Skip symlinks for analysis (#611)

* Exclude symlinks from analysis

* Attempt to capture Semgrep SARIF upon failure

* Add unit test for symlink exclusion

src/codemodder/codemodder.py

@@ -199,11 +199,15 @@ def run(original_args) -> int:
     log_list(logging.INFO, "including paths", included_paths)
     log_list(logging.INFO, "excluding paths", argv.path_exclude)
 
-    files_to_analyze: list[Path] = match_files(
-        context.directory,
-        argv.path_exclude,
-        included_paths,
-    )
+    files_to_analyze: list[Path] = [
+        path
+        for path in match_files(
+            context.directory,
+            argv.path_exclude,
+            included_paths,
+        )
+        if path.is_file() and not path.is_symlink()
+    ]
 
     full_names = [str(path) for path in files_to_analyze]
     log_list(logging.DEBUG, "matched files", full_names)

src/codemodder/semgrep.py

@@ -110,6 +110,11 @@ def run(
         if call.returncode != 0:
             if not execution_context.verbose:
                 logger.error("captured semgrep stderr: %s", call.stderr)
+            try:
+                logger.error("semgrep sarif output: %s", temp_sarif_file.read())
+            except Exception as e:
+                logger.error("failed to read semgrep sarif output: %s", e)
+
             raise subprocess.CalledProcessError(call.returncode, command)
         # semgrep prepends the folders into the rule-id, we want the base name only
         results = InternalSemgrepResultSet.from_sarif(

tests/test_codemodder.py

@@ -8,6 +8,7 @@
 from codemodder.diff import create_diff_from_tree
 from codemodder.registry import load_registered_codemods
 from codemodder.result import ResultSet
+from codemodder.semgrep import run as semgrep_run
 
 
 @pytest.fixture(autouse=True, scope="module")
@@ -74,6 +75,20 @@ def test_no_files_matched(self, mock_parse, dir_structure):
         mock_parse.assert_not_called()
         assert codetf.exists()
 
+    def test_skip_symlinks(self, mocker, dir_structure):
+        # Override fixture for this specific test case
+        mocker.patch("codemodder.codemods.semgrep.semgrep_run", semgrep_run)
+        code_dir, codetf = dir_structure
+        (code_dir / "symlink.py").symlink_to(code_dir / "test_request.py")
+        args = [
+            str(code_dir),
+            "--output",
+            str(codetf),
+            "--codemod-include=url-sandbox",
+        ]
+        res = run(args)
+        assert res == 0
+
     @mock.patch("libcst.parse_module", side_effect=Exception)
     @mock.patch("codemodder.codetf.CodeTF.build")
     def test_cst_parsing_fails(self, build_report, mock_parse, dir_structure):