merge: resolve .gitignore conflict, keep remote memory ignore pattern

apps/cli/run_gene_family_report.py

@@ -0,0 +1,70 @@
+#!/usr/bin/env python3
+"""CLI for the plan-scoped formal gene-family result report."""
+
+from __future__ import annotations
+
+import argparse
+import json
+from pathlib import Path
+import sys
+from typing import Sequence
+
+PROJECT_ROOT = Path(__file__).resolve().parents[2]
+if str(PROJECT_ROOT) not in sys.path:
+    sys.path.insert(0, str(PROJECT_ROOT))
+
+from gfa_core.gene_family_report import GeneFamilyReportResult, generate_gene_family_report
+
+
+def _parser() -> argparse.ArgumentParser:
+    parser = argparse.ArgumentParser(description="Generate or open a gene-family result report")
+    parser.add_argument("--workspace", type=Path, required=True)
+    parser.add_argument("--prefix", required=True)
+    parser.add_argument("--job-id", default="")
+    parser.add_argument("--expected-stages", default="")
+    parser.add_argument("--stage-statuses-json", default="{}")
+    parser.add_argument("--scope-id", default="")
+    parser.add_argument("--analysis-route", default="")
+    parser.add_argument("--member-set-id", default="")
+    parser.add_argument("--rnaseq-scope-id", default="")
+    parser.add_argument("--action", choices=("generate", "open"), default="generate")
+    parser.add_argument("--no-model", action="store_true")
+    return parser
+
+
+def main(argv: Sequence[str] | None = None) -> GeneFamilyReportResult:
+    args = _parser().parse_args(argv)
+    statuses = json.loads(args.stage_statuses_json)
+    if not isinstance(statuses, dict):
+        raise ValueError("--stage-statuses-json must contain a JSON object")
+    result = generate_gene_family_report(
+        args.workspace,
+        args.prefix,
+        expected_stages=[value.strip() for value in args.expected_stages.split(",") if value.strip()],
+        stage_statuses={str(key): str(value) for key, value in statuses.items()},
+        scope_id=args.scope_id,
+        analysis_route=args.analysis_route,
+        member_set_id=args.member_set_id,
+        rnaseq_scope_id=args.rnaseq_scope_id,
+        use_model=not args.no_model,
+        action=args.action,
+        job_id=args.job_id,
+    )
+    print(
+        json.dumps(
+            {
+                "status": "success",
+                "report_path": str(result.report_path),
+                "manifest_path": str(result.manifest_path),
+                "report_status": result.report_status,
+                "generation_mode": result.generation_mode,
+                "reused": result.reused,
+            },
+            ensure_ascii=False,
+        )
+    )
+    return result
+
+
+if __name__ == "__main__":
+    main()

apps/web/pipeline_backend.py

@@ -6054,8 +6054,9 @@ def run_stage(
 
     target_species = kwargs.get("target_species")
     interspecies_ref_species = kwargs.get("interspecies_ref_species")
-    scope_file = str(kwargs.get("scope_file") or kwargs.get("scopeFile") or "").strip()
-    analysis_route = str(kwargs.get("analysis_route") or kwargs.get("analysisRoute") or "").strip()
+    scope_file = str(kwargs.get("scope_file") or kwargs.get("scopeFile") or "").strip()
+    scope_id = str(kwargs.get("scope_id") or kwargs.get("scopeId") or "").strip()
+    analysis_route = str(kwargs.get("analysis_route") or kwargs.get("analysisRoute") or "").strip()
     analysis_mode = str(kwargs.get("analysis_mode") or kwargs.get("analysisMode") or "").strip()
     member_set_id = str(kwargs.get("member_set_id") or kwargs.get("memberSetId") or "").strip()
     combo_output_label = str(combo_output_label or kwargs.get("comboOutputLabel") or kwargs.get("combo_output_label") or "").strip()
@@ -8374,7 +8375,62 @@ def run_stage(
         else:
             return f"❌ PEP failed (exit code: {code}). Log: {log_file}", manifest
 
-    if stage == "summary":
+    if stage == "gene_family_report":
+        expected_stages = kwargs.get("expected_stages") or kwargs.get("expectedStages") or []
+        if isinstance(expected_stages, str):
+            expected_stages = [value.strip() for value in expected_stages.split(",") if value.strip()]
+        else:
+            expected_stages = [str(value).strip() for value in expected_stages if str(value).strip()]
+        report_action = str(kwargs.get("report_action") or kwargs.get("reportAction") or "generate").strip()
+        if report_action == "generate" and not expected_stages:
+            return "❌ 基因家族结果报告生成需要非空 expected_stages", manifest
+        stage_statuses = kwargs.get("stage_statuses") or kwargs.get("stageStatuses") or {}
+        if isinstance(stage_statuses, str):
+            try:
+                stage_statuses = json.loads(stage_statuses)
+            except json.JSONDecodeError:
+                return "❌ 基因家族结果报告的 stage_statuses 不是合法 JSON", manifest
+        if not isinstance(stage_statuses, dict):
+            return "❌ 基因家族结果报告的 stage_statuses 必须是对象", manifest
+        report_use_model_raw = kwargs.get("report_use_model", kwargs.get("reportUseModel", True))
+        rnaseq_scope_id = str(kwargs.get("rnaseq_scope_id") or kwargs.get("rnaseqScopeId") or "").strip()
+        cmd = [
+            sys.executable,
+            "apps/cli/run_gene_family_report.py",
+            "--workspace",
+            str(ws),
+            "--prefix",
+            prefix,
+            "--job-id",
+            job.job_id,
+            "--expected-stages",
+            ",".join(expected_stages),
+            "--stage-statuses-json",
+            json.dumps(stage_statuses, ensure_ascii=False, separators=(",", ":")),
+            "--action",
+            report_action,
+        ]
+        for flag, value in (
+            ("--scope-id", scope_id),
+            ("--analysis-route", analysis_route),
+            ("--member-set-id", member_set_id),
+            ("--rnaseq-scope-id", rnaseq_scope_id),
+        ):
+            if value:
+                cmd += [flag, value]
+        if not _truthy(report_use_model_raw):
+            cmd.append("--no-model")
+        code = run_cmd_logged(cmd, log_file, cwd=Path("."))
+        report_manifests = sorted(
+            final_dir.glob(f"{prefix}*.gene_family_report.manifest.json"),
+            key=lambda path: path.stat().st_mtime,
+        )
+        report_manifest = report_manifests[-1] if report_manifests else manifest
+        if code != 0:
+            return f"❌ 基因家族结果报告生成失败，日志：{log_file}", report_manifest
+        return f"✅ 基因家族结果报告已生成。日志：{log_file}", report_manifest
+
+    if stage == "summary":
         summary_manifest_seed = (
             ws / "final" / f"{prefix}.identify.manifest.json"
             if (ws / "final" / f"{prefix}.identify.manifest.json").exists()

apps/web/vue3/agent_status_component_ml.html

@@ -0,0 +1,416 @@
+<!-- Agent状态显示组件 - 可嵌入index.html -->
+<template id="agent-status-component">
+  <div class="agent-status-panel">
+    <div class="agent-header">
+      <h3>{{ t('agent-assistant') }}</h3>
+      <span class="agent-mode">{{ currentMode }}</span>
+    </div>
+    
+    <div class="agent-messages" ref="messageContainer">
+      <div v-for="(msg, index) in messages" :key="index" 
+           :class="['message', msg.role]">
+        <div class="message-role">{{ getRoleLabel(msg.role) }}</div>
+        <div class="message-content" v-html="formatMessage(msg.content)"></div>
+        <div class="message-time">{{ formatTime(msg.timestamp) }}</div>
+      </div>
+    </div>
+    
+    <div class="agent-input">
+      <textarea v-model="userInput" 
+                :placeholder="t('enter-question')"
+                @keydown.enter.prevent="sendMessage"
+                rows="3"></textarea>
+      <button @click="sendMessage" :disabled="isProcessing">
+        {{ isProcessing ? t('processing') : t('send') }}
+      </button>
+    </div>
+    
+    <div class="agent-tasks" v-if="tasks.length > 0">
+      <h4>{{ t('task-list') }}</h4>
+      <div v-for="task in tasks" :key="task.task_id" 
+           :class="['task-item', task.status]"
+           @click="selectTask(task)">
+        <span class="task-status">{{ getStatusIcon(task.status) }}</span>
+        <span class="task-message">{{ task.message }}</span>
+        <span class="task-progress">{{ task.progress }}%</span>
+      </div>
+    </div>
+  </div>
+</template>
+
+<script src="/static/i18n.js"></script>
+// Agent状态组件
+const AgentStatusComponent = {
+  template: '#agent-status-component',
+  
+  data() {
+    return {
+      messages: [],
+      userInput: '',
+      isProcessing: false,
+      currentMode: '',
+      sessionId: '',
+      tasks: [],
+      currentTask: null,
+      pollingInterval: null
+    };
+  },
+  
+  mounted() {
+    this.sessionId = 'session_' + Date.now();
+    this.currentMode = t('standby');
+    this.loadTasks();
+    this.startPolling();
+  },
+  
+  beforeUnmount() {
+    this.stopPolling();
+  },
+  
+  methods: {
+    async sendMessage() {
+      if (!this.userInput.trim() || this.isProcessing) return;
+      
+      const message = this.userInput.trim();
+      this.userInput = '';
+      this.isProcessing = true;
+      
+      // 添加用户消息
+      this.addMessage('user', message);
+      
+      try {
+        // 调用Agent执行API
+        const response = await fetch('/api/agent/execute', {
+          method: 'POST',
+          headers: { 'Content-Type': 'application/json' },
+          body: JSON.stringify({
+            message: message,
+            session_id: this.sessionId,
+            model: 'kimi'
+          })
+        });
+        
+        const data = await response.json();
+        
+        if (data.success) {
+          this.currentTask = data.task_id;
+          this.addMessage('system', t('msg-task-submitted') + data.task_id);
+          this.loadTasks();
+        } else {
+          this.addMessage('error', data.message || t('msg-submit-failed'));
+        }
+      } catch (error) {
+        this.addMessage('error', t('msg-request-failed') + error.message);
+      }
+      
+      this.isProcessing = false;
+    },
+    
+    async loadTasks() {
+      try {
+        const response = await fetch('/api/agent/tasks');
+        const data = await response.json();
+        
+        if (data.success) {
+          this.tasks = data.tasks;
+        }
+      } catch (error) {
+        console.error(t('msg-load-task-failed'), error);
+      }
+    },
+    
+    async checkTaskStatus(taskId) {
+      try {
+        const response = await fetch(`/api/agent/status/${taskId}`);
+        const data = await response.json();
+        
+        if (data.success && data.task) {
+          const task = data.task;
+          
+          // 更新任务状态
+          const taskIndex = this.tasks.findIndex(t => t.task_id === taskId);
+          if (taskIndex >= 0) {
+            this.tasks[taskIndex] = { ...this.tasks[taskIndex], ...task };
+          }
+          
+          // 如果任务完成，显示结果
+          if (task.status === 'completed' && task.result) {
+            this.addMessage('assistant', task.result.response || t('msg-task-completed'));
+            
+            // 显示执行结果摘要
+            if (task.result.execution_result) {
+              const execResult = task.result.execution_result;
+              if (execResult.status === 'success') {
+                const manifest = execResult.manifest || {};
+                const metrics = manifest.metrics || {};
+                this.addMessage('system',
+                  t('msg-analysis-complete') + (metrics.final_members || 0) + t('msg-gene-members'));
+              }
+            }
+          } else if (task.status === 'failed') {
+            this.addMessage('error', task.result?.response || t('msg-task-failed'));
+          }
+        }
+      } catch (error) {
+        console.error(t('msg-check-task-status-failed'), error);
+      }
+    },
+    
+    selectTask(task) {
+      this.currentTask = task.task_id;
+      this.checkTaskStatus(task.task_id);
+    },
+    
+    startPolling() {
+      this.pollingInterval = setInterval(() => {
+        if (this.currentTask) {
+          this.checkTaskStatus(this.currentTask);
+        }
+        this.loadTasks();
+      }, 3000); // 每3秒轮询一次
+    },
+    
+    stopPolling() {
+      if (this.pollingInterval) {
+        clearInterval(this.pollingInterval);
+      }
+    },
+    
+    addMessage(role, content) {
+      this.messages.push({
+        role: role,
+        content: content,
+        timestamp: new Date().toISOString()
+      });
+      
+      // 滚动到底部
+      setTimeout(() => {
+        const container = this.$refs.messageContainer;
+        if (container) {
+          container.scrollTop = container.scrollHeight;
+        }
+      }, 100);
+    },
+    
+    getRoleLabel(role) {
+      const keys = {
+        'user': 'user-role',
+        'assistant': 'agent-role',
+        'system': 'system-role',
+        'error': 'error-role',
+        'execution': 'execution-role',
+        'planning': 'planning-role',
+        'diagnosis': 'diagnosis-role'
+      };
+      return keys[role] ? t(keys[role]) : role;
+    },
+    
+    getStatusIcon(status) {
+      const icons = {
+        'pending': '⏳',
+        'running': '🔄',
+        'completed': '✅',
+        'failed': '❌',
+        'cancelled': '🚫'
+      };
+      return icons[status] || '❓';
+    },
+    
+    formatMessage(content) {
+      // 简单的Markdown格式化
+      return content
+        .replace(/\*\*(.+?)\*\*/g, '<strong>$1</strong>')
+        .replace(/\n/g, '<br>');
+    },
+    
+    formatTime(timestamp) {
+      if (!timestamp) return '';
+      const date = new Date(timestamp);
+      return date.toLocaleTimeString('zh-CN', {
+        hour: '2-digit',
+        minute: '2-digit',
+        second: '2-digit'
+      });
+    },
+
+    t(key) {
+      return window.t ? window.t(key) : key;
+    }
+  }
+};
+</script>
+
+<style>
+.agent-status-panel {
+  border: 1px solid #ddd;
+  border-radius: 8px;
+  padding: 16px;
+  background: #f9f9f9;
+  height: 100%;
+  display: flex;
+  flex-direction: column;
+}
+
+.agent-header {
+  display: flex;
+  justify-content: space-between;
+  align-items: center;
+  margin-bottom: 12px;
+  padding-bottom: 8px;
+  border-bottom: 1px solid #eee;
+}
+
+.agent-header h3 {
+  margin: 0;
+  font-size: 16px;
+}
+
+.agent-mode {
+  font-size: 12px;
+  color: #666;
+  background: #e0e0e0;
+  padding: 2px 8px;
+  border-radius: 4px;
+}
+
+.agent-messages {
+  flex: 1;
+  overflow-y: auto;
+  max-height: 400px;
+  margin-bottom: 12px;
+}
+
+.message {
+  margin-bottom: 12px;
+  padding: 8px 12px;
+  border-radius: 8px;
+  background: white;
+  border-left: 3px solid #ddd;
+}
+
+.message.user {
+  border-left-color: #4CAF50;
+  background: #E8F5E9;
+}
+
+.message.assistant {
+  border-left-color: #2196F3;
+  background: #E3F2FD;
+}
+
+.message.error {
+  border-left-color: #f44336;
+  background: #FFEBEE;
+}
+
+.message.system {
+  border-left-color: #9E9E9E;
+  background: #F5F5F5;
+  font-size: 12px;
+}
+
+.message-role {
+  font-size: 12px;
+  color: #666;
+  margin-bottom: 4px;
+}
+
+.message-content {
+  font-size: 14px;
+  line-height: 1.5;
+}
+
+.message-time {
+  font-size: 11px;
+  color: #999;
+  text-align: right;
+  margin-top: 4px;
+}
+
+.agent-input {
+  display: flex;
+  gap: 8px;
+  margin-bottom: 12px;
+}
+
+.agent-input textarea {
+  flex: 1;
+  padding: 8px;
+  border: 1px solid #ddd;
+  border-radius: 4px;
+  resize: none;
+  font-family: inherit;
+}
+
+.agent-input button {
+  padding: 8px 16px;
+  background: #2196F3;
+  color: white;
+  border: none;
+  border-radius: 4px;
+  cursor: pointer;
+}
+
+.agent-input button:disabled {
+  background: #ccc;
+  cursor: not-allowed;
+}
+
+.agent-tasks {
+  border-top: 1px solid #eee;
+  padding-top: 12px;
+}
+
+.agent-tasks h4 {
+  margin: 0 0 8px 0;
+  font-size: 14px;
+}
+
+.task-item {
+  display: flex;
+  align-items: center;
+  gap: 8px;
+  padding: 6px 8px;
+  border-radius: 4px;
+  cursor: pointer;
+  margin-bottom: 4px;
+  background: white;
+}
+
+.task-item:hover {
+  background: #f0f0f0;
+}
+
+.task-item.pending {
+  border-left: 3px solid #FFC107;
+}
+
+.task-item.running {
+  border-left: 3px solid #2196F3;
+}
+
+.task-item.completed {
+  border-left: 3px solid #4CAF50;
+}
+
+.task-item.failed {
+  border-left: 3px solid #f44336;
+}
+
+.task-status {
+  font-size: 14px;
+}
+
+.task-message {
+  flex: 1;
+  font-size: 12px;
+  overflow: hidden;
+  text-overflow: ellipsis;
+  white-space: nowrap;
+}
+
+.task-progress {
+  font-size: 11px;
+  color: #666;
+}
+</style>

apps/web/vue3/index-with-sidebar_ml.html

@@ -0,0 +1,391 @@
+<!DOCTYPE html>
+<html lang="zh-CN">
+<head>
+    <meta charset="UTF-8">
+    <script src="/static/i18n.js"></script>
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>BotanicalBaseAgent</title>
+    <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/element-plus@2.3.14/dist/index.css">
+    <script src="https://cdn.jsdelivr.net/npm/vue@3.3.4/dist/vue.global.prod.js"></script>
+    <script src="https://cdn.jsdelivr.net/npm/element-plus@2.3.14/dist/index.full.js"></script>
+    <script src="https://cdn.jsdelivr.net/npm/@element-plus/icons-vue@2.1.0/dist/index.iife.js"></script>
+    <link rel="stylesheet" href="conversation-sidebar.css">
+    <style>
+        * { box-sizing: border-box; }
+        body { 
+            margin: 0; 
+            font-family: 'Helvetica Neue', Arial, sans-serif; 
+            background: #f5f7fa; 
+        }
+        .header { 
+            background: linear-gradient(135deg, #667eea 0%, #764ba2 100%); 
+            color: white; 
+            padding: 15px 20px; 
+        }
+        .header h1 { margin: 0; font-size: 22px; }
+        .main-container { 
+            display: flex; 
+            height: calc(100vh - 60px); 
+            overflow: hidden;
+        }
+        
+        /* 左侧控制面板 */
+        .left-panel {
+            width: 280px;
+            background: white;
+            border-right: 1px solid #e4e7ed;
+            display: flex;
+            flex-direction: column;
+            padding: 15px;
+            gap: 15px;
+            overflow-y: auto;
+        }
+        
+        /* 中间内容区 */
+        .center-panel {
+            flex: 1;
+            display: flex;
+            flex-direction: column;
+            padding: 15px;
+            gap: 15px;
+            overflow: hidden;
+        }
+        
+        /* 右侧结果区 */
+        .right-panel {
+            width: 350px;
+            background: white;
+            border-left: 1px solid #e4e7ed;
+            padding: 15px;
+            overflow-y: auto;
+        }
+        
+        .panel-section {
+            background: white;
+            border-radius: 8px;
+            padding: 15px;
+            box-shadow: 0 2px 8px rgba(0,0,0,0.08);
+        }
+        
+        .panel-title {
+            font-size: 14px;
+            font-weight: bold;
+            color: #409EFF;
+            margin-bottom: 12px;
+            padding-bottom: 8px;
+            border-bottom: 2px solid #409EFF;
+        }
+        
+        .chat-area {
+            flex: 1;
+            background: white;
+            border-radius: 8px;
+            padding: 15px;
+            overflow-y: auto;
+            box-shadow: 0 2px 8px rgba(0,0,0,0.08);
+        }
+        
+        .chat-message {
+            margin-bottom: 15px;
+            padding: 12px 16px;
+            border-radius: 8px;
+            max-width: 80%;
+        }
+        
+        .chat-message.user {
+            background: #ecf5ff;
+            margin-left: auto;
+            text-align: right;
+        }
+        
+        .chat-message.assistant {
+            background: #f0f9eb;
+        }
+        
+        .input-area {
+            display: flex;
+            gap: 10px;
+        }
+        
+        .stage-tag {
+            display: inline-block;
+            padding: 4px 12px;
+            border-radius: 4px;
+            font-size: 12px;
+            margin: 4px;
+        }
+        
+        .stage-tag.success { background: #67C23A; color: white; }
+        .stage-tag.running { background: #E6A23C; color: white; }
+        .stage-tag.pending { background: #909399; color: white; }
+    </style>
+</head>
+<body>
+    <div id="app">
+        <!-- Header -->
+        <div class="header">
+            <h1>{{ t('gf-analysis-system') }}</h1>
+        </div>
+
+        <div class="main-container">
+            <!-- 左侧：会话侧边栏 + 控制面板 -->
+            <div class="left-panel">
+                <!-- 会话侧边栏 -->
+                <div class="conversation-sidebar" style="width: 100%; margin: -15px; margin-bottom: 0;">
+                    <div class="sidebar-header">
+                        <button class="new-chat-btn" @click="createNewConversation" style="flex: 1;">
+                            <el-icon><plus /></el-icon>
+                            <span>New Chat</span>
+                        </button>
+                    </div>
+                    
+                    <div class="search-box" style="padding: 12px;">
+                        <el-input 
+                            v-model="searchQuery" 
+                            :placeholder="t('search-conv')"
+                            prefix-icon="search" 
+                            clearable 
+                            size="small">
+                        </el-input>
+                    </div>
+                    
+                    <div class="conversation-list" style="max-height: 300px;">
+                        <div class="list-section">
+                            <div class="section-title">{{ t('conv-list') }}</div>
+                            <div v-for="conv in filteredConversations" 
+                                 :key="conv.id"
+                                 class="conversation-item" 
+                                 :class="{ active: currentConv?.id === conv.id }"
+                                 @click="selectConversation(conv)">
+                                <div class="item-icon">
+                                    <el-icon><chat-dot-round /></el-icon>
+                                </div>
+                                <div class="item-content">
+                                    <div class="item-title">{{ conv.title }}</div>
+                                    <div class="item-meta">
+                                        <span class="gene-family" v-if="conv.gene_family">{{ conv.gene_family }}</span>
+                                        <span class="message-count">{{ conv.message_count }}{{ t('msg-count') }}</span>
+                                    </div>
+                                </div>
+                            </div>
+                        </div>
+                    </div>
+                </div>
+                
+                <!-- 分析控制 -->
+                <div class="panel-section">
+                    <div class="panel-title">{{ t('analysis-stage') }}</div>
+                    <el-select v-model="selectedStage" :placeholder="t('select-stage')" style="width: 100%;">
+                        <el-option :label="t('identify-label')" value="identify"></el-option>
+                        <el-option :label="t('phylogeny-label')" value="phylogeny"></el-option>
+                        <el-option :label="t('motif-label')" value="motif"></el-option>
+                        <el-option :label="t('domain-label')" value="domain"></el-option>
+                        <el-option :label="t('expression-label')" value="expression"></el-option>
+                    </el-select>
+                    <el-button type="primary" style="width: 100%; margin-top: 10px;" @click="executeAnalysis">
+                        {{ t('execute-analysis') }}
+                    </el-button>
+                </div>
+
+                <!-- 参数设置 -->
+                <div class="panel-section">
+                    <div class="panel-title">{{ t('param-settings') }}</div>
+                    <el-form :model="params" label-width="80px" size="small">
+                        <el-form-item :label="t('prefix')">
+                            <el-input v-model="params.prefix" :placeholder="t('prefix-placeholder')"></el-input>
+                        </el-form-item>
+                        <el-form-item label="CPU">
+                            <el-input-number v-model="params.cpu" :min="1" :max="32" style="width: 100%;"></el-input-number>
+                        </el-form-item>
+                    </el-form>
+                </div>
+            </div>
+            
+            <!-- 中间：对话区 -->
+            <div class="center-panel">
+                <div class="chat-area">
+                    <div v-for="(msg, index) in messages" :key="index" 
+                         class="chat-message" :class="msg.role">
+                        <div style="font-size: 12px; color: #666; margin-bottom: 4px;">
+                            {{ msg.role === 'user' ? t('user') : t('ai-assistant') }} · {{ msg.time }}
+                        </div>
+                        <div>{{ msg.content }}</div>
+                    </div>
+                    <div v-if="messages.length === 0" style="text-align: center; color: #999; padding: 40px;">
+                        <el-icon :size="48" style="display: block; margin-bottom: 10px;"><chat-line-round /></el-icon>
+                        <p>{{ t('start-new-chat') }}</p>
+                        <p style="font-size: 12px;">{{ t('or-continue') }}</p>
+                    </div>
+                </div>
+                
+                <div class="input-area">
+                    <el-input 
+                        v-model="userInput" 
+                        type="textarea" 
+                        :rows="3" 
+                        :placeholder="t('describe-need')"
+                        @keyup.enter.ctrl="sendMessage">
+                    </el-input>
+                    <el-button type="primary" size="large" @click="sendMessage" :disabled="!userInput.trim()">
+                        {{ t('send') }}
+                    </el-button>
+                </div>
+            </div>
+            
+            <!-- 右侧：结果展示 -->
+            <div class="right-panel">
+                <div class="panel-title">📊 Analysis Results</div>
+                
+                <div v-for="stage in stages" :key="stage.name" style="margin-bottom: 15px;">
+                    <div style="display: flex; justify-content: space-between; align-items: center; margin-bottom: 8px;">
+                        <span style="font-weight: 500;">{{ stage.label }}</span>
+                        <span class="stage-tag" :class="stage.status">{{ stage.statusText }}</span>
+                    </div>
+                    <el-progress :percentage="stage.progress" :status="stage.status"></el-progress>
+                </div>
+                
+                <el-divider></el-divider>
+                
+                <div style="text-align: center; color: #999; padding: 20px;">
+                    <el-icon :size="48" style="display: block; margin-bottom: 10px;"><picture /></el-icon>
+                    <p>{{ t('results-here') }}</p>
+                </div>
+            </div>
+        </div>
+    </div>
+
+    <script>
+        const { createApp, ref, reactive, computed } = Vue;
+        
+        const app = createApp({
+            setup() {
+                const t = window.t;
+                document.title = 'BotanicalBaseAgent - ' + t('gf-analysis');
+                // 会话管理
+                const conversations = ref([
+                    { id: 1, title: 'Ft.SPL基因家族分析', gene_family: 'SPL', message_count: 12 },
+                    { id: 2, title: 'Os.TCP进化分析', gene_family: 'TCP', message_count: 5 },
+                    { id: 3, title: 'HMMER参数配置咨询', gene_family: null, message_count: 8 },
+                ]);
+                const currentConv = ref(null);
+                const searchQuery = ref('');
+                
+                const filteredConversations = computed(() => {
+                    if (!searchQuery.value) return conversations.value;
+                    const query = searchQuery.value.toLowerCase();
+                    return conversations.value.filter(conv => 
+                        conv.title.toLowerCase().includes(query) ||
+                        (conv.gene_family && conv.gene_family.toLowerCase().includes(query))
+                    );
+                });
+                
+                const createNewConversation = () => {
+                    const newConv = {
+                        id: Date.now(),
+                        title: t('new-chat') + ' ' + new Date().toLocaleTimeString(),
+                        gene_family: null,
+                        message_count: 0
+                    };
+                    conversations.value.unshift(newConv);
+                    selectConversation(newConv);
+                };
+                
+                const selectConversation = (conv) => {
+                    currentConv.value = conv;
+                    // 清空消息并添加欢迎语
+                    messages.value = [{
+                        role: 'assistant',
+                        content: t('initial-welcome').replace('{title}', conv.title),
+                        time: new Date().toLocaleTimeString()
+                    }];
+                };
+                
+                // 分析参数
+                const selectedStage = ref('');
+                const params = reactive({
+                    prefix: 'Ft.SPL',
+                    cpu: 8
+                });
+                
+                // 消息
+                const messages = ref([]);
+                const userInput = ref('');
+                
+                const sendMessage = () => {
+                    if (!userInput.value.trim()) return;
+                    
+                    // 添加用户消息
+                    messages.value.push({
+                        role: 'user',
+                        content: userInput.value,
+                        time: new Date().toLocaleTimeString()
+                    });
+                    
+                    // 更新当前会话消息数
+                    if (currentConv.value) {
+                        currentConv.value.message_count++;
+                    }
+                    
+                    // 模拟AI回复
+                    setTimeout(() => {
+                        messages.value.push({
+                            role: 'assistant',
+                            content: `Received: "${userInput.value}". I will help analyze the gene family. Confirm parameters and click "${t('execute-analysis')}".`,
+                            time: new Date().toLocaleTimeString()
+                        });
+                        if (currentConv.value) {
+                            currentConv.value.message_count++;
+                        }
+                    }, 500);
+                    
+                    userInput.value = '';
+                };
+                
+                // 分析阶段
+                const stages = ref([
+                    { name: 'identify', label: 'Identify', status: 'success', statusText: t('completed'), progress: 100 },
+                    { name: 'phylogeny', label: 'Phylogeny', status: 'running', statusText: t('running'), progress: 60 },
+                    { name: 'motif', label: 'Motif', status: 'pending', statusText: t('pending'), progress: 0 },
+                    { name: 'domain', label: 'Domain', status: 'pending', statusText: t('pending'), progress: 0 },
+                ]);
+                
+                const executeAnalysis = () => {
+                    if (!selectedStage.value) {
+                        ElementPlus.ElMessage.warning(t('msg-select-stage-first'));
+                        return;
+                    }
+                    ElementPlus.ElMessage.success(t('msg-executing') + selectedStage.value + t('msg-analysis-text'));
+                };
+                
+                return {
+                    t,
+                    conversations,
+                    currentConv,
+                    searchQuery,
+                    filteredConversations,
+                    createNewConversation,
+                    selectConversation,
+                    selectedStage,
+                    params,
+                    messages,
+                    userInput,
+                    sendMessage,
+                    stages,
+                    executeAnalysis
+                };
+            }
+        });
+        
+        app.use(ElementPlus);
+        // 注册 i18n 翻译函数到 Vue 模板作用域
+        app.config.globalProperties.t = window.t || ((key) => key);
+
+        // 注册图标
+        for (const [key, component] of Object.entries(ElementPlusIconsVue)) {
+            app.component(key, component);
+        }
+        
+        app.mount('#app');
+    </script>
+</body>
+</html>

apps/web/vue3/index.html

@@ -995,7 +995,7 @@
         }
 
         .execution-log-item.assistant .log-content.structured-content {
-            /* 结构化内容使用rag样式 */
+            font-size: 13px;
         }
 
         .execution-log-item.assistant .log-content.short-content {
@@ -1363,7 +1363,8 @@
 
                     <el-divider style="margin: 12px 0;"></el-divider>
 
-                    <div v-if="false" style="padding:10px; background:#fff; border:1px solid #dcdfe6; border-radius:0px;">
+                    <div @dragover.prevent @drop.prevent="handleLightweightExtensionFolderDrop($event)"
+                        style="padding:10px; background:#fff; border:1px dashed #409EFF; border-radius:0px;">
                         <div style="display:flex; align-items:center; justify-content:space-between; gap:8px; margin-bottom:8px;">
                             <el-tooltip content="上传已跑通过的代码和测试数据；执行通过自然语言触发。" placement="top">
                                 <h4 style="margin:0; color:#303133; cursor:help;">拓展分析阶段</h4>
@@ -1389,10 +1390,13 @@
                             <span>名称</span><el-input v-model="extensionBuild.displayName" size="small" placeholder="例如 HMMER hmmsearch"></el-input>
                             <span>原始命令</span><el-input v-model="extensionBuild.command" size="small" placeholder="例如 bash run.sh input.fa"></el-input>
                             <span>环境</span>
-                            <el-select v-model="extensionBuild.runtimeEnv" size="small">
-                                <el-option label="test4py311" value="test4py311"></el-option>
-                                <el-option label="rnaseq" value="rnaseq"></el-option>
-                                <el-option label="rnaR" value="rnaR"></el-option>
+                            <el-select v-model="extensionBuild.runtimeEnv" size="small" filterable>
+                                <el-option
+                                    v-for="env in extensionEnvOptions"
+                                    :key="env"
+                                    :label="env"
+                                    :value="env">
+                                </el-option>
                             </el-select>
                             <span>原始代码</span><input type="file" multiple @change="onExtensionCodeFilesChange" style="font-size:12px; min-width:0;">
                             <span v-if="extensionBuild.codeFiles.length"></span>
@@ -1777,6 +1781,20 @@
                             📂 Select
                         </el-button>
                     </div>
+                    <!-- lightWeightExtensionTest:start -->
+                    <div id="lightweight-extension-test-drop-zone"
+                        style="display:none;margin-top:8px;border:1px dashed #409EFF;padding:10px;font-size:12px;color:#606266;background:#f8fbff;"
+                         @dragover.prevent
+                         @drop.prevent="handleLightweightExtensionFolderDrop($event)">
+                        <div style="font-weight:600;color:#303133;">拖入固定结构拓展包</div>
+                        <div style="margin-top:4px;line-height:1.5;">要求包含 raw_code/run.sh 与 raw_test_data/，系统会自动创建 Job、解析环境并开始 lightweight upload。</div>
+                        <input id="lightweight-extension-test-folder-input" type="file" webkitdirectory directory multiple style="display:none" @change="handleLightweightExtensionFolderPick($event)">
+                        <div style="display:flex;justify-content:space-between;align-items:center;gap:8px;margin-top:8px;">
+                            <span>{{ lightweightExtensionTestStatus }}</span>
+                            <el-button size="small" type="success" @click="openLightweightExtensionFolderPicker">选择文件夹</el-button>
+                        </div>
+                    </div>
+                    <!-- lightWeightExtensionTest:end -->
                 </div>
             </div>
 
@@ -7774,6 +7792,7 @@ RNA-seq KEGG/fgsea 会优先使用物种级 KEGG gene set；没有物种级缓
                     working_dir: '',
                     output_dir: ''
                 });
+                const lightweightExtensionTestStatus = ref('拖入固定结构文件夹，系统将自动创建 Job、解析环境并开始 upload。');
                 const activeRnaseqScopeId = ref('');
                 const activeGenotypeScopeId = ref('');
 
@@ -7950,6 +7969,7 @@ RNA-seq KEGG/fgsea 会优先使用物种级 KEGG gene set；没有物种级缓
                         pop_snp_density: 'SNP密度分析',
                         rnaseq_de: 'RNA-seq DE',
                         combo: '组合图',
+                        gene_family_report: '基因家族结果报告',
                         reference_classification: '参考亚家族分类',
                         subfamily_confirm: '亚家族标签确认',
                         ppi_kaks_reference_data: 'PPI/KaKs 参考数据',
@@ -9127,6 +9147,7 @@ RNA-seq KEGG/fgsea 会优先使用物种级 KEGG gene set；没有物种级缓
                     statusDialogVisible: false,
                     statusEvents: []
                 });
+                const extensionEnvOptions = ref(['test4py311', 'rnaseq', 'rnaR']);
                 const lightweightExtensions = ref([]);
                 const lightweightExtensionConversation = reactive({
                     cards: [],
@@ -10111,6 +10132,7 @@ compare: [[flesh, peel]]`;
                     { name: 'pep', label: '1️⃣2️⃣ PEP', status: 'pending', images: [], files: [], elapsed_time: 0 },
                     { name: 'expression', label: '1️⃣3️⃣ Expression (FPKM)', status: 'pending', images: [], files: [], elapsed_time: 0 },
                     { name: 'combo', label: '6️⃣ Combo', status: 'pending', images: [], files: [], elapsed_time: 0 },
+                    { name: 'gene_family_report', label: '📄 基因家族结果报告', status: 'pending', images: [], files: [], elapsed_time: 0 },
                     // RNA-seq stages
                     { name: 'rnaseq_qc', label: '1️⃣5️⃣ RNA-seq QC', status: 'pending', images: [], files: [], elapsed_time: 0 },
                     { name: 'rnaseq_align', label: '1️⃣6️⃣ RNA-seq Align', status: 'pending', images: [], files: [], elapsed_time: 0 },
@@ -15080,6 +15102,54 @@ compare: [[flesh, peel]]`;
                     return `⏸️ 批量执行已暂停：成功 ${completedCount}/${totalCount}，暂停 ${pausedCount}/${totalCount}。真实原因：${reasonText}。`;
                 };
 
+                const openGeneratedGeneFamilyReport = async () => {
+                    await refreshResults(jobInfo.job_id, 'gene_family_report');
+                    const reportStage = stages.find(stage => stage.name === 'gene_family_report');
+                    const reportFile = (reportStage?.files || []).find(file =>
+                        file.role === 'gene_family_report' || String(file.name || '').endsWith('.gene_family_report.md')
+                    );
+                    if (!reportFile) return false;
+                    rightPanelTab.value = 'results';
+                    selectFile('gene_family_report', reportFile);
+                    return true;
+                };
+
+                const submitGeneFamilyReportForBatch = async (stages, pausedCount) => {
+                    if (pausedCount > 0) return false;
+                    const plannedIds = (stages || []).map(stage => getStageId(stage)).filter(
+                        stageId => stageId && !['summary', 'gene_family_report', 'subfamily_confirm'].includes(stageId)
+                    );
+                    const geneFamilyStages = new Set([
+                        'identify', 'phylogeny', 'motif', 'domain', 'structure', 'promoter',
+                        'synteny', 'interspecies_synteny', 'karyotype', 'combo', 'ppi', 'expression', 'pep'
+                    ]);
+                    if (!plannedIds.some(stageId => geneFamilyStages.has(stageId))) return false;
+                    const stageStatuses = Object.fromEntries(plannedIds.map(stageId => {
+                        const status = stageExecutionStatus.value[stageId];
+                        return [stageId, status === 'completed' ? 'success' : status === 'failed' ? 'failed' : 'missing'];
+                    }));
+                    const batchParams = batchExecuteParams.value || {};
+                    const planParams = batchParams.plan?.params || {};
+                    const stageParams = (stages || []).find(stage => stage && typeof stage === 'object' && stage.params)?.params || {};
+                    try {
+                        await executeSingleStageWithParams('gene_family_report', {
+                            expectedStages: plannedIds,
+                            stageStatuses,
+                            reportAction: 'generate',
+                            reportUseModel: true,
+                            scopeId: batchParams.scopeId || planParams.scopeId || stageParams.scopeId || '',
+                            analysisRoute: batchParams.analysisRoute || planParams.analysisRoute || stageParams.analysisRoute || '',
+                            memberSetId: batchParams.memberSetId || planParams.memberSetId || stageParams.memberSetId || '',
+                            rnaseqScopeId: batchParams.rnaseqScopeId || planParams.rnaseqScopeId || stageParams.rnaseqScopeId || ''
+                        });
+                        addAgentMessage('assistant', '📄 基因家族结果报告已生成。');
+                        return true;
+                    } catch (err) {
+                        addAgentMessage('assistant', `⚠️ 基因家族结果报告生成失败：${err.message || err}`);
+                        return false;
+                    }
+                };
+
                 const confirmAndStartBatchExecute = async (event) => {
                     if (!event?.isTrusted) return;
                     batchExecutionUserConfirmed.value = true;
@@ -15195,6 +15265,7 @@ compare: [[flesh, peel]]`;
                         }).length;
                         const totalCount = stages.length;
 
+                        let continuationOpened = false;
                         if (failedCount > 0) {
                             addAgentMessage('assistant', `⚠️ 批量执行完成：成功 ${completedCount}/${totalCount}，失败 ${failedCount}/${totalCount}`);
                         } else if (pausedCount > 0) {
@@ -15202,13 +15273,16 @@ compare: [[flesh, peel]]`;
 	                        } else {
 	                            addAgentMessage('assistant', `🎉 批量执行完成！成功: ${completedCount}/${totalCount}`);
                                 if (isMethodologyDataPreparationContinuationCandidate(stages, completedCount, totalCount, failedCount, pausedCount)) {
-                                    await openMethodologyDataPreparationContinuation();
+                                    continuationOpened = await openMethodologyDataPreparationContinuation();
                                 } else if (isMethodologyPostConfirmContinuationCandidate(stages, completedCount, totalCount, failedCount, pausedCount)) {
-                                    await openMethodologyPostConfirmContinuation();
+                                    continuationOpened = await openMethodologyPostConfirmContinuation();
                                 } else if (isContextualPostConfirmContinuationCandidate(stages, completedCount, totalCount, failedCount, pausedCount)) {
-                                    await openContextualPostConfirmContinuation();
+                                    continuationOpened = await openContextualPostConfirmContinuation();
                                 }
 	                        }
+                            if (pausedCount === 0 && !continuationOpened) {
+                                await submitGeneFamilyReportForBatch(stages, pausedCount);
+                            }
                     }
                 };
 
@@ -17496,6 +17570,16 @@ compare: [[flesh, peel]]`;
                         requestBody.geoId = confirmParams.geoId || '';
                         requestBody.idTransform = confirmParams.idTransform || 'remove_T01';
                     }
+                    if (stageName === 'gene_family_report') {
+                        requestBody.expectedStages = activeStageParams.expectedStages || [];
+                        requestBody.stageStatuses = activeStageParams.stageStatuses || {};
+                        requestBody.reportAction = activeStageParams.reportAction || 'generate';
+                        requestBody.reportUseModel = activeStageParams.reportUseModel !== false;
+                        requestBody.scopeId = activeStageParams.scopeId || '';
+                        requestBody.analysisRoute = activeStageParams.analysisRoute || '';
+                        requestBody.memberSetId = activeStageParams.memberSetId || '';
+                        requestBody.rnaseqScopeId = activeStageParams.rnaseqScopeId || '';
+                    }
                     if (stageName === 'promoter_plot_revise') {
                         const elements = Array.isArray(confirmParams.promoterElements) ? confirmParams.promoterElements : [];
                         const categories = Array.isArray(confirmParams.promoterCategories) ? confirmParams.promoterCategories : [];
@@ -17586,6 +17670,9 @@ compare: [[flesh, peel]]`;
                         } else if (data.async === false) {
                             // 同步执行完成，直接返回结果
                             console.log(`[DEBUG-EXEC] ${stageName}: sync completed`);
+                            if (stageName === 'gene_family_report') {
+                                await openGeneratedGeneFamilyReport();
+                            }
                             return data;
                         } else {
                             throw createStructuredExecuteError(data);
@@ -18851,6 +18938,9 @@ compare: [[flesh, peel]]`;
                                 result: data
                             });
                             await handleStageCompleted(stageName, data, {});
+                            if (stageName === 'gene_family_report') {
+                                await openGeneratedGeneFamilyReport();
+                            }
 
                             // 更新阶段结果 - 如果有分stage的文件，则更新所有stage的文件
                             if (stageIdx >= 0 && data.result) {
@@ -19419,6 +19509,10 @@ compare: [[flesh, peel]]`;
                 };
 
                 const extensionFileKey = (file) => `${file?.name || ''}::${file?.size || 0}::${file?.lastModified || 0}`;
+                const extensionUploadPath = (file) => {
+                    const relative = String(file?.lightweightRelativePath || '').trim().replace(/^\/+/, '');
+                    return relative || String(file?.name || '').trim();
+                };
                 const appendExtensionFiles = (target, files) => {
                     const current = Array.isArray(target) ? target : [];
                     const merged = [...current];
@@ -19444,6 +19538,53 @@ compare: [[flesh, peel]]`;
                     if (selected.length) ElMessage.success(`已选择 ${selected.length} 个测试数据文件`);
                     event.target.value = '';
                 };
+                const handleLightweightExtensionFolderDrop = (event) => {
+                    const droppedFiles = Array.from(event?.dataTransfer?.files || []);
+                    if (!droppedFiles.length) {
+                        ElMessage.warning('未检测到可用文件');
+                        return;
+                    }
+
+                    const codeExtPattern = /\.(py|r|sh|bash|pl|js|ts|java|c|cc|cpp|go|rs|jl|rb|m|smk|nf|ipynb)$/i;
+                    const dataExtPattern = /\.(fastq|fq|gz|fa|fasta|fna|faa|pep|cds|gff|gff3|gtf|csv|tsv|txt|xlsx|xls|vcf|sam|bam)$/i;
+
+                    const normalized = droppedFiles.map((file) => {
+                        const relativePath = file.webkitRelativePath || file.name;
+                        if (!file.lightweightRelativePath) {
+                            Object.defineProperty(file, 'lightweightRelativePath', {
+                                value: relativePath,
+                                configurable: true
+                            });
+                        }
+                        return file;
+                    });
+
+                    const codeFiles = [];
+                    const dataFiles = [];
+                    normalized.forEach((file) => {
+                        const filePath = extensionUploadPath(file).toLowerCase();
+                        if (codeExtPattern.test(filePath)) {
+                            codeFiles.push(file);
+                        } else if (dataExtPattern.test(filePath)) {
+                            dataFiles.push(file);
+                        } else {
+                            codeFiles.push(file);
+                        }
+                    });
+
+                    extensionBuild.codeFiles = appendExtensionFiles(extensionBuild.codeFiles, codeFiles);
+                    extensionBuild.dataFiles = appendExtensionFiles(extensionBuild.dataFiles, dataFiles);
+
+                    if (!extensionBuild.displayName) {
+                        const firstPath = normalized[0]?.webkitRelativePath || normalized[0]?.name || '';
+                        const folder = firstPath.includes('/') ? firstPath.split('/')[0] : '';
+                        if (folder) {
+                            extensionBuild.displayName = folder.replace(/[^a-zA-Z0-9_-]+/g, '_');
+                        }
+                    }
+
+                    ElMessage.success(`已拖入 ${normalized.length} 个文件，已自动填充拓展包`);
+                };
                 const removeExtensionFile = (kind, file) => {
                     const key = extensionFileKey(file);
                     if (kind === 'code') {
@@ -19476,9 +19617,10 @@ compare: [[flesh, peel]]`;
                 };
                 const extensionApiUrl = (path) => {
                     const value = String(path || '');
-                    if (!value.startsWith('/api/extension-stages') && !value.startsWith('/api/extension-stage-runs')) return value;
+                    if (!value.startsWith('/api/extension-stages') && !value.startsWith('/api/extension-stage-runs') && !value.startsWith('/api/lightweight-extension-stages')) return value;
                     const host = window.location.hostname || '127.0.0.1';
-                    return `${window.location.protocol}//${host}:7880${value}`;
+                    const port = window.location.port;
+                    return port ? `${window.location.protocol}//${host}:${port}${value}` : `${window.location.protocol}//${host}${value}`;
                 };
                 const extensionApiFetch = async (path, options = {}) => fetch(extensionApiUrl(path), options);
                 const pushExtensionStatus = (message, type = 'info', showDialog = false) => {
@@ -19839,9 +19981,10 @@ compare: [[flesh, peel]]`;
                         form.append('extension_id', extensionId);
                         if (hasCommand) form.append('original_command', extensionBuild.command);
                         form.append('operation_token', token);
-                        extensionBuild.codeFiles.forEach(file => form.append('raw_code_files', file));
-                        extensionBuild.dataFiles.forEach(file => form.append('raw_data_files', file));
+                        extensionBuild.codeFiles.forEach(file => form.append('raw_code_files', file, extensionUploadPath(file)));
+                        extensionBuild.dataFiles.forEach(file => form.append('raw_data_files', file, extensionUploadPath(file)));
                         if (hasDataPaths) form.append('raw_data_paths', extensionBuild.dataPaths);
+                        form.append('runtime_env', extensionBuild.runtimeEnv);
                         const response = await extensionApiFetch('/api/lightweight-extension-stages/upload', { method: 'POST', body: form });
                         if (!response.ok) throw new Error(await extensionApiError(response, '原始包可复现检查提交失败'));
                         ElMessage.success('文件上传成功，已开始生成并验收');
@@ -20086,6 +20229,18 @@ compare: [[flesh, peel]]`;
                         console.warn('[lightweight extension] list failed', err);
                     }
                 };
+                const loadExtensionEnvOptions = async () => {
+                    try {
+                        const response = await extensionApiFetch('/api/extension-stages/envs');
+                        if (!response.ok) return;
+                        const data = await response.json();
+                        if (data.success && Array.isArray(data.envs) && data.envs.length) {
+                            extensionEnvOptions.value = data.envs;
+                        }
+                    } catch (err) {
+                        console.warn('[extension env options] load failed', err);
+                    }
+                };
                 const answerLightweightExtensionHelp = async (message) => {
                     const query = String(message || '');
                     const matched = (lightweightExtensions.value || []).find(item => query.includes(item.extension_id));
@@ -23318,6 +23473,7 @@ compare: [[flesh, peel]]`;
                     startRuntimeMonitor();
                     loadExtensionStages();
                     loadLightweightExtensionStages();
+                    loadExtensionEnvOptions();
                     resumeLightweightOperation();
                     loadExtensionRuns();
                     loadMethodologyJobs();
@@ -23648,6 +23804,7 @@ compare: [[flesh, peel]]`;
                     intentHistory,
                     uploadedFiles,
                     extensionBuild,
+                    extensionEnvOptions,
                     extensionStages,
                     extensionCompletedStages,
                     lightweightExtensionConversation,
@@ -23666,6 +23823,7 @@ compare: [[flesh, peel]]`;
                     extensionFileKey,
                     onExtensionCodeFilesChange,
                     onExtensionDataFilesChange,
+                    handleLightweightExtensionFolderDrop,
                     removeExtensionFile,
                     buildExtensionStage,
                     confirmLightweightCandidate,
@@ -23685,6 +23843,7 @@ compare: [[flesh, peel]]`;
                     validateExtensionStage,
                     publishExtensionStage,
                     loadExtensionStages,
+                    loadExtensionEnvOptions,
                     loadExtensionRuns,
                     runExtensionStage,
                     runExtensionStageFromIntent,
@@ -23804,6 +23963,24 @@ compare: [[flesh, peel]]`;
                     openPreview,
                     redrawImage,
                     createNewJob,
+                    lightweightExtensionTestStatus,
+                    handleLightweightExtensionFolderDrop: (event) => window.LightWeightExtensionTest && window.LightWeightExtensionTest.handleDrop({
+                        jobInfo,
+                        extensionBuild,
+                        createNewJob,
+                        appendExtensionFiles,
+                        buildLightweightExtensionStage,
+                        lightweightExtensionTestStatus,
+                    }, event),
+                    handleLightweightExtensionFolderPick: (event) => window.LightWeightExtensionTest && window.LightWeightExtensionTest.handlePick({
+                        jobInfo,
+                        extensionBuild,
+                        createNewJob,
+                        appendExtensionFiles,
+                        buildLightweightExtensionStage,
+                        lightweightExtensionTestStatus,
+                    }, event),
+                    openLightweightExtensionFolderPicker: () => window.LightWeightExtensionTest && window.LightWeightExtensionTest.openPicker(),
                     // Working DirectorySelect
                     existingJobs,
                     jobSelectorVisible,
@@ -23920,6 +24097,9 @@ compare: [[flesh, peel]]`;
         document.getElementById('app').style.display = 'block';
         console.log('App mounted successfully');
     </script>
+    <!-- lightWeightExtensionTest:wiring:start -->
+    <script src="/lightWeightExtensionTest.js"></script>
+    <!-- lightWeightExtensionTest:wiring:end -->
     <!-- 深度解读弹窗样式 -->
     <style>
         .interpretation-dialog .el-dialog__body { padding: 0; max-height: 70vh; overflow-y: auto; }

apps/web/vue3/kg_ml.html

@@ -0,0 +1,712 @@
+<!DOCTYPE html>
+<html lang="zh-CN">
+<head>
+    <meta charset="UTF-8">
+    <meta name="viewport" content="width=device-width, initial-scale=1.0">
+    <title>Knowledge Graph</title>
+    <link rel="stylesheet" href="https://cdn.jsdelivr.net/npm/element-plus@2.7.1/dist/index.css">
+    <script src="https://cdn.jsdelivr.net/npm/vue@3/dist/vue.global.prod.js"></script>
+    <script src="https://cdn.jsdelivr.net/npm/element-plus@2.7.1/dist/index.full.min.js"></script>
+    <script src="https://cdn.jsdelivr.net/npm/@element-plus/icons-vue"></script>
+    <script src="https://cdn.jsdelivr.net/npm/echarts@5.4.3/dist/echarts.min.js"></script>
+    <script src="/static/i18n.js"></script>
+    <style>
+        body { margin: 0; font-family: 'Helvetica Neue', Arial, sans-serif; background: #f5f7fa; }
+        .header { background: linear-gradient(135deg, #667eea 0%, #764ba2 100%); color: white; padding: 15px 20px; display: flex; align-items: center; justify-content: space-between; }
+        .header h1 { margin: 0; font-size: 22px; }
+        .header .subtitle { font-size: 12px; opacity: 0.8; margin-top: 4px; }
+        .main-container { display: flex; padding: 15px; gap: 15px; height: calc(100vh - 70px); }
+        .left-panel { width: 300px; display: flex; flex-direction: column; gap: 10px; }
+        .control-section { background: white; border-radius: 8px; padding: 15px; box-shadow: 0 2px 8px rgba(0,0,0,0.08); }
+        .control-section h4 { margin: 0 0 10px 0; color: #409EFF; font-size: 14px; border-bottom: 2px solid #409EFF; padding-bottom: 8px; }
+        .stat-item { display: flex; justify-content: space-between; padding: 8px 0; border-bottom: 1px solid #eee; }
+        .stat-item:last-child { border-bottom: none; }
+        .stat-label { color: #666; }
+        .stat-value { font-weight: bold; color: #409EFF; }
+        .filter-section { margin-top: 10px; }
+        .filter-tag { margin: 4px; cursor: pointer; }
+        .filter-tag.active { background: #409EFF; color: white; }
+        .main-panel { flex: 1; display: flex; flex-direction: column; background: white; border-radius: 8px; box-shadow: 0 2px 8px rgba(0,0,0,0.08); overflow: hidden; }
+        .toolbar { padding: 10px 15px; border-bottom: 1px solid #eee; display: flex; align-items: center; gap: 10px; }
+        #graph-container { flex: 1; position: relative; }
+        .right-panel { width: 350px; background: white; border-radius: 8px; box-shadow: 0 2px 8px rgba(0,0,0,0.08); padding: 15px; overflow-y: auto; }
+        .right-panel h4 { margin: 0 0 10px 0; color: #67C23A; border-bottom: 2px solid #67C23A; padding-bottom: 8px; }
+        .node-detail { padding: 10px; background: #f5f7fa; border-radius: 6px; margin-top: 10px; }
+        .node-detail .label { color: #666; font-size: 12px; margin-bottom: 4px; }
+        .node-detail .value { font-weight: 500; color: #333; }
+        .relation-list { margin-top: 10px; }
+        .relation-item { padding: 8px; background: #f0f9eb; border-radius: 4px; margin-bottom: 8px; font-size: 13px; }
+        .relation-item .source { color: #409EFF; font-weight: 500; }
+        .relation-item .rel { color: #67C23A; margin: 0 4px; }
+        .relation-item .target { color: #E6A23C; font-weight: 500; }
+        .search-box { margin-bottom: 10px; }
+        .legend { display: flex; flex-wrap: wrap; gap: 8px; margin-top: 10px; }
+        .legend-item { display: flex; align-items: center; gap: 4px; font-size: 12px; }
+        .legend-color { width: 12px; height: 12px; border-radius: 50%; }
+        .legend-symbol { width: 12px; height: 12px; border-radius: 2px; }
+        .legend-line { width: 20px; height: 2px; }
+        
+        /* PC语义分类样式 */
+        .pc-category-header {
+            font-size: 11px;
+            color: #666;
+            font-weight: bold;
+            margin: 8px 0 4px 0;
+            padding-left: 4px;
+            border-left: 3px solid #409EFF;
+        }
+    </style>
+</head>
+<body>
+    <div id="app">
+        <div class="header">
+            <div>
+                <h1>{{ t('kg-visualization') }}</h1>
+                <div class="subtitle">{{ t('kg-subtitle') }}</div>
+            </div>
+            <el-button type="primary" @click="goBack">
+                <el-icon><arrow-left /></el-icon> {{ t('back-to-main') }}
+            </el-button>
+        </div>
+        
+        <div class="main-container">
+            <!-- 左侧面板 -->
+            <div class="left-panel">
+                <div class="control-section">
+                    <h4>{{ t('kg-stats') }}</h4>
+                    <div class="stat-item">
+                        <span class="stat-label">{{ t('node-count') }}</span>
+                        <span class="stat-value">{{ stats.nodes }}</span>
+                    </div>
+                    <div class="stat-item">
+                        <span class="stat-label">{{ t('edge-count') }}</span>
+                        <span class="stat-value">{{ stats.edges }}</span>
+                    </div>
+                    <div class="stat-item">
+                        <span class="stat-label">{{ t('node-types') }}</span>
+                        <span class="stat-value">{{ stats.nodeTypes }}</span>
+                    </div>
+                    <div class="stat-item">
+                        <span class="stat-label">{{ t('edge-types') }}</span>
+                        <span class="stat-value">{{ stats.edgeTypes }}</span>
+                    </div>
+                </div>
+                
+                <div class="control-section">
+                    <h4>{{ t('node-search') }}</h4>
+                    <el-input
+                        v-model="searchQuery"
+                        :placeholder="t('enter-gene-name')"
+                        clearable
+                        @keyup.enter="searchNode"
+                    >
+                        <template #append>
+                            <el-button @click="searchNode">
+                                <el-icon><search /></el-icon>
+                            </el-button>
+                        </template>
+                    </el-input>
+                </div>
+                
+                <div class="control-section">
+                    <h4>{{ t('relation-filter-pc') }}</h4>
+                    <div class="filter-section">
+                        <div v-for="(types, category) in relationTypesByCategory" :key="category" style="margin-bottom: 10px;">
+                            <div style="font-size: 12px; color: #666; margin-bottom: 5px; font-weight: bold;">
+                                {{ category === 'activation' ? t('activation-induction') :
+                                   category === 'repression' ? t('repression-inhibition') :
+                                   category === 'regulation' ? t('regulation-control') :
+                                   category === 'expression' ? t('expression-detection') :
+                                   category === 'association' ? t('association-interaction') :
+                                   category === 'localization' ? t('localization') :
+                                   category === 'containment' ? t('containment-composition') :
+                                   category === 'participation' ? t('participation-function') : t('other-rel') }}
+                            </div>
+                            <el-tag 
+                                v-for="type in types" 
+                                :key="type"
+                                class="filter-tag"
+                                :class="{ active: selectedRelations.includes(type) }"
+                                @click="toggleRelationFilter(type)"
+                                size="small"
+                                :style="{ borderColor: relationEdgeStyles[category].color, color: selectedRelations.includes(type) ? '#fff' : relationEdgeStyles[category].color }"
+                            >
+                                {{ type }} ({{ relationCounts[type] }})
+                            </el-tag>
+                        </div>
+                    </div>
+                </div>
+                
+                <div class="control-section">
+                    <h4>{{ t('node-legend-pc') }}</h4>
+                    <div class="pc-category-header">Gene/Protein</div>
+                    <div class="legend">
+                        <div class="legend-item" v-for="type in ['gene', 'gene_id', 'gene_group', 'gene_family']" :key="type">
+                            <div class="legend-symbol" :style="{ background: nodeColors[type] }"></div>
+                            <span>{{ nodeTypeLabels[type] }}</span>
+                        </div>
+                    </div>
+                    <div class="pc-category-header">Phenotype</div>
+                    <div class="legend">
+                        <div class="legend-item" v-for="type in ['phenotype', 'attribute']" :key="type">
+                            <div class="legend-symbol" :style="{ background: nodeColors[type] }"></div>
+                            <span>{{ nodeTypeLabels[type] }}</span>
+                        </div>
+                    </div>
+                    <div class="pc-category-header">Cell/Organ/Organism</div>
+                    <div class="legend">
+                        <div class="legend-item" v-for="type in ['tissue', 'species']" :key="type">
+                            <div class="legend-symbol" :style="{ background: nodeColors[type] }"></div>
+                            <span>{{ nodeTypeLabels[type] }}</span>
+                        </div>
+                    </div>
+                    <div class="pc-category-header">Biological Process</div>
+                    <div class="legend">
+                        <div class="legend-item" v-for="type in ['process', 'time', 'condition', 'stress']" :key="type">
+                            <div class="legend-symbol" :style="{ background: nodeColors[type] }"></div>
+                            <span>{{ nodeTypeLabels[type] }}</span>
+                        </div>
+                    </div>
+                    <div class="pc-category-header">Genomic</div>
+                    <div class="legend">
+                        <div class="legend-item" v-for="type in ['location', 'sra_dataset', 'data_type', 'count']" :key="type">
+                            <div class="legend-symbol" :style="{ background: nodeColors[type] }"></div>
+                            <span>{{ nodeTypeLabels[type] }}</span>
+                        </div>
+                    </div>
+                    <h4 style="margin-top: 15px;">🔗 {{ t('edge-legend-pc') }}</h4>
+                    <div class="legend">
+                        <div class="legend-item" v-for="(style, cat) in relationEdgeStyles" :key="cat">
+                            <div class="legend-line" :style="{ background: style.color, height: style.width + 'px', borderTop: style.type === 'dashed' ? '2px dashed ' + style.color : 'none' }"></div>
+                            <span>{{ cat === 'activation' ? 'Activation/Induction' : 
+                                    cat === 'repression' ? 'Repression/Inhibition' :
+                                    cat === 'regulation' ? 'Regulation/Control' :
+                                    cat === 'expression' ? 'Expression/Detection' :
+                                    cat === 'association' ? 'Association/Interaction' :
+                                    cat === 'localization' ? 'Localization' :
+                                    cat === 'containment' ? 'Containment/Composition' :
+                                    cat === 'participation' ? 'Participation/Function' : 'Other' }}</span>
+                        </div>
+                    </div>
+                </div>
+            </div>
+            
+            <!-- 主面板 -->
+            <div class="main-panel">
+                <div class="toolbar">
+                    <el-button-group>
+                        <el-button @click="fitGraph">
+                            <el-icon><full-screen /></el-icon> {{ t('fit-view') }}
+                        </el-button>
+                        <el-button @click="resetFilters">
+                            <el-icon><refresh /></el-icon> {{ t('reset-filters') }}
+                        </el-button>
+                    </el-button-group>
+                    <el-divider direction="vertical"></el-divider>
+                    <span style="color: #666; font-size: 13px;">
+                        {{ t('click-drag-hint') }}
+                    </span>
+                </div>
+                <div id="graph-container"></div>
+            </div>
+            
+            <!-- 右侧面板 -->
+            <div class="right-panel">
+                <h4>{{ t('node-detail') }}</h4>
+                <div v-if="selectedNode" class="node-detail">
+                    <div style="margin-bottom: 15px;">
+                        <div class="label">{{ t('node-name') }}</div>
+                        <div class="value" style="font-size: 18px; color: #409EFF;">{{ selectedNode.name }}</div>
+                    </div>
+                    <div style="margin-bottom: 15px;">
+                        <div class="label">{{ t('node-type-pc') }}</div>
+                        <div class="value">
+                            <el-tag :type="getNodeTypeTag(selectedNode.category)" :style="{ backgroundColor: nodeColors[selectedNode.category] + '20', borderColor: nodeColors[selectedNode.category], color: nodeColors[selectedNode.category] }">
+                                {{ nodeTypeLabels[selectedNode.category] || selectedNode.category }}
+                            </el-tag>
+                        </div>
+                    </div>
+                    <div>
+                        <div class="label">{{ t('connection-count') }}</div>
+                        <div class="value">{{ selectedNode.degree }}{{ t('num-connections') }}</div>
+                    </div>
+                </div>
+                <div v-else style="color: #999; text-align: center; padding: 40px;">
+                    {{ t('click-node-detail') }}
+                </div>
+                
+                <template v-if="selectedNodeRelations.length > 0">
+                    <h4 style="margin-top: 20px;">🔗 {{ t('related-relations') }} ({{ selectedNodeRelations.length }})</h4>
+                    <div class="relation-list">
+                        <div 
+                            v-for="rel in selectedNodeRelations.slice(0, 10)" 
+                            :key="rel.id"
+                            class="relation-item"
+                            :style="{ borderLeft: '3px solid ' + relationEdgeStyles[rel.category || relationCategories[rel.name] || 'other'].color }"
+                        >
+                            <span class="source">{{ rel.source }}</span>
+                            <span class="rel" :style="{ color: relationEdgeStyles[rel.category || relationCategories[rel.name] || 'other'].color }">--{{ rel.name }}--></span>
+                            <span class="target">{{ rel.target }}</span>
+                        </div>
+                        <div v-if="selectedNodeRelations.length > 10" style="text-align: center; color: #999; padding: 10px;">
+                            {{ tp('more-relations', { count: selectedNodeRelations.length - 10 }) }}
+                        </div>
+                    </div>
+                </template>
+            </div>
+        </div>
+    </div>
+
+    <script>
+        const { createApp, ref, onMounted, computed } = Vue;
+        const { ElMessage } = ElementPlus;
+
+        createApp({
+            setup() {
+                const t = window.t || ((key) => key);
+                const tp = window.tp || ((key, params) => {
+                    let s = t(key);
+                    if (params) Object.keys(params).forEach(k => { s = s.replace('{' + k + '}', params[k]); });
+                    return s;
+                });
+                document.title = t('kg-title');
+                const graphData = ref({ nodes: [], edges: [] });
+                const chart = ref(null);
+                const searchQuery = ref('');
+                const selectedNode = ref(null);
+                const selectedRelations = ref([]);
+                
+                // PC (Pathway Commons) 语义分类颜色映射
+                const nodeColors = {
+                    // Gene/Protein - 蓝色
+                    'gene': '#5DADE2',
+                    'gene_id': '#85C1E9',
+                    'gene_group': '#AED6F1',
+                    'gene_family': '#5DADE2',
+                    
+                    // Phenotype - 绿色
+                    'phenotype': '#58D68D',
+                    'attribute': '#82E0AA',
+                    
+                    // Cell/Organ/Organism - 粉色
+                    'tissue': '#F5B7B1',
+                    'species': '#F1948A',
+                    
+                    // Process - 紫色菱形
+                    'process': '#AF7AC5',
+                    'time': '#C39BD3',
+                    'condition': '#D7BDE2',
+                    'stress': '#E8DAEF',
+                    
+                    // Location - 浅绿色
+                    'location': '#82E0AA',
+                    
+                    // Data - 橙色（更显眼）
+                    'sra_dataset': '#E67E22',
+                    'data_type': '#F39C12',
+                    'count': '#EAEDED',
+                    
+                    'unknown': '#95A5A6'
+                ,
+            'article': '#2ecc71',
+            'paper_title': '#9b59b6'
+        };
+                
+                // PC 语义分类显示名称
+                const nodeTypeLabels = {
+                    'gene': 'Gene/Protein',
+                    'gene_id': 'Gene Identifier',
+                    'gene_group': 'Gene Group',
+                    'gene_family': 'Gene Family',
+                    'phenotype': 'Phenotype',
+                    'attribute': 'Attribute',
+                    'tissue': 'Cell/Organ/Tissue',
+                    'species': 'Organism',
+                    'process': 'Biological Process',
+                    'time': 'Time/Stage',
+                    'condition': 'Condition',
+                    'stress': 'Stress',
+                    'location': 'Genomic Location',
+                    'sra_dataset': 'SRA Dataset',
+                    'geo_dataset': 'GEO Dataset',
+                    'data_type': 'Data Type',
+                    'count': 'Count/Statistic',
+                    'article': 'Article (PMID)',
+                    'paper_title': 'Paper Title',
+                    'unknown': 'Other'
+                };
+                
+                // PC 关系类型分类
+                const relationCategories = {
+                    // Activation/Induction - 绿色箭头
+                    'induces': 'activation',
+                    'promote': 'activation',
+                    'overexpression_increases': 'activation',
+                    'enhanced_tolerance_to': 'activation',
+                    
+                    // Repression/Inhibition - 红色T型
+                    'down_regulated_during': 'repression',
+                    'down_regulation_improves': 'repression',
+                    
+                    // Regulation - 蓝色
+                    'regulate': 'regulation',
+                    'regulates': 'regulation',
+                    'regulating': 'regulation',
+                    
+                    // Expression - 橙色
+                    'expressed_in': 'expression',
+                    'expressed_during': 'expression',
+                    'was_expressed_during': 'expression',
+                    'expression_reached_peak_at': 'expression',
+                    
+                    // Association - 紫色
+                    'collinear_with': 'association',
+                    'was_highly_orthologous_to': 'association',
+                    'related_to': 'association',
+                    'affect': 'association',
+                    
+                    // Localization - 深绿
+                    'located_on': 'localization',
+                    'identified_in': 'localization',
+                    
+                    // Containment - 青色
+                    'contain': 'containment',
+                    'had': 'containment',
+                    'has_gene_id': 'containment',
+                    'has_data_type': 'containment',
+                    
+                    // Participation - 深红
+                    'involved_in': 'participation',
+                    'participate_in': 'participation',
+                    
+                    'default': 'other'
+                };
+                
+                const relationEdgeStyles = {
+                    'activation': { color: '#27AE60', width: 2, type: 'solid' },
+                    'repression': { color: '#E74C3C', width: 2, type: 'solid' },
+                    'regulation': { color: '#3498DB', width: 2, type: 'solid' },
+                    'expression': { color: '#E67E22', width: 1.5, type: 'solid' },
+                    'association': { color: '#9B59B6', width: 1.5, type: 'dashed' },
+                    'localization': { color: '#16A085', width: 1.5, type: 'solid' },
+                    'containment': { color: '#1ABC9C', width: 1.5, type: 'solid' },
+                    'participation': { color: '#C0392B', width: 2, type: 'solid' },
+                    'other': { color: '#95A5A6', width: 1, type: 'solid' }
+                };
+                
+                const stats = computed(() => ({
+                    nodes: graphData.value.nodes.length,
+                    edges: graphData.value.edges.length,
+                    nodeTypes: Object.keys(nodeColors).length,
+                    edgeTypes: relationTypes.value.length
+                }));
+                
+                // 按 PC 语义分类的关系类型
+                const relationTypesByCategory = computed(() => {
+                    const cats = {};
+                    graphData.value.edges.forEach(e => {
+                        const cat = relationCategories[e.relation] || 'other';
+                        if (!cats[cat]) cats[cat] = [];
+                        cats[cat].push(e.relation);
+                    });
+                    // 去重并排序
+                    for (const cat in cats) {
+                        cats[cat] = [...new Set(cats[cat])].sort();
+                    }
+                    return cats;
+                });
+                
+                const relationTypes = computed(() => {
+                    const types = new Set();
+                    graphData.value.edges.forEach(e => types.add(e.relation));
+                    return Array.from(types).sort();
+                });
+                
+                const relationCounts = computed(() => {
+                    const counts = {};
+                    graphData.value.edges.forEach(e => {
+                        counts[e.relation] = (counts[e.relation] || 0) + 1;
+                    });
+                    return counts;
+                });
+                
+                const selectedNodeRelations = computed(() => {
+                    if (!selectedNode.value) return [];
+                    return graphData.value.edges.filter(e => 
+                        e.source === selectedNode.value.id || e.target === selectedNode.value.id
+                    );
+                });
+                
+                const loadData = async () => {
+                    try {
+                        // 优先加载包含多组学数据的知识图谱
+                        let response = await fetch('knowledge_graph_with_omics.json');
+                        if (!response.ok) {
+                            // 回退到标准知识图谱
+                            response = await fetch('knowledge_graph.json');
+                        }
+                        if (!response.ok) {
+                            throw new Error(`HTTP ${response.status}: ${response.statusText}`);
+                        }
+                        const data = await response.json();
+                        
+                        // 验证数据结构
+                        if (!data.nodes || !Array.isArray(data.nodes)) {
+                            throw new Error(t('err-data-format'));
+                        }
+                        if (!data.edges || !Array.isArray(data.edges)) {
+                            console.warn(t('warn-edges-undefined'));
+                            data.edges = [];
+                        }
+                        
+                        // 计算节点度数
+                        const nodeDegrees = {};
+                        data.edges.forEach(e => {
+                            nodeDegrees[e.source] = (nodeDegrees[e.source] || 0) + 1;
+                            nodeDegrees[e.target] = (nodeDegrees[e.target] || 0) + 1;
+                        });
+                        
+                        // 根据 PC 语义分类设置节点形状
+                        const getNodeSymbol = (type) => {
+                            const symbolMap = {
+                                'gene': 'circle',
+                                'gene_id': 'circle',
+                                'gene_group': 'circle',
+                                'gene_family': 'circle',
+                                'phenotype': 'rect',
+                                'attribute': 'rect',
+                                'tissue': 'roundRect',
+                                'species': 'roundRect',
+                                'process': 'diamond',
+                                'time': 'diamond',
+                                'condition': 'diamond',
+                                'stress': 'diamond',
+                                'location': 'triangle',
+                                'sra_dataset': 'pin',
+                                'data_type': 'pin',
+                                'count': 'pin'
+                            };
+                            return symbolMap[type] || 'circle';
+                        };
+                        
+                        graphData.value = {
+                            nodes: data.nodes.map(n => ({
+                                id: n.id,
+                                name: n.id,
+                                category: n.type || 'unknown',
+                                degree: nodeDegrees[n.id] || 0,
+                                symbol: getNodeSymbol(n.type),
+                                symbolSize: (n.type === 'gene' ? 20 : n.type === 'sra_dataset' ? 18 : 12) + Math.min((nodeDegrees[n.id] || 0) * 0.3, 15),
+                                itemStyle: { 
+                                    color: nodeColors[n.type] || nodeColors.unknown,
+                                    borderColor: '#fff',
+                                    borderWidth: 1
+                                }
+                            })),
+                            edges: data.edges.map((e, i) => {
+                                const cat = relationCategories[e.relation] || 'other';
+                                const style = relationEdgeStyles[cat];
+                                return {
+                                    id: i,
+                                    source: e.source,
+                                    target: e.target,
+                                    name: e.relation,
+                                    relation: e.relation,
+                                    category: cat,
+                                    lineStyle: {
+                                        color: style.color,
+                                        width: style.width,
+                                        type: style.type,
+                                        curveness: 0.1
+                                    }
+                                };
+                            })
+                        };
+                        
+                        initChart();
+                        ElMessage.success(t('msg-kg-loaded'));
+                    } catch (error) {
+                        ElMessage.error(t('msg-load-data-failed') + error.message);
+                    }
+                };
+                
+                const initChart = () => {
+                    const container = document.getElementById('graph-container');
+                    chart.value = echarts.init(container);
+                    
+                    const option = {
+                        tooltip: {
+                            formatter: params => {
+                                if (params.dataType === 'node') {
+                                    const pcType = nodeTypeLabels[params.data.category] || params.data.category;
+                                    return `<b>${params.name}</b><br/>PC: ${pcType}<br/>${t('connection-count').replace('Connections', 'Deg')}: ${params.data.degree}`;
+                                }
+                                const cat = params.data.category || relationCategories[params.name] || 'other';
+                                const catName = cat === 'activation' ? 'Activation' : 
+                                               cat === 'repression' ? 'Repression' :
+                                               cat === 'regulation' ? 'Regulation' :
+                                               cat === 'expression' ? 'Expression' :
+                                               cat === 'association' ? 'Association' :
+                                               cat === 'localization' ? 'Localization' :
+                                               cat === 'containment' ? 'Containment' :
+                                               cat === 'participation' ? 'Participation' : 'Other';
+                                return `<b>${params.data.source}</b> <span style="color:${relationEdgeStyles[cat].color}">--${params.name}--></span> <b>${params.data.target}</b><br/><small>PC: ${catName}</small>`;
+                            }
+                        },
+                        series: [{
+                            type: 'graph',
+                            layout: 'force',
+                            data: graphData.value.nodes,
+                            links: graphData.value.edges,
+                            roam: true,
+                            draggable: true,
+                            label: {
+                                show: true,
+                                position: 'right',
+                                formatter: '{b}'
+                            },
+                            force: {
+                                repulsion: 300,
+                                gravity: 0.1,
+                                edgeLength: 100,
+                                layoutAnimation: true
+                            },
+                            emphasis: {
+                                focus: 'adjacency',
+                                lineStyle: { width: 4 }
+                            }
+                        }]
+                    };
+                    
+                    chart.value.setOption(option);
+                    
+                    chart.value.on('click', params => {
+                        if (params.dataType === 'node') {
+                            selectedNode.value = params.data;
+                        } else {
+                            selectedNode.value = null;
+                        }
+                    });
+                    
+                    window.addEventListener('resize', () => chart.value.resize());
+                };
+                
+                const searchNode = () => {
+                    if (!searchQuery.value || !chart.value) return;
+                    
+                    const node = graphData.value.nodes.find(n => 
+                        n.id.toLowerCase().includes(searchQuery.value.toLowerCase())
+                    );
+                    
+                    if (node) {
+                        chart.value.dispatchAction({
+                            type: 'highlight',
+                            seriesIndex: 0,
+                            name: node.id
+                        });
+                        selectedNode.value = node;
+                        ElMessage.success(t('msg-node-found') + node.name);
+                    } else {
+                        ElMessage.warning(t('msg-node-not-found'));
+                    }
+                };
+                
+                const toggleRelationFilter = (type) => {
+                    const index = selectedRelations.value.indexOf(type);
+                    if (index > -1) {
+                        selectedRelations.value.splice(index, 1);
+                    } else {
+                        selectedRelations.value.push(type);
+                    }
+                    
+                    if (selectedRelations.value.length === 0) {
+                        chart.value.setOption({
+                            series: [{ data: graphData.value.nodes, links: graphData.value.edges }]
+                        });
+                    } else {
+                        const filteredEdges = graphData.value.edges.filter(e => 
+                            selectedRelations.value.includes(e.relation)
+                        );
+                        const connectedNodes = new Set();
+                        filteredEdges.forEach(e => {
+                            connectedNodes.add(e.source);
+                            connectedNodes.add(e.target);
+                        });
+                        const filteredNodes = graphData.value.nodes.filter(n => 
+                            connectedNodes.has(n.id)
+                        );
+                        
+                        chart.value.setOption({
+                            series: [{ data: filteredNodes, links: filteredEdges }]
+                        });
+                    }
+                };
+                
+                const fitGraph = () => {
+                    if (chart.value) {
+                        chart.value.dispatchAction({ type: 'restore' });
+                    }
+                };
+                
+                const resetFilters = () => {
+                    selectedRelations.value = [];
+                    selectedNode.value = null;
+                    searchQuery.value = '';
+                    if (chart.value) {
+                        chart.value.setOption({
+                            series: [{ data: graphData.value.nodes, links: graphData.value.edges }]
+                        });
+                        chart.value.dispatchAction({ type: 'restore' });
+                    }
+                };
+                
+                const getNodeTypeTag = (type) => {
+                    const typeMap = { 'gene': '', 'gene_id': 'success', 'tissue': 'warning', 'location': 'info' };
+                    return typeMap[type] || '';
+                };
+                
+                const goBack = () => {
+                    window.location.href = '/';
+                };
+                
+                onMounted(() => {
+                    loadData().then(() => {
+                        // 检查URL参数，如果有highlight则自动搜索高亮
+                        const urlParams = new URLSearchParams(window.location.search);
+                        const highlightEntity = urlParams.get('highlight');
+                        if (highlightEntity) {
+                            searchQuery.value = highlightEntity;
+                            setTimeout(() => {
+                                searchNode();
+                            }, 500); // 等待图表初始化完成
+                        }
+                    });
+                });
+                
+                return {
+                    t,
+                    tp,
+                    stats,
+                    searchQuery,
+                    selectedNode,
+                    selectedRelations,
+                    relationTypes,
+                    relationTypesByCategory,
+                    relationCounts,
+                    relationEdgeStyles,
+                    relationCategories,
+                    nodeTypeLabels,
+                    selectedNodeRelations,
+                    nodeColors,
+                    searchNode,
+                    toggleRelationFilter,
+                    fitGraph,
+                    resetFilters,
+                    getNodeTypeTag,
+                    goBack
+                };
+            }
+        }).use(ElementPlus).mount('#app');
+    </script>
+</body>
+</html>

apps/web/vue3/lightWeightExtensionTest.js

@@ -0,0 +1,304 @@
+(function () {
+    const PY_EXTENSIONS = new Set(['.py']);
+    const R_EXTENSIONS = new Set(['.r']);
+
+    function normalizedRelativePath(file) {
+        const relative = String(file.webkitRelativePath || file.relativePath || file.name || '').replace(/^\/+/, '');
+        return relative.split('\\').join('/');
+    }
+
+    function parsePythonImports(content) {
+        const imports = new Set();
+        const lines = String(content || '').split(/\r?\n/);
+        for (const line of lines) {
+            let match = line.match(/^\s*import\s+([A-Za-z0-9_.,\s]+)/);
+            if (match) {
+                match[1].split(',').forEach((item) => {
+                    const token = item.trim().split(/\s+as\s+/i)[0].split('.')[0].trim();
+                    if (token) imports.add(token);
+                });
+            }
+            match = line.match(/^\s*from\s+([A-Za-z0-9_.]+)\s+import\s+/);
+            if (match) {
+                const token = match[1].split('.')[0].trim();
+                if (token) imports.add(token);
+            }
+        }
+        return Array.from(imports);
+    }
+
+    function parseRPackages(content) {
+        const packages = new Set();
+        const pattern = /(?:library|require)\(\s*["']?([A-Za-z0-9_.-]+)["']?\s*\)/g;
+        let match;
+        const text = String(content || '');
+        while ((match = pattern.exec(text)) !== null) {
+            if (match[1]) packages.add(match[1]);
+        }
+        return Array.from(packages);
+    }
+
+    function commonPathPrefix(files) {
+        const paths = files.map((f) => normalizedRelativePath(f).split('/')).filter((parts) => parts.length > 0);
+        if (!paths.length) return '';
+        const first = paths[0];
+        let prefixLen = 0;
+        for (let i = 0; i < first.length; i++) {
+            if (!paths.every((parts) => parts[i] === first[i])) break;
+            prefixLen = i + 1;
+        }
+        return first.slice(0, prefixLen).join('/');
+    }
+
+    function sanitizeDisplayName(raw) {
+        return String(raw || '').replace(/[^A-Za-z0-9_-]+/g, '_').replace(/^_+|_+$/g, '') || 'lightweight_extension';
+    }
+
+    function extractRootName(files) {
+        const prefix = commonPathPrefix(files);
+        const base = (prefix && prefix !== 'raw_code' && prefix !== 'raw_test_data')
+            ? sanitizeDisplayName(prefix.split('/')[0])
+            : 'lightweight_extension_drop';
+        const ts = Date.now();
+        return base + '_' + ts;
+    }
+
+    function splitFixedStructure(files) {
+        const codeFiles = [];
+        const dataFiles = [];
+        let hasRunScript = false;
+        let prefix = commonPathPrefix(files);
+        if (prefix && !prefix.endsWith('/')) prefix += '/';
+
+        const sampled = [];
+        for (const file of files) {
+            let relativePath = normalizedRelativePath(file);
+            if (prefix && relativePath.startsWith(prefix)) {
+                relativePath = relativePath.slice(prefix.length);
+            }
+            if (sampled.length < 10) sampled.push(relativePath);
+            if (relativePath.startsWith('raw_code/')) {
+                file.lightweightRelativePath = relativePath.slice('raw_code/'.length) || file.name;
+                codeFiles.push(file);
+                if (relativePath === 'raw_code/run.sh') {
+                    hasRunScript = true;
+                }
+            } else if (relativePath.startsWith('raw_test_data/')) {
+                file.lightweightRelativePath = relativePath.slice('raw_test_data/'.length) || file.name;
+                dataFiles.push(file);
+            }
+        }
+        if (!codeFiles.length) {
+            const preview = sampled.length ? sampled.slice(0, 10).join(', ') : '(无)';
+            throw new Error('缺少 raw_code/ 目录（检测到的路径样例: ' + preview + '）');
+        }
+        if (!dataFiles.length) {
+            throw new Error('缺少 raw_test_data/ 目录');
+        }
+        if (!hasRunScript) {
+            throw new Error('缺少 raw_code/run.sh');
+        }
+        return { codeFiles, dataFiles };
+    }
+
+    async function extractDependencies(files) {
+        const pythonImports = new Set();
+        const rPackages = new Set();
+        for (const file of files) {
+            const path = normalizedRelativePath(file);
+            const lower = path.toLowerCase();
+            const extension = lower.includes('.') ? lower.slice(lower.lastIndexOf('.')) : '';
+            if (!PY_EXTENSIONS.has(extension) && !R_EXTENSIONS.has(extension)) {
+                continue;
+            }
+            const content = await file.text();
+            if (PY_EXTENSIONS.has(extension)) {
+                parsePythonImports(content).forEach((name) => pythonImports.add(name));
+            } else {
+                parseRPackages(content).forEach((name) => rPackages.add(name));
+            }
+        }
+        return {
+            python_imports: Array.from(pythonImports),
+            r_packages: Array.from(rPackages),
+        };
+    }
+
+    async function encodeBase64(file) {
+        const buffer = await file.arrayBuffer();
+        const bytes = new Uint8Array(buffer);
+        let binary = '';
+        const chunkSize = 0x8000;
+        for (let index = 0; index < bytes.length; index += chunkSize) {
+            binary += String.fromCharCode(...bytes.subarray(index, index + chunkSize));
+        }
+        return btoa(binary);
+    }
+
+    async function importFolderToJob(hooks, rootName, files) {
+        const payload = {
+            job_id: String(hooks.jobInfo.job_id || '').trim(),
+            root_name: rootName,
+            files: [],
+            relative_paths: [],
+        };
+        for (const file of files) {
+            payload.files.push(await encodeBase64(file));
+            payload.relative_paths.push(normalizedRelativePath(file));
+        }
+        const response = await fetch('/api/job/import-folder', {
+            method: 'POST',
+            headers: { 'Content-Type': 'application/json' },
+            body: JSON.stringify(payload),
+        });
+        const data = await response.json();
+        if (!response.ok || !data.success) {
+            throw new Error(data.detail || data.error || data.message || 'Job 导入失败');
+        }
+        return data;
+    }
+
+    async function resolveRuntimeEnv(files) {
+        const dependencies = await extractDependencies(files);
+        console.log('[lightWeightExtensionTest] 提取的依赖:', JSON.stringify(dependencies), '| 扫描文件数:', files.length);
+        try {
+            const response = await fetch('/api/extension-stages/envs/resolve', {
+                method: 'POST',
+                headers: { 'Content-Type': 'application/json' },
+                body: JSON.stringify(dependencies),
+            });
+            const data = await response.json();
+            console.log('[lightWeightExtensionTest] 后端 env/resolve 原始响应:', response.status, JSON.stringify(data).slice(0, 500));
+            if (!response.ok || !data.success) {
+                throw new Error(data.detail || data.error || data.message || '运行环境解析失败');
+            }
+            return data;
+        } catch (e) {
+            console.error('[lightWeightExtensionTest] env/resolve 调用失败:', e);
+            throw e;
+        }
+    }
+
+    function notifyError(message) {
+        if (window.ElementPlus && window.ElementPlus.ElMessage) {
+            window.ElementPlus.ElMessage.error(message);
+        }
+    }
+
+    async function ensureJob(hooks) {
+        if (String(hooks.jobInfo.job_id || '').trim() && String(hooks.jobInfo.job_id) !== 'default_job') {
+            return;
+        }
+        await hooks.createNewJob();
+        if (!String(hooks.jobInfo.job_id || '').trim() || String(hooks.jobInfo.job_id) === 'default_job') {
+            throw new Error('自动创建 Job 失败');
+        }
+    }
+
+    async function processFolderFiles(hooks, inputFiles) {
+        const files = Array.from(inputFiles || []).filter((file) => normalizedRelativePath(file));
+        if (!files.length) {
+            throw new Error('未读取到任何文件');
+        }
+        hooks.lightweightExtensionTestStatus.value = '正在校验目录结构...';
+        const rootName = extractRootName(files);
+        const fixed = splitFixedStructure(files);
+        hooks.lightweightExtensionTestStatus.value = '正在确保 Job 可用...';
+        await ensureJob(hooks);
+        hooks.lightweightExtensionTestStatus.value = '正在解析运行环境...';
+        const envResult = await resolveRuntimeEnv(files);
+        hooks.extensionBuild.runtimeEnv = envResult.runtime_env || 'test4py311';
+        console.log(
+            '[lightWeightExtensionTest] ✓ 选定环境: ' + hooks.extensionBuild.runtimeEnv,
+            '| 原因: ' + (envResult.reason || 'unknown'),
+            '| 兜底: ' + (envResult.fallback ? '是' : '否'),
+            envResult.matches ? '| 候选: ' + JSON.stringify(envResult.matches.map(m => m.env + '(py:' + (m.python_hits || []).join(',') + ' r:' + (m.r_hits || []).join(',') + ')')) : '',
+        );
+        hooks.lightweightExtensionTestStatus.value = '正在镜像导入当前 Job...';
+        await importFolderToJob(hooks, rootName, files);
+        hooks.extensionBuild.displayName = rootName;
+        hooks.extensionBuild.command = 'bash run.sh';
+        hooks.extensionBuild.codeFiles = hooks.appendExtensionFiles([], fixed.codeFiles);
+        hooks.extensionBuild.dataFiles = hooks.appendExtensionFiles([], fixed.dataFiles);
+        hooks.extensionBuild.dataPaths = '';
+        hooks.lightweightExtensionTestStatus.value = `运行环境 ${hooks.extensionBuild.runtimeEnv} 已确定，正在触发 upload...`;
+        await hooks.buildLightweightExtensionStage();
+        hooks.lightweightExtensionTestStatus.value = '已开始 upload，系统正在自动轮询并等待候选卡。';
+    }
+
+    async function readEntry(entry, basePath) {
+        if (entry.isFile) {
+            return new Promise((resolve) => {
+                entry.file((file) => {
+                    Object.defineProperty(file, 'webkitRelativePath', {
+                        value: basePath ? basePath + '/' + entry.name : entry.name,
+                        writable: false,
+                    });
+                    resolve([file]);
+                });
+            });
+        }
+        if (entry.isDirectory) {
+            const reader = entry.createReader();
+            const entries = await new Promise((resolve) => {
+                reader.readEntries(resolve);
+            });
+            const subPath = basePath ? basePath + '/' + entry.name : entry.name;
+            const nested = await Promise.all(entries.map((e) => readEntry(e, subPath)));
+            return nested.flat();
+        }
+        return [];
+    }
+
+    async function readDroppedFiles(dataTransfer) {
+        if (!dataTransfer || !dataTransfer.items) {
+            return Array.from(dataTransfer?.files || []);
+        }
+        const items = Array.from(dataTransfer.items);
+        const entries = items
+            .map((item) => item.webkitGetAsEntry && item.webkitGetAsEntry())
+            .filter(Boolean);
+        if (!entries.length) {
+            return Array.from(dataTransfer.files || []);
+        }
+        const results = await Promise.all(entries.map((entry) => readEntry(entry, '')));
+        return results.flat();
+    }
+
+    function mountApi() {
+        window.LightWeightExtensionTest = {
+            async handleDrop(hooks, event) {
+                try {
+                    const files = await readDroppedFiles(event?.dataTransfer);
+                    await processFolderFiles(hooks, files);
+                } catch (error) {
+                    const message = `失败：${error.message || '目录处理失败'}`;
+                    hooks.lightweightExtensionTestStatus.value = message;
+                    notifyError(message);
+                }
+            },
+            async handlePick(hooks, event) {
+                const files = event?.target?.files || [];
+                try {
+                    await processFolderFiles(hooks, files);
+                } catch (error) {
+                    const message = `失败：${error.message || '目录处理失败'}`;
+                    hooks.lightweightExtensionTestStatus.value = message;
+                    notifyError(message);
+                } finally {
+                    if (event?.target) {
+                        event.target.value = '';
+                    }
+                }
+            },
+            openPicker() {
+                const input = document.getElementById('lightweight-extension-test-folder-input');
+                if (input) {
+                    input.click();
+                }
+            },
+        };
+    }
+
+    mountApi();
+})();

apps/web/vue3/main.py

@@ -6,6 +6,7 @@ BotanicalBaseAgent - FastAPI Backend
 import os
 import sys
 import json
+import base64
 import csv
 import asyncio
 import hashlib
@@ -41,6 +42,7 @@ _builtins.print = _safe_print
 
 # 添加项目路径
 PROJECT_ROOT = Path(__file__).parent.parent.parent.parent
+DEFAULT_RUNTIME_ENV = os.environ.get("BBAV5_DEFAULT_RUNTIME_ENV", "test4py311")
 sys.path.insert(0, str(PROJECT_ROOT))
 from gfa_core.project_paths import get_conda_env_bin, get_conda_env_rscript, get_configured_path, get_wgs_bcftools, get_wgs_java, get_wgs_samtools
 
@@ -6876,9 +6878,14 @@ class ExecuteRequest(BaseModel):
     domCoverage: float = 30.0
     idTransform: str = "none"
     scopeFile: str = ""
+    scopeId: str = ""
     scopeMode: str = ""
     analysisRoute: str = ""
     memberSetId: str = ""
+    expectedStages: List[str] = []
+    stageStatuses: Dict[str, str] = {}
+    reportAction: str = "generate"
+    reportUseModel: bool = True
     contextRoute: str = ""
     subfamilyLabelSource: str = ""
     requiresConfirmedSubfamily: bool = False
@@ -6911,6 +6918,10 @@ class ExecuteRequest(BaseModel):
     speciesCode: str = ""
     rnaseqPrefix: str = ""
     rnaseqOutputPrefix: str = ""
+    rnaseqScopeId: str = ""
+    rnaseqExpectedStages: List[str] = Field(default_factory=list)
+    rnaseqReportAction: str = "generate"
+    rnaseqReportUseModel: bool = True
     # RNA-seq QC 参数
     rnaseqDataMode: str = "upload"
     rnaseqDataPath: str = ""
@@ -7794,6 +7805,10 @@ def run_stage_sync(task_id: str, stage: str, job_id: str, params: dict):
             wgcna_powers=params.get("wgcnaPowers", "1,2,3,4,5,6,7,8,9,10,12,14,16,18,20"),
             candidate_max_deg_proteins=params.get("candidateMaxDegProteins", 500),
             candidate_run_interproscan=params.get("candidateRunInterproscan", "auto"),
+            rnaseq_scope_id=params.get("rnaseqScopeId", ""),
+            rnaseq_expected_stages=params.get("rnaseqExpectedStages") or params.get("expectedStages") or [],
+            rnaseq_report_action=params.get("rnaseqReportAction", "generate"),
+            rnaseq_report_use_model=_bool_param("rnaseqReportUseModel", "report_use_model", default=True),
             # PPI参数
             ppi_species=params.get("ppiSpecies") or params.get("ppi_species") or "auto",
             normalization_species_label=params.get("normalizationSpeciesLabel") or params.get("normalization_species_label") or "",
@@ -7808,8 +7823,13 @@ def run_stage_sync(task_id: str, stage: str, job_id: str, params: dict):
             # Genome Prepare参数
             genome_prepare_type=params.get("genomePrepareType", "auto"),
             scope_file=params.get("scopeFile", ""),
+            scope_id=params.get("scopeId", ""),
             analysis_route=params.get("analysisRoute", ""),
             member_set_id=params.get("memberSetId", ""),
+            expected_stages=params.get("expectedStages", []),
+            stage_statuses=params.get("stageStatuses", {}),
+            report_action=params.get("reportAction", "generate"),
+            report_use_model=params.get("reportUseModel", True),
             analysis_mode=params.get("analysisMode", ""),
             species_queue=params.get("speciesQueue", []),
             subfamily_label_source=params.get("subfamilyLabelSource", ""),
@@ -8555,6 +8575,19 @@ async def root():
     )
 
 
+@app.get("/ml")
+async def root_ml():
+    """返回Vue3前端多语言页面"""
+    return FileResponse(
+        Path(__file__).parent / "index_ml.html",
+        headers={
+            "Cache-Control": "no-cache, no-store, must-revalidate",
+            "Pragma": "no-cache",
+            "Expires": "0"
+        }
+    )
+
+
 @app.post("/api/new_job")
 async def create_new_job():
     """创建新工作目录"""
@@ -8762,6 +8795,56 @@ async def upload_file(files: List[UploadFile] = File(...), job_id: str = Form(""
     }
 
 
+class JobImportFolderRequest(BaseModel):
+    job_id: str
+    root_name: str = ""
+    files: List[str] = Field(default_factory=list)
+    relative_paths: List[str] = Field(default_factory=list)
+
+
+@app.post("/api/job/import-folder")
+async def import_job_folder(req: JobImportFolderRequest):
+    job_id = str(req.job_id or "").strip()
+    if not job_id:
+        raise HTTPException(status_code=400, detail="job_id is required")
+    if len(req.files) != len(req.relative_paths):
+        raise HTTPException(status_code=400, detail="files and relative_paths length mismatch")
+
+    root_name = _safe_upload_name(req.root_name or "lightweight_extension_drop")
+    import_root = INPUT_ROOT / job_id / root_name
+    import_root.mkdir(parents=True, exist_ok=True)
+    saved_files: List[str] = []
+
+    for encoded, raw_relative in zip(req.files, req.relative_paths):
+        relative = Path(str(raw_relative or "").strip())
+        if not raw_relative or relative.is_absolute() or any(part in {"", ".", ".."} for part in relative.parts):
+            raise HTTPException(status_code=400, detail=f"invalid relative path: {raw_relative}")
+        try:
+            content = base64.b64decode(str(encoded or "").encode("utf-8"), validate=True)
+        except Exception as exc:
+            raise HTTPException(status_code=400, detail=f"invalid base64 payload for {raw_relative}: {exc}") from exc
+        destination = import_root / relative
+        destination.parent.mkdir(parents=True, exist_ok=True)
+        destination.write_bytes(content)
+        saved_files.append(relative.as_posix())
+
+    return {
+        "success": True,
+        "job_id": job_id,
+        "root_name": root_name,
+        "import_root": str(import_root),
+        "saved_files": saved_files,
+    }
+
+
+@app.get("/lightWeightExtensionTest.js")
+async def get_lightweight_extension_test_script():
+    script_path = WEB_DIR / "lightWeightExtensionTest.js"
+    if not script_path.exists():
+        raise HTTPException(status_code=404, detail="lightWeightExtensionTest.js not found")
+    return FileResponse(str(script_path), media_type="application/javascript")
+
+
 class ExtensionStageRunRequest(BaseModel):
     extension_id: str
     job_id: str = ""
@@ -8832,6 +8915,137 @@ class ExtensionStageResolveIntentRequest(BaseModel):
     job_id: str = ""
 
 
+class ExtensionStageEnvResolveRequest(BaseModel):
+    python_imports: List[str] = Field(default_factory=list)
+    r_packages: List[str] = Field(default_factory=list)
+
+
+
+@app.get("/api/extension-stages/envs")
+async def list_extension_stage_envs():
+    """Return available conda environment names for the extension stage runtime dropdown."""
+    import json as _json
+    try:
+        proc = await asyncio.create_subprocess_exec(
+            "conda", "env", "list", "--json",
+            stdout=asyncio.subprocess.PIPE,
+            stderr=asyncio.subprocess.PIPE,
+        )
+        stdout, stderr = await proc.communicate()
+        if proc.returncode != 0:
+            # fallback: try parsing plain-text output
+            proc2 = await asyncio.create_subprocess_exec(
+                "conda", "env", "list",
+                stdout=asyncio.subprocess.PIPE,
+                stderr=asyncio.subprocess.PIPE,
+            )
+            stdout2, _ = await proc2.communicate()
+            envs = []
+            for line in stdout2.decode("utf-8", errors="replace").splitlines():
+                stripped = line.strip()
+                if not stripped or stripped.startswith("#"):
+                    continue
+                # format: "env_name    /path/to/env"
+                parts = stripped.split()
+                if parts:
+                    envs.append(parts[0])
+            return {"success": True, "envs": envs}
+        data = _json.loads(stdout.decode("utf-8"))
+        envs = [entry.split("/")[-1] if "/" in str(entry) else str(entry) for entry in data.get("envs", [])]
+        return {"success": True, "envs": envs}
+    except Exception as exc:
+        return {"success": False, "envs": ["test4py311", "rnaseq", "rnaR"], "error": str(exc)}
+
+
+def _normalized_dependency_names(values: List[str]) -> List[str]:
+    normalized: List[str] = []
+    seen: set[str] = set()
+    stdlib_names = set(getattr(sys, "stdlib_module_names", set()))
+    for raw in values or []:
+        token = re.split(r"[<>=\[\]()\s]", str(raw or "").strip(), maxsplit=1)[0].strip()
+        if not token:
+            continue
+        top_level = token.split(".")[0].strip()
+        key = top_level.lower().replace("_", "-")
+        if top_level in stdlib_names or key in seen:
+            continue
+        seen.add(key)
+        normalized.append(top_level)
+    return normalized
+
+
+async def _available_extension_env_names() -> List[str]:
+    result = await list_extension_stage_envs()
+    envs = result.get("envs") if isinstance(result, dict) else []
+    if isinstance(envs, list) and envs:
+        return [str(item) for item in envs if str(item).strip()]
+    return ["test4py311", "rnaseq", "rnaR"]
+
+
+async def _python_packages_for_env(env_name: str) -> set[str]:
+    proc = await asyncio.create_subprocess_exec(
+        "conda", "run", "-n", env_name, "python", "-c",
+        "import json, importlib.metadata as m; print(json.dumps(sorted({dist.metadata.get('Name', '') for dist in m.distributions() if dist.metadata.get('Name', '')})))",
+        stdout=asyncio.subprocess.PIPE,
+        stderr=asyncio.subprocess.PIPE,
+    )
+    stdout, _stderr = await proc.communicate()
+    if proc.returncode != 0:
+        return set()
+    try:
+        values = json.loads(stdout.decode("utf-8", errors="replace"))
+    except Exception:
+        return set()
+    return {str(item).strip().lower().replace("_", "-") for item in values if str(item).strip()}
+
+
+async def _r_packages_for_env(env_name: str) -> set[str]:
+    proc = await asyncio.create_subprocess_exec(
+        "conda", "run", "-n", env_name, "Rscript", "-e",
+        "cat(paste(sort(rownames(installed.packages())), collapse='\n'))",
+        stdout=asyncio.subprocess.PIPE,
+        stderr=asyncio.subprocess.PIPE,
+    )
+    stdout, _stderr = await proc.communicate()
+    if proc.returncode != 0:
+        return set()
+    return {line.strip().lower() for line in stdout.decode("utf-8", errors="replace").splitlines() if line.strip()}
+
+
+@app.post("/api/extension-stages/envs/resolve")
+async def resolve_extension_stage_env(req: ExtensionStageEnvResolveRequest):
+    python_imports = _normalized_dependency_names(req.python_imports)
+    r_packages = _normalized_dependency_names(req.r_packages)
+    if not python_imports and not r_packages:
+        return {
+            "success": True,
+            "runtime_env": "test4py311",
+            "reason": "no_dependencies_detected",
+            "fallback": True,
+        }
+
+    for dep in list(dict.fromkeys(d.lower() for d in python_imports + r_packages)):
+        proc = await asyncio.create_subprocess_exec(
+            "conda", "run", "-n", dep, "python", "--version",
+            stdout=asyncio.subprocess.PIPE,
+            stderr=asyncio.subprocess.PIPE,
+        )
+        await proc.communicate()
+        if proc.returncode == 0:
+            return {
+                "success": True,
+                "runtime_env": dep,
+                "reason": "env_name_matches_dependency",
+                "dependency": dep,
+                "fallback": False,
+            }
+
+    return {
+        "success": True,
+        "runtime_env": "test4py311",
+        "reason": "no_conda_env_matches_dependency",
+        "fallback": True,
+    }
 @app.post("/api/extension-stages/build")
 async def build_extension_stage(
     display_name: str = Form(...),
@@ -9732,7 +9946,7 @@ async def get_config_autofill_template():
 async def draft_config_autofill(req: AutofillDraftRequest):
     job_id, input_dir, workspace_dir = _autofill_job_dirs(req.job_id)
     cmd = [
-        "/home/xzq/miniconda3/envs/test4py311/bin/python",
+        f"/home/xzq/miniconda3/envs/{DEFAULT_RUNTIME_ENV}/bin/python",
         "apps/cli/run_config_autofill.py",
         "--input-dir", str(input_dir),
         "--workspace", str(workspace_dir),
@@ -9761,7 +9975,7 @@ async def draft_config_autofill(req: AutofillDraftRequest):
 async def draft_samples_autofill(req: AutofillDraftRequest):
     job_id, input_dir, workspace_dir = _autofill_job_dirs(req.job_id)
     cmd = [
-        "/home/xzq/miniconda3/envs/test4py311/bin/python",
+        f"/home/xzq/miniconda3/envs/{DEFAULT_RUNTIME_ENV}/bin/python",
         "apps/cli/run_samples_autofill.py",
         "--input-dir", str(input_dir),
         "--workspace", str(workspace_dir),
@@ -9892,7 +10106,7 @@ async def confirm_config_autofill(req: AutofillDraftRequest):
         _write_config_draft_rows(draft_path, req.rows, family, primary_reference_species, identify_blast_reference_species)
         draft_to_use = str(draft_path)
     cmd = [
-        "/home/xzq/miniconda3/envs/test4py311/bin/python",
+        f"/home/xzq/miniconda3/envs/{DEFAULT_RUNTIME_ENV}/bin/python",
         "apps/cli/run_config_autofill.py",
         "--input-dir", str(input_dir),
         "--workspace", str(workspace_dir),
@@ -9940,7 +10154,7 @@ async def confirm_samples_autofill(req: AutofillDraftRequest):
             req,
         )
     cmd = [
-        "/home/xzq/miniconda3/envs/test4py311/bin/python",
+        f"/home/xzq/miniconda3/envs/{DEFAULT_RUNTIME_ENV}/bin/python",
         "apps/cli/run_samples_autofill.py",
         "--input-dir", str(input_dir),
         "--workspace", str(workspace_dir),
@@ -10266,7 +10480,7 @@ async def confirm_identify_domain_review(req: IdentifyDomainReviewConfirmRequest
     curated_file.parent.mkdir(parents=True, exist_ok=True)
     curated_file.write_text("\n".join(selected) + "\n", encoding="utf-8")
     cmd = [
-        "/home/xzq/miniconda3/envs/test4py311/bin/python",
+        f"/home/xzq/miniconda3/envs/{DEFAULT_RUNTIME_ENV}/bin/python",
         "apps/cli/run_identify_refine.py",
         "--input-dir", str(input_dir),
         "--workspace", str(workspace_dir),
@@ -10749,7 +10963,7 @@ def _split_joint_subfamily_confirmation(job_id: str, prefix: str, rows: list[dic
                     f"{row.get('confidence','')}\t{row.get('note','')}\n"
                 )
         cmd = [
-            "/home/xzq/miniconda3/envs/test4py311/bin/python",
+            f"/home/xzq/miniconda3/envs/{DEFAULT_RUNTIME_ENV}/bin/python",
             "apps/cli/run_subfamily_confirm.py",
             "--input-dir", str(input_dir),
             "--workspace", str(workspace_dir),
@@ -11086,7 +11300,7 @@ async def confirm_subfamily_review(req: SubfamilyReviewConfirmRequest):
     member_set_changed = bool(current_ids and confirmed_ids and not current_ids.issubset(confirmed_ids))
 
     cmd = [
-        "/home/xzq/miniconda3/envs/test4py311/bin/python",
+        f"/home/xzq/miniconda3/envs/{DEFAULT_RUNTIME_ENV}/bin/python",
         "apps/cli/run_subfamily_confirm.py",
         "--input-dir", str(input_dir),
         "--workspace", str(workspace_dir),
@@ -11597,7 +11811,7 @@ async def execute_stage(req: ExecuteRequest):
         })
         if req.stage == "gwas_fmt":
             stage_context["genotype_scope_id"] = trusted_genotype_scope
-        if req.stage in {"genome_prepare", "genome_prepare_v2"} or req.stage in RNA_SEQ_STAGES:
+        if req.stage in {"genome_prepare", "genome_prepare_v2", "gene_family_report"} or req.stage in RNA_SEQ_STAGES:
             stage_context.pop("scope_id", None)
             stage_context.pop("scope_mode", None)
             stage_context.pop("analysis_route", None)
@@ -11730,6 +11944,7 @@ async def execute_stage(req: ExecuteRequest):
         skip_completed_check = (
             is_utility_stage(req.stage)
             or is_repair_stage(req.stage)
+            or req.stage == "gene_family_report"
             or force_rerun_requested
             or (req.stage == "gwas_fmt" and not trusted_genotype_scope)
             or (req.stage == "gwas_mlm" and not gwas_mlm_full_identity)
@@ -11958,9 +12173,15 @@ async def execute_stage(req: ExecuteRequest):
         "domCoverage": req.domCoverage,
         "idTransform": req.idTransform,
         "scopeFile": scope_params.get("scopeFile", ""),
+        "scopeId": getattr(req, "scopeId", ""),
+        "rnaseqScopeId": getattr(req, "rnaseqScopeId", ""),
         "scopeMode": scope_params.get("scopeMode", ""),
         "analysisRoute": stage_context.get("analysis_route") or getattr(req, "analysisRoute", ""),
         "memberSetId": stage_context.get("member_set_id") or getattr(req, "memberSetId", ""),
+        "expectedStages": list(getattr(req, "expectedStages", []) or []),
+        "stageStatuses": dict(getattr(req, "stageStatuses", {}) or {}),
+        "reportAction": getattr(req, "reportAction", "generate"),
+        "reportUseModel": bool(getattr(req, "reportUseModel", True)),
         "contextRoute": getattr(req, "contextRoute", ""),
         "subfamilyLabelSource": getattr(req, "subfamilyLabelSource", ""),
         "requiresConfirmedSubfamily": bool(getattr(req, "requiresConfirmedSubfamily", False)),
@@ -12093,6 +12314,10 @@ async def execute_stage(req: ExecuteRequest):
         "wgcnaPowers": getattr(req, 'wgcnaPowers', "1,2,3,4,5,6,7,8,9,10,12,14,16,18,20"),
         "candidateMaxDegProteins": getattr(req, 'candidateMaxDegProteins', 500),
         "candidateRunInterproscan": getattr(req, 'candidateRunInterproscan', "auto"),
+        "rnaseqScopeId": getattr(req, 'rnaseqScopeId', ""),
+        "rnaseqExpectedStages": getattr(req, 'rnaseqExpectedStages', []),
+        "rnaseqReportAction": getattr(req, 'rnaseqReportAction', "generate"),
+        "rnaseqReportUseModel": getattr(req, 'rnaseqReportUseModel', True),
         "ncbiQuery": getattr(req, 'ncbiQuery', ''),
         "ncbiGeneIds": getattr(req, 'ncbiGeneIds', ''),
         "ncbiMode": getattr(req, 'ncbiMode', 'gene'),
@@ -12716,6 +12941,69 @@ def _confirmed_execute_request(
     return ExecuteRequest(**params)
 
 
+def _confirmed_plan_identity(ordered: List[ConfirmedPlanStage]) -> Dict[str, str]:
+    identity: Dict[str, str] = {}
+    for stage in reversed(ordered):
+        params = stage.params or {}
+        for target, keys in {
+            "scopeId": ("scopeId", "scope_id"),
+            "analysisRoute": ("analysisRoute", "analysis_route"),
+            "memberSetId": ("memberSetId", "member_set_id"),
+            "rnaseqScopeId": ("rnaseqScopeId", "rnaseq_scope_id"),
+        }.items():
+            if identity.get(target):
+                continue
+            identity[target] = next((str(params.get(key) or "").strip() for key in keys if params.get(key)), "")
+    return identity
+
+
+def _confirmed_plan_report_request(
+    request: ConfirmedPlanExecutionRequest,
+    ordered: List[ConfirmedPlanStage],
+    status: Dict[str, Any],
+) -> Optional[ExecuteRequest]:
+    """Build the one formal-report submission for a terminal confirmed plan."""
+    terminal = str(status.get("status") or "")
+    if terminal not in {"success", "failed"}:
+        return None
+    planned = [stage.id for stage in ordered if stage.id not in {"summary", "gene_family_report", "subfamily_confirm"}]
+    if not planned:
+        return None
+    completed = set(status.get("completed_stages") or [])
+    failed_stage = str((status.get("failure") or {}).get("stage") or "")
+    stage_statuses = {
+        stage: "success" if stage in completed else "failed" if stage == failed_stage else "not_run"
+        for stage in planned
+    }
+    if terminal == "success":
+        stage_statuses = {stage: "success" for stage in planned}
+    return ExecuteRequest(
+        stage="gene_family_report",
+        session_id=request.session_id,
+        job_id=request.job_id,
+        prefix=request.prefix,
+        expectedStages=planned,
+        stageStatuses=stage_statuses,
+        reportAction="generate",
+        reportUseModel=True,
+        **_confirmed_plan_identity(ordered),
+    )
+
+
+async def _submit_confirmed_plan_report(
+    request: ConfirmedPlanExecutionRequest,
+    ordered: List[ConfirmedPlanStage],
+    status: Dict[str, Any],
+) -> None:
+    report_request = _confirmed_plan_report_request(request, ordered, status)
+    if report_request is None:
+        return
+    try:
+        status["report_submission"] = await execute_stage(report_request)
+    except Exception as exc:
+        status["report_submission"] = {"success": False, "error_type": type(exc).__name__}
+
+
 async def _wait_for_submitted_stage(
     task_id: str,
     stage_id: str,
@@ -12765,6 +13053,8 @@ async def _run_confirmed_plan_execution(
         "run_id": run_id,
         "plan_id": request.plan_id,
         "job_id": request.job_id,
+        "prefix": request.prefix,
+        **_confirmed_plan_identity(ordered),
         "status": "running",
         "stages": [stage.id for stage in ordered],
         "completed_stages": [],
@@ -12808,9 +13098,11 @@ async def _run_confirmed_plan_execution(
                     },
                 }
             )
+            await _submit_confirmed_plan_report(request, ordered, status)
             _write_confirmed_plan_status(status_path, status)
             return
     status.update({"status": "success", "current_stage": ""})
+    await _submit_confirmed_plan_report(request, ordered, status)
     _write_confirmed_plan_status(status_path, status)
 
 
@@ -12838,6 +13130,8 @@ async def agent_execute_confirmed(request: ConfirmedPlanExecutionRequest):
         "run_id": run_id,
         "plan_id": request.plan_id,
         "job_id": request.job_id,
+        "prefix": request.prefix,
+        **_confirmed_plan_identity(_confirmed_plan_stages(request)),
         "status": "queued",
         "stages": [stage.id for stage in _confirmed_plan_stages(request)],
     }
@@ -13679,6 +13973,7 @@ async def get_results(
         "rnaseq_fgsea": {"images": [], "files": [], "elapsed_time": 0},
         "rnaseq_wgcna": {"images": [], "files": [], "elapsed_time": 0},
         "rnaseq_candidate_family": {"images": [], "files": [], "elapsed_time": 0},
+        "rnaseq_report": {"images": [], "files": [], "elapsed_time": 0},
         "genome_prepare": {"images": [], "files": [], "elapsed_time": 0},
         "prepare_organize": {"images": [], "files": [], "elapsed_time": 0},
         "prepare_normalize_gff": {"images": [], "files": [], "elapsed_time": 0},
@@ -13780,6 +14075,7 @@ async def get_results(
         "rnaseq_fgsea",
         "rnaseq_wgcna",
         "rnaseq_candidate_family",
+        "rnaseq_report",
         "expression",
     }
     RNASEQ_FILE_TOKENS = (
@@ -14801,6 +15097,7 @@ async def get_results(
                 "genome_prepare": ["genome_prepare", "species_config"],
                 "msa_region_plot": ["msa_region", "region.tsv", "conservation_profile"],
                 "subfamily_confirm": ["subfamily_confirm", "confirmed_subfamily"],
+                "rnaseq_report": ["rnaseq_report"],
                 "rnaseq_fgsea": ["rnaseq_fgsea", "fgsea"],
                 "rnaseq_go_enrich": ["rnaseq_go_enrich", ".go_enrich", "_go_"],
                 "rnaseq_kegg_enrich": ["rnaseq_kegg_enrich", ".kegg_enrich", "_kegg_", "kegg_pathway", "kegg_pathview"],
@@ -16029,6 +16326,7 @@ def parse_natural_language(message: str) -> dict:
         "rnaseq_align": ["rnaseq比对", "rna比对", "hisat2", "比对"],
         "rnaseq_quant": ["rnaseq定量", "rna定量", "stringtie", "定量"],
         "rnaseq_sample_qc": ["样本质量", "样本检测", "sample qc", "sample quality", "pca", "样本相关性"],
+        "rnaseq_report": ["rnaseq结果报告", "rna-seq结果报告", "转录组结果报告", "rnaseq报告"],
         "rnaseq_wgcna": ["wgcna", "共表达", "加权共表达", "模块性状", "module trait"],
         "rnaseq_de": ["rnaseq差异", "rna差异", "差异表达", "de分析"],
         "rnaseq_fgsea": ["fgsea", "gsea", "基因集富集", "排序富集"],
@@ -16743,6 +17041,93 @@ def _answer_methodology_sandbox_qa(message: str) -> dict[str, Any]:
     return payload
 
 
+def _gene_family_report_plan_context(job_id: str, prefix: str = "") -> Optional[Dict[str, Any]]:
+    """Recover only a user-confirmed or previously reported stage plan."""
+    safe_job_id = str(job_id or "").strip()
+    requested_prefix = str(prefix or "").strip()
+    if not re.fullmatch(r"[A-Za-z0-9][A-Za-z0-9_.-]{0,127}", safe_job_id):
+        return None
+    final_dir = WORKSPACE_ROOT / safe_job_id / "final"
+    excluded = {"summary", "gene_family_report", "subfamily_confirm"}
+
+    confirmed: list[tuple[float, Dict[str, Any]]] = []
+    confirmed_dir = final_dir / ".confirmed_plans"
+    for path in confirmed_dir.glob("*.json") if confirmed_dir.is_dir() else ():
+        try:
+            payload = json.loads(path.read_text(encoding="utf-8"))
+        except (OSError, json.JSONDecodeError):
+            continue
+        terminal = str(payload.get("status") or "")
+        plan_prefix = str(payload.get("prefix") or "").strip()
+        if (
+            terminal not in {"success", "failed"}
+            or str(payload.get("job_id") or "") != safe_job_id
+            or not plan_prefix
+            or (requested_prefix and plan_prefix != requested_prefix)
+        ):
+            continue
+        planned = [
+            str(stage).strip()
+            for stage in (payload.get("stages") or [])
+            if str(stage).strip() and str(stage).strip() not in excluded
+        ]
+        if not planned:
+            continue
+        completed = {str(stage) for stage in (payload.get("completed_stages") or [])}
+        failed_stage = str((payload.get("failure") or {}).get("stage") or "")
+        statuses = {
+            stage: "success" if terminal == "success" or stage in completed else "failed" if stage == failed_stage else "not_run"
+            for stage in planned
+        }
+        context = {
+            "prefix": plan_prefix,
+            "expectedStages": planned,
+            "stageStatuses": statuses,
+            "scopeId": str(payload.get("scopeId") or payload.get("scope_id") or ""),
+            "analysisRoute": str(payload.get("analysisRoute") or payload.get("analysis_route") or ""),
+            "memberSetId": str(payload.get("memberSetId") or payload.get("member_set_id") or ""),
+            "rnaseqScopeId": str(payload.get("rnaseqScopeId") or payload.get("rnaseq_scope_id") or ""),
+        }
+        confirmed.append((path.stat().st_mtime, context))
+    if confirmed:
+        return max(confirmed, key=lambda item: item[0])[1]
+
+    pattern = f"{requested_prefix}.gene_family_report.manifest.json" if requested_prefix else "*.gene_family_report.manifest.json"
+    reports: list[tuple[float, Dict[str, Any]]] = []
+    for path in final_dir.glob(pattern) if final_dir.is_dir() else ():
+        try:
+            manifest = json.loads(path.read_text(encoding="utf-8"))
+        except (OSError, json.JSONDecodeError):
+            continue
+        report_prefix = str(manifest.get("prefix") or "").strip()
+        parameters = manifest.get("parameters") or {}
+        planned = [
+            str(stage).strip()
+            for stage in (parameters.get("expected_stages") or [])
+            if str(stage).strip() and str(stage).strip() not in excluded
+        ]
+        if (
+            manifest.get("stage") != "gene_family_report"
+            or manifest.get("status") != "success"
+            or not report_prefix
+            or (requested_prefix and report_prefix != requested_prefix)
+            or not planned
+        ):
+            continue
+        recorded_statuses = parameters.get("stage_statuses") or {}
+        context = {
+            "prefix": report_prefix,
+            "expectedStages": planned,
+            "stageStatuses": {stage: str(recorded_statuses.get(stage) or "missing") for stage in planned},
+            "scopeId": "",
+            "analysisRoute": "",
+            "memberSetId": "",
+            "rnaseqScopeId": "",
+        }
+        reports.append((path.stat().st_mtime, context))
+    return max(reports, key=lambda item: item[0])[1] if reports else None
+
+
 async def _run_agent_chat(
     request: AgentChatRequest,
     progress_callback=None,
@@ -16838,7 +17223,11 @@ async def _run_agent_chat(
         )
         router_context_terms = dict(terms)
 
-    from gfa_core.mas.utils.intent_parser import parse_sequence_extract_request
+    from gfa_core.mas.utils.intent_parser import (
+        deterministic_agent_chat_intent,
+        parse_sequence_extract_request,
+        resolve_gene_family_report_intent,
+    )
 
     utility_params = parse_sequence_extract_request(request.message)
     if utility_params:
@@ -16884,6 +17273,127 @@ async def _run_agent_chat(
             "session_id": session_id,
         }
 
+    compact_message = re.sub(r"\s+", "", str(request.message or "").lower())
+    deterministic_intent = None if "基因家族" in compact_message else deterministic_agent_chat_intent(
+        request.message,
+        rnaseq_context=any(str(stage).startswith("rnaseq_") for stage in completed_stages),
+    )
+    if deterministic_intent is not None:
+        report_action = str(
+            (deterministic_intent.get("params") or {}).get("rnaseqReportAction")
+            or "generate"
+        )
+        report_message = (
+            "已识别为打开 RNA-seq 结果报告。"
+            if report_action == "open"
+            else "已识别为生成 RNA-seq 结果报告。"
+        )
+        report_intent = {
+            **deterministic_intent,
+            "stage": "rnaseq_report",
+            "primary_stage": "rnaseq_report",
+            "taskType": "analysis",
+            "task_kind": "analysis",
+            "job_id": request.job_id,
+            "workspace": (
+                str(PROJECT_ROOT / "workspace" / request.job_id)
+                if request.job_id
+                else ""
+            ),
+            "message": report_message,
+        }
+        if conversation_turn is not None:
+            active_store.finish_turn(
+                conversation_turn,
+                assistant_message=report_message,
+                interaction_kind="independent",
+                action="propose_analysis",
+                intent=report_intent,
+            )
+        return {
+            "success": True,
+            "status": "ok",
+            "action": "propose_analysis",
+            "intent": report_intent,
+            "sources": [],
+            "tool_trace": [],
+            "mode": "analysis",
+            "completed_stages": completed_stages,
+            "model_used": "rule",
+            "session_id": session_id,
+            "handoff_request": request.message,
+        }
+
+    gene_report_intent = resolve_gene_family_report_intent(request.message)
+    if gene_report_intent is not None:
+        plan_context = _gene_family_report_plan_context(
+            request.job_id,
+            str(router_context_terms.get("prefix") or ""),
+        )
+        report_action = str((gene_report_intent.get("params") or {}).get("reportAction") or "generate")
+        if plan_context is None:
+            report_message = "已识别为基因家族结果报告请求，但当前 job 缺少可验证的分析计划，无法生成或打开正式报告。"
+            if conversation_turn is not None:
+                active_store.finish_turn(
+                    conversation_turn,
+                    assistant_message=report_message,
+                    interaction_kind="independent",
+                    action="reply",
+                    intent=None,
+                )
+            return {
+                "success": False,
+                "status": "report_plan_missing",
+                "action": None,
+                "intent": None,
+                "message": report_message,
+                "sources": [],
+                "tool_trace": [],
+                "mode": "analysis",
+                "completed_stages": completed_stages,
+                "model_used": "rule",
+                "session_id": session_id,
+            }
+        report_message = (
+            "已识别为打开基因家族结果报告。"
+            if report_action == "open"
+            else "已识别为生成基因家族结果报告。"
+        )
+        report_params = {**(gene_report_intent.get("params") or {}), **plan_context}
+        resolved_intent = {
+            **gene_report_intent,
+            "stage": "gene_family_report",
+            "primary_stage": "gene_family_report",
+            "taskType": "analysis",
+            "task_kind": "report",
+            "prefix": plan_context["prefix"],
+            "params": report_params,
+            "job_id": request.job_id,
+            "workspace": str(WORKSPACE_ROOT / request.job_id) if request.job_id else "",
+            "message": report_message,
+        }
+        if conversation_turn is not None:
+            active_store.finish_turn(
+                conversation_turn,
+                assistant_message=report_message,
+                interaction_kind="independent",
+                action="propose_analysis",
+                intent=resolved_intent,
+            )
+        return {
+            "success": True,
+            "status": "ok",
+            "action": "propose_analysis",
+            "intent": resolved_intent,
+            "sources": [],
+            "tool_trace": [],
+            "mode": "analysis",
+            "completed_stages": completed_stages,
+            "model_used": "rule",
+            "session_id": session_id,
+            "handoff_request": request.message,
+        }
+
     global llm_manager
     active_llm_manager = llm_manager
     if active_llm_manager is None:
@@ -19989,6 +20499,63 @@ async def agent_plan(request: AgentPlanRequest):
         extension_intent = _match_extension_stage_intent(request.message, request.job_id or "")
         if extension_intent:
             return _extension_stage_plan_response(extension_intent, session_id, request.job_id or "")
+        report_intent = dict(request.intent or {})
+        if report_intent.get("stages") == ["gene_family_report"]:
+            report_params = dict(report_intent.get("params") or {})
+            report_prefix = str(
+                report_intent.get("prefix")
+                or report_params.get("prefix")
+                or request.prefix
+                or ""
+            ).strip()
+            if not report_params.get("expectedStages"):
+                recovered = _gene_family_report_plan_context(request.job_id, report_prefix)
+                if recovered:
+                    report_params.update(recovered)
+                    report_prefix = recovered["prefix"]
+            if not report_params.get("expectedStages"):
+                return {
+                    "success": False,
+                    "mode": "gene_family_report_deterministic",
+                    "status": "report_plan_missing",
+                    "message": "当前 job 缺少可验证的基因家族分析计划，无法生成或打开正式报告。",
+                    "session_id": session_id,
+                }
+            report_params["prefix"] = report_prefix
+            report_intent.update(
+                {
+                    "stage": "gene_family_report",
+                    "primary_stage": "gene_family_report",
+                    "stages": ["gene_family_report"],
+                    "prefix": report_prefix,
+                    "params": report_params,
+                }
+            )
+            detail = _stage_detail_defaults("gene_family_report")
+            detail.update({"order": 1, "dependencies": [], "params": dict(report_params)})
+            return {
+                "success": True,
+                "mode": "gene_family_report_deterministic",
+                "plan": {
+                    "analysis_type": "gene_family",
+                    "prefix": report_prefix,
+                    "description": "生成或打开基因家族结果报告",
+                    "estimated_time": "2分钟",
+                    "estimated_total_time": "2分钟",
+                    "execution_strategy": "sequential",
+                    "max_parallel": 1,
+                    "total_stages": 1,
+                    "stages": ["gene_family_report"],
+                    "stages_detail": [detail],
+                    "all_stages": ["gene_family_report"],
+                    "all_stages_detail": [detail],
+                    "parallel_groups": [],
+                    "params": report_params,
+                },
+                "intent": report_intent,
+                "completed_stages": [],
+                "session_id": session_id,
+            }
         plan_role_resolution = (
             _reconcile_confirmed_gene_family_species(
                 request.job_id,
@@ -20012,6 +20579,63 @@ async def agent_plan(request: AgentPlanRequest):
             request.intent["params"] = dict(request.intent.get("params") or {})
             _apply_reconciled_species_to_intent(request.intent, plan_role_resolution)
         query_lower_for_context = (request.message or "").lower()
+        result_report_query = (
+            "结果报告" in query_lower_for_context
+            and any(action in query_lower_for_context for action in ["生成", "打开"])
+        )
+        if result_report_query:
+            from gfa_core.rnaseq_evidence import is_rnaseq_evidence_stage, manifest_identity_value
+
+            current_intent = dict(request.intent or {})
+            current_params = dict(current_intent.get("params") or {})
+            current_stages = [str(stage) for stage in (current_intent.get("stages") or [])]
+            explicit_rnaseq_report = any(
+                marker in query_lower_for_context
+                for marker in ["rnaseq", "rna-seq", "rna seq", "转录组"]
+            )
+            rnaseq_context = any(is_rnaseq_evidence_stage(stage) for stage in current_stages)
+            latest_rnaseq_manifest = None
+            if request.job_id:
+                report_final_dir = WORKSPACE_ROOT / request.job_id / "final"
+                report_prefix = _nonempty_prefix(request.prefix or current_intent.get("prefix") or current_params.get("prefix"))
+                report_pattern = f"{report_prefix}.*.manifest.json" if report_prefix else "*.manifest.json"
+                candidates = []
+                for candidate in report_final_dir.glob(report_pattern) if report_final_dir.exists() else []:
+                    try:
+                        payload = json.loads(candidate.read_text(encoding="utf-8"))
+                    except Exception:
+                        continue
+                    if (
+                        is_rnaseq_evidence_stage(str(payload.get("stage") or ""))
+                        and str(payload.get("status") or "") in {"success", "partial_success"}
+                    ):
+                        candidates.append((candidate.stat().st_mtime, candidate, payload))
+                if candidates:
+                    _mtime, _path, latest_rnaseq_manifest = max(candidates, key=lambda item: item[0])
+                    rnaseq_context = True
+            if explicit_rnaseq_report or rnaseq_context:
+                current_params["rnaseqReportAction"] = "open" if "打开" in query_lower_for_context else "generate"
+                if latest_rnaseq_manifest:
+                    current_params.setdefault(
+                        "rnaseqScopeId",
+                        manifest_identity_value(latest_rnaseq_manifest, "rnaseq_scope_id"),
+                    )
+                report_prefix = _nonempty_prefix(
+                    request.prefix
+                    or current_intent.get("prefix")
+                    or current_params.get("prefix")
+                    or (latest_rnaseq_manifest or {}).get("prefix")
+                )
+                request.intent = {
+                    **current_intent,
+                    "stages": ["rnaseq_report"],
+                    "primary_stage": "rnaseq_report",
+                    "task_type": "report",
+                    "task_kind": "pipeline",
+                    "prefix": report_prefix,
+                    "params": {**current_params, "prefix": report_prefix},
+                    "confidence": 0.99,
+                }
         subfamily_confirm_query_for_context = any(
             kw in query_lower_for_context
             for kw in ["确认亚家族", "亚家族确认", "确认亚家族标签", "人工确认亚家族", "subfamily confirm", "confirmed subfamily"]
@@ -20907,7 +21531,10 @@ async def agent_plan(request: AgentPlanRequest):
                             "manifest_path": str(status.manifest_path) if status.manifest_path else "",
                             "missing_count": len(status.missing_artifacts or []) + len(status.errors or []),
                         }
-                        if status.completed:
+                        # Report requests are actions, not a request to skip an
+                        # already completed computation. The CLI decides whether
+                        # an "open" request can reuse the fresh snapshot.
+                        if status.completed and stage_id != "rnaseq_report":
                             completed_rnaseq_stages.append(stage_id)
                         else:
                             remaining_rnaseq_stages.append(stage_id)
@@ -20923,6 +21550,7 @@ async def agent_plan(request: AgentPlanRequest):
                         "rnaseq_fgsea": "RNA-seq fgsea",
                         "rnaseq_wgcna": "RNA-seq WGCNA",
                         "rnaseq_candidate_family": "RNA-seq Candidate Family",
+                        "rnaseq_report": "RNA-seq Result Report",
                     }
                     plan_prefix = effective_plan_prefix or request.prefix or incoming_intent.get("prefix", "")
                     final_dir_for_rnaseq = PROJECT_ROOT / "workspace" / request.job_id / "final"
@@ -20942,6 +21570,7 @@ async def agent_plan(request: AgentPlanRequest):
                         "rnaseq_fgsea": ["rnaseq_de"],
                         "rnaseq_wgcna": ["rnaseq_sample_qc"],
                         "rnaseq_candidate_family": ["rnaseq_de", "rnaseq_go_enrich", "rnaseq_kegg_enrich", "rnaseq_fgsea"],
+                        "rnaseq_report": [],
                     }
                     if (
                         "rnaseq_fgsea" in remaining_rnaseq_stages
@@ -20965,6 +21594,7 @@ async def agent_plan(request: AgentPlanRequest):
                         "rnaseq_fgsea": 10,
                         "rnaseq_wgcna": 20,
                         "rnaseq_candidate_family": 10,
+                        "rnaseq_report": 2,
                     }
                     stages_detail = []
                     for order, stage_id in enumerate(remaining_rnaseq_stages, start=1):

apps/web/vue3/static/cdn/en.js

@@ -0,0 +1,165 @@
+// global wrapper
+/*! Element Plus v2.3.14 */
+
+window.en = {
+  name: "en",
+  el: {
+    colorpicker: {
+      confirm: "OK",
+      clear: "Clear",
+      defaultLabel: "color picker",
+      description: "current color is {color}. press enter to select a new color."
+    },
+    datepicker: {
+      now: "Now",
+      today: "Today",
+      cancel: "Cancel",
+      clear: "Clear",
+      confirm: "OK",
+      dateTablePrompt: "Use the arrow keys and enter to select the day of the month",
+      monthTablePrompt: "Use the arrow keys and enter to select the month",
+      yearTablePrompt: "Use the arrow keys and enter to select the year",
+      selectedDate: "Selected date",
+      selectDate: "Select date",
+      selectTime: "Select time",
+      startDate: "Start Date",
+      startTime: "Start Time",
+      endDate: "End Date",
+      endTime: "End Time",
+      prevYear: "Previous Year",
+      nextYear: "Next Year",
+      prevMonth: "Previous Month",
+      nextMonth: "Next Month",
+      year: "",
+      month1: "January",
+      month2: "February",
+      month3: "March",
+      month4: "April",
+      month5: "May",
+      month6: "June",
+      month7: "July",
+      month8: "August",
+      month9: "September",
+      month10: "October",
+      month11: "November",
+      month12: "December",
+      week: "week",
+      weeks: {
+        sun: "Sun",
+        mon: "Mon",
+        tue: "Tue",
+        wed: "Wed",
+        thu: "Thu",
+        fri: "Fri",
+        sat: "Sat"
+      },
+      weeksFull: {
+        sun: "Sunday",
+        mon: "Monday",
+        tue: "Tuesday",
+        wed: "Wednesday",
+        thu: "Thursday",
+        fri: "Friday",
+        sat: "Saturday"
+      },
+      months: {
+        jan: "Jan",
+        feb: "Feb",
+        mar: "Mar",
+        apr: "Apr",
+        may: "May",
+        jun: "Jun",
+        jul: "Jul",
+        aug: "Aug",
+        sep: "Sep",
+        oct: "Oct",
+        nov: "Nov",
+        dec: "Dec"
+      }
+    },
+    inputNumber: {
+      decrease: "decrease number",
+      increase: "increase number"
+    },
+    select: {
+      loading: "Loading",
+      noMatch: "No matching data",
+      noData: "No data",
+      placeholder: "Select"
+    },
+    dropdown: {
+      toggleDropdown: "Toggle Dropdown"
+    },
+    cascader: {
+      noMatch: "No matching data",
+      loading: "Loading",
+      placeholder: "Select",
+      noData: "No data"
+    },
+    pagination: {
+      goto: "Go to",
+      pagesize: "/page",
+      total: "Total {total}",
+      pageClassifier: "",
+      page: "Page",
+      prev: "Go to previous page",
+      next: "Go to next page",
+      currentPage: "page {pager}",
+      prevPages: "Previous {pager} pages",
+      nextPages: "Next {pager} pages",
+      deprecationWarning: "Deprecated usages detected, please refer to the el-pagination documentation for more details"
+    },
+    dialog: {
+      close: "Close this dialog"
+    },
+    drawer: {
+      close: "Close this dialog"
+    },
+    messagebox: {
+      title: "Message",
+      confirm: "OK",
+      cancel: "Cancel",
+      error: "Illegal input",
+      close: "Close this dialog"
+    },
+    upload: {
+      deleteTip: "press delete to remove",
+      delete: "Delete",
+      preview: "Preview",
+      continue: "Continue"
+    },
+    slider: {
+      defaultLabel: "slider between {min} and {max}",
+      defaultRangeStartLabel: "pick start value",
+      defaultRangeEndLabel: "pick end value"
+    },
+    table: {
+      emptyText: "No Data",
+      confirmFilter: "Confirm",
+      resetFilter: "Reset",
+      clearFilter: "All",
+      sumText: "Sum"
+    },
+    tree: {
+      emptyText: "No Data"
+    },
+    transfer: {
+      noMatch: "No matching data",
+      noData: "No data",
+      titles: ["List 1", "List 2"],
+      filterPlaceholder: "Enter keyword",
+      noCheckedFormat: "{total} items",
+      hasCheckedFormat: "{checked}/{total} checked"
+    },
+    image: {
+      error: "FAILED"
+    },
+    pageHeader: {
+      title: "Back"
+    },
+    popconfirm: {
+      confirmButtonText: "Yes",
+      cancelButtonText: "No"
+    }
+  }
+};

apps/web/vue3/static/cdn/en.mjs

@@ -0,0 +1,165 @@
+/*! Element Plus v2.3.14 */
+
+var en = {
+  name: "en",
+  el: {
+    colorpicker: {
+      confirm: "OK",
+      clear: "Clear",
+      defaultLabel: "color picker",
+      description: "current color is {color}. press enter to select a new color."
+    },
+    datepicker: {
+      now: "Now",
+      today: "Today",
+      cancel: "Cancel",
+      clear: "Clear",
+      confirm: "OK",
+      dateTablePrompt: "Use the arrow keys and enter to select the day of the month",
+      monthTablePrompt: "Use the arrow keys and enter to select the month",
+      yearTablePrompt: "Use the arrow keys and enter to select the year",
+      selectedDate: "Selected date",
+      selectDate: "Select date",
+      selectTime: "Select time",
+      startDate: "Start Date",
+      startTime: "Start Time",
+      endDate: "End Date",
+      endTime: "End Time",
+      prevYear: "Previous Year",
+      nextYear: "Next Year",
+      prevMonth: "Previous Month",
+      nextMonth: "Next Month",
+      year: "",
+      month1: "January",
+      month2: "February",
+      month3: "March",
+      month4: "April",
+      month5: "May",
+      month6: "June",
+      month7: "July",
+      month8: "August",
+      month9: "September",
+      month10: "October",
+      month11: "November",
+      month12: "December",
+      week: "week",
+      weeks: {
+        sun: "Sun",
+        mon: "Mon",
+        tue: "Tue",
+        wed: "Wed",
+        thu: "Thu",
+        fri: "Fri",
+        sat: "Sat"
+      },
+      weeksFull: {
+        sun: "Sunday",
+        mon: "Monday",
+        tue: "Tuesday",
+        wed: "Wednesday",
+        thu: "Thursday",
+        fri: "Friday",
+        sat: "Saturday"
+      },
+      months: {
+        jan: "Jan",
+        feb: "Feb",
+        mar: "Mar",
+        apr: "Apr",
+        may: "May",
+        jun: "Jun",
+        jul: "Jul",
+        aug: "Aug",
+        sep: "Sep",
+        oct: "Oct",
+        nov: "Nov",
+        dec: "Dec"
+      }
+    },
+    inputNumber: {
+      decrease: "decrease number",
+      increase: "increase number"
+    },
+    select: {
+      loading: "Loading",
+      noMatch: "No matching data",
+      noData: "No data",
+      placeholder: "Select"
+    },
+    dropdown: {
+      toggleDropdown: "Toggle Dropdown"
+    },
+    cascader: {
+      noMatch: "No matching data",
+      loading: "Loading",
+      placeholder: "Select",
+      noData: "No data"
+    },
+    pagination: {
+      goto: "Go to",
+      pagesize: "/page",
+      total: "Total {total}",
+      pageClassifier: "",
+      page: "Page",
+      prev: "Go to previous page",
+      next: "Go to next page",
+      currentPage: "page {pager}",
+      prevPages: "Previous {pager} pages",
+      nextPages: "Next {pager} pages",
+      deprecationWarning: "Deprecated usages detected, please refer to the el-pagination documentation for more details"
+    },
+    dialog: {
+      close: "Close this dialog"
+    },
+    drawer: {
+      close: "Close this dialog"
+    },
+    messagebox: {
+      title: "Message",
+      confirm: "OK",
+      cancel: "Cancel",
+      error: "Illegal input",
+      close: "Close this dialog"
+    },
+    upload: {
+      deleteTip: "press delete to remove",
+      delete: "Delete",
+      preview: "Preview",
+      continue: "Continue"
+    },
+    slider: {
+      defaultLabel: "slider between {min} and {max}",
+      defaultRangeStartLabel: "pick start value",
+      defaultRangeEndLabel: "pick end value"
+    },
+    table: {
+      emptyText: "No Data",
+      confirmFilter: "Confirm",
+      resetFilter: "Reset",
+      clearFilter: "All",
+      sumText: "Sum"
+    },
+    tree: {
+      emptyText: "No Data"
+    },
+    transfer: {
+      noMatch: "No matching data",
+      noData: "No data",
+      titles: ["List 1", "List 2"],
+      filterPlaceholder: "Enter keyword",
+      noCheckedFormat: "{total} items",
+      hasCheckedFormat: "{checked}/{total} checked"
+    },
+    image: {
+      error: "FAILED"
+    },
+    pageHeader: {
+      title: "Back"
+    },
+    popconfirm: {
+      confirmButtonText: "Yes",
+      cancelButtonText: "No"
+    }
+  }
+};
+

apps/web/vue3/static/cdn/zh-cn.js

@@ -0,0 +1,130 @@
+// global wrapper
+/*! Element Plus v2.3.14 */
+
+window.zhCn = {
+  name: "zh-cn",
+  el: {
+    colorpicker: {
+      confirm: "\u786E\u5B9A",
+      clear: "\u6E05\u7A7A"
+    },
+    datepicker: {
+      now: "\u6B64\u523B",
+      today: "\u4ECA\u5929",
+      cancel: "\u53D6\u6D88",
+      clear: "\u6E05\u7A7A",
+      confirm: "\u786E\u5B9A",
+      selectDate: "\u9009\u62E9\u65E5\u671F",
+      selectTime: "\u9009\u62E9\u65F6\u95F4",
+      startDate: "\u5F00\u59CB\u65E5\u671F",
+      startTime: "\u5F00\u59CB\u65F6\u95F4",
+      endDate: "\u7ED3\u675F\u65E5\u671F",
+      endTime: "\u7ED3\u675F\u65F6\u95F4",
+      prevYear: "\u524D\u4E00\u5E74",
+      nextYear: "\u540E\u4E00\u5E74",
+      prevMonth: "\u4E0A\u4E2A\u6708",
+      nextMonth: "\u4E0B\u4E2A\u6708",
+      year: "\u5E74",
+      month1: "1 \u6708",
+      month2: "2 \u6708",
+      month3: "3 \u6708",
+      month4: "4 \u6708",
+      month5: "5 \u6708",
+      month6: "6 \u6708",
+      month7: "7 \u6708",
+      month8: "8 \u6708",
+      month9: "9 \u6708",
+      month10: "10 \u6708",
+      month11: "11 \u6708",
+      month12: "12 \u6708",
+      weeks: {
+        sun: "\u65E5",
+        mon: "\u4E00",
+        tue: "\u4E8C",
+        wed: "\u4E09",
+        thu: "\u56DB",
+        fri: "\u4E94",
+        sat: "\u516D"
+      },
+      months: {
+        jan: "\u4E00\u6708",
+        feb: "\u4E8C\u6708",
+        mar: "\u4E09\u6708",
+        apr: "\u56DB\u6708",
+        may: "\u4E94\u6708",
+        jun: "\u516D\u6708",
+        jul: "\u4E03\u6708",
+        aug: "\u516B\u6708",
+        sep: "\u4E5D\u6708",
+        oct: "\u5341\u6708",
+        nov: "\u5341\u4E00\u6708",
+        dec: "\u5341\u4E8C\u6708"
+      }
+    },
+    select: {
+      loading: "\u52A0\u8F7D\u4E2D",
+      noMatch: "\u65E0\u5339\u914D\u6570\u636E",
+      noData: "\u65E0\u6570\u636E",
+      placeholder: "\u8BF7\u9009\u62E9"
+    },
+    cascader: {
+      noMatch: "\u65E0\u5339\u914D\u6570\u636E",
+      loading: "\u52A0\u8F7D\u4E2D",
+      placeholder: "\u8BF7\u9009\u62E9",
+      noData: "\u6682\u65E0\u6570\u636E"
+    },
+    pagination: {
+      goto: "\u524D\u5F80",
+      pagesize: "\u6761/\u9875",
+      total: "\u5171 {total} \u6761",
+      pageClassifier: "\u9875",
+      page: "\u9875",
+      prev: "\u4E0A\u4E00\u9875",
+      next: "\u4E0B\u4E00\u9875",
+      currentPage: "\u7B2C {pager} \u9875",
+      prevPages: "\u5411\u524D {pager} \u9875",
+      nextPages: "\u5411\u540E {pager} \u9875",
+      deprecationWarning: "\u4F60\u4F7F\u7528\u4E86\u4E00\u4E9B\u5DF2\u88AB\u5E9F\u5F03\u7684\u7528\u6CD5\uFF0C\u8BF7\u53C2\u8003 el-pagination \u7684\u5B98\u65B9\u6587\u6863"
+    },
+    messagebox: {
+      title: "\u63D0\u793A",
+      confirm: "\u786E\u5B9A",
+      cancel: "\u53D6\u6D88",
+      error: "\u8F93\u5165\u7684\u6570\u636E\u4E0D\u5408\u6CD5!"
+    },
+    upload: {
+      deleteTip: "\u6309 delete \u952E\u53EF\u5220\u9664",
+      delete: "\u5220\u9664",
+      preview: "\u67E5\u770B\u56FE\u7247",
+      continue: "\u7EE7\u7EED\u4E0A\u4F20"
+    },
+    table: {
+      emptyText: "\u6682\u65E0\u6570\u636E",
+      confirmFilter: "\u7B5B\u9009",
+      resetFilter: "\u91CD\u7F6E",
+      clearFilter: "\u5168\u90E8",
+      sumText: "\u5408\u8BA1"
+    },
+    tree: {
+      emptyText: "\u6682\u65E0\u6570\u636E"
+    },
+    transfer: {
+      noMatch: "\u65E0\u5339\u914D\u6570\u636E",
+      noData: "\u65E0\u6570\u636E",
+      titles: ["\u5217\u8868 1", "\u5217\u8868 2"],
+      filterPlaceholder: "\u8BF7\u8F93\u5165\u641C\u7D22\u5185\u5BB9",
+      noCheckedFormat: "\u5171 {total} \u9879",
+      hasCheckedFormat: "\u5DF2\u9009 {checked}/{total} \u9879"
+    },
+    image: {
+      error: "\u52A0\u8F7D\u5931\u8D25"
+    },
+    pageHeader: {
+      title: "\u8FD4\u56DE"
+    },
+    popconfirm: {
+      confirmButtonText: "\u786E\u5B9A",
+      cancelButtonText: "\u53D6\u6D88"
+    }
+  }
+};

apps/web/vue3/static/cdn/zh-cn.mjs

@@ -0,0 +1,130 @@
+/*! Element Plus v2.3.14 */
+
+var zhCn = {
+  name: "zh-cn",
+  el: {
+    colorpicker: {
+      confirm: "\u786E\u5B9A",
+      clear: "\u6E05\u7A7A"
+    },
+    datepicker: {
+      now: "\u6B64\u523B",
+      today: "\u4ECA\u5929",
+      cancel: "\u53D6\u6D88",
+      clear: "\u6E05\u7A7A",
+      confirm: "\u786E\u5B9A",
+      selectDate: "\u9009\u62E9\u65E5\u671F",
+      selectTime: "\u9009\u62E9\u65F6\u95F4",
+      startDate: "\u5F00\u59CB\u65E5\u671F",
+      startTime: "\u5F00\u59CB\u65F6\u95F4",
+      endDate: "\u7ED3\u675F\u65E5\u671F",
+      endTime: "\u7ED3\u675F\u65F6\u95F4",
+      prevYear: "\u524D\u4E00\u5E74",
+      nextYear: "\u540E\u4E00\u5E74",
+      prevMonth: "\u4E0A\u4E2A\u6708",
+      nextMonth: "\u4E0B\u4E2A\u6708",
+      year: "\u5E74",
+      month1: "1 \u6708",
+      month2: "2 \u6708",
+      month3: "3 \u6708",
+      month4: "4 \u6708",
+      month5: "5 \u6708",
+      month6: "6 \u6708",
+      month7: "7 \u6708",
+      month8: "8 \u6708",
+      month9: "9 \u6708",
+      month10: "10 \u6708",
+      month11: "11 \u6708",
+      month12: "12 \u6708",
+      weeks: {
+        sun: "\u65E5",
+        mon: "\u4E00",
+        tue: "\u4E8C",
+        wed: "\u4E09",
+        thu: "\u56DB",
+        fri: "\u4E94",
+        sat: "\u516D"
+      },
+      months: {
+        jan: "\u4E00\u6708",
+        feb: "\u4E8C\u6708",
+        mar: "\u4E09\u6708",
+        apr: "\u56DB\u6708",
+        may: "\u4E94\u6708",
+        jun: "\u516D\u6708",
+        jul: "\u4E03\u6708",
+        aug: "\u516B\u6708",
+        sep: "\u4E5D\u6708",
+        oct: "\u5341\u6708",
+        nov: "\u5341\u4E00\u6708",
+        dec: "\u5341\u4E8C\u6708"
+      }
+    },
+    select: {
+      loading: "\u52A0\u8F7D\u4E2D",
+      noMatch: "\u65E0\u5339\u914D\u6570\u636E",
+      noData: "\u65E0\u6570\u636E",
+      placeholder: "\u8BF7\u9009\u62E9"
+    },
+    cascader: {
+      noMatch: "\u65E0\u5339\u914D\u6570\u636E",
+      loading: "\u52A0\u8F7D\u4E2D",
+      placeholder: "\u8BF7\u9009\u62E9",
+      noData: "\u6682\u65E0\u6570\u636E"
+    },
+    pagination: {
+      goto: "\u524D\u5F80",
+      pagesize: "\u6761/\u9875",
+      total: "\u5171 {total} \u6761",
+      pageClassifier: "\u9875",
+      page: "\u9875",
+      prev: "\u4E0A\u4E00\u9875",
+      next: "\u4E0B\u4E00\u9875",
+      currentPage: "\u7B2C {pager} \u9875",
+      prevPages: "\u5411\u524D {pager} \u9875",
+      nextPages: "\u5411\u540E {pager} \u9875",
+      deprecationWarning: "\u4F60\u4F7F\u7528\u4E86\u4E00\u4E9B\u5DF2\u88AB\u5E9F\u5F03\u7684\u7528\u6CD5\uFF0C\u8BF7\u53C2\u8003 el-pagination \u7684\u5B98\u65B9\u6587\u6863"
+    },
+    messagebox: {
+      title: "\u63D0\u793A",
+      confirm: "\u786E\u5B9A",
+      cancel: "\u53D6\u6D88",
+      error: "\u8F93\u5165\u7684\u6570\u636E\u4E0D\u5408\u6CD5!"
+    },
+    upload: {
+      deleteTip: "\u6309 delete \u952E\u53EF\u5220\u9664",
+      delete: "\u5220\u9664",
+      preview: "\u67E5\u770B\u56FE\u7247",
+      continue: "\u7EE7\u7EED\u4E0A\u4F20"
+    },
+    table: {
+      emptyText: "\u6682\u65E0\u6570\u636E",
+      confirmFilter: "\u7B5B\u9009",
+      resetFilter: "\u91CD\u7F6E",
+      clearFilter: "\u5168\u90E8",
+      sumText: "\u5408\u8BA1"
+    },
+    tree: {
+      emptyText: "\u6682\u65E0\u6570\u636E"
+    },
+    transfer: {
+      noMatch: "\u65E0\u5339\u914D\u6570\u636E",
+      noData: "\u65E0\u6570\u636E",
+      titles: ["\u5217\u8868 1", "\u5217\u8868 2"],
+      filterPlaceholder: "\u8BF7\u8F93\u5165\u641C\u7D22\u5185\u5BB9",
+      noCheckedFormat: "\u5171 {total} \u9879",
+      hasCheckedFormat: "\u5DF2\u9009 {checked}/{total} \u9879"
+    },
+    image: {
+      error: "\u52A0\u8F7D\u5931\u8D25"
+    },
+    pageHeader: {
+      title: "\u8FD4\u56DE"
+    },
+    popconfirm: {
+      confirmButtonText: "\u786E\u5B9A",
+      cancelButtonText: "\u53D6\u6D88"
+    }
+  }
+};
+

apps/web/vue3/static/conversation-sidebar.js

@@ -1,373 +1,373 @@
 /**
  * Conversation Sidebar Component
- * 类似ChatGPT的会话侧边栏组件
+ * Conversation Sidebar component
  */
 
 const ConversationSidebar = {
-    template: `
-        <div class="conversation-sidebar" :class="{ collapsed: isCollapsed }">
-            <!-- 头部：New Chat按钮 -->
-            <div class="sidebar-header">
-                <button class="new-chat-btn" @click="createNewConversation">
-                    <el-icon><plus /></el-icon>
-                    <span v-if="!isCollapsed">New Chat</span>
-                </button>
-                <button class="toggle-btn" @click="toggleSidebar">
-                    <el-icon><arrow-left v-if="!isCollapsed" /><arrow-right v-else /></el-icon>
-                </button>
-            </div>
-            
-            <!-- 搜索框 -->
-            <div class="search-box" v-if="!isCollapsed">
-                <el-input
-                    v-model="searchQuery"
-                    placeholder="搜索会话..."
-                    prefix-icon="search"
-                    clearable
-                    size="small"
-                />
-            </div>
-            
-            <!-- 会话列表 -->
-            <div class="conversation-list" v-if="!isCollapsed">
-                <!-- 今日会话 -->
-                <div class="list-section" v-if="todayConversations.length > 0">
-                    <div class="section-title">今天</div>
-                    <div
-                        v-for="conv in todayConversations"
-                        :key="conv.conversation_id"
-                        class="conversation-item"
-                        :class="{ active: currentConversationId === conv.conversation_id }"
-                        @click="selectConversation(conv)"
-                    >
-                        <div class="item-icon">
-                            <el-icon><chat-dot-round /></el-icon>
-                        </div>
-                        <div class="item-content">
-                            <div class="item-title">{{ conv.title }}</div>
-                            <div class="item-meta">
-                                <span class="gene-family" v-if="conv.gene_family">{{ conv.gene_family }}</span>
-                                <span class="message-count">{{ conv.message_count }}条消息</span>
-                            </div>
-                            <div class="item-preview">{{ conv.last_message }}</div>
-                        </div>
-                        <div class="item-actions" @click.stop>
-                            <el-dropdown trigger="click">
-                                <el-icon><more /></el-icon>
-                                <template #dropdown>
-                                    <el-dropdown-menu>
-                                        <el-dropdown-item @click="renameConversation(conv)">
-                                            <el-icon><edit /></el-icon>重命名
-                                        </el-dropdown-item>
-                                        <el-dropdown-item @click="archiveConversation(conv)">
-                                            <el-icon><folder /></el-icon>归档
-                                        </el-dropdown-item>
-                                        <el-dropdown-item divided @click="deleteConversation(conv)" type="danger">
-                                            <el-icon><delete /></el-icon>删除
-                                        </el-dropdown-item>
-                                    </el-dropdown-menu>
-                                </template>
-                            </el-dropdown>
-                        </div>
-                    </div>
-                </div>
-                
-                <!-- 昨日会话 -->
-                <div class="list-section" v-if="yesterdayConversations.length > 0">
-                    <div class="section-title">昨天</div>
-                    <div
-                        v-for="conv in yesterdayConversations"
-                        :key="conv.conversation_id"
-                        class="conversation-item"
-                        :class="{ active: currentConversationId === conv.conversation_id }"
-                        @click="selectConversation(conv)"
-                    >
-                        <div class="item-icon">
-                            <el-icon><chat-dot-round /></el-icon>
-                        </div>
-                        <div class="item-content">
-                            <div class="item-title">{{ conv.title }}</div>
-                            <div class="item-meta">
-                                <span class="gene-family" v-if="conv.gene_family">{{ conv.gene_family }}</span>
-                                <span class="message-count">{{ conv.message_count }}条</span>
-                            </div>
-                        </div>
-                    </div>
-                </div>
-                
-                <!-- 更早会话 -->
-                <div class="list-section" v-if="olderConversations.length > 0">
-                    <div class="section-title">过去7天</div>
-                    <div
-                        v-for="conv in olderConversations"
-                        :key="conv.conversation_id"
-                        class="conversation-item"
-                        :class="{ active: currentConversationId === conv.conversation_id }"
-                        @click="selectConversation(conv)"
-                    >
-                        <div class="item-icon">
-                            <el-icon><chat-dot-round /></el-icon>
-                        </div>
-                        <div class="item-content">
-                            <div class="item-title">{{ conv.title }}</div>
-                            <div class="item-meta">
-                                <span class="gene-family" v-if="conv.gene_family">{{ conv.gene_family }}</span>
-                            </div>
-                        </div>
-                    </div>
-                </div>
-                
-                <!-- 空状态 -->
-                <div v-if="filteredConversations.length === 0" class="empty-state">
-                    <el-icon><chat-line-round /></el-icon>
-                    <p>暂无会话</p>
-                    <p class="hint">点击上方"New Chat"开始新的基因家族分析</p>
-                </div>
-            </div>
-            
-            <!-- 底部：用户信息 -->
-            <div class="sidebar-footer" v-if="!isCollapsed">
-                <div class="user-info">
-                    <el-avatar :size="32" :icon="UserFilled" />
-                    <span class="username">{{ userId }}</span>
-                </div>
-            </div>
-        </div>
-    `,
-    
-    props: {
-        userId: {
-            type: String,
-            default: 'xia-lab'
-        },
-        apiBaseUrl: {
-            type: String,
-            default: 'http://localhost:8000/api'
-        }
-    },
-    
-    data() {
-        return {
-            isCollapsed: false,
-            searchQuery: '',
-            conversations: [],
-            currentConversationId: null,
-            loading: false,
-            // 图标
-            Plus: ElementPlusIconsVue.Plus,
-            ArrowLeft: ElementPlusIconsVue.ArrowLeft,
-            ArrowRight: ElementPlusIconsVue.ArrowRight,
-            ChatDotRound: ElementPlusIconsVue.ChatDotRound,
-            ChatLineRound: ElementPlusIconsVue.ChatLineRound,
-            More: ElementPlusIconsVue.More,
-            Edit: ElementPlusIconsVue.Edit,
-            Folder: ElementPlusIconsVue.Folder,
-            Delete: ElementPlusIconsVue.Delete,
-            UserFilled: ElementPlusIconsVue.UserFilled,
-        }
-    },
-    
-    computed: {
-        filteredConversations() {
-            if (!this.searchQuery) return this.conversations;
-            const query = this.searchQuery.toLowerCase();
-            return this.conversations.filter(conv => 
-                conv.title.toLowerCase().includes(query) ||
-                (conv.gene_family && conv.gene_family.toLowerCase().includes(query)) ||
-                conv.last_message.toLowerCase().includes(query)
-            );
-        },
-        
-        todayConversations() {
-            const today = new Date().toDateString();
-            return this.filteredConversations.filter(conv => {
-                const convDate = new Date(conv.updated_at).toDateString();
-                return convDate === today;
-            });
-        },
-        
-        yesterdayConversations() {
-            const yesterday = new Date(Date.now() - 86400000).toDateString();
-            return this.filteredConversations.filter(conv => {
-                const convDate = new Date(conv.updated_at).toDateString();
-                return convDate === yesterday;
-            });
-        },
-        
-        olderConversations() {
-            const yesterday = new Date(Date.now() - 86400000).toDateString();
-            return this.filteredConversations.filter(conv => {
-                const convDate = new Date(conv.updated_at).toDateString();
-                return convDate < yesterday;
-            });
-        }
-    },
-    
-    mounted() {
-        this.loadConversations();
-        // 定时刷新
-        this.refreshInterval = setInterval(() => {
-            this.loadConversations();
-        }, 30000); // 30秒刷新一次
-    },
-    
-    beforeUnmount() {
-        if (this.refreshInterval) {
-            clearInterval(this.refreshInterval);
-        }
-    },
-    
-    methods: {
-        async loadConversations() {
-            try {
-                this.loading = true;
-                const response = await fetch(`${this.apiBaseUrl}/conversations/list/${this.userId}`);
-                if (response.ok) {
-                    const data = await response.json();
-                    this.conversations = data.conversations || [];
-                }
-            } catch (error) {
-                console.error('Failed to load conversations:', error);
-                // 使用模拟数据
-                this.conversations = this.getMockConversations();
-            } finally {
-                this.loading = false;
-            }
-        },
-        
-        getMockConversations() {
-            // 模拟数据，用于测试
-            return [
-                {
-                    conversation_id: 'conv_001',
-                    title: 'At.WRKY基因家族分析',
-                    gene_family: 'WRKY',
-                    species: 'At',
-                    message_count: 12,
-                    last_message: '系统发育树已生成完成',
-                    updated_at: new Date().toISOString()
-                },
-                {
-                    conversation_id: 'conv_002',
-                    title: 'Os.TCP进化分析',
-                    gene_family: 'TCP',
-                    species: 'Os',
-                    message_count: 5,
-                    last_message: '正在构建进化树...',
-                    updated_at: new Date(Date.now() - 3600000).toISOString()
-                },
-                {
-                    conversation_id: 'conv_003',
-                    title: 'HMMER参数配置咨询',
-                    message_count: 8,
-                    last_message: 'E-value建议设置为1e-5',
-                    updated_at: new Date(Date.now() - 86400000).toISOString()
-                }
-            ];
-        },
-        
-        toggleSidebar() {
-            this.isCollapsed = !this.isCollapsed;
-            this.$emit('toggle', this.isCollapsed);
-        },
-        
-        async createNewConversation() {
-            try {
-                const response = await fetch(`${this.apiBaseUrl}/conversations/create`, {
-                    method: 'POST',
-                    headers: { 'Content-Type': 'application/json' },
-                    body: JSON.stringify({
-                        user_id: this.userId,
-                        title: '新会话 ' + new Date().toLocaleTimeString()
-                    })
-                });
-                
-                if (response.ok) {
-                    const data = await response.json();
-                    this.currentConversationId = data.conversation_id;
-                    this.$emit('new-conversation', data);
-                    await this.loadConversations();
-                }
-            } catch (error) {
-                console.error('Failed to create conversation:', error);
-                // 创建本地会话
-                const newConv = {
-                    conversation_id: 'conv_' + Date.now(),
-                    title: '新会话',
-                    message_count: 0,
-                    last_message: '',
-                    updated_at: new Date().toISOString()
-                };
-                this.conversations.unshift(newConv);
-                this.currentConversationId = newConv.conversation_id;
-                this.$emit('new-conversation', newConv);
-            }
-        },
-        
-        selectConversation(conv) {
-            this.currentConversationId = conv.conversation_id;
-            this.$emit('select-conversation', conv);
-        },
-        
-        async renameConversation(conv) {
-            const newTitle = prompt('请输入新标题:', conv.title);
-            if (newTitle && newTitle !== conv.title) {
-                try {
-                    await fetch(`${this.apiBaseUrl}/conversations/update-title`, {
-                        method: 'POST',
-                        headers: { 'Content-Type': 'application/json' },
-                        body: JSON.stringify({
-                            conversation_id: conv.conversation_id,
-                            title: newTitle
-                        })
-                    });
-                    conv.title = newTitle;
-                } catch (error) {
-                    console.error('Failed to rename:', error);
-                    conv.title = newTitle; // 本地更新
-                }
-            }
-        },
-        
-        async archiveConversation(conv) {
-            try {
-                await fetch(`${this.apiBaseUrl}/conversations/archive`, {
-                    method: 'POST',
-                    headers: { 'Content-Type': 'application/json' },
-                    body: JSON.stringify({
-                        conversation_id: conv.conversation_id
-                    })
-                });
-                await this.loadConversations();
-            } catch (error) {
-                console.error('Failed to archive:', error);
-            }
-        },
-        
-        async deleteConversation(conv) {
-            if (confirm(`确定要删除会话 "${conv.title}" 吗？`)) {
-                try {
-                    await fetch(`${this.apiBaseUrl}/conversations/delete`, {
-                        method: 'POST',
-                        headers: { 'Content-Type': 'application/json' },
-                        body: JSON.stringify({
-                            conversation_id: conv.conversation_id
-                        })
-                    });
-                    await this.loadConversations();
-                    if (this.currentConversationId === conv.conversation_id) {
-                        this.currentConversationId = null;
-                        this.$emit('select-conversation', null);
-                    }
-                } catch (error) {
-                    console.error('Failed to delete:', error);
-                }
-            }
-        }
-    }
+ template: `
+ <div class="conversation-sidebar" :class="{ collapsed: isCollapsed }">
+ <!-- Header: New Chat button -->
+ <div class="sidebar-header">
+ <button class="new-chat-btn" @click="createNewConversation">
+ <el-icon><plus /></el-icon>
+ <span v-if="!isCollapsed">New Chat</span>
+ </button>
+ <button class="toggle-btn" @click="toggleSidebar">
+ <el-icon><arrow-left v-if="!isCollapsed" /><arrow-right v-else /></el-icon>
+ </button>
+ </div>
+ 
+ <!-- Search box -->
+ <div class="search-box" v-if="!isCollapsed">
+ <el-input
+ v-model="searchQuery"
+ placeholder="Search conversations..."
+ prefix-icon="search"
+ clearable
+ size="small"
+ />
+ </div>
+ 
+ <!-- Conversation list -->
+ <div class="conversation-list" v-if="!isCollapsed">
+ <!-- Todays conversations -->
+ <div class="list-section" v-if="todayConversations.length > 0">
+ <div class="section-title">Today</div>
+ <div
+ v-for="conv in todayConversations"
+ :key="conv.conversation_id"
+ class="conversation-item"
+ :class="{ active: currentConversationId === conv.conversation_id }"
+ @click="selectConversation(conv)"
+ >
+ <div class="item-icon">
+ <el-icon><chat-dot-round /></el-icon>
+ </div>
+ <div class="item-content">
+ <div class="item-title">{{ conv.title }}</div>
+ <div class="item-meta">
+ <span class="gene-family" v-if="conv.gene_family">{{ conv.gene_family }}</span>
+ <span class="message-count">{{ conv.message_count }} messages</span>
+ </div>
+ <div class="item-preview">{{ conv.last_message }}</div>
+ </div>
+ <div class="item-actions" @click.stop>
+ <el-dropdown trigger="click">
+ <el-icon><more /></el-icon>
+ <template #dropdown>
+ <el-dropdown-menu>
+ <el-dropdown-item @click="renameConversation(conv)">
+ <el-icon><edit /></el-icon>Rename
+ </el-dropdown-item>
+ <el-dropdown-item @click="archiveConversation(conv)">
+ <el-icon><folder /></el-icon>Archive
+ </el-dropdown-item>
+ <el-dropdown-item divided @click="deleteConversation(conv)" type="danger">
+ <el-icon><delete /></el-icon>Delete
+ </el-dropdown-item>
+ </el-dropdown-menu>
+ </template>
+ </el-dropdown>
+ </div>
+ </div>
+ </div>
+ 
+ <!-- Yesterdays conversations -->
+ <div class="list-section" v-if="yesterdayConversations.length > 0">
+ <div class="section-title">Yesterday</div>
+ <div
+ v-for="conv in yesterdayConversations"
+ :key="conv.conversation_id"
+ class="conversation-item"
+ :class="{ active: currentConversationId === conv.conversation_id }"
+ @click="selectConversation(conv)"
+ >
+ <div class="item-icon">
+ <el-icon><chat-dot-round /></el-icon>
+ </div>
+ <div class="item-content">
+ <div class="item-title">{{ conv.title }}</div>
+ <div class="item-meta">
+ <span class="gene-family" v-if="conv.gene_family">{{ conv.gene_family }}</span>
+ <span class="message-count">{{ conv.message_count }}</span>
+ </div>
+ </div>
+ </div>
+ </div>
+ 
+ <!-- Older conversations -->
+ <div class="list-section" v-if="olderConversations.length > 0">
+ <div class="section-title">Past 7 days</div>
+ <div
+ v-for="conv in olderConversations"
+ :key="conv.conversation_id"
+ class="conversation-item"
+ :class="{ active: currentConversationId === conv.conversation_id }"
+ @click="selectConversation(conv)"
+ >
+ <div class="item-icon">
+ <el-icon><chat-dot-round /></el-icon>
+ </div>
+ <div class="item-content">
+ <div class="item-title">{{ conv.title }}</div>
+ <div class="item-meta">
+ <span class="gene-family" v-if="conv.gene_family">{{ conv.gene_family }}</span>
+ </div>
+ </div>
+ </div>
+ </div>
+ 
+ <!-- Empty state -->
+ <div v-if="filteredConversations.length === 0" class="empty-state">
+ <el-icon><chat-line-round /></el-icon>
+ <p>No conversations yet</p>
+ <p class="hint">Click "New Chat" to start gene family analysis</p>
+ </div>
+ </div>
+ 
+ <!-- footer: user info -->
+ <div class="sidebar-footer" v-if="!isCollapsed">
+ <div class="user-info">
+ <el-avatar :size="32" :icon="UserFilled" />
+ <span class="username">{{ userId }}</span>
+ </div>
+ </div>
+ </div>
+ `,
+ 
+ props: {
+ userId: {
+ type: String,
+ default: 'xia-lab'
+ },
+ apiBaseUrl: {
+ type: String,
+ default: 'http://localhost:8000/api'
+ }
+ },
+ 
+ data() {
+ return {
+ isCollapsed: false,
+ searchQuery: '',
+ conversations: [],
+ currentConversationId: null,
+ loading: false,
+ // Icons
+ Plus: ElementPlusIconsVue.Plus,
+ ArrowLeft: ElementPlusIconsVue.ArrowLeft,
+ ArrowRight: ElementPlusIconsVue.ArrowRight,
+ ChatDotRound: ElementPlusIconsVue.ChatDotRound,
+ ChatLineRound: ElementPlusIconsVue.ChatLineRound,
+ More: ElementPlusIconsVue.More,
+ Edit: ElementPlusIconsVue.Edit,
+ Folder: ElementPlusIconsVue.Folder,
+ Delete: ElementPlusIconsVue.Delete,
+ UserFilled: ElementPlusIconsVue.UserFilled,
+ }
+ },
+ 
+ computed: {
+ filteredConversations() {
+ if (!this.searchQuery) return this.conversations;
+ const query = this.searchQuery.toLowerCase();
+ return this.conversations.filter(conv => 
+ conv.title.toLowerCase().includes(query) ||
+ (conv.gene_family && conv.gene_family.toLowerCase().includes(query)) ||
+ conv.last_message.toLowerCase().includes(query)
+ );
+ },
+ 
+ todayConversations() {
+ const today = new Date().toDateString();
+ return this.filteredConversations.filter(conv => {
+ const convDate = new Date(conv.updated_at).toDateString();
+ return convDate === today;
+ });
+ },
+ 
+ yesterdayConversations() {
+ const yesterday = new Date(Date.now() - 86400000).toDateString();
+ return this.filteredConversations.filter(conv => {
+ const convDate = new Date(conv.updated_at).toDateString();
+ return convDate === yesterday;
+ });
+ },
+ 
+ olderConversations() {
+ const yesterday = new Date(Date.now() - 86400000).toDateString();
+ return this.filteredConversations.filter(conv => {
+ const convDate = new Date(conv.updated_at).toDateString();
+ return convDate < yesterday;
+ });
+ }
+ },
+ 
+ mounted() {
+ this.loadConversations();
+ // Auto-refresh
+ this.refreshInterval = setInterval(() => {
+ this.loadConversations();
+ }, 30000); // 30 seconds refresh interval
+ },
+ 
+ beforeUnmount() {
+ if (this.refreshInterval) {
+ clearInterval(this.refreshInterval);
+ }
+ },
+ 
+ methods: {
+ async loadConversations() {
+ try {
+ this.loading = true;
+ const response = await fetch(`${this.apiBaseUrl}/conversations/list/${this.userId}`);
+ if (response.ok) {
+ const data = await response.json();
+ this.conversations = data.conversations || [];
+ }
+ } catch (error) {
+ console.error('Failed to load conversations:', error);
+ // Use mock data
+ this.conversations = this.getMockConversations();
+ } finally {
+ this.loading = false;
+ }
+ },
+ 
+ getMockConversations() {
+ // Mock data for testing
+ return [
+ {
+ conversation_id: 'conv_001',
+ title: 'At.WRKY gene family analysis',
+ gene_family: 'WRKY',
+ species: 'At',
+ message_count: 12,
+ last_message: 'Phylogenetic tree done',
+ updated_at: new Date().toISOString()
+ },
+ {
+ conversation_id: 'conv_002',
+ title: 'Os.TCP evolution analysis',
+ gene_family: 'TCP',
+ species: 'Os',
+ message_count: 5,
+ last_message: 'Building tree...',
+ updated_at: new Date(Date.now() - 3600000).toISOString()
+ },
+ {
+ conversation_id: 'conv_003',
+ title: 'HMMER config consultation',
+ message_count: 8,
+ last_message: 'E-value 1e-5 recommended',
+ updated_at: new Date(Date.now() - 86400000).toISOString()
+ }
+ ];
+ },
+ 
+ toggleSidebar() {
+ this.isCollapsed = !this.isCollapsed;
+ this.$emit('toggle', this.isCollapsed);
+ },
+ 
+ async createNewConversation() {
+ try {
+ const response = await fetch(`${this.apiBaseUrl}/conversations/create`, {
+ method: 'POST',
+ headers: { 'Content-Type': 'application/json' },
+ body: JSON.stringify({
+ user_id: this.userId,
+ title: 'New Chat ' + new Date().toLocaleTimeString()
+ })
+ });
+ 
+ if (response.ok) {
+ const data = await response.json();
+ this.currentConversationId = data.conversation_id;
+ this.$emit('new-conversation', data);
+ await this.loadConversations();
+ }
+ } catch (error) {
+ console.error('Failed to create conversation:', error);
+ // Create local conversation
+ const newConv = {
+ conversation_id: 'conv_' + Date.now(),
+ title: 'New Chat',
+ message_count: 0,
+ last_message: '',
+ updated_at: new Date().toISOString()
+ };
+ this.conversations.unshift(newConv);
+ this.currentConversationId = newConv.conversation_id;
+ this.$emit('new-conversation', newConv);
+ }
+ },
+ 
+ selectConversation(conv) {
+ this.currentConversationId = conv.conversation_id;
+ this.$emit('select-conversation', conv);
+ },
+ 
+ async renameConversation(conv) {
+ const newTitle = prompt('Enter new title:', conv.title);
+ if (newTitle && newTitle !== conv.title) {
+ try {
+ await fetch(`${this.apiBaseUrl}/conversations/update-title`, {
+ method: 'POST',
+ headers: { 'Content-Type': 'application/json' },
+ body: JSON.stringify({
+ conversation_id: conv.conversation_id,
+ title: newTitle
+ })
+ });
+ conv.title = newTitle;
+ } catch (error) {
+ console.error('Failed to rename:', error);
+ conv.title = newTitle; // local update
+ }
+ }
+ },
+ 
+ async archiveConversation(conv) {
+ try {
+ await fetch(`${this.apiBaseUrl}/conversations/archive`, {
+ method: 'POST',
+ headers: { 'Content-Type': 'application/json' },
+ body: JSON.stringify({
+ conversation_id: conv.conversation_id
+ })
+ });
+ await this.loadConversations();
+ } catch (error) {
+ console.error('Failed to archive:', error);
+ }
+ },
+ 
+ async deleteConversation(conv) {
+ if (confirm(`Delete conversation "${conv.title}"?`)) {
+ try {
+ await fetch(`${this.apiBaseUrl}/conversations/delete`, {
+ method: 'POST',
+ headers: { 'Content-Type': 'application/json' },
+ body: JSON.stringify({
+ conversation_id: conv.conversation_id
+ })
+ });
+ await this.loadConversations();
+ if (this.currentConversationId === conv.conversation_id) {
+ this.currentConversationId = null;
+ this.$emit('select-conversation', null);
+ }
+ } catch (error) {
+ console.error('Failed to delete:', error);
+ }
+ }
+ }
+ }
 };
 
-// 导出组件
+// Export component
 if (typeof module !== 'undefined' && module.exports) {
-    module.exports = { ConversationSidebar };
+ module.exports = { ConversationSidebar };
 }

apps/web/vue3/static/i18n_en.js

@@ -0,0 +1,380 @@
+window.__I18N_EN__ = {
+  "Agent状态": "AgentStatus",
+  "Self-RAG反思": "Self-RAG Reflection",
+  "三角形": "Triangle",
+  "下一步": "Next Step",
+  "下载": "Download",
+  "不受支持标记处理策略": "Unsupported Marker Handling Policy",
+  "中性替换率": "Neutral Substitution Rate",
+  "中性速率": "Neutral Rate",
+  "中文": "Chinese",
+  "丰度引擎": "Abundance Engine",
+  "主参考": "Primary Reference",
+  "主参考物种": "Primary reference species",
+  "主要结果": "Main Results",
+  "亚家族分类确认": "Subfamily Classification Confirmation",
+  "亚家族名称距离": "Subfamily Name Distance",
+  "亚家族外圈弧线": "Subfamily Outer Arc",
+  "亚家族确认参数": "Subfamily Confirmation Parameters",
+  "交集": "Intersection",
+  "仅圈图": "Circle Plot Only",
+  "仅比较物种": "Comparative Species Only",
+  "仅目标": "Target Only",
+  "仅目标物种": "Target Species Only",
+  "仅矩形图": "Rectangular Only",
+  "任务列表": "Task List",
+  "位置分布图": "Position Distribution Map",
+  "使用拟南芥作为显式兜底": "Use Arabidopsis as Explicit Fallback",
+  "使用推荐区间": "Use Recommended Range",
+  "保存方法学方案": "Save Methodology Plan",
+  "保留": "Retain",
+  "修订": "Revision",
+  "倒计时已暂停": "Countdown paused",
+  "全屏": "Full Screen",
+  "全屏展示": "Full Screen Display",
+  "全部": "All",
+  "全部行": "All Rows",
+  "关系总数": "Total Edges",
+  "关闭": "Close",
+  "内容": "Content",
+  "内置物种代码": "Built-in Species Code",
+  "分析家族": "Analysis Family",
+  "分组角色": "Group Role",
+  "分组角色不改": "Group Role (Unchanged)",
+  "删除": "Deleted",
+  "删除会话": "Delete Session",
+  "刷新": "Refresh",
+  "刷新结果": "Refresh Results",
+  "前景基因": "Foreground Genes",
+  "功能类别": "Feature Category",
+  "加入正式列表": "Add to Formal List",
+  "包含关键词": "Contains Keyword",
+  "匹配方式": "Match Mode",
+  "匹配行": "Matched Rows",
+  "原因": "Reason",
+  "原始代码": "Original Code",
+  "原始命令": "Original Command",
+  "原始文件名": "Original Filename",
+  "原始证据": "Original Evidence",
+  "原推荐参考": "Original Recommended Reference",
+  "参数": "Parameters",
+  "参考分类": "Reference Classification",
+  "参考前缀": "Reference Prefix",
+  "参考基因": "Reference Gene",
+  "参考基因编号": "Reference Gene ID",
+  "参考文献": "References",
+  "参考物种": "Reference Species",
+  "发送": "Send",
+  "取消": "Cancel",
+  "取消预览": "Cancel Preview",
+  "只会执行已勾选且可执行的阶段": "Only checked and executable stages will run",
+  "可改": "Editable",
+  "同时处理的样本数": "Number of Samples Processed Simultaneously",
+  "名称": "Name",
+  "后续主参考物种": "Downstream Primary Reference Species",
+  "启动子元件": "Promoter Elements",
+  "启动子自定义绘图": "Promoter Custom Plot",
+  "图例颜色": "Legend Color",
+  "图类型": "Plot Type",
+  "图表标题清单": "Chart Title List",
+  "图表标题驱动复现规划预览": "Chart Title-Driven Reproduction Plan Preview",
+  "圆形": "Circle",
+  "基因注释": "Gene Annotation",
+  "基本参数": "Basic Parameters",
+  "基础参数": "Basic Parameters",
+  "处理中...": "Processing...",
+  "处理方式": "Processing Method",
+  "多物种处理方式": "Multi-species Processing",
+  "大小": "Size",
+  "定量模式": "Quantification Mode",
+  "实验设计": "Experimental Design",
+  "实验设计模块": "Experimental Design Module",
+  "审核备注": "Review Notes",
+  "富集类型": "Enrichment Type",
+  "差异表达范围": "Differential Expression Scope",
+  "已写阶段": "Registered Stages",
+  "已完成": "Completed",
+  "已完成阶段": "Completed Stages",
+  "已应用": "Applied",
+  "建议参数": "Suggested Parameters",
+  "开始验证": "Start Validation",
+  "弧线避让距离": "Arc Avoidance Distance",
+  "当前参数": "Current Parameters",
+  "当前参考物种": "Current Reference Species",
+  "当前选择": "Current Selection",
+  "待补数据": "Awaiting Data",
+  "必填": "Required",
+  "我知道了": "Got It",
+  "手动区间": "Manual Range",
+  "执行": "Execute",
+  "扫描双链": "Scan Both Strands",
+  "批量执行确认": "Batch Execution Confirmation",
+  "拉丁名": "Latin Name",
+  "拓展分析运行参数确认": "Extension Analysis Run Parameter Confirmation",
+  "拓展分析阶段": "Extension Analysis Stage",
+  "拓展分析阶段状态": "Extension Analysis Stage Status",
+  "拓展分析阶段确认": "Extension Analysis Stage Confirmation",
+  "拓展分析阶段运行结果": "Extension Analysis Stage Run Result",
+  "按元件": "By Element",
+  "按单个物种分别分析与确认": "Per-Species Analysis & Confirmation",
+  "按当前筛选重建成员蛋白": "Rebuild Member Proteins by Current Filter",
+  "按类别": "By Category",
+  "授权发布": "Authorize Publish",
+  "推荐参考数据下载失败": "Recommended Ref Data Download Failed",
+  "提出修订意见": "Submit Revision Suggestions",
+  "操作": "Operation",
+  "数据准备": "Data Preparation",
+  "数据路径": "Data Path",
+  "数据需求": "Data Needs",
+  "文件": "File",
+  "文件类型": "File Type",
+  "文件范围": "File Scope",
+  "文献参数": "Literature Parameters",
+  "文献工具": "Literature Tools",
+  "文章涉及物种与下载入口": "Article Species & Download Entry",
+  "新增": "Added",
+  "方形": "Square",
+  "方法参考": "Method Reference",
+  "方法学文献": "Methodology Papers",
+  "无": "None",
+  "明确指定": "Explicitly Specify",
+  "显示": "Show",
+  "暂停倒计时": "Pause Countdown",
+  "暂无已上传文件": "No Uploaded Files Yet",
+  "暂无拓展分析阶段结果": "No Extension Analysis Stage Results Yet",
+  "暂无状态记录": "No Status Record Yet",
+  "最大宽度": "Max Width",
+  "最小宽度": "Min Width",
+  "最小非缺口比例": "Min Non-gap Ratio",
+  "最近到属": "Closest to Genus",
+  "最近到目": "Closest to Order",
+  "最近到科": "Closest to Family",
+  "最近到纲": "Closest to Class",
+  "有损转换警告": "Lossy Conversion Warning",
+  "服务器测试数据路径": "Server Test Data Path",
+  "未从图表标题推断出额外阶段": "No Additional Stages Inferred from Chart Titles",
+  "未提取到图表标题": "No Chart Title Extracted",
+  "未识别到内置下载链接": "No Built-in DL Link Identified",
+  "未识别到参数": "No Parameters Identified",
+  "未识别到文献工具": "No Literature Tool Identified",
+  "本次成员鉴定物种": "Current Member Identification Species",
+  "来源": "Sources",
+  "染色体标注位置": "Chromosome Annotation Position",
+  "染色体标注大小": "Chromosome Annotation Size",
+  "染色体策略": "Chromosome Strategy",
+  "染色体色块粗细": "Chromosome Block Width",
+  "查看本次知识检索过程": "View knowledge retrieval process",
+  "标记大小": "Mark Size",
+  "标记模式": "Mark Mode",
+  "标题推断的候选阶段": "Candidate Stages Inferred from Titles",
+  "树枝粗细": "Branch Width",
+  "树枝颜色": "Branch Color",
+  "样本并行数量": "Sample Parallel Count",
+  "检索结果": "Retrieval Results",
+  "检索表格内容": "Search Table Content",
+  "正则匹配": "Regex Match",
+  "此拓展阶段没有可配置参数": "No Configurable Parameters",
+  "测试数据": "Test Data",
+  "涉及阶段": "Involved Stages",
+  "添加行": "Add Row",
+  "灰色": "Gray",
+  "物种": "Species",
+  "物种代码": "Species Code",
+  "物种代码不改": "Species Code (Unchanged)",
+  "物种名": "Species Name",
+  "物种角色": "Species Role",
+  "物种角色不改": "Species Role (Unchanged)",
+  "环境": "Environment",
+  "留空则自动发现": "Leave empty for auto-discovery",
+  "目标前缀": "Target Prefix",
+  "目标物种": "Target Species",
+  "知识图谱": "Knowledge Graph",
+  "确定": "Confirm",
+  "确认亚家族标签": "Confirm Subfamily Labels",
+  "确认保存": "Confirm Save",
+  "确认并写入正式配置": "Confirm & Write to Official Config",
+  "确认并执行": "Confirm & Execute",
+  "确认执行": "Confirm Execution",
+  "确认自动注释": "Confirm Auto-Annotation",
+  "确认重绘": "Confirm Replot",
+  "种间共线性比较物种": "Interspecies Synteny Comparative Species",
+  "种间共线性绘图设置": "Interspecies Synteny Plot Settings",
+  "移除": "Remove",
+  "窗口长度": "Window Length",
+  "类型": "Types",
+  "精确匹配": "Exact Match",
+  "红色": "Red",
+  "终止位点": "End Site",
+  "终止残基": "End Residue",
+  "绘图模式": "Plot Mode",
+  "绿色": "Green",
+  "置信度": "Confidence",
+  "置信度阈值": "Confidence Threshold",
+  "群体遗传输入": "Population Genetic Input",
+  "背景来源": "Background Source",
+  "背景知识": "Background knowledge",
+  "自动": "Auto",
+  "自动从注释提取": "Auto-extract from Annotation",
+  "自动保守窗口": "Auto Conserved Window",
+  "自动判断": "Auto-detect",
+  "节点名称": "Node Name",
+  "节点总数": "Total Nodes",
+  "节点类型": "Node Types",
+  "菱形": "Diamond",
+  "蓝色": "Blue",
+  "蛋白": "Protein",
+  "蛋白文件": "Protein Files",
+  "表达矩阵": "Expression Matrix",
+  "诊断动作": "Diagnostic Actions",
+  "说明": "Description",
+  "请先试运行以记录真实输出": "Please Run a Trial First to Record Actual Output",
+  "请选择共线性分析类型": "Please select synteny analysis type",
+  "请选择模式物种": "Select Model Species",
+  "起始位点": "Start Site",
+  "起始残基": "Start Residue",
+  "跳数": "Hops",
+  "输出": "Output",
+  "输出前缀": "Output Prefix",
+  "输出标签": "Output Label",
+  "运行值": "Run Value",
+  "运行结果": "Run Result",
+  "进化树图修订参数": "Phylogenetic Tree Revision Parameters",
+  "连接关系数": "Connections",
+  "迭代": "Iteration",
+  "选择其他提取结果": "Select Other Extraction Result",
+  "选择工具": "Select Tool",
+  "选择已完成撰写的拓展阶段": "Select Completed Extension Stage",
+  "通常留空": "Usually leave empty",
+  "重写查询": "Rewrite Query",
+  "重新生成说明": "Regenerate Description",
+  "重置": "Reset",
+  "重置视图": "Reset View",
+  "链接": "Link",
+  "链特异性": "Library Strandedness",
+  "隐藏": "Hide",
+  "需检查": "Needs Review",
+  "需要补充": "Need to Supplement",
+  "非时间实验留空": "Leave empty for non-time experiments",
+  "项目": "Project",
+  "预览": "Preview",
+  "预览到表格": "Preview to Table",
+  "预览命令": "Preview Commands",
+  "黑色": "Black",
+  "默认值": "Default Value",
+  "提取方法学": "Extract",
+  "刷新记录": "Refresh",
+  "打开最新提取结果": "Open Latest Extraction",
+  "查看最新提取状态": "View Latest Status",
+  "打开所选提取结果": "Open Selected Extraction",
+  "查看所选提取状态": "View Selected Status",
+  "生成并发布": "Generate & Publish",
+  "运行已发布": "Run Published",
+  "当前会话": "Current Session",
+  "更多会话": "More Sessions",
+  "新建": "New",
+  "新建会话": "New Session",
+  "使用小Tip": "Tips",
+  "一、分析模块快速指令": "1. Analysis Module Quick Commands",
+  "选择输入框上方\"Analysis\"": "Select \"Analysis\" above input box",
+  "粘贴数据位置": "Paste data location",
+  "核对配置文件": "Review config files",
+  "执行数据准备": "Run data preparation",
+  "执行XX物种的亚家族分类": "Run subfamily classification for XX species",
+  "执行XX物种的基因家族分析": "Run gene family analysis for XX species",
+  "执行rnaseq分析": "Run RNA-seq analysis",
+  "二、文章复现步骤": "2. Article Reproduction Steps",
+  "点击\"浏览\"上传文献": "Click \"Browse\" to upload paper",
+  "点击提取方法学": "Click Extract Methodology",
+  "核对分析步骤": "Review analysis steps",
+  "点击保存方案": "Click Save Plan",
+  "上传数据": "Upload data",
+  "发送\"按已保存的方法学方案继续执行\"": "Send \"Continue with saved methodology plan\"",
+  "三、RAG快速指令": "3. RAG Quick Commands",
+  "选择输入框上方\"RAG\"": "Select \"RAG\" above input box",
+  "输入问题": "Enter question",
+  "点击\"知识图谱\"查看关系": "Click \"Knowledge Graph\" to view relations",
+  "知识图谱": "Knowledge Graph",
+  "重新加载": "Reload",
+  "重置视图": "Reset View",
+  "2.2 MSA Replot / 区间重绘": "2.2 MSA Replot",
+  "2.3 Tree Replot / 进化树重绘": "2.3 Tree Replot",
+  "2.5 亚家族确认": "2.5 Subfamily Confirmation",
+  "6.1 启动子自定义绘图": "6.1 Promoter Custom Plot",
+  "7️⃣ 种内Synteny": "7️⃣ Intraspecies Synteny",
+  "7.1 种内共线性 Circos 重绘": "7.1 Intraspecies Synteny Circos Replot",
+  "8️⃣ Karyotype": "8️⃣ Karyotype",
+  "9️⃣ 种间Synteny": "9️⃣ Interspecies Synteny",
+  "基因家族": "Gene Family",
+  "WGS2GWAS（遗传变异与群体分析）": "WGS2GWAS",
+  "基因家族 promoter 扫描": "Gene family promoter scanning",
+  "新会话": "New Session",
+  "新会话已创建，请选择或创建 Working Directory": "New session created. Please select or create a Working Directory",
+  "创建会话失败": "Failed to create session",
+  "会话已删除": "Session deleted",
+  "删除会话失败": "Failed to delete session",
+  "对话历史已清空": "Chat history cleared",
+  "错误日志已清空": "Error logs cleared",
+  "重启 Celery": "Restart Celery",
+  "重启项目": "Restart Project",
+  "提交配置好的项目重启脚本": "Submit configured project restart script",
+  "未配置 PLANTAI_RESTART_SCRIPT 或 restart_plantai_9000.sh": "PLANTAI_RESTART_SCRIPT or restart_plantai_9000.sh not configured",
+  "未配置项目重启脚本": "Project restart script not configured",
+  "这会提交项目重启脚本，当前页面可能短暂断开。": "This will submit the project restart script. The page may briefly disconnect.",
+  "确认重启": "Confirm Restart",
+  "项目重启脚本已提交": "Project restart script submitted",
+  "项目重启未提交": "Project restart not submitted",
+  "基因家族鉴定": "Gene Family Identification",
+  "系统发育分析": "Phylogenetic Analysis",
+  "Motif分析": "Motif Analysis",
+  "结构域分析": "Domain Analysis",
+  "基因结构分析": "Gene Structure Analysis",
+  "启动子元件预测": "Promoter Element Prediction",
+  "TF结合位点预测": "TF Binding Site Prediction",
+  "种内共线性分析": "Intraspecies Synteny Analysis",
+  "种间共线性分析": "Interspecies Synteny Analysis",
+  "核型/染色体分布分析": "Karyotype/Chromosome Distribution",
+  "PPI分析": "PPI Analysis",
+  "Ka/Ks分析": "Ka/Ks Analysis",
+  "蛋白理化性质与亚细胞定位": "Protein Properties & Subcellular Localization",
+  "表达矩阵分析": "Expression Matrix Analysis",
+  "RNA-seq QC": "RNA-seq QC",
+  "RNA-seq Align": "RNA-seq Align",
+  "RNA-seq Quant": "RNA-seq Quant",
+  "RNA-seq Sample QC": "RNA-seq Sample QC",
+  "GWAS VCF排序与HapMap转换": "GWAS VCF Sort & HapMap Conversion",
+  "GWAS TASSEL亲缘关系矩阵": "GWAS TASSEL Kinship Matrix",
+  "GWAS表型准备": "GWAS Phenotype Preparation",
+  "GWAS协变量准备": "GWAS Covariate Preparation",
+  "GWAS TASSEL MLM/CMLM": "GWAS TASSEL MLM/CMLM",
+  "GWAS MLM/CMLM绘图": "GWAS MLM/CMLM Plotting",
+  "GWAS EMMAX": "GWAS EMMAX",
+  "GWAS EMMAX绘图": "GWAS EMMAX Plotting",
+  "GWAS TASSEL GLM": "GWAS TASSEL GLM",
+  "群体PCA分析": "Population PCA Analysis",
+  "群体系统树分析": "Population Phylogenetic Tree",
+  "群体结构分析": "Population Structure Analysis",
+  "群体LD衰减分析": "Population LD Decay Analysis",
+  "SNP密度分析": "SNP Density Analysis",
+  "RNA-seq DE": "RNA-seq DE",
+  "组合图": "Combo Plot",
+  "参考亚家族分类": "Reference Subfamily Classification",
+  "亚家族标签确认": "Subfamily Label Confirmation",
+  "PPI/KaKs 参考数据": "PPI/KaKs Reference Data",
+  "PPI/KaKs 兜底确认": "PPI/KaKs Fallback Confirmation",
+  "亚家族确认输出": "Subfamily Confirmation Output",
+  "MSA区间重绘": "MSA Region Replot",
+  "MSA区间重绘已提交": "MSA Replot submitted",
+  "MSA区间重绘完成": "MSA Replot completed",
+  "MSA区间重绘失败": "MSA Replot failed",
+  "启动子自定义绘图已提交": "Promoter custom plot submitted",
+  "启动子自定义绘图完成": "Promoter custom plot completed",
+  "启动子自定义绘图失败": "Promoter custom plot failed",
+  "种内共线性 Circos 重绘已提交": "Intraspecies Circos replot submitted",
+  "种内共线性 Circos 重绘完成，已切换到新图": "Intraspecies Circos replot completed, switched to new figure",
+  "种内共线性 Circos 重绘失败": "Intraspecies Circos replot failed",
+  "亚家族确认 - Reference Classification": "Subfamily Confirmation - Reference Classification",
+  "这会停止当前 profile 的 Celery worker 并重新启动。若有任务正在运行，后端会默认拒绝执行。": "This will stop and restart the Celery worker for the current profile. Running tasks will be rejected by default.",
+  "Celery 已重启并完成队列检查": "Celery restarted and queue check complete",
+  "Celery 重启未完成": "Celery restart incomplete"
+};
+