From 4b463761a6c5190ce50890b0ba5c9e56847b71b6 Mon Sep 17 00:00:00 2001
From: Manasa Venkatakrishnan <14958785+manasaV3@users.noreply.github.com>
Date: Mon, 4 Nov 2024 13:21:51 -0800
Subject: [PATCH] chore: Handle no neuroglancer config file (#339)

* Handle no neuroglancer config file

* Handling for api v2

* Fix tests
---
 apiv2/db_import/importers/tomogram.py                       | 6 +++++-
 ingestion_tools/scripts/importers/db/tomogram.py            | 6 ++++--
 .../scripts/tests/db_import/test_db_tomo_import.py          | 2 +-
 3 files changed, 10 insertions(+), 4 deletions(-)

diff --git a/apiv2/db_import/importers/tomogram.py b/apiv2/db_import/importers/tomogram.py
index 22b67227e..28d0af45d 100644
--- a/apiv2/db_import/importers/tomogram.py
+++ b/apiv2/db_import/importers/tomogram.py
@@ -34,7 +34,11 @@ class TomogramItem(ItemDBImporter):
     def normalize_to_unknown_str(self, value: str) -> str:
         return value.replace(" ", "_") if value else "Unknown"
 
-    def generate_neuroglancer_data(self, path) -> str:
+    def generate_neuroglancer_data(self, path) -> str | None:
+        if not path:
+            # Handle the case where there is no neuroglancer config file specified which is expected when
+            # visualization_default is set to False.
+            return None
         config = self.config.load_key_json(path, is_file_required=False)
         # TODO: Log warning
         return json.dumps(config, separators=(",", ":")) if config else "{}"
diff --git a/ingestion_tools/scripts/importers/db/tomogram.py b/ingestion_tools/scripts/importers/db/tomogram.py
index 0396ee9ca..1c3795bb0 100644
--- a/ingestion_tools/scripts/importers/db/tomogram.py
+++ b/ingestion_tools/scripts/importers/db/tomogram.py
@@ -72,9 +72,11 @@ def get_tomogram_type(self) -> str:
             return "CANONICAL"
         return "UNKOWN"  # TYPO that's also reflected in the db :'(
 
-    def generate_neuroglancer_data(self, config_path) -> str:
+    def generate_neuroglancer_data(self, config_path) -> str | None:
         if not config_path:
-            return "{}"
+            # Handle the case where there is no neuroglancer config file specified, which is expected when
+            # visualization_default is set to False.
+            return None
         config = self.config.load_key_json(config_path, is_file_required=True)
         # TODO: Log warning
         return json.dumps(config, separators=(",", ":")) if config else "{}"
diff --git a/ingestion_tools/scripts/tests/db_import/test_db_tomo_import.py b/ingestion_tools/scripts/tests/db_import/test_db_tomo_import.py
index 3cef1ea82..383706431 100644
--- a/ingestion_tools/scripts/tests/db_import/test_db_tomo_import.py
+++ b/ingestion_tools/scripts/tests/db_import/test_db_tomo_import.py
@@ -120,7 +120,7 @@ def expected_tomograms_by_run(http_prefix: str) -> dict[str, dict[float, list[di
         "offset_x": 0,
         "offset_y": 0,
         "offset_z": 0,
-        "neuroglancer_config": "{}",
+        "neuroglancer_config": None,
         "type": "CANONICAL",
         "deposition_id": 300,
     }