fix(onboarding): six defects in self-host deploy path (#443) - #833
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Friction surfaced on a fresh clone → start.sh → login walkthrough. Each fix is small and independent; bundled here per the issue's "all are onboarding hygiene" framing. 1. scripts/deploy/start.sh — auto-generate SECRET_KEY and INTERNAL_API_SECRET if blank (same pattern as the existing CREDENTIAL_ENCRYPTION_KEY block, extracted to a helper). Fail fast with a clear message if ADMIN_PASSWORD is blank rather than booting into a state the operator can't log into. 2. .env.example — document FRONTEND_PORT=80 with an inline comment explaining "remap if your host's port 80 is taken." The var was already read by docker-compose.yml and start.sh but wasn't reachable from the quickstart. 3. scripts/deploy/start.sh — replace "login: admin/password" hint with "login: admin / ADMIN_PASSWORD from .env". New users took "password" as the literal default. 4. src/mcp-server/src/index.ts + README.md — drop hardcoded http://localhost:3000/api-keys hint. Port was wrong (frontend default is 80) and ignored FRONTEND_PORT overrides. Replaced with "your Trinity web UI → Settings → MCP Keys". 5. scripts/deploy/clean.sh — new script. Stops compose + removes leftover agent-* containers + trinity-agent-network. Without this, a fresh install inherits Exited zombie agents from previous tests and the first new agent collides on AGENT_SSH_PORT_START (2222). Preserves data volumes intentionally — operators can wipe those manually. 6. src/mcp-server/Dockerfile — point healthcheck at /health, not /mcp. The /mcp endpoint rejects HEAD requests with 400 (which `wget --spider` sends), so `docker compose ps` reported the container as unhealthy despite serving traffic. /health returns 200 to both HEAD and GET. Verified live: post-rebuild, trinity-mcp-server reports `healthy` within 30s. No schema, API, or runtime-behavior changes. No migration needed. Related to #443 Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
…form_default_model The lint job on #443's PR went red on a file that is NOT in the PR's diff — `tests/test_platform_default_model.py` carries 6 bare `sys.modules` mutations that were merged to dev without an entry in `tests/lint_sys_modules_baseline.txt`. Same #802 rebase-race shape as the original #791 vs #783 incident: baseline-introducing PR (#791) and violation-introducing PR landed disjointly, both green pre-merge, dev went red post-merge, the next PR off dev (this one) inherits it. Ratcheting the baseline here unblocks #443. Same precedent as #796 which baselined `test_cleanup_unreachable_orphan.py` for the same reason. The proper fix is to convert the file's bare sys.modules writes to `monkeypatch.setitem` / `monkeypatch.delitem`; that's scope-creep relative to the onboarding work this PR is doing and should land separately. (That file's count is currently 0 against the lint, so a follow-up that converts it can drop the baseline line altogether.) Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
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Clean, focused fix — all six defects verified. Dockerfile healthcheck and ADMIN_PASSWORD guard are the highest-value changes. Second commit correctly resolves the pre-existing sys_modules baseline rebase-race from #831. ✅ Approved to merge.
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…ts (#678) (#797) * fix(executor): salvage telemetry + auto-retry reader-race empty results Issue #678: when claude's stdout reader thread wedges mid-turn (a tool subprocess inherits the stdout fd), the trailing `result` line is lost and `chat_with_agent` returns null cost/context/response while the schedule_executions row is written as FAILED with no telemetry. Recovery pipeline (agent-server side): - `_classify_empty_result` now returns a structured dict body (message + sanitized partial metadata + raw_message_count) so the backend can salvage what telemetry was captured before the race - `_recover_metadata_from_jsonl` back-fills cost_usd, duration_ms, num_turns, per-call usage, model_name from the on-disk JSONL — Claude Code writes turns to the JSONL via a side channel independent of stdout - `_attempt_empty_result_recovery` shared helper wires JSONL metadata back-fill → text recovery from response_parts → text recovery from JSONL → structured 502 dict body, used by both sync and async paths - session_id_fallback (the UUID we passed via --session-id) closes the recovery gap when the race wedges before claude echoes its session_id - Long-running headless tasks (timeout > 600s) auto-enable JSONL persistence so recovery can fire; short fan-out stays disk-cheap. Session cleanup service reaps the stale JSONLs on its existing sweep - jsonl_recovery hardened: safe session_id regex + resolve()/is_relative_to containment so a corrupted stdout line can't drive the reader outside the projects dir - stream_parser captures model_name from assistant.message.model so it survives the reader-race even when the trailing result line is lost Auto-retry (backend side): - task_execution_service detects the reader-race signature on 502 dict bodies and fires one in-line retry with the same execution_id when num_turns < 5, raw_message_count == 0, parse_failure_count == 0 - retry caps timeout at 300s on both sides so a 30-min task that ate 28 min before failing doesn't get another 30 min on top - CB re-check between attempts; previous-attempt cost rolled into the terminal cost write so spend isn't silently absorbed - audit log `auto_retry` event (fire-and-forget, non-blocking) Salvage path (backend HTTPError handler): - routers/chat.py + task_execution_service.py both parse the structured dict detail and update_execution_status with salvaged cost/context/ context_max instead of null-everything - `_compute_context_used` shared helper keeps success and salvage paths computing context_used the same way Schema: - migration 59: schedule_executions.retry_count INTEGER DEFAULT 0 - ScheduleExecution.retry_count surfaces through get_execution_result - update_execution_status retry_count is COALESCE-preserved so cleanup and scheduler paths don't accidentally zero it Tests: 3 new files (auto_retry signature, dict body shape, JSONL metadata recovery) + dict-body migration in existing classification tests + persist-session flag now combines persist_session OR timeout threshold. Closes #678 Co-Authored-By: Claude <noreply@anthropic.com> * docs(security): add CSO branch-diff audits for #678 work Two daily diff audits run during issue #678 development: - 2026-05-11: scoped to the initial recovery pipeline + auto-retry - 2026-05-12: post mid-audit fix on jsonl_recovery (shape whitelist + is_relative_to containment, 12 parametrized tests for hostile session_id shapes) Refs #678 Co-Authored-By: Claude <noreply@anthropic.com> * fix(tests): drop redundant agent_server sys.modules stubs (#678) `tests/unit/conftest.py:_preload_real_agent_server()` already registers `agent_server` as a namespace package globally before any unit test collection — the per-file `if "agent_server" not in sys.modules: ...` blocks in the two new #678 test files are dead code that just trip `tests/lint_sys_modules.py`. Removes the dead block from `test_error_classifier_dict_body.py` and `test_jsonl_metadata_recovery.py`, plus the now-unused `sys`/`types` imports and supporting path constants. Keeps `from pathlib import Path` in the JSONL-recovery file (used by `_write_jsonl(tmp_path: Path, ...)`) and the agent_server imports themselves (resolve via the conftest namespace shim). All 32 tests in the two files still pass; the lint stops growing the `tests/lint_sys_modules_baseline.txt` baseline by 2. Refs #678 Co-Authored-By: Claude <noreply@anthropic.com> * docs(architecture): document #678 retry_count + auto-retry + headless JSONL reaping Three additive doc edits matching what shipped in the executor recovery work but wasn't reflected in `docs/memory/architecture.md`: 1. `schedule_executions` DDL block now lists the `retry_count INTEGER DEFAULT 0` column added by migration 59. 2. `task_execution_service.py` service-row gains a clause describing the in-line auto-retry (502 dict body / num_turns < 5 / raw_message_count == 0 / parse_failure_count == 0; capped at 300s, previous-attempt cost rolled into the terminal write). 3. `session_cleanup_service` Background-Services row gains a clause noting that headless-task JSONLs (timeout > 600s, auto-enabled by `agent_server/services/jsonl_recovery.py`) are reaped by the same sweep — they aren't in `agent_sessions` so they fall out of the keep set and the existing 1h age guard + 6h cycle removes them. No new component descriptions for the agent-server internal services themselves — `architecture.md` documents the agent-server surface, not its internal services. Refs #678 Co-Authored-By: Claude <noreply@anthropic.com> * fix(tests): restore unit-suite sys.modules between tests (#678) The parent tests/conftest.py #762 baseline-restore never loads for the unit suite because tests/unit/pytest.ini makes tests/unit/ the pytest rootdir. That blind spot let collection-time sys.modules stubs leak across files under pytest-randomly, manifesting on PR #797 as three test_voice_auth regressions (close_code 4001 instead of 4003/accept) across all three CI seeds. Adds an autouse mirror fixture in tests/unit/conftest.py that captures config + database in the baseline, restores before+after each test, and pops non-baseline keys matching a narrow prefix policy. Uses a per-process TRINITY_DB_PATH so two concurrent local pytest invocations don't race on the eager DB init. Converts tests/unit/test_cleanup_unreachable_orphan.py to the lint-exempt _STUBBED_MODULE_NAMES + _restore_sys_modules helper-pair pattern (tests/lint_sys_modules.py:96-115). Drops the now-dead `database` stub since the conftest preload supersedes it. Net: lint (sys.modules pollution check) passes; test_voice_auth's three ownership-gate tests go green across seeds 12345/67890/99999; only the two pre-existing test_orphaned_execution_recovery failures remain (both in CI base baseline). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * fix(tests): add sanitize_dict to credential_sanitizer stub (#678) test_cb_probe_execution_close.py stubs utils.credential_sanitizer in sys.modules to keep the unit tests self-contained, but the stub was missing sanitize_dict. The #678 salvage path in src/backend/services/task_execution_service.py:35 added `from utils.credential_sanitizer import sanitize_dict, ...`, so the test module now fails to import the SUT with: ImportError: cannot import name 'sanitize_dict' from 'utils.credential_sanitizer' That import error is what the 03:07 BST full-suite run mis-attributed to a MagicMock-vs-AsyncMock mismatch. The 7 cluster-A failures actually all share the same ImportError root cause; promoting the circuit mocks would not have helped (production calls circuit.allow_request() synchronously). The one-line stub addition makes all 10 tests in the file green. Verified locally with ADMIN_PASSWORD set: 10 passed, 14 warnings in 0.48s Refs #678 * fix(tests): defeat cross-file sanitizer pollution in cluster-A (#678) The previous sanitize_dict stub commit (b4cc5dde) was correct in isolation but didn't survive the full-suite run. test_validation.py overwrites sys.modules["utils.credential_sanitizer"] with an incomplete stub at module-collection time: _sanitizer_mod = types.ModuleType("utils.credential_sanitizer") _sanitizer_mod.sanitize_text = lambda x: x # only one fn sys.modules["utils.credential_sanitizer"] = _sanitizer_mod Our file used sys.modules.setdefault(...) (a no-op once polluted), so the incomplete stub wins. When the test re-imports services.task_execution_service, the `from utils.credential_sanitizer import sanitize_dict, ...` line raises ImportError. That's the real source of all 7 cluster-A failures the 03:07 BST run misdiagnosed as a MagicMock-vs-AsyncMock issue — production code calls circuit.allow_request() synchronously, so the mock type was never the problem. In parallel, services.task_execution_service itself can be stubbed as a MagicMock by other test files. tests/conftest.py's _SYS_MODULES_BASELINE captures None for that key (not preloaded), so its autouse restore is a no-op. The MagicMock persists; the re-import returns a MagicMock class; svc.execute_task is not awaitable. Defense: a new autouse fixture re-asserts our complete sanitizer stub and evicts services.task_execution_service before every test in this file, so the test's import statement loads the real class against our complete stub. Verified: - test_cb_probe_execution_close.py alone: 10 passed - test_validation.py + test_cb_probe_execution_close.py (in that deterministic order, which previously reproduced the pollution): 29 passed, 3 skipped Refs #678 * docs(test-runs): comprehensive after-fix test plan report for #797 (#678) Three data points: - Control (dev, paper, excl. slow): ~10 pre-existing failures - Treatment 1 (PR unfixed, full): 3465 pass / 24 fail (03:07 BST) - Treatment 2 (PR + cluster-A fix, excl. slow): 3457 / 12 / 127 Net-new failures attributable to PR #797: 0. Cluster A (7 failures) cleared by commit 3b0653b0 — the 03:07 root- cause label was wrong (it blamed MagicMock vs AsyncMock, but production calls circuit.allow_request() synchronously). Actual cause was cross- file sys.modules pollution: test_validation.py overwrites utils.credential_sanitizer with an incomplete stub, defeating our setdefault. The autouse fixture re-asserts our complete stub and evicts services.task_execution_service so each test re-imports the real class. Verified 10/10 isolated and 29 passed when test_validation is collected first. The remaining 12 failures are all pre-existing on dev or seed-dependent flakes in unrelated test files (clusters B, D, E, G + one unit flake). Live verification on the running macau stack confirmed: - Migration 59 applied (retry_count INTEGER DEFAULT 0) - 5 recent rows show retry_count=0 (happy-path correct) - _is_reader_race_signature gate exercises positive + negative cases correctly against deployed code - session_cleanup_service documents the #678 headless JSONL reap Operational note: agent base image built 2026-05-09 pre-dates #678 agent-side commits. Before agent-side fixes (structured error body, JSONL metadata salvage) are live in production agent containers, run ./scripts/deploy/build-base-image.sh and recreate agents. Refs #678, PR #797 * docs(test-runs): live-DB acceptance evidence for #678 reviewer items Documents the two acceptance criteria from PR #797's reviewer comment: 1. Trigger a long-running headless task, kill its stdout reader, verify the failure row carries cost + recovered_from_jsonl=True instead of null telemetry. 2. Confirm retry_count=1 appears on the row when the reader-race signature fires and the retry succeeds. The reader-race itself is non-deterministic (fd inheritance timing), so the script validates the recovery pipeline by mocking only agent_post_with_retry to return the exact structured 502 body that error_classifier._classify_empty_result emits. Everything else runs unmodified against the live trinity.db inside trinity-backend. Results — both PASS: Acceptance #2 (retry-success): Execution ID: 6AmUgSbpF-dMU0kL-xRH2A status=success, retry_count=1, cost=$0.08 ($0.05 failed first attempt rolled in + $0.03 retry) Acceptance #1 (salvage on double-failure): Execution ID: Q06wdBqFtPegQlGzqIVvWw status=failed, retry_count=1, cost=$0.10, context_used=100 (would have been all NULL before #678) Plus 63/63 supporting unit tests pass across the four #678 test files: test_jsonl_metadata_recovery.py (24 — covers JSONL salvage + 12 hostile session_id shapes) test_auto_retry_reader_race.py (14 — gate semantics) test_empty_result_classification.py (7 — dict body shape) test_error_classifier_dict_body.py (18 — sanitization invariants) Refs #678, PR #797 * fix(tests): switch _restore_complete_stubs to monkeypatch (#678) The autouse fixture introduced in 170fc23 to defeat cross-file sanitizer pollution did bare sys.modules writes, which the Issue #762 lint (tests/lint_sys_modules.py) bans for any *new* violations in an already-baselined file. Rewriting via monkeypatch.setitem / monkeypatch.delitem brings the file back to its 5-line baseline and adds auto-revert on teardown. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * fix(tests): read detail['message'] from 502 dict body (#678) PR #797 (#678) changed _classify_empty_result's HTTP 502 detail from a plain string to a structured dict carrying salvage telemetry. The test added by #813 (test_clean_exit_but_missing_cost_falls_to_empty_result_classifier) still called .lower() on the raw detail and now hits AttributeError. Mirror the canonical pattern from tests/unit/test_empty_result_classification.py: assert detail is a dict, then read the human-readable text out of detail['message'] before doing substring checks. No production behavior change — only the assertion plumbing was stale. Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * docs(feature-flows): sync task-execution-service + parallel-headless-execution for #678 PR #797 lands a coupled refactor + behavioral change pair the flow docs needed to capture: - task-execution-service.md: new top-of-doc blockquote for the auto-retry gate on reader-race signature, structured 502 dict body salvage path (cost/context written onto FAILED rows instead of null), shared _compute_context_used helper, and migration 59's retry_count column. - parallel-headless-execution.md: new 2026-05-13 row in Revision History documenting the claude_code.py decomposition (956+465+461+ 448 LOC across new headless_executor, error_classifier, jsonl_recovery, stream_parser modules), dict-body shape evolution, two-step JSONL metadata + text recovery, auto-enable JSONL persistence for timeout > 600s, and path-containment hardening in jsonl_recovery. Closes the optional polish item flagged by /validate-pr (#797). Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com> * docs(test-runs): add #797 full-suite run report 2026-05-12 (#678) Captures the full pytest run (non-unit + unit halves) at HEAD 1b8651e, before the rebase that picked up #833's baseline fix. 2026 pass / 24 fail / 163 skip on the non-unit half in 41:49. Refs #678 * test(acceptance): add live-stack harness for #678 acceptance criteria One-off harness that runs against live trinity.db inside trinity-backend. Mocks only \`agent_post_with_retry\` so the real DB write path, capacity manager, activity service, and audit log fire as they would in production. Verifies the two acceptance criteria: 1. Failure rows carry cost + context (salvaged from the 502 dict body's partial metadata) instead of null when the reader-race signature fires and the retry also fails. 2. \`retry_count=1\` appears on the row when the reader-race signature fires and the retry succeeds. Refs #678 --------- Co-authored-by: Claude <noreply@anthropic.com>
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Summary
Six small fixes on the fresh-clone →
start.sh→ login walkthrough. Each independent, no schema/API/runtime-behavior change.SECRET_KEY+INTERNAL_API_SECRETif blank; fail-fast on blankADMIN_PASSWORDscripts/deploy/start.shFRONTEND_PORT=80with remap comment.env.examplelogin: admin/passwordhint withadmin / ADMIN_PASSWORD from .envscripts/deploy/start.shlocalhost:3000/api-keysURL — replace with "your Trinity web UI → Settings → MCP Keys"src/mcp-server/src/index.ts,README.mdclean.sh— removes leftoveragent-*containers +trinity-agent-network; preserves data volumesscripts/deploy/clean.sh/mcp→/health(the/mcpendpoint rejects HEAD with 400, which is whatwget --spidersends)src/mcp-server/DockerfileVerification (live)
.env, confirmedCREDENTIAL_ENCRYPTION_KEYleft alone when set;SECRET_KEY/INTERNAL_API_SECRETgenerated when blank;ADMIN_PASSWORDguard tripped correctly when blank.bash -non bothclean.shandstart.shclean.mcp-serveragainst this PR's Dockerfile and watcheddocker compose ps mcp-server— wasunhealthybefore, reportsUp (healthy)within 30s now.docker inspect'sState.Health.Statusflipped tohealthywithFailingStreak=0.Out of scope (deferred / separate tracking)
agent-*zombies from previous test runs. The newclean.shwould remove them, but I'm not running it on the dev box as part of this PR — operator's call.docs.ability.ai/getting-started) — issue notes these are tracked separately; in-repodocs/user-docs/guides/*was already corrected alongside thegenerate-user-docsplaybook.feature/443-onboarding-fixesalready exists on remote with @vybe's WIP (refactor(skills): prevent duplicate validation issues, 2026-04-21, same day issue was filed — likely abandoned start at this work). Didn't touch it. This PR ships underfeature/443-onboarding-six-defectsinstead.Related to #443
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