Only upload simularium file once

cellpack/autopack/DBRecipeHandler.py

@@ -529,7 +529,7 @@ def upload_config(self, config_data, source_path):
         self.db.update_doc("configs", id, config_data)
         return id
 
-    def upload_result_metadata(self, file_name, url, dedup_hash=None):
+    def upload_result_metadata(self, file_name, url):
         """
         Upload the metadata of the result file to the database.
         """
@@ -543,11 +543,8 @@ def upload_result_metadata(self, file_name, url, dedup_hash=None):
                     "user": username,
                     "timestamp": timestamp,
                     "url": url,
-                    "dedup_hash": dedup_hash,
                 },
             )
-        if dedup_hash:
-            self.upload_job_status(dedup_hash, "DONE", result_path=url)
 
     def upload_job_status(
         self,
@@ -644,6 +641,7 @@ def upload_packing_results_workflow(
                 self.upload_job_status(
                     dedup_hash,
                     "DONE",
+                    result_path=upload_result.get("simularium_url"),
                     outputs_directory=upload_result.get("outputs_directory"),
                 )
 
@@ -675,8 +673,11 @@ def upload_outputs_to_s3(self, output_folder, recipe_name, dedup_hash):
                     f"{base_url}/{file_info['s3_key']}"
                     for file_info in upload_result["uploaded_files"]
                 ]
+                simularium_url = None
+                for url in public_urls:
+                    if url.endswith(".simularium"):
+                        simularium_url = url
                 outputs_directory = f"https://us-west-2.console.aws.amazon.com/s3/buckets/{bucket_name}/{s3_prefix}/"
-
                 logging.info(
                     f"Successfully uploaded {upload_result['total_files']} files to {outputs_directory}"
                 )
@@ -694,6 +695,7 @@ def upload_outputs_to_s3(self, output_folder, recipe_name, dedup_hash):
                     "total_size": upload_result["total_size"],
                     "urls": public_urls,
                     "outputs_directory": outputs_directory,
+                    "simularium_url": simularium_url,
                 }
         except Exception as e:
             logging.error(e)

cellpack/autopack/upy/simularium/simularium_helper.py

@@ -1387,36 +1387,28 @@ def raycast_test(self, obj, start, end, length, **kw):
 
     def post_and_open_file(self, file_name, open_results_in_browser, dedup_hash=None):
         simularium_file = Path(f"{file_name}.simularium")
-        file_name, url = simulariumHelper.store_result_file(
-            simularium_file, storage="aws", batch_job_id=dedup_hash
-        )
-        if file_name and url:
-            simulariumHelper.store_metadata(
-                file_name, url, db="firebase", dedup_hash=dedup_hash
+        if dedup_hash is None:
+            file_name, url = simulariumHelper.store_result_file(
+                simularium_file, storage="aws"
             )
-            if open_results_in_browser:
-                simulariumHelper.open_in_simularium(url)
+            if file_name and url:
+                simulariumHelper.store_metadata(
+                    file_name, url, db="firebase"
+                )
+                if open_results_in_browser:
+                    simulariumHelper.open_in_simularium(url)
 
     @staticmethod
     def store_result_file(
-        file_path, storage=None, batch_job_id=None, sub_folder="simularium"
+        file_path, storage=None, sub_folder="simularium"
     ):
         if storage == "aws":
             handler = DATABASE_IDS.handlers().get(storage)
-            # if batch_job_id is not None, then we are in a batch job and should use the temp bucket
-            # TODO: use cellpack-results bucket for batch jobs once we have the correct permissions
-            if batch_job_id:
-                initialized_handler = handler(
-                    bucket_name="cellpack-demo",
-                    sub_folder_name=sub_folder,
-                    region_name="us-west-2",
-                )
-            else:
-                initialized_handler = handler(
-                    bucket_name="cellpack-results",
-                    sub_folder_name=sub_folder,
-                    region_name="us-west-2",
-                )
+            initialized_handler = handler(
+                bucket_name="cellpack-results",
+                sub_folder_name=sub_folder,
+                region_name="us-west-2",
+            )
             file_name, url = initialized_handler.save_file_and_get_url(file_path)
             if not file_name or not url:
                 db_maintainer = DBMaintenance(initialized_handler)
@@ -1426,15 +1418,15 @@ def store_result_file(
         return file_name, url
 
     @staticmethod
-    def store_metadata(file_name, url, db=None, dedup_hash=None):
+    def store_metadata(file_name, url, db=None):
         if db == "firebase":
             handler = DATABASE_IDS.handlers().get(db)
             initialized_db = handler(
                 default_db="staging"
             )  # default to staging for metadata uploads
             if initialized_db._initialized:
                 db_uploader = DBUploader(initialized_db)
-                db_uploader.upload_result_metadata(file_name, url, dedup_hash)
+                db_uploader.upload_result_metadata(file_name, url)
             else:
                 db_maintainer = DBMaintenance(initialized_db)
                 logging.warning(