Merge branch 'feature/resovle-grads-in-comp' into feature/run-recipes…

…-from-firebase

cellpack/autopack/DBRecipeHandler.py

@@ -361,14 +361,6 @@ def is_nested_list(item):
             and isinstance(item[0], (list, tuple))
         )
 
-    @staticmethod
-    def is_db_dict(item):
-        if isinstance(item, dict) and len(item) > 0:
-            for key, value in item.items():
-                if key.isdigit() and isinstance(value, list):
-                    return True
-        return False
-
     @staticmethod
     def prep_data_for_db(data):
         """
@@ -440,6 +432,8 @@ def upload_objects(self, objects):
             _, doc_id = object_doc.should_write(self.db)
             if doc_id:
                 print(f"objects/{object_doc.name} is already in firestore")
+                obj_path = self.db.create_path("objects", doc_id)
+                self.objects_to_path_map[obj_name] = obj_path
             else:
                 _, obj_path = self.upload_data("objects", object_doc.as_dict())
                 self.objects_to_path_map[obj_name] = obj_path
@@ -541,34 +535,3 @@ def upload_recipe(self, recipe_meta_data, recipe_data):
         recipe_to_save = self.upload_collections(recipe_meta_data, recipe_data)
         key = self.get_recipe_id(recipe_to_save)
         self.upload_data("recipes", recipe_to_save, key)
-
-    def prep_db_doc_for_download(self, db_doc):
-        """
-        convert data from db and resolve references.
-        """
-        prep_data = {}
-        if isinstance(db_doc, dict):
-            for key, value in db_doc.items():
-                if self.is_db_dict(value):
-                    unpack_dict = [value[str(i)] for i in range(len(value))]
-                    prep_data[key] = unpack_dict
-                elif key == "composition":
-                    compositions = db_doc["composition"]
-                    for comp_name, reference in compositions.items():
-                        ref_link = reference["inherit"]
-                        comp_doc = CompositionDoc(
-                            comp_name,
-                            object_key=None,
-                            count=None,
-                            regions={},
-                            molarity=None,
-                        )
-                        composition_data, _ = comp_doc.get_reference_data(
-                            ref_link, self.db
-                        )
-                        comp_doc.resolve_db_regions(composition_data, self.db)
-                        compositions[comp_name] = composition_data
-                    prep_data[key] = compositions
-                else:
-                    prep_data[key] = value
-        return prep_data

cellpack/autopack/__init__.py

@@ -386,7 +386,6 @@ def read_text_file(filename, destination="", cache="collisionTrees", force=None)
 
 
 def load_file(filename, destination="", cache="geometries", force=None):
-    # what is the param destination for? should we use it to store db names?
     if is_remote_path(filename):
         database_name, file_path = convert_db_shortname_to_url(filename)
         # command example: `pack -r firebase:recipes/peroxisomes_surface_gradient_v-linear -c examples/packing-configs/peroxisome_packing_config.json`
@@ -405,7 +404,7 @@ def load_file(filename, destination="", cache="geometries", force=None):
         local_file_path = get_local_file_location(
             filename, destination=destination, cache=cache, force=force
         )
-    return json.load(open(local_file_path, "r")), None
+    return json.load(open(local_file_path, "r"))
 
 
 def fixPath(adict):  # , k, v):

cellpack/autopack/loaders/migrate_v1_to_v2.py

@@ -121,7 +121,7 @@ def split_ingredient_data(object_key, ingredient_data):
 
 def get_and_store_v2_object(ingredient_key, ingredient_data, region_list, objects_dict):
     if "include" in ingredient_data:
-        ingredient_data, _ = load_file(ingredient_data["include"], cache="recipes")
+        ingredient_data = load_file(ingredient_data["include"], cache="recipes")
     check_required_attributes(ingredient_data)
     converted_ingredient = migrate_ingredient(ingredient_data)
     object_info, composition_info = split_ingredient_data(