molecule-core/workspace
Hongming Wang 427300f3a4 feat: make molecule-mcp standalone (built-in register + heartbeat) + recover awaiting_agent on heartbeat
Two paired fixes that together let an external operator run a single
process (molecule-mcp) and see their workspace come up online in the
canvas — the bug surfaced live when status stuck at "awaiting_agent /
OFFLINE" despite an active MCP server.

Platform side (workspace-server/internal/handlers/registry.go):
  Heartbeat handler already auto-recovers offline → online and
  provisioning → online, but NOT awaiting_agent → online. Healthsweep
  flips stale-heartbeat external workspaces TO awaiting_agent, and
  with no recovery path the workspace stays "OFFLINE — Restart" in the
  canvas forever. Add the symmetric branch: if currentStatus ==
  "awaiting_agent" and a heartbeat arrives, flip to online + broadcast
  WORKSPACE_ONLINE. Mirrors the existing offline/provisioning patterns
  exactly. Test: TestHeartbeatHandler_AwaitingAgentToOnline asserts
  the SQL UPDATE fires with the awaiting_agent guard clause.

Wheel side (workspace/mcp_cli.py):
  molecule-mcp was outbound-only — operators had to run a separate
  SDK process to register + heartbeat. Now mcp_cli.main():
    1. Calls /registry/register at startup (idempotent upsert flips
       status awaiting_agent → online via the existing register path).
    2. Spawns a daemon thread that POSTs /registry/heartbeat every
       20s. 20s is comfortably under the healthsweep stale window so
       a single missed beat doesn't cause status churn.
    3. Runs the MCP stdio loop in the foreground.

  Both calls set Origin: ${PLATFORM_URL} so the SaaS edge WAF accepts
  them. Threaded heartbeat (not asyncio) chosen because it doesn't
  need to share an event loop with the MCP stdio server — daemon=True
  cleanly dies when the operator's runtime exits.

  MOLECULE_MCP_DISABLE_HEARTBEAT=1 escape hatch lets in-container
  callers (which have heartbeat.py running already) reuse the entry
  point without double-heartbeating. Default is enabled.

End-to-end verification (live, against
hongmingwang.moleculesai.app, workspace 8dad3e29-...):
  pre-fix:  status=awaiting_agent → canvas shows OFFLINE forever
  post-fix: ran `molecule-mcp` for 5s standalone → canvas state:
            status=online runtime=external agent=molecule-mcp-8dad3e29

Test coverage: 7 new mcp_cli tests (register-at-startup, heartbeat-
thread-spawned, disable-env-skips-both, env-and-file token resolution,
register payload shape, heartbeat endpoint + headers); 1 new platform
test (awaiting_agent → online recovery). Full workspace + handlers
suites green: 1355 Python, full Go handlers passing.

Co-Authored-By: Claude Opus 4.7 (1M context) <noreply@anthropic.com>
2026-04-30 15:42:44 -07:00
..
adapters fix: comprehensive a2a-sdk 1.x migration sweep across workspace/ 2026-04-27 09:42:57 -07:00
builtin_tools feat(harness): coordinator phase-boundary instrumentation for RFC #2251 2026-04-28 20:11:46 -07:00
lib feat(workspace): pre-stop serialization for pause/resume (closes #1386) 2026-04-21 12:40:44 +00:00
molecule_audit chore: open-source restructure — rename dirs, remove internal files, scrub secrets 2026-04-18 00:24:44 -07:00
platform_tools Merge pull request #2261 from Molecule-AI/fix/harness-cleanup-failed-event 2026-04-29 05:35:43 +00:00
plugins_registry feat(plugin): implement MCPServerAdaptor (issue #847) 2026-04-24 01:42:13 +00:00
policies feat(platform): single-source-of-truth tool registry — adapters consume, no drift 2026-04-28 17:11:36 -07:00
scripts fix(git-token-helper): close TOCTOU window + stop swallowing chmod errors (closes #1552) 2026-04-26 08:22:29 -07:00
skill_loader feat(skills): per-skill runtime compatibility (#119, hermes pattern) 2026-04-27 01:57:43 -07:00
tests feat: make molecule-mcp standalone (built-in register + heartbeat) + recover awaiting_agent on heartbeat 2026-04-30 15:42:44 -07:00
.coveragerc test(workspace): centralize pytest-cov config + 92% floor (closes #1817) 2026-04-26 06:21:22 -07:00
a2a_cli.py fix(runtime): use lowercase wire role for v0.3 JSON-RPC compat layer 2026-04-27 12:40:11 -07:00
a2a_client.py feat(workspace): surface peer-discovery failure reason instead of "may be isolated" 2026-04-30 11:09:26 -07:00
a2a_executor.py fix: comprehensive a2a-sdk 1.x migration sweep across workspace/ 2026-04-27 09:42:57 -07:00
a2a_mcp_server.py feat(workspace-runtime): expose universal MCP server to runtime=external operators 2026-04-30 15:20:19 -07:00
a2a_tools.py feat(workspace): surface peer-discovery failure reason instead of "may be isolated" 2026-04-30 11:09:26 -07:00
adapter_base.py feat(platform): single-source-of-truth tool registry — adapters consume, no drift 2026-04-28 17:11:36 -07:00
agent.py chore: open-source restructure — rename dirs, remove internal files, scrub secrets 2026-04-18 00:24:44 -07:00
agents_md.py chore: open-source restructure — rename dirs, remove internal files, scrub secrets 2026-04-18 00:24:44 -07:00
build-all.sh fix: update workspace script comments for workspace-template → workspace rename 2026-04-18 01:48:05 -07:00
config.py fix(compliance): flip default mode to owasp_agentic (detect-only) 2026-04-24 11:52:09 -07:00
consolidation.py fix: apply #1124 env-var defaults + scrub F1088 credentials from INCIDENT_LOG.md (#1347) 2026-04-21 08:11:44 +00:00
coordinator.py feat(harness): coordinator phase-boundary instrumentation for RFC #2251 2026-04-28 20:11:46 -07:00
Dockerfile feat(workspace): 45-min gh-token refresh daemon + credential helper cache 2026-04-22 19:52:46 -07:00
entrypoint.sh fix(workspace): credential helper security hardening (#1797) 2026-04-23 18:14:55 +00:00
events.py chore: open-source restructure — rename dirs, remove internal files, scrub secrets 2026-04-18 00:24:44 -07:00
executor_helpers.py feat(prompt): Platform Capabilities preamble at top of system prompt 2026-04-29 21:31:13 -07:00
heartbeat.py fix(runtime): use lowercase wire role for v0.3 JSON-RPC compat layer 2026-04-27 12:40:11 -07:00
initial_prompt.py chore: open-source restructure — rename dirs, remove internal files, scrub secrets 2026-04-18 00:24:44 -07:00
internal_chat_uploads.py feat(workspace): /internal/chat/uploads/ingest endpoint (RFC #2312, PR-B) 2026-04-29 14:16:32 -07:00
internal_file_read.py feat(chat_files): rewrite Download as HTTP-forward (RFC #2312, PR-D) 2026-04-29 15:19:02 -07:00
main.py feat(chat_files): rewrite Download as HTTP-forward (RFC #2312, PR-D) 2026-04-29 15:19:02 -07:00
mcp_cli.py feat: make molecule-mcp standalone (built-in register + heartbeat) + recover awaiting_agent on heartbeat 2026-04-30 15:42:44 -07:00
molecule_ai_status.py fix(runtime): replace remaining /app/ legacy paths in agent prompts + docstrings 2026-04-27 11:22:00 -07:00
platform_auth.py fix(workspace-runtime): add Origin header so SaaS edge WAF accepts MCP tool calls 2026-04-30 15:30:15 -07:00
platform_inbound_auth.py feat(saas): deliver platform_inbound_secret via /registry/register (RFC #2312, PR-F) 2026-04-29 15:12:34 -07:00
plugins.py chore: open-source restructure — rename dirs, remove internal files, scrub secrets 2026-04-18 00:24:44 -07:00
preflight.py feat(preflight): replace SUPPORTED_RUNTIMES static list with adapter discovery 2026-04-27 00:44:51 -07:00
prompt.py feat(prompt): Platform Capabilities preamble at top of system prompt 2026-04-29 21:31:13 -07:00
pytest.ini feat(preflight): replace SUPPORTED_RUNTIMES static list with adapter discovery 2026-04-27 00:44:51 -07:00
rebuild-runtime-images.sh fix: update workspace script comments for workspace-template → workspace rename 2026-04-18 01:48:05 -07:00
requirements.txt feat(workspace): /internal/chat/uploads/ingest endpoint (RFC #2312, PR-B) 2026-04-29 14:16:32 -07:00
runtime_wedge.py chore(workspace): drop claude_sdk_executor — Phase 2 of #87 2026-04-27 00:52:55 -07:00
shared_runtime.py feat(platform): single-source-of-truth tool registry — adapters consume, no drift 2026-04-28 17:11:36 -07:00
transcript_auth.py chore: open-source restructure — rename dirs, remove internal files, scrub secrets 2026-04-18 00:24:44 -07:00
watcher.py chore: open-source restructure — rename dirs, remove internal files, scrub secrets 2026-04-18 00:24:44 -07:00