Add formatting and exceptions

ASTGrep/VERSION

@@ -1 +1 @@
-24
+25

ASTGrep/requirements.txt

@@ -3,4 +3,5 @@ ast-grep-cli >0.25.0, <0.26.0
 pylspclient
 cryptography
 ast-grep-py
-jinja2
+jinja2
+ruff

ASTGrep/service/al_run.py

@@ -1,6 +1,7 @@
 import hashlib
 import json
 import os
+import subprocess
 import tempfile
 from collections import defaultdict
 from copy import copy
@@ -205,6 +206,7 @@ def _process_file(self, request: ServiceRequest, file_path, file_type):
             request.add_supplementary(f.name, "astgrep_raw_results.json", "AST-Grep Results")
 
         if self._should_deobfuscate:
+            reformat_code = request.get_param("reformat_deobfuscated_code")
             extracted_layers = []
             result_no = 1
             for deobf_result, layer in self._deobfuscator.deobfuscate_file(file_path, file_type):
@@ -220,10 +222,20 @@ def _process_file(self, request: ServiceRequest, file_path, file_type):
                         )
                     )
                 else:
+                    if reformat_code:
+                        try:
+                            subprocess.run(
+                                ["ruff", "format", "--no-cache", "--isolated", path],
+                                timeout=5,
+                                check=False,
+                            )
+                        except Exception:
+                            self.log.warning("Error reformatting deobfuscated code", exc_info=True)
                     request.add_extracted(
                         path,
                         f"_deobfuscated_code_FINAL{LANGUAGE_TO_EXT[file_type]}",
                         "Final deobfuscation layer",
+                        safelist_interface=self.api_interface,
                     )
                 result_no += 1
             deobf_section = ResultTextSection(

ASTGrep/service_manifest.yml

@@ -11,7 +11,7 @@ stage: CORE
 category: Static Analysis
 uses_tags: false
 file_required: true
-timeout: 120
+timeout: 150
 is_external: false
 
 config:
@@ -22,12 +22,11 @@ config:
   EXTRACT_INTERMEDIATE_LAYERS: false
   TRY_LANGUAGE_FROM_EXTENSION: true
 
-# submission_params:
-#   - default: "auto"
-#     name: platform
-#     type: list
-#     value: "auto"
-#     list: ["auto", "linux"]
+submission_params:
+  - default: true
+    name: reformat_deobfuscated_code
+    type: bool
+    value: true
 
 heuristics:
   - description: Suspicious code pattern