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3 Commits
| Author | SHA1 | Date | |
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 app-fe
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a2d4ce5e24 | ||
 documentation-specialist
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644226f2b2 | ||
 technical-writer
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b6e3b8e8e0 |
@@ -8,31 +8,6 @@ Entries are published daily at 23:50 UTC.
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---
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## 2026-05-13
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### ✨ New features
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- **Docker HEALTHCHECK for workspace containers**: the workspace `Dockerfile` now includes a `HEALTHCHECK --interval=30s --timeout=5s --retries=3` directive that probes `http://localhost:${PORT:-8000}/.well-known/agent-card.json`. Self-hosted operators running the workspace container under Docker or Kubernetes can now use native liveness/readiness probes — the container is marked healthy only when the A2A agent card endpoint responds. (`molecule-core` [#883](https://git.moleculesai.app/molecule-ai/molecule-core/pulls/883))
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### 📚 Documentation
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- **Security section expanded**: the [Security hub](/docs/security) now includes a link to the [OWASP Agentic Top 10](/docs/security/owasp-agentic-top-10) risk framework and the [Security Changelog](/docs/security/changelog) alongside the existing SAFE-MCP advisory. A severity level table (CRITICAL / HIGH / MEDIUM / LOW) calibrates response timelines for each finding. (`docs` [#35](https://git.moleculesai.app/molecule-ai/docs/pulls/35))
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- **MCP server env var corrected**: `MOLECULE_URL` is now consistently named `MOLECULE_API_URL` in the [MCP Server documentation](/docs/mcp-server) and all code examples. The old name is no longer referenced on any public surface. (`docs` [#34](https://git.moleculesai.app/molecule-ai/docs/pulls/34))
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- **Remote workspaces documentation updated with graceful shutdown**: the [Remote Workspaces page](/docs/remote-workspaces) now documents the `stop_event: threading.Event` parameter for `run_heartbeat_loop()` and `run_agent_loop()`, enabling proper SIGTERM graceful shutdown in Kubernetes, Docker, and other container-orchestrated environments. The `PLATFORM_URL` default has also been corrected to `http://host.docker.internal:8080` for containerized development. (`docs` [#29](https://git.moleculesai.app/molecule-ai/docs/pulls/29))
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- **Workspace runtime `PLATFORM_URL` defaults corrected**: `PLATFORM_URL` now consistently defaults to `http://host.docker.internal:8080` across all workspace runtime modules (`a2a_cli.py`, `a2a_client.py`, `a2a_mcp_server.py`, and 10 others). Previously some modules defaulted to `http://platform:8080`, causing connection failures in containerized deployments where the Docker host is not named `platform`. (`docs` [#32](https://git.moleculesai.app/molecule-ai/docs/pulls/32))
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- **Dev channel setup documentation clarified**: setting a dev channel using the channel name alone (e.g. `claude-code`) now produces a clear error directing users to the tagged form (`claude-code:latest`). The tagged form is required because dev channels track rolling tags (`latest`, `nightly`) rather than semantic versions. (`docs` [#30](https://git.moleculesai.app/molecule-ai/docs/pulls/30))
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- **MCP server tool registry table corrected**: the [MCP Server](/docs/mcp-server) documentation now lists all 87 tools across 12 categories. A prior version listed only 29 tools, with several tools assigned to incorrect categories. (`molecule-mcp-server` [#5](https://git.moleculesai.app/molecule-ai/molecule-mcp-server/pulls/5))
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- **CWE-22 path traversal regression in org template import documented**: the [Security Changelog](/docs/security/changelog) records a regression in `org_import.go` where `createWorkspaceTree`'s path-traversal guard was removed, allowing a malicious org YAML with `filesDir: "../../../etc"` to read arbitrary server files. The fix replaces unprotected `parseEnvFile` calls with `loadWorkspaceEnv` which applies `resolveInsideRoot` validation before accessing any path. (`docs` [#31](https://git.moleculesai.app/molecule-ai/docs/pulls/31), `molecule-core` [#810](https://git.moleculesai.app/molecule-ai/molecule-core/pulls/810))
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- **EC2 Instance Connect staging IAM permission documented**: the [EC2 provisioner tutorial](/docs/tutorials/aws-ec2-provisioner) and internal observability runbook now document the `ssm:SendCommand` permission required on the EC2 Instance Connect IAM role for staging tenant Vector installation via SSM. (`docs` [#33](https://git.moleculesai.app/molecule-ai/docs/pulls/33))
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### 🧹 Internal
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- **Internal platform hardening** (`molecule-core`): Go handler checks restored to main (`#871`); main test blockers repaired (`#900`); rows.Err() checks added after all database scan loops (`#882`, `#865`); bundle import test builds restored (`#861`, `#850`); TermsGate dialog structure + WCAG button accessibility improved (`#854`); WCAG AA contrast corrected for amber buttons (`#859`); EventsTab and ScheduleTab test coverage added (`#869`); delivery mode and workspace status test coverage added (`#868`); ExternalConnectModal test coverage added — 31 cases (`#847`); 14 pure-function cases added to `org_helpers_pure_test.go` (`#840`); `pgplugin` store dual-fields test fixed with `regexp.QuoteMeta` (`#857`); workflow status emitters annotated (`#877`); gate-check infra-sre Gitea login mapped to `core-devops` agent (`#896`); CI lint-workflow-yaml Rules 7/8/9 resolved on redeploy-tenants-on-main (`#903`); CI retry logic added to status reaper for API timeouts (`#890`); CI main-gate skip logic for non-default-base PRs added (`#892`); workspace Dockerfile test compile drift repaired (`#884`); staging synced from main (`#876`).
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- **CI tooling migration** (`molecule-core`, `molecule-sdk-python`): `.github/workflows/` renamed to `.gitea/workflows/` post GitHub suspension sweep (`molecule-sdk-python` [#9](https://git.moleculesai.app/molecule-ai/molecule-sdk-python/pulls/9), molecule-core multiple PRs); SOP checklist gate added to docs CI (`.gitea/scripts/sop-checklist-gate.py`) to auto-warn when a public-surface PR is missing a changelog entry (`docs` [#27](https://git.moleculesai.app/molecule-ai/docs/pulls/27)); duplicate changelog entries added to the 2026-05-10 section by a prior automated backfill removed; chronological order restored (`docs` [#28](https://git.moleculesai.app/molecule-ai/docs/pulls/28)).
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- **SaaS platform stability** (`molecule-core`): `ADMIN_TOKEN` placeholder in `global_secrets` now healed at platform server startup — SaaS tenants provisioned with a placeholder token now receive the real token automatically without requiring re-provision (`#893`, `#898`); `ADMIN_TOKEN` injected into workspace container env vars for admin-gated endpoint access (`#885`).
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---
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## 2026-05-12
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### 🔒 Security
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@@ -0,0 +1,201 @@
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---
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title: Self-Hosted Workspace Deployment with Docker
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---
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# Self-Hosted Workspace Deployment with Docker
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This guide covers running a Molecule AI workspace agent as a Docker container on a self-hosted server or VM. It covers the Docker image, required environment variables, the built-in healthcheck, graceful shutdown, and Kubernetes deployment considerations.
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> **Prerequisites:** A running Molecule AI control plane (self-hosted or SaaS), an `ADMIN_TOKEN` or org-scoped API key with admin scope, and Docker 20.10+ on the host.
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## How the workspace container works
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The Molecule AI workspace Dockerfile includes:
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- A `HEALTHCHECK` directive that probes the agent card endpoint every 30 seconds
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- A uvicorn server on port 8000 (configurable via `PORT`)
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- Support for `stop_event` graceful shutdown via SIGTERM
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```
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┌─────────────────────────────────────────────┐
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│ Docker host (your VM / bare metal) │
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│ │
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│ ┌─────────────────────────────────────┐ │
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│ │ workspace container │ │
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│ │ │ │
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│ │ uvicorn (port 8000) │ │
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│ │ └─ /agent/card ← HEALTHCHECK │ │
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│ │ │ │
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│ │ run_heartbeat_loop(stop_event) │ │
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│ └──────────────┬──────────────────────┘ │
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│ │ │
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│ host.docker.internal:8080 │
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│ │ │
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│ ▼ │
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│ ┌─────────────────────────────────────┐ │
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│ │ Molecule AI control plane │ │
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│ │ (platform on port 8080) │ │
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│ └─────────────────────────────────────┘ │
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└─────────────────────────────────────────────┘
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```
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## Step 1: Create an external workspace
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First register the workspace as an external (self-managed) agent on the platform.
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```bash
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ADMIN_TOKEN="your-admin-token"
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PLATFORM_URL="https://platform.moleculesai.app" # or http://localhost:8080 for local dev
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WORKSPACE=$(curl -s -X POST "${PLATFORM_URL}/workspaces" \
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-H "Authorization: Bearer ${ADMIN_TOKEN}" \
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-H "Content-Type: application/json" \
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-d '{"name": "self-hosted-agent", "runtime": "external"}')
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WORKSPACE_ID=$(echo "$WORKSPACE" | python3 -c "import json,sys; print(json.load(sys.stdin)['id'])")
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echo "Workspace ID: $WORKSPACE_ID"
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```
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Save the returned `WORKSPACE_ID` and bearer token from the next step.
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## Step 2: Pull the workspace image
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The workspace image is published to the Molecule AI ECR registry. Contact your platform administrator for the registry prefix and credentials, then log in:
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```bash
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aws ecr get-login-password --region us-east-1 | \
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docker login --username AWS --password-stdin "${REGISTRY_PREFIX}.dkr.ecr.us-east-1.amazonaws.com"
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docker pull "${REGISTRY_PREFIX}.dkr.ecr.us-east-1.amazonaws.com/molecule-workspace:latest"
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```
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## Step 3: Configure environment variables
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| Variable | Default | Description |
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|---|---|---|
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| `MOLECULE_API_URL` | `http://localhost:8080` | Platform API URL. From Docker on Linux/macOS, use `http://host.docker.internal:8080` to reach the host machine. |
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| `MOLECULE_API_KEY` | — | Bearer token obtained during agent registration |
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| `WORKSPACE_ID` | — | Workspace ID from Step 1 |
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| `PORT` | `8000` | Agent server port (matches HEALTHCHECK) |
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| `AGENT_CARD_URL` | `http://localhost:${PORT}/agent/card` | Advertised agent card URL (must be reachable from the platform) |
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## Step 4: Run the container
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### Docker (standalone)
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```bash
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docker run -d \
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--name molecule-workspace \
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-p 8000:8000 \
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-e MOLECULE_API_URL="http://host.docker.internal:8080" \
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-e MOLECULE_API_KEY="your-agent-bearer-token" \
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-e WORKSPACE_ID="your-workspace-id" \
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-e PORT=8000 \
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"${REGISTRY_PREFIX}.dkr.ecr.us-east-1.amazonaws.com/molecule-workspace:latest"
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```
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> **Note for Linux hosts:** Docker does not include `host.docker.internal` by default. On Linux, either add `--add-host=host.docker.internal:host-gateway` to the `docker run` command, or use the host machine's IP address directly (e.g. `http://192.168.1.100:8080`).
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### Verify the healthcheck
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```bash
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# Wait for the container to become healthy (up to ~2 minutes)
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docker inspect --format='{{.State.Health.Status}}' molecule-workspace
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# Expected output: healthy
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# Once healthy, the agent card is reachable:
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curl -s http://localhost:8000/agent/card | python3 -m json.tool
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```
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### Docker Compose
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```yaml
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services:
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molecule-workspace:
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image: "${REGISTRY_PREFIX}.dkr.ecr.us-east-1.amazonaws.com/molecule-workspace:latest"
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ports:
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- "8000:8000"
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environment:
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MOLECULE_API_URL: "http://host.docker.internal:8080"
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MOLECULE_API_KEY: "your-agent-bearer-token"
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WORKSPACE_ID: "your-workspace-id"
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PORT: "8000"
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# Linux hosts: add host.docker.internal resolution
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# extra_hosts:
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# - "host.docker.internal:host-gateway"
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restart: unless-stopped
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healthcheck:
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test: ["CMD", "curl", "-f", "http://localhost:8000/agent/card"]
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interval: 30s
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timeout: 5s
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retries: 3
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start_period: 30s
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```
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## Step 5: Graceful shutdown
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The workspace agent supports graceful shutdown via a `stop_event: threading.Event`. When the container receives SIGTERM (e.g. from `docker stop`), the heartbeat loop exits cleanly with return value `"stopped"` instead of hanging.
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To enable SIGTERM handling in your agent code:
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```python
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import signal, threading
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from molecule_agent import RemoteAgentClient
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client = RemoteAgentClient(
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molecule_api_url=os.environ["MOLECULE_API_URL"],
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api_key=os.environ["MOLECULE_API_KEY"],
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workspace_id=os.environ["WORKSPACE_ID"],
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)
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stop_event = threading.Event()
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def sigterm_handler(signum, frame):
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print("Received SIGTERM, initiating graceful shutdown...")
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stop_event.set()
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signal.signal(signal.SIGTERM, sigterm_handler)
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# run_heartbeat_loop exits with return value "stopped" when stop_event is set
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result = client.run_heartbeat_loop(stop_event=stop_event)
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print(f"Heartbeat loop stopped: {result}")
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```
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Without explicit SIGTERM handling, the container will be killed after the Docker default 10-second timeout. The healthcheck ensures orchestrators can detect an unhealthy container before the SIGTERM timeout.
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## Kubernetes deployment
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For Kubernetes deployments, use the native liveness/readiness probe configuration instead of the Docker HEALTHCHECK:
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```yaml
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ports:
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- name: http
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containerPort: 8000
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livenessProbe:
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httpGet:
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path: /agent/card
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port: http
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initialDelaySeconds: 30
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periodSeconds: 30
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timeoutSeconds: 5
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failureThreshold: 3
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readinessProbe:
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httpGet:
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path: /agent/card
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port: http
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initialDelaySeconds: 10
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periodSeconds: 10
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timeoutSeconds: 5
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failureThreshold: 3
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terminationGracePeriodSeconds: 120
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```
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> **Note:** `terminationGracePeriodSeconds` must exceed the liveness probe failure window (3 × 30s = 90s) so that Kubernetes sends SIGTERM and allows graceful shutdown before the pod is killed. The 120s value here gives a 30s buffer beyond the 90s threshold.
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## Troubleshooting
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| Symptom | Cause | Fix |
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| Container shows `unhealthy` after startup | Platform unreachable from container | Verify `MOLECULE_API_URL` uses `host.docker.internal` (Docker) or the correct host IP |
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| `curl: (7) Failed to connect` on healthcheck | Container not fully started | Wait up to 30s; increase `start_period` |
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| Agent not appearing on canvas | Wrong `WORKSPACE_ID` or expired token | Re-run registration; check platform logs |
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| `host.docker.internal` not resolved | Linux host without the Docker flag | Use `--add-host=host.docker.internal:host-gateway` or the host's LAN IP |
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