infra/reingest_canonical_ids.sh

@@ -0,0 +1,110 @@
+#!/usr/bin/env bash
+# One-time migration to canonical paper IDs (audit C-7).
+#
+# Before the C-7 fix, ingest stored OpenAlex's URL-form doi/id as papers.id
+# (e.g. "https://doi.org/10.48550/arxiv.math/0603097"). After the fix, ingest
+# keys papers.id on the bare caller id ("math/0603097"). The existing rows keep
+# their old URL-form primary keys, so a plain re-ingest would DUPLICATE every
+# paper (new bare-id row alongside the old URL-id row). This script wipes the
+# corpus and rebuilds it on canonical ids.
+#
+# DESTRUCTIVE: `TRUNCATE papers CASCADE` removes papers + chunks + citations +
+# formulas + figures + paper_identifiers (code_links.paper_id is set NULL). All
+# content is rebuilt by ingest_all.sh, which re-fetches OpenAlex and re-embeds
+# (minutes for ~36 papers).
+#
+# Prerequisites: SSH tunnel on :5433 (see ingest_all.sh) and .env.jetson-ingest.
+# Usage: bash infra/reingest_canonical_ids.sh
+set -euo pipefail
+
+CODEX_DIR="$(cd "$(dirname "$0")/.." && pwd)"
+ENV_FILE="$CODEX_DIR/.env.jetson-ingest"
+PY="$CODEX_DIR/.venv/bin/python"
+TUNNEL_PORT=5433
+
+# ── 1. Preconditions ─────────────────────────────────────────────────────────
+if ! nc -z localhost "$TUNNEL_PORT" 2>/dev/null; then
+  echo "ERROR: SSH tunnel not active on :$TUNNEL_PORT"
+  echo "Run: ssh -f -N -L 5433:localhost:5432 alfred@192.168.178.103"
+  exit 1
+fi
+[[ -f "$ENV_FILE" ]] || { echo "ERROR: $ENV_FILE missing"; exit 1; }
+[[ -x "$PY" ]] || { echo "ERROR: venv python not found at $PY (run uv sync)"; exit 1; }
+# Load DATABASE_URL into the environment (not echoed — keeps the password out of logs).
+set -a; source "$ENV_FILE"; set +a
+
+# run_sql <SQL>: execute one statement via psycopg, print any result rows.
+# Reads DATABASE_URL from the environment; suppresses the DSN on error.
+run_sql() {
+  "$PY" - "$1" <<'PYEOF'
+import os, sys, psycopg
+from psycopg.rows import dict_row
+try:
+    with psycopg.connect(os.environ["DATABASE_URL"], row_factory=dict_row, connect_timeout=10) as c:
+        cur = c.execute(sys.argv[1])
+        if cur.description:
+            for row in cur.fetchall():
+                print("   " + "  ".join(f"{k}={v!r}" for k, v in row.items()))
+        c.commit()
+except Exception as e:
+    print(f"   DB ERROR: {type(e).__name__} (details suppressed to avoid DSN leak)")
+    sys.exit(1)
+PYEOF
+}
+
+# ── 2. BEFORE snapshot ───────────────────────────────────────────────────────
+echo "── BEFORE migration ──────────────────────────────────────────"
+run_sql "SELECT count(*) AS papers, count(*) FILTER (WHERE starts_with(id, 'https://')) AS url_form_ids FROM papers"
+echo "   sample ids:"
+run_sql "SELECT id FROM papers ORDER BY added_at LIMIT 3"
+
+# ── 3. Confirmation gate (destructive) ───────────────────────────────────────
+echo ""
+echo "This TRUNCATEs papers CASCADE (papers/chunks/citations/formulas/figures/"
+echo "paper_identifiers) and re-ingests via ingest_all.sh. The DB content is"
+echo "rebuilt from scratch."
+read -r -p "Type 'MIGRATE' to proceed: " confirm
+[[ "$confirm" == "MIGRATE" ]] || { echo "Aborted — nothing changed."; exit 1; }
+
+# ── 4. Wipe ──────────────────────────────────────────────────────────────────
+echo "── TRUNCATE papers CASCADE ───────────────────────────────────"
+run_sql "TRUNCATE papers CASCADE"
+echo "   wiped."
+
+# ── 5. Re-ingest on canonical ids ────────────────────────────────────────────
+echo "── Re-ingest (ingest_all.sh) ─────────────────────────────────"
+bash "$CODEX_DIR/ingest_all.sh"
+
+# ── 6. AFTER snapshot + live verification ────────────────────────────────────
+echo "── AFTER migration ───────────────────────────────────────────"
+echo "   C-7 — url_form_ids should now be 0; sample ids should be bare:"
+run_sql "SELECT count(*) AS papers, count(*) FILTER (WHERE starts_with(id, 'https://')) AS url_form_ids FROM papers"
+run_sql "SELECT id FROM papers ORDER BY added_at LIMIT 3"
+
+# C-1 must be verified through the REAL resolver-based discovery_leads(), not a
+# raw cited_id check: cited_id/openalex_id stay in OpenAlex form, so the raw
+# "cited_id NOT IN papers.id" count is non-zero by design — the resolver is what
+# excludes ingested papers. Check that no ingested paper leaks into the leads.
+echo "   C-1 — real discovery_leads() must contain no already-ingested paper:"
+PYTHONPATH="$CODEX_DIR" "$PY" - <<'PYEOF'
+import os, psycopg
+from psycopg.rows import dict_row
+from codex.discover import discovery_leads
+try:
+    leads = discovery_leads(limit=100000)
+    with psycopg.connect(os.environ["DATABASE_URL"], row_factory=dict_row, connect_timeout=10) as c:
+        ingested = {r["id"] for r in c.execute("SELECT id FROM papers").fetchall()}
+        ingested |= {
+            r["openalex_id"]
+            for r in c.execute("SELECT openalex_id FROM papers WHERE openalex_id IS NOT NULL").fetchall()
+        }
+    leaked = sum(1 for lead in leads if lead["cited_id"] in ingested)
+    print(f"   leads={len(leads)}  ingested-papers-leaked-into-leads={leaked}")
+except Exception as e:
+    print(f"   DB ERROR: {type(e).__name__} (details suppressed)")
+PYEOF
+
+echo ""
+echo "✓ Migration complete."
+echo "  Expected: url_form_ids=0 (C-7 verified) and leaked=0 (C-1 verified) above."
+echo "  Next: re-run 'codex graph report' and refresh the ADR-F15 spike table (audit D-1)."