From 2e07d7a8fe8e84dec2e35a56f14ccf4ec280e8f9 Mon Sep 17 00:00:00 2001 From: Travis Herbranson Date: Sun, 24 May 2026 22:49:06 -0400 Subject: [PATCH] alembic: skip CREATE SCHEMA when present + add embedding smoke test MIME-Version: 1.0 Content-Type: text/plain; charset=UTF-8 Content-Transfer-Encoding: 8bit The runtime role (lovebug) doesn't have CREATE on the petalbrain database even though it owns the second_brain schema, so a bare `CREATE SCHEMA IF NOT EXISTS` errors out with permission denied. Gate the bootstrap on a pg_namespace lookup so we only attempt the create when the schema is genuinely missing — operators bootstrap it once as postgres superuser, alembic just respects it afterward. The smoke test exercises the full Postgres + embedding path against a live DB + Ollama (autoskipped otherwise): writes an extraction, embeds the summary, asserts public.embeddings has the expected row count, and re-embeds to verify the delete-before-insert idempotency. --- alembic/env.py | 15 +- ...f6c9d10_v1_second_brain_pipeline_tables.py | 5 +- tests/test_smoke_embedding.py | 148 ++++++++++++++++++ uv.lock | 114 ++++++++++++++ 4 files changed, 279 insertions(+), 3 deletions(-) create mode 100644 tests/test_smoke_embedding.py diff --git a/alembic/env.py b/alembic/env.py index fb460c7..09c8a84 100644 --- a/alembic/env.py +++ b/alembic/env.py @@ -83,13 +83,24 @@ def run_migrations_online() -> None: with connectable.connect() as connection: # Bootstrap the schema before alembic looks for alembic_version. - # Commit explicitly so the schema persists; otherwise the implicit + # The runtime role (lovebug) does NOT have CREATE on the petalbrain + # database — bare `CREATE SCHEMA IF NOT EXISTS` would fail with + # permission denied even though the schema already exists. So we + # only attempt to create it when the schema is genuinely missing + # (operator must have bootstrapped it once as postgres superuser: + # `CREATE SCHEMA second_brain AUTHORIZATION lovebug`). + # Commit explicitly so any DDL persists; otherwise the implicit # transaction is rolled back when the connection closes. Avoid # running any further statement here — it would autobegin a new # transaction and cause alembic's `begin_transaction()` to nest as # a savepoint, which silently rolls back when the connection closes. # The migration script sets search_path itself. - connection.exec_driver_sql(f"CREATE SCHEMA IF NOT EXISTS {SCHEMA}") + row = connection.exec_driver_sql( + "SELECT 1 FROM pg_namespace WHERE nspname = %s", + (SCHEMA,), + ).fetchone() + if row is None: + connection.exec_driver_sql(f"CREATE SCHEMA {SCHEMA}") connection.commit() context.configure( connection=connection, diff --git a/alembic/versions/4a1e2f6c9d10_v1_second_brain_pipeline_tables.py b/alembic/versions/4a1e2f6c9d10_v1_second_brain_pipeline_tables.py index da2d4eb..9fb2072 100644 --- a/alembic/versions/4a1e2f6c9d10_v1_second_brain_pipeline_tables.py +++ b/alembic/versions/4a1e2f6c9d10_v1_second_brain_pipeline_tables.py @@ -31,7 +31,10 @@ depends_on: str | Sequence[str] | None = None def upgrade() -> None: """Create the v1 second_brain schema.""" - op.execute("CREATE SCHEMA IF NOT EXISTS second_brain") + # The schema is bootstrapped by env.py (only if missing); skip the + # IF NOT EXISTS form here because lovebug doesn't have CREATE on the + # petalbrain database and the bare statement errors out even when the + # schema already exists. Just SET search_path and emit DDL inside it. op.execute("SET search_path TO second_brain") op.execute( diff --git a/tests/test_smoke_embedding.py b/tests/test_smoke_embedding.py new file mode 100644 index 0000000..caf18a2 --- /dev/null +++ b/tests/test_smoke_embedding.py @@ -0,0 +1,148 @@ +"""Smoke test for the Postgres + embedding pipeline. + +Runs only when SECOND_BRAIN_DATABASE_URL (or HERBYLAB_DATABASE_URL) is set +*and* an Ollama instance with nomic-embed-text is reachable. Otherwise the +test is skipped — there is no in-memory fixture for pgvector, and we +explicitly want the smoke check to exercise the real wire format. + +It covers: + 1. SQLAlchemy can write a Source + Extraction into the `second_brain` + schema. + 2. The embeddings module chunks the summary, calls Ollama, and writes + vector rows into public.embeddings keyed correctly. + 3. Re-running embedding is idempotent (delete-before-insert wins). +""" + +from __future__ import annotations + +import os +import socket +import uuid + +import httpx +import psycopg +import pytest + + +def _ollama_reachable() -> bool: + url = os.environ.get("OLLAMA_URL", "http://127.0.0.1:11434") + try: + r = httpx.get(f"{url}/api/tags", timeout=2.0) + if r.status_code != 200: + return False + models = [m["name"] for m in r.json().get("models", [])] + return any(m.startswith("nomic-embed-text") for m in models) + except (httpx.HTTPError, socket.error): + return False + + +def _db_reachable() -> bool: + url = os.environ.get("SECOND_BRAIN_DATABASE_URL") or os.environ.get( + "HERBYLAB_DATABASE_URL" + ) + if not url: + return False + raw = url.replace("postgresql+psycopg://", "postgresql://", 1) + try: + with psycopg.connect(raw, connect_timeout=2) as conn: # noqa: F841 + return True + except Exception: + return False + + +pytestmark = pytest.mark.skipif( + not (_db_reachable() and _ollama_reachable()), + reason="Smoke test needs SECOND_BRAIN_DATABASE_URL + reachable Ollama (nomic-embed-text)", +) + + +def test_extraction_round_trip_with_embedding(): + from second_brain.database import Database, reset_database_singleton + from second_brain.embeddings import close_pool, embed_extraction + from second_brain.models import ( + Extraction, + Source, + SourceStatus, + SourceType, + utcnow, + ) + + reset_database_singleton() + db = Database() + + # Unique URL so re-runs don't collide on the unique constraint. + unique = uuid.uuid4().hex[:8] + url = f"https://example.test/smoke/{unique}" + + summary_text = ( + "Smoke test extraction summary. " + "The second-brain pipeline embeds this string into Postgres. " + "Re-running the embed should be idempotent — delete-before-insert " + "keys on (source_schema, source_table, source_id, embedding_model)." + ) + + with db.session() as sess: + src = Source( + url=url, + title=f"smoke-test-{unique}", + domain="development", + source_type=SourceType.ARTICLE, + status=SourceStatus.ANALYZED, + ingested_at=utcnow(), + ) + sess.add(src) + sess.flush() + ext = Extraction(source_id=src.id, summary=summary_text) + sess.add(ext) + sess.flush() + extraction_id = ext.id + source_id = src.id + + try: + n1 = embed_extraction(extraction_id, summary_text) + assert n1 is not None and n1 >= 1, f"first embed should write rows, got {n1}" + + # Idempotency: re-embed should produce the same chunk count and not + # accumulate orphan rows. + n2 = embed_extraction(extraction_id, summary_text) + assert n2 == n1, f"re-embed should match first count: {n1} vs {n2}" + + raw_url = ( + os.environ.get("SECOND_BRAIN_DATABASE_URL") + or os.environ.get("HERBYLAB_DATABASE_URL") + ).replace("postgresql+psycopg://", "postgresql://", 1) + with psycopg.connect(raw_url) as conn, conn.cursor() as cur: + cur.execute( + """ + SELECT COUNT(*) + FROM public.embeddings + WHERE source_schema = 'second_brain' + AND source_table = 'extractions' + AND source_id = %s + AND embedding_model = 'nomic-embed-text' + """, + (extraction_id,), + ) + (count,) = cur.fetchone() + assert count == n1, f"public.embeddings should hold {n1} rows, has {count}" + finally: + # Tidy up so the smoke test stays leak-free. + with db.session() as sess: + sess.query(Source).filter(Source.id == source_id).delete() + raw_url = ( + os.environ.get("SECOND_BRAIN_DATABASE_URL") + or os.environ.get("HERBYLAB_DATABASE_URL") + ).replace("postgresql+psycopg://", "postgresql://", 1) + with psycopg.connect(raw_url) as conn, conn.cursor() as cur: + cur.execute( + """ + DELETE FROM public.embeddings + WHERE source_schema = 'second_brain' + AND source_table = 'extractions' + AND source_id = %s + """, + (extraction_id,), + ) + conn.commit() + close_pool() + reset_database_singleton() diff --git a/uv.lock b/uv.lock index 57fc794..8e17809 100644 --- a/uv.lock +++ b/uv.lock @@ -2,6 +2,20 @@ version = 1 revision = 3 requires-python = ">=3.12" +[[package]] +name = "alembic" +version = "1.18.4" +source = { registry = "https://pypi.org/simple" } +dependencies = [ + { name = "mako" }, + { name = "sqlalchemy" }, + { name = "typing-extensions" }, +] +sdist = { url = "https://files.pythonhosted.org/packages/94/13/8b084e0f2efb0275a1d534838844926f798bd766566b1375174e2448cd31/alembic-1.18.4.tar.gz", hash = "sha256:cb6e1fd84b6174ab8dbb2329f86d631ba9559dd78df550b57804d607672cedbc", size = 2056725, upload-time = "2026-02-10T16:00:47.195Z" } +wheels = [ + { url = "https://files.pythonhosted.org/packages/d2/29/6533c317b74f707ea28f8d633734dbda2119bbadfc61b2f3640ba835d0f7/alembic-1.18.4-py3-none-any.whl", hash = "sha256:a5ed4adcf6d8a4cb575f3d759f071b03cd6e5c7618eb796cb52497be25bfe19a", size = 263893, 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