Add scripts that help debug bugs from simulator

1. Add script that cleans simulator logs into just the SQL statements
2. Add script that bisects a set of SQL statements to find the minimal
   prefix set of statements that fails SQLite integrity check

.gitignore

@@ -44,3 +44,4 @@ profile.json.gz
 simulator-output/
 
 &1
+bisected.sql

scripts/clean_interactions.sh

@@ -0,0 +1,39 @@
+#!/usr/bin/env bash
+set -euo pipefail
+
+# Clean lines from simulator output by:
+# 1) Removing everything up to and including "interaction="
+# 2) Replacing everything from "}:" to the end with a single semicolon
+# 3) Only retaining lines containing CREATE/INSERT/UPDATE/DELETE/DROP (the rest are usually meaningless for debugging)
+#
+# The purpose of this is to transform the interaction plan into a list of executable SQL statements
+# in cases where:
+# 1. Shrinking the plan failed
+# 2. We know the point at which the simulator failure occurred.
+#
+# I use this script like this in the simulator directory:
+# cargo run &> raw_output.txt
+# manually edit out the shrinking parts and the WarGames intro graphics etc and save the file
+# then run:
+# ./clean_interactions.sh raw_output.txt > interactions.sql
+#
+# Usage:
+#   clean_interactions.sh INPUT [OUTPUT]
+#
+# If OUTPUT is omitted, the result is written to stdout.
+
+if [[ $# -lt 1 || $# -gt 2 ]]; then
+  echo "Usage: $0 INPUT [OUTPUT]" >&2
+  exit 1
+fi
+
+input_path="$1"
+output_path="${2:-}"
+
+if [[ -z "${output_path}" ]]; then
+  awk '{ line=$0; sub(/^[^\n]*interaction=/, "", line); sub(/}:.*/, ";", line); print line }' "${input_path}" | grep -E 'CREATE|INSERT|UPDATE|DELETE|DROP'
+else
+  awk '{ line=$0; sub(/^[^\n]*interaction=/, "", line); sub(/}:.*/, ";", line); print line }' "${input_path}" | grep -E 'CREATE|INSERT|UPDATE|DELETE|DROP' > "${output_path}"
+fi
+
+

scripts/corruption_bisecter.py

@@ -0,0 +1,195 @@
+#!/usr/bin/env python3
+# Usage e.g.: uv run scripts/corruption_bisecter.py -i corruption.sql -o bisected.sql
+# To clean up input data for this script, consider using `scripts/clean_interactions.sh`
+import argparse
+import shutil
+import subprocess
+import sys
+import tempfile
+from pathlib import Path
+from typing import Callable, List, Literal, Sequence
+
+def read_statements(input_path: Path) -> List[str]:
+    with input_path.open("r", encoding="utf-8", errors="replace") as f:
+        lines = [line.rstrip("\n") for line in f]
+    return [line for line in lines if line.strip()]
+
+
+# Run a set of SQL statements using tursodb and then run integrity_check on the given db file using sqlite3.
+# Return whether the integrity check passed or failed.
+def run_sql_and_do_integrity_check(
+    workspace_root: Path,
+    db_path: Path,
+    statements: Sequence[str],
+) -> bool:
+    # Apply statements (if any) and then run integrity_check on the given db file
+    if statements:
+        sql_input = "\n".join(statements) + "\n"
+        run_cmd = ["cargo", "run", "--quiet", "--", str(db_path)]
+        run_proc = subprocess.run(
+            run_cmd,
+            input=sql_input,
+            text=True,
+            stdout=subprocess.PIPE,
+            stderr=subprocess.PIPE,
+            cwd=str(workspace_root),
+            check=False,
+        )
+        if run_proc.returncode != 0:
+            raise RuntimeError(f"cargo run failed (code {run_proc.returncode}) for candidate with {len(statements)} statements")
+
+    sqlite_cmd = [
+        "sqlite3",
+        str(db_path),
+        "pragma integrity_check;",
+    ]
+    sqlite_proc = subprocess.run(
+        sqlite_cmd,
+        text=True,
+        stdout=subprocess.PIPE,
+        stderr=subprocess.PIPE,
+        cwd=str(workspace_root),
+        check=False,
+    )
+
+    output = (sqlite_proc.stdout or "").strip()
+    if sqlite_proc.returncode != 0:
+        raise RuntimeError(f"sqlite3 returned code {sqlite_proc.returncode} with output: {output}")
+
+    return output.lower() == "ok"
+
+
+# Find a minimal subset of SQL statements that still fails integrity check.
+# This is done by binary searching for the minimal prefix.
+# We don't care about scenarios where some prefix P fails and then a larger prefix P' does not fail anymore;
+# We just want to find the minimal prefix that fails in some manner.
+def find_min_failing_prefix(
+    workspace_root: Path,
+    statements: Sequence[str],
+) -> List[str]:
+    # For performance reasons, reuse DB across attempts: keep last passing DB snapshot and apply only deltas.
+    with tempfile.TemporaryDirectory(prefix="limbo-bisect-") as tmpdir:
+        tmpdir_path = Path(tmpdir)
+        db_pass = tmpdir_path / "pass.db"
+        db_work = tmpdir_path / "work.db"
+
+        def delete_db(base: Path) -> None:
+            for suffix in ("", "-wal", "-shm"):
+                p = Path(str(base) + suffix)
+                if p.exists():
+                    try:
+                        p.unlink()
+                    except FileNotFoundError:
+                        pass
+
+        def copy_db(src: Path, dst: Path) -> None:
+            delete_db(dst)
+            for suffix in ("", "-wal", "-shm"):
+                s = Path(str(src) + suffix)
+                d = Path(str(dst) + suffix)
+                if s.exists():
+                    d.parent.mkdir(parents=True, exist_ok=True)
+                    shutil.copy2(s, d)
+
+        last_pass_len = 0
+
+        def check_prefix(k: int) -> bool:
+            nonlocal last_pass_len
+            # Prepare working DB starting from last passing snapshot when possible
+            if last_pass_len > 0 and k > last_pass_len and db_pass.exists():
+                copy_db(db_pass, db_work)
+                delta = statements[last_pass_len:k]
+                integrity_check_ok = run_sql_and_do_integrity_check(workspace_root, db_work, delta)
+            else:
+                delete_db(db_work)
+                initial = statements[:k]
+                integrity_check_ok = run_sql_and_do_integrity_check(workspace_root, db_work, initial)
+
+            sys.stderr.write(f"Test prefix {k} -> {integrity_check_ok}\n")
+            if integrity_check_ok:
+                copy_db(db_work, db_pass)
+                last_pass_len = k
+            return not integrity_check_ok
+
+        # Binary search minimal k such that prefix of length k FAILS.
+        low = 1
+        high = len(statements)
+        answer_k = None
+
+        # Initialize with empty DB as passing baseline
+        delete_db(db_pass)
+        delete_db(db_work)
+
+        while low <= high:
+            mid = (low + high) // 2
+            failed = check_prefix(mid)
+            if failed:
+                answer_k = mid
+                high = mid - 1
+            else:
+                low = mid + 1
+
+        if answer_k is None:
+            raise RuntimeError("Could not find a failing prefix despite full set failing.")
+
+        return list(statements[:answer_k])
+
+def main(argv: List[str]) -> int:
+    parser = argparse.ArgumentParser(
+        description=(
+            "Find a minimal subset of SQL statements that still FAILS pragma integrity_check."
+        )
+    )
+    parser.add_argument(
+        "-i",
+        "--input",
+        type=Path,
+        help="Path to input SQL file (one statement per line)",
+        required=True,
+    )
+    parser.add_argument(
+        "-o",
+        "--output",
+        type=Path,
+        default=Path("bisected.sql"),
+        help="Path to write the minimized failing prefix (default: bisected.sql)",
+    )
+
+    args = parser.parse_args(argv)
+
+    # Assume the script is placed under <repo>/scripts/ and use repo root as workspace
+    workspace_root = Path(__file__).resolve().parent.parent
+
+    if not args.input.exists():
+        raise RuntimeError(f"Input file not found: {args.input}")
+
+    statements = read_statements(args.input)
+    if not statements:
+        raise RuntimeError("Input file has no statements after filtering empty lines.")
+
+    # Confirm the full input fails integrity check on a fresh DB
+    with tempfile.TemporaryDirectory(prefix="limbo-bisect-precheck-") as pretmp:
+        pre_db = Path(pretmp) / "check.db"
+        integrity_check_ok = run_sql_and_do_integrity_check(workspace_root, pre_db, statements)
+        if integrity_check_ok:
+            raise RuntimeError("Full input did not FAIL integrity check")
+
+    result_lines = find_min_failing_prefix(workspace_root, statements)
+    summary = (
+        f"Reduced failing subset to {len(result_lines)} of {len(statements)} statements.\n"
+    )
+
+    args.output.parent.mkdir(parents=True, exist_ok=True)
+    with args.output.open("w", encoding="utf-8") as f:
+        for line in result_lines:
+            f.write(line + "\n")
+    sys.stderr.write(f"Wrote minimized failing prefix to {args.output}\n")
+
+    sys.stderr.write(summary)
+    return 0
+
+
+if __name__ == "__main__":
+    sys.exit(main(sys.argv[1:]))
+
+