From 63223a8f8959760f769ee5e5d9b5abf179a37ebe Mon Sep 17 00:00:00 2001 From: Logan Drescher Date: Wed, 5 Feb 2025 12:10:11 -0500 Subject: [PATCH] More nightly test result updates --- .github/workflows/NightlyBMDB_CLI.yml | 2 +- .../src/main/resources/test_cases.ndjson | 78 +++++++++---------- .../testsupport/OmexTestingDatabase.java | 1 + 3 files changed, 41 insertions(+), 40 deletions(-) diff --git a/.github/workflows/NightlyBMDB_CLI.yml b/.github/workflows/NightlyBMDB_CLI.yml index 0e979a6db5..90b50b86b7 100644 --- a/.github/workflows/NightlyBMDB_CLI.yml +++ b/.github/workflows/NightlyBMDB_CLI.yml @@ -205,7 +205,7 @@ jobs: sim_input="/root/${base_name}" sim_output="/root/${base_extless_name}_output" echo -n "Running \"${file}\" in output folder \"${base_extless_name}_output\"..." - docker run -v $GITHUB_WORKSPACE/set_${{ matrix.sets }}:/root $(docker image ls | grep "" | awk '{print $3;}') execute-omex -i ${sim_input} -o ${sim_output} --timeout_ms=1200000 + docker run -v $GITHUB_WORKSPACE/set_${{ matrix.sets }}:/root $(docker image ls | grep "" | awk '{print $3;}') execute-omex -i ${sim_input} -o ${sim_output} --timeout_ms=900000 echo "Done!" # Grab Summary echo -n "Obtaining Summary..." diff --git a/vcell-cli/src/main/resources/test_cases.ndjson b/vcell-cli/src/main/resources/test_cases.ndjson index 2f5d33781e..2ea476fc40 100644 --- a/vcell-cli/src/main/resources/test_cases.ndjson +++ b/vcell-cli/src/main/resources/test_cases.ndjson @@ -702,7 +702,7 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000592.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SEDML_NO_SEDMLS_TO_EXECUTE","known_failure_desc":"writeErrorList(): BIOMD0000000592 java.lang.RuntimeException: There are no SED-MLs in the archive to execute"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000593.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SEDML_NO_SEDMLS_TO_EXECUTE","known_failure_desc":"writeErrorList(): BIOMD0000000593 java.lang.RuntimeException: There are no SED-MLs in the archive to execute"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000594.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000595.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":"timeout > 12 minutes"} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000595.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"TIMEOUT_ENCOUNTERED","known_failure_desc":"takes time (> 12 minutes), but otherwise passes"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000596.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_XML_NODE_FAILURE","known_failure_desc":"java.lang.ClassCastException: 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":"BIOMD0000000597.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000598.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -1116,7 +1116,7 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001010.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001011.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001012.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001013.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SOLVER_FAILURE","known_failure_desc":"Failed execution: Model 'BIOMD0000001013_Leon-Triana2021 - eqs 1 and 2 - fig 3b.sedml_model15' Task 'task1'. java.lang.RuntimeException: Could not execute code: Unexpected error: Process timed out\n\n(/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 \"/tmp/VCell_CLI_193f9b57e146875651314089006626/BIOMD0000001013/Leon-Triana2021 - eqs 1 and 2 - fig 3b.sedml/SimID_1601148481_0_.cvodeInput\" \"/tmp/VCell_CLI_193f9b57e146875651314089006626/BIOMD0000001013/Leon-Triana2021 - eqs 1 and 2 - fig 3b.sedml/SimID_1601148481_0_.ida\") "} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001013.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"TIMEOUT_ENCOUNTERED","known_failure_desc":"Failed execution: Model 'BIOMD0000001013_Leon-Triana2021 - eqs 1 and 2 - fig 3b.sedml_model15' Task 'task1'. java.lang.RuntimeException: Could not execute code: Unexpected error: Process timed out\n\n(/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 \"/tmp/VCell_CLI_193f9b57e146875651314089006626/BIOMD0000001013/Leon-Triana2021 - eqs 1 and 2 - fig 3b.sedml/SimID_1601148481_0_.cvodeInput\" \"/tmp/VCell_CLI_193f9b57e146875651314089006626/BIOMD0000001013/Leon-Triana2021 - eqs 1 and 2 - fig 3b.sedml/SimID_1601148481_0_.ida\") "} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001014.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001015.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001016.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -1125,27 +1125,27 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001019.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001020.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001021.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"Error binding global parameter 'Metabolite_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":"BIOMD0000001022.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SOLVER_FAILURE","known_failure_desc":"Failed execution: Model 'BIOMD0000001022_Creemers2021 - Fig 2(B) inset 2.sedml_model6' Task 'task1'. java.lang.RuntimeException: Could not execute code: Unexpected error: Process timed out\n\n(/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 \"/tmp/VCell_CLI_193f9b4214e7972318304477051167/BIOMD0000001022/Creemers2021 - Fig 2(B) inset 2.sedml/SimID_1038023516_0_.cvodeInput\" \"/tmp/VCell_CLI_193f9b4214e7972318304477051167/BIOMD0000001022/Creemers2021 - Fig 2(B) inset 2.sedml/SimID_1038023516_0_.ida\") "} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001022.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"TIMEOUT_ENCOUNTERED","known_failure_desc":"Failed execution: Model 'BIOMD0000001022_Creemers2021 - Fig 2(B) inset 2.sedml_model6' Task 'task1'. java.lang.RuntimeException: Could not execute code: Unexpected error: Process timed out\n\n(/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 \"/tmp/VCell_CLI_193f9b4214e7972318304477051167/BIOMD0000001022/Creemers2021 - Fig 2(B) inset 2.sedml/SimID_1038023516_0_.cvodeInput\" \"/tmp/VCell_CLI_193f9b4214e7972318304477051167/BIOMD0000001022/Creemers2021 - Fig 2(B) inset 2.sedml/SimID_1038023516_0_.ida\") "} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001023.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001024.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001025.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SOLVER_FAILURE","known_failure_desc":"Failed execution: Model 'BIOMD0000001025_Chaudhury2020 Eq 7-9 - Fig 4(B) simulation.sedml_model5' Task 'task1'. java.lang.RuntimeException: Could not execute code: Unexpected error: Process timed out\n\n(/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 \"/tmp/VCell_CLI_193f9b43fd52760581088069625327/BIOMD0000001025/Chaudhury2020 Eq 7-9 - Fig 4(B) simulation.sedml/SimID_1974748314_0_.cvodeInput\" \"/tmp/VCell_CLI_193f9b43fd52760581088069625327/BIOMD0000001025/Chaudhury2020 Eq 7-9 - Fig 4(B) simulation.sedml/SimID_1974748314_0_.ida\") "} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001025.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"TIMEOUT_ENCOUNTERED","known_failure_desc":"Failed execution: Model 'BIOMD0000001025_Chaudhury2020 Eq 7-9 - Fig 4(B) simulation.sedml_model5' Task 'task1'. java.lang.RuntimeException: Could not execute code: Unexpected error: Process timed out\n\n(/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 \"/tmp/VCell_CLI_193f9b43fd52760581088069625327/BIOMD0000001025/Chaudhury2020 Eq 7-9 - Fig 4(B) simulation.sedml/SimID_1974748314_0_.cvodeInput\" \"/tmp/VCell_CLI_193f9b43fd52760581088069625327/BIOMD0000001025/Chaudhury2020 Eq 7-9 - Fig 4(B) simulation.sedml/SimID_1974748314_0_.ida\") "} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001026.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"Error binding global parameter 'Summary_flux_to_RBC' to model: 'Vin' is either not found in your model or is not allowed to be used in the current context"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001027.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_NON_CONSTANT_COMPARTMENTS","known_failure_desc":"Error adding Feature to vcModel org.vcell.sbml.vcell.SBMLImportException: compartment 'Liver' has constant attribute set to False, not currently supported."} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001028.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_NON_CONSTANT_COMPARTMENTS","known_failure_desc":"Error adding Feature to vcModel org.vcell.sbml.vcell.SBMLImportException: compartment 'Liver' has constant attribute set to False, not currently supported."} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001029.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_NON_CONSTANT_COMPARTMENTS","known_failure_desc":"Error adding Feature to vcModel org.vcell.sbml.vcell.SBMLImportException: compartment 'Liver' has constant attribute set to False, not currently supported."} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001030.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SOLVER_FAILURE","known_failure_desc":"Failed execution: Model 'BIOMD0000001030_Sontag2017 - Fig 1D shifted exponential simulation.sedml_model4' Task 'task1'. java.lang.RuntimeException: Could not execute code: Unexpected error: Process timed out\n\n(/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 \"/tmp/VCell_CLI_193f9b42ace2198722070284996283/BIOMD0000001030/Sontag2017 - Fig 1D shifted exponential simulation.sedml/SimID_1085451342_0_.cvodeInput\" \"/tmp/VCell_CLI_193f9b42ace2198722070284996283/BIOMD0000001030/Sontag2017 - Fig 1D shifted exponential simulation.sedml/SimID_1085451342_0_.ida\") "} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001030.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"TIMEOUT_ENCOUNTERED","known_failure_desc":"Failed execution: Model 'BIOMD0000001030_Sontag2017 - Fig 1D shifted exponential simulation.sedml_model4' Task 'task1'. java.lang.RuntimeException: Could not execute code: Unexpected error: Process timed out\n\n(/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 \"/tmp/VCell_CLI_193f9b42ace2198722070284996283/BIOMD0000001030/Sontag2017 - Fig 1D shifted exponential simulation.sedml/SimID_1085451342_0_.cvodeInput\" \"/tmp/VCell_CLI_193f9b42ace2198722070284996283/BIOMD0000001030/Sontag2017 - Fig 1D shifted exponential simulation.sedml/SimID_1085451342_0_.ida\") "} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001031.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"TIMEOUT_ENCOUNTERED","known_failure_desc":"Failed execution: Model 'BIOMD0000001031_Al-Tuwairqi2020 - Fig2b simulation.sedml_model6' Task 'task1'. java.lang.RuntimeException: Could not execute code: Unexpected error: Process timed out\n\n(/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 \"/tmp/VCell_CLI_193f9b4239d16177731767565387322/BIOMD0000001031/Al-Tuwairqi2020 - Fig2b simulation.sedml/SimID_1472540734_0_.cvodeInput\" \"/tmp/VCell_CLI_193f9b4239d16177731767565387322/BIOMD0000001031/Al-Tuwairqi2020 - Fig2b simulation.sedml/SimID_1472540734_0_.ida\") "} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001032.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001033.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001034.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001035.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SOLVER_FAILURE","known_failure_desc":"Failed execution: Model 'BIOMD0000001035_Al-Tuwairqi2020 - Fig7(a) simulation.sedml_model11' Task 'task1'. java.lang.RuntimeException: Could not execute code: Unexpected error: Process timed out\n\n(/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 \"/tmp/VCell_CLI_193f9b48bb36616768759896770720/BIOMD0000001035/Al-Tuwairqi2020 - Fig7(a) simulation.sedml/SimID_724140336_0_.cvodeInput\" \"/tmp/VCell_CLI_193f9b48bb36616768759896770720/BIOMD0000001035/Al-Tuwairqi2020 - Fig7(a) simulation.sedml/SimID_724140336_0_.ida\") "} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001035.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"TIMEOUT_ENCOUNTERED","known_failure_desc":"Failed execution: Model 'BIOMD0000001035_Al-Tuwairqi2020 - Fig7(a) simulation.sedml_model11' Task 'task1'. java.lang.RuntimeException: Could not execute code: Unexpected error: Process timed out\n\n(/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 \"/tmp/VCell_CLI_193f9b48bb36616768759896770720/BIOMD0000001035/Al-Tuwairqi2020 - Fig7(a) simulation.sedml/SimID_724140336_0_.cvodeInput\" \"/tmp/VCell_CLI_193f9b48bb36616768759896770720/BIOMD0000001035/Al-Tuwairqi2020 - Fig7(a) simulation.sedml/SimID_724140336_0_.ida\") "} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001036.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001037.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001038.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001039.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_NON_CONSTANT_COMPARTMENTS","known_failure_desc":"Error adding Feature to vcModel org.vcell.sbml.vcell.SBMLImportException: compartment 'Liver' has constant attribute set to False, not currently supported."} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001040.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"Error binding global parameter 'Summary_flux_to_RBC' to model: 'Vin' is either not found in your model or is not allowed to be used in the current context"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001041.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001042.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SOLVER_FAILURE","known_failure_desc":"Failed execution: Model 'BIOMD0000001042_Makhlouf2020 - Fig1(b).sedml_model1' Task 'task1'. java.lang.RuntimeException: Could not execute code: Unexpected error: Process timed out\n\n(/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 \"/tmp/VCell_CLI_193fa3dcefc8848860965362711991/BIOMD0000001042/Makhlouf2020 - Fig1(b).sedml/SimID_1236394790_0_.cvodeInput\" \"/tmp/VCell_CLI_193fa3dcefc8848860965362711991/BIOMD0000001042/Makhlouf2020 - Fig1(b).sedml/SimID_1236394790_0_.ida\") "} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001042.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"TIMEOUT_ENCOUNTERED","known_failure_desc":"Failed execution: Model 'BIOMD0000001042_Makhlouf2020 - Fig1(b).sedml_model1' Task 'task1'. java.lang.RuntimeException: Could not execute code: Unexpected error: Process timed out\n\n(/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 \"/tmp/VCell_CLI_193fa3dcefc8848860965362711991/BIOMD0000001042/Makhlouf2020 - Fig1(b).sedml/SimID_1236394790_0_.cvodeInput\" \"/tmp/VCell_CLI_193fa3dcefc8848860965362711991/BIOMD0000001042/Makhlouf2020 - Fig1(b).sedml/SimID_1236394790_0_.ida\") "} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001043.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"TIMEOUT_ENCOUNTERED","known_failure_desc":"Failed execution: Model 'BIOMD0000001043_Wodarz2001 - Fig3A non-cytotoxic.sedml_model' Task 'task1'. java.lang.RuntimeException: Could not execute code: Unexpected error: Process timed out\n\n(/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 \"/tmp/VCell_CLI_193f9b4ce9c2304006454824128300/BIOMD0000001043/Wodarz2001 - Fig3A non-cytotoxic.sedml/SimID_1036516481_0_.cvodeInput\" \"/tmp/VCell_CLI_193f9b4ce9c2304006454824128300/BIOMD0000001043/Wodarz2001 - Fig3A non-cytotoxic.sedml/SimID_1036516481_0_.ida\") "} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001044.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_XML_NODE_FAILURE","known_failure_desc":"java.lang.ClassCastException: 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":"BIOMD0000001045.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -1184,7 +1184,7 @@ {"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_10829774.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"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} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_116898345.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -1197,13 +1197,13 @@ {"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":true,"known_status":"FAIL","known_failure_type": "TIMEOUT_ENCOUNTERED","known_failure_desc":null} +{"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_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":true,"known_status":"FAIL","known_failure_type": "TIMEOUT_ENCOUNTERED","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_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_168717401.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} +{"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} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_171423486.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -1212,9 +1212,9 @@ {"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":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":true,"known_status":"FAIL","known_failure_type": "TIMEOUT_ENCOUNTERED","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_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.) "} @@ -1222,14 +1222,14 @@ {"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":"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_205406319.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_206022012.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} +{"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":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_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} @@ -1259,7 +1259,7 @@ {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_31584491.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_32288619.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_32579611.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_34855932.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_34855932.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SEDML_IMPORT_FAILURE","known_failure_desc":null} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_35789302.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SEDML_IMPORT_FAILURE","known_failure_desc":null} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_36053554.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_36230715.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -1268,11 +1268,11 @@ {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_40883478.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_40883509.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_43726934.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SEDML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sedml.SEDMLImportException: BioModel `ess_biomodel_43726934.sedml_compartmental` not found in mapping; mismatch in SedMLImporter!!"} -{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_49411430.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} +{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_49411430.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SEDML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sedml.SEDMLImportException: BioModel `ess_biomodel_49411430.sedml__0930` not found in mapping; mismatch in SedMLImporter!!"} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_50584157.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_59280306.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_59361239.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_60113862.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} +{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_59280306.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_59361239.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SEDML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sedml.SEDMLImportException: BioModel `ess_biomodel_59361239.sedml_individual_knockouts_with_delay` not found in mapping; mismatch in SedMLImporter!!"} +{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_60113862.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SEDML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sedml.SEDMLImportException: BioModel `ess_biomodel_60113862.sedml_psGDIfactor_R1_0_1__find_SS_with_no_gluc` not found in mapping; mismatch in SedMLImporter!!"} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_60647264.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_60647373.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_60705749.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -1281,12 +1281,12 @@ {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_61340695.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SEDML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sedml.SEDMLImportException: BioModel `ess_biomodel_61340695.sedml_VSP_PHD_Geo` not found in mapping; mismatch in SedMLImporter!!"} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_61414583.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_61629922.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_61680876.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_61699798.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_62467093.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_61680876.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SEDML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sedml.SEDMLImportException: BioModel `ess_biomodel_61680876.sedml_Ca_buffered_pulses` not found in mapping; mismatch in SedMLImporter!!"} +{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_61699798.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SEDML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sedml.SEDMLImportException: BioModel `ess_biomodel_61699798.sedml_Ca_buffered__pulses` not found in mapping; mismatch in SedMLImporter!!"} +{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_62467093.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SEDML_IMPORT_FAILURE","known_failure_desc":null} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_62477836.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_62585003.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_62849940.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_62849940.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SEDML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sedml.SEDMLImportException: BioModel `ess_biomodel_62849940.sedml_Temporal_stimulation__decay_` not found in mapping; mismatch in SedMLImporter!!"} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_6436213.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_65182838.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SEDML_IMPORT_FAILURE","known_failure_desc":null} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_65183024.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SEDML_IMPORT_FAILURE","known_failure_desc":null} @@ -1297,20 +1297,20 @@ {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_74924130.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_7681482.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SEDML_IMPORT_FAILURE","known_failure_desc":null} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_81992349.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_82065439.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_82065439.omex","should_fail":false,"known_status":"FAIL","known_failure_type": "SEDML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sedml.SEDMLImportException: BioModel `ess_biomodel_82065439.sedml_circle` not found in mapping; mismatch in SedMLImporter!!"} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_82798486.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_82799056.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} +{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_82799056.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SEDML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sedml.SEDMLImportException: BioModel `ess_biomodel_82799056.sedml_Basic_1_2_3_system___PA5_006_3_` not found in mapping; mismatch in SedMLImporter!!"} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_82799247.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_82799266.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_83446023.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_83932776.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_83932806.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} +{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_83932806.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SEDML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sedml.SEDMLImportException: BioModel `ess_biomodel_83932806.sedml__10x10x10_numbered_geometry` not found in mapping; mismatch in SedMLImporter!!"} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_84069156.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_84235320.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_84275910.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_84982814.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} +{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_84982814.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SEDML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sedml.SEDMLImportException: BioModel `ess_biomodel_84982814.sedml_GMO_Compartmental` not found in mapping; mismatch in SedMLImporter!!"} {"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_84985561.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SEDML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sedml.SEDMLImportException: BioModel `ess_biomodel_84985561.sedml_steady_state` not found in mapping; mismatch in SedMLImporter!!"} -{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_89712092.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_89712092.omex","should_fail":false,"known_status":"FAIL","known_failure_type": "SEDML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sedml.SEDMLImportException: BioModel `ess_biomodel_89712092.sedml_steady_state_compartment` not found in mapping; 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} @@ -1325,16 +1325,16 @@ {"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":"PASS","known_failure_type":null,"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":"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":true,"known_status":"FAIL","known_failure_type": "TIMEOUT_ENCOUNTERED","known_failure_desc":null} -{"test_collection":"VCELL_PUBLISHED_OMEX","file_path":"VCDB_published_95675197.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_95675441.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_95676312.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_95682290.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_95686613.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_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} 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 288c40488f..30857639cb 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 @@ -139,6 +139,7 @@ private static FailureType determineFault(TraceEvent traceEvent){ if (traceEvent.exception instanceof SolverException solverException) { 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; }