Updating Post-small mesh

virtualcell · Feb 6, 2025 · 8243b64 · 8243b64
1 parent 0288e52
commit 8243b64
Show file tree

Hide file tree

Showing 6 changed files with 82 additions and 73 deletions.
diff --git a/vcell-cli/src/main/java/org/vcell/cli/run/RunUtils.java b/vcell-cli/src/main/java/org/vcell/cli/run/RunUtils.java
@@ -578,7 +578,6 @@ private static void exportDocument(ExportServiceImpl exportServiceImpl, DataServ
         try {
             exportOutputs = asciiExporter.makeASCIIData(outputContext, jobRequest, vcId.getOwner(), dataServerImpl, exportSpecs, fileDataContainerManager);
         } catch (DataAccessException | IOException e) {
-            logger.error(e);
             throw e;
         }
 

diff --git a/vcell-cli/src/main/java/org/vcell/cli/run/SolverHandler.java b/vcell-cli/src/main/java/org/vcell/cli/run/SolverHandler.java
@@ -51,6 +51,7 @@
 import org.vcell.sbml.vcell.SBMLNonspatialSimResults;
 import org.vcell.sbml.vcell.SBMLSymbolMapping;
 import org.vcell.sedml.SEDMLImporter;
+import org.vcell.util.DataAccessException;
 import org.vcell.util.ISize;
 import org.apache.commons.lang.NotImplementedException;
 import org.apache.logging.log4j.LogManager;
@@ -318,7 +319,7 @@ public TempSimulation getTempSimulation() {
     public Map<AbstractTask, BiosimulationLog.Status> simulateAllTasks(ExternalDocInfo externalDocInfo, SedML sedmlRequested, CLIRecordable cliLogger,
                                  File outputDirForSedml, String outDir, String sedmlLocation,
                                  boolean keepTempFiles, boolean exactMatchOnly, boolean bSmallMeshOverride)
-			throws XMLException, IOException, SEDMLImportException, ExpressionException, PropertyVetoException, SolverException {
+			throws XMLException, IOException, SEDMLImportException, ExpressionException, PropertyVetoException, SolverException, DataAccessException {
         // create the VCDocument(s) (bioModel(s) + application(s) + simulation(s)), do sanity checks
 		Map<AbstractTask, BiosimulationLog.Status> biosimStatusMap = new LinkedHashMap<>();
         cbit.util.xml.VCLogger sedmlImportLogger = new LocalLogger();
@@ -526,6 +527,7 @@ public Map<AbstractTask, BiosimulationLog.Status> simulateAllTasks(ExternalDocIn
 							Tracer.failure(e, "Failed to export PDE2HDF5 for " + task.getId() + " " + e.getMessage());
 							logger.error(e.getMessage(), e);
 							spatialResults.put(new TaskJob(task.getId(), tempSimulationJob.getJobIndex()), null);
+							throw e;
 						}
 					} else {
 						logger.info("Processing non-spatial results of execution...");