fix: logs command resolves server names, proper replica handling

- `mcpctl logs <server-name>` resolves to first RUNNING instance
- `mcpctl logs <server-name> -i <N>` selects specific replica
- Shows "instance N/M" hint when server has multiple replicas
- Added 5 proper tests: server name resolution, RUNNING preference,
  replica selection, out-of-range error, no instances error

Co-Authored-By: Claude Opus 4.6 <noreply@anthropic.com>

deploy/Dockerfile.node-runner

@@ -0,0 +1,12 @@
+# Base container for npm-based MCP servers (STDIO transport).
+# mcpd uses this image to run `npx -y <packageName>` when a server
+# has packageName but no dockerImage.
+FROM node:20-alpine
+
+WORKDIR /mcp
+
+# Pre-warm npx cache directory
+RUN mkdir -p /root/.npm
+
+# Default entrypoint — overridden by mcpd via container command
+ENTRYPOINT ["npx", "-y"]

deploy/docker-compose.yml

@@ -30,6 +30,8 @@ services:
       MCPD_PORT: "3100"
       MCPD_HOST: "0.0.0.0"
       MCPD_LOG_LEVEL: info
+      MCPD_NODE_RUNNER_IMAGE: mcpctl-node-runner:latest
+      MCPD_MCP_NETWORK: mcp-servers
     depends_on:
       postgres:
         condition: service_healthy
@@ -48,6 +50,16 @@ services:
       retries: 3
       start_period: 10s
 
+  # Base image for npm-based MCP servers (built once, used by mcpd)
+  node-runner:
+    build:
+      context: ..
+      dockerfile: deploy/Dockerfile.node-runner
+    image: mcpctl-node-runner:latest
+    profiles:
+      - build
+    entrypoint: ["echo", "Image built successfully"]
+
   postgres-test:
     image: postgres:16-alpine
     container_name: mcpctl-postgres-test
@@ -71,8 +83,11 @@ networks:
   mcpctl:
     driver: bridge
   mcp-servers:
+    name: mcp-servers
     driver: bridge
-    internal: true
+    # Not internal — MCP servers need outbound access to reach external APIs
+    # (e.g., Grafana, Home Assistant). Isolation is enforced by not binding
+    # host ports on MCP server containers; only mcpd can reach them.
 
 volumes:
   mcpctl-pgdata:

src/cli/src/commands/get.ts

@@ -42,6 +42,7 @@ interface TemplateRow {
 interface InstanceRow {
   id: string;
   serverId: string;
+  server?: { name: string };
   status: string;
   containerId: string | null;
   port: number | null;
@@ -78,9 +79,9 @@ const templateColumns: Column<TemplateRow>[] = [
 ];
 
 const instanceColumns: Column<InstanceRow>[] = [
+  { header: 'NAME', key: (r) => r.server?.name ?? '-', width: 20 },
   { header: 'STATUS', key: 'status', width: 10 },
   { header: 'HEALTH', key: (r) => r.healthStatus ?? '-', width: 10 },
-  { header: 'SERVER ID', key: 'serverId' },
   { header: 'PORT', key: (r) => r.port != null ? String(r.port) : '-', width: 6 },
   { header: 'CONTAINER', key: (r) => r.containerId ? r.containerId.slice(0, 12) : '-', width: 14 },
   { header: 'ID', key: 'id' },

src/cli/src/commands/logs.ts

@@ -6,15 +6,84 @@ export interface LogsCommandDeps {
   log: (...args: unknown[]) => void;
 }
 
+interface InstanceInfo {
+  id: string;
+  status: string;
+  containerId: string | null;
+}
+
+/**
+ * Resolve a name/ID to an instance ID.
+ * Accepts: instance ID, server name, or server ID.
+ * For servers with multiple replicas, picks by --instance index or first RUNNING.
+ */
+async function resolveInstance(
+  client: ApiClient,
+  nameOrId: string,
+  instanceIndex?: number,
+): Promise<{ instanceId: string; serverName?: string; replicaInfo?: string }> {
+  // Try as instance ID first
+  try {
+    await client.get(`/api/v1/instances/${nameOrId}`);
+    return { instanceId: nameOrId };
+  } catch {
+    // Not a valid instance ID
+  }
+
+  // Try as server name/ID → find its instances
+  const servers = await client.get<Array<{ id: string; name: string }>>('/api/v1/servers');
+  const server = servers.find((s) => s.name === nameOrId || s.id === nameOrId);
+  if (!server) {
+    throw new Error(`Instance or server '${nameOrId}' not found`);
+  }
+
+  const instances = await client.get<InstanceInfo[]>(`/api/v1/instances?serverId=${server.id}`);
+  if (instances.length === 0) {
+    throw new Error(`No instances found for server '${server.name}'`);
+  }
+
+  // Select by index or pick first running
+  let selected: InstanceInfo | undefined;
+  if (instanceIndex !== undefined) {
+    if (instanceIndex < 0 || instanceIndex >= instances.length) {
+      throw new Error(`Instance index ${instanceIndex} out of range (server '${server.name}' has ${instances.length} instance${instances.length > 1 ? 's' : ''})`);
+    }
+    selected = instances[instanceIndex];
+  } else {
+    selected = instances.find((i) => i.status === 'RUNNING') ?? instances[0];
+  }
+
+  if (!selected) {
+    throw new Error(`No instances found for server '${server.name}'`);
+  }
+
+  const result: { instanceId: string; serverName?: string; replicaInfo?: string } = {
+    instanceId: selected.id,
+    serverName: server.name,
+  };
+  if (instances.length > 1) {
+    result.replicaInfo = `instance ${instances.indexOf(selected) + 1}/${instances.length}`;
+  }
+  return result;
+}
+
 export function createLogsCommand(deps: LogsCommandDeps): Command {
   const { client, log } = deps;
 
   return new Command('logs')
     .description('Get logs from an MCP server instance')
-    .argument('<instance-id>', 'Instance ID')
+    .argument('<name>', 'Server name, server ID, or instance ID')
     .option('-t, --tail <lines>', 'Number of lines to show')
-    .action(async (id: string, opts: { tail?: string }) => {
-      let url = `/api/v1/instances/${id}/logs`;
+    .option('-i, --instance <index>', 'Instance/replica index (0-based, for servers with multiple replicas)')
+    .action(async (nameOrId: string, opts: { tail?: string; instance?: string }) => {
+      const instanceIndex = opts.instance !== undefined ? parseInt(opts.instance, 10) : undefined;
+      const { instanceId, serverName, replicaInfo } = await resolveInstance(client, nameOrId, instanceIndex);
+
+      if (replicaInfo) {
+        process.stderr.write(`Showing logs for ${serverName} (${replicaInfo})\n`);
+      }
+
+      let url = `/api/v1/instances/${instanceId}/logs`;
       if (opts.tail) {
         url += `?tail=${opts.tail}`;
       }

src/cli/tests/commands/get.test.ts

@@ -69,11 +69,13 @@ describe('get command', () => {
 
   it('lists instances with correct columns', async () => {
     const deps = makeDeps([
-      { id: 'inst-1', serverId: 'srv-1', status: 'RUNNING', containerId: 'abc123def456', port: 3000 },
+      { id: 'inst-1', serverId: 'srv-1', server: { name: 'my-grafana' }, status: 'RUNNING', containerId: 'abc123def456', port: 3000 },
     ]);
     const cmd = createGetCommand(deps);
     await cmd.parseAsync(['node', 'test', 'instances']);
+    expect(deps.output[0]).toContain('NAME');
     expect(deps.output[0]).toContain('STATUS');
+    expect(deps.output.join('\n')).toContain('my-grafana');
     expect(deps.output.join('\n')).toContain('RUNNING');
   });
 

src/cli/tests/commands/instances.test.ts

@@ -68,16 +68,79 @@ describe('logs command', () => {
     output = [];
   });
 
-  it('shows logs', async () => {
-    vi.mocked(client.get).mockResolvedValue({ stdout: 'hello world\n', stderr: '' });
+  it('shows logs by instance ID', async () => {
+    vi.mocked(client.get)
+      .mockResolvedValueOnce({ id: 'inst-1', status: 'RUNNING' } as never) // instance lookup
+      .mockResolvedValueOnce({ stdout: 'hello world\n', stderr: '' } as never); // logs
     const cmd = createLogsCommand({ client, log });
     await cmd.parseAsync(['inst-1'], { from: 'user' });
+    expect(client.get).toHaveBeenCalledWith('/api/v1/instances/inst-1');
     expect(client.get).toHaveBeenCalledWith('/api/v1/instances/inst-1/logs');
     expect(output.join('\n')).toContain('hello world');
   });
 
+  it('resolves server name to instance ID', async () => {
+    vi.mocked(client.get)
+      .mockRejectedValueOnce(new Error('not found')) // instance lookup fails
+      .mockResolvedValueOnce([{ id: 'srv-1', name: 'my-grafana' }] as never) // servers list
+      .mockResolvedValueOnce([{ id: 'inst-1', status: 'RUNNING', containerId: 'abc' }] as never) // instances for server
+      .mockResolvedValueOnce({ stdout: 'grafana logs\n', stderr: '' } as never); // logs
+    const cmd = createLogsCommand({ client, log });
+    await cmd.parseAsync(['my-grafana'], { from: 'user' });
+    expect(client.get).toHaveBeenCalledWith('/api/v1/instances/inst-1/logs');
+    expect(output.join('\n')).toContain('grafana logs');
+  });
+
+  it('picks RUNNING instance over others', async () => {
+    vi.mocked(client.get)
+      .mockRejectedValueOnce(new Error('not found'))
+      .mockResolvedValueOnce([{ id: 'srv-1', name: 'ha-mcp' }] as never)
+      .mockResolvedValueOnce([
+        { id: 'inst-err', status: 'ERROR', containerId: null },
+        { id: 'inst-ok', status: 'RUNNING', containerId: 'abc' },
+      ] as never)
+      .mockResolvedValueOnce({ stdout: 'running instance\n', stderr: '' } as never);
+    const cmd = createLogsCommand({ client, log });
+    await cmd.parseAsync(['ha-mcp'], { from: 'user' });
+    expect(client.get).toHaveBeenCalledWith('/api/v1/instances/inst-ok/logs');
+  });
+
+  it('selects specific replica with --instance', async () => {
+    vi.mocked(client.get)
+      .mockRejectedValueOnce(new Error('not found'))
+      .mockResolvedValueOnce([{ id: 'srv-1', name: 'ha-mcp' }] as never)
+      .mockResolvedValueOnce([
+        { id: 'inst-0', status: 'RUNNING', containerId: 'a' },
+        { id: 'inst-1', status: 'RUNNING', containerId: 'b' },
+      ] as never)
+      .mockResolvedValueOnce({ stdout: 'replica 1\n', stderr: '' } as never);
+    const cmd = createLogsCommand({ client, log });
+    await cmd.parseAsync(['ha-mcp', '-i', '1'], { from: 'user' });
+    expect(client.get).toHaveBeenCalledWith('/api/v1/instances/inst-1/logs');
+  });
+
+  it('throws on out-of-range --instance index', async () => {
+    vi.mocked(client.get)
+      .mockRejectedValueOnce(new Error('not found'))
+      .mockResolvedValueOnce([{ id: 'srv-1', name: 'ha-mcp' }] as never)
+      .mockResolvedValueOnce([{ id: 'inst-0', status: 'RUNNING' }] as never);
+    const cmd = createLogsCommand({ client, log });
+    await expect(cmd.parseAsync(['ha-mcp', '-i', '5'], { from: 'user' })).rejects.toThrow('out of range');
+  });
+
+  it('throws when server has no instances', async () => {
+    vi.mocked(client.get)
+      .mockRejectedValueOnce(new Error('not found'))
+      .mockResolvedValueOnce([{ id: 'srv-1', name: 'empty-srv' }] as never)
+      .mockResolvedValueOnce([] as never);
+    const cmd = createLogsCommand({ client, log });
+    await expect(cmd.parseAsync(['empty-srv'], { from: 'user' })).rejects.toThrow('No instances found');
+  });
+
   it('passes tail option', async () => {
-    vi.mocked(client.get).mockResolvedValue({ stdout: '', stderr: '' });
+    vi.mocked(client.get)
+      .mockResolvedValueOnce({ id: 'inst-1' } as never)
+      .mockResolvedValueOnce({ stdout: '', stderr: '' } as never);
     const cmd = createLogsCommand({ client, log });
     await cmd.parseAsync(['inst-1', '-t', '50'], { from: 'user' });
     expect(client.get).toHaveBeenCalledWith('/api/v1/instances/inst-1/logs?tail=50');

src/mcpd/src/repositories/mcp-instance.repository.ts

@@ -11,6 +11,7 @@ export class McpInstanceRepository implements IMcpInstanceRepository {
     }
     return this.prisma.mcpInstance.findMany({
       where,
+      include: { server: { select: { name: true } } },
       orderBy: { createdAt: 'desc' },
     });
   }

src/mcpd/src/services/docker/container-manager.ts

@@ -5,7 +5,7 @@ import type {
   ContainerInfo,
   ContainerLogs,
 } from '../orchestrator.js';
-import { DEFAULT_MEMORY_LIMIT, DEFAULT_NANO_CPUS } from '../orchestrator.js';
+import { DEFAULT_MEMORY_LIMIT } from '../orchestrator.js';
 
 const MCPCTL_LABEL = 'mcpctl.managed';
 
@@ -54,7 +54,7 @@ export class DockerContainerManager implements McpOrchestrator {
 
   async createContainer(spec: ContainerSpec): Promise<ContainerInfo> {
     const memoryLimit = spec.memoryLimit ?? DEFAULT_MEMORY_LIMIT;
-    const nanoCpus = spec.nanoCpus ?? DEFAULT_NANO_CPUS;
+    const nanoCpus = spec.nanoCpus;
 
     const portBindings: Record<string, Array<{ HostPort: string }>> = {};
     const exposedPorts: Record<string, Record<string, never>> = {};
@@ -83,7 +83,7 @@ export class DockerContainerManager implements McpOrchestrator {
       HostConfig: {
         PortBindings: portBindings,
         Memory: memoryLimit,
-        NanoCpus: nanoCpus,
+        ...(nanoCpus ? { NanoCpus: nanoCpus } : {}),
         NetworkMode: spec.network ?? 'bridge',
       },
     };

src/mcpd/src/services/instance.service.ts

@@ -4,6 +4,12 @@ import type { McpOrchestrator, ContainerSpec, ContainerInfo } from './orchestrat
 import { NotFoundError } from './mcp-server.service.js';
 import { resolveServerEnv } from './env-resolver.js';
 
+/** Default image for npm-based MCP servers (STDIO with packageName, no dockerImage). */
+const DEFAULT_NODE_RUNNER_IMAGE = process.env['MCPD_NODE_RUNNER_IMAGE'] ?? 'mysources.co.uk/michal/mcpctl-node-runner:latest';
+
+/** Network for MCP server containers (matches docker-compose mcp-servers network). */
+const MCP_SERVERS_NETWORK = process.env['MCPD_MCP_NETWORK'] ?? 'mcp-servers';
+
 export class InvalidStateError extends Error {
   readonly statusCode = 409;
   constructor(message: string) {
@@ -139,7 +145,23 @@ export class InstanceService {
       });
     }
 
-    const image = server.dockerImage ?? server.packageName ?? server.name;
+    // Determine image + command based on server config:
+    // 1. Explicit dockerImage → use as-is
+    // 2. packageName (npm) → use node-runner image + npx command
+    // 3. Fallback → server name (legacy)
+    let image: string;
+    let npmCommand: string[] | undefined;
+
+    if (server.dockerImage) {
+      image = server.dockerImage;
+    } else if (server.packageName) {
+      image = DEFAULT_NODE_RUNNER_IMAGE;
+      // Build npx command: entrypoint is ["npx", "-y"], so CMD = [packageName, ...args]
+      const serverCommand = server.command as string[] | null;
+      npmCommand = [server.packageName, ...(serverCommand ?? [])];
+    } else {
+      image = server.name;
+    }
 
     let instance = await this.instanceRepo.create({
       serverId,
@@ -151,6 +173,7 @@ export class InstanceService {
         image,
         name: `mcpctl-${server.name}-${instance.id}`,
         hostPort: null,
+        network: MCP_SERVERS_NETWORK,
         labels: {
           'mcpctl.server-id': serverId,
           'mcpctl.instance-id': instance.id,
@@ -159,10 +182,16 @@ export class InstanceService {
       if (server.transport === 'SSE' || server.transport === 'STREAMABLE_HTTP') {
         spec.containerPort = server.containerPort ?? 3000;
       }
+      // npm-based servers: command = [packageName, ...args] (entrypoint handles npx -y)
+      // Docker-image servers: use explicit command if provided
+      if (npmCommand) {
+        spec.command = npmCommand;
+      } else {
         const command = server.command as string[] | null;
         if (command) {
           spec.command = command;
         }
+      }
 
       // Resolve env vars from inline values and secret refs
       if (this.secretRepo) {
@@ -177,6 +206,13 @@ export class InstanceService {
         }
       }
 
+      // Pull image if not available locally
+      try {
+        await this.orchestrator.pullImage(image);
+      } catch {
+        // Image may already be available locally
+      }
+
       const containerInfo = await this.orchestrator.createContainer(spec);
 
       const updateFields: { containerId: string; port?: number } = {

stack/docker-compose.yml

@@ -28,6 +28,8 @@ services:
       MCPD_PORT: "3100"
       MCPD_HOST: "0.0.0.0"
       MCPD_LOG_LEVEL: ${MCPD_LOG_LEVEL:-info}
+      MCPD_NODE_RUNNER_IMAGE: mysources.co.uk/michal/mcpctl-node-runner:latest
+      MCPD_MCP_NETWORK: mcp-servers
     depends_on:
       postgres:
         condition: service_healthy
@@ -47,8 +49,10 @@ networks:
   mcpctl:
     driver: bridge
   mcp-servers:
+    name: mcp-servers
     driver: bridge
-    internal: true
+    # Not internal — MCP servers need outbound access for external APIs.
+    # Isolation enforced by not binding host ports on MCP containers.
 
 volumes:
   mcpctl-pgdata: