diff --git a/.github/workflows/NightlyBMDB_CLI.yml b/.github/workflows/NightlyBMDB_CLI.yml index f9f13478f6..9514f724ec 100644 --- a/.github/workflows/NightlyBMDB_CLI.yml +++ b/.github/workflows/NightlyBMDB_CLI.yml @@ -175,7 +175,7 @@ jobs: echo "Skipping ${file_name}" continue fi - if [ $number -eq 235 ] || [ $number -eq 255 ] || [ $number -eq 595 ] || [ $number -eq 1008 ]; then + if [ $number -eq 235 ] || [ $number -eq 255 ] || [ $number -eq 595 ] || [ $number -eq 711 ] || [ $number -eq 1008 ]; then echo "Skipping ${file_name} - too slow or otherwise misbehaved" continue fi diff --git a/vcell-cli/src/main/resources/test_cases.ndjson b/vcell-cli/src/main/resources/test_cases.ndjson index acbed10e27..401c39f518 100644 --- a/vcell-cli/src/main/resources/test_cases.ndjson +++ b/vcell-cli/src/main/resources/test_cases.ndjson @@ -709,44 +709,44 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000605.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000606.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000607.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000608.omex","should_fail":false,"known_status":null,"known_failure_type":null,"known_failure_desc":null} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000608.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('0.5' for reactant 'x_18' in reaction 'R_18') not handled in VCell at this time."} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000609.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000610.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000611.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000612.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000613.omex","should_fail":false,"known_status":null,"known_failure_type":null,"known_failure_desc":null} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000613.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"Error binding global parameter 'Q0' 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":"BIOMD0000000614.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000615.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000616.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000617.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000618.omex","should_fail":false,"known_status":null,"known_failure_type":null,"known_failure_desc":null} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000618.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"Error processing model: model2 - couldn't find SBase with sid=null in SBMLSymbolMapping org.vcell.sbml.vcell.SBMLImportException: couldn't find SBase with sid=null in SBMLSymbolMapping"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000619.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000620.omex","should_fail":false,"known_status":null,"known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000621.omex","should_fail":false,"known_status":null,"known_failure_type":null,"known_failure_desc":null} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000620.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNCATETORIZED_FAULT","known_failure_desc":"Failed execution: Model 'BIOMD0000000620_BIOMD0000000620_url.sedml_BIOMD0000000620_url' Task 'task1'. java.lang.RuntimeException: Could not execute code: CVODE solver failed : at time 5.5, discontinuity (t == Anakinra_dose_counter) evaluated to TRUE, solver assumed FALSE"} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000621.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNCATETORIZED_FAULT","known_failure_desc":"Failed execution: Model 'BIOMD0000000621_BIOMD0000000621_url.sedml_BIOMD0000000621_url' Task 'task1'. java.lang.RuntimeException: Could not execute code: CVODE solver failed : at time 5.5, discontinuity (t == Anakinra_dose_counter) evaluated to TRUE, solver assumed FALSE"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000622.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000623.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000624.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000625.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000626.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000627.omex","should_fail":false,"known_status":null,"known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000628.omex","should_fail":false,"known_status":null,"known_failure_type":null,"known_failure_desc":null} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000627.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"Error adding Feature to vcModel org.vcell.sbml.vcell.SBMLImportException: compartment 'venous_balloon' has constant attribute set to False, not currently supported."} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000628.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"Error binding global parameter 'Metabolite_8' 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":"BIOMD0000000629.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000630.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000631.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000632.omex","should_fail":false,"known_status":null,"known_failure_type":null,"known_failure_desc":null} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000632.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"Error binding global parameter 'k4b' 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":"BIOMD0000000633.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000634.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000635.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000636.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000637.omex","should_fail":false,"known_status":null,"known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000638.omex","should_fail":false,"known_status":null,"known_failure_type":null,"known_failure_desc":null} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000637.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNCATETORIZED_FAULT","known_failure_desc":"Cannot invoke \"cbit.vcell.solver.Simulation.getImportedTaskID()\" because \"simulation\" is null"} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000638.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNCATETORIZED_FAULT","known_failure_desc":"Cannot invoke \"cbit.vcell.solver.Simulation.getImportedTaskID()\" because \"simulation\" is null"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000639.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000640.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000641.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000642.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000643.omex","should_fail":false,"known_status":null,"known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000644.omex","should_fail":false,"known_status":null,"known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000645.omex","should_fail":false,"known_status":null,"known_failure_type":null,"known_failure_desc":null} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000643.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNCATETORIZED_FAULT","known_failure_desc":"Cannot invoke \"cbit.vcell.solver.Simulation.getImportedTaskID()\" because \"simulation\" is null"} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000644.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNCATETORIZED_FAULT","known_failure_desc":"Cannot invoke \"cbit.vcell.solver.Simulation.getImportedTaskID()\" because \"simulation\" is null"} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000645.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNCATETORIZED_FAULT","known_failure_desc":"Cannot invoke \"cbit.vcell.solver.Simulation.getImportedTaskID()\" because \"simulation\" is null"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000646.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000647.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000648.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -773,7 +773,7 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000670.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000671.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000672.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000673.omex","should_fail":false,"known_status":null,"known_failure_type":null,"known_failure_desc":null} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000673.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNCATETORIZED_FAULT","known_failure_desc":"Failed execution: Model 'BIOMD0000000673_MODEL1006230054_edited.sedml_model' Task 'task1'. java.lang.RuntimeException: Could not execute code: \n[CVDENSE ERROR] CVDense\n A memory request failed.\n\nCVODE solver failed : CV_CONV_FAILURE: convergence test failures occurred too many times during one internal step"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000674.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000675.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000676.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -795,7 +795,7 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000692.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000693.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000695.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000696.omex","should_fail":false,"known_status":null,"known_failure_type":null,"known_failure_desc":null} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000696.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"Error binding global parameter 'Metabolite_16' 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":"BIOMD0000000697.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000698.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000699.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -804,13 +804,13 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000702.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000703.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000704.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000705.omex","should_fail":false,"known_status":null,"known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000706.omex","should_fail":false,"known_status":null,"known_failure_type":null,"known_failure_desc":null} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000705.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"Error binding global parameter 'Metabolite_21' 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":"BIOMD0000000706.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"found more than one SBase match for sid=v, matched [org.vcell.sbml.vcell.SBMLSymbolMapping$SBaseWrapper@4c5da4f9, org.vcell.sbml.vcell.SBMLSymbolMapping$SBaseWrapper@6987a133]"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000707.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"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":null,"known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000711.omex","should_fail":false,"known_status":null,"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":"UNCATETORIZED_FAULT","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} @@ -818,7 +818,7 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000716.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000717.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000718.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000719.omex","should_fail":false,"known_status":null,"known_failure_type":null,"known_failure_desc":null} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000719.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNCATETORIZED_FAULT","known_failure_desc":"Failed execution: Model 'BIOMD0000000719_tsai2014.sedml_model' Task 'task1'. java.lang.RuntimeException: Could not execute code: \n[CVODE ERROR] CVode\n The right-hand side routine failed at the first call.\n\nCVODE solver failed : CV_FIRST_RHSFUNC_ERR: The right-hand side routine failed at the first call : DivideByZeroException : DivideByZeroException : divide by zero in \"( - (1.5 * (APC_C_active - APC_C_total) / (1 + ((0.5 / Plx1_active) ^ 4))) - (0.14999999999999999445 * APC_C_active))\"\n where:\n\tAPC_C_active = 1.000000\n\tAPC_C_total = 1.000000\n\tPlx1_active = 0.000000"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000720.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000721.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000722.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -830,15 +830,15 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000728.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000729.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000730.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000731.omex","should_fail":false,"known_status":null,"known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000732.omex","should_fail":false,"known_status":null,"known_failure_type":null,"known_failure_desc":null} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000731.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"Error binding global parameter 'Treg_origin_fraction_CD4' to model: 'func_TRegs_Production_from_CD4' is either not found in your model or is not allowed to be used in the current context"} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000732.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNCATETORIZED_FAULT","known_failure_desc":"Failed execution: Model 'BIOMD0000000732_Kirschner_1998.sedml_model' Task 'task1'. java.lang.RuntimeException: Could not execute code: \n[CVODE WARNING] CVode\n Internal t = 737.903 and h = 3.5563e-14 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 737.903 and h = 3.5563e-14 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 737.903 and h = 3.5563e-14 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 737.903 and h = 3.5563e-14 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 737.903 and h = 2.21887e-14 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 737.903 and h = 2.21887e-14 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 737.903 and h = 2.21887e-14 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 737.903 and h = 2.21887e-14 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 737.903 and h = 1.36968e-14 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 737.903 and h = 1.36968e-14 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n The above warning has been issued mxhnil times and will not be issued again for this problem.\n\n\n[CVODE ERROR] CVode\n At t = 737.903, mxstep steps taken before reaching tout.\n\nCVODE solver failed : CV_TOO_MUCH_WORK: took mxstep internal steps but could not reach tout.\n\nTry reducing maximum time step."} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000733.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000734.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000735.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000736.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000737.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000738.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000739.omex","should_fail":false,"known_status":null,"known_failure_type":null,"known_failure_desc":null} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000739.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"Error binding global parameter 'Metabolite_19' 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":"BIOMD0000000740.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000741.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000742.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -863,7 +863,7 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000761.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000762.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000763.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000764.omex","should_fail":false,"known_status":null,"known_failure_type":null,"known_failure_desc":null} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000764.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"Error binding global parameter 'Metabolite_3' 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":"BIOMD0000000765.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000766.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000767.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -885,7 +885,7 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000783.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000784.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000785.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000786.omex","should_fail":false,"known_status":null,"known_failure_type":null,"known_failure_desc":null} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000786.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNCATETORIZED_FAULT","known_failure_desc":"class org.sbml.jsbml.xml.XMLNode cannot be cast to class org.sbml.jsbml.Annotation (org.sbml.jsbml.xml.XMLNode and org.sbml.jsbml.Annotation are in unnamed module of loader 'app')"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000787.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000788.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000789.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -893,7 +893,7 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000791.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000792.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000793.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000794.omex","should_fail":false,"known_status":null,"known_failure_type":null,"known_failure_desc":null} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000794.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNCATETORIZED_FAULT","known_failure_desc":"class org.sbml.jsbml.xml.XMLNode cannot be cast to class org.sbml.jsbml.Annotation (org.sbml.jsbml.xml.XMLNode and org.sbml.jsbml.Annotation are in unnamed module of loader 'app')"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000795.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000796.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000797.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null}