From 51371c35fd136439cd3c44d8772b85eaac4a87cc Mon Sep 17 00:00:00 2001
From: oplantalech <oleguer@thehyve.nl>
Date: Wed, 14 Feb 2024 12:22:41 +0100
Subject: [PATCH] Ignore gene described in the CNA Discrete Long file if it
 cannot be found in the database

---
 .../mskcc/cbio/portal/scripts/ImportCnaDiscreteLongData.java | 5 +++++
 1 file changed, 5 insertions(+)

diff --git a/src/main/java/org/mskcc/cbio/portal/scripts/ImportCnaDiscreteLongData.java b/src/main/java/org/mskcc/cbio/portal/scripts/ImportCnaDiscreteLongData.java
index af67c17a..f03e5b45 100644
--- a/src/main/java/org/mskcc/cbio/portal/scripts/ImportCnaDiscreteLongData.java
+++ b/src/main/java/org/mskcc/cbio/portal/scripts/ImportCnaDiscreteLongData.java
@@ -260,6 +260,11 @@ private CanonicalGene getGene(
             if (genes.size() > 1) {
                 throw new IllegalStateException("Found multiple genes for Hugo symbol " + hugoSymbol + " while importing cna");
             }
+            // Ignore gene if it cannot be found in the database
+            if (genes.size() < 1) {
+                ProgressMonitor.logWarning("Ignoring Hugo symbol " + hugoSymbol + "not found in the database");
+                return null;
+            }
             return genes.get(0);
         }
         ProgressMonitor.logWarning("Entrez_Id " + entrez + " not found. Record will be skipped for this gene.");