Rename document_meta identity column document_id to id

CHANGELOG.md

@@ -9,6 +9,7 @@
 ### Fixed
 
 - Concurrent ingestion of the same URI no longer creates duplicate documents; the URI is re-checked under the write lock and a colliding create becomes an update.
+- Document filters can reference `id` (`list_documents`/`count_documents`/`search`/`analyze` `filter=`); the `document_meta` identity column is renamed `document_id` → `id` with a migration.
 
 ## [0.63.2] - 2026-07-03
 

app/backend/pyproject.toml

@@ -8,7 +8,7 @@ dependencies = [
     "uvicorn[standard]>=0.40.0",
     "pydantic-ai-slim[ag-ui,anthropic,openai]>=1.81.0",
     "python-dotenv>=1.2.1",
-    "haiku.rag-slim>=0.63.2",
+    "haiku.rag-slim>=0.64.0",
     "logfire[pydantic-ai]>=3.17.0",
 ]
 

evaluations/pyproject.toml

@@ -2,7 +2,7 @@
 
 name = "haiku.rag-evals"
 description = "Benchmarking and evaluation scripts for haiku.rag"
-version = "0.63.2"
+version = "0.64.0"
 authors = [{ name = "Yiorgis Gozadinos", email = "ggozadinos@gmail.com" }]
 license = { text = "MIT" }
 requires-python = ">=3.12"

haiku_rag_slim/haiku/rag/client/rebuild.py

@@ -520,7 +520,7 @@ async def _flush_rebuild_batch(
         )
         meta_records.append(
             DocumentMetaRecord(
-                document_id=doc.id,
+                id=doc.id,
                 uri=doc.uri,
                 title=doc.title,
                 metadata=json.dumps(doc.metadata),
@@ -535,7 +535,7 @@ async def _flush_rebuild_batch(
         .execute(doc_records)
     )
     await (
-        client.store.document_meta_table.merge_insert("document_id")
+        client.store.document_meta_table.merge_insert("id")
         .when_matched_update_all()
         .when_not_matched_insert_all()
         .execute(meta_records)

haiku_rag_slim/haiku/rag/doctor.py

@@ -454,18 +454,16 @@ async def run_db_checks(
     doc_ids = set(await _column_values(store.documents_table, "id"))
     meta_rows = (
         await store.document_meta_table.query()
-        .select(["document_id", "metadata", "uri", "title"])
+        .select(["id", "metadata", "uri", "title"])
         .to_list()
     )
-    meta_doc_ids = {row["document_id"] for row in meta_rows}
+    meta_doc_ids = {row["id"] for row in meta_rows}
     content_type_by_doc = {
-        row["document_id"]: json.loads(row.get("metadata") or "{}").get(
-            "content_type", ""
-        )
+        row["id"]: json.loads(row.get("metadata") or "{}").get("content_type", "")
         for row in meta_rows
     }
-    uri_by_doc = {row["document_id"]: row.get("uri") for row in meta_rows}
-    title_by_doc = {row["document_id"]: row.get("title") for row in meta_rows}
+    uri_by_doc = {row["id"]: row.get("uri") for row in meta_rows}
+    title_by_doc = {row["id"]: row.get("title") for row in meta_rows}
 
     notify("Reading chunks")
     chunk_rows = (

haiku_rag_slim/haiku/rag/store/engine.py

@@ -87,7 +87,7 @@ class DocumentMetaRecord(LanceModel):
     write-once content/blobs in `documents`. Updating these (metadata, title,
     source_revision) must not rewrite the multi-MB docling row."""
 
-    document_id: str
+    id: str
     uri: str | None = None
     title: str | None = None
     metadata: str = Field(default="{}")
@@ -610,7 +610,7 @@ class Store:
                 "document_meta", schema=DocumentMetaRecord
             )
             await self.document_meta_table.create_index(
-                "document_id", config=BTree(), replace=True
+                "id", config=BTree(), replace=True
             )
             await self.document_meta_table.create_index(
                 "uri", config=BTree(), replace=True

haiku_rag_slim/haiku/rag/store/repositories/chunk.py

@@ -272,13 +272,13 @@ class ChunkRepository:
             # whenever the top-N window lacked `limit` matching chunks.
             docs_df = await (
                 self.store.document_meta_table.query()
-                .select(["document_id"])
+                .select(["id"])
                 .where(filter)
                 .to_pandas()
             )
             if docs_df.empty:
                 return []
-            id_list = ", ".join(f"'{d}'" for d in docs_df["document_id"])
+            id_list = ", ".join(f"'{d}'" for d in docs_df["id"])
             chunk_filter = f"document_id IN ({id_list})"
 
         if query_vector is not None:
@@ -346,8 +346,8 @@ class ChunkRepository:
         # Get document info from the mutable attributes table
         doc_rows = await (
             self.store.document_meta_table.query()
-            .select(["document_id", "uri", "title", "metadata"])
-            .where(f"document_id = '{document_id}'")
+            .select(["id", "uri", "title", "metadata"])
+            .where(f"id = '{document_id}'")
             .limit(1)
             .to_list()
         )
@@ -503,14 +503,14 @@ class ChunkRepository:
         documents_map: dict[str, dict] = {}
         if document_ids:
             id_list = "', '".join(document_ids)
-            where_clause = f"document_id IN ('{id_list}')"
+            where_clause = f"id IN ('{id_list}')"
             doc_rows = await (
                 self.store.document_meta_table.query()
-                .select(["document_id", "uri", "title", "metadata"])
+                .select(["id", "uri", "title", "metadata"])
                 .where(where_clause)
                 .to_list()
             )
-            documents_map = {str(row["document_id"]): row for row in doc_rows}
+            documents_map = {str(row["id"]): row for row in doc_rows}
 
         # Build final results with document info
         chunks_with_scores = []

haiku_rag_slim/haiku/rag/store/repositories/document.py

@@ -94,7 +94,7 @@ class DocumentRepository:
         updated_at: str,
     ) -> DocumentMetaRecord:
         return DocumentMetaRecord(
-            document_id=doc_id,
+            id=doc_id,
             uri=entity.uri,
             title=entity.title,
             metadata=json.dumps(entity.metadata),
@@ -105,9 +105,7 @@ class DocumentRepository:
     async def _meta_by_id(self, doc_id: str) -> DocumentMetaRecord | None:
         safe_id = escape_sql_string(doc_id)
         results = await query_to_pydantic(
-            self.store.document_meta_table.query()
-            .where(f"document_id = '{safe_id}'")
-            .limit(1),
+            self.store.document_meta_table.query().where(f"id = '{safe_id}'").limit(1),
             DocumentMetaRecord,
         )
         return results[0] if results else None
@@ -146,9 +144,7 @@ class DocumentRepository:
                 )
             except Exception:
                 safe_id = escape_sql_string(doc_id)
-                await self.store.document_meta_table.delete(
-                    f"document_id = '{safe_id}'"
-                )
+                await self.store.document_meta_table.delete(f"id = '{safe_id}'")
                 raise
             entity.id = doc_id
             entity.created_at = datetime.fromisoformat(now)
@@ -178,7 +174,7 @@ class DocumentRepository:
             await self.store.documents_table.add(doc_records)
         except Exception:
             ids = ", ".join(f"'{escape_sql_string(d)}'" for d in doc_ids)
-            await self.store.document_meta_table.delete(f"document_id IN ({ids})")
+            await self.store.document_meta_table.delete(f"id IN ({ids})")
             raise
         return documents
 
@@ -271,7 +267,7 @@ class DocumentRepository:
         # from create()/migration; inserting on no-match would manufacture a
         # ghost row (visible to list_all/count) for an id with no documents row.
         await (
-            self.store.document_meta_table.merge_insert("document_id")
+            self.store.document_meta_table.merge_insert("id")
             .when_matched_update_all()
             .execute([record])
         )
@@ -310,7 +306,7 @@ class DocumentRepository:
         # Delete the document row, its mutable attributes
         safe_id = escape_sql_string(entity_id)
         await self.store.documents_table.delete(f"id = '{safe_id}'")
-        await self.store.document_meta_table.delete(f"document_id = '{safe_id}'")
+        await self.store.document_meta_table.delete(f"id = '{safe_id}'")
         return True
 
     async def list_all(
@@ -348,13 +344,13 @@ class DocumentRepository:
 
         if not include_content:
             return [
-                self._merge_to_document(DocumentRecord(id=m.document_id, content=""), m)
+                self._merge_to_document(DocumentRecord(id=m.id, content=""), m)
                 for m in meta_records
             ]
 
         documents: list[Document] = []
         for meta in meta_records:
-            safe_id = escape_sql_string(meta.document_id)
+            safe_id = escape_sql_string(meta.id)
             doc_results = await query_to_pydantic(
                 self.store.documents_table.query().where(f"id = '{safe_id}'").limit(1),
                 DocumentRecord,
@@ -362,7 +358,7 @@ class DocumentRepository:
             doc_record = (
                 doc_results[0]
                 if doc_results
-                else DocumentRecord(id=meta.document_id, content="")
+                else DocumentRecord(id=meta.id, content="")
             )
             documents.append(self._merge_to_document(doc_record, meta))
         return documents
@@ -385,7 +381,7 @@ class DocumentRepository:
             return None
 
         meta = meta_results[0]
-        safe_id = escape_sql_string(meta.document_id)
+        safe_id = escape_sql_string(meta.id)
         doc_results = await query_to_pydantic(
             self.store.documents_table.query().where(f"id = '{safe_id}'").limit(1),
             DocumentRecord,
@@ -433,7 +429,7 @@ class DocumentRepository:
                 "document_meta", schema=DocumentMetaRecord
             )
             await self.store.document_meta_table.create_index(
-                "document_id", config=BTree(), replace=True
+                "id", config=BTree(), replace=True
             )
             await self.store.document_meta_table.create_index(
                 "uri", config=BTree(), replace=True

haiku_rag_slim/haiku/rag/store/upgrades/__init__.py

@@ -96,6 +96,9 @@ from haiku.rag.store.upgrades.v0_50_0 import (
 from haiku.rag.store.upgrades.v0_58_0 import (
     upgrade_split_document_meta as upgrade_0_58_0_split_document_meta,
 )
+from haiku.rag.store.upgrades.v0_64_0 import (
+    upgrade_rename_document_meta_id as upgrade_0_64_0_rename_document_meta_id,
+)
 
 upgrades.append(upgrade_0_20_0_docling)
 upgrades.append(upgrade_0_23_1_contextualize)
@@ -106,3 +109,4 @@ upgrades.append(upgrade_0_45_0_extract_picture_bytes)
 upgrades.append(upgrade_0_48_0_heading_hierarchy)
 upgrades.append(upgrade_0_50_0_canonical_metadata_keys)
 upgrades.append(upgrade_0_58_0_split_document_meta)
+upgrades.append(upgrade_0_64_0_rename_document_meta_id)

haiku_rag_slim/haiku/rag/store/upgrades/v0_58_0.py

@@ -31,10 +31,8 @@ async def _apply_split_document_meta(store: Store) -> None:
 
     # Resume support: skip documents whose meta row already exists.
     existing_meta = {
-        row["document_id"]
-        for row in await store.document_meta_table.query()
-        .select(["document_id"])
-        .to_list()
+        row["id"]
+        for row in await store.document_meta_table.query().select(["id"]).to_list()
     }
 
     rows = await store.documents_table.query().select(["id", *present]).to_list()
@@ -45,7 +43,7 @@ async def _apply_split_document_meta(store: Store) -> None:
         meta = row.get("metadata")
         records.append(
             DocumentMetaRecord(
-                document_id=row["id"],
+                id=row["id"],
                 uri=row.get("uri"),
                 title=row.get("title"),
                 metadata=meta if isinstance(meta, str) and meta else "{}",

haiku_rag_slim/haiku/rag/store/upgrades/v0_64_0.py

@@ -0,0 +1,35 @@
+import logging
+
+from lancedb.index import BTree
+
+from haiku.rag.store.engine import Store
+from haiku.rag.store.upgrades import Upgrade
+
+logger = logging.getLogger(__name__)
+
+
+async def _apply_rename_document_meta_id(store: Store) -> None:
+    """Rename the `document_meta` identity column `document_id` → `id`.
+
+    In `document_meta` the column is the document's own identity (1:1 with the
+    row), so `id` matches the `documents` table and the public `Document.id`.
+    Callers filter/list/count against `document_meta`, so with the old name a
+    filter on `id` raised "No field named id". Idempotent: skips if the column
+    is already `id`.
+    """
+    schema = await store.document_meta_table.schema()
+    if "id" in schema.names:
+        logger.info("document_meta.id already present; nothing to rename")
+        return
+
+    await store.document_meta_table.alter_columns(
+        {"path": "document_id", "rename": "id"}  # ty: ignore[invalid-argument-type]
+    )
+    await store.document_meta_table.create_index("id", config=BTree(), replace=True)
+
+
+upgrade_rename_document_meta_id = Upgrade(
+    version="0.64.0",
+    apply=_apply_rename_document_meta_id,
+    description="Rename the document_meta identity column document_id to id",
+)

haiku_rag_slim/pyproject.toml

@@ -2,7 +2,7 @@
 
 name = "haiku.rag-slim"
 description = "Opinionated agentic RAG powered by LanceDB, Pydantic AI, and Docling - Minimal dependencies"
-version = "0.63.2"
+version = "0.64.0"
 authors = [{ name = "Yiorgis Gozadinos", email = "ggozadinos@gmail.com" }]
 license = { text = "MIT" }
 readme = { file = "README.md", content-type = "text/markdown" }

pyproject.toml

@@ -2,7 +2,7 @@
 
 name = "haiku.rag"
 description = "Opinionated agentic RAG powered by LanceDB, Pydantic AI, and Docling"
-version = "0.63.2"
+version = "0.64.0"
 authors = [{ name = "Yiorgis Gozadinos", email = "ggozadinos@gmail.com" }]
 license = { text = "MIT" }
 readme = { file = "README.md", content-type = "text/markdown" }
@@ -30,7 +30,7 @@ classifiers = [
 ]
 
 dependencies = [
-    "haiku.rag-slim[docling,voyageai,mxbai,cohere,zeroentropy,tui,cross-encoder]==0.63.2",
+    "haiku.rag-slim[docling,voyageai,mxbai,cohere,zeroentropy,tui,cross-encoder]==0.64.0",
 ]
 
 [project.scripts]
@@ -38,9 +38,9 @@ haiku-rag = "haiku.rag.cli:cli"
 
 [project.optional-dependencies]
 tui = ["textual>=8.2.4"]
-s3 = ["haiku.rag-slim[s3]==0.63.2"]
-cross-encoder = ["haiku.rag-slim[cross-encoder]==0.63.2"]
-ingester = ["haiku.rag-slim[ingester]==0.63.2"]
+s3 = ["haiku.rag-slim[s3]==0.64.0"]
+cross-encoder = ["haiku.rag-slim[cross-encoder]==0.64.0"]
+ingester = ["haiku.rag-slim[ingester]==0.64.0"]
 
 [build-system]
 requires = ["hatchling"]

tests/store/test_document_meta_split.py

@@ -156,6 +156,6 @@ async def test_get_by_uri_with_orphan_meta_returns_none(temp_db_path):
     async with Store(temp_db_path, create=True, skip_migration_check=True) as store:
         repo = DocumentRepository(store)
         await store.document_meta_table.add(
-            [DocumentMetaRecord(document_id="ghost", uri="u-ghost", metadata="{}")]
+            [DocumentMetaRecord(id="ghost", uri="u-ghost", metadata="{}")]
         )
         assert await repo.get_by_uri("u-ghost") is None

tests/store/test_v0_58_0_migration.py

@@ -52,7 +52,7 @@ class TestV0_58_0Migration:
             meta_rows = await store.document_meta_table.query().to_list()
             assert len(meta_rows) == 1
             row = meta_rows[0]
-            assert row["document_id"] == "doc-1"
+            assert row["id"] == "doc-1"
             assert row["uri"] == "s3://b/one"
             assert row["title"] == "One"
             assert json.loads(row["metadata"]) == {"source_revision": "r1", "md5": "a"}
@@ -95,7 +95,7 @@ class TestV0_58_0Migration:
 
             meta_rows = await store.document_meta_table.query().to_list()
             assert len(meta_rows) == 1
-            assert meta_rows[0]["document_id"] == "doc-1"
+            assert meta_rows[0]["id"] == "doc-1"
 
 
 @pytest.mark.asyncio
@@ -115,14 +115,14 @@ class TestV0_58_0MigrationEdgeCases:
             )
             # Pretend a prior run already moved doc "a".
             await store.document_meta_table.add(
-                [DocumentMetaRecord(document_id="a", uri="u-a", metadata="{}")]
+                [DocumentMetaRecord(id="a", uri="u-a", metadata="{}")]
             )
             await store.set_haiku_version("0.57.0")
 
         async with Store(temp_db_path, skip_migration_check=True) as store:
             await store.migrate()
             rows = await store.document_meta_table.query().to_list()
-            by_id = {r["document_id"]: r for r in rows}
+            by_id = {r["id"]: r for r in rows}
             assert set(by_id) == {"a", "b"}  # exactly one row each, no duplicates
             assert len(rows) == 2
 

tests/store/test_v0_64_0_migration.py

@@ -0,0 +1,51 @@
+import pytest
+from lancedb.pydantic import LanceModel
+
+from haiku.rag.store.engine import Store
+from haiku.rag.store.upgrades.v0_64_0 import _apply_rename_document_meta_id
+
+
+class LegacyMetaRecord(LanceModel):
+    """The pre-0.63.2 `document_meta` record (identity column `document_id`)."""
+
+    document_id: str
+    uri: str | None = None
+    title: str | None = None
+    metadata: str = "{}"
+    created_at: str = ""
+    updated_at: str = ""
+
+
+async def _seed_legacy_meta(store: Store, doc_id: str) -> None:
+    await store.db.drop_table("document_meta")
+    store.document_meta_table = await store.db.create_table(
+        "document_meta", schema=LegacyMetaRecord
+    )
+    await store.document_meta_table.add(
+        [LegacyMetaRecord(document_id=doc_id, uri="u", metadata="{}")]
+    )
+
+
+@pytest.mark.asyncio
+async def test_renames_document_id_to_id_and_keeps_rows(temp_db_path):
+    async with Store(temp_db_path, create=True, skip_migration_check=True) as store:
+        await _seed_legacy_meta(store, "doc-1")
+
+        await _apply_rename_document_meta_id(store)
+
+        names = {f.name for f in await store.document_meta_table.schema()}
+        assert "id" in names and "document_id" not in names
+        rows = await store.document_meta_table.query().to_list()
+        assert [r["id"] for r in rows] == ["doc-1"]
+
+
+@pytest.mark.asyncio
+async def test_idempotent_when_already_renamed(temp_db_path):
+    async with Store(temp_db_path, create=True, skip_migration_check=True) as store:
+        await _seed_legacy_meta(store, "doc-1")
+        await _apply_rename_document_meta_id(store)
+        # Second run must be a no-op, not an error.
+        await _apply_rename_document_meta_id(store)
+
+        names = {f.name for f in await store.document_meta_table.schema()}
+        assert "id" in names and "document_id" not in names

tests/test_doctor.py

@@ -114,7 +114,7 @@ async def _build_db(
         ]
     )
     await docs_tbl.add([DocumentRecord(id="d1", content="hello")])
-    await meta_tbl.add([DocumentMetaRecord(document_id="d1", uri="test://d1")])
+    await meta_tbl.add([DocumentMetaRecord(id="d1", uri="test://d1")])
     await items_tbl.add(
         [
             DocumentItemRecord(
@@ -240,7 +240,7 @@ async def _add_doc(db, doc_id, *, items, metadata=None, chunks=None):
     await meta_tbl.add(
         [
             DocumentMetaRecord(
-                document_id=doc_id,
+                id=doc_id,
                 uri=f"test://{doc_id}",
                 metadata=json.dumps(metadata or {}),
             )
@@ -1143,9 +1143,7 @@ async def _build_dup_db(path, docs: dict[str, list[int]], *, vector_dim: int = 8
     )
     for doc_id, idxs in docs.items():
         await docs_tbl.add([DocumentRecord(id=doc_id, content="x")])
-        await meta_tbl.add(
-            [DocumentMetaRecord(document_id=doc_id, uri=f"test://{doc_id}")]
-        )
+        await meta_tbl.add([DocumentMetaRecord(id=doc_id, uri=f"test://{doc_id}")])
         await items_tbl.add(
             [
                 DocumentItemRecord(

tests/test_filter.py

@@ -37,6 +37,32 @@ async def test_search_with_uri_filter(temp_db_path):
             assert result.document_uri == "https://other.com/java.html"
 
 
+@pytest.mark.vcr()
+async def test_filter_by_document_id(temp_db_path):
+    """A document's identity is `id` everywhere user-facing, so filtering by
+    `id` must resolve against the document_meta table (list/count/search)."""
+    async with HaikuRAG(db_path=temp_db_path, create=True) as client:
+        doc = await client.create_document(
+            content="Filterable content about pelicans",
+            uri="https://example.com/pelican.html",
+            title="Pelican Guide",
+        )
+        await client.create_document(
+            content="Other content about penguins",
+            uri="https://example.com/penguin.html",
+            title="Penguin Guide",
+        )
+
+        listed = await client.list_documents(filter=f"id = '{doc.id}'")
+        assert [d.id for d in listed] == [doc.id]
+
+        assert await client.count_documents(filter=f"id = '{doc.id}'") == 1
+
+        results = await client.search("content", limit=5, filter=f"id = '{doc.id}'")
+        assert len(results) > 0
+        assert all(r.document_id == doc.id for r in results)
+
+
 @pytest.mark.vcr()
 async def test_search_with_title_filter(temp_db_path):
     """Test filtering by document title."""

uv.lock

@@ -751,7 +751,7 @@ name = "cuda-bindings"
 version = "13.2.0"
 source = { registry = "https://pypi.org/simple" }
 dependencies = [
-    { name = "cuda-pathfinder", marker = "sys_platform != 'darwin' and sys_platform != 'emscripten' and sys_platform != 'win32'" },
+    { name = "cuda-pathfinder" },
 ]
 wheels = [
     { url = "https://files.pythonhosted.org/packages/52/c8/b2589d68acf7e3d63e2be330b84bc25712e97ed799affbca7edd7eae25d6/cuda_bindings-13.2.0-cp312-cp312-manylinux_2_24_aarch64.manylinux_2_28_aarch64.whl", hash = "sha256:e865447abfb83d6a98ad5130ed3c70b1fc295ae3eeee39fd07b4ddb0671b6788", size = 5722404, upload-time = "2026-03-11T00:12:44.041Z" },
@@ -782,37 +782,37 @@ wheels = [
 
 [package.optional-dependencies]
 cublas = [
-    { name = "nvidia-cublas", marker = "sys_platform == 'linux'" },
+    { name = "nvidia-cublas" },
 ]
 cudart = [
-    { name = "nvidia-cuda-runtime", marker = "sys_platform == 'linux'" },
+    { name = "nvidia-cuda-runtime" },
 ]
 cufft = [
-    { name = "nvidia-cufft", marker = "sys_platform == 'linux'" },
+    { name = "nvidia-cufft" },
 ]
 cufile = [
-    { name = "nvidia-cufile", marker = "sys_platform == 'linux'" },
+    { name = "nvidia-cufile" },
 ]
 cupti = [
-    { name = "nvidia-cuda-cupti", marker = "sys_platform == 'linux'" },
+    { name = "nvidia-cuda-cupti" },
 ]
 curand = [
-    { name = "nvidia-curand", marker = "sys_platform == 'linux'" },
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+    { name = "jsonpatch" },
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+    { name = "langsmith" },
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