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fix: audit remediation Wave 3 — M-1, MED/LOW sweep, ingest robustness + D-1 close-out #14

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user2595 merged 15 commits from fix/audit-wave-3 into main 2026-06-16 04:54:00 +00:00
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2 changed files with 13 additions and 8 deletions
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6
.env.example
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@@ -5,6 +5,12 @@
# Example: postgresql://researcher:change_me@localhost:5432/papers
DATABASE_URL=postgresql://researcher:change_me@localhost:5432/papers
# Optional: privileged connection used by `codex migrate` to apply schema DDL.
# The app DATABASE_URL is often a least-privilege DML role that cannot CREATE/
# ALTER owner-held tables; point this at an owner/superuser connection.
# Falls back to DATABASE_URL when unset.
# MIGRATION_DATABASE_URL=postgresql://postgres:change_me@localhost:5432/papers
# GROBID service base URL (containerised — see infra/docker-compose.yml)
GROBID_URL=http://localhost:8070

15
README.md
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@@ -19,13 +19,11 @@ $EDITOR .env
# 3. Install Python dependencies (requires uv)
uv sync
# 4. Apply the database schema (first run only)
uv run python -c "
from codex.db import get_conn, apply_schema
with get_conn() as conn:
apply_schema(conn)
print('Schema applied.')
"
# 4. Apply the database schema (idempotent — safe to re-run after upgrades)
# Needs a role that can run DDL. If DATABASE_URL is a least-privilege app
# role, point MIGRATION_DATABASE_URL at an owner/superuser connection first:
# MIGRATION_DATABASE_URL=postgresql://postgres:...@host:5432/papers
uv run codex migrate
```
---
@@ -34,7 +32,8 @@ print('Schema applied.')
| Variable | Default | Description |
|---|---|---|
| `DATABASE_URL` | `postgresql://researcher:change_me@localhost:5432/papers` | libpq connection string |
| `DATABASE_URL` | `postgresql://researcher:change_me@localhost:5432/papers` | libpq connection string (app role; DML) |
| `MIGRATION_DATABASE_URL` | *(falls back to `DATABASE_URL`)* | Privileged connection used by `codex migrate` for schema DDL (owner/superuser) |
| `GROBID_URL` | `http://localhost:8070` | GROBID HTTP API base URL |
| `OLLAMA_BASE_URL` | `http://localhost:11434` | Local Ollama endpoint (optional) |
| `EMBEDDING_MODEL` | `BAAI/bge-m3` | sentence-transformers model name |