Dev

requirements-dev.txt

@@ -22,7 +22,7 @@ click==8.1.3
     # via pip-tools
 coverage==5.1
     # via -r requirements-dev.in
-django==4.2.22
+django==4.2.24
     # via
     #   -c requirements.txt
     #   django-appconf

requirements.txt

@@ -28,7 +28,7 @@ defusedxml==0.7.1
     # via
     #   python3-openid
     #   social-auth-core
-django==4.2.22
+django==4.2.24
     # via
     #   -r requirements.in
     #   django-anymail

seqr/views/apis/anvil_workspace_api_tests.py

@@ -800,7 +800,7 @@ def _assert_valid_operation(self, project, test_add_data=True):
             '\n'.join(['\t'.join(row) for row in [header] + rows])
         )
 
-        self.mock_gzip_temp_open.assert_called_with(f'{TEMP_PATH}/db_id_to_gene_id.csv.gz', 'w')
+        self.mock_gzip_temp_open.assert_called_with(f'{TEMP_PATH}/db_id_to_gene_id.csv.gz', 'wt')
         gene_file = self.mock_gzip_temp_open.return_value.__enter__.return_value.write.call_args.args[0].split('\n')
         self.assertEqual(len(gene_file), 52)
         self.assertListEqual(gene_file[:3], ['db_id,gene_id', '1,ENSG00000223972', '2,ENSG00000227232'])

seqr/views/apis/data_manager_api_tests.py

@@ -1507,7 +1507,7 @@ def _has_expected_ped_files(self, mock_open, mock_gzip_open, mock_mkdir, dataset
         if has_gene_id_file:
             mock_gzip_open.assert_not_called()
         else:
-            mock_gzip_open.assert_called_once_with(f'{self.LOCAL_WRITE_DIR}/db_id_to_gene_id.csv.gz', 'w')
+            mock_gzip_open.assert_called_once_with(f'{self.LOCAL_WRITE_DIR}/db_id_to_gene_id.csv.gz', 'wt')
             file = [
                 row.split(',') for row in mock_gzip_open.return_value.__enter__.return_value.write.call_args.args[0].split('\n')
             ]

seqr/views/utils/export_utils.py

@@ -97,11 +97,12 @@ def write_multiple_files(files, file_path, user, gzip_file=False, **kwargs):
     with TemporaryDirectory() as temp_dir_name:
         dir_name = temp_dir_name if is_gs_path else file_path
         open_func = gzip.open if gzip_file else open
+        open_mode = 'wt' if gzip_file else 'w'
         for filename, content in _format_files_content(files, **kwargs):
             current_file = f'{dir_name}/{filename}'
             if gzip_file:
                 current_file += '.gz'
-            with open_func(current_file, 'w') as f:
+            with open_func(current_file, open_mode) as f:
                 f.write(content)
         if is_gs_path:
             mv_file_to_gs(f'{temp_dir_name}/*', f'{file_path}/', user)