fix(db): add timeout=30s to all sqlite3.connect() calls across app

Watcher, REST endpoints, services (search, incidents, blocklist),
MCP server, context retriever, embedder, glean_scheduler, and
doc_upload all used the default 5-second SQLite busy timeout.
During collect glean write phases, watcher flush threads were hitting
'database is locked' errors when the glean held the write lock longer
than 5 seconds.

All connections now use timeout=30.0, matching the pipeline fix
from commit ee39ffb. No logic changes.

.nfs0000000000bbcf52000002e7

@@ -0,0 +1,308 @@
+#!/usr/bin/env bash
+# manage.sh — Turnstone diagnostic intelligence layer
+# Usage: ./manage.sh <command> [args]
+set -euo pipefail
+
+# Only emit color codes when stdout is a real terminal
+if [[ -t 1 ]]; then
+    RED='\033[0;31m'; GREEN='\033[0;32m'; YELLOW='\033[1;33m'; BLUE='\033[0;34m'; NC='\033[0m'
+else
+    RED=''; GREEN=''; YELLOW=''; BLUE=''; NC=''
+fi
+info()    { echo -e "${BLUE}[turnstone]${NC} $*"; }
+success() { echo -e "${GREEN}[turnstone]${NC} $*"; }
+warn()    { echo -e "${YELLOW}[turnstone]${NC} $*"; }
+error()   { echo -e "${RED}[turnstone]${NC} $*" >&2; exit 1; }
+
+SCRIPT_DIR="$(cd "$(dirname "${BASH_SOURCE[0]}")" && pwd)"
+cd "$SCRIPT_DIR"
+
+API_PORT=8534           # FastAPI: serves REST API + built Vue SPA
+VITE_PORT=5174          # Vite HMR port in dev mode (proxies /api → 8534)
+
+LOG_DIR="log"
+API_PID_FILE=".turnstone-api.pid"
+
+DB="${TURNSTONE_DB:-${SCRIPT_DIR}/data/turnstone.db}"
+
+CONDA_BASE="${CONDA_BASE:-/devl/miniconda3}"
+PYTHON="${CONDA_BASE}/envs/cf/bin/python"
+
+# ── Helpers ───────────────────────────────────────────────────────────────────
+
+_is_alive() {
+    local pid_file="$1"
+    [[ -f "$pid_file" ]] && kill -0 "$(<"$pid_file")" 2>/dev/null
+}
+
+_kill_pid_file() {
+    local pid_file="$1" label="$2"
+    if [[ -f "$pid_file" ]]; then
+        local pid
+        pid=$(<"$pid_file")
+        if kill -0 "$pid" 2>/dev/null; then
+            kill "$pid" && rm -f "$pid_file"
+            success "$label stopped (PID $pid)."
+        else
+            warn "Stale PID file for $label (PID $pid not running). Cleaning up."
+            rm -f "$pid_file"
+        fi
+    else
+        warn "$label not running."
+    fi
+}
+
+_wait_for_port() {
+    local port="$1" label="$2" pid_file="$3"
+    for _i in $(seq 1 20); do
+        sleep 0.5
+        (echo "" >/dev/tcp/127.0.0.1/"$port") 2>/dev/null && return 0
+        if ! _is_alive "$pid_file"; then
+            rm -f "$pid_file"
+            error "$label died during startup. Check ${LOG_DIR}/api.log"
+        fi
+    done
+    error "$label did not bind to port $port within 10 s."
+}
+
+# ── Usage ─────────────────────────────────────────────────────────────────────
+
+usage() {
+    echo ""
+    echo -e "  ${BLUE}Turnstone — Diagnostic Log Intelligence${NC}"
+    echo ""
+    echo "  Usage: ./manage.sh <command> [args]"
+    echo ""
+    echo "  Production-like (built SPA + uvicorn):"
+    echo -e "    ${GREEN}start${NC}                    Build Vue SPA, start FastAPI + SPA on :${API_PORT}"
+    echo -e "    ${GREEN}stop${NC}                     Stop the server"
+    echo -e "    ${GREEN}restart${NC}                  Stop then start"
+    echo -e "    ${GREEN}status${NC}                   Show running process"
+    echo -e "    ${GREEN}logs${NC}                     Tail server log"
+    echo -e "    ${GREEN}open${NC}                     Open UI in browser"
+    echo ""
+    echo "  Development (hot-reload):"
+    echo -e "    ${GREEN}dev${NC}                      uvicorn --reload (:${API_PORT}) + Vite HMR (:${VITE_PORT})"
+    echo ""
+    echo "  Data:"
+    echo -e "    ${GREEN}ingest PATH [DB]${NC}         Ingest a log file or corpus directory"
+    echo -e "    ${GREEN}ingest-plex [HOST]${NC}       Pull Plex log from Cass (or HOST) and ingest"
+    echo -e "    ${GREEN}ingest-qbit [HOST]${NC}       Pull qBittorrent log locally or from HOST via SSH"
+    echo -e "    ${GREEN}build-fts${NC}                Rebuild the FTS search index"
+    echo ""
+    echo "  Tests:"
+    echo -e "    ${GREEN}test [args]${NC}              Run pytest suite"
+    echo ""
+    echo "  DB: ${DB}"
+    echo "  Conda env: cf"
+    echo ""
+    echo "  Examples:"
+    echo "    ./manage.sh start"
+    echo "    ./manage.sh dev"
+    echo "    ./manage.sh ingest corpus/raw/"
+    echo "    ./manage.sh ingest corpus/raw/ data/custom.db"
+    echo ""
+}
+
+# ── Commands ──────────────────────────────────────────────────────────────────
+
+CMD="${1:-help}"
+shift || true
+
+case "$CMD" in
+
+    start)
+        if _is_alive "$API_PID_FILE"; then
+            warn "Already running (PID $(<"$API_PID_FILE")) — use 'restart' to rebuild."
+            exit 0
+        fi
+        mkdir -p "$LOG_DIR" data
+
+        info "Building Vue SPA…"
+        (cd web && npm run build) 2>&1 | tee "${LOG_DIR}/build.log" | grep -E "built in|error" || true
+        success "SPA built → web/dist/"
+
+        info "Starting on port ${API_PORT}…"
+        TURNSTONE_DB="$DB" nohup "$PYTHON" -m uvicorn app.rest:app \
+            --host 0.0.0.0 --port "$API_PORT" \
+            >> "${LOG_DIR}/api.log" 2>&1 &
+        echo $! > "$API_PID_FILE"
+        _wait_for_port "$API_PORT" "Turnstone" "$API_PID_FILE"
+        success "Running → http://localhost:${API_PORT}  (PID $(<"$API_PID_FILE"))"
+        ;;
+
+    stop)
+        _kill_pid_file "$API_PID_FILE" "Turnstone"
+        ;;
+
+    restart)
+        bash "$0" stop
+        exec bash "$0" start
+        ;;
+
+    status)
+        echo ""
+        if _is_alive "$API_PID_FILE"; then
+            success "Turnstone RUNNING  PID $(<"$API_PID_FILE")  → http://localhost:${API_PORT}"
+        else
+            echo -e "  Turnstone ${RED}STOPPED${NC}"
+        fi
+        echo ""
+        ;;
+
+    logs)
+        tail -f "${LOG_DIR}/api.log"
+        ;;
+
+    open)
+        URL="http://localhost:${API_PORT}"
+        info "Opening ${URL}"
+        if command -v xdg-open &>/dev/null; then xdg-open "$URL"
+        elif command -v open &>/dev/null; then open "$URL"
+        else echo "$URL"
+        fi
+        ;;
+
+    dev)
+        DEV_API_PID=".turnstone-dev-api.pid"
+        mkdir -p "$LOG_DIR" data
+
+        if _is_alive "$DEV_API_PID"; then
+            warn "Dev API already running (PID $(<"$DEV_API_PID"))"
+        else
+            info "Starting uvicorn --reload on port ${API_PORT}…"
+            TURNSTONE_DB="$DB" nohup "$PYTHON" -m uvicorn app.rest:app \
+                --host 0.0.0.0 --port "$API_PORT" --reload \
+                >> "${LOG_DIR}/api.log" 2>&1 &
+            echo $! > "$DEV_API_PID"
+            _wait_for_port "$API_PORT" "FastAPI (dev)" "$DEV_API_PID"
+            success "API (hot-reload) → http://localhost:${API_PORT}"
+        fi
+
+        _cleanup_dev() {
+            local pid
+            pid=$(<"$DEV_API_PID" 2>/dev/null) || true
+            [[ -n "${pid:-}" ]] && kill "$pid" 2>/dev/null && rm -f "$DEV_API_PID"
+            info "Dev servers stopped."
+        }
+        trap _cleanup_dev EXIT INT TERM
+
+        info "Starting Vite HMR on port ${VITE_PORT}…"
+        success "Frontend (HMR) → http://localhost:${VITE_PORT}"
+        (cd web && npm run dev -- --port "$VITE_PORT")
+        ;;
+
+    ingest)
+        if [[ $# -lt 1 ]]; then
+            error "Usage: ./manage.sh ingest <file_or_dir> [DB_PATH]"
+        fi
+        info "Ingesting $1 → ${2:-$DB}…"
+        "$PYTHON" scripts/ingest_corpus.py "$1" "${2:-$DB}"
+        ;;
+
+    ingest-plex)
+        PLEX_HOST="${1:-cass}"
+        PLEX_LOG_DIR="/var/lib/plexmediaserver/Library/Application Support/Plex Media Server/Logs"
+        TMP_DIR="/tmp/turnstone-plex-$$"
+        mkdir -p "$TMP_DIR"
+
+        info "Listing Plex logs on ${PLEX_HOST}…"
+        # Get list of all rotated + active Plex logs
+        mapfile -t REMOTE_LOGS < <(ssh "$PLEX_HOST" \
+            "ls '${PLEX_LOG_DIR}'/Plex\ Media\ Server*.log 2>/dev/null") \
+            || { rm -rf "$TMP_DIR"; error "SSH to ${PLEX_HOST} failed."; }
+
+        if [[ ${#REMOTE_LOGS[@]} -eq 0 ]]; then
+            rm -rf "$TMP_DIR"
+            error "No Plex logs found on ${PLEX_HOST} at ${PLEX_LOG_DIR}"
+        fi
+
+        for remote_path in "${REMOTE_LOGS[@]}"; do
+            # Plex Media Server.1.log → cass-plex_media_server.1.log
+            local_name="${PLEX_HOST}-$(basename "$remote_path" | tr ' ' '_' | tr '[:upper:]' '[:lower:]')"
+            local_path="${TMP_DIR}/${local_name}"
+            info "  ← $(basename "$remote_path")"
+            ssh "$PLEX_HOST" "cat '${remote_path}'" > "$local_path"
+        done
+
+        info "Ingesting ${#REMOTE_LOGS[@]} log file(s) into ${DB}…"
+        for f in "$TMP_DIR"/*.log; do
+            "$PYTHON" scripts/ingest_corpus.py "$f" "$DB"
+        done
+        rm -rf "$TMP_DIR"
+        info "Done. Restarting server…"
+        exec bash "$0" restart
+        ;;
+
+    ingest-qbit)
+        QBIT_HOST="${1:-}"
+        # Default log locations in priority order
+        QBIT_LOG_PATHS=(
+            "$HOME/.local/share/qBittorrent/logs/qbittorrent.log"
+            "$HOME/.config/qBittorrent/logs/qbittorrent.log"
+            "/var/log/qbittorrent/qbittorrent.log"
+        )
+        TMP_DIR="/tmp/turnstone-qbit-$$"
+        mkdir -p "$TMP_DIR"
+
+        if [[ -n "$QBIT_HOST" ]]; then
+            info "Fetching qBittorrent log from ${QBIT_HOST}…"
+            REMOTE_LOG=""
+            for p in "${QBIT_LOG_PATHS[@]}"; do
+                if ssh "$QBIT_HOST" "test -f '$p'" 2>/dev/null; then
+                    REMOTE_LOG="$p"
+                    break
+                fi
+            done
+            if [[ -z "$REMOTE_LOG" ]]; then
+                rm -rf "$TMP_DIR"
+                error "No qBittorrent log found on ${QBIT_HOST}. Tried: ${QBIT_LOG_PATHS[*]}"
+            fi
+            local_name="${QBIT_HOST}-qbittorrent.log"
+            ssh "$QBIT_HOST" "cat '$REMOTE_LOG'" > "${TMP_DIR}/${local_name}"
+            info "  ← ${REMOTE_LOG} (${QBIT_HOST})"
+        else
+            LOCAL_LOG=""
+            for p in "${QBIT_LOG_PATHS[@]}"; do
+                if [[ -f "$p" ]]; then
+                    LOCAL_LOG="$p"
+                    break
+                fi
+            done
+            if [[ -z "$LOCAL_LOG" ]]; then
+                rm -rf "$TMP_DIR"
+                error "No qBittorrent log found locally. Tried: ${QBIT_LOG_PATHS[*]}"
+            fi
+            cp "$LOCAL_LOG" "${TMP_DIR}/qbittorrent.log"
+            info "  ← ${LOCAL_LOG}"
+        fi
+
+        info "Ingesting into ${DB}…"
+        "$PYTHON" scripts/ingest_corpus.py "${TMP_DIR}"/*.log "$DB"
+        rm -rf "$TMP_DIR"
+        info "Done. Restarting server…"
+        exec bash "$0" restart
+        ;;
+
+    build-fts)
+        info "Rebuilding FTS index for ${DB}…"
+        TURNSTONE_DB="$DB" "$PYTHON" scripts/build_fts_index.py "$DB"
+        success "FTS index rebuilt."
+        ;;
+
+    test)
+        info "Running test suite…"
+        PYTEST="${CONDA_BASE}/envs/cf/bin/pytest"
+        [[ -x "$PYTEST" ]] || error "pytest not found in cf env at ${PYTEST}"
+        TURNSTONE_DB=":memory:" "$PYTEST" tests/ -v "$@"
+        ;;
+
+    help|--help|-h)
+        usage
+        ;;
+
+    *)
+        error "Unknown command: ${CMD}. Run './manage.sh help' for usage."
+        ;;
+
+esac

app/context/embedder.py

@@ -45,7 +45,7 @@ def embed_chunks(
     if embedder is None:
         return 0
 
-    conn = sqlite3.connect(str(db_path))
+    conn = sqlite3.connect(str(db_path), timeout=30.0)
     conn.execute("PRAGMA journal_mode=WAL")
     conn.row_factory = sqlite3.Row
 

app/context/retriever.py

@@ -37,7 +37,7 @@ class RetrievedContext:
 def get_relevant_facts(db_path: Path, query: str) -> list[dict[str, str]]:
     """Keyword match against context_facts. Always runs — Free tier."""
     try:
-        conn = sqlite3.connect(str(db_path))
+        conn = sqlite3.connect(str(db_path), timeout=30.0)
         conn.execute("PRAGMA journal_mode=WAL")
         conn.row_factory = sqlite3.Row
         keywords = [w.lower() for w in query.split() if len(w) > 2]
@@ -92,7 +92,7 @@ def _search_chunks_vector(
         return []
 
     try:
-        conn = sqlite3.connect(str(db_path))
+        conn = sqlite3.connect(str(db_path), timeout=30.0)
         conn.execute("PRAGMA journal_mode=WAL")
         conn.row_factory = sqlite3.Row
         rows = conn.execute(
@@ -127,7 +127,7 @@ def _search_chunks_vector(
 def _search_chunks_keyword(db_path: Path, query: str) -> list[dict[str, str]]:
     """LIKE-based keyword search across context_chunks. Fallback when no embedder."""
     try:
-        conn = sqlite3.connect(str(db_path))
+        conn = sqlite3.connect(str(db_path), timeout=30.0)
         conn.execute("PRAGMA journal_mode=WAL")
         conn.row_factory = sqlite3.Row
         keywords = [w.lower() for w in query.split() if len(w) > 2][:5]

app/glean/doc_upload.py

@@ -25,7 +25,7 @@ def glean_upload(db_path: Path, filename: str, content: bytes) -> dict[str, Any]
     for fact in facts:
         add_fact(db_path, fact.category, fact.key, fact.value, source="upload")
 
-    conn = sqlite3.connect(str(db_path))
+    conn = sqlite3.connect(str(db_path), timeout=30.0)
     conn.execute("PRAGMA journal_mode=WAL")
     for i, chunk_text in enumerate(chunks):
         conn.execute(

app/glean/mqtt_subscriber.py

@@ -59,7 +59,7 @@ def _make_entry_id(source_id: str, seq: int, text: str) -> str:
 
 
 def _write_entry(db_path: Path, entry: RetrievedEntry) -> None:
-    with sqlite3.connect(db_path) as conn:
+    with sqlite3.connect(db_path, timeout=30.0) as conn:
         conn.execute(
             """
             INSERT OR IGNORE INTO log_entries

app/mcp_server.py

@@ -59,7 +59,7 @@ def _ensure_index() -> None:
         return
 
     try:
-        conn = sqlite3.connect(str(DB_PATH))
+        conn = sqlite3.connect(str(DB_PATH), timeout=30.0)
         count = conn.execute("SELECT COUNT(*) FROM log_fts").fetchone()[0]
         conn.close()
         if count > 0:

app/rest.py

@@ -509,7 +509,7 @@ def list_configured_sources() -> dict:
 @router.delete("/api/sources/{source_id}")
 def delete_source(source_id: str) -> dict:
     """Delete all log entries (and FTS index rows) for a given source."""
-    conn = sqlite3.connect(str(DB_PATH))
+    conn = sqlite3.connect(str(DB_PATH), timeout=30.0)
     conn.execute("PRAGMA journal_mode=WAL")
     try:
         conn.execute("DELETE FROM log_fts WHERE source_id = ?", (source_id,))
@@ -616,7 +616,7 @@ def glean_batch(payload: BatchGleanRequest, background_tasks: BackgroundTasks) -
     """
     if not payload.entries:
         return {"gleaned": 0}
-    conn = sqlite3.connect(str(DB_PATH))
+    conn = sqlite3.connect(str(DB_PATH), timeout=30.0)
     conn.execute("PRAGMA journal_mode=WAL")
     conn.executemany(
         """
@@ -710,7 +710,7 @@ async def glean_wazuh_alert(
     compiled = load_compiled_patterns(PATTERN_FILE)
     entries = list(_parse_wazuh(iter([json.dumps(alert)]), sid, compiled, ingest_time))
     if entries:
-        conn = sqlite3.connect(str(DB_PATH))
+        conn = sqlite3.connect(str(DB_PATH), timeout=30.0)
         conn.execute("PRAGMA journal_mode=WAL")
         conn.executemany(
             """
@@ -892,7 +892,7 @@ def glean_tautulli(
     compiled = _compiled_patterns
     entry = _parse_tautulli(payload, compiled)
 
-    conn = sqlite3.connect(str(DB_PATH))
+    conn = sqlite3.connect(str(DB_PATH), timeout=30.0)
     conn.execute("PRAGMA journal_mode=WAL")
     try:
         _tautulli_write_entry(conn, entry)

app/services/blocklist.py

@@ -172,7 +172,7 @@ def run_scan(
     now = _now_iso()
     count = 0
 
-    conn = sqlite3.connect(str(db_path))
+    conn = sqlite3.connect(str(db_path), timeout=30.0)
     try:
         rows = conn.execute(
             f"SELECT id, text FROM log_entries WHERE source_id IN ({placeholders})",
@@ -226,7 +226,7 @@ def list_candidates(
     status: str | None = None,
     device_ip: str | None = None,
 ) -> list[BlocklistCandidate]:
-    conn = sqlite3.connect(str(db_path))
+    conn = sqlite3.connect(str(db_path), timeout=30.0)
     try:
         query = f"{_CANDIDATE_SELECT} WHERE 1=1"
         params: list = []
@@ -255,7 +255,7 @@ def _get_candidate(conn: sqlite3.Connection, candidate_id: str) -> BlocklistCand
 
 def get_candidate(db_path: Path, candidate_id: str) -> BlocklistCandidate:
     """Fetch a single candidate by ID. Raises KeyError if not found."""
-    conn = sqlite3.connect(str(db_path))
+    conn = sqlite3.connect(str(db_path), timeout=30.0)
     try:
         return _get_candidate(conn, candidate_id)
     finally:
@@ -265,7 +265,7 @@ def get_candidate(db_path: Path, candidate_id: str) -> BlocklistCandidate:
 def update_candidate_status(db_path: Path, candidate_id: str, new_status: str) -> BlocklistCandidate:
     if new_status not in _VALID_STATUSES:
         raise ValueError(f"Invalid status {new_status!r}. Must be one of {_VALID_STATUSES}")
-    conn = sqlite3.connect(str(db_path))
+    conn = sqlite3.connect(str(db_path), timeout=30.0)
     try:
         conn.execute("UPDATE blocklist_candidates SET status=? WHERE id=?", (new_status, candidate_id))
         conn.commit()
@@ -275,7 +275,7 @@ def update_candidate_status(db_path: Path, candidate_id: str, new_status: str) -
 
 
 def mark_pushed(db_path: Path, candidate_id: str) -> BlocklistCandidate:
-    conn = sqlite3.connect(str(db_path))
+    conn = sqlite3.connect(str(db_path), timeout=30.0)
     try:
         conn.execute(
             "UPDATE blocklist_candidates SET status='pushed', pushed_at=? WHERE id=?",
@@ -288,7 +288,7 @@ def mark_pushed(db_path: Path, candidate_id: str) -> BlocklistCandidate:
 
 
 def mark_unblocked(db_path: Path, candidate_id: str) -> BlocklistCandidate:
-    conn = sqlite3.connect(str(db_path))
+    conn = sqlite3.connect(str(db_path), timeout=30.0)
     try:
         conn.execute("UPDATE blocklist_candidates SET status='unblocked' WHERE id=?", (candidate_id,))
         conn.commit()

app/services/diagnose/suppressor.py

@@ -72,7 +72,7 @@ def _fetch_resolved_incidents(db_path: Path) -> list[str]:
     Returns an empty list on any error (missing table, connection failure, etc.).
     """
     try:
-        with sqlite3.connect(str(db_path)) as conn:
+        with sqlite3.connect(str(db_path), timeout=30.0) as conn:
             cursor = conn.execute(
                 "SELECT label, notes FROM incidents WHERE ended_at IS NOT NULL LIMIT 200"
             )

app/services/incidents.py

@@ -57,7 +57,7 @@ def create_incident(
         created_at=now_iso(),
         severity=severity,
     )
-    conn = sqlite3.connect(str(db_path))
+    conn = sqlite3.connect(str(db_path), timeout=30.0)
     conn.execute("PRAGMA journal_mode=WAL")
     conn.execute(
         "INSERT INTO incidents (id, label, issue_type, started_at, ended_at, notes, created_at, severity) "
@@ -71,7 +71,7 @@ def create_incident(
 
 
 def list_incidents(db_path: Path) -> list[Incident]:
-    conn = sqlite3.connect(str(db_path))
+    conn = sqlite3.connect(str(db_path), timeout=30.0)
     conn.execute("PRAGMA journal_mode=WAL")
     conn.row_factory = sqlite3.Row
     rows = conn.execute(
@@ -82,7 +82,7 @@ def list_incidents(db_path: Path) -> list[Incident]:
 
 
 def get_incident(db_path: Path, incident_id: str) -> Incident | None:
-    conn = sqlite3.connect(str(db_path))
+    conn = sqlite3.connect(str(db_path), timeout=30.0)
     conn.execute("PRAGMA journal_mode=WAL")
     conn.row_factory = sqlite3.Row
     row = conn.execute(
@@ -93,7 +93,7 @@ def get_incident(db_path: Path, incident_id: str) -> Incident | None:
 
 
 def delete_incident(db_path: Path, incident_id: str) -> bool:
-    conn = sqlite3.connect(str(db_path))
+    conn = sqlite3.connect(str(db_path), timeout=30.0)
     conn.execute("PRAGMA journal_mode=WAL")
     cur = conn.execute("DELETE FROM incidents WHERE id = ?", (incident_id,))
     conn.commit()
@@ -186,7 +186,7 @@ def store_bundle(db_path: Path, bundle: dict) -> ReceivedBundle:
         entry_count=len(bundle.get("log_entries", [])),
         bundle_json=json.dumps(bundle),
     )
-    conn = sqlite3.connect(str(db_path))
+    conn = sqlite3.connect(str(db_path), timeout=30.0)
     conn.execute("PRAGMA journal_mode=WAL")
     conn.execute(
         "INSERT INTO received_bundles "
@@ -201,7 +201,7 @@ def store_bundle(db_path: Path, bundle: dict) -> ReceivedBundle:
 
 
 def list_bundles(db_path: Path) -> list[ReceivedBundle]:
-    conn = sqlite3.connect(str(db_path))
+    conn = sqlite3.connect(str(db_path), timeout=30.0)
     conn.execute("PRAGMA journal_mode=WAL")
     conn.row_factory = sqlite3.Row
     rows = conn.execute(
@@ -213,7 +213,7 @@ def list_bundles(db_path: Path) -> list[ReceivedBundle]:
 
 
 def get_bundle(db_path: Path, bundle_id: str) -> ReceivedBundle | None:
-    conn = sqlite3.connect(str(db_path))
+    conn = sqlite3.connect(str(db_path), timeout=30.0)
     conn.execute("PRAGMA journal_mode=WAL")
     conn.row_factory = sqlite3.Row
     row = conn.execute(

app/services/search.py

@@ -30,7 +30,7 @@ def build_fts_index(db_path: Path) -> None:
 
     Drops and recreates the table if the schema is stale (missing sequence column).
     """
-    conn = sqlite3.connect(str(db_path))
+    conn = sqlite3.connect(str(db_path), timeout=30.0)
     conn.execute("PRAGMA journal_mode=WAL")
 
     # Check whether existing table has the sequence column; rebuild if not.
@@ -98,7 +98,7 @@ def search(
     or_mode: bool = False,
 ) -> list[SearchResult]:
     """Full-text search with optional filters. Returns results ranked by relevance."""
-    conn = sqlite3.connect(str(db_path))
+    conn = sqlite3.connect(str(db_path), timeout=30.0)
     conn.execute("PRAGMA journal_mode=WAL")
     conn.row_factory = sqlite3.Row
 
@@ -181,7 +181,7 @@ def entries_in_window(
     (e.g. network-syslog) don't crowd out lower-volume but more interesting ones.
     Errors/warnings are ranked first within each source partition.
     """
-    conn = sqlite3.connect(str(db_path))
+    conn = sqlite3.connect(str(db_path), timeout=30.0)
     conn.execute("PRAGMA journal_mode=WAL")
     conn.row_factory = sqlite3.Row
 
@@ -275,7 +275,7 @@ def recent_source_errors(
     Bypasses FTS ranking so text content doesn't affect which errors surface.
     Used by diagnose when FTS keyword search returns nothing for a known source.
     """
-    conn = sqlite3.connect(str(db_path))
+    conn = sqlite3.connect(str(db_path), timeout=30.0)
     conn.execute("PRAGMA journal_mode=WAL")
     conn.row_factory = sqlite3.Row
 
@@ -328,7 +328,7 @@ def recent_source_errors(
 
 def list_sources(db_path: Path) -> list[dict]:
     """Return distinct sources with entry counts and time ranges."""
-    conn = sqlite3.connect(str(db_path))
+    conn = sqlite3.connect(str(db_path), timeout=30.0)
     conn.execute("PRAGMA journal_mode=WAL")
     rows = conn.execute("""
         SELECT
@@ -381,7 +381,7 @@ def stats_summary(db_path: Path, window_hours: int = 24, severity_overrides: lis
     """
     rules = _compile_overrides(severity_overrides or [])
 
-    conn = sqlite3.connect(str(db_path))
+    conn = sqlite3.connect(str(db_path), timeout=30.0)
     conn.execute("PRAGMA journal_mode=WAL")
     conn.row_factory = sqlite3.Row
 

app/tasks/glean_scheduler.py

@@ -49,7 +49,7 @@ def get_state() -> IngestState:
 
 def _query_matched_since(db_path: Path, since: str | None) -> list[dict]:
     """Return entries with non-empty matched_patterns, optionally filtered by ingest_time."""
-    conn = sqlite3.connect(str(db_path))
+    conn = sqlite3.connect(str(db_path), timeout=30.0)
     conn.row_factory = sqlite3.Row
     try:
         if since:

app/watch/watcher.py

@@ -111,7 +111,7 @@ class WatchSource:
         patterns = load_patterns(self.pattern_file)
         compiled = _compile(patterns)
 
-        conn = sqlite3.connect(str(self.db_path))
+        conn = sqlite3.connect(str(self.db_path), timeout=30.0)
         conn.execute("PRAGMA journal_mode=WAL")
         conn.executescript(_SCHEMA)
         conn.commit()

scripts/collect_cluster_logs.sh

@@ -99,6 +99,21 @@ else
   echo "navi: unreachable, skipping docker logs"
 fi
 
+# ── Navi qBittorrent app logs (volume-mounted files, not in docker logs) ──────
+# qBit writes rich per-torrent events to a file inside the compose volume.
+# These are NOT captured by `docker logs` — must be pulled directly.
+QBIT_LOG_BASE="/opt/containers/arr"
+for instance in qbit-tb0 qbit-tb1 qbit-tb2; do
+  remote_log="${QBIT_LOG_BASE}/${instance}/qBittorrent/logs/qbittorrent.log"
+  local_out="${NAVI_DIR}/${instance}-app.log"
+  if ssh ${SSH_OPTS} navi "test -f '${remote_log}'" 2>/dev/null; then
+    ssh ${SSH_OPTS} navi "cat '${remote_log}'" > "${local_out}" 2>/dev/null || : > "${local_out}"
+  else
+    : > "${local_out}"
+  fi
+done
+echo "navi qbit app logs: $(cat "${NAVI_DIR}"/qbit-tb*.log 2>/dev/null | wc -l) lines"
+
 # ── Strahl Docker containers ──────────────────────────────────────────────────
 STRAHL_DIR="${DATA_DIR}/docker-strahl"
 mkdir -p "${STRAHL_DIR}"