Fix sast_only flag behavior to include other sast input flags

integration_tests/test_program.py

@@ -1,4 +1,8 @@
 import subprocess
+from pathlib import Path
+
+import pytest
+from sarif_pydantic.sarif import Run, Sarif, Tool, ToolDriver
 
 from core_codemods.remove_assertion_in_pytest_raises import (
     RemoveAssertionInPytestRaises,
@@ -26,14 +30,50 @@ def test_codemods_include_exclude_conflict(self):
         )
         assert completed_process.returncode == 3
 
-    def test_load_sast_only_by_flag(self, tmp_path):
+    @pytest.mark.parametrize(
+        "cli_args",
+        [
+            "--sonar-issues-json",
+            "--sonar-hotspots-json",
+            "--sonar-json",
+        ],
+    )
+    def test_load_sast_only_by_sonar_flag(self, tmp_path, cli_args):
         tmp_file_path = tmp_path / "sonar.json"
         tmp_file_path.touch()
         completed_process = subprocess.run(
             [
                 "codemodder",
                 "tests/samples/",
-                "--sonar-issues-json",
+                cli_args,
+                f"{tmp_file_path}",
+                "--dry-run",
+            ],
+            check=False,
+            capture_output=True,
+            text=True,
+        )
+        print(completed_process.stdout)
+        print(completed_process.stderr)
+        assert completed_process.returncode == 0
+        assert RemoveAssertionInPytestRaises.id not in completed_process.stdout
+
+    def test_load_sast_only_by_sarif_flag(self, tmp_path: Path):
+        tmp_file_path = tmp_path / "sarif.json"
+        sarif_run = Run(
+            tool=Tool(driver=ToolDriver(name="test")),
+            results=[],
+        )
+        sarif = Sarif(runs=[sarif_run], **{"$schema": ""})
+        tmp_file_path.write_text(
+            sarif.model_dump_json(indent=2, exclude_none=True, by_alias=True)
+        )
+
+        completed_process = subprocess.run(
+            [
+                "codemodder",
+                "tests/samples/",
+                "--sarif",
                 f"{tmp_file_path}",
                 "--dry-run",
             ],

src/codemodder/codemodder.py

@@ -285,7 +285,10 @@ def _run_cli(original_args, remediation=False) -> int:
         max_workers=argv.max_workers,
         original_cli_args=original_args,
         codemod_registry=codemod_registry,
-        sast_only=argv.sonar_issues_json or argv.sarif,
+        sast_only=argv.sonar_issues_json
+        or argv.sarif
+        or argv.sonar_hotspots_json
+        or argv.sonar_json,
         log_matched_files=True,
         remediation=remediation,
     )