perf(task-sources): run store schema DDL once per process, not per query

[mysma-9403]

Summary

• task_sources::store's with_connection re-ran the full schema DDL + both column migrations on every single query — the identical un-gated pattern PR perf(cron): run store schema DDL once per process, not per query #5708 proposed for cron::store, and the same idiom all three stores inherited from their shared with_connection origin.
• The DDL batch (2 CREATE TABLE + 1 CREATE INDEX) and both add_column_if_missing probes now run once per process per database file, gated behind PRAGMA user_version (on-disk schema authority) with a lock-free fast path. Every call still gets its own fresh connection.
• Behaviour-preserving: the open-time pragmas (busy_timeout, journal_mode = WAL, foreign_keys = ON) are unchanged 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 (Major) and Codex (P2) reviewed the first commit; both are addressed in 44c19911c, and the design now supersedes the original flows::store precedent rather than merely mirroring it (note: flows::store no longer has per-op DDL gating in this repo — its schema init moved to tinyflows-sqlite upstream; cron::store (#5708) is a sibling proposal, still open):

• Complete-schema validation. The cache-hit verify no longer trusts the presence of one table. init_schema stamps PRAGMA user_version = TASK_SOURCES_SCHEMA_VERSION after a full migration, and a hit is honoured only when the on-disk version is at least the expected version — so a runtime-replaced older/partial DB (missing ingested_tasks or a migrated column like card_id/assigned_executor) is re-migrated, not trusted then failed on the incomplete schema.
• Forward-compatible version check (Copilot reviewer, 684433d227): the comparison uses >= rather than ==, treating a DB created by a newer binary (higher user_version) as already-initialized rather than unnecessarily re-running DDL and downgrading the stamp. Matches the repo's idiom in security/approval/store.rs.
• Atomic per-path init. The INITIALIZED_SCHEMAS guard is now held across the verify + init_schema + insert, so two first callers for the same path can't both run the DDL. The fast path is lock-free — the mutex is taken only on a version mismatch, with a double-check under the lock.
• New older_on_disk_schema_under_a_cached_path_is_remigrated test pins the column-drift case (drops assigned_executor, resets user_version, asserts re-migration).

On the flows::store precedent: the original flows::store gating (single-table sqlite_master probe + lock released before init_schema) no longer exists on main — flows::store was reduced to a directory-substitution shim when the schema migrated to tinyflows-sqlite upstream. Both gaps this PR fixed (complete-schema validation, atomic-per-path init) are therefore now resolved for flows as part of that extraction rather than by an in-repo follow-up.

Known tradeoff: TASK_SOURCES_SCHEMA_VERSION must be bumped whenever a table/migration is added to init_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, so user_version is the right call.

Problem

Every store op funnels through with_connection, and before this change each call paid, as pure fixed overhead before its one real query:

• Connection::open (kept — unavoidable, Connection is !Sync),
• an execute_batch of the DDL (2 CREATE TABLE, 1 CREATE INDEX),
• 2 add_column_if_missing calls, each preparing and running PRAGMA table_info(...) and scanning the table's columns.

None of it was gated. This is worse than a per-op tax: the periodic-poll fetch loop (task_sources::pipeline) calls is_ingested, get_card_id, and mark_ingested per task, so a fetch of N tasks paid the full DDL+migration setup 3N times — on top of every RPC-driven list_sources / get_source / add_source.

Solution

Introduce per-process, per-path schema initialization gating via PRAGMA user_version (the repo's established idiom, already used by security/approval/store.rs):

• INITIALIZED_SCHEMAS: OnceLock<Mutex<HashSet<PathBuf>>> — keyed by db path (not a bare flag) so each test's per-TempDir workspace still initializes. Used only as a diagnostic marker for runtime DB replacement detection; the on-disk version check is lock-free and the authority.
• init_schema(conn) — the DDL batch + the 2 migrations, split out of with_connection.
• ensure_schema_initialized(conn, db_path) — lock-free fast path returns immediately when user_version >= TASK_SOURCES_SCHEMA_VERSION; on a version mismatch it serializes init under the mutex with a double-check verify, runs init_schema, stamps the version, and marks the path.

Correctness — the connection setup is byte-identical. The three open-time pragmas still run on every open: busy_timeout and journal_mode = WAL stay in with_connection exactly as before, and foreign_keys = ON was moved out of the gated DDL batch and into with_connection (it is per-connection — not persisted in the db file — so it must run every open for the ingested_tasks ON DELETE CASCADE FK to stay enforced). journal_mode = WAL is persistent and could be gated too, but is left with the other open-time pragmas to keep the connection setup identical and the diff minimal; it is idempotent per open.

Not extracting a shared helper across the three stores is intentional and matches the existing convention: flows::store's add_column_if_missing doc already states it is "kept per-domain rather than shared — each store owns its own connection helper and this is a handful of lines."

Impact

• Runtime: core / CLI (the integrations family is always-compiled, no feature gate). No wire, schema, or config change; no migration.
• Performance: removes the DDL batch + 2 PRAGMA table_info scans from every store op after the first per process, replaced by a single database-header read (PRAGMA user_version) — most impactful inside the per-task fetch loop, which paid it 3× per task. "Remove redundant repeated work on a recurring path," not a hot-loop micro-opt.
• Lock contention: the hot path is entirely lock-free. The process-wide mutex is only entered on a version mismatch (init/re-init), with a second header read under the lock (double-check). Independent database paths contend only during that rare init window.
• Security/compat: none.

Submission Checklist

• Tests added or updated (happy path + at least one failure / edge case) — new schema_reinitializes_when_the_database_file_is_deleted_at_runtime regression pins the verify-on-hit self-heal branch (the one path the gate could regress; WAL sidecars removed too); older_on_disk_schema_under_a_cached_path_is_remigrated pins the column-drift re-migration case. The existing task_sources::store suite all still exercises the cache miss+hit legs through with_connection.
• Diff coverage ≥ 80% — the new gating functions are covered by the new self-heal test plus the whole existing task_sources::store suite routing through with_connection. See "Validation Blocked" for why the focused run used --no-default-features.
• N/A: behaviour-only / perf change — no feature rows added, removed, or renamed in docs/TEST-COVERAGE-MATRIX.md.
• N/A: no matrix feature IDs are affected by this change.
• No new external network dependencies introduced.
• N/A: does not touch a release-cut surface in docs/RELEASE-MANUAL-SMOKE.md.
• N/A: no linked tracking issue — found via a code audit of the store's per-call overhead; the companion cron::store change (perf(cron): run store schema DDL once per process, not per query #5708) is the sibling proposal.

Related

• Closes: N/A (no tracking issue — see checklist)
• Follow-up PR(s)/TODOs: companion cron::store fix is perf(cron): run store schema DDL once per process, not per query #5708 (same pattern). This PR is the deferred follow-up noted there; it touches only task_sources/store.rs and does not overlap my open fix(task-sources): don't prune board cards on a truncated (full-page) fetch #5521 (which is task_sources/pipeline.rs).

---

AI Authored PR Metadata (required for Codex/Linear PRs)

Linear Issue

• Key: N/A
• URL: N/A

Commit & Branch

• Branch: perf/task-sources-store-schema-init-gate
• Commit SHA: 150974713

Validation Run

• N/A: no app/ frontend changes — pnpm --filter openhuman-app format:check not applicable.
• N/A: no TypeScript changes — pnpm typecheck not applicable.
• Focused tests: GGML_NATIVE=OFF cargo test --lib --no-default-features task_sources::store — 12/12 pass, incl. the new self-heal test.
• Rust fmt/check: cargo fmt (clean); core lib + task_sources::store tests compiled and passed under --no-default-features; core lib under product features compiled via the shell's cargo check in the pre-push hook.
• N/A: no app/src-tauri shell changes — Tauri fmt/check not applicable.

Validation Blocked

• command: cargo test --lib task_sources::store (default features)
• error: pre-existing compile break in flows test code on main — tinyflows::observability::ExecutionStep gained a transcript field that src/openhuman/flows/{ops_tests.rs, tinyflows/observability.rs}'s #[cfg(test)] constructors don't set (E0063 ×4). Unrelated to this PR (I touch only src/openhuman/integrations/task_sources/).
• impact: I ran the focused suite with --no-default-features, which excludes the gated flows test code entirely while still compiling the always-on integrations family; the task_sources::store tests pass there (12/12). The break is #[cfg(test)]-only, so the core library itself still compiles — verified via the shell's pre-push cargo check (product features, non-test), which builds openhuman_core as a path dep.

Behavior Changes

• Intended behavior change: none — this is a performance change; observable store behaviour (including deleted-DB self-heal and FK enforcement) is preserved.
• User-visible effect: none.

Summary by CodeRabbit

• Bug Fixes

  • Improved task source database initialization to reliably detect missing or outdated schemas.
  • Preserved existing task source data during schema recovery and migration.
  • Prevented duplicate concurrent schema initialization.
  • Ensured new task sources can be created and retrieved after recovery.
  • Improved consistency when multiple connections access the task source database during initialization.

• Tests

  • Added coverage for recovering partially initialized or outdated cached databases.

[tinysweeper]

tinysweeper found nothing blocking. Approving.

$0.0000 · 0 in / 0 out · 524 embedded · openrouter/openai/text-embedding-3-small

[tinysweeper]

How this change flows

1 changed behaviour across 17 relationships. 6 surrounding behaviours are shown (60 graph nodes walked). 39 further behaviours left out to keep the diagram readable.

flowchart LR
  n0["clear_all_removes_every_source<br/>changed"]:::changed
  n1["github_filter"]:::impacted
  n2["test_config"]:::impacted
  n3["vec"]:::impacted
  n4["mark_ingested"]:::impacted
  n5["dedup_detects_seen_and_edited_tasks"]:::impacted
  n6["list_ingested_orders_newest_first"]:::impacted
  n0 -->|calls| n1
  n0 -->|tests| n1
  n0 -->|calls| n2
  n0 -->|tests| n2
  n1 -->|calls| n3
  n5 -->|calls| n1
  n5 -->|tests| n1
  n5 -->|calls| n2
  n5 -->|tests| n2
  n5 -->|calls| n4
  n5 -->|tests| n4
  n6 -->|calls| n1
  n6 -->|tests| n1
  n6 -->|calls| n2
  n6 -->|tests| n2
  n6 -->|calls| n4
  n6 -->|tests| n4
  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

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_{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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📝 Walkthrough

Walkthrough

The task-source store validates cached schemas with PRAGMA user_version and performs guarded transactional initialization. JSON-RPC readiness checks now use BUS.get(). Tests cover schema remigration and asynchronous bus setup.

Changes

Task-source database lifecycle

Layer / File(s)	Summary
Versioned schema initialization src/openhuman/integrations/task_sources/store.rs	The store validates schema versions, serializes stale-schema initialization, applies connection pragmas on every open, and stamps version 1 after successful migrations.
Cached schema migration coverage src/openhuman/integrations/task_sources/store_tests.rs	The regression test verifies column restoration, existing-row preservation, and continued source creation and retrieval after remigration.

Event-bus readiness checks

Layer / File(s)	Summary
Current event-bus readiness path src/core/jsonrpc.rs, src/core/jsonrpc_tests.rs	Subscriber readiness checks use BUS.get(). The related test initializes BUS asynchronously with init_in_process.

Priority: ⬇️ Low

Estimated code review effort: 4 (Complex) | ~45 minutes

Change: Refactor

Sequence Diagram(s)

sequenceDiagram
  participant StoreOperation
  participant with_connection
  participant SchemaInitializer
  participant SQLite
  StoreOperation->>with_connection: request connection
  with_connection->>SQLite: apply connection pragmas
  with_connection->>SchemaInitializer: validate user_version
  SchemaInitializer->>SQLite: run transactional DDL and migrations
  SchemaInitializer->>SQLite: write user_version 1
  SchemaInitializer-->>with_connection: initialization complete
  with_connection-->>StoreOperation: execute store operation

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Suggested reviewers: senamakel

Merge Risk: ⚪ Minimal · up to 76a54

The schema initialization and event-bus readiness changes are covered by focused tests, with no remaining merge-blocking risk identified.

🚥 Pre-merge checks | ✅ 4 | ❌ 1

❌ Failed checks (1 warning)

Check name	Status	Explanation	Resolution
Docstring Coverage	⚠️ Warning	Docstring coverage is 50.00% which is insufficient. The required threshold is 80.00%. Docstring coverage is scoped to functions touched by this diff. Analyzed 8 functions across 3 files.	Write docstrings for the functions missing them to satisfy the coverage threshold.

✅ Passed checks (4 passed)

Check name	Status	Explanation
Description Check	✅ Passed	Check skipped - CodeRabbit’s high-level summary is enabled.
Title check	✅ Passed	The title clearly and concisely describes the main change: schema DDL now runs once per process instead of once per query.
Linked Issues check	✅ Passed	Check skipped because no linked issues were found for this pull request.
Out of Scope Changes check	✅ Passed	Check skipped because no linked issues were found for this pull request.

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Inline comments:
In `@src/openhuman/integrations/task_sources/store.rs`:
- Around line 496-506: Update the schema-presence validation before the early
return in the task-source initialization flow to verify the complete current
schema, including both required tables and migrated columns, rather than only
checking task_sources. Ensure incomplete or outdated databases continue through
init_schema, and return early only after validation succeeds.

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[M3gA-Mind]

Maintainer review pass — findings only, nothing pushed to your branch.

Short version: the change is sound and still applies cleanly (MERGEABLE against fa044d388); the red CI is not yours; but two of the three precedents the PR argues from no longer hold on main, and that is worth knowing before this lands.

1. The red check is 10-day-old vendor drift, not your code

Rust Core Coverage fails with:

error[E0063]: missing field `transcript` in initializer of `tinyflows::observability::ExecutionStep`
  --> src/openhuman/flows/ops_tests.rs:3202:30
  --> src/openhuman/flows/tinyflows/observability.rs:243:34

Neither file is in this PR (you touch task_sources/store.rs and store_tests.rs only). That run is from 2026-08-23, before the vendored tinyflows pin moved; main @ fa044d388 is green on every lane. Push any no-op rebase onto current main and it should clear — nothing to fix in the diff.

2. Two of your three precedents are gone from main

This is the part I'd want a second pair of eyes on, because the PR body leans on them:

• flows::store "accepted R-m8 gating" — no longer exists. src/openhuman/flows/store.rs on main has been reduced to a directory-substitution shim; its header now reads "The store itself is tinyflows_sqlite::flows — schema, SQL, migrations and concurrency all live there." There is no INITIALIZED_SCHEMAS, no init_schema, no sqlite_master probe left in this repo. So the "mirrors the accepted precedent" argument no longer describes the tree, and your stated follow-up ("applying the same two fixes to flows::store") is not actionable here — it would be an upstream change in tinyflows_sqlite.
• cron::store (perf(cron): run store schema DDL once per process, not per query #5708) — the PR body says perf(cron): run store schema DDL once per process, not per query #5708 "just fixed" this pattern. perf(cron): run store schema DDL once per process, not per query #5708 is still OPEN; cron/store*.rs on main has no gating either. It is a sibling proposal, not landed precedent.

Neither makes this PR wrong — the per-op DDL tax in task_sources is real, still present on main at store.rs:464, and the fetch loop really does pay it 3× per task. But the direction of travel on main is evicting store schema into vendored crates rather than gating it in-repo, so a maintainer should decide whether task_sources is heading the same way before taking an in-repo optimisation of it. Please update those two claims in the PR body either way — as written they assert a convention that isn't there.

The one precedent that does hold is the good one: PRAGMA user_version for schema-version stamping is already the repo's idiom in security/approval/store.rs:141-154. Your TASK_SOURCES_SCHEMA_VERSION follows it faithfully.

3. On the implementation

No objection. Specifically checked and happy with:

• foreign_keys = ON moved out of the gated batch into with_connection. This is the one change that could have silently broken ingested_tasks ON DELETE CASCADE — it is per-connection and not persisted, so it must run every open. You caught it and the comment says why. Good.
• Guard held across verify + init_schema + insert. Correctly closes the double-init race CodeRabbit raised.
• Marking the path only after init_schema succeeds, so a transient failure retries rather than wedging.
• user_version checked on the hit path rather than a single-table sqlite_master probe — this is strictly what both @chatgpt-codex-connector and CodeRabbit asked for, and it covers the missing-column case their single-table version would not have.

One observation, not a blocker: the hit path now takes a process-wide Mutex and runs a PRAGMA user_version query on every store op. That is much cheaper than the DDL batch plus two PRAGMA table_info scans it replaces, so the trade is clearly positive, but it does introduce a single global lock on a path that previously had none. Worth a sentence in the PR body under Impact so nobody has to rediscover it.

4. Threads

Two, both about the same finding (validate the whole schema, not one table), both addressed in 44c19911c. CodeRabbit resolved theirs and re-approved. @chatgpt-codex-connector's is still open but outdated — the user_version design answers it. Reply pointing at 44c19911c and resolve it; don't wait on a re-review.

To get this green: rebase onto fa044d388, correct the two precedent claims in the body, resolve the Codex thread. No code changes needed from my side of the review.

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[mysma-9403]

Follow-up push (5b14aa6bb): proactively simplified ensure_schema_initialized to a lock-free fast path, keeping this PR in lockstep with the sibling store-init-gate change on #5708.

The on-disk PRAGMA user_version is already authoritative (init_schema stamps it only after a full, successful migration), so it's now read lock-free first and the common already-initialized call returns without acquiring the process-global mutex at all. The mutex is taken only on a version mismatch (init/re-init), with a second user_version read under the lock (double-check). This:

• removes the global lock from the hot path (no cross-path serialization on the common case);
• preserves atomic-per-path init — two first callers racing on the same fresh path run the DDL exactly once, the loser observing the winner's stamp on the recheck;
• preserves migrated-column validation — a stale/partial on-disk schema carries a non-matching user_version and falls through to the idempotent init_schema.

INITIALIZED_SCHEMAS no longer gates the DDL (the on-disk version does); it's kept purely as a diagnostic marker so the "deleted/replaced at runtime" warn! fires only for a path this process already initialized, not on every fresh-boot init (user_version 0). Both existing regression tests still pass.

This mirrors the exact change CodeRabbit verified on #5708 ("the original hot-path serialization finding is addressed; a path-specific lock registry is not required" — #5708 (comment)). Framing honestly: this is a code-clarity / correctness-of-locking change, not a measured speedup — the real win of the PR (DDL batch + metadata scans → one header read per call) is unchanged.

[Copilot]

🟡 Changes recommended

The new user_version check treats newer on-disk versions as a mismatch and can stamp the schema version downward, which is a correctness/compatibility bug on downgrade scenarios.

Once you've addressed the issues Copilot identified, you can request another Copilot review.

Pull request overview

This PR improves the Rust core’s task_sources SQLite store performance by avoiding repeated schema initialization work on every store operation, while preserving the “self-heal” behavior when the DB is deleted/replaced at runtime.

Changes:

• Added a per-db-path, process-wide schema initialization gate using PRAGMA user_version, so DDL + additive migrations run only when needed.
• Kept per-connection pragmas (busy_timeout, journal_mode=WAL, foreign_keys=ON) applied on every connection open.
• Added regression tests covering runtime DB deletion self-heal and “older schema swapped under cached path” re-migration.

File summaries

File	Description
src/openhuman/integrations/task_sources/store.rs	Introduces user_version-based schema init gating and factors schema setup into init_schema / ensure_schema_initialized.
src/openhuman/integrations/task_sources/store_tests.rs	Adds regression tests for deleted-DB re-init and schema drift re-migration under a cached path.

Review details

• Files reviewed: 2/2 changed files
• Comments generated: 1
• Review effort level: Lite

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Codex Review Summary

This comment shows the latest Codex review activity on this pull request.

Review	Status	Commit	Review trigger
📝 Code Review	✅ Completed 2026-09-12T00:35:00.717488Z	5f302d2	New commits
🔒 Security Review	✅ Completed 2026-09-11T16:16:32.887139Z	684433d	New commits

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Inline comments:
In `@src/openhuman/integrations/task_sources/store.rs`:
- Around line 611-612: Update init_schema to wrap task-sources schema
initialization in an immediate SQLite transaction: recheck user_version after
beginning it, run any required migration, stamp TASK_SOURCES_SCHEMA_VERSION, and
commit the transaction atomically. Preserve the existing initialization guard
and avoid stamping when the rechecked version is already current or newer.

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