Added VCML conversion failure type in preparation for VCML processing

virtualcell · Jan 29, 2025 · 44b082f · 44b082f
1 parent f574f8d
commit 44b082f
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Showing 2 changed files with 10 additions and 2 deletions.
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
@@ -45,5 +45,6 @@ public enum FailureType {
     UNSUPPORTED_DELAY_SBML,
     UNSUPPORTED_NON_CONSTANT_COMPARTMENTS,
     BIOMODEL_IMPORT_SEDML_FAILURE,
+    VCML_EXPORT_FAILURE,
     TIMEOUT_ENCOUNTERED
 }
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
@@ -14,6 +14,7 @@
 import java.nio.file.Paths;
 import java.util.ArrayList;
 import java.util.List;
+import java.util.concurrent.TimeoutException;
 import java.util.stream.Collectors;
 
 public class OmexTestingDatabase {
@@ -29,7 +30,8 @@ public enum TestCollection {
         VCELL_BSTS_SYNTHS(TestDataRepo.vcell, "vcell-cli/src/test/resources/bsts-omex/synths"),
         VCELL_SPATIAL(TestDataRepo.vcell, "vcell-cli/src/test/resources/spatial"),
         SYSBIO_BIOMD(TestDataRepo.sysbio, "omex_files"),
-        VCELL_PUBLISHED(TestDataRepo.vcdb,"published/biomodel/omex/sbml");
+        VCELL_PUBLISHED_OMEX(TestDataRepo.vcdb,"published/biomodel/omex/sbml"),
+        VCELL_PUBLISHED_VCML(TestDataRepo.vcdb,"published/biomodel/vcml");
 
         public final TestDataRepo repo;
         public final String pathPrefix;
@@ -120,6 +122,9 @@ private static FailureType determineFault(TraceEvent traceEvent){
             return (sbmlFailureType = determineFault(traceEvent.exception)) != null ? sbmlFailureType : FailureType.SBML_IMPORT_FAILURE;
         }
 
+        if (traceEvent.message.contains("convert necessary file to sbml/sedml combine archive"))
+            return FailureType.VCML_EXPORT_FAILURE;
+
         if (traceEvent.exception instanceof RuntimeException && traceEvent.message.contains("Failed execution")){
             if (traceEvent.message.contains("divide by zero")) return FailureType.DIVIDE_BY_ZERO;
             if (traceEvent.message.contains("infinite loop")) return FailureType.SOLVER_FAILURE;
@@ -147,7 +152,9 @@ private static FailureType determineFault(TraceEvent traceEvent){
     private static FailureType determineFault(Exception caughtException){
         String errorMessage = caughtException.getMessage();
 
-        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)"
+        if (caughtException instanceof TimeoutException) {
+            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;
         } else if (errorMessage.contains("Non-integer stoichiometry")) {
             return FailureType.UNSUPPORTED_NON_INT_STOCH;