enhanced simularium url and firebase recipe path validation

cellpack/autopack/AWSHandler.py

@@ -89,10 +89,11 @@ def create_presigned_url(self, object_name, expiration=3600):
         # https://{self.bucket_name}.s3.{region}.amazonaws.com/{object_key}
         return url
 
-    def save_file(self, file_path):
+    def save_file_and_get_url(self, file_path):
         """
         Uploads a file to S3 and returns the presigned url
         """
         file_name = self.upload_file(file_path)
         if file_name:
-            return file_name, self.create_presigned_url(file_name)
+            base_url = self.create_presigned_url(file_name).split("?")[0]
+            return file_name, base_url

cellpack/autopack/DBRecipeHandler.py

@@ -572,6 +572,7 @@ def upload_recipe(self, recipe_meta_data, recipe_data):
             print(f"{recipe_id} is already in firestore")
             return
         recipe_to_save = self.upload_collections(recipe_meta_data, recipe_data)
+        recipe_to_save["recipe_path"] = self.db.create_path("recipes", recipe_id)
         self.upload_data("recipes", recipe_to_save, recipe_id)
 
     def upload_result_metadata(self, file_name, url):
@@ -584,7 +585,7 @@ def upload_result_metadata(self, file_name, url):
             self.db.update_or_create(
                 "results",
                 file_name,
-                {"user": username, "timestamp": timestamp, "url": url.split("?")[0]},
+                {"user": username, "timestamp": timestamp, "url": url},
             )
 
 
@@ -630,6 +631,18 @@ def prep_db_doc_for_download(self, db_doc):
     def collect_docs_by_id(self, collection, id):
         return self.db.get_doc_by_id(collection, id)
 
+    def validate_input_recipe_path(self, path):
+        """
+        Validates if the input path corresponds to a recipe path in the database.
+        Format of a recipe path: firebase:recipes/[RECIPE-ID]
+        """
+        collection, id = self.db.get_collection_id_from_path(path)
+        recipe_path = self.db.get_value(collection, id, "recipe_path")
+        if not recipe_path:
+            raise ValueError(
+                f"No recipe found at the input path: '{path}'. Please ensure the recipe exists in the database and is spelled correctly. Expected path format: 'firebase:recipes/[RECIPE-ID]'"
+            )
+
     @staticmethod
     def _get_grad_and_obj(obj_data, obj_dict, grad_dict):
         """

cellpack/autopack/FirebaseHandler.py

@@ -5,6 +5,9 @@
 from dotenv import load_dotenv
 from google.cloud.exceptions import NotFound
 from cellpack.autopack.loaders.utils import read_json_file, write_json_file
+from cellpack.autopack.interface_objects.default_values import (
+    default_firebase_collection_names,
+)
 
 
 class FirebaseHandler(object):
@@ -65,10 +68,18 @@ def get_path_from_ref(doc):
 
     @staticmethod
     def get_collection_id_from_path(path):
-        # path example = firebase:composition/uid_1
-        components = path.split(":")[1].split("/")
-        collection = components[0]
-        id = components[1]
+        try:
+            components = path.split(":")[1].split("/")
+            collection = components[0]
+            id = components[1]
+            if collection not in default_firebase_collection_names:
+                raise ValueError(
+                    f"Invalid collection name: '{collection}'. Choose from: {default_firebase_collection_names}"
+                )
+        except IndexError:
+            raise ValueError(
+                "Invalid path provided. Expected format: firebase:collection/id"
+            )
         return collection, id
 
     # Create methods
@@ -141,6 +152,12 @@ def get_doc_by_ref(self, path):
         collection, id = FirebaseHandler.get_collection_id_from_path(path)
         return self.get_doc_by_id(collection, id)
 
+    def get_value(self, collection, id, field):
+        doc, _ = self.get_doc_by_id(collection, id)
+        if doc is None:
+            return None
+        return doc[field]
+
     # Update methods
     def update_doc(self, collection, id, data):
         doc_ref = self.db.collection(collection).document(id)

cellpack/autopack/__init__.py

@@ -387,6 +387,7 @@ def load_file(filename, destination="", cache="geometries", force=None):
         if database_name == "firebase":
             db = DATABASE_IDS.handlers().get(database_name)
             db_handler = DBRecipeLoader(db)
+            db_handler.validate_input_recipe_path(filename)
             recipe_id = file_path.split("/")[-1]
             db_doc, _ = db_handler.collect_docs_by_id(
                 collection="recipes", id=recipe_id

cellpack/autopack/interface_objects/default_values.py

@@ -13,3 +13,11 @@
     "mode_settings": {},
     "weight_mode_settings": {},
 }
+
+default_firebase_collection_names = [
+    "composition",
+    "objects",
+    "gradients",
+    "recipes",
+    "results",
+]

cellpack/autopack/loaders/recipe_loader.py

@@ -196,7 +196,7 @@ def _read(self, resolve_inheritance=True):
                     atomic=reps.get("atomic", None),
                     packing=reps.get("packing", None),
                 )
-                # the key "all_partners" exists in obj["partners"] if the recipe is downloaded from a remote db
+                # the key "all_partners" already exists in obj["partners"] if the recipe is downloaded from firebase
                 partner_settings = (
                     []
                     if (

cellpack/autopack/upy/simularium/simularium_helper.py

@@ -1416,7 +1416,7 @@ def store_result_file(file_path, storage=None):
                 sub_folder_name="simularium/",
                 region_name="us-west-2",
             )
-        file_name, url = initialized_handler.save_file(file_path)
+        file_name, url = initialized_handler.save_file_and_get_url(file_path)
         simulariumHelper.store_metadata(file_name, url, db="firebase")
         return file_name, url