From ef0101d0a002be8d30ad4f40b6b7ba6dc03a516b Mon Sep 17 00:00:00 2001
From: Andrey Fedorov <andrey.fedorov@gmail.com>
Date: Mon, 7 Oct 2024 15:34:41 -0400
Subject: [PATCH] BUG: clean up after conflict resolution

---
 idc_index/index.py | 12 +++++-------
 tests/idcindex.py  |  3 +++
 2 files changed, 8 insertions(+), 7 deletions(-)

diff --git a/idc_index/index.py b/idc_index/index.py
index 0d113bc1..c6d0ea5b 100644
--- a/idc_index/index.py
+++ b/idc_index/index.py
@@ -153,7 +153,7 @@ def _safe_filter_by_selection(
         patientId,
         studyInstanceUID,
         seriesInstanceUID,
-        sopInstanceUID=None,
+        sopInstanceUID,
         crdc_series_uuid,
     ):
         if collection_id is not None:
@@ -205,10 +205,10 @@ def _safe_filter_by_selection(
 
         if sopInstanceUID is not None:
             result_df = IDCClient._filter_by_dicom_instance_uid(
-                result_df, sopInstanceUID
+                df_index, sopInstanceUID
             )
             return result_df
-          
+
         if seriesInstanceUID is not None:
             result_df = IDCClient._filter_by_dicom_series_uid(
                 df_index, seriesInstanceUID
@@ -1512,6 +1512,7 @@ def citations_from_selection(
             patientId=patientId,
             studyInstanceUID=studyInstanceUID,
             seriesInstanceUID=seriesInstanceUID,
+            sopInstanceUID=None,
             crdc_series_uuid=None,
         )
 
@@ -1604,10 +1605,7 @@ def download_from_selection(
                 raise ValueError(
                     "Instance-level access not possible because instance-level index not installed."
                 )
-        else:
-            download_df = self.index
-
-        if crdc_series_uuid is not None:
+        elif crdc_series_uuid is not None:
             download_df = pd.concat(
                 [
                     self.index[
diff --git a/tests/idcindex.py b/tests/idcindex.py
index 18c8311a..66b875b9 100644
--- a/tests/idcindex.py
+++ b/tests/idcindex.py
@@ -15,6 +15,9 @@
 
 # Run tests using the following command from the root of the repository:
 # python -m unittest -vv tests/idcindex.py
+#
+# run specific tests with this:
+# pytest ./tests/idcindex.py::TestIDCClient.test_download_dicom_instance
 
 logging.basicConfig(level=logging.DEBUG)