Account for status that indicates Cromwell server issue

oicr-gsi · Nov 11, 2024 · 2fa4aa4 · 2fa4aa4
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diff --git a/changes/fix_fail.md b/changes/fix_fail.md
@@ -0,0 +1,2 @@
+Account for Cromwell server issue
+
diff --git a/vidarr-cromwell/src/main/java/ca/on/oicr/gsi/vidarr/cromwell/CromwellWorkflowEngine.java b/vidarr-cromwell/src/main/java/ca/on/oicr/gsi/vidarr/cromwell/CromwellWorkflowEngine.java
@@ -173,6 +173,11 @@ private void check(EngineState state, WorkMonitor<Result<String>, EngineState> m
                               return null;
                             });
                     break;
+                  // Cromwell has become unavailable or there was a problem initializing the
+                  // Cromwell job. Don't ask Cromwell for more information, just die
+                  case "fail":
+                    monitor.permanentFailure("Cromwell server issue for " + result.getId() + ": " + result.getStatus());
+                    break;
                   case "Succeeded":
                     finish(state, monitor);
                     break;