "
                         "this product")
        must = [models.FieldCondition(key="product_id", match=models.MatchValue(value=pid))]
        if doc_type:
            must.append(models.FieldCondition(key="doc_type", match=models.MatchValue(value=doc_type)))
        points, mode = _query(DOCS_COLLECTION, q, models.Filter(must=must), max(top_k, 20), prefetch=40)
        points, reranked = _maybe_rerank(q, points, top_k, rerank)
        results = [{
            "doc_type": p.payload.get("doc_type"),
            "doc_id": p.payload.get("doc_id"),
            "section": p.payload.get("section_path"),
            "text": (p.payload.get("text_raw") or "")[:MAX_TEXT],
            "score": getattr(p, "score", None),
        } for p in points[:top_k]]
        return {"ok": True, "product_id": pid, "product_title": prod["product_title"],
                "matched_by": "product_id" if dataset_or_product_id == pid else "dataset_id/fuzzy",
                "doc_types_available": prod.get("doc_types", []),
                "dataset_ids": prod.get("dataset_ids", []),
                "query": q, "retrieval": mode, "reranked": reranked,
                "n_results": len(results), "results": results,
                "next_step": ("read_document(doc_id) pulls a full document; "
                              "then subset data via the copernicus MCP server")}
    except Exception as e:
        _log(f"get_dataset_docs failed: {repr(e)}")
        return _err(f"lookup failed: {repr(e)[:200]}")


@mcp.tool()
def search_docs(query: str, doc_type: str | None = None, top_k: int = 8,
                rerank: bool = True) -> dict:
    """Global semantic search across ALL CMEMS quality documentation
    (~29k chunks of PUM/QUID/SQO for 306 products), not limited to one product.

    Use for cross-product questions like "which products are validated against
    Argo floats" or "sea level trend uncertainty methodology".

    Args:
        query: natural-language question.
        doc_type: optional filter — PUM, QUID or SQO.
        top_k: number of chunks to return (default 8).
        rerank: also rerank with Google semantic-ranker (needs GCP ADC).
    """
    try:
        if doc_type:
            doc_type = doc_type.upper()
            if doc_type not in DOC_TYPES:
                return _err(f"unknown doc_type '{doc_type}'", valid=list(DOC_TYPES))
        top_k = max(1, min(int(top_k), 20))
        flt = models.Filter(must=[models.FieldCondition(
            key="doc_type", match=models.MatchValue(value=doc_type))]) if doc_type else None
        points, mode = _query(DOCS_COLLECTION, query, flt, max(top_k, 20))
        points, reranked = _maybe_rerank(query, points, top_k, rerank)
        results = [{
            "product_id": p.payload.get("product_id"),
            "product_title": p.payload.get("product_title"),
            "doc_type": p.payload.get("doc_type"),
            "doc_id": p.payload.get("doc_id"),
            "section": p.payload.get("section_path"),
            "text": (p.payload.get("text_raw") or "")[:MAX_TEXT],
            "score": getattr(p, "score", None),
        } for p in points[:top_k]]
        return {"ok": True, "query": query, "retrieval": mode, "reranked": reranked,
                "n_results": len(results), "results": results}
    except Exception as e:
        _log(f"search_docs failed: {repr(e)}")
        return _err(f"search failed: {repr(e)[:200]}")


@mcp.tool()
def list_dataset_documents(dataset_or_product_id: str) -> dict:
    """List the full EQC documents available for a CMEMS product/dataset:
    doc_id, type (PUM/QUID/SQO) and size. Feed a doc_id to read_document
    to pull the complete text.

    Args:
        dataset_or_product_id: CMEMS product_id or dataset_id.
    """
    try:
        pid = resolve_product(dataset_or_product_id)
        if not pid:
            return _err(f"unknown dataset/product id: {dataset_or_product_id}")
        by_pid, _ = _catalog()
        prod = by_pid[pid]
        docs = [{"doc_id": d["doc_id"], "doc_type": d["doc_type"],
                 "size_bytes": d.get("md_bytes"), "available": d.get("has_md", False)}
                for d in prod.get("docs", [])]
        return {"ok": True, "product_id": pid, "product_title": prod["product_title"],
                "dataset_ids": prod.get("dataset_ids", []),
                "doi": prod.get("doi"), "regions": prod.get("regions", []),
                "domains": prod.get("domains", []),
                "n_documents": len(docs), "documents": docs}
    except Exception as e:
        _log(f"list_dataset_documents failed: {repr(e)}")
        return _err(f"lookup failed: {repr(e)[:200]}")


@lru_cache(maxsize=1)
def _unified_meta() -> dict:
    """Full harvested upstream metadata, all 4 stores (meta_harvest)."""
    path = ROOT.parent / "meta_harvest" / "unified_metadata.json"
    return json.loads(path.read_text()) if path.exists() else {}


@mcp.tool()
def dataset_metadata(dataset_or_collection_id: str) -> dict:
    """FULL harvested metadata for one dataset (any store) — much richer than
    the card returned by search_datasets: variables with units/standard_name/
    bbox/depth/time ranges, services, processing level, production centre,
    update frequency, documentation links, scientific references, licence.

    Use before subsetting data: it tells you exact variable names, units and
    coverage bounds. Accepts a CMEMS dataset_id, a CDS/ADS/EWDS collection id,
    or a CMEMS product_id (then lists the product's datasets).

    Args:
        dataset_or_collection_id: e.g. "antarctic_omi_si_extent",
            "reanalysis-era5-single-levels", or a CMEMS product_id.
    """
    try:
        meta = _unified_meta()
        if not meta:
            return _err("unified_metadata.json not found — run the meta_harvest pipeline")
        key = dataset_or_collection_id
        entry = meta.get(key) or meta.get(key.lower())
        if entry is None:
            # maybe a CMEMS product_id → group its datasets
            low = key.lower()
            members = {k: v for k, v in meta.items()
                       if (v.get("product_id") or "").lower() == low}
            if members:
                first = next(iter(members.values()))
                return {"ok": True, "matched_by": "product_id",
                        "product_id": first.get("product_id"),
                        "title": first.get("title"), "doi": first.get("doi"),
                        "store": first.get("store"),
                        "n_datasets": len(members),
                        "dataset_ids": sorted(members),
                        "next_step": "call dataset_metadata with one dataset_id"}
            close = [k for k in meta if low in k.lower()][:10]
            return _err(f"unknown id: {key}",
                        similar_ids=close,
                        hint="use ids from search_datasets / list_dataset_documents")
        out = dict(entry)
        out["dataset_id"] = key if key in meta else key.lower()
        for field, cap in (("variables", 120), ("references", 30),
                           ("documentation_links", 40), ("keywords", 40)):
            v = out.get(field)
            if isinstance(v, list) and len(v) > cap:
                out[field] = v[:cap]
                out[f"{field}_truncated"] = f"{len(v) - cap} more omitted"
        return {"ok": True, "matched_by": "dataset_id", **out}
    except Exception as e:
        _log(f"dataset_metadata failed: {repr(e)}")
        return _err(f"lookup failed: {repr(e)[:200]}")


@lru_cache(maxsize=1)
def _doc_index() -> dict:
    """doc_id -> absolute md path, from the catalog."""
    by_pid, _ = _catalog()
    idx = {}
    for prod in by_pid.values():
        for d in prod.get("docs", []):
            if d.get("has_md") and d.get("md_path"):
                idx[d["doc_id"]] = ROOT.parent / d["md_path"]
    return idx


@mcp.tool()
def read_document(doc_id: str, offset: int = 0, max_chars: int = READ_DEFAULT) -> dict:
    """Pull the full markdown text of one EQC document (PUM/QUID/SQO), paginated.
    Get doc_id from list_dataset_documents or from get_dataset_docs results.
    The first page includes an outline (headings + char offsets) so you can jump
    straight to a section with the offset argument.

    Args:
        doc_id: e.g. "CMEMS-MED-QUID-006-013".
        offset: character offset to start from (default 0).
        max_chars: page size (default 20000, max 60000).
    """
    try:
        path = _doc_index().get(doc_id)
        if path is None:
            return _err(f"unknown doc_id: {doc_id}",
                        hint="use list_dataset_documents to get valid doc_ids")
        if not path.exists():
            return _err(f"document file missing on disk: {path.name}")
        text = path.read_text(encoding="utf-8", errors="replace")
        offset = max(0, int(offset))
        max_chars = max(1000, min(int(max_chars), 60_000))
        page = text[offset:offset + max_chars]
        out = {"ok": True, "doc_id": doc_id, "total_chars": len(text),
               "offset": offset, "returned_chars": len(page),
               "next_offset": offset + len(page) if offset + len(page) < len(text) else None,
               "text": page}
        if offset == 0:
            outline, pos = [], 0
            for line in text.splitlines(keepends=True):
                if line.startswith("#"):
                    outline.append({"heading": line.strip()[:120], "offset": pos})
                pos += len(line)
            out["outline"] = outline[:60]
        return out
    except Exception as e:
        _log(f"read_document failed: {repr(e)}")
        return _err(f"read failed: {repr(e)[:200]}")


@lru_cache(maxsize=1)
def _registry() -> list[dict]:
    # cached for process lifetime: restart server to pick up registry updates
    if not REGISTRY.exists():
        return []
    return [json.loads(l) for l in REGISTRY.read_text().splitlines() if l.strip()]


@lru_cache(maxsize=1)
def _links_by_dataset() -> dict:
    # dataset_id -> [paper records] materialized by pubs_rag/build_links_sidecar.py
    # (registry direct + flagship citations, same logic as relink_full.py)
    if not LINKS_SIDECAR.exists():
        return {}
    return json.loads(LINKS_SIDECAR.read_text(encoding="utf-8"))


@lru_cache(maxsize=1)
def _papers_by_id() -> dict:
    """Orphan-corpus parsed papers: paper_id and doi -> record with md_path.

    Cached for process lifetime (like _registry): restart to pick up new papers.
    """
    idx = {}
    if PAPERS.exists():
        for line in PAPERS.read_text().splitlines():
            if not line.strip():
                continue
            p = json.loads(line)
            idx[p["paper_id"]] = p
            if p.get("doi"):
                idx[p["doi"].lower()] = p
    return idx


@mcp.tool()
def search_publications(query: str, domain: str | None = None,
                        dataset_or_product_id: str | None = None,
                        orphan_only: bool = False, top_k: int = 8,
                        rerank: bool = True) -> dict:
    """Level-3 METHODOLOGY search: semantic search over the scientific
    publications RAG (parsed full-text paper chunks). Use it to learn HOW to
    analyze data: methods, validation approaches, known analysis pitfalls.

    Args:
        query: natural-language question (e.g. "how to compute ocean heat
            content trends from reanalysis").
        domain: optional filter — one of ocean/marine, atmosphere, cryosphere,
            land, climate-modeling, climate-general, emergency.
        dataset_or_product_id: only papers LINKED to this Copernicus
            product/collection (cited in its documentation).
        orphan_only: only the general (non-dataset-linked) methodology corpus.
        top_k: number of chunks to return (default 8).
        rerank: also rerank with Google semantic-ranker (needs GCP ADC).
    """
    try:
        client = _pubs_qdrant()
        if client is None:
            return _err("publications index not built yet", status=_pubs_status())
        if domain and domain not in PUB_DOMAINS:
            return _err(f"unknown domain '{domain}'", valid=list(PUB_DOMAINS))
        top_k = max(1, min(int(top_k), 20))
        must = []
        if domain:
            must.append(models.FieldCondition(key="domains", match=models.MatchValue(value=domain)))
        if orphan_only:
            must.append(models.FieldCondition(key="orphan", match=models.MatchValue(value=True)))
        if dataset_or_product_id:
            pid = resolve_product(dataset_or_product_id) or dataset_or_product_id
            must.append(models.FieldCondition(key="linked_products", match=models.MatchValue(value=pid)))
        flt = models.Filter(must=must) if must else None
        points, mode = _query(PUBS_COLLECTION, query, flt, max(top_k, 20), client=client)
        points, reranked = _maybe_rerank(query, points, top_k, rerank)
        results = [{
            "doi": p.payload.get("doi"),
            "title": p.payload.get("title"),
            "journal": p.payload.get("journal"),
            "year": p.payload.get("year"),
            "domains": p.payload.get("domains"),
            "section": p.payload.get("section"),
            "orphan": p.payload.get("orphan"),
            "linked_products": (p.payload.get("linked_products") or [])[:8],
            "text": (p.payload.get("text_raw") or "")[:MAX_TEXT],
            "score": getattr(p, "score", None),
        } for p in points[:top_k]]
        return {"ok": True, "query": query, "retrieval": mode, "reranked": reranked,
                "n_results": len(results), "results": results,
                "next_step": "read_publication(doi) pulls a paper's full parsed text"}
    except Exception as e:
        _log(f"search_publications failed: {repr(e)}")
        return _err(f"search failed: {repr(e)[:200]}")


@mcp.tool()
def get_dataset_publications(dataset_or_product_id: str, top_k: int = 15) -> dict:
    """List the scientific publications LINKED to one Copernicus dataset —
    i.e. papers cited in its quality documentation (CMEMS PUM/QUID/SQO) or on
    its CDS/ADS/EWDS references section. This is the dataset's literature:
    validation papers, method papers, foundational references.

    Args:
        dataset_or_product_id: CMEMS product/dataset id or CDS/ADS/EWDS
            collection id.
        top_k: max publications to return (default 15), most-cited first.
    """
    try:
        pid = resolve_product(dataset_or_product_id) or dataset_or_product_id
        low = {pid.lower(), dataset_or_product_id.lower()}
        parsed = _papers_by_id()

        # primary: materialized links sidecar (registry direct + flagship citers)
        seen: set[str] = set()
        merged: list[dict] = []
        by_ds = _links_by_dataset()
        for ds, recs in by_ds.items():
            if ds.lower() not in low:
                continue
            for r in recs:
                doi = (r.get("doi") or "").lower()
                if doi in seen:
                    continue
                seen.add(doi)
                merged.append({
                    "doi": r.get("doi"), "title": r.get("title"),
                    "journal": r.get("journal"), "year": r.get("year"),
                    "citations_count": r.get("cited_by_count"),
                    "link_via": r.get("via"),
                    "flagship_labels": r.get("flagship_labels") or None,
                    "full_text_available": doi in parsed,
                })

        # secondary: registry papers not in the parsed corpus (metadata-only)
        for r in _registry():
            doi = (r.get("doi") or "").lower()
            if doi in seen:
                continue
            if not any((p or "").lower() in low for p in r.get("linked_products", [])):
                continue
            seen.add(doi)
            merged.append({
                "doi": r["doi"], "title": r.get("title"),
                "journal": r.get("journal"), "year": r.get("year"),
                "authors": (r.get("authors") or [])[:6],
                "n_mentions": r.get("n_mentions"),
                "citations_count": r.get("citations_count"),
                "pdf_status": r.get("pdf_status"),
                "link_via": ["registry"],
                "full_text_available": doi in parsed,
            })

        merged.sort(key=lambda r: (-int(bool(r.get("full_text_available"))),
                                   -(r.get("citations_count") or 0)))
        results = merged[:max(1, min(int(top_k), 50))]
        return {"ok": True, "id": pid, "n_linked_publications": len(merged),
                "results": results,
                "next_step": ("read_publication(doi) for full text where "
                              "full_text_available; otherwise metadata only for now")}
    except Exception as e:
        _log(f"get_dataset_publications failed: {repr(e)}")
        return _err(f"lookup failed: {repr(e)[:200]}")


@mcp.tool()
def read_publication(doi_or_paper_id: str, offset: int = 0,
                     max_chars: int = READ_DEFAULT) -> dict:
    """Pull the full parsed markdown text of one publication, paginated
    (same contract as read_document: page 0 includes a heading outline).
    Works for papers in the parsed corpus; for registry papers whose PDF is
    not parsed yet it returns their metadata + abstract instead.

    Args:
        doi_or_paper_id: canonical DOI ("10.x/...") or underscored paper_id.
        offset: character offset (default 0).
        max_chars: page size (default 20000, max 60000).
    """
    try:
        key = doi_or_paper_id.strip()
        paper = _papers_by_id().get(key) or _papers_by_id().get(key.lower())
        if paper and paper.get("md_path") and Path(paper["md_path"]).exists():
            text = Path(paper["md_path"]).read_text(encoding="utf-8", errors="replace")
            offset = max(0, int(offset))
            max_chars = max(1000, min(int(max_chars), 60_000))
            page = text[offset:offset + max_chars]
            out = {"ok": True, "doi": paper.get("doi"), "title": paper.get("title"),
                   "journal": paper.get("journal"), "year": paper.get("year"),
                   "total_chars": len(text), "offset": offset,
                   "returned_chars": len(page),
                   "next_offset": offset + len(page) if offset + len(page) < len(text) else None,
                   "text": page}
            if offset == 0:
                outline, pos = [], 0
                for line in text.splitlines(keepends=True):
                    if line.startswith("#"):
                        outline.append({"heading": line.strip()[:120], "offset": pos})
                    pos += len(line)
                out["outline"] = outline[:60]
            return out
        # not parsed — fall back to registry metadata
        low = key.lower()
        rec = next((r for r in _registry() if r["doi"].lower() == low), None)
        if rec:
            return {"ok": True, "full_text": False,
                    "reason": f"not parsed yet (pdf_status: {rec.get('pdf_status')})",
                    "doi": rec["doi"], "title": rec.get("title"),
                    "journal": rec.get("journal"), "year": rec.get("year"),
                    "authors": rec.get("authors"), "abstract": rec.get("abstract"),
                    "linked_products": (rec.get("linked_products") or [])[:15]}
        return _err(f"unknown publication: {key}",
                    hint="use a DOI from search_publications / get_dataset_publications")
    except Exception as e:
        _log(f"read_publication failed: {repr(e)}")
        return _err(f"read failed: {repr(e)[:200]}")


@mcp.tool()
def get_eqc_quality_report(query: str, dataset_id: str | None = None,
                           aspect: str | None = None, top_k: int = 8,
                           rerank: bool = True) -> dict:
    """CDS/C3S EQC Quality Assessment reports — the curated fitness-for-purpose
    assessments (consistency, completeness, etc.) for ~27 climate datasets that
    carry the "Quality Assurance" badge in the CDS catalogue. Use this to judge
    whether a CDS/ADS/EWDS dataset is suitable for a use case, to compare
    alternative datasets on quality criteria, or to surface known limitations.

    Complements get_dataset_docs (which serves CMEMS Marine PUM/QUID/SQO):
    this tool serves the CDS-side quality knowledge.

    Args:
        query: natural-language question (e.g. "is the C3S atlas temperature
            consistent across origins", "completeness of satellite soil moisture").
        dataset_id: optional filter — a CDS collection id (e.g.
            "multi-origin-c3s-atlas", "satellite-sea-surface-temperature").
        aspect: optional filter — quality aspect prefix (e.g. "consistency",
            "completeness").
        top_k: number of report chunks to return (default 8).
        rerank: also rerank with Google semantic-ranker (needs GCP ADC).
    """
    try:
        client = _eqc_qdrant()
        if client is None:
            return _err("EQC-QA index not built yet",
                        status="CDS quality-assessment reports are being embedded "
                               "and indexed — retry shortly")
        top_k = max(1, min(int(top_k), 20))
        must = []
        if dataset_id:
            must.append(models.FieldCondition(key="dataset_id",
                                              match=models.MatchValue(value=dataset_id)))
        if aspect:
            must.append(models.FieldCondition(key="aspect_base",
                                              match=models.MatchValue(value=aspect.lower())))
        flt = models.Filter(must=must) if must else None
        points, mode = _query(EQC_QA_COLLECTION, query, flt, max(top_k, 20), client=client)
        points, reranked = _maybe_rerank(query, points, top_k, rerank)
        results = [{
            "dataset_id": p.payload.get("dataset_id"),
            "report_id": p.payload.get("report_id"),
            "aspect": p.payload.get("aspect"),
            "title": p.payload.get("title"),
            "section": p.payload.get("section"),
            "text": (p.payload.get("text_raw") or "")[:MAX_TEXT],
            "code_notebooks": _nb_refs(p.payload.get("dataset_id")),
            "score": getattr(p, "score", None),
        } for p in points[:top_k]]
        return {"ok": True, "query": query, "retrieval": mode, "reranked": reranked,
                "n_results": len(results), "results": results,
                "source": "c3s2-eqc-quality-assessment (CDS EQC QA reports)",
                "next_step": ("where a result has code_notebooks[], call "
                              "get_dataset_code(dataset_id, notebook_id=...) for the runnable code")}
    except Exception as e:
        _log(f"get_eqc_quality_report failed: {repr(e)}")
        return _err(f"lookup failed: {repr(e)[:200]}")


@mcp.tool()
def get_dataset_code(dataset_id: str, notebook_id: str | None = None,
                     kind: str | None = None, offset: int = 0,
                     max_chars: int = READ_DEFAULT) -> dict:
    """Runnable CODE examples (Jupyter notebook cells) ATTACHED to a Copernicus
    dataset: how to DOWNLOAD and ANALYZE it. Code is not embedded/searched on its
    own — it rides along on the dataset, sourced from official example notebooks
    (e.g. the C3S EQC quality-assessment notebooks). Reach it from a
    search_datasets / get_eqc_quality_report hit whose notebooks[] is non-empty.

    Two modes:
      • dataset_id only  -> LIST the notebooks attached to that dataset (id, title,
        recipe kinds download/analyze/plot, size, source repo + licence).
      • + notebook_id    -> the FULL reconstructed notebook (verbatim ```python
        cells + markdown + text outputs), paginated like read_document.

    Args:
        dataset_id: a CDS/ADS/EWDS collection id or CMEMS product/dataset id
            (e.g. "satellite-sea-surface-temperature", "projections-cmip6").
        notebook_id: pull one notebook's full code (from the list mode).
        kind: optional filter for list mode — download, analyze or plot.
        offset: character offset for the full-notebook mode (default 0).
        max_chars: page size for the full-notebook mode (default 20000, max 60000).
    """
    try:
        by_ds, by_id, generic = _notebooks()
        if not by_ds and not generic:
            return _err("notebook code layer not built yet",
                        status="example notebooks are being extracted and attached")
        if notebook_id:
            rec = by_id.get(notebook_id)
            if not rec:
                return _err(f"unknown notebook_id: {notebook_id}",
                            hint="call get_dataset_code(dataset_id) to list attached notebooks")
            path = ROOT.parent / rec["md_path"]
            if not path.exists():
                return _err(f"notebook file missing on disk: {path.name}")
            text = path.read_text(encoding="utf-8", errors="replace")
            offset = max(0, int(offset))
            max_chars = max(1000, min(int(max_chars), 60_000))
            page = text[offset:offset + max_chars]
            return {"ok": True, "notebook_id": notebook_id, "title": rec.get("title"),
                    "dataset_id": rec.get("matched_dataset_id"), "store": rec.get("store"),
                    "recipe_kinds": rec.get("recipe_kinds"),
                    "source_repo": rec.get("source_repo"), "license": rec.get("license"),
                    "src_path": rec.get("src_path"),
                    "total_chars": len(text), "offset": offset,
                    "returned_chars": len(page),
                    "next_offset": offset + len(page) if offset + len(page) < len(text) else None,
                    "text": page}
        # list mode — dataset-specific notebooks + a store-level generic how-to fallback
        recs = by_ds.get(dataset_id) or by_ds.get(dataset_id.lower())
        if not recs:
            pid = resolve_product(dataset_id)
            if pid:
                recs = by_ds.get(pid)
        recs = recs or []
        store = next((r.get("store") for r in recs if r.get("store")), None)
        if not store:
            store = "CMEMS" if resolve_product(dataset_id) else None

        def _brief(r, scope):
            return {"notebook_id": r["notebook_id"], "title": r.get("title"),
                    "scope": scope, "recipe_kinds": r.get("recipe_kinds"),
                    "n_code_cells": r.get("n_code_cells"),
                    "n_code_lines": r.get("n_code_lines"), "aspect": r.get("aspect"),
                    "source_repo": r.get("source_repo"), "license": r.get("license")}

        notebooks = [_brief(r, "dataset") for r in recs
                     if not kind or kind in (r.get("recipe_kinds") or [])]
        generic_how_to = [_brief(r, "generic") for r in (generic.get(store) or [])
                          if not kind or kind in (r.get("recipe_kinds") or [])]
        if not notebooks and not generic_how_to:
            return _err(f"no notebooks attached to '{dataset_id}'",
                        hint="notebooks cover CDS/ADS/EWDS + CMEMS example datasets",
                        example_ids=sorted(by_ds)[:12])
        return {"ok": True, "dataset_id": dataset_id, "store": store,
                "n_notebooks": len(notebooks), "notebooks": notebooks,
                "generic_how_to": generic_how_to,
                "next_step": ("call get_dataset_code(dataset_id, notebook_id=...) "
                              "for one notebook's full runnable code")}
    except Exception as e:
        _log(f"get_dataset_code failed: {repr(e)}")
        return _err(f"lookup failed: {repr(e)[:200]}")


@mcp.tool()
def search_deep_docs(query: str, store: str | None = None, top_k: int = 8,
                     rerank: bool = True) -> dict:
    """Global semantic search across the DEEP documentation of the non-marine
    stores — CDS (climate/ERA5), ADS (atmosphere/CAMS), EWDS (emergency/flood/
    fire): Confluence user guides, ATBDs, product specs and PDFs (~23k chunks
    over 165 datasets). The non-marine counterpart to search_docs (which covers
    CMEMS PUM/QUID/SQO). Use for cross-dataset climate/atmosphere/emergency
    questions ("ERA5-Land soil moisture accuracy", "CAMS aerosol assimilation").

    Args:
        query: natural-language question.
        store: optional filter — CDS, ADS or EWDS.
        top_k: number of chunks to return (default 8).
        rerank: also rerank with Google semantic-ranker (needs GCP ADC).
    """
    try:
        client = _deep_qdrant()
        if client is None:
            return _err("deep-docs index not built yet",
                        status="CDS/ADS/EWDS documentation is being fetched, chunked "
                               "and embedded — retry shortly")
        if store:
            store = store.upper()
            if store not in ("CDS", "ADS", "EWDS"):
                return _err(f"unknown store '{store}'", valid=["CDS", "ADS", "EWDS"])
        top_k = max(1, min(int(top_k), 20))
        flt = models.Filter(must=[models.FieldCondition(
            key="store", match=models.MatchValue(value=store))]) if store else None
        points, mode = _query(DEEP_COLLECTION, query, flt, max(top_k, 20), client=client)
        points, reranked = _maybe_rerank(query, points, top_k, rerank)
        results = [{
            "store": p.payload.get("store"),
            "dataset_ids": (p.payload.get("dataset_ids") or [])[:6],
            "doc_title": p.payload.get("doc_title"),
            "doc_url": p.payload.get("doc_url"),
            "section": p.payload.get("section"),
            "text": (p.payload.get("text_raw") or "")[:MAX_TEXT],
            "score": getattr(p, "score", None),
        } for p in points[:top_k]]
        return {"ok": True, "query": query, "store": store or "CDS/ADS/EWDS",
                "retrieval": mode, "reranked": reranked,
                "n_results": len(results), "results": results}
    except Exception as e:
        _log(f"search_deep_docs failed: {repr(e)}")
        return _err(f"search failed: {repr(e)[:200]}")


if __name__ == "__main__":
    _log("starting copernicus-rag MCP server (stdio)")
    mcp.run()