Studio: add recipe and config json to outputs for downloading (#435)

* add recipe and config to output

* refactor

* path guard

* Potential fix for code scanning alert no. 21: Uncontrolled data used in path expression

Co-authored-by: Copilot Autofix powered by AI <62310815+github-advanced-security[bot]@users.noreply.github.com>

* format

* fix 404 comment

* handle firebase recipe, serialize it before passing to s3

* save recipe data directly to outputs

* remove unused import

* one more unused import

---------

Co-authored-by: Copilot Autofix powered by AI <62310815+github-advanced-security[bot]@users.noreply.github.com>

Author: rugeli

cellpack/autopack/DBRecipeHandler.py

@@ -566,7 +566,27 @@ def upload_job_status(self, job_id, status, result_path=None, error_message=None
                 },
             )
 
-    def upload_packing_results_workflow(self, source_folder, recipe_name, job_id):
+    def save_recipe_and_config_to_output(self, output_folder, config_data, recipe_data):
+        output_path = Path(output_folder)
+
+        recipe_output_path = output_path / "recipe.json"
+        with open(recipe_output_path, "w") as f:
+            json.dump(recipe_data, f, indent=2)
+        logging.debug(f"Saved recipe to {recipe_output_path}")
+
+        config_path = output_path / "config.json"
+        with open(config_path, "w") as f:
+            json.dump(config_data, f, indent=2)
+        logging.debug(f"Saved config to {config_path}")
+
+    def upload_packing_results_workflow(
+        self,
+        source_folder,
+        recipe_name,
+        job_id,
+        config_data,
+        recipe_data,
+    ):
         """
         Complete packing results upload workflow including folder preparation and s3 upload
         """
@@ -586,10 +606,15 @@ def upload_packing_results_workflow(self, source_folder, recipe_name, job_id):
 
                 logging.debug(f"outputs will be copied to: {s3_upload_folder}")
 
-                # copy outputs to unique upload folder
                 s3_upload_folder.mkdir(parents=True, exist_ok=True)
                 shutil.copytree(source_folder, s3_upload_folder, dirs_exist_ok=True)
 
+                if recipe_data and config_data:
+                    self.save_recipe_and_config_to_output(
+                        output_folder=s3_upload_folder,
+                        config_data=config_data,
+                        recipe_data=recipe_data,
+                    )
                 upload_result = self.upload_outputs_to_s3(
                     output_folder=s3_upload_folder,
                     recipe_name=recipe_name,

cellpack/autopack/loaders/recipe_loader.py

@@ -208,6 +208,10 @@ def _read(self, resolve_inheritance=True, use_docker=False):
             formatted_error = RecipeValidator.format_validation_error(e)
             raise ValueError(f"Recipe validation failed:\n{formatted_error}")
 
+        # keep a serializable copy before converting to class instances
+        # this ensures the original data (human-readable) is available for download in the UI
+        self.serializable_recipe_data = copy.deepcopy(recipe_data)
+
         if "objects" in recipe_data:
             for _, obj in recipe_data["objects"].items():
                 reps = obj["representations"] if "representations" in obj else {}

cellpack/bin/pack.py

@@ -39,9 +39,10 @@ def pack(
     """
     packing_config_data = ConfigLoader(config_path, docker).config
 
-    recipe_data = RecipeLoader(
+    recipe_loader = RecipeLoader(
         recipe, packing_config_data["save_converted_recipe"], docker
-    ).recipe_data
+    )
+    recipe_data = recipe_loader.recipe_data
     analysis_config_data = {}
     if analysis_config_path is not None:
         analysis_config_data = AnalysisConfigLoader(analysis_config_path).config
@@ -92,6 +93,8 @@ def pack(
                 source_folder=env.out_folder,
                 recipe_name=recipe_data["name"],
                 job_id=job_id,
+                config_data=packing_config_data,
+                recipe_data=recipe_loader.serializable_recipe_data,
             )