merge-cli 2.0.2__tar.gz → 3.0.0__tar.gz

{merge_cli-2.0.2 → merge_cli-3.0.0}/PKG-INFO

@@ -1,13 +1,12 @@
 Metadata-Version: 2.4
 Name: merge-cli
-Version: 2.0.2
-Summary: MERGE 变异致病性预测 CLI（支持远程服务器和完全本地模式）
-Project-URL: Homepage, https://github.com/your-org/merge-cli
+Version: 3.0.0
+Summary: MERGE 变异致病性预测 CLI（服务器固定，集成模型内嵌，无需手动配置）
+Project-URL: Homepage, https://merge.fanglab.cn
 Requires-Python: >=3.11
 Requires-Dist: click>=8.1
 Requires-Dist: rich>=13.0
 Requires-Dist: requests>=2.31
-Requires-Dist: keyring>=24.0
 Requires-Dist: pysam>=0.22; sys_platform != "win32"
 Requires-Dist: numpy>=1.26
 Requires-Dist: pandas>=2.1

{merge_cli-2.0.2 → merge_cli-3.0.0}/merge_cli/api.py

@@ -1,44 +1,31 @@
 """
-merge_cli/api.py
+merge_cli/api.py  —  v3.0.0
 封装所有对 Django 后端的 HTTP 请求。
-每个函数对应 views.py 里的一个端点，参数名与 views.py 完全一致。
+服务器地址固定为 https://merge.fanglab.cn/，无需 Token 认证。
 """
 import sys
 from typing import Optional
 
 import requests
 
-from .config import get_api_url, get_token
+from .config import FIXED_API_URL
 
-# 所有请求的默认超时（秒）
-_TIMEOUT_SINGLE = 180   # 单变异：Evo2 最慢，约 2 分钟
-_TIMEOUT_BATCH  = 60    # 批量提交：只是上传文件，后台异步处理
+_TIMEOUT_SINGLE = 180
+_TIMEOUT_BATCH  = 60
 
-
-def _headers() -> dict:
-    token = get_token()
-    h = {"Accept": "application/json"}
-    if token:
-        h["Authorization"] = f"Token {token}"
-    return h
+_BASE = FIXED_API_URL
 
 
-def _base() -> str:
-    url = get_api_url()
-    if not url:
-        print("错误：未配置 API 地址。请先运行：merge config set-url https://your-server.com")
-        sys.exit(1)
-    return url
+def _headers() -> dict:
+    return {"Accept": "application/json"}
 
 
 # ─────────────────────────────────────────────────────────────
 # 1. 单变异预测  POST /predict/
-# 对应 views.py: combined_prediction_view
 # ─────────────────────────────────────────────────────────────
 def predict_single(
     chrom: str, pos: int, ref: str, alt: str,
     genome_version: str = "hg38",
-    # 模型开关，与 views.py POST 参数名一一对应
     use_alphagenome:   bool = True,
     use_hyenadna:      bool = True,
     use_nt:            bool = True,
@@ -49,10 +36,6 @@ def predict_single(
     use_evo2:          bool = True,
     use_evo1:          bool = True,
 ) -> dict:
-    """
-    调用 /predict/ 端点，返回完整 prediction 字典。
-    包含 dbnsfp / alphagenome / hyenadna / nt / gpn_msa / popeve / evo2 / evo1 / errors。
-    """
     payload = {
         "chr": chrom, "pos": pos, "ref": ref, "alt": alt,
         "genome_version": genome_version,
@@ -67,7 +50,7 @@ def predict_single(
         "use_evo1":          str(use_evo1).lower(),
     }
     resp = requests.post(
-        f"{_base()}/predict/",
+        f"{_BASE}/predict/",
         json=payload,
         headers=_headers(),
         timeout=_TIMEOUT_SINGLE,
@@ -78,17 +61,11 @@ def predict_single(
 
 # ─────────────────────────────────────────────────────────────
 # 2. 集成模型评分  POST /ensemble/
-# 对应 views.py: ensemble_predict_view
-# 通常在 predict_single 成功后自动调用
 # ─────────────────────────────────────────────────────────────
 def predict_ensemble(prediction: dict, all_transcripts: list) -> dict:
-    """
-    用 /predict/ 返回的 prediction 字典再调用 /ensemble/，
-    获取 MERGE 集成得分和 SHAP 图（base64 PNG）。
-    """
     payload = {"prediction": prediction, "all_transcripts": all_transcripts}
     resp = requests.post(
-        f"{_base()}/ensemble/",
+        f"{_BASE}/ensemble/",
         json=payload,
         headers=_headers(),
         timeout=_TIMEOUT_SINGLE,
@@ -99,7 +76,6 @@ def predict_ensemble(prediction: dict, all_transcripts: list) -> dict:
 
 # ─────────────────────────────────────────────────────────────
 # 3. 批量提交  POST /api/submit_batch_job/
-# 对应 views.py: submit_batch_job
 # ─────────────────────────────────────────────────────────────
 def submit_batch(
     vcf_path: str,
@@ -115,10 +91,6 @@ def submit_batch(
     use_evo2:          bool = True,
     use_evo1:          bool = True,
 ) -> dict:
-    """
-    上传 VCF 文件，异步批量预测，结果发送至 email。
-    返回 job_id 供后续查询状态。
-    """
     data = {
         "notify_email":    email,
         "genome_version":  genome_version,
@@ -134,7 +106,7 @@ def submit_batch(
     }
     with open(vcf_path, "rb") as f:
         resp = requests.post(
-            f"{_base()}/api/submit_batch_job/",
+            f"{_BASE}/api/submit_batch_job/",
             data=data,
             files={"vcf_file": (vcf_path.split("/")[-1], f)},
             headers=_headers(),
@@ -146,45 +118,12 @@ def submit_batch(
 
 # ─────────────────────────────────────────────────────────────
 # 4. 查询批量任务状态  GET /api/batch_job/<job_id>/
-# 对应 views.py: batch_job_status
 # ─────────────────────────────────────────────────────────────
 def get_batch_status(job_id: str) -> dict:
     resp = requests.get(
-        f"{_base()}/api/batch_job/{job_id}/",
+        f"{_BASE}/api/batch_job/{job_id}/",
         headers=_headers(),
         timeout=30,
     )
     resp.raise_for_status()
     return resp.json()
-
-
-# ─────────────────────────────────────────────────────────────
-# 5. 开放注册  POST /api/register/
-# 对应 views.py: register_and_get_token
-# 公开接口，不需要携带 Token
-# ─────────────────────────────────────────────────────────────
-def register(username: str, email: str, password: str) -> dict:
-    resp = requests.post(
-        f"{_base()}/api/register/",
-        json={"username": username, "email": email, "password": password},
-        headers={"Content-Type": "application/json", "Accept": "application/json"},
-        timeout=30,
-    )
-    resp.raise_for_status()
-    return resp.json()
-
-
-# ─────────────────────────────────────────────────────────────
-# 6. 已有账号重新登录取 Token  POST /api/login/
-# 对应 views.py: login_and_get_token
-# 公开接口，不需要携带 Token
-# ─────────────────────────────────────────────────────────────
-def login(username: str, password: str) -> dict:
-    resp = requests.post(
-        f"{_base()}/api/login/",
-        json={"username": username, "password": password},
-        headers={"Content-Type": "application/json", "Accept": "application/json"},
-        timeout=30,
-    )
-    resp.raise_for_status()
-    return resp.json()