databases initiation handling

cellpack/autopack/DBRecipeHandler.py

@@ -574,6 +574,19 @@ def upload_recipe(self, recipe_meta_data, recipe_data):
         key = self._get_recipe_id(recipe_to_save)
         self.upload_data("recipes", recipe_to_save, key)
 
+    def upload_result_metadata(self, file_name, url):
+        """
+        Upload the metadata of the result file to the database.
+        """
+        if self.db:
+            username = self.db.get_username()
+            timestamp = self.db.create_timestamp()
+            self.db.update_or_create(
+                "results",
+                file_name,
+                {"user": username, "timestamp": timestamp, "url": url.split("?")[0]},
+            )
+
 
 class DBRecipeLoader(object):
     """

cellpack/autopack/__init__.py

@@ -48,7 +48,6 @@
 import ssl
 import json
 from cellpack.autopack.DBRecipeHandler import DBRecipeLoader
-from cellpack.autopack.FirebaseHandler import FirebaseHandler
 from cellpack.autopack.interface_objects.database_ids import DATABASE_IDS
 
 from cellpack.autopack.loaders.utils import read_json_file, write_json_file
@@ -384,9 +383,9 @@ def read_text_file(filename, destination="", cache="collisionTrees", force=None)
 def load_file(filename, destination="", cache="geometries", force=None):
     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-nucleus_cube -c examples/packing-configs/peroxisome_packing_config.json`
+        # command example: `pack -r firebase:recipes/[FIREBASE-RECIPE-ID] -c [CONFIG-FILE-PATH]`
         if database_name == "firebase":
-            db = FirebaseHandler()
+            db = DATABASE_IDS.handlers().get(database_name)
             db_handler = DBRecipeLoader(db)
             recipe_id = file_path.split("/")[-1]
             db_doc, _ = db_handler.collect_docs_by_id(

cellpack/autopack/interface_objects/database_ids.py

@@ -1,10 +1,28 @@
 from .meta_enum import MetaEnum
+from cellpack.autopack.AWSHandler import AWSHandler
+from cellpack.autopack.FirebaseHandler import FirebaseHandler
 
 
 class DATABASE_IDS(MetaEnum):
     FIREBASE = "firebase"
     GITHUB = "github"
+    AWS = "aws"
 
     @classmethod
     def with_colon(cls):
         return [f"{ele}:" for ele in cls.values()]
+
+    @classmethod
+    def handlers(cls):
+        def create_aws_handler(bucket_name, sub_folder_name, region_name):
+            return AWSHandler(
+                bucket_name=bucket_name,
+                sub_folder_name=sub_folder_name,
+                region_name=region_name,
+            )
+
+        handlers_dict = {
+            cls.FIREBASE: FirebaseHandler(),
+            cls.AWS: create_aws_handler,
+        }
+        return handlers_dict

cellpack/autopack/upy/simularium/simularium_helper.py

@@ -23,7 +23,8 @@
 from simulariumio.constants import DISPLAY_TYPE, VIZ_TYPE
 
 from cellpack.autopack.upy import hostHelper
-from cellpack.autopack.AWSHandler import AWSHandler
+from cellpack.autopack.DBRecipeHandler import DBUploader
+from cellpack.autopack.interface_objects.database_ids import DATABASE_IDS
 import collada
 
 
@@ -1387,7 +1388,7 @@ def post_and_open_file(self, file_name):
         simularium_file = Path(f"{file_name}.simularium")
         url = None
         try:
-            url = simulariumHelper.store_results_to_s3(simularium_file)
+            _, url = simulariumHelper.store_result_file(simularium_file, storage="aws")
         except Exception as e:
             aws_readme_url = "https://github.com/mesoscope/cellpack/blob/feature/main/README.md#aws-s3"
             if isinstance(e, NoCredentialsError):
@@ -1402,14 +1403,23 @@ def post_and_open_file(self, file_name):
             simulariumHelper.open_in_simularium(url)
 
     @staticmethod
-    def store_results_to_s3(file_path):
-        handler = AWSHandler(
-            bucket_name="cellpack-results",
-            sub_folder_name="simularium/",
-            region_name="us-west-2",
-        )
-        url = handler.save_file(file_path)
-        return url
+    def store_result_file(file_path, storage=None):
+        if storage == "aws":
+            handler = DATABASE_IDS.handlers().get(storage)
+            initialized_handler = handler(
+                bucket_name="cellpack-results",
+                sub_folder_name="simularium/",
+                region_name="us-west-2",
+            )
+        file_name, url = initialized_handler.save_file(file_path)
+        simulariumHelper.store_metadata(file_name, url, db="firebase")
+        return file_name, url
+
+    @staticmethod
+    def store_metadata(file_name, url, db=None):
+        if db == "firebase":
+            db_handler = DBUploader(DATABASE_IDS.handlers().get(db))
+            db_handler.upload_result_metadata(file_name, url)
 
     @staticmethod
     def open_in_simularium(aws_url):