修改测试案例

backend/app/utils/docker_client.py

@@ -7,6 +7,7 @@ import logging
 import time
 from pathlib import Path
 from typing import Dict, Any, Optional, List
+import sys
 
 try:
     import docker  # type: ignore
@@ -76,6 +77,14 @@ class DockerContainerManager:
         remove: bool = True,
     ) -> Dict[str, Any]:
         """在容器中执行命令，返回执行结果。"""
+        # 确保挂载目录存在且可写
+        for host_path, spec in volumes.items():
+            p = Path(host_path)
+            p.mkdir(parents=True, exist_ok=True)
+            try:
+                p.chmod(0o777)
+            except Exception:
+                pass
         if self._engine == "docker-sdk" and self._client is not None:
             return self._run_with_docker_sdk(
                 command, volumes, environment, working_dir, name, detach, remove
@@ -144,12 +153,36 @@ class DockerContainerManager:
         threads: int = 4,
         **kwargs: Any,
     ) -> Dict[str, Any]:
-        """在容器中运行 BtToxin_Digger 主分析（工作目录挂载到 /workspace）。"""
+        """在容器中运行 BtToxin_Digger 主分析（单目录方案）。"""
-        command: List[str] = [
+
+        # 1) 在宿主输出目录下准备 input_files，并复制输入文件
+        work_input_dir = (output_dir / "input_files").resolve()
+        work_input_dir.mkdir(parents=True, exist_ok=True)
+
+        import shutil
+        if sequence_type == "nucl":
+            pattern = f"*{scaf_suffix}"
+        elif sequence_type == "orfs":
+            pattern = f"*{kwargs.get('orfs_suffix', '.ffn')}"
+        elif sequence_type == "prot":
+            pattern = f"*{kwargs.get('prot_suffix', '.faa')}"
+        elif sequence_type == "reads":
+            pattern = "*"
+        else:
+            pattern = "*"
+
+        copied_files = 0
+        for f in input_dir.glob(pattern):
+            if f.is_file():
+                shutil.copy2(f, work_input_dir / f.name)
+                copied_files += 1
+        logger.info(f"已复制 {copied_files} 个输入文件到 {work_input_dir}")
+
+        base_cmd: List[str] = [
             "/usr/local/env-execute",
             "BtToxin_Digger",
             "--SeqPath",
-            "/data/input",
+            "/workspace/input_files",
             "--SequenceType",
             sequence_type,
             "--threads",
@@ -157,32 +190,32 @@ class DockerContainerManager:
         ]
 
         if sequence_type == "nucl":
-            command += ["--Scaf_suffix", scaf_suffix]
+            base_cmd += ["--Scaf_suffix", scaf_suffix]
         elif sequence_type == "orfs":
-            command += ["--orfs_suffix", kwargs.get("orfs_suffix", ".ffn")]
+            base_cmd += ["--orfs_suffix", kwargs.get("orfs_suffix", ".ffn")]
         elif sequence_type == "prot":
-            command += ["--prot_suffix", kwargs.get("prot_suffix", ".faa")]
+            base_cmd += ["--prot_suffix", kwargs.get("prot_suffix", ".faa")]
         elif sequence_type == "reads":
             platform = kwargs.get("platform", "illumina")
-            command += ["--platform", platform]
+            base_cmd += ["--platform", platform]
             if platform == "illumina":
                 r1 = kwargs.get("reads1_suffix", "_R1.fastq.gz")
                 r2 = kwargs.get("reads2_suffix", "_R2.fastq.gz")
                 sfx = kwargs.get("suffix_len") or len(r1)
-                v = self.validate_reads_filenames(input_dir, platform, r1, r2, sfx)
+                v = self.validate_reads_filenames(work_input_dir, platform, r1, r2, sfx)
                 if not v.get("valid"):
                     raise ValueError(f"Reads 文件验证失败: {v.get('error')}")
                 sfx = v.get("suggested_suffix_len", sfx)
-                command += ["--reads1", r1, "--reads2", r2, "--suffix_len", str(sfx)]
+                base_cmd += ["--reads1", r1, "--reads2", r2, "--suffix_len", str(sfx)]
             elif platform in ("pacbio", "oxford"):
                 r = kwargs.get("reads1_suffix", ".fastq.gz")
                 gsize = kwargs.get("genome_size", "6.07m")
                 sfx = kwargs.get("suffix_len") or len(r)
-                v = self.validate_reads_filenames(input_dir, platform, r, None, sfx)
+                v = self.validate_reads_filenames(work_input_dir, platform, r, None, sfx)
                 if not v.get("valid"):
                     raise ValueError(f"Reads 文件验证失败: {v.get('error')}")
                 sfx = v.get("suggested_suffix_len", sfx)
-                command += ["--reads1", r, "--genomeSize", gsize, "--suffix_len", str(sfx)]
+                base_cmd += ["--reads1", r, "--genomeSize", gsize, "--suffix_len", str(sfx)]
             elif platform == "hybrid":
                 short1 = kwargs.get("short1")
                 short2 = kwargs.get("short2")
@@ -190,9 +223,9 @@ class DockerContainerManager:
                 if not all([short1, short2, long]):
                     raise ValueError("hybrid 需要 short1/short2/long 三个完整文件名")
                 for fn in (short1, short2, long):
-                    if not (input_dir / fn).exists():
+                    if not (work_input_dir / fn).exists():
                         raise ValueError(f"文件不存在: {fn}")
-                command += [
+                base_cmd += [
                     "--short1",
                     short1,
                     "--short2",
@@ -204,19 +237,23 @@ class DockerContainerManager:
                 ]
 
         if kwargs.get("assemble_only"):
-            command.append("--assemble_only")
+            base_cmd.append("--assemble_only")
 
+        # 2) 只挂载输出目录（含 input_files）与日志目录
         volumes = {
-            str(input_dir.resolve()): {"bind": "/data/input", "mode": "ro"},
             str(output_dir.resolve()): {"bind": "/workspace", "mode": "rw"},
             str(log_dir.resolve()): {"bind": "/data/logs", "mode": "rw"},
         }
 
         logger.info("开始 BtToxin_Digger 分析...")
+
+        final_cmd = base_cmd
+        working_dir = "/workspace"
+
         result = self.run_command_in_container(
-            command=command,
+            command=final_cmd,
             volumes=volumes,
-            working_dir="/workspace",
+            working_dir=working_dir,
             name=f"bttoxin_digger_{int(time.time())}",
         )
 
@@ -270,6 +307,8 @@ class DockerContainerManager:
     ) -> Dict[str, Any]:
         assert self._client is not None
         try:
+            # 注意：docker SDK 在 detach=False 时返回的是日志字节串，而非容器对象。
+            # 这里统一以 detach=True 运行，然后等待并抓取日志，最后按需删除容器。
             container = self._client.containers.run(
                 image=self.image,
                 command=command,
@@ -278,13 +317,12 @@ class DockerContainerManager:
                 working_dir=working_dir,
                 platform=self.platform,
                 name=name,
-                detach=detach,
+                user="0:0",  # 以 root 运行，避免挂载目录权限问题
-                remove=False,  # 等获取日志后再删
+                detach=True,
+                remove=False,  # 获取日志后再删
                 stdout=True,
                 stderr=True,
             )
-            if detach:
-                return {"success": True, "container_id": container.id, "status": "running"}
             exit_info = container.wait()
             code = exit_info.get("StatusCode", 1)
             logs = container.logs().decode("utf-8", errors="ignore")
@@ -312,12 +350,18 @@ class DockerContainerManager:
         cmd: List[str] = [cli, "run", "--rm" if remove and not detach else ""]
         cmd = [c for c in cmd if c]
         cmd += ["--platform", self.platform]
+        # 以 root 运行，避免权限问题
+        cmd += ["--user", "0:0"]
         if name:
             cmd += ["--name", name]
         for host, spec in volumes.items():
             bind = spec.get("bind")
             mode = spec.get("mode", "rw")
-            cmd += ["-v", f"{host}:{bind}:{mode}"]
+            # Podman(Linux) 下附加 :Z 处理 SELinux 标注；其他平台保持不变
+            mount_mode = mode
+            if self._engine == "podman-cli" and os.name == "posix" and sys.platform.startswith("linux"):
+                mount_mode = f"{mode},Z"
+            cmd += ["-v", f"{host}:{bind}:{mount_mode}"]
         for k, v in (environment or {}).items():
             cmd += ["-e", f"{k}={v}"]
         cmd += ["-w", working_dir, self.image]