From ac7fdcecf2b3687bd3414cf55534ea9d8d7aa5bf Mon Sep 17 00:00:00 2001
From: X-iZhang <zacharyzhang2022@gmail.com>
Date: Thu, 19 Mar 2026 18:38:57 +0000
Subject: [PATCH] refactor: improve readability of command validation and path
 extraction logic

---
 EvoScientist/backends.py | 31 ++++++++++++++++++-------------
 tests/test_backends.py   | 14 +++++++++++---
 2 files changed, 29 insertions(+), 16 deletions(-)

diff --git a/EvoScientist/backends.py b/EvoScientist/backends.py
index b05a4d8..7c23545 100644
--- a/EvoScientist/backends.py
+++ b/EvoScientist/backends.py
@@ -110,7 +110,11 @@ def _collect_executable_positions(command: str) -> set[int]:
             # First token is the executable itself — mark its offset
             offsets.add(seg_start)
             # pip install <path> — mark the install-target token
-            if len(tokens) >= 3 and tokens[0] in ("pip", "pip3") and tokens[1] == "install":
+            if (
+                len(tokens) >= 3
+                and tokens[0] in ("pip", "pip3")
+                and tokens[1] == "install"
+            ):
                 # Find position of the 3rd token (the package arg) onwards
                 rest = pipe_seg_stripped
                 for t in tokens[:2]:
@@ -134,8 +138,8 @@ def _extract_all_paths(command: str) -> list[str]:
     # dashes, slashes. Looks inside quotes and unquoted tokens alike.
     # Excludes URL-like patterns (preceded by ://)
     path_re = re.compile(
-        r'(?<![:=/\w])'       # not preceded by :, =, /, or word char (avoid URLs, env vars)
-        r'(/(?:Users|home|tmp|var|etc|opt|usr|bin|sbin|dev|proc|sys|root)'
+        r"(?<![:=/.\w])"  # not preceded by :, =, /, ., or word char (avoid URLs, env vars, ./paths)
+        r"(/(?:Users|home|tmp|var|etc|opt|usr|bin|sbin|dev|proc|sys|root)"
         r'(?:/[^\s\'",;|&<>)}\]]*)?)'  # rest of the path
     )
     for m in path_re.finditer(command):
@@ -472,17 +476,9 @@ class CustomSandboxBackend(LocalShellBackend):
 
         Then delegates to LocalShellBackend.execute() for actual execution.
         """
-        # Validate command safety
-        error = validate_command(command)
-        if error:
-            return ExecuteResponse(
-                output=error,
-                exit_code=1,
-                truncated=False,
-            )
-
         # Replace literal workspace-root absolute paths with ./
-        # Catches cases where the agent uses the exact real path.
+        # Must happen BEFORE validation so workspace paths (e.g. /tmp/...)
+        # are sanitized before the system-path check fires.
         ws = str(self.cwd).rstrip("/") + "/"
         if ws in command:
             command = command.replace(ws, "./")
@@ -494,6 +490,15 @@ class CustomSandboxBackend(LocalShellBackend):
                 workspace_name=Path(str(self.cwd)).name,
             )
 
+        # Validate command safety (after path sanitization)
+        error = validate_command(command)
+        if error:
+            return ExecuteResponse(
+                output=error,
+                exit_code=1,
+                truncated=False,
+            )
+
         # Delegate to parent for subprocess execution
         response = super().execute(command, timeout=timeout)
 
diff --git a/tests/test_backends.py b/tests/test_backends.py
index b36867f..c5495c6 100644
--- a/tests/test_backends.py
+++ b/tests/test_backends.py
@@ -395,12 +395,16 @@ class TestAbsolutePathDetection:
 
     def test_python_os_remove(self):
         """python -c with os.remove targeting system path."""
-        result = validate_command("python -c \"import os; os.remove('/Users/foo/file')\"")
+        result = validate_command(
+            "python -c \"import os; os.remove('/Users/foo/file')\""
+        )
         assert result is not None
         assert "absolute system path" in result.lower()
 
     def test_python_shutil_rmtree(self):
-        result = validate_command("python -c \"import shutil; shutil.rmtree('/home/user/project')\"")
+        result = validate_command(
+            "python -c \"import shutil; shutil.rmtree('/home/user/project')\""
+        )
         assert result is not None
         assert "/home/" in result
 
@@ -473,6 +477,7 @@ class TestAbsolutePathDetection:
         # dd itself is blocked by BLOCKED_COMMANDS, but the /dev path
         # should not trigger the absolute-path check due to = prefix
         from EvoScientist.backends import _extract_all_paths
+
         assert _extract_all_paths("if=/dev/zero") == []
 
     def test_safe_system_executable(self):
@@ -494,7 +499,10 @@ class TestAbsolutePathDetection:
         assert validate_command("echo hello | /usr/bin/grep pattern") is None
 
     def test_safe_executable_in_chain(self):
-        assert validate_command("/usr/bin/python3 a.py && /opt/homebrew/bin/node b.js") is None
+        assert (
+            validate_command("/usr/bin/python3 a.py && /opt/homebrew/bin/node b.js")
+            is None
+        )
 
     def test_dangerous_second_arg_still_blocked(self):
         """System path as a non-executable argument should still be blocked."""