@dsh-bio/dsh-bio-gem 0.1.1

package/src/python.js

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+// python.js — dsh-bio-gem Python 子进程调用器（JSON stdin 协议）
+// bridge 契约同 dsh-bio-genie：stdout 最后一行是 JSON；stderr 含
+// "Traceback (most recent call last)" 头 = 代码级失败（恒 ok:true 时靠它判定）。
+import { spawn } from 'node:child_process'
+import { dirname, join } from 'node:path'
+import { fileURLToPath } from 'node:url'
+import { existsSync } from 'node:fs'
+
+const PYTHON_DIR = join(dirname(fileURLToPath(import.meta.url)), '..', 'python')
+
+// 运行时探测 Python：优先 miniconda（本机分析环境，cobra 已装），回退 env GEM_PYTHON / PATH
+function pythonExe() {
+  const cands = [
+    process.env.GEM_PYTHON,
+    'C:/Users/shuai/miniconda3/python.exe',
+    'python',
+  ]
+  for (const c of cands) {
+    if (!c) continue
+    try {
+      if (c === 'python' || existsSync(c)) return c
+    } catch { /* ignore */ }
+  }
+  return 'python'
+}
+
+/** 调用 gem_ops.py（op 协议）：{op, args} -> result；异常/代码级失败抛 Error。 */
+export function callGem(op, args, opts = {}) {
+  return new Promise((resolve, reject) => {
+    const py = pythonExe()
+    const script = join(PYTHON_DIR, 'gem_ops.py')
+    const cp = spawn(py, ['-I', script], { cwd: PYTHON_DIR, windowsHide: true })
+    let out = ''
+    let err = ''
+    cp.stdout.on('data', (d) => { out += d })
+    cp.stderr.on('data', (d) => { err += d })
+    cp.on('error', (e) => reject(new Error(`python spawn failed: ${e.message}`)))
+    const timer = opts.timeoutMs
+      ? setTimeout(() => { cp.kill(); reject(new Error(`gem op ${op} timeout after ${opts.timeoutMs}ms`)) }, opts.timeoutMs)
+      : null
+    cp.on('close', (code) => {
+      if (timer) clearTimeout(timer)
+      const lines = out.trim().split(/\r?\n/).filter(Boolean)
+      if (!lines.length) {
+        return reject(new Error(`gem_ops.py produced no output (op=${op}); stderr: ${err.slice(-400)}`))
+      }
+      if (err.includes('Traceback (most recent call last)')) {
+        return reject(new Error(`gem op ${op} code-level failure: ${err.slice(-400)}`))
+      }
+      let parsed
+      try {
+        parsed = JSON.parse(lines[lines.length - 1])
+      } catch (e) {
+        return reject(new Error(`gem op ${op} bad JSON: ${lines[lines.length - 1].slice(0, 300)}`))
+      }
+      if (parsed.ok === false) return reject(new Error(parsed.error || `gem op ${op} failed (ok:false)`))
+      resolve(parsed.result)
+    })
+    cp.stdin.write(JSON.stringify({ op, args }))
+    cp.stdin.end()
+  })
+}
+
+export { pythonExe, PYTHON_DIR }

package/src/skills.js

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+// skills.js — dsh-bio-gem skill 注册（M1：gem-expert 主 skill）
+// 工具选择决策树 + 工作流 + 实测坑位；遵循 dsh-bio-genie 注册模式（ctx.skills.register）。
+import { readFileSync } from 'node:fs'
+import { join, dirname } from 'node:path'
+import { fileURLToPath } from 'node:url'
+
+const SKILLS_DIR = join(dirname(fileURLToPath(import.meta.url)), '..', 'skills')
+
+export function registerSkills(ctx) {
+  const disposers = []
+  let content = ''
+  try {
+    content = readFileSync(join(SKILLS_DIR, 'gem-expert.md'), 'utf8')
+  } catch {
+    content = `Skill body missing from plugin package (skills/gem-expert.md)。`
+  }
+  disposers.push(ctx.skills.register({
+    name: 'gem-expert',
+    description:
+      '基因组尺度代谢模型（GEM）主指引：工具分层选择（gem_report/validate/gapfind/gapfill/build）、构建→验证→补洞→报告工作流、' +
+      '跨引擎培养基自然名规则、CarveMe M9 介质边界、C58 回归锚。任何代谢模型需求先加载本 skill。',
+    whenToUse:
+      '用户提出代谢模型/GEM/基因组建模型/模型验证/模型补洞/为什么模型不长/FBA 模型准备/底盘代谢分析等需求时。',
+    source: 'custom',
+    provider: 'dsh-bio-gem',
+    content,
+  }))
+  return () => disposers.forEach((d) => d())
+}