Fix recurring 60s timeout in logs MCP tool degrading audit datasets by Copilot · Pull Request #45714 · github/gh-aw

Copilot · 2026-07-15T10:22:34Z

The logs MCP tool was hitting the MCP gateway's default 60s tool-execution deadline mid-download on daily audit runs (safe-output-health, api-consumption), killing the gh aw logs subprocess via context cancellation before it could write continuation data — leaving reports on partial datasets.

Changes

Immediate fix: `safe-output-health.md`

Expands engine: claude to set engine.mcp.tool-timeout: 10m, matching api-consumption-report.md (already fixed). Raises the gateway per-tool deadline from 60s to 10m.

Systemic fix: deadline-aware subprocess timeout (`mcp_tools_privileged.go`)

Adds effectiveMCPLogsToolTimeoutMinutesWithDeadline(ctx, requestedTimeout, count) that caps the subprocess --timeout to floor((remaining − 30s buffer) / 1min) when the context carries a deadline shorter than the auto-scaled value. The 30s buffer gives the subprocess time to write continuation data before the gateway context fires.
Examples with mcpLogsDeadlineBufferSeconds = 30:
- 10m deadline, 100 runs (auto=3m) → 3m (no cap needed)
- 2m deadline, 100 runs (auto=3m) → 1m (caps: truncate((2m−30s)/1m) = 1)
- 60s deadline → 3m (buffer exhausted; no useful cap; workflow fix is required)
Adds a targeted error message when the subprocess is killed by context.DeadlineExceeded, directing users to set engine.mcp.tool-timeout: 10m.

Documentation fix: `gh-aw-as-mcp-server.md`

timeout parameter was documented as "Max seconds"; corrected to minutes with auto-scaling description.

Tests

Adds TestEffectiveMCPLogsToolTimeoutMinutesWithDeadline covering: no deadline, generous deadline (no cap), tight deadlines triggering caps, sub-buffer deadline (no cap), and explicit timeout capping.

- Add engine.mcp.tool-timeout: 10m to safe-output-health.md so the MCP gateway allows enough time for the logs subprocess to complete - Make the logs MCP tool handler context-deadline-aware: compute a bounded internal --timeout that leaves a 30s buffer for the subprocess to write continuation data before the MCP gateway context expires - Improve error message when subprocess is killed by context deadline exceeded to guide users to set engine.mcp.tool-timeout - Fix documentation: timeout parameter is in minutes, not seconds - Add tests for effectiveMCPLogsToolTimeoutMinutesWithDeadline Closes #45510 Co-authored-by: pelikhan <4175913+pelikhan@users.noreply.github.com>

…tion Co-authored-by: pelikhan <4175913+pelikhan@users.noreply.github.com>

pelikhan · 2026-07-15T12:32:22Z

 - `after_run_id`, `before_run_id` (optional): Pagination by run ID
 - `artifacts` (array of strings, optional): Artifact sets to download. Valid values: `all`, `activation`, `agent`, `detection`, `experiment`, `firewall`, `github-api`, `mcp`, `usage`. Defaults to `usage`.
- `timeout` (optional): Max seconds to download (default: 50)
+- `timeout` (optional): Max minutes to download (default: auto-scales with count in the MCP server, rounded up in 40-run increments; e.g. 1 minute up to 40 runs, 2 minutes for 41-80, 3 minutes for 81-120). For large date-range fetches set this explicitly (e.g. `5`) and also configure `engine.mcp.tool-timeout: 10m` in the workflow frontmatter so the MCP gateway allows enough time.


@copilot review this value

Updated in 0026d77: changed the explicit timeout example from 5 to 10 in the logs reference entry so it lines up with the engine.mcp.tool-timeout: 10m guidance.

Copilot

Pull request overview

Attempts to prevent MCP log downloads from being interrupted before continuation data is written.

Changes:

Adds deadline-aware subprocess timeout calculation and timeout guidance.
Configures the health workflow with a 10-minute gateway timeout.
Corrects timeout documentation and adds unit tests.

Show a summary per file

File	Description
`pkg/cli/mcp_tools_privileged.go`	Adds deadline-aware log timeout handling.
`pkg/cli/logs_timeout_test.go`	Tests deadline-based timeout calculations.
`docs/src/content/docs/reference/gh-aw-as-mcp-server.md`	Documents timeout units and scaling.
`.github/workflows/safe-output-health.md`	Sets the MCP tool timeout to 10 minutes.
`.github/workflows/safe-output-health.lock.yml`	Recompiles the workflow configuration.

Review details

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Files reviewed: 5/5 changed files
Comments generated: 3
Review effort level: Medium

+	deadline, ok := ctx.Deadline()
+	if !ok {
+		return baseTimeout
+	}


+			if errors.Is(ctx.Err(), context.DeadlineExceeded) ||
+				strings.Contains(err.Error(), "context deadline exceeded") {


+				mainMsg += "\n\nThe logs tool exceeded the MCP gateway tool timeout. " +
+					"Add 'engine.mcp.tool-timeout: 10m' (or higher) to your workflow frontmatter to allow more time."


Co-authored-by: pelikhan <4175913+pelikhan@users.noreply.github.com>

github-actions · 2026-07-15T12:47:38Z

🤖 PR Triage

Field	Value
Category	`bug`
Risk	🟡 Medium
Priority Score	62/100
Recommended Action	⚡ `fast_track`

Score breakdown: Impact 32 + Urgency 20 + Quality 10

Rationale: Fixes recurring 60s timeout that degrades audit dataset quality on daily workflow runs. Moderate risk (5 files, adds timeout test). CI test job failing — investigate before merge.

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gh-aw-bot · 2026-07-15T13:52:47Z

pr-sous-chef
@copilot please run the pr-finisher skill, address unresolved review comments, and rerun checks once finished.

Run: https://github.com/github/gh-aw/actions/runs/29420425558

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Copilot · 2026-07-15T14:10:14Z

pr-sous-chef
@copilot please run the pr-finisher skill, address unresolved review comments, and rerun checks once finished.
...

Done in 952f8b6. I addressed the unresolved review findings by removing the deadline-based timeout capping and deadline-exceeded hint path in pkg/cli/mcp_tools_privileged.go, and removed the corresponding deadline-specific test in pkg/cli/logs_timeout_test.go. I reran local checks (go test ./pkg/cli -run 'TestEffectiveMCPLogsToolTimeoutMinutes|TestTimeoutFlagParsing|TestTimeoutLogic', make fmt, make agent-report-progress) and final validation (parallel_validation). CI on the new head still needs a maintainer re-trigger.

pelikhan · 2026-07-15T14:19:20Z

@copilot resolve the merge conflicts on this branch.

Co-authored-by: pelikhan <4175913+pelikhan@users.noreply.github.com>

Copilot · 2026-07-15T14:38:41Z

@copilot resolve the merge conflicts on this branch.

Resolved in aad2da1 by merging origin/main into this branch and fixing the conflict in .github/workflows/safe-output-health.lock.yml.

gh-aw-bot · 2026-07-15T15:18:26Z

pr-sous-chef
@copilot please run the pr-finisher skill, address unresolved review feedback, and rerun checks once finished.

Run: https://github.com/github/gh-aw/actions/runs/29426851914

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Copilot · 2026-07-15T15:30:59Z

pr-sous-chef
@copilot please run the pr-finisher skill, address unresolved review feedback, and rerun checks once finished.
...

Completed on 605d1ed (no additional file changes in this pass). I ran PR-finisher triage, reviewed unresolved feedback, and reran checks locally: make fmt, make lint, make test-unit, make test, make recompile, plus parallel_validation.

Current status: unresolved review threads are all outdated against older commits, and the latest PR workflow runs are action_required with zero jobs (so CI on this head remains stale/unverified until a maintainer re-triggers it).

gh-aw-bot · 2026-07-15T16:50:28Z

@copilot please run the pr-finisher skill, address unresolved review comments, and rerun checks once the branch is up to date.

Generated by 👨‍🍳 PR Sous Chef · 15.3 AIC · ⌖ 6.97 AIC · ⊞ 5.1K · ◷
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Copilot · 2026-07-15T17:01:27Z

@copilot please run the pr-finisher skill, address unresolved review comments, and rerun checks once the branch is up to date.

...

Ran pr-finisher on the up-to-date branch at 605d1ed with no additional file changes needed. I rechecked unresolved review threads (all are outdated), reviewed recent CI runs/logs (current runs are action_required with zero jobs or in-progress), and reran local checks: make fmt, make lint, make test-unit, make test, and make recompile. Local test failures are unchanged and environment-related (Blocked by DNS monitoring proxy in bootstrap tests), so CI on this head remains unverified until a maintainer re-triggers workflows.

…ix-60s-timeout Co-authored-by: gh-aw-bot <259018956+gh-aw-bot@users.noreply.github.com>

gh-aw-bot · 2026-07-15T17:28:39Z

pr-sous-chef
@copilot please run the pr-finisher skill, address these unresolved review threads:

pelikhan: Fix recurring 60s timeout in logs MCP tool degrading audit datasets #45714 (comment), and rerun checks once the branch is up to date.

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Copilot · 2026-07-15T17:42:37Z

pr-sous-chef
@copilot please run the pr-finisher skill, address these unresolved review threads:

pelikhan: Fix recurring 60s timeout in logs MCP tool degrading audit datasets #45714 (comment), and rerun checks onc...

Ran pr-finisher triage on the current head (a4c08bf). The unresolved thread at #45714 (comment) is outdated and already satisfied by the docs update (timeout example is 10 and guidance matches engine.mcp.tool-timeout: 10m).

I reran local checks:

make fmt ✅
make lint ✅
make test-unit ❌ (pre-existing env failure: Blocked by DNS monitoring proxy in bootstrap tests)
make test ❌ (same pre-existing env failure)
make recompile ✅

CI on this branch head remains action_required with 0 jobs (stale/unverified in agent context). A maintainer needs to re-trigger CI from GitHub to get fresh check results on this head.

github-actions · 2026-07-16T06:42:10Z

🎉 This pull request is included in a new release.

Release: v0.82.10

Initial plan

30608f0

Copilot AI assigned Copilot and pelikhan Jul 15, 2026

Copilot AI linked an issue Jul 15, 2026 that may be closed by this pull request

[deep-report] Fix recurring 60s timeout in gh-aw logs MCP tool degrading audit datasets #45510

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Copilot started work on behalf of pelikhan July 15, 2026 10:22 View session

Copilot AI and others added 2 commits July 15, 2026 10:45

Clarify test comments: use truncate() notation for int() floor trunca…

ca436dd

…tion Co-authored-by: pelikhan <4175913+pelikhan@users.noreply.github.com>

Copilot AI changed the title ~~[WIP] Fix recurring 60s timeout in gh-aw logs MCP tool~~ Fix recurring 60s timeout in logs MCP tool degrading audit datasets Jul 15, 2026

Copilot finished work on behalf of pelikhan July 15, 2026 10:50

Copilot AI requested a review from pelikhan July 15, 2026 10:50

pelikhan marked this pull request as ready for review July 15, 2026 12:31

Copilot AI review requested due to automatic review settings July 15, 2026 12:31

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pelikhan reviewed Jul 15, 2026

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Copilot started work on behalf of pelikhan July 15, 2026 12:36 View session

Adjust logs timeout example value in MCP server reference

0026d77

Co-authored-by: pelikhan <4175913+pelikhan@users.noreply.github.com>

github-actions Bot added pr-action:fast_track pr-agent:copilot-swe-agent pr-priority:high pr-risk:medium pr-type:bug labels Jul 15, 2026

Copilot finished work on behalf of pelikhan July 15, 2026 12:47

github-actions Bot mentioned this pull request Jul 15, 2026

[PR Triage Report] PR Triage Report — 2026-07-15 [Run 29416064927] #45730

Closed

Copilot AI requested a review from pelikhan July 15, 2026 12:47

This was referenced Jul 15, 2026

[pr-sous-chef] Run report — 0 nudged, 0 skipped #45581

Closed

[Contribution Check Report] Contribution Check — 2026-07-15 #45590

Closed

Copilot started work on behalf of gh-aw-bot July 15, 2026 13:53 View session

Remove ineffective deadline-based logs timeout handling

952f8b6

Co-authored-by: gh-aw-bot <259018956+gh-aw-bot@users.noreply.github.com>

Copilot finished work on behalf of gh-aw-bot July 15, 2026 14:11

Copilot AI requested a review from gh-aw-bot July 15, 2026 14:11

Copilot started work on behalf of pelikhan July 15, 2026 14:19 View session

Merge origin/main and resolve safe-output-health lock conflict

aad2da1

Co-authored-by: pelikhan <4175913+pelikhan@users.noreply.github.com>

Copilot finished work on behalf of pelikhan July 15, 2026 14:39

Copilot started work on behalf of gh-aw-bot July 15, 2026 15:18 View session

Plan: triage PR and resolve remaining feedback

605d1ed

Co-authored-by: gh-aw-bot <259018956+gh-aw-bot@users.noreply.github.com>

Copilot finished work on behalf of gh-aw-bot July 15, 2026 15:31

Copilot started work on behalf of gh-aw-bot July 15, 2026 16:50 View session

Merge remote-tracking branch 'origin/main' into copilot/deep-report-f…

9e3e76b

…ix-60s-timeout Co-authored-by: gh-aw-bot <259018956+gh-aw-bot@users.noreply.github.com>

Copilot finished work on behalf of gh-aw-bot July 15, 2026 17:15

Copilot started work on behalf of gh-aw-bot July 15, 2026 17:28 View session

chore: start pr-finisher pass plan

a4c08bf

Co-authored-by: gh-aw-bot <259018956+gh-aw-bot@users.noreply.github.com>

Copilot finished work on behalf of gh-aw-bot July 15, 2026 17:43

pelikhan merged commit 3fb2526 into main Jul 15, 2026

pelikhan deleted the copilot/deep-report-fix-60s-timeout branch July 15, 2026 18:05

		if errors.Is(ctx.Err(), context.DeadlineExceeded) \|\|
		strings.Contains(err.Error(), "context deadline exceeded") {

		mainMsg += "\n\nThe logs tool exceeded the MCP gateway tool timeout. " +
		"Add 'engine.mcp.tool-timeout: 10m' (or higher) to your workflow frontmatter to allow more time."

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Changes

Immediate fix: safe-output-health.md

Systemic fix: deadline-aware subprocess timeout (mcp_tools_privileged.go)

Documentation fix: gh-aw-as-mcp-server.md

Tests

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Pull request overview

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🤖 PR Triage

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Copilot AI commented Jul 15, 2026 •

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Immediate fix: `safe-output-health.md`

Systemic fix: deadline-aware subprocess timeout (`mcp_tools_privileged.go`)

Documentation fix: `gh-aw-as-mcp-server.md`