From cdba0f94edbba5fa3374332ec4eed36544e523d4 Mon Sep 17 00:00:00 2001
From: Vicky Daiya <37933641+vickydaiya@users.noreply.github.com>
Date: Tue, 28 Nov 2023 18:07:54 -0500
Subject: [PATCH] fix for NaN gene_expr value

---
 containers/gene-expression/context/main.py | 1 +
 1 file changed, 1 insertion(+)

diff --git a/containers/gene-expression/context/main.py b/containers/gene-expression/context/main.py
index 71d2910..8ab0181 100644
--- a/containers/gene-expression/context/main.py
+++ b/containers/gene-expression/context/main.py
@@ -71,6 +71,7 @@ def get_gene_expr(matrix: anndata.AnnData, clid_column: str, gene_expr_column: s
     merged_obs = matrix.obs.merge(
         ct_marker_genes_df[[clid_column, gene_expr_column]], how="left"
     )
+    merged_obs.fillna({gene_expr_column: '[]'}, inplace=True)
     merged_obs[gene_expr_column] = merged_obs[gene_expr_column].apply(json.dumps)
     merged_obs.index = matrix.obs.index
     matrix.obs = merged_obs