@dsh-bio/dsh-bio-gem 0.1.14 → 0.1.15

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@dsh-bio/dsh-bio-gem",
-  "version": "0.1.14",
+  "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",
@@ -52,8 +52,8 @@
   },
   "scripts": {
     "smoke": "node test/smoke.js",
-    "test": "node test/check-version-source.mjs && 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"
+    "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": "*"

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 {