MCP Client  <──stdio──>  mcp_server  <──HTTP/JSON──>  backend_service
                                                     ├── Django Ninja API
                                                     ├── django-q2 worker
                                                     ├── PlantCARE provider
                                                     └── 分析结果存储

gene-family-mcp/
├── mcp_server/
│   ├── server.py             # MCP tools 和 stdio 入口
│   ├── backend_client.py     # 后端 HTTP client
│   ├── settings.py           # MCP 侧配置
│   └── requirements.txt
├── backend_service/
│   ├── config/               # Django 配置与 API 路由
│   ├── core/                 # 健康检查等基础 API
│   ├── cis_elements/         # PlantCARE API 与 provider 原型
│   ├── jobs/                 # 业务任务、事件、产物与 q2 worker 入口
│   │   └── local_tools/      # MAFFT、FastTree 适配器与能力探测
│   ├── scripts/              # PlantCARE 独立调试脚本
│   ├── tests/fixtures/       # 测试输入
│   ├── manage.py
│   └── requirements.txt
├── docs/
│   ├── architecture.md       # 架构边界与演进方案
│   ├── operations.md         # 部署、备份与故障排查
│   └── plantcare-cli.md      # 独立脚本使用说明
└── README.md

python -m venv venv
.\venv\Scripts\python.exe -m pip install -r .\requirements-dev.txt

$env:BACKEND_API_TOKEN = "replace-with-a-random-token"
$env:GENE_FAMILY_BACKEND_TOKEN = $env:BACKEND_API_TOKEN

$env:MAFFT_EXECUTABLE = "mafft"
$env:FASTTREE_EXECUTABLE = "FastTree"

$env:PLANTCARE_EMAIL = "your-email@qq.com"
$env:PLANTCARE_AUTH_CODE = "your-imap-auth-code"
$env:PLANTCARE_IMAP_HOST = "imap.qq.com"

Set-Location .\backend_service
..\venv\Scripts\python.exe manage.py migrate
..\venv\Scripts\python.exe manage.py runserver

Set-Location .\backend_service
..\venv\Scripts\python.exe manage.py qcluster

$env:GENE_FAMILY_BACKEND_URL = "http://127.0.0.1:8000/api"
.\venv\Scripts\python.exe -m mcp_server.server

$headers = @{ Authorization = "Bearer $env:BACKEND_API_TOKEN" }

$body = @{
  analysis_type = "cis_elements"
  parameters = @{ sequence = "ACGTACGTNNACGT" }
} | ConvertTo-Json -Depth 3
Invoke-RestMethod `
  -Method Post `
  -Uri http://127.0.0.1:8000/api/jobs `
  -Headers $headers `
  -ContentType application/json `
  -Body $body

Invoke-RestMethod `
  -Uri http://127.0.0.1:8000/api/jobs/<job_id> `
  -Headers $headers

$input = Invoke-RestMethod `
  -Method Post `
  -Uri http://127.0.0.1:8000/api/inputs/fasta `
  -Headers $headers `
  -ContentType application/json `
  -Body (@{
    filename = "family.fa"
    content = ">gene1`nACGTACGT`n>gene2`nACGTTCGT`n>gene3`nACGGACGT`n"
  } | ConvertTo-Json)

$jobBody = @{
  analysis_type = "fasta_validation"
  parameters = @{
    input_artifact_id = $input.input_artifact_id
    alphabet = "auto"
  }
} | ConvertTo-Json -Depth 3

Invoke-RestMethod `
  -Method Post `
  -Uri http://127.0.0.1:8000/api/jobs `
  -Headers $headers `
  -ContentType application/json `
  -Body $jobBody

$workflowBody = @{
  analysis_type = "sequence_phylogeny"
  parameters = @{
    input_artifact_id = $input.input_artifact_id
    alphabet = "dna"
    alignment_strategy = "auto"
    tree_model = "auto"
    threads = 2
  }
} | ConvertTo-Json -Depth 3

Invoke-RestMethod `
  -Method Post `
  -Uri http://127.0.0.1:8000/api/jobs `
  -Headers $headers `
  -ContentType application/json `
  -Body $workflowBody

flowchart LR
    A["输入序列或基因 ID"] --> B["标准化与校验"]
    B --> C["同源检索"]
    C --> D["结构域验证"]
    D --> E["多序列比对"]
    E --> F["系统发育树"]
    D --> G["基因结构与保守基序"]
    D --> H["启动子顺式元件"]
    F --> I["家族结果与报告"]
    G --> I
    H --> I

.\scripts\check.ps1