From 8243b64ad1a9d5e98852152e155c4dcf2d037009 Mon Sep 17 00:00:00 2001 From: Logan Drescher Date: Thu, 6 Feb 2025 14:27:51 -0500 Subject: [PATCH] Updating Post-small mesh --- .../main/java/org/vcell/cli/run/RunUtils.java | 1 - .../java/org/vcell/cli/run/SolverHandler.java | 4 +- .../src/main/resources/test_cases.ndjson | 110 +++++++++--------- .../vcell/sedml/testsupport/FailureType.java | 1 + .../sedml/testsupport/OmexTestReport.java | 12 +- .../testsupport/OmexTestingDatabase.java | 27 +++-- 6 files changed, 82 insertions(+), 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 index 9c87bf9474..c34eec0464 100644 --- 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 index eec4eb2c7b..39508d8d9c 100644 --- 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 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 biosimStatusMap = new LinkedHashMap<>(); cbit.util.xml.VCLogger sedmlImportLogger = new LocalLogger(); @@ -526,6 +527,7 @@ public Map 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..."); diff --git a/vcell-cli/src/main/resources/test_cases.ndjson b/vcell-cli/src/main/resources/test_cases.ndjson index 2ea476fc40..b59d4dc617 100644 --- a/vcell-cli/src/main/resources/test_cases.ndjson +++ b/vcell-cli/src/main/resources/test_cases.ndjson @@ -1180,10 +1180,10 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001078.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001079.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001080.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_101962320.omex","should_fail":true,"known_status":"FAIL","known_failure_type": "TIMEOUT_ENCOUNTERED","known_failure_desc":null} -{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_101981216.omex","should_fail":true,"known_status":"FAIL","known_failure_type": "TIMEOUT_ENCOUNTERED","known_failure_desc":null} +{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_101962320.omex","should_fail":true,"known_status":"FAIL","known_failure_type":"TIMEOUT_ENCOUNTERED","known_failure_desc":null} +{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_101981216.omex","should_fail":true,"known_status":"FAIL","known_failure_type":"TIMEOUT_ENCOUNTERED","known_failure_desc":null} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_102802266.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SOLVER_FAILURE","known_failure_desc":null} -{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_105608907.omex","should_fail":true,"known_status":"FAIL","known_failure_type": "TIMEOUT_ENCOUNTERED","known_failure_desc":null} +{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_105608907.omex","should_fail":true,"known_status":"FAIL","known_failure_type":"TIMEOUT_ENCOUNTERED","known_failure_desc":null} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_10829774.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SEDML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sedml.SEDMLImportException: BioModel `ess_biomodel_10829774.sedml_typicalModuleResponseFig2` not found in mapping; mismatch in SedMLImporter!!"} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_116704767.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_116898182.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -1193,16 +1193,16 @@ {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_12522025.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SPECIES_NOT_LOCATED_IN_RESULTS","known_failure_desc":null} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_13714636.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_13717231.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SPECIES_NOT_LOCATED_IN_RESULTS","known_failure_desc":null} -{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_13717282.omex","should_fail":true,"known_status":"FAIL","known_failure_type": "TIMEOUT_ENCOUNTERED","known_failure_desc":null} +{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_13717282.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SPECIES_NOT_LOCATED_IN_RESULTS","known_failure_desc":"RuntimeException: Encountered spatial dataset collection failure. java.lang.RuntimeException: Encountered spatial dataset collection failure."} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_13736736.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_14647285.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_147699816.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SEDML_IMPORT_FAILURE","known_failure_desc":" org.vcell.sedml.SEDMLImportException: BioModel `ess_biomodel_147699816.sedml__sorafenib` not found in mapping; mismatch in SedMLImporter!!"} -{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_148700996.omex","should_fail":false,"known_status":"FAIL","known_failure_type": "SEDML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sedml.SEDMLImportException: BioModel `ess_biomodel_148700996.sedml__2DGeom_nonuniform_dens_v2` not found in mapping; mismatch in SedMLImporter!!"} +{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_148700996.omex","should_fail":false,"known_status":"SKIP","known_failure_type":"MODIFIED_MESH_INVALID","known_failure_desc":"Solver (FVSolverStandalone) status: `Aborted` (Could not execute code: Exception : With current mesh sampling, unexpected membrane found in between Nucleus and Extracellular, considering using finer mesh."} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_154208982.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_154210963.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_155016832.omex","should_fail":false,"known_status":"FAIL","known_failure_type": "SEDML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sedml.SEDMLImportException: BioModel `ess_biomodel_155016832.sedml_Stochastic` not found in mapping; mismatch in SedMLImporter!!"} +{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_155016832.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SEDML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sedml.SEDMLImportException: BioModel `ess_biomodel_155016832.sedml_Stochastic` not found in mapping; mismatch in SedMLImporter!!"} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_158495696.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_16404713.omex","should_fail":true,"known_status":"FAIL","known_failure_type": "TIMEOUT_ENCOUNTERED","known_failure_desc":null} +{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_16404713.omex","should_fail":true,"known_status":"SKIP","known_failure_type":"MODIFIED_MESH_INVALID","known_failure_desc":"Solver (FVSolverStandalone) status: `Aborted` (Could not execute code: Exception : With current mesh sampling, unexpected membrane found in between subVolume2 and subVolume0, considering using finer mesh.\\n\\n\\n(/Users/logandrescher/Development/VCell/app/localsolvers/mac64/FiniteVolume_x64 /var/folders/5t/47gxcbn94td37pk5hmkwszl00000gr/T/VCell_CLI_194dc149b1215510415499069194946/ess/biomodel_16404713.sedml/SimID_986322307_0_.fvinput)) cbit.vcell.solver.SolverException: Solver (FVSolverStandalone) status: `Aborted` (Could not execute code: Exception : With current mesh sampling, unexpected membrane found in between subVolume2 and subVolume0, considering using finer mesh."} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_168717401.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SEDML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sedml.SEDMLImportException: BioModel `ess_biomodel_168717401.sedml_Deterministic` not found in mapping; mismatch in SedMLImporter!!"} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_17028306.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_171423478.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -1211,33 +1211,33 @@ {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_171423851.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_171423920.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_171423957.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_172076998.omex","should_fail":true,"known_status":"FAIL","known_failure_type": "TIMEOUT_ENCOUNTERED","known_failure_desc":null} -{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_17257105.omex","should_fail":false,"known_status":"FAIL","known_failure_type": "SEDML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sedml.SEDMLImportException: BioModel `ess_biomodel_17257105.sedml_spatial` not found in mapping; mismatch in SedMLImporter!!"} +{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_172076998.omex","should_fail":true,"known_status":"FAIL","known_failure_type":"TIMEOUT_ENCOUNTERED","known_failure_desc":null} +{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_17257105.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SEDML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sedml.SEDMLImportException: BioModel `ess_biomodel_17257105.sedml_spatial` not found in mapping; mismatch in SedMLImporter!!"} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_17263179.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_17326658.omex","should_fail":false,"known_status":"FAIL","known_failure_type": "SEDML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sedml.SEDMLImportException: BioModel `ess_biomodel_17326658.sedml_Mg_Green` not found in mapping; mismatch in SedMLImporter!!"} +{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_17326658.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SEDML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sedml.SEDMLImportException: BioModel `ess_biomodel_17326658.sedml_Mg_Green` not found in mapping; mismatch in SedMLImporter!!"} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_174341395.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_176334674.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_185577495.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_INITIAL_CONDITIONS","known_failure_desc":"Failed execution:\\n\\t> Elapsed Time:\\t25ms\\n\\t> Model:\\t\\tess_biomodel_185577495.sedml_Copy_of_Application0_1\\n\\t> Task:\\t\\t\\tdone 1 2 1\\n\\t> Cause:\\t\\tSolverException\\n\\t> Message:\\t\\tSolver (GibsonSolver) status: `Aborted` (solver input file exception: The Initial count for Species 'AC_Count' is 900000000000000\\nwhich is higher than the internal vCell limit of 1000000000.\\nPlease reduce the Initial Condition value for this Species or reduce the compartment size.) cbit.vcell.solver.SolverException: Solver (GibsonSolver) status: `Aborted` (solver input file exception: The Initial count for Species 'AC_Count' is 900000000000000\\nwhich is higher than the internal vCell limit of 1000000000.\\nPlease reduce the Initial Condition value for this Species or reduce the compartment size.) "} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_18894555.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_200301029.omex","should_fail":true,"known_status":"FAIL","known_failure_type": "TIMEOUT_ENCOUNTERED","known_failure_desc":null} -{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_200301683.omex","should_fail":true,"known_status":"FAIL","known_failure_type": "TIMEOUT_ENCOUNTERED","known_failure_desc":null} +{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_200301029.omex","should_fail":true,"known_status":"FAIL","known_failure_type":"TIMEOUT_ENCOUNTERED","known_failure_desc":null} +{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_200301683.omex","should_fail":true,"known_status":"FAIL","known_failure_type":"TIMEOUT_ENCOUNTERED","known_failure_desc":null} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_200965116.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_200999311.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SEDML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sedml.SEDMLImportException: BioModel `ess_biomodel_200999311.sedml_Stochastic1` not found in mapping; mismatch in SedMLImporter!!"} -{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_201022999.omex","should_fail":true,"known_status":"FAIL","known_failure_type": "TIMEOUT_ENCOUNTERED","known_failure_desc":null} -{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_203052143.omex","should_fail":true,"known_status":"FAIL","known_failure_type": "TIMEOUT_ENCOUNTERED","known_failure_desc":null} -{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_203656156.omex","should_fail":true,"known_status":"FAIL","known_failure_type": "TIMEOUT_ENCOUNTERED","known_failure_desc":null} +{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_201022999.omex","should_fail":true,"known_status":"FAIL","known_failure_type":"TIMEOUT_ENCOUNTERED","known_failure_desc":null} +{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_203052143.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} +{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_203656156.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNKNOWN_IDENTIFIER","known_failure_desc":"Failed to export PDE2HDF5 for tsk_0_0 'production' is either not found in your model or is not allowed to be used in the current context. Check that you have provided the correct and full name (e.g. Ca_Cytosol). org.vcell.util.DataAccessException: 'production' is either not found in your model or is not allowed to be used in the current context. Check that you have provided the correct and full name (e.g. Ca_Cytosol)"} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_205406319.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SEDML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sedml.SEDMLImportException: BioModel `ess_biomodel_205406319.sedml__0_3___PKAk0_05_ERKd0_035` not found in mapping; mismatch in SedMLImporter!!"} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_206022012.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SEDML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sedml.SEDMLImportException: BioModel `ess_biomodel_206022012.sedml__5` not found in mapping; mismatch in SedMLImporter!!"} -{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_20754836.omex","should_fail":true,"known_status":"FAIL","known_failure_type": "TIMEOUT_ENCOUNTERED","known_failure_desc":null} -{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_209284198.omex","should_fail":false,"known_status":"FAIL","known_failure_type": "SEDML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sedml.SEDMLImportException: BioModel `ess_biomodel_209284198.sedml_fast_compart_with_3D_S_V___V_V` not found in mapping; mismatch in SedMLImporter!!"} +{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_20754836.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SPECIES_NOT_LOCATED_IN_RESULTS","known_failure_desc":"RuntimeException: Encountered spatial dataset collection failure. java.lang.RuntimeException: Encountered spatial dataset collection failure."} +{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_209284198.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SEDML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sedml.SEDMLImportException: BioModel `ess_biomodel_209284198.sedml_fast_compart_with_3D_S_V___V_V` not found in mapping; mismatch in SedMLImporter!!"} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_217669650.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_220138697.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_22523922.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_22681429.omex","should_fail":true,"known_status":"FAIL","known_failure_type": "TIMEOUT_ENCOUNTERED","known_failure_desc":null} -{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_229605883.omex","should_fail":true,"known_status":"FAIL","known_failure_type": "TIMEOUT_ENCOUNTERED","known_failure_desc":null} +{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_22681429.omex","should_fail":true,"known_status":"SKIP","known_failure_type":"MODIFIED_MESH_INVALID","known_failure_desc":"Solver (FVSolverStandalone) status: `Aborted` (Could not execute code: Exception : With current mesh sampling, unexpected membrane found in between subVolume2 and subVolume0, considering using finer mesh."} +{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_229605883.omex","should_fail":true,"known_status":"FAIL","known_failure_type":"TIMEOUT_ENCOUNTERED","known_failure_desc":null} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_26454052.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SPECIES_NOT_LOCATED_IN_RESULTS","known_failure_desc":null} -{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_26454463.omex","should_fail":true,"known_status":"FAIL","known_failure_type": "TIMEOUT_ENCOUNTERED","known_failure_desc":null} -{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_26455186.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"TIMEOUT_ENCOUNTERED","known_failure_desc":null} +{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_26454463.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SPECIES_NOT_LOCATED_IN_RESULTS","known_failure_desc":"java.lang.RuntimeException: Encountered spatial dataset collection failure."} +{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_26455186.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SPECIES_NOT_LOCATED_IN_RESULTS","known_failure_desc":null} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_26581203.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_26928347.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_27071354.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SPECIES_NOT_LOCATED_IN_RESULTS","known_failure_desc":null} @@ -1247,70 +1247,70 @@ {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_27087758.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} 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mismatch in SedMLImporter!!"} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_91133993.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SOLVER_FAILURE","known_failure_desc":null} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_91134220.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_91134296.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -1322,23 +1322,23 @@ {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_91162818.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_91164078.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_91164682.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_91986407.omex","should_fail":true,"known_status":"FAIL","known_failure_type": "TIMEOUT_ENCOUNTERED","known_failure_desc":null} -{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_93313420.omex","should_fail":true,"known_status":"FAIL","known_failure_type": "TIMEOUT_ENCOUNTERED","known_failure_desc":null} +{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_91986407.omex","should_fail":true,"known_status":"FAIL","known_failure_type":"TIMEOUT_ENCOUNTERED","known_failure_desc":null} +{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_93313420.omex","should_fail":true,"known_status":"FAIL","known_failure_type":"TIMEOUT_ENCOUNTERED","known_failure_desc":null} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_93386467.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SPECIES_NOT_LOCATED_IN_RESULTS","known_failure_desc":null} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_94538871.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SEDML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sedml.SEDMLImportException: BioModel `ess_biomodel_94538871.sedml_test_pH_outside` not found in mapping; mismatch in SedMLImporter!!"} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_94891280.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_95094548.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SEDML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sedml.SEDMLImportException: BioModel `ess_biomodel_95094548.sedml_Copy_of_PLB_0_2uM` not found in mapping; mismatch in SedMLImporter!!"} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_95177642.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_95674618.omex","should_fail":false,"known_status":"FAIL","known_failure_type": "SOLVER_FAILURE","known_failure_desc":null} -{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_95675197.omex","should_fail":true,"known_status":"FAIL","known_failure_type": "SOLVER_FAILURE","known_failure_desc":null} -{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_95675441.omex","should_fail":true,"known_status":"FAIL","known_failure_type": "SEDML_IMPORT_FAILURE","known_failure_desc":null} -{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_95676312.omex","should_fail":true,"known_status":"FAIL","known_failure_type": "SOLVER_FAILURE","known_failure_desc":null} -{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_95682290.omex","should_fail":true,"known_status":"FAIL","known_failure_type": "SOLVER_FAILURE","known_failure_desc":null} -{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_95686613.omex","should_fail":true,"known_status":"FAIL","known_failure_type": "SOLVER_FAILURE","known_failure_desc":null} -{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_95693513.omex","should_fail":true,"known_status":"FAIL","known_failure_type": "TIMEOUT_ENCOUNTERED","known_failure_desc":null} -{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_95693624.omex","should_fail":true,"known_status":"FAIL","known_failure_type": "TIMEOUT_ENCOUNTERED","known_failure_desc":null} -{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_95706942.omex","should_fail":true,"known_status":"FAIL","known_failure_type": "TIMEOUT_ENCOUNTERED","known_failure_desc":null} -{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_95707047.omex","should_fail":true,"known_status":"FAIL","known_failure_type": "TIMEOUT_ENCOUNTERED","known_failure_desc":null} -{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_9590643.omex","should_fail":true,"known_status":"FAIL","known_failure_type": "TIMEOUT_ENCOUNTERED","known_failure_desc":null} -{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_98139292.omex","should_fail":true,"known_status":"FAIL","known_failure_type": "TIMEOUT_ENCOUNTERED","known_failure_desc":null} -{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_98139299.omex","should_fail":true,"known_status":"FAIL","known_failure_type": "SPECIES_NOT_LOCATED_IN_RESULTS","known_failure_desc":"writeDetailedErrorList(): VCDB_published_98139299, doc: RuntimeException: Encountered spatial dataset collection failure. java.lang.RuntimeException: Encountered spatial dataset collection failure"} \ No newline at end of file +{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_95674618.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"MODIFIED_MESH_INVALID","known_failure_desc":"With current mesh sampling, unexpected membrane found in between SR and roi_255, considering using finer mesh"} +{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_95675197.omex","should_fail":true,"known_status":"FAIL","known_failure_type":"SOLVER_FAILURE","known_failure_desc":null} +{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_95675441.omex","should_fail":true,"known_status":"FAIL","known_failure_type":"SEDML_IMPORT_FAILURE","known_failure_desc":null} +{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_95676312.omex","should_fail":true,"known_status":"FAIL","known_failure_type":"SEDML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sedml.SEDMLImportException: BioModel `ess_biomodel_95676312.sedml_ode` not found in mapping; mismatch in SedMLImporter!!"} +{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_95682290.omex","should_fail":true,"known_status":"FAIL","known_failure_type":"SOLVER_FAILURE","known_failure_desc":null} +{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_95686613.omex","should_fail":true,"known_status":"FAIL","known_failure_type":"SOLVER_FAILURE","known_failure_desc":null} +{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_95693513.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} +{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_95693624.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} +{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_95706942.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SEDML_IMPORT_FAILURE","known_failure_desc":"BioModel `ess_biomodel_95706942.sedml_ode` not found in mapping; mismatch in SedMLImporter!!"} +{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_95707047.omex","should_fail":true,"known_status":"FAIL","known_failure_type":"TIMEOUT_ENCOUNTERED","known_failure_desc":null} +{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_9590643.omex","should_fail":true,"known_status":"FAIL","known_failure_type":"SPECIES_NOT_LOCATED_IN_RESULTS","known_failure_desc":null} +{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_98139292.omex","should_fail":true,"known_status":"FAIL","known_failure_type":"SPECIES_NOT_LOCATED_IN_RESULTS","known_failure_desc":null} +{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_98139299.omex","should_fail":true,"known_status":"FAIL","known_failure_type":"SPECIES_NOT_LOCATED_IN_RESULTS","known_failure_desc":"writeDetailedErrorList(): VCDB_published_98139299, doc: RuntimeException: Encountered spatial dataset collection failure. java.lang.RuntimeException: Encountered spatial dataset collection failure"} \ No newline at end of file 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 index 167e6b96fb..ac58963d02 100644 --- a/vcell-core/src/main/java/org/vcell/sedml/testsupport/FailureType.java +++ b/vcell-core/src/main/java/org/vcell/sedml/testsupport/FailureType.java @@ -14,6 +14,7 @@ public enum FailureType { MATH_GENERATION_FAILURE, MATH_OVERRIDES_A_FUNCTION, MATH_OVERRIDES_INVALID, + MODIFIED_MESH_INVALID, NESTED_SEDML_REPEATED_TASK, // We can do a repeated task of a normal task, but not another repeated task. NULL_POINTER_EXCEPTION, OPERATION_NOT_SUPPORTED, // VCell simply doesn't have the necessary features to run this archive. diff --git a/vcell-core/src/main/java/org/vcell/sedml/testsupport/OmexTestReport.java b/vcell-core/src/main/java/org/vcell/sedml/testsupport/OmexTestReport.java index 1bccfd4df9..ea736a62c1 100644 --- a/vcell-core/src/main/java/org/vcell/sedml/testsupport/OmexTestReport.java +++ b/vcell-core/src/main/java/org/vcell/sedml/testsupport/OmexTestReport.java @@ -88,17 +88,19 @@ public OmexTestReport(List testCases, List execSu matchingTestCase.should_fail, OmexTestCase.Status.PASS, null, null); } } - if (execSummary.status == OmexExecSummary.ActualStatus.FAILED){ + if (execSummary.status == OmexExecSummary.ActualStatus.FAILED){ // Includes things we should skip if (matchingTestCase.known_status == OmexTestCase.Status.PASS || matchingTestCase.known_status == null) { System.out.println("Test case marked as "+matchingTestCase.known_status+", but failed "+execSummary.failure_type+": "+execSummary.failure_desc+", "+execSummary.file_path); updatedTestCase = new OmexTestCase(matchingTestCase.test_collection, matchingTestCase.file_path, matchingTestCase.should_fail, OmexTestCase.Status.FAIL, execSummary.failure_type, execSummary.failure_desc); } else if (matchingTestCase.known_status == OmexTestCase.Status.SKIP) { - System.out.println("Test case marked as SKIP and failed with "+execSummary.failure_type+": "+execSummary.failure_desc+", "+execSummary.file_path); - updatedTestCase = new OmexTestCase(matchingTestCase.test_collection, matchingTestCase.file_path, - matchingTestCase.should_fail, OmexTestCase.Status.SKIP, - execSummary.failure_type, execSummary.failure_desc); + if (execSummary.failure_type != matchingTestCase.known_failure_type) { // If we set to skip, and it failed as expected, we're fine! + System.out.println("Test case marked as SKIP ("+matchingTestCase.known_failure_type+") but failed unexpectedly with "+execSummary.failure_type+": "+execSummary.failure_desc+", "+execSummary.file_path); + updatedTestCase = new OmexTestCase(matchingTestCase.test_collection, matchingTestCase.file_path, + matchingTestCase.should_fail, OmexTestCase.Status.SKIP, + execSummary.failure_type, execSummary.failure_desc); + } } else if (matchingTestCase.known_status == OmexTestCase.Status.FAIL) { if (matchingTestCase.known_failure_type == null || !matchingTestCase.known_failure_type.equals(execSummary.failure_type)) { System.out.println("Test case marked as FAIL with different type "+matchingTestCase.known_failure_type+", but failed with "+execSummary.failure_type+": "+execSummary.failure_desc+", "+execSummary.file_path); 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 index 30857639cb..340c2e2b1b 100644 --- a/vcell-core/src/main/java/org/vcell/sedml/testsupport/OmexTestingDatabase.java +++ b/vcell-core/src/main/java/org/vcell/sedml/testsupport/OmexTestingDatabase.java @@ -8,6 +8,7 @@ import org.vcell.sedml.SEDMLImportException; import org.vcell.trace.Span; import org.vcell.trace.TraceEvent; +import org.vcell.util.DataAccessException; import java.io.*; import java.nio.file.FileAlreadyExistsException; @@ -95,18 +96,15 @@ public static List parseOmexTestCases(String testCasesNdjson) thro public static OmexExecSummary summarize(File inputFilePath, Exception exception, List errorEvents, long elapsedTime_ms) { OmexExecSummary execSummary = new OmexExecSummary(); execSummary.file_path = inputFilePath.toString(); - execSummary.status = OmexExecSummary.ActualStatus.FAILED; + execSummary.status = OmexExecSummary.ActualStatus.FAILED; // We assume it's a normal failure right off the bat. execSummary.elapsed_time_ms = elapsedTime_ms; - if (exception != null || !errorEvents.isEmpty()) { - execSummary.failure_type = determineFault(exception, errorEvents); - execSummary.failure_desc = null; - if (exception != null) { - execSummary.failure_desc = exception.getMessage(); - } - if (!errorEvents.isEmpty()) { - execSummary.failure_desc = errorEvents.get(0).message + " " + errorEvents.get(0).exception; - } - } + if (exception == null && errorEvents.isEmpty()) return execSummary; + + // We can do some additional parsing + execSummary.failure_type = determineFault(exception, errorEvents); + + // Either exception must be null, or we must have no events; not both! + execSummary.failure_desc = exception != null ? exception.getMessage() : errorEvents.get(0).message + " " + errorEvents.get(0).exception; return execSummary; } @@ -137,12 +135,19 @@ private static FailureType determineFault(TraceEvent traceEvent){ } if (traceEvent.exception instanceof SolverException solverException) { + if (solverException.getMessage().contains("ith current mesh sampling") + || solverException.getMessage().contains("is too coarse, found isolated membrane element")) + return FailureType.MODIFIED_MESH_INVALID; if (solverException.getMessage().contains("is higher than the internal vCell limit of")) return FailureType.UNSUPPORTED_INITIAL_CONDITIONS; if (solverException.getMessage().contains("divide by zero")) return FailureType.DIVIDE_BY_ZERO; if (solverException.getMessage().contains("timed out")) return FailureType.TIMEOUT_ENCOUNTERED; return FailureType.SOLVER_FAILURE; } + if (traceEvent.exception instanceof DataAccessException dataAccessException) { + if (dataAccessException.getMessage().contains("either not found in your model or is not allowed to be used")) return FailureType.UNKNOWN_IDENTIFIER; + } + if (traceEvent.message.contains("convert necessary file to sbml/sedml combine archive")) return FailureType.VCML_EXPORT_FAILURE;