DocsGPT/application/scripts/reembed.py

"""Re-embed an existing index with the currently configured embedding model.

Changing ``EMBEDDINGS_NAME`` does not change vectors already stored. Because
several models share a width -- granite-311m and all-mpnet-base-v2 are both
768-dimensional -- a swapped model does not fail any dimension check. It simply
retrieves against vectors that mean something else, which shows up as bad
answers rather than as an error.

This script rebuilds the vectors from the chunk text already held in the store,
so it never re-downloads, re-parses or re-chunks anything: no source files, no
crawl, no docling. It works against pgvector and FAISS. With ``GRAPHRAG_ENABLED``
it also rewrites ``graph_nodes.name_embedding``, which seeds graph traversal and
would otherwise be left behind in the previous model's space.

Usage::

    python -m application.scripts.reembed --dry-run     # report, change nothing
    python -m application.scripts.reembed               # re-embed everything
    python -m application.scripts.reembed --sources a,b # only these sources
"""

from __future__ import annotations

import argparse
import logging
import sys
import time
from dataclasses import dataclass
from typing import Any, Dict, Iterable, List, Optional, Sequence, Tuple

from psycopg import sql

from application.core.settings import settings
from application.vectorstore.model_registry import resolve
from application.vectorstore.vector_creator import VectorCreator

logger = logging.getLogger("reembed")

#: Stores this script knows how to rewrite in place.
SUPPORTED_STORES = ("pgvector", "faiss")

#: Chunks embedded (and, for pgvector, written) per transaction.
DEFAULT_BATCH_SIZE = 64


@dataclass
class _RebuildDoc:
    """Minimal document shape ``FaissStore(docs_init=...)`` accepts."""

    page_content: str
    metadata: Dict[str, Any]


class ReembedError(RuntimeError):
    """Raised for a misconfiguration the user needs to fix before running."""


def _log_setup(verbose: bool) -> None:
    logging.basicConfig(
        level=logging.DEBUG if verbose else logging.INFO,
        format="%(asctime)s %(levelname)s %(message)s",
    )


def _batched(items: Sequence[Any], size: int) -> Iterable[Sequence[Any]]:
    for start in range(0, len(items), size):
        yield items[start : start + size]


def list_source_ids(store_type: str) -> List[str]:
    """Every source id that has vectors in the configured store.

    Args:
        store_type: ``"pgvector"`` or ``"faiss"``.

    Returns:
        Source ids, sorted for a stable and resumable ordering.
    """
    if store_type == "pgvector":
        return _pgvector_source_ids()
    return _faiss_source_ids()


def _pgvector_source_ids() -> List[str]:
    store = VectorCreator.create_vectorstore("pgvector", source_id="")
    # ``_get_connection`` hands back a pooled connection, not a context
    # manager: closing it via ``with`` would cost the pool a slot.
    conn = store._get_connection()
    cursor = conn.cursor()
    try:
        # Table and column names cannot be bound as parameters, so they go
        # through ``sql.Identifier``, which quotes them. They are internal
        # constants rather than user input, but composing SQL by f-string is
        # the habit worth not having.
        cursor.execute(
            sql.SQL(
                "SELECT DISTINCT source_id FROM {table} "
                "WHERE source_id IS NOT NULL ORDER BY source_id"
            ).format(table=sql.Identifier(store._table_name))
        )
        return [row[0] for row in cursor.fetchall()]
    finally:
        cursor.close()
        store.close()


def _faiss_source_ids() -> List[str]:
    """Directories under the FAISS root that hold an index."""
    from application.storage.storage_creator import StorageCreator

    storage = StorageCreator.get_storage()
    root = "indexes"
    ids: List[str] = []
    try:
        for path in storage.list_files(root):
            # ``indexes/<source_id>/index.faiss``
            parts = str(path).split("/")
            if parts and parts[-1].endswith(".faiss") and len(parts) >= 2:
                ids.append(parts[-2])
    except Exception as exc:  # noqa: BLE001 -- surfaced to the user below
        raise ReembedError(
            f"Could not list FAISS indexes under {root!r}: {exc}"
        ) from exc
    return sorted(set(ids))


def _graph_nodes_exist(conn) -> bool:
    """True when the GraphRAG node table is present in this database."""
    cursor = conn.cursor()
    try:
        cursor.execute("SELECT to_regclass('public.graph_nodes')")
        row = cursor.fetchone()
        return bool(row and row[0])
    finally:
        cursor.close()


def reembed_graph_nodes(store, conn, source_id: str, batch_size: int, dry_run: bool) -> int:
    """Rewrite one source's GraphRAG node name vectors.

    ``graph_nodes.name_embedding`` is what every graph traversal starts from:
    the retriever embeds the query and takes the nearest node names as seeds.
    It is written once at extraction time and never revisited, so re-embedding
    only the chunk table leaves the graph seeding against the previous model.
    Nothing errors -- mpnet and granite-311m are both 768-dimensional, so the
    column accepts the mismatch -- the graph just walks from the wrong nodes.

    The embedded text is ``graph_nodes.name``, which is already stored, so this
    needs no LLM re-extraction.

    Args:
        store: The pgvector store, for its embeddings client.
        conn: Open connection to the same database.
        source_id: Source whose nodes to re-embed.
        batch_size: Names per embed call and per transaction.
        dry_run: When true, count the work and change nothing.

    Returns:
        Number of node rows seen (dry run) or rewritten.
    """
    if not _graph_nodes_exist(conn):
        return 0

    cursor = conn.cursor()
    try:
        cursor.execute(
            "SELECT id, name FROM graph_nodes "
            "WHERE source_id = %s AND name_embedding IS NOT NULL ORDER BY id",
            (source_id,),
        )
        rows = cursor.fetchall()
    finally:
        cursor.close()

    if dry_run or not rows:
        return len(rows)

    written = 0
    for batch in _batched(rows, batch_size):
        vectors = store._embedding.embed_documents([row[1] or "" for row in batch])
        cursor = conn.cursor()
        try:
            cursor.executemany(
                "UPDATE graph_nodes SET name_embedding = %s::vector WHERE id = %s",
                [
                    (str(list(vector)), row[0])
                    for vector, row in zip(vectors, batch)
                ],
            )
            conn.commit()
        except Exception:
            conn.rollback()
            raise
        finally:
            cursor.close()
        written += len(batch)
    return written


def reembed_pgvector(source_id: str, batch_size: int, dry_run: bool) -> Tuple[int, int]:
    """Rewrite one source's vectors in place.

    Rows are updated, never deleted and re-inserted, so an interrupted run
    leaves every chunk present and simply re-does its batch next time.

    Args:
        source_id: Source whose chunks to re-embed.
        batch_size: Chunks per embed call and per transaction.
        dry_run: When true, count the work and change nothing.

    Returns:
        ``(chunks_seen, chunks_written)``.
    """
    store = VectorCreator.create_vectorstore("pgvector", source_id=source_id)
    table, vector_column = store._table_name, store._vector_column
    conn = store._get_connection()

    cursor = conn.cursor()
    try:
        cursor.execute(
            sql.SQL("SELECT id, text FROM {table} WHERE source_id = %s ORDER BY id").format(
                table=sql.Identifier(table)
            ),
            (source_id,),
        )
        rows = cursor.fetchall()
    finally:
        cursor.close()

    written = 0
    try:
        if not dry_run:
            for batch in _batched(rows, batch_size):
                vectors = store._embedding.embed_documents([row[1] or "" for row in batch])
                cursor = conn.cursor()
                try:
                    cursor.executemany(
                        sql.SQL(
                            "UPDATE {table} SET {column} = %s::vector WHERE id = %s"
                        ).format(
                            table=sql.Identifier(table),
                            column=sql.Identifier(vector_column),
                        ),
                        [
                            (str(list(vector)), row[0])
                            for vector, row in zip(vectors, batch)
                        ],
                    )
                    conn.commit()
                except Exception:
                    conn.rollback()
                    raise
                finally:
                    cursor.close()
                written += len(batch)

        # The graph seeds every traversal from its own vectors, so leaving them
        # in the old model's space is the same silent mismatch this script
        # exists to remove -- and at equal widths nothing would report it.
        if getattr(settings, "GRAPHRAG_ENABLED", False):
            nodes = reembed_graph_nodes(store, conn, source_id, batch_size, dry_run)
            if nodes:
                logger.info(
                    "  %s: %d graph node name(s)%s",
                    source_id,
                    nodes,
                    "" if dry_run else " re-embedded",
                )
    finally:
        store.close()
    return len(rows), written


def reembed_faiss(source_id: str, batch_size: int, dry_run: bool) -> Tuple[int, int]:
    """Rebuild one FAISS index from the chunk text in its sidecar.

    A FAISS index is a flat array, so this rebuilds rather than updates. Every
    new vector is computed *before* the old index is touched, so an interrupt
    during embedding leaves the existing index intact.

    Args:
        source_id: Source whose index to rebuild.
        batch_size: Chunks per embed call.
        dry_run: When true, count the work and change nothing.

    Returns:
        ``(chunks_seen, chunks_written)``.
    """
    # A width change is the main reason to run this, and it is exactly what
    # ``assert_embedding_dimensions`` refuses to open. The chunk text lives in
    # the sidecar rather than the index, so reading it needs no matching width,
    # and the index this reads is replaced below.
    store = VectorCreator.create_vectorstore(
        "faiss",
        source_id=source_id,
        embeddings_key=settings.EMBEDDINGS_KEY,
        skip_dimension_check=True,
    )
    chunks: List[Dict[str, Any]] = store.get_chunks() or []
    if dry_run or not chunks:
        return len(chunks), 0

    docs = [
        _RebuildDoc(chunk.get("text") or "", chunk.get("metadata") or {})
        for chunk in chunks
    ]

    # Constructing with ``docs_init`` embeds everything into a fresh in-memory
    # index and touches nothing on disk. The existing index is only replaced by
    # ``save_local`` below, so a failure while embedding leaves it intact.
    # Keep the existing ids: GraphRAG's ``graph_node_chunks`` rows and any id a
    # client already holds point at them.
    ids = [chunk.get("doc_id") for chunk in chunks]
    rebuilt = VectorCreator.create_vectorstore(
        "faiss",
        source_id=source_id,
        embeddings_key=settings.EMBEDDINGS_KEY,
        docs_init=docs,
        ids=ids if all(ids) else None,
        batch_size=batch_size,
    )
    rebuilt.save_local()
    return len(chunks), len(docs)


def record_source_model(source_id: str) -> None:
    """Stamp ``sources.model`` with the model these vectors were just built by.

    ``sources`` lives in the user-data database while the vectors may not, so
    this takes its own session. Left unwritten, the column keeps naming the old
    model and every consumer that trusts it -- the boot mismatch check above
    all -- reports a source as stale immediately after it was migrated.
    """
    from sqlalchemy import text

    from application.storage.db.session import db_session

    try:
        with db_session() as conn:
            conn.execute(
                text("UPDATE sources SET model = :model WHERE id = :id"),
                {"model": settings.EMBEDDINGS_NAME, "id": source_id},
            )
    except Exception as exc:  # noqa: BLE001 — the vectors are already rewritten
        logger.warning(
            "  %s: re-embedded, but could not update sources.model (%s). Retrieval "
            "is correct; the mismatch warning may persist until it is.",
            source_id,
            exc,
        )


def run(
    store_type: str,
    source_ids: Optional[Sequence[str]],
    batch_size: int,
    dry_run: bool,
) -> int:
    """Re-embed the requested sources. Returns a process exit code."""
    model = settings.EMBEDDINGS_NAME
    spec = resolve(model)
    logger.info(
        "Re-embedding %s with %s (%s)",
        store_type,
        model,
        f"{spec.dimension} dims" if spec else "width determined at runtime",
    )
    if dry_run:
        logger.info("Dry run: nothing will be written.")

    ids = list(source_ids) if source_ids else list_source_ids(store_type)
    if not ids:
        logger.warning("No sources found; nothing to do.")
        return 0
    logger.info("%d source(s) to process", len(ids))

    handler = reembed_pgvector if store_type == "pgvector" else reembed_faiss
    total_seen = total_written = 0
    failures: List[str] = []
    started = time.monotonic()

    for position, source_id in enumerate(ids, start=1):
        try:
            seen, written = handler(source_id, batch_size, dry_run)
            if written and not dry_run:
                record_source_model(source_id)
            total_seen += seen
            total_written += written
            logger.info(
                "[%d/%d] %s: %d chunk(s)%s",
                position,
                len(ids),
                source_id,
                seen,
                "" if dry_run else f", {written} re-embedded",
            )
        except Exception as exc:  # noqa: BLE001 -- one bad source must not stop the run
            failures.append(source_id)
            logger.error("[%d/%d] %s FAILED: %s", position, len(ids), source_id, exc)

    elapsed = time.monotonic() - started
    logger.info(
        "Done in %.1fs: %d chunk(s) seen, %d re-embedded, %d source(s) failed",
        elapsed,
        total_seen,
        total_written,
        len(failures),
    )
    if failures:
        logger.error("Failed sources: %s", ", ".join(failures))
        logger.error("Re-run with --sources %s to retry just those.", ",".join(failures))
        return 1
    if dry_run:
        logger.info("Re-run without --dry-run to apply.")
    return 0


def build_parser() -> argparse.ArgumentParser:
    parser = argparse.ArgumentParser(
        prog="python -m application.scripts.reembed",
        description=__doc__.split("\n\n")[0],
    )
    parser.add_argument(
        "--dry-run", action="store_true", help="report what would change, write nothing"
    )
    parser.add_argument(
        "--sources", help="comma-separated source ids; default is every source"
    )
    parser.add_argument(
        "--batch-size",
        type=int,
        default=DEFAULT_BATCH_SIZE,
        help=f"chunks per embed call (default {DEFAULT_BATCH_SIZE})",
    )
    parser.add_argument("-v", "--verbose", action="store_true", help="debug logging")
    return parser


def main(argv: Optional[Sequence[str]] = None) -> int:
    args = build_parser().parse_args(argv)
    _log_setup(args.verbose)

    # Which model this installation uses may live in ``app_metadata`` rather
    # than the environment -- ``application.app`` resolves it at boot, and this
    # script never imports that. Without this, an install pinned to granite
    # with no EMBEDDINGS_NAME set (every stock Kubernetes deployment: the
    # manifests carry no embedding config at all) would re-embed its whole
    # index with the *legacy* code default and stamp ``sources.model`` to
    # match -- the silent cross-model index this script exists to repair.
    from application.storage.db.embeddings_pin import resolve_embeddings_pin

    resolve_embeddings_pin(logger)

    # Embed in this process. ``EMBEDDINGS_DELEGATE_TO_WORKER`` exists to keep a
    # model out of the API, which serves one query at a time and holds the
    # model for nothing in between. This is the opposite case: a batch job that
    # embeds every chunk in the index, where a broker round trip per batch adds
    # latency and a dependency on a worker running. Loading the model here also
    # means the script reports a real failure for a model it cannot load,
    # instead of timing out against an empty queue.
    if getattr(settings, "EMBEDDINGS_DELEGATE_TO_WORKER", False):
        logger.info("Embedding in-process; worker delegation does not apply here.")
        settings.EMBEDDINGS_DELEGATE_TO_WORKER = False

    store_type = (settings.VECTOR_STORE or "").lower()
    if store_type not in SUPPORTED_STORES:
        logger.error(
            "VECTOR_STORE is %r; this script supports %s. For other stores, "
            "delete and re-ingest the affected sources.",
            settings.VECTOR_STORE,
            " and ".join(SUPPORTED_STORES),
        )
        return 2

    sources = (
        [s.strip() for s in args.sources.split(",") if s.strip()]
        if args.sources
        else None
    )
    try:
        return run(store_type, sources, max(1, args.batch_size), args.dry_run)
    except ReembedError as exc:
        logger.error("%s", exc)
        return 2


if __name__ == "__main__":
    sys.exit(main())