user2595/codex-py
1
0
Fork 0
Code Issues Pull Requests Actions Packages Projects Releases Wiki Activity

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

Merged
user2595 merged 15 commits from fix/audit-wave-3 into main 2026-06-16 04:54:00 +00:00
Conversation 0 Commits 15 Files Changed 25 +13 -8
2 changed files with 13 additions and 8 deletions
Download Patch File Download Diff File Expand all files Collapse all files
Showing only changes of commit ae5e9a528b - Show all commits

6
.env.example
View File

@@ -5,6 +5,12 @@
# Example: postgresql://researcher:change_me@localhost:5432/papers # Example: postgresql://researcher:change_me@localhost:5432/papers
DATABASE_URL=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 service base URL (containerised — see infra/docker-compose.yml)
GROBID_URL=http://localhost:8070 GROBID_URL=http://localhost:8070

15
README.md
View File

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