Fixing fault case labeling

virtualcell · Jan 30, 2025 · 537c9f1 · 537c9f1
1 parent e9bed12
commit 537c9f1
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Showing 3 changed files with 2 additions and 5 deletions.
diff --git a/vcell-cli/src/main/resources/test_cases.ndjson b/vcell-cli/src/main/resources/test_cases.ndjson
@@ -816,7 +816,7 @@
 {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000708.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null}
 {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000709.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null}
 {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000710.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"Error binding global parameter 'Metabolite_0_0' to model: 'UNRESOLVED.initConc' is either not found in your model or is not allowed to be used in the current context"}
-{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000711.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"TOO_SLOW","known_failure_desc":"> 5 minutes - Failed execution: Model 'BIOMD0000000711_Hancioglu2007 - Human Immune Response to Influenza A virus.sedml_model' Task 'task1'.  java.lang.RuntimeException: Could not execute code: Unexpected error: Process timed out"}
+{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000711.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"TIMEOUT_ENCOUNTERED","known_failure_desc":"> 5 minutes - Failed execution: Model 'BIOMD0000000711_Hancioglu2007 - Human Immune Response to Influenza A virus.sedml_model' Task 'task1'.  java.lang.RuntimeException: Could not execute code: Unexpected error: Process timed out"}
 {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000712.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null}
 {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000713.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null}
 {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000714.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null}

diff --git a/vcell-core/src/main/java/org/vcell/sedml/testsupport/FailureType.java b/vcell-core/src/main/java/org/vcell/sedml/testsupport/FailureType.java
@@ -31,7 +31,6 @@ public enum FailureType {
     SEDML_UNSUPPORTED_MODEL_REFERENCE, // Model refers to either a non-existent model (invalid SED-ML) or to another model with changes (not supported yet)
     SEDML_NON_UTC_SIMULATION_FOUND,
     SEDML_SBML_LEVEL_CHANGE, // unsupported SBML Level change within the SED-ML
-    TOO_SLOW,
     UNCATEGORIZED_FAULT,
     UNITS_EXCEPTION,
     UNKNOWN_IDENTIFIER,

diff --git a/vcell-core/src/main/java/org/vcell/sedml/testsupport/OmexTestingDatabase.java b/vcell-core/src/main/java/org/vcell/sedml/testsupport/OmexTestingDatabase.java
@@ -152,7 +152,7 @@ private static FailureType determineFault(TraceEvent traceEvent){
     private static FailureType determineFault(Exception caughtException){
         String errorMessage = caughtException.getMessage();
 
-        if (caughtException instanceof TimeoutException) {
+        if (caughtException instanceof TimeoutException || errorMessage.contains("Process timed out")) {
             return FailureType.TIMEOUT_ENCOUNTERED;
         } else if (errorMessage.contains("refers to either a non-existent model")) { //"refers to either a non-existent model (invalid SED-ML) or to another model with changes (not supported yet)"
             return FailureType.SEDML_UNSUPPORTED_MODEL_REFERENCE;
@@ -189,8 +189,6 @@ private static FailureType determineFault(Exception caughtException){
             return FailureType.UNSUPPORTED_DELAY_SBML;
         } else if (errorMessage.contains("are in unnamed module of loader")){
             return FailureType.SBML_IMPORT_FAILURE;
-        } else if (errorMessage.contains("Process timed out")) {
-            return FailureType.TOO_SLOW;
         }
         return null;
     }