@dsh-bio/dsh-bio-gem 0.1.13 → 0.1.15

package/package.json

@@ -1,52 +1,66 @@
-{
-  "name": "@dsh-bio/dsh-bio-gem",
-  "version": "0.1.13",
-  "description": "基因组尺度代谢模型（GEM）构建插件：输入细菌全基因组（蛋白FASTA，支持多质粒/多染色体），自动构建+验证+补洞+出报告（SBML + 模型卡），供 dsh-bio-genie 消费工具加载使用 | Genome-scale metabolic model builder for dsh",
-  "repository": {
-    "type": "git",
-    "url": "https://github.com/moonbowterfly/dsh-bio-gem.git"
-  },
-  "homepage": "https://github.com/moonbowterfly/dsh-bio-gem",
-  "bugs": {
-    "url": "https://github.com/moonbowterfly/dsh-bio-gem/issues"
-  },
-  "publishConfig": {
-    "access": "public"
-  },
-  "type": "module",
-  "main": "index.js",
-  "exports": {
-    ".": "./index.js",
-    "./cordis.patch.yml": "./cordis.patch.yml",
-    "./package.json": "./package.json"
-  },
-  "files": [
-    "index.js",
-    "cordis.patch.yml",
-    "src/**/*.js",
-    "python/**/*.py",
-    "skills/**/*.md",
-    "docs/**/*.md",
-    "README.md",
-    "LICENSE"
-  ],
-  "keywords": ["dsh", "deepseek-harness", "dsh-plugin", "metabolic-model", "GEM", "SBML", "carveme", "cobra", "bioinformatics"],
-  "license": "MIT",
-  "engines": { "node": "^22.19 || >=24" },
-  "dsh": {
-    "bundle": {
-      "patch": "./cordis.patch.yml"
-    }
-  },
-  "scripts": {
-    "smoke": "node test/smoke.js",
-    "test": "node test/smoke.js --skip-build && node test/integration.js && node --import ./test/register-dsh-tools.mjs test/optional-injection.js && node --import ./test/register-dsh-tools.mjs test/check-capabilities.mjs && node test/check-counts.mjs",
-    "test:full": "node test/smoke.js && node test/integration.js && node --import ./test/register-dsh-tools.mjs test/optional-injection.js && node --import ./test/register-dsh-tools.mjs test/check-capabilities.mjs && node test/check-counts.mjs"
-  },
-  "peerDependencies": {
-    "@deepseek-ai/dsh-tools": "*"
-  },
-  "peerDependenciesMeta": {
-    "@deepseek-ai/dsh-tools": { "optional": true }
-  }
-}
+{
+  "name": "@dsh-bio/dsh-bio-gem",
+  "version": "0.1.15",
+  "description": "基因组尺度代谢模型（GEM）构建插件：输入细菌全基因组（蛋白FASTA，支持多质粒/多染色体），自动构建+验证+补洞+出报告（SBML + 模型卡），供 dsh-bio-genie 消费工具加载使用 | Genome-scale metabolic model builder for dsh",
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/moonbowterfly/dsh-bio-gem.git"
+  },
+  "homepage": "https://github.com/moonbowterfly/dsh-bio-gem",
+  "bugs": {
+    "url": "https://github.com/moonbowterfly/dsh-bio-gem/issues"
+  },
+  "publishConfig": {
+    "access": "public"
+  },
+  "type": "module",
+  "main": "index.js",
+  "exports": {
+    ".": "./index.js",
+    "./cordis.patch.yml": "./cordis.patch.yml",
+    "./package.json": "./package.json"
+  },
+  "files": [
+    "index.js",
+    "cordis.patch.yml",
+    "src/**/*.js",
+    "python/**/*.py",
+    "skills/**/*.md",
+    "docs/**/*.md",
+    "README.md",
+    "LICENSE"
+  ],
+  "keywords": [
+    "dsh",
+    "deepseek-harness",
+    "dsh-plugin",
+    "metabolic-model",
+    "GEM",
+    "SBML",
+    "carveme",
+    "cobra",
+    "bioinformatics"
+  ],
+  "license": "MIT",
+  "engines": {
+    "node": "^22.19 || >=24"
+  },
+  "dsh": {
+    "bundle": {
+      "patch": "./cordis.patch.yml"
+    }
+  },
+  "scripts": {
+    "smoke": "node test/smoke.js",
+    "test": "node test/check-version-source.mjs && node test/smoke.js --skip-build && node test/integration.js && node test/capabilities.js && node --import ./test/register-dsh-tools.mjs test/optional-injection.js && node --import ./test/register-dsh-tools.mjs test/check-capabilities.mjs && node test/check-counts.mjs && node test/capabilities-warn-state.mjs",
+    "test:full": "node test/smoke.js && node test/integration.js && node test/capabilities.js && node --import ./test/register-dsh-tools.mjs test/optional-injection.js && node --import ./test/register-dsh-tools.mjs test/check-capabilities.mjs && node test/check-counts.mjs"
+  },
+  "peerDependencies": {
+    "@deepseek-ai/dsh-tools": "*"
+  },
+  "peerDependenciesMeta": {
+    "@deepseek-ai/dsh-tools": {
+      "optional": true
+    }
+  }
+}

package/src/capabilities.js

@@ -12,7 +12,7 @@
 // cost_class:  light  (<10s)  | medium (10s–2min) | heavy (>2min)
 // network:     none | optional | required
 // mutability:  read_only | writes_output | model_mutating
-// status:      ready | experimental | data-not-initialized  （依赖级状态由 integration 动态覆盖）
+// status:      ready | experimental | data-not-initialized  （依赖级状态由 integration 动态覆盖为 unavailable / unknown）
 // requires:    动态依赖 id 列表（对齐 integration status 的 check id；缺省即 ready）
 
 export const TOOLS_MANIFEST = [
@@ -124,11 +124,19 @@ export const CONTRACT_VERSION = '1'
 export function buildCapabilitiesReport({ pluginVersion, checks = [] } = {}) {
   const checkStatus = new Map(checks.map((c) => [c.id, c.status]))
   const tools = TOOLS_MANIFEST.map((t) => {
-    const missingDeps = (t.requires ?? []).filter((id) => {
+    const required = t.requires ?? []
+    // 三态与 status 层对齐：missing = 确认缺；warn = 探测未完成或进行中
+    // （runtime.gapseq 在 WSL 冷启动期间就是 warn）；未出现在 checks = 未观测到。
+    // warn 不可归入 missing——否则"还在探测"会被说成"gapseq 不可用"。
+    const missingDeps = required.filter((id) => checkStatus.get(id) === 'missing')
+    const unprobedDeps = required.filter((id) => {
       const st = checkStatus.get(id)
-      return st !== undefined && st !== 'ok'
+      return st !== undefined && st !== 'ok' && st !== 'missing'
     })
-    const effectiveStatus = missingDeps.length > 0 ? 'unavailable' : (t.status ?? 'ready')
+    const unknownDeps = required.filter((id) => !checkStatus.has(id))
+    const effectiveStatus = missingDeps.length > 0 ? 'unavailable'
+      : unprobedDeps.length > 0 ? 'unknown'
+        : unknownDeps.length > 0 ? 'unknown' : (t.status ?? 'ready')
     return {
       name: t.name,
       capability: t.capability,
@@ -140,6 +148,11 @@ export function buildCapabilitiesReport({ pluginVersion, checks = [] } = {}) {
       summary: t.summary,
       ...(t.requires ? { requires: t.requires } : {}),
       ...(missingDeps.length > 0 ? { missing_dependencies: missingDeps } : {}),
+      // 未观测到（check缺席）与探测未完成（warn）都归入 unknown_dependencies：
+      // 两者都无法证明依赖缺失，前端据此提示"待确认"而非"不可用"。
+      ...(unknownDeps.length + unprobedDeps.length > 0
+        ? { unknown_dependencies: [...unprobedDeps, ...unknownDeps] }
+        : {}),
     }
   })
   return {

package/src/integration.js

@@ -1,507 +1,511 @@
-import { spawn } from 'node:child_process'
-import { existsSync, readFileSync, readdirSync, statSync } from 'node:fs'
-import os from 'node:os'
-import { join } from 'node:path'
-import { pythonCandidates } from './python.js'
-import { TOOLS_MANIFEST, buildCapabilitiesReport } from './capabilities.js'
-
-/**
- * dsh-bio-gem — hosted-domain integration protocol v1 (read-only batch).
- *
- * This module deliberately has no import-time probes: loading the plugin and
- * serving /health must never spawn Python or modify the data directory.
- */
-
-export const INTEGRATION_PREFIX = '/api/dsh-bio-gem/integration'
-export const PROTOCOL_MAJOR = 1
-export const PROTOCOL_MINORS = [0]
-export const RUNTIME_PROBE_CACHE_MS = 60_000
-/** WSL/gapseq 探测更重（wsl.exe 冷启动可达十秒级），缓存更久且**非阻塞**。 */
-export const GAPSEQ_PROBE_CACHE_MS = 300_000
-export const INTEGRATION_FEATURES = [
-  'status',
-  'capabilities',
-  'model-store',
-  'ledger',
-  'exports',
-  'carveme-runtime',
-  'gapseq-probe',
-]
-
-const PLUGIN_ID = 'dsh-bio-gem'
-const PLUGIN_VERSION = '0.1.13'
-
-function defaultDataRoot() {
-  const dshHome = process.env.DSH_HOME ?? join(os.homedir(), '.dsh')
-  return join(dshHome, 'dsh-bio-gem')
-}
-
-function listFiles(dir, predicate = () => true) {
-  try {
-    return readdirSync(dir, { withFileTypes: true })
-      .filter((entry) => entry.isFile() && predicate(entry.name))
-      .map((entry) => {
-        const fullPath = join(dir, entry.name)
-        const stat = statSync(fullPath)
-        return {
-          name: entry.name,
-          sizeBytes: stat.size,
-          modifiedAt: stat.mtime.toISOString(),
-        }
-      })
-      .sort((a, b) => b.modifiedAt.localeCompare(a.modifiedAt))
-  } catch {
-    return []
-  }
-}
-
-function boundedSummary(dir, predicate) {
-  const all = listFiles(dir, predicate)
-  return { count: all.length, items: all.slice(0, 50) }
-}
-
-function ledgerSummary(root) {
-  const dir = join(root, 'ledger')
-  const files = listFiles(dir, (name) => name.endsWith('.jsonl'))
-  const ledgers = files.map((file) => {
-    let entries = 0
-    try {
-      entries = readFileSync(join(dir, file.name), 'utf8').split(/\r?\n/).filter((line) => line.trim()).length
-    } catch { /* unreadable ledgers are represented as zero entries */ }
-    return {
-      model: file.name.replace(/\.jsonl$/, ''),
-      entries,
-      modifiedAt: file.modifiedAt,
-    }
-  })
-  return {
-    count: ledgers.length,
-    totalEntries: ledgers.reduce((total, ledger) => total + ledger.entries, 0),
-    dir,
-    ledgers: ledgers.slice(0, 50),
-  }
-}
-
-function carvemeStatus(root) {
-  const scripts = join(root, 'venv-carveme', 'Scripts')
-  const carve = existsSync(join(scripts, 'carve.exe'))
-  const diamond = existsSync(join(scripts, 'diamond.exe'))
-  return {
-    available: carve && diamond,
-    hint: carve && diamond
-      ? 'carve.exe 与 diamond.exe 均可读。'
-      : 'gem_build(carveme) 需要私有 venv 中的 carve.exe 与 diamond.exe。',
-  }
-}
-
-function statusCheck(id, status, detail) {
-  return { id, status, detail }
-}
-
-function remediationsFor(checks) {
-  const codes = new Set(checks.filter((check) => check.status !== 'ok').map((check) => check.id))
-  const remediations = []
-  if (codes.has('python.cobra')) {
-    remediations.push({
-      code: 'genie.bootstrap-python', owner: 'genie',
-      detail: '准备 BioGenie 共享 Python/cobra 环境后重新探测。',
-    })
-  }
-  if (codes.has('runtime.carveme')) {
-    remediations.push({
-      code: 'gem.install-carveme-runtime', owner: 'gem',
-      detail: '准备 gem 私有 CarveMe 运行时（含 diamond）后重新探测。',
-    })
-  }
-  if (codes.has('runtime.gapseq')) {
-    remediations.push({
-      code: 'genie.install-wsl-gapseq', owner: 'genie',
-      detail: '准备 WSL/gapseq 共享前置能力后重新探测。',
-    })
-  }
-  return remediations
-}
-
-/** Read only the installed cobra version; output and failures stay local. */
-function probeCobraVersion(executable) {
-  return new Promise((resolve) => {
-    let settled = false
-    let timer = null
-    const finish = (value) => {
-      if (settled) return
-      settled = true
-      if (timer) clearTimeout(timer)
-      resolve(value)
-    }
-    try {
-      const child = spawn(executable, ['-I', '-c', 'import cobra; print(cobra.__version__)'], {
-        windowsHide: true,
-        stdio: ['ignore', 'pipe', 'ignore'],
-      })
-      let stdout = ''
-      child.stdout?.on('data', (chunk) => { stdout += chunk.toString('utf8') })
-      child.on('error', () => finish(null))
-      child.on('close', (code) => finish(code === 0 ? stdout.trim() || 'available' : null))
-      timer = setTimeout(() => {
-        try { child.kill() } catch { /* already exited */ }
-        finish(null)
-      }, 20_000)
-    } catch {
-      finish(null)
-    }
-  })
-}
-
-async function probePythonEnvironment(candidateProvider, fileExists, probeCobra) {
-  const candidates = candidateProvider().map((candidate) => ({
-    ...candidate,
-    exists: candidate.path === 'python' ? true : fileExists(candidate.path),
-  }))
-  let selected = null
-  for (const candidate of candidates) {
-    if (!candidate.exists) continue
-    let cobraVersion = null
-    try {
-      cobraVersion = await probeCobra(candidate.path)
-    } catch { /* individual candidate failures are an expected degraded state */ }
-    if (cobraVersion) {
-      selected = {
-        path: candidate.path,
-        source: candidate.source,
-        cobraVersion,
-      }
-      break
-    }
-  }
-  return {
-    selected,
-    candidates,
-    note: selected ? undefined : '所有候选均未通过 import cobra 的只读探测。',
-  }
-}
-
-/** Execute a fixed, read-only WSL command and retain only a tiny version response. */
-function runGapseqVersionCommand(command, args) {
-  return new Promise((resolve) => {
-    let settled = false
-    let stdout = ''
-    let timer = null
-    const finish = (result) => {
-      if (settled) return
-      settled = true
-      if (timer) clearTimeout(timer)
-      resolve(result)
-    }
-    try {
-      // stdin 必须保持 pipe（并立即 end）：实测 wsl.exe 在 stdin=ignore 下会极慢
-      // （同一条 `echo ok`：ignore 14.9s vs pipe 0.26s，约 50 倍），
-      // 这是之前 gapseq 探测频繁超时的真正根因。
-      const child = spawn(command, args, {
-        windowsHide: true,
-        stdio: ['pipe', 'pipe', 'ignore'],
-      })
-      child.stdin?.end()
-      child.stdout?.on('data', (chunk) => {
-        if (stdout.length < 512) stdout += chunk.toString('utf8').slice(0, 512 - stdout.length)
-      })
-      child.on('error', () => finish({ ok: false }))
-      child.on('close', (code) => finish({ ok: code === 0, stdout }))
-      timer = setTimeout(() => {
-        try { child.kill() } catch { /* already exited */ }
-        finish({ ok: false, timeout: true })
-      }, 30_000)
-    } catch {
-      finish({ ok: false })
-    }
-  })
-}
-
-async function probeGapseqEnvironment({ isWindows, distro, runner }) {
-  if (!isWindows) {
-    return { available: false, detail: 'gapseq 仅支持 Windows WSL 的只读探测。' }
-  }
-  // 快速预检：先确认目标发行版存在（wsl.exe -l -q 亚秒级），避免发行版缺失时
-  // 白等一次 bash 长命令直到超时刹车（真实运行时实测：本机 bash 启动即 ~3s）。
-  try {
-    const listed = await runner('wsl.exe', ['-l', '-q'])
-    const names = String(listed?.stdout ?? '')
-      .replace(/\u0000/g, '')
-      .split(/\r?\n/)
-      .map((name) => name.trim())
-      .filter(Boolean)
-    if (listed?.ok && !names.includes(distro)) {
-      return {
-        available: false,
-        detail: names.length > 0
-          ? `WSL 发行版 ${distro} 不存在（现有：${names.join(', ')}）。`
-          : `WSL 未发现发行版（期望 ${distro}）。`,
-      }
-    }
-  } catch { /* 预检失败不阻断后续只读探测 */ }
-  let result
-  try {
-    result = await runner('wsl.exe', [
-      '-d', distro, '-u', 'root', '--', 'bash', '-lc',
-      'source /opt/miniforge3/etc/profile.d/conda.sh && conda activate gapseq && gapseq -v',
-    ])
-  } catch {
-    return { available: false, detail: 'WSL/gapseq 只读探测未完成。' }
-  }
-  const output = String(result?.stdout ?? '').slice(0, 512)
-  if (!result?.ok || !/\bgapseq\b/i.test(output)) {
-    return {
-      available: false,
-      detail: result?.timeout
-        ? 'gapseq 探测超时（WSL 冷启动可能超过 30s），后台将自动重试。'
-        : 'WSL/gapseq 只读探测未就绪。',
-    }
-  }
-  const version = output.match(/gapseq(?:\s+version)?\s*[:v]?\s*([0-9][0-9.]*)/i)?.[1]
-  return {
-    available: true,
-    detail: version ? `gapseq ${version}（WSL 只读探测通过）。` : 'gapseq（WSL 只读探测通过）。',
-  }
-}
-
-function writeJson(res, status, body) {
-  res.writeHead(status, {
-    'content-type': 'application/json; charset=utf-8',
-    'referrer-policy': 'no-referrer',
-  })
-  res.end(JSON.stringify(body))
-}
-
-/**
- * Loopback + same-origin guard copied from the host integration boundary.
- *
- * It independently verifies socket address, Host, browser cross-site intent,
- * and Origin when one is present. Loopback alone is not treated as a general
- * authorization mechanism for future write routes.
- */
-export function isLoopbackRequest(req) {
-  const address = req.socket?.remoteAddress
-  if (address !== '127.0.0.1' && address !== '::1' && address !== '::ffff:127.0.0.1') return false
-  const host = req.headers?.host
-  if (typeof host !== 'string') return false
-  let hostUrl
-  try {
-    hostUrl = new URL(`http://${host}`)
-  } catch {
-    return false
-  }
-  if (hostUrl.hostname !== '127.0.0.1' && hostUrl.hostname !== 'localhost' && hostUrl.hostname !== '[::1]') return false
-  if (req.headers?.['sec-fetch-site'] === 'cross-site') return false
-  const origin = req.headers?.origin
-  if (origin === undefined) return true
-  try {
-    return new URL(origin).host === hostUrl.host
-  } catch {
-    return false
-  }
-}
-
-function guardedGet(handler) {
-  return async (req, res) => {
-    if (!isLoopbackRequest(req)) {
-      return writeJson(res, 403, {
-        ok: false,
-        code: 'loopback-required',
-        message: 'loopback requests only',
-      })
-    }
-    if (req.method !== 'GET') {
-      return writeJson(res, 405, {
-        ok: false,
-        code: 'method-not-allowed',
-        message: `method not allowed: ${req.method}`,
-      })
-    }
-    try {
-      const response = await handler()
-      if (response?.ok !== true) {
-        return writeJson(res, 500, {
-          ok: false,
-          code: 'internal',
-          message: 'integration endpoint failed',
-        })
-      }
-      return writeJson(res, 200, response)
-    } catch {
-      return writeJson(res, 500, {
-        ok: false,
-        code: 'internal',
-        message: 'integration endpoint failed',
-      })
-    }
-  }
-}
-
-/** Register the two fixed read-only integration routes when webServer exists. */
-export function registerIntegrationRoutes(ctx, options = {}) {
-  const webServer = options.webServer ?? ctx?.webServer
-  if (!webServer?.register) return () => {}
-  const service = options.service ?? createIntegrationService(options)
-  const routes = [
-    {
-      kind: 'exact',
-      path: `${INTEGRATION_PREFIX}/health`,
-      handler: guardedGet(() => service.health()),
-    },
-    {
-      kind: 'exact',
-      path: `${INTEGRATION_PREFIX}/v1/status`,
-      handler: guardedGet(() => service.status()),
-    },
-    {
-      kind: 'exact',
-      path: `${INTEGRATION_PREFIX}/v1/capabilities`,
-      handler: guardedGet(() => service.capabilities()),
-    },
-  ]
-  const disposers = routes.map((route) => webServer.register(route))
-  return () => {
-    for (const dispose of disposers) dispose?.()
-  }
-}
-
-/**
- * Create the stateless portion of the integration API.
- *
- * Options exist solely to make protocol behavior testable without a dsh host;
- * production callers use the package defaults.
- */
-export function createIntegrationService(options = {}) {
-  const pluginVersion = options.pluginVersion ?? PLUGIN_VERSION
-  const dataRoot = options.dataRoot ?? defaultDataRoot()
-  const now = options.now ?? Date.now
-  const candidateProvider = options.pythonCandidates ?? pythonCandidates
-  const fileExists = options.fileExists ?? existsSync
-  const probeCobra = options.probeCobra ?? probeCobraVersion
-  const probePython = options.probePython
-    ?? (() => probePythonEnvironment(candidateProvider, fileExists, probeCobra))
-  const probeGapseq = options.probeGapseq
-    ?? (() => probeGapseqEnvironment({
-      isWindows: options.isWindows ?? process.platform === 'win32',
-      distro: options.gapseqDistro ?? process.env.GEM_GAPSEQ_DISTRO ?? 'Ubuntu-22.04',
-      runner: options.runGapseqProbe ?? runGapseqVersionCommand,
-    }))
-  let cachedPython = null
-  let cachedPythonAt = 0
-  let pendingPython = null
-  let cachedGapseq = null
-  let cachedGapseqAt = 0
-  let pendingGapseq = null
-
-  /** Python 探测快（≈3s）且有 60s 缓存：保持同步等待，语义简单。 */
-  function readPython() {
-    const current = now()
-    if (cachedPython && current - cachedPythonAt < RUNTIME_PROBE_CACHE_MS) return Promise.resolve(cachedPython)
-    if (pendingPython) return pendingPython
-    pendingPython = Promise.resolve()
-      .then(probePython)
-      .then((value) => {
-        cachedPython = value
-        cachedPythonAt = now()
-        return value
-      })
-      .finally(() => { pendingPython = null })
-    return pendingPython
-  }
-
-  /**
-   * gapseq 探测**非阻塞**（stale-while-revalidate）：缓存未过期直接返回；
-   * 过期时立即返回旧值并后台刷新；从未探测过则返回 `available: null` 占位
-   * （契约语义：null = 尚未探测，探测在后台进行，后续请求即得布尔结果）。
-   * 这样 status 永远不会被 WSL 冷启动拖到消费端超时。
-   */
-  function readGapseq() {
-    const current = now()
-    // 失败结果（含超时）只缓存 60s，让后台尽快重试（WSL 冷启动是暂时性状态）。
-    const ttl = cachedGapseq?.available === false ? 60_000 : GAPSEQ_PROBE_CACHE_MS
-    if (cachedGapseq && current - cachedGapseqAt < ttl) return cachedGapseq
-    if (!pendingGapseq) {
-      pendingGapseq = Promise.resolve()
-        .then(probeGapseq)
-        .then((value) => {
-          cachedGapseq = value
-          cachedGapseqAt = now()
-          return value
-        })
-        .catch(() => cachedGapseq)
-        .finally(() => { pendingGapseq = null })
-    }
-    return cachedGapseq ?? {
-      available: null,
-      probing: true,
-      detail: 'gapseq 只读探测进行中（WSL 冷启动可能需数秒），稍后刷新可见结果。',
-    }
-  }
-
-  /** 依赖检查（status 与 capabilities 共用；语义与既有 status 一致）。 */
-  async function collectChecks() {
-    const python = await readPython()
-    const gapseq = readGapseq()
-    const carveme = carvemeStatus(dataRoot)
-    const checks = [
-      statusCheck(
-        'python.cobra',
-        python.selected ? 'ok' : 'missing',
-        python.selected
-          ? `cobra ${python.selected.cobraVersion ?? 'available'} @ ${python.selected.path}`
-          : '未找到可 import cobra 的 Python 解释器。',
-      ),
-      statusCheck(
-        'runtime.carveme',
-        carveme.available ? 'ok' : 'missing',
-        carveme.hint,
-      ),
-      statusCheck(
-        'runtime.gapseq',
-        gapseq.available === true ? 'ok' : gapseq.available === null ? 'warn' : 'missing',
-        gapseq.detail ?? (gapseq.available ? 'gapseq 只读探测通过。' : 'gapseq 只读探测未就绪。'),
-      ),
-    ]
-    return { python, gapseq, carveme, checks }
-  }
-
-  return {
-    async health() {
-      return {
-        ok: true,
-        value: {
-          pluginId: PLUGIN_ID,
-          pluginVersion,
-          protocolMajor: PROTOCOL_MAJOR,
-          protocolMinors: PROTOCOL_MINORS,
-          features: INTEGRATION_FEATURES,
-        },
-      }
-    },
-
-    async capabilities() {
-      const { checks } = await collectChecks()
-      return { ok: true, value: buildCapabilitiesReport({ pluginVersion, checks }) }
-    },
-
-    async status() {
-      const { python, gapseq, carveme, checks } = await collectChecks()
-      return {
-        ok: true,
-        value: {
-          state: checks.every((check) => check.status === 'ok') ? 'ready' : 'degraded',
-          generatedAt: new Date(now()).toISOString(),
-          pluginVersion,
-          features: INTEGRATION_FEATURES,
-          checks,
-          data: {
-            models: boundedSummary(join(dataRoot, 'models'), (name) => name.endsWith('.xml')),
-            ledger: ledgerSummary(dataRoot),
-            exports: boundedSummary(join(dataRoot, 'exports')),
-          },
-          env: { python, engines: { carveme, gapseq } },
-          remediations: remediationsFor(checks),
-        },
-      }
-    },
-  }
-}
+import { spawn } from 'node:child_process'
+import { existsSync, readFileSync, readdirSync, statSync } from 'node:fs'
+import os from 'node:os'
+import { join } from 'node:path'
+import { pythonCandidates } from './python.js'
+import { TOOLS_MANIFEST, buildCapabilitiesReport } from './capabilities.js'
+
+/**
+ * dsh-bio-gem — hosted-domain integration protocol v1 (read-only batch).
+ *
+ * This module deliberately has no import-time probes: loading the plugin and
+ * serving /health must never spawn Python or modify the data directory.
+ */
+
+export const INTEGRATION_PREFIX = '/api/dsh-bio-gem/integration'
+export const PROTOCOL_MAJOR = 1
+export const PROTOCOL_MINORS = [0]
+export const RUNTIME_PROBE_CACHE_MS = 60_000
+/** WSL/gapseq 探测更重（wsl.exe 冷启动可达十秒级），缓存更久且**非阻塞**。 */
+export const GAPSEQ_PROBE_CACHE_MS = 300_000
+export const INTEGRATION_FEATURES = [
+  'status',
+  'capabilities',
+  'model-store',
+  'ledger',
+  'exports',
+  'carveme-runtime',
+  'gapseq-probe',
+]
+
+const PLUGIN_ID = 'dsh-bio-gem'
+// 版本号从 package.json 实时读，避免 bump 版本时漏改此处导致 /health 自报旧版本
+// （第二真值源曾导致 galatea 报 0.1.2 而磁盘已是 0.1.3；重启无效、非缓存）。
+const PLUGIN_VERSION = JSON.parse(
+  readFileSync(new URL('../package.json', import.meta.url), 'utf8'),
+).version
+
+function defaultDataRoot() {
+  const dshHome = process.env.DSH_HOME ?? join(os.homedir(), '.dsh')
+  return join(dshHome, 'dsh-bio-gem')
+}
+
+function listFiles(dir, predicate = () => true) {
+  try {
+    return readdirSync(dir, { withFileTypes: true })
+      .filter((entry) => entry.isFile() && predicate(entry.name))
+      .map((entry) => {
+        const fullPath = join(dir, entry.name)
+        const stat = statSync(fullPath)
+        return {
+          name: entry.name,
+          sizeBytes: stat.size,
+          modifiedAt: stat.mtime.toISOString(),
+        }
+      })
+      .sort((a, b) => b.modifiedAt.localeCompare(a.modifiedAt))
+  } catch {
+    return []
+  }
+}
+
+function boundedSummary(dir, predicate) {
+  const all = listFiles(dir, predicate)
+  return { count: all.length, items: all.slice(0, 50) }
+}
+
+function ledgerSummary(root) {
+  const dir = join(root, 'ledger')
+  const files = listFiles(dir, (name) => name.endsWith('.jsonl'))
+  const ledgers = files.map((file) => {
+    let entries = 0
+    try {
+      entries = readFileSync(join(dir, file.name), 'utf8').split(/\r?\n/).filter((line) => line.trim()).length
+    } catch { /* unreadable ledgers are represented as zero entries */ }
+    return {
+      model: file.name.replace(/\.jsonl$/, ''),
+      entries,
+      modifiedAt: file.modifiedAt,
+    }
+  })
+  return {
+    count: ledgers.length,
+    totalEntries: ledgers.reduce((total, ledger) => total + ledger.entries, 0),
+    dir,
+    ledgers: ledgers.slice(0, 50),
+  }
+}
+
+function carvemeStatus(root) {
+  const scripts = join(root, 'venv-carveme', 'Scripts')
+  const carve = existsSync(join(scripts, 'carve.exe'))
+  const diamond = existsSync(join(scripts, 'diamond.exe'))
+  return {
+    available: carve && diamond,
+    hint: carve && diamond
+      ? 'carve.exe 与 diamond.exe 均可读。'
+      : 'gem_build(carveme) 需要私有 venv 中的 carve.exe 与 diamond.exe。',
+  }
+}
+
+function statusCheck(id, status, detail) {
+  return { id, status, detail }
+}
+
+function remediationsFor(checks) {
+  const codes = new Set(checks.filter((check) => check.status !== 'ok').map((check) => check.id))
+  const remediations = []
+  if (codes.has('python.cobra')) {
+    remediations.push({
+      code: 'genie.bootstrap-python', owner: 'genie',
+      detail: '准备 BioGenie 共享 Python/cobra 环境后重新探测。',
+    })
+  }
+  if (codes.has('runtime.carveme')) {
+    remediations.push({
+      code: 'gem.install-carveme-runtime', owner: 'gem',
+      detail: '准备 gem 私有 CarveMe 运行时（含 diamond）后重新探测。',
+    })
+  }
+  if (codes.has('runtime.gapseq')) {
+    remediations.push({
+      code: 'genie.install-wsl-gapseq', owner: 'genie',
+      detail: '准备 WSL/gapseq 共享前置能力后重新探测。',
+    })
+  }
+  return remediations
+}
+
+/** Read only the installed cobra version; output and failures stay local. */
+function probeCobraVersion(executable) {
+  return new Promise((resolve) => {
+    let settled = false
+    let timer = null
+    const finish = (value) => {
+      if (settled) return
+      settled = true
+      if (timer) clearTimeout(timer)
+      resolve(value)
+    }
+    try {
+      const child = spawn(executable, ['-I', '-c', 'import cobra; print(cobra.__version__)'], {
+        windowsHide: true,
+        stdio: ['ignore', 'pipe', 'ignore'],
+      })
+      let stdout = ''
+      child.stdout?.on('data', (chunk) => { stdout += chunk.toString('utf8') })
+      child.on('error', () => finish(null))
+      child.on('close', (code) => finish(code === 0 ? stdout.trim() || 'available' : null))
+      timer = setTimeout(() => {
+        try { child.kill() } catch { /* already exited */ }
+        finish(null)
+      }, 20_000)
+    } catch {
+      finish(null)
+    }
+  })
+}
+
+async function probePythonEnvironment(candidateProvider, fileExists, probeCobra) {
+  const candidates = candidateProvider().map((candidate) => ({
+    ...candidate,
+    exists: candidate.path === 'python' ? true : fileExists(candidate.path),
+  }))
+  let selected = null
+  for (const candidate of candidates) {
+    if (!candidate.exists) continue
+    let cobraVersion = null
+    try {
+      cobraVersion = await probeCobra(candidate.path)
+    } catch { /* individual candidate failures are an expected degraded state */ }
+    if (cobraVersion) {
+      selected = {
+        path: candidate.path,
+        source: candidate.source,
+        cobraVersion,
+      }
+      break
+    }
+  }
+  return {
+    selected,
+    candidates,
+    note: selected ? undefined : '所有候选均未通过 import cobra 的只读探测。',
+  }
+}
+
+/** Execute a fixed, read-only WSL command and retain only a tiny version response. */
+function runGapseqVersionCommand(command, args) {
+  return new Promise((resolve) => {
+    let settled = false
+    let stdout = ''
+    let timer = null
+    const finish = (result) => {
+      if (settled) return
+      settled = true
+      if (timer) clearTimeout(timer)
+      resolve(result)
+    }
+    try {
+      // stdin 必须保持 pipe（并立即 end）：实测 wsl.exe 在 stdin=ignore 下会极慢
+      // （同一条 `echo ok`：ignore 14.9s vs pipe 0.26s，约 50 倍），
+      // 这是之前 gapseq 探测频繁超时的真正根因。
+      const child = spawn(command, args, {
+        windowsHide: true,
+        stdio: ['pipe', 'pipe', 'ignore'],
+      })
+      child.stdin?.end()
+      child.stdout?.on('data', (chunk) => {
+        if (stdout.length < 512) stdout += chunk.toString('utf8').slice(0, 512 - stdout.length)
+      })
+      child.on('error', () => finish({ ok: false }))
+      child.on('close', (code) => finish({ ok: code === 0, stdout }))
+      timer = setTimeout(() => {
+        try { child.kill() } catch { /* already exited */ }
+        finish({ ok: false, timeout: true })
+      }, 30_000)
+    } catch {
+      finish({ ok: false })
+    }
+  })
+}
+
+async function probeGapseqEnvironment({ isWindows, distro, runner }) {
+  if (!isWindows) {
+    return { available: false, detail: 'gapseq 仅支持 Windows WSL 的只读探测。' }
+  }
+  // 快速预检：先确认目标发行版存在（wsl.exe -l -q 亚秒级），避免发行版缺失时
+  // 白等一次 bash 长命令直到超时刹车（真实运行时实测：本机 bash 启动即 ~3s）。
+  try {
+    const listed = await runner('wsl.exe', ['-l', '-q'])
+    const names = String(listed?.stdout ?? '')
+      .replace(/\u0000/g, '')
+      .split(/\r?\n/)
+      .map((name) => name.trim())
+      .filter(Boolean)
+    if (listed?.ok && !names.includes(distro)) {
+      return {
+        available: false,
+        detail: names.length > 0
+          ? `WSL 发行版 ${distro} 不存在（现有：${names.join(', ')}）。`
+          : `WSL 未发现发行版（期望 ${distro}）。`,
+      }
+    }
+  } catch { /* 预检失败不阻断后续只读探测 */ }
+  let result
+  try {
+    result = await runner('wsl.exe', [
+      '-d', distro, '-u', 'root', '--', 'bash', '-lc',
+      'source /opt/miniforge3/etc/profile.d/conda.sh && conda activate gapseq && gapseq -v',
+    ])
+  } catch {
+    return { available: false, detail: 'WSL/gapseq 只读探测未完成。' }
+  }
+  const output = String(result?.stdout ?? '').slice(0, 512)
+  if (!result?.ok || !/\bgapseq\b/i.test(output)) {
+    return {
+      available: false,
+      detail: result?.timeout
+        ? 'gapseq 探测超时（WSL 冷启动可能超过 30s），后台将自动重试。'
+        : 'WSL/gapseq 只读探测未就绪。',
+    }
+  }
+  const version = output.match(/gapseq(?:\s+version)?\s*[:v]?\s*([0-9][0-9.]*)/i)?.[1]
+  return {
+    available: true,
+    detail: version ? `gapseq ${version}（WSL 只读探测通过）。` : 'gapseq（WSL 只读探测通过）。',
+  }
+}
+
+function writeJson(res, status, body) {
+  res.writeHead(status, {
+    'content-type': 'application/json; charset=utf-8',
+    'referrer-policy': 'no-referrer',
+  })
+  res.end(JSON.stringify(body))
+}
+
+/**
+ * Loopback + same-origin guard copied from the host integration boundary.
+ *
+ * It independently verifies socket address, Host, browser cross-site intent,
+ * and Origin when one is present. Loopback alone is not treated as a general
+ * authorization mechanism for future write routes.
+ */
+export function isLoopbackRequest(req) {
+  const address = req.socket?.remoteAddress
+  if (address !== '127.0.0.1' && address !== '::1' && address !== '::ffff:127.0.0.1') return false
+  const host = req.headers?.host
+  if (typeof host !== 'string') return false
+  let hostUrl
+  try {
+    hostUrl = new URL(`http://${host}`)
+  } catch {
+    return false
+  }
+  if (hostUrl.hostname !== '127.0.0.1' && hostUrl.hostname !== 'localhost' && hostUrl.hostname !== '[::1]') return false
+  if (req.headers?.['sec-fetch-site'] === 'cross-site') return false
+  const origin = req.headers?.origin
+  if (origin === undefined) return true
+  try {
+    return new URL(origin).host === hostUrl.host
+  } catch {
+    return false
+  }
+}
+
+function guardedGet(handler) {
+  return async (req, res) => {
+    if (!isLoopbackRequest(req)) {
+      return writeJson(res, 403, {
+        ok: false,
+        code: 'loopback-required',
+        message: 'loopback requests only',
+      })
+    }
+    if (req.method !== 'GET') {
+      return writeJson(res, 405, {
+        ok: false,
+        code: 'method-not-allowed',
+        message: `method not allowed: ${req.method}`,
+      })
+    }
+    try {
+      const response = await handler()
+      if (response?.ok !== true) {
+        return writeJson(res, 500, {
+          ok: false,
+          code: 'internal',
+          message: 'integration endpoint failed',
+        })
+      }
+      return writeJson(res, 200, response)
+    } catch {
+      return writeJson(res, 500, {
+        ok: false,
+        code: 'internal',
+        message: 'integration endpoint failed',
+      })
+    }
+  }
+}
+
+/** Register the two fixed read-only integration routes when webServer exists. */
+export function registerIntegrationRoutes(ctx, options = {}) {
+  const webServer = options.webServer ?? ctx?.webServer
+  if (!webServer?.register) return () => {}
+  const service = options.service ?? createIntegrationService(options)
+  const routes = [
+    {
+      kind: 'exact',
+      path: `${INTEGRATION_PREFIX}/health`,
+      handler: guardedGet(() => service.health()),
+    },
+    {
+      kind: 'exact',
+      path: `${INTEGRATION_PREFIX}/v1/status`,
+      handler: guardedGet(() => service.status()),
+    },
+    {
+      kind: 'exact',
+      path: `${INTEGRATION_PREFIX}/v1/capabilities`,
+      handler: guardedGet(() => service.capabilities()),
+    },
+  ]
+  const disposers = routes.map((route) => webServer.register(route))
+  return () => {
+    for (const dispose of disposers) dispose?.()
+  }
+}
+
+/**
+ * Create the stateless portion of the integration API.
+ *
+ * Options exist solely to make protocol behavior testable without a dsh host;
+ * production callers use the package defaults.
+ */
+export function createIntegrationService(options = {}) {
+  const pluginVersion = options.pluginVersion ?? PLUGIN_VERSION
+  const dataRoot = options.dataRoot ?? defaultDataRoot()
+  const now = options.now ?? Date.now
+  const candidateProvider = options.pythonCandidates ?? pythonCandidates
+  const fileExists = options.fileExists ?? existsSync
+  const probeCobra = options.probeCobra ?? probeCobraVersion
+  const probePython = options.probePython
+    ?? (() => probePythonEnvironment(candidateProvider, fileExists, probeCobra))
+  const probeGapseq = options.probeGapseq
+    ?? (() => probeGapseqEnvironment({
+      isWindows: options.isWindows ?? process.platform === 'win32',
+      distro: options.gapseqDistro ?? process.env.GEM_GAPSEQ_DISTRO ?? 'Ubuntu-22.04',
+      runner: options.runGapseqProbe ?? runGapseqVersionCommand,
+    }))
+  let cachedPython = null
+  let cachedPythonAt = 0
+  let pendingPython = null
+  let cachedGapseq = null
+  let cachedGapseqAt = 0
+  let pendingGapseq = null
+
+  /** Python 探测快（≈3s）且有 60s 缓存：保持同步等待，语义简单。 */
+  function readPython() {
+    const current = now()
+    if (cachedPython && current - cachedPythonAt < RUNTIME_PROBE_CACHE_MS) return Promise.resolve(cachedPython)
+    if (pendingPython) return pendingPython
+    pendingPython = Promise.resolve()
+      .then(probePython)
+      .then((value) => {
+        cachedPython = value
+        cachedPythonAt = now()
+        return value
+      })
+      .finally(() => { pendingPython = null })
+    return pendingPython
+  }
+
+  /**
+   * gapseq 探测**非阻塞**（stale-while-revalidate）：缓存未过期直接返回；
+   * 过期时立即返回旧值并后台刷新；从未探测过则返回 `available: null` 占位
+   * （契约语义：null = 尚未探测，探测在后台进行，后续请求即得布尔结果）。
+   * 这样 status 永远不会被 WSL 冷启动拖到消费端超时。
+   */
+  function readGapseq() {
+    const current = now()
+    // 失败结果（含超时）只缓存 60s，让后台尽快重试（WSL 冷启动是暂时性状态）。
+    const ttl = cachedGapseq?.available === false ? 60_000 : GAPSEQ_PROBE_CACHE_MS
+    if (cachedGapseq && current - cachedGapseqAt < ttl) return cachedGapseq
+    if (!pendingGapseq) {
+      pendingGapseq = Promise.resolve()
+        .then(probeGapseq)
+        .then((value) => {
+          cachedGapseq = value
+          cachedGapseqAt = now()
+          return value
+        })
+        .catch(() => cachedGapseq)
+        .finally(() => { pendingGapseq = null })
+    }
+    return cachedGapseq ?? {
+      available: null,
+      probing: true,
+      detail: 'gapseq 只读探测进行中（WSL 冷启动可能需数秒），稍后刷新可见结果。',
+    }
+  }
+
+  /** 依赖检查（status 与 capabilities 共用；语义与既有 status 一致）。 */
+  async function collectChecks() {
+    const python = await readPython()
+    const gapseq = readGapseq()
+    const carveme = carvemeStatus(dataRoot)
+    const checks = [
+      statusCheck(
+        'python.cobra',
+        python.selected ? 'ok' : 'missing',
+        python.selected
+          ? `cobra ${python.selected.cobraVersion ?? 'available'} @ ${python.selected.path}`
+          : '未找到可 import cobra 的 Python 解释器。',
+      ),
+      statusCheck(
+        'runtime.carveme',
+        carveme.available ? 'ok' : 'missing',
+        carveme.hint,
+      ),
+      statusCheck(
+        'runtime.gapseq',
+        gapseq.available === true ? 'ok' : gapseq.available === null ? 'warn' : 'missing',
+        gapseq.detail ?? (gapseq.available ? 'gapseq 只读探测通过。' : 'gapseq 只读探测未就绪。'),
+      ),
+    ]
+    return { python, gapseq, carveme, checks }
+  }
+
+  return {
+    async health() {
+      return {
+        ok: true,
+        value: {
+          pluginId: PLUGIN_ID,
+          pluginVersion,
+          protocolMajor: PROTOCOL_MAJOR,
+          protocolMinors: PROTOCOL_MINORS,
+          features: INTEGRATION_FEATURES,
+        },
+      }
+    },
+
+    async capabilities() {
+      const { checks } = await collectChecks()
+      return { ok: true, value: buildCapabilitiesReport({ pluginVersion, checks }) }
+    },
+
+    async status() {
+      const { python, gapseq, carveme, checks } = await collectChecks()
+      return {
+        ok: true,
+        value: {
+          state: checks.every((check) => check.status === 'ok') ? 'ready' : 'degraded',
+          generatedAt: new Date(now()).toISOString(),
+          pluginVersion,
+          features: INTEGRATION_FEATURES,
+          checks,
+          data: {
+            models: boundedSummary(join(dataRoot, 'models'), (name) => name.endsWith('.xml')),
+            ledger: ledgerSummary(dataRoot),
+            exports: boundedSummary(join(dataRoot, 'exports')),
+          },
+          env: { python, engines: { carveme, gapseq } },
+          remediations: remediationsFor(checks),
+        },
+      }
+    },
+  }
+}