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perf(cron): run store schema DDL once per process, not per query - #5708
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`cron::store::with_connection` re-ran the full schema DDL (8 statements) plus all 11 `add_column_if_missing` migration probes on *every* call — i.e. before every one of the 16 store ops: `due_jobs` on each scheduler tick, `record_run`/`reschedule_after_run`/`record_last_run` per executed job, and every RPC-driven `list_jobs`/`get_job`/`add_*`. Each `add_column_if_missing` prepares and runs `PRAGMA table_info(cron_jobs)` and scans ~17 columns, so this was ~187 discarded column comparisons on top of the DDL batch, as pure fixed overhead ahead of the real query. Gate the DDL + migrations behind a per-path "already initialized" set so they run once per process per database file, mirroring the accepted `flows::store` R-m8 gating — which was itself derived from this very `with_connection` idiom, so this brings the fix back to the store it was copied from. Every call still opens its own fresh `Connection` (`Connection` is `!Sync`); only the redundant schema work is elided. - `INITIALIZED_SCHEMAS: OnceLock<Mutex<HashSet<PathBuf>>>` keyed by db path (not a bare flag) so each test's per-`TempDir` workspace still initializes. - `ensure_schema_initialized` does a "trust, but verify" indexed `sqlite_master` lookup on a cache hit, so a database deleted or replaced at runtime self-heals instead of wedging at `no such table`. - `PRAGMA foreign_keys = ON` is per-connection (not persisted in the db file), so it moves *out* of the gated DDL into `with_connection` and still runs on every open — the `cron_runs ON DELETE CASCADE` FK stays enforced. No `journal_mode = WAL` / `busy_timeout` added: behaviour is otherwise byte-identical, gating only what already ran. New `schema_reinitializes_when_the_database_file_is_deleted_at_runtime` test pins the verify-on-hit self-heal branch (the one path the gate could regress). Claude-Session: https://claude.ai/code/session_01ACB4Ugi5pJMQqoCbZnVo6f
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Included review availability: Your plan provides up to 10 included reviews per hour; 9 remain after this review. 📝 WalkthroughWalkthroughThe cron store now caches schema initialization per database path, validates SQLite ChangesCron schema lifecycle
Estimated code review effort: 3 (Moderate) | ~25 minutes Merge Risk: 🔵 Low · up to The change removes repeated schema work from cron store operations but holds a process-wide lock while verifying and initializing schemas, so first access to different database files can briefly serialize. The PR is mergeable with explicit owner awareness or a follow-up if broader initialization parallelism is needed. Sequence Diagram(s)sequenceDiagram
participant with_connection
participant schema_cache_mutex
participant SQLite_database
with_connection->>schema_cache_mutex: verify cached database path
schema_cache_mutex->>SQLite_database: read user_version
SQLite_database-->>schema_cache_mutex: return schema version
schema_cache_mutex->>SQLite_database: run DDL and migrations when stale
SQLite_database-->>schema_cache_mutex: complete initialization
schema_cache_mutex->>SQLite_database: stamp CRON_SCHEMA_VERSION
Suggested reviewers: Poem
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Inline comments:
In `@src/openhuman/cron/store.rs`:
- Around line 816-845: Update the schema initialization flow around
INITIALIZED_SCHEMAS and init_schema so cache verification and initialization are
atomic per database path. Hold a path-specific guard across the cache check and
init_schema, or recheck the cache after acquiring that guard, ensuring
concurrent callers cannot both run initialization for the same path while
preserving the existing schema-presence recovery behavior.
- Around line 821-831: Update the schema-present cache-hit logic in the cron
database initialization flow to verify that cron_jobs includes the required
agent_id and profile_id columns before returning Ok(()); otherwise continue
through init_schema/migrations. Add a regression test that replaces the database
file with an older cron_jobs schema and confirms initialization migrates it
successfully.
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How this change flows1 changed behaviour across 9 relationships. 6 surrounding behaviours are shown (60 graph nodes walked). 51 further behaviours left out to keep the diagram readable. flowchart LR
n0["dedup_named_jobs_ignores_unnamed_jobs<br/>changed"]:::changed
n1["test_config"]:::impacted
n2["add_job"]:::impacted
n3["with_connection"]:::impacted
n4["list_jobs"]:::impacted
n5["get_job"]:::impacted
n6["add_shell_job"]:::impacted
n0 -->|calls| n1
n0 -->|tests| n1
n0 -->|calls| n2
n0 -->|tests| n2
n2 -->|calls| n6
n4 -->|calls| n3
n5 -->|calls| n3
n6 -->|calls| n3
n6 -->|calls| n5
classDef changed fill:#0d4429,stroke:#238636,color:#e6edf3
classDef impacted fill:#161b22,stroke:#6e7681,color:#c9d1d9
classDef flagged fill:#5a1e02,stroke:#d93f0b,color:#ffffff
classDef blocking fill:#67060c,stroke:#f85149,color:#ffffff
Green: changed behaviour. Grey: surrounding behaviour. Arrows name the call, use, implementation, or test relationship. Orange: has findings. Red: has a finding that blocks the merge. |
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priority: p3
Addresses the CodeRabbit (2× Major) and Codex (P2) review on tinyhumansai#5708. 1. Complete-schema validation. The cache-hit verify probed only for the `cron_jobs` table via `sqlite_master`, so a database replaced at runtime with an older/partial schema (that table present but missing a migrated column such as `agent_id`/`profile_id`, or the `cron_runs` table) was trusted and later failed with `no such column`. Replace the single-table probe with a `PRAGMA user_version` check: `init_schema` now stamps `CRON_SCHEMA_VERSION` after a full, successful migration, and a cache hit is honoured only when the on-disk version matches. Any deleted (fresh file => version 0) or drifted database re-runs the idempotent `init_schema`, restoring the pre-gating self-heal for column drift as well as a missing table. 2. Atomic per-path init. The `INITIALIZED_SCHEMAS` guard was released before `init_schema`, so two first callers for the same path could both run the DDL. Hold the guard across the verify + `init_schema` + insert so initialization happens exactly once per process per database file. On a cache hit the critical section is a single `PRAGMA user_version` read. New `older_on_disk_schema_under_a_cached_path_is_remigrated` test drops a migrated column and clears the version stamp under a cached path, then asserts the next store op re-migrates rather than failing `no such column`. Claude-Session: https://claude.ai/code/session_01ACB4Ugi5pJMQqoCbZnVo6f
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Inline comments:
In `@src/openhuman/cron/store.rs`:
- Around line 826-852: Replace the single global initialization lock around the
verification and init_schema call with a short-lived registry lock that
retrieves or creates an Arc<Mutex<()>> for the current db_path, then hold only
that path-specific mutex during PRAGMA user_version validation and init_schema.
Keep INITIALIZED_SCHEMAS access brief and separate so initialization of one
database path does not block independent paths.
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@coderabbitai review — both Major findings (complete-schema validation via |
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Maintainer triage pass — review only, no changes pushed, not an approval. Good news first: your red CI is not your fault and is already fixed on
That is a vendored- The conflict is the file split
Review threadscodex's "verify the complete schema before skipping migrations" (marked outdated) — you already fixed this. The current diff stamps and validates CodeRabbit's "use a path-specific initialization guard" — technically correct, and I would push back on the priority. It is true that the single global The optimisation itself is worth having: 16 store operations each paying a |
Round-2 review follow-up (CodeRabbit): the process-global INITIALIZED_SCHEMAS mutex was held across the PRAGMA user_version read and init_schema, so every with_connection call took the lock on the hot path and independent db paths serialized during init. The on-disk user_version is already authoritative (init_schema stamps it only after a full migration), so read it lock-free first and return on a match — the common already-initialized case never touches the mutex. Only a version mismatch takes the lock, re-reads under it (double-check), and runs the DDL, so initialization stays atomic per path (the earlier round-1 fix) and migrated columns are still validated via the version gate (also round-1). INITIALIZED_SCHEMAS no longer gates the DDL; it is kept purely as a diagnostic marker so the "deleted/replaced at runtime" warning fires only for a path this process already initialized, not on every fresh-boot init (version 0). Both round-1 regression tests still pass (deletion self-heal + older-on-disk schema re-migration); 24/24 cron::store green. Claude-Session: https://claude.ai/code/session_01ACB4Ugi5pJMQqoCbZnVo6f
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@coderabbitai review — the round-2 finding on |
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🟢 Approval recommended
The change is behavior-preserving with targeted regression tests for the key failure modes, and the remaining feedback is a minor diagnostics improvement.
Pull request overview
This PR removes redundant per-query SQLite schema initialization work in the Rust core’s cron::store by gating the DDL+migrations behind a per-database-path, per-process initialization check using PRAGMA user_version, while preserving per-connection pragmas and the store’s self-healing behavior if the DB file is deleted/replaced at runtime.
Changes:
- Add a per-process, per-DB-path schema init gate (
ensure_schema_initialized) and move DDL+migrations intoinit_schema, stampingPRAGMA user_versionon successful migration. - Keep
PRAGMA foreign_keys = ONas a per-connection setup inwith_connection(behavior-preserving for FK enforcement). - Add regression tests covering runtime DB deletion self-heal and “older/partial schema swapped under cached path” re-migration.
File summaries
| File | Description |
|---|---|
| src/openhuman/cron/store.rs | Introduces schema init gating via user_version, moves schema work into init_schema, and keeps per-connection pragmas in with_connection. |
| src/openhuman/cron/store_tests.rs | Adds regression tests ensuring schema reinitialization after DB deletion and re-migration when an older/partial schema is swapped in under a cached path. |
Review details
- Files reviewed: 2/2 changed files
- Comments generated: 1
- Review effort level: Lite
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| let is_current = || -> bool { | ||
| conn.query_row("PRAGMA user_version", [], |row| row.get::<_, i64>(0)) | ||
| .unwrap_or(0) | ||
| == CRON_SCHEMA_VERSION | ||
| }; |
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Mirrors the verified sibling change on tinyhumansai#5708. The process-global INITIALIZED_SCHEMAS mutex was held across the PRAGMA user_version read and init_schema, so every with_connection call took the lock on the hot path and independent db paths serialized during init. The on-disk user_version is already authoritative (init_schema stamps it only after a full migration), so read it lock-free first and return on a match — the common already-initialized case never touches the mutex. Only a version mismatch takes the lock, re-reads under it (double-check), and runs the DDL, so initialization stays atomic per path and migrated columns are still validated via the version gate (both earlier fixes preserved). INITIALIZED_SCHEMAS no longer gates the DDL; it is kept purely as a diagnostic marker so the "deleted/replaced at runtime" warning fires only for a path this process already initialized, not on every fresh-boot init (version 0). Both regression tests still pass (deletion self-heal + older-on-disk schema re-migration); 13/13 integrations::task_sources::store green. Claude-Session: https://claude.ai/code/session_01ACB4Ugi5pJMQqoCbZnVo6f
Mirrors the verified sibling change on tinyhumansai#5708 (and tinyhumansai#5709). The process-global INITIALIZED_SCHEMAS mutex was held across the PRAGMA user_version read and init_schema, so every with_connection call took the lock — and in flows that runs once per node per live run via upsert_flow_run_step, not just at open, so the hot-path serialization is the most reachable of the three stores. The on-disk user_version is already authoritative (init_schema stamps it only after a full migration), so read it lock-free first and return on a match — the common already-initialized case never touches the mutex. Only a version mismatch takes the lock, re-reads under it (double-check), and runs the DDL, so initialization stays atomic per path and migrated columns are still validated via the version gate (both preserved). INITIALIZED_SCHEMAS no longer gates the DDL; it is kept purely as a diagnostic marker so the "deleted/replaced at runtime" warning fires only for a path this process already initialized, not on every fresh-boot init (version 0). All flows::store regression tests still pass (deletion self-heal, older-on-disk re-migration, per-path independence, fresh-init idempotence); 47/47 green. Claude-Session: https://claude.ai/code/session_01ACB4Ugi5pJMQqoCbZnVo6f
`ensure_schema_initialized` confirmed a cached "already initialized" path with a single-table `sqlite_master` presence probe for `flow_definitions`. That honours the cache whenever the table merely exists, so a `flows.db` replaced at runtime with an older/partial schema — the table present but missing a migrated column (`require_approval` / `graph_hash`) or one of the other tables — passed the probe, and the next query then failed with `no such column` / `no such table` until the process restarted. The probe only restored self-healing for a deleted (empty) database, not a drifted one. The gate also dropped the `INITIALIZED_SCHEMAS` guard before `init_schema`, so two first callers for the same path could both run the DDL. Replace the presence probe with a `PRAGMA user_version` gate and make the fast path lock-free: - `init_schema` stamps `FLOWS_DB_SCHEMA_VERSION` into `user_version` only after a full, successful migration. - `ensure_schema_initialized` reads `user_version` lock-free first and returns on a match, so the common already-initialized case — which runs once per node per live run via `upsert_flow_run_step`, not just at store open — never acquires the process mutex. - Only a version mismatch takes the `INITIALIZED_SCHEMAS` lock, re-reads `user_version` under it (double-check), then runs the idempotent `init_schema`, so init is atomic per path and a stale/partial on-disk schema (including a drifted column) is re-migrated instead of trusted. - `INITIALIZED_SCHEMAS` no longer gates the DDL; it is kept as a diagnostic marker so the "deleted/replaced at runtime" warning fires only for a path this process already initialized, not on every fresh-boot init (version 0). Add `flows::older_on_disk_schema_under_a_cached_path_is_remigrated`, which drops the `require_approval` migrated column and resets `user_version` under a cached path, then asserts the next op re-migrates rather than failing `no such column`. These two findings were raised (CodeRabbit/Codex) on the equivalent in-repo fix in the host before this store was extracted here; the lock-free variant was verified on tinyhumansai/openhuman#5708.
Mirrors the verified sibling change on tinyhumansai#5708. The process-global INITIALIZED_SCHEMAS mutex was held across the PRAGMA user_version read and init_schema, so every with_connection call took the lock on the hot path and independent db paths serialized during init. The on-disk user_version is already authoritative (init_schema stamps it only after a full migration), so read it lock-free first and return on a match — the common already-initialized case never touches the mutex. Only a version mismatch takes the lock, re-reads under it (double-check), and runs the DDL, so initialization stays atomic per path and migrated columns are still validated via the version gate (both earlier fixes preserved). INITIALIZED_SCHEMAS no longer gates the DDL; it is kept purely as a diagnostic marker so the "deleted/replaced at runtime" warning fires only for a path this process already initialized, not on every fresh-boot init (version 0). Both regression tests still pass (deletion self-heal + older-on-disk schema re-migration); 13/13 integrations::task_sources::store green. Claude-Session: https://claude.ai/code/session_01ACB4Ugi5pJMQqoCbZnVo6f Co-authored-by: Medulla <medulla@tinyhumans.ai>
Summary
cron::store'swith_connectionre-ran the full schema DDL + all 11 column migrations on every single query. This closes that drift withflows::store, which was derived from this exactwith_connectionidiom and later got the fix (R-m8) thatcronnever received.add_column_if_missingprobes now run once per process per database file, gated behind a per-path "already initialized" set — every call still gets its own fresh connection.PRAGMA foreign_keys = ON(a per-connection setting) still runs on every open; the self-healing on a deleted/replaced DB is preserved by a verify-on-hit and pinned by a new regression test.Review updates (post-open)
CodeRabbit (2× Major) and Codex (P2) reviewed the first commit; both are addressed in
cc7f7626a, and the design now supersedes theflows::storeprecedent rather than merely mirroring it:init_schemastampsPRAGMA user_version = CRON_SCHEMA_VERSIONafter a full migration, and a hit is honoured only when the on-disk version matches — so a runtime-replaced older/partial DB (missing a migrated column such asagent_id/profile_id, or thecron_runstable) is re-migrated, not trusted then failed withno such column. This is exactly CodeRabbit's suggestion ("record and validate a schema version").INITIALIZED_SCHEMASguard is now held across the verify +init_schema+ insert, so two first callers for the same path can't both run the DDL.older_on_disk_schema_under_a_cached_path_is_remigratedtest pins the column-drift case (dropsprofile_id, resetsuser_version, asserts re-migration).On the
flows::storeprecedent:flows::storestill uses the single-tablesqlite_masterprobe and releases its lock beforeinit_schema— i.e. both gaps flagged here are latent there too. Applying the same two fixes toflows::storeis a sensible follow-up, not bundled here to keep this PR single-concern.Known tradeoff:
CRON_SCHEMA_VERSIONmust be bumped whenever a table/migration is added toinit_schema(documented on the const). A future migration added without bumping it would silently skip drift-detection for older DBs. The alternative — enumerating expected columns on each hit — carries the same discipline with more surface, souser_versionis the right call.Problem
Every one of the 16 store ops funnels through
with_connection, and before this change each call paid, as pure fixed overhead before its one real query:Connection::open(kept — unavoidable,Connectionis!Sync),execute_batchof 8 DDL statements (2CREATE TABLE, 5CREATE INDEX/partial-unique-index, and — pulled out here — 1PRAGMA),add_column_if_missingcalls, each of which prepares and runsPRAGMA table_info(cron_jobs)and linearly scans all ~17 columns (~187 discarded column comparisons per op).None of it was gated. The call sites are a steady, process-lifetime load, not one-off startup:
due_jobs— every scheduler tick (scheduler::tick_once,reliability.scheduler_poll_secs),record_run+reschedule_after_run+record_last_run— per executed job,list_jobs/get_job/add_*— every RPC-driven cron interaction.Solution
Mirror the accepted
flows::storegating exactly (it documents itself as mirroringcron::store's idiom, so this is bringing the fix home):INITIALIZED_SCHEMAS: OnceLock<Mutex<HashSet<PathBuf>>>— keyed by db path (not a bare flag) so each test's per-TempDirworkspace still initializes.init_schema(conn)— the DDL batch + the 11 migrations, split out ofwith_connection.ensure_schema_initialized(conn, db_path)— runsinit_schemaon a miss and marks the path only after success; on a hit it does one indexedsqlite_masterlookup to confirm the table is really on disk before trusting the cache (trust, but verify), so a DB deleted/replaced at runtime still self-heals instead of wedging atno such table.Correctness — the one behaviour that must not move:
PRAGMA foreign_keys = ONis per-connection (it is not persisted in the db file), so it was moved out of the gated DDL batch and intowith_connection, where it still runs on every open — thecron_runs ON DELETE CASCADEFK stays enforced on every connection exactly as before. I deliberately did not addjournal_mode = WALorbusy_timeout(whichflowscarries) —cronnever had them, and this PR keeps behaviour otherwise byte-identical, gating only what already ran.Not extracting a shared helper is intentional and matches the existing convention:
flows::store'sadd_column_if_missingdoc already states it is "kept per-domain rather than shared — each store owns its own connection helper and this is a handful of lines." The same reasoning applies to the ~35-line init gate.Impact
sqlite_masterprobe. This is a "remove redundant repeated work on a recurring path" change, not a hot-loop micro-opt.Submission Checklist
schema_reinitializes_when_the_database_file_is_deleted_at_runtimeregression pins the verify-on-hit self-heal branch (the one path the gate could regress); the existing 20+cron::storetests all still exercise the cache miss+hit legs throughwith_connection.cron::storesuite routing throughwith_connection. See "Validation Blocked" for why the focused run used--no-default-features(a pre-existingflowstest-code break onmain, unrelated to this PR).docs/TEST-COVERAGE-MATRIX.md.docs/RELEASE-MANUAL-SMOKE.md.flows::storeR-m8 precedent is the reference.Impact
(see Impact section above)
Related
integrations::task_sources::store'swith_connectionhas the identical un-gated DDL-per-call pattern (hit 3× per task inside the fetch loop). It is intentionally not bundled here to keep this single-concern and because those files overlap my open fix(task-sources): don't prune board cards on a truncated (full-page) fetch #5521 — separate follow-up.AI Authored PR Metadata (required for Codex/Linear PRs)
Linear Issue
Commit & Branch
perf/cron-store-schema-init-gate93d5e5ad9Validation Run
app/frontend changes —pnpm --filter openhuman-app format:checknot applicable.pnpm typechecknot applicable.cargo test --lib --no-default-features cron::store(see below for why--no-default-features).cargo fmt(clean); core lib +cron::storetests compiled and passed under--no-default-features(23/23); core lib under product features compiled via the shell'scargo checkin the pre-push hook (exit 0). The core crate's own literaldefault-featurecargo checkwas not run locally — the change is feature-agnostic (std + rusqlite), so that is left to the Quality lane.app/src-taurishell changes — Tauri fmt/check not applicable.Validation Blocked
command:cargo test --lib cron::store(default features)error:pre-existing compile break inflowstest code onmain—tinyflows::observability::ExecutionStepgained atranscriptfield thatsrc/openhuman/flows/{ops_tests.rs, tinyflows/observability.rs}'s#[cfg(test)]constructors don't set (E0063 ×4). Unrelated to this PR (I touch onlysrc/openhuman/cron/).impact:I ran the focused suite with--no-default-features, which excludes the gatedflowstest code entirely while still compiling the always-oncrondomain; thecron::storetests pass there (23/23). The break is#[cfg(test)]-only, so the core library itself still compiles — verified via the shell's pre-pushcargo check(product features, non-test), which buildsopenhuman_coreas a path dep and passed (exit 0).Behavior Changes
Summary by CodeRabbit
Bug Fixes
Tests