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fix test fixtures and update fault list for Linux
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@jcschaff
jcschaff committed Nov 21, 2024
1 parent 6cec020 commit ef59564
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Showing 11 changed files with 2,513 additions and 17 deletions.
32 changes: 16 additions & 16 deletions vcell-cli/src/test/java/org/vcell/cli/run/BSTSBasedOmexExecTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -140,22 +140,22 @@ static Map<String, FAULT> knownFaults() {
//faults.put("misc-projects/BIOMD0000000718.omex", null); // works!!
//faults.put("misc-projects/BIOMD0000000842.omex", null); // works!!
//faults.put("misc-projects/BIOMD0000000843.omex", null); // works!!
faults.put("misc-projects/BIOMD0000000932.omex", FAULT.SEDML_PREPROCESS_FAILURE); // | Root(root) | OMEX_EXECUTE(BSTS_OmexFile_299806559413585814omex) | PROCESSING_SEDML(preProcessDoc) | **** Error: SED-ML processing for /var/folders/zz/gcfcvgtd5v1cdgj2sw4bjzdr0000gr/T/vcell_temp_05f4edae-1193-4e1d-80a9-bf99016edf3d13374866975883240909/Garde2020-Fig2.sedml failed with error: | java.lang.RuntimeException: Failed to create plot file /var/folders/zz/gcfcvgtd5v1cdgj2sw4bjzdr0000gr/T/BSTS_OmexExecTest9311079708082702671/temp/simulation_Garde2020-Fig2.sedml
faults.put("misc-projects/BIOMD0000000944.omex", FAULT.SEDML_PREPROCESS_FAILURE); // | Root(root) | OMEX_EXECUTE(BSTS_OmexFile_10652422074989094828omex) | PROCESSING_SEDML(preProcessDoc) | **** Error: SED-ML processing for /var/folders/zz/gcfcvgtd5v1cdgj2sw4bjzdr0000gr/T/vcell_temp_c678fc1e-c809-4281-a929-b697475fad5d11034735503698684353/Goldbeter2013.sedml failed with error: | java.lang.RuntimeException: Failed to create plot file /var/folders/zz/gcfcvgtd5v1cdgj2sw4bjzdr0000gr/T/BSTS_OmexExecTest4404087004775987568/temp/simulation_Goldbeter2013.sedml
faults.put("misc-projects/BIOMD0000000951.omex", FAULT.SEDML_PREPROCESS_FAILURE); // | Root(root) | OMEX_EXECUTE(BSTS_OmexFile_18094892223264859678omex) | PROCESSING_SEDML(preProcessDoc) | **** Error: SED-ML processing for /var/folders/zz/gcfcvgtd5v1cdgj2sw4bjzdr0000gr/T/vcell_temp_9fe6c239-0047-464f-ba8d-033f9950ef5616996166662536534590/Mitrophanov2015.sedml failed with error: | java.lang.RuntimeException: Failed to create plot file /var/folders/zz/gcfcvgtd5v1cdgj2sw4bjzdr0000gr/T/BSTS_OmexExecTest17248149207139727689/temp/simulation_Mitrophanov2015.sedml
faults.put("misc-projects/BIOMD0000000957.omex", FAULT.SEDML_PREPROCESS_FAILURE); // | Root(root) | OMEX_EXECUTE(BSTS_OmexFile_15398452662216167908omex) | PROCESSING_SEDML(preProcessDoc) | **** Error: SED-ML processing for /var/folders/zz/gcfcvgtd5v1cdgj2sw4bjzdr0000gr/T/vcell_temp_d40b4a5d-9a59-43f3-87fa-6836a78ea0268242714171608426821/Roda2020.sedml failed with error: | java.lang.RuntimeException: Failed to create plot file /var/folders/zz/gcfcvgtd5v1cdgj2sw4bjzdr0000gr/T/BSTS_OmexExecTest15618790497998059623/temp/simulation_Roda2020.sedml
faults.put("misc-projects/BIOMD0000000968.omex", FAULT.SEDML_PREPROCESS_FAILURE); // | Root(root) | OMEX_EXECUTE(BSTS_OmexFile_1952836001547640998omex) | PROCESSING_SEDML(preProcessDoc) | **** Error: SED-ML processing for /var/folders/zz/gcfcvgtd5v1cdgj2sw4bjzdr0000gr/T/vcell_temp_d2ee93af-bb6c-48ca-97f2-98a106e0b7e26203677341757147488/Palmer2008.sedml failed with error: | java.lang.RuntimeException: Failed to create plot file /var/folders/zz/gcfcvgtd5v1cdgj2sw4bjzdr0000gr/T/BSTS_OmexExecTest14998574499587823528/temp/simulation_Palmer2008.sedml
faults.put("misc-projects/BIOMD0000000972.omex", FAULT.SEDML_PREPROCESS_FAILURE); // | Root(root) | OMEX_EXECUTE(BSTS_OmexFile_16129466033006731360omex) | PROCESSING_SEDML(preProcessDoc) | **** Error: SED-ML processing for /var/folders/zz/gcfcvgtd5v1cdgj2sw4bjzdr0000gr/T/vcell_temp_65e8c60c-c8bd-41fe-973e-49b215ee11b71447845804155630300/Tang2020.sedml failed with error: | java.lang.RuntimeException: Failed to create plot file /var/folders/zz/gcfcvgtd5v1cdgj2sw4bjzdr0000gr/T/BSTS_OmexExecTest17277361648850041020/temp/simulation_Tang2020.sedml
faults.put("misc-projects/BIOMD0000000983.omex", FAULT.SEDML_PREPROCESS_FAILURE); // | Root(root) | OMEX_EXECUTE(BSTS_OmexFile_12538305798901592382omex) | PROCESSING_SEDML(preProcessDoc) | **** Error: SED-ML processing for /var/folders/zz/gcfcvgtd5v1cdgj2sw4bjzdr0000gr/T/vcell_temp_0591fd03-88b3-4ad7-a988-c2478671a68812551187952687659692/Zongo2020.sedml failed with error: | java.lang.RuntimeException: Failed to create plot file /var/folders/zz/gcfcvgtd5v1cdgj2sw4bjzdr0000gr/T/BSTS_OmexExecTest12116210176998446933/temp/simulation_Zongo2020.sedml
faults.put("misc-projects/BIOMD0000000985.omex", FAULT.SEDML_PREPROCESS_FAILURE); // | Root(root) | OMEX_EXECUTE(BSTS_OmexFile_11036490625279901942omex) | PROCESSING_SEDML(preProcessDoc) | **** Error: SED-ML processing for /var/folders/zz/gcfcvgtd5v1cdgj2sw4bjzdr0000gr/T/vcell_temp_321f50e0-1f6e-48fc-a4f8-7233662b5f8b12358921756946262823/Gex-Fabry1984.sedml failed with error: | java.lang.RuntimeException: Failed to create plot file /var/folders/zz/gcfcvgtd5v1cdgj2sw4bjzdr0000gr/T/BSTS_OmexExecTest914620207324900201/temp/simulation_Gex-Fabry1984.sedml
faults.put("misc-projects/BIOMD0000000989.omex", FAULT.SEDML_PREPROCESS_FAILURE); // | Root(root) | OMEX_EXECUTE(BSTS_OmexFile_17814250350066747412omex) | PROCESSING_SEDML(preProcessDoc) | **** Error: SED-ML processing for /var/folders/zz/gcfcvgtd5v1cdgj2sw4bjzdr0000gr/T/vcell_temp_20fc8778-795e-4ca2-87e5-954ebc6fde8617940965203697577620/MODEL1712050001.sedml failed with error: | java.lang.RuntimeException: Failed to create plot file /var/folders/zz/gcfcvgtd5v1cdgj2sw4bjzdr0000gr/T/BSTS_OmexExecTest8507375305898450638/temp/simulation_MODEL1712050001.sedml
faults.put("misc-projects/BIOMD0000000991.omex", FAULT.SEDML_PREPROCESS_FAILURE); // | Root(root) | OMEX_EXECUTE(BSTS_OmexFile_2522047989779973244omex) | PROCESSING_SEDML(preProcessDoc) | **** Error: SED-ML processing for /var/folders/zz/gcfcvgtd5v1cdgj2sw4bjzdr0000gr/T/vcell_temp_156e5fee-cd1a-4c28-af49-e6c00cce446e10964600217313052640/Okuonghae2020.sedml failed with error: | java.lang.RuntimeException: Failed to create plot file /var/folders/zz/gcfcvgtd5v1cdgj2sw4bjzdr0000gr/T/BSTS_OmexExecTest10045148909541837809/temp/simulation_Okuonghae2020.sedml
faults.put("misc-projects/BIOMD0000000997.omex", FAULT.SEDML_PREPROCESS_FAILURE); // | Root(root) | OMEX_EXECUTE(BSTS_OmexFile_17043350583827454685omex) | PROCESSING_SEDML(preProcessDoc) | **** Error: BSTS_OmexFile_17043350583827454685omex,MODEL1712050006.sedml,Failed to create plot file /var/folders/zz/gcfcvgtd5v1cdgj2sw4bjzdr0000gr/T/BSTS_OmexExecTest9820394719800166079/temp/simulation_MODEL1712050006.sedml
faults.put("misc-projects/BIOMD0000001010.omex", FAULT.SEDML_PREPROCESS_FAILURE); // | Root(root) | OMEX_EXECUTE(BSTS_OmexFile_901594480328185461omex) | PROCESSING_SEDML(preProcessDoc) | **** Error: BSTS_OmexFile_901594480328185461omex,Zhang2007_M3_low_DD.sedml,Failed to create plot file /var/folders/zz/gcfcvgtd5v1cdgj2sw4bjzdr0000gr/T/BSTS_OmexExecTest1961470606014028473/temp/simulation_Zhang2007_M3_low_DD.sedml
faults.put("misc-projects/BIOMD0000001014.omex", FAULT.SEDML_PREPROCESS_FAILURE); // | Root(root) | OMEX_EXECUTE(BSTS_OmexFile_1371059216516510527omex) | PROCESSING_SEDML(preProcessDoc) | **** Error: BSTS_OmexFile_1371059216516510527omex,Leon-Triana2021 (eqs 3-6).sedml,Failed to create plot file /var/folders/zz/gcfcvgtd5v1cdgj2sw4bjzdr0000gr/T/BSTS_OmexExecTest145372853658544068/temp/simulation_Leon-Triana2021 (eqs 3-6).sedml
faults.put("misc-projects/BIOMD0000001018.omex", FAULT.SEDML_PREPROCESS_FAILURE); // | Root(root) | OMEX_EXECUTE(BSTS_OmexFile_17092676956014497901omex) | PROCESSING_SEDML(preProcessDoc) | **** Error: BSTS_OmexFile_17092676956014497901omex,Bakshi2020 properdin model.sedml,Failed to create plot file /var/folders/zz/gcfcvgtd5v1cdgj2sw4bjzdr0000gr/T/BSTS_OmexExecTest9940912637860611784/temp/simulation_Bakshi2020 properdin model.sedml
faults.put("misc-projects/BIOMD0000001072.omex", FAULT.SEDML_PREPROCESS_FAILURE); // | Root(root) | OMEX_EXECUTE(BSTS_OmexFile_4412450965004248264omex) | PROCESSING_SEDML(preProcessDoc) | **** Error: BSTS_OmexFile_4412450965004248264omex,Phillips2013.sedml,Failed to create plot file /var/folders/zz/gcfcvgtd5v1cdgj2sw4bjzdr0000gr/T/BSTS_OmexExecTest16782612435251983142/temp/simulation_Phillips2013.sedml
faults.put("misc-projects/BIOMD0000001077.omex", FAULT.SEDML_PREPROCESS_FAILURE); // | Root(root) | OMEX_EXECUTE(BSTS_OmexFile_11225596004044316029omex) | PROCESSING_SEDML(preProcessDoc) | **** Error: BSTS_OmexFile_11225596004044316029omex,Adlung2021 _model_jakstat_pa.sedml,Failed to create plot file /var/folders/zz/gcfcvgtd5v1cdgj2sw4bjzdr0000gr/T/BSTS_OmexExecTest7806933134886966313/temp/simulation_Adlung2021 _model_jakstat_pa.sedml
//faults.put("misc-projects/BIOMD0000000932.omex", null); // works!!
//faults.put("misc-projects/BIOMD0000000944.omex", null); // works!!
//faults.put("misc-projects/BIOMD0000000951.omex", null); // works!!
//faults.put("misc-projects/BIOMD0000000957.omex", null); // works!!
//faults.put("misc-projects/BIOMD0000000968.omex", null); // works!!
//faults.put("misc-projects/BIOMD0000000972.omex", null); // works!!
//faults.put("misc-projects/BIOMD0000000983.omex", null); // works!!
//faults.put("misc-projects/BIOMD0000000985.omex", null); // works!!
//faults.put("misc-projects/BIOMD0000000989.omex", null); // works!!
//faults.put("misc-projects/BIOMD0000000991.omex", null); // works!!
//faults.put("misc-projects/BIOMD0000000997.omex", null); // works!!
//faults.put("misc-projects/BIOMD0000001010.omex", null); // works!!
//faults.put("misc-projects/BIOMD0000001014.omex", null); // works!!
//faults.put("misc-projects/BIOMD0000001018.omex", null); // works!!
//faults.put("misc-projects/BIOMD0000001072.omex", null); // works!!
//faults.put("misc-projects/BIOMD0000001077.omex", null); // works!!

return faults;
}
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3 changes: 2 additions & 1 deletion vcell-cli/src/test/java/org/vcell/cli/run/BiosimulationsExecTest.java
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Original file line number Diff line number Diff line change
Expand Up @@ -151,7 +151,8 @@ public void testBiosimulationsProject(String testCaseProjectID) throws Exception
ExecuteImpl.singleMode(omexFile.toFile(), outdirPath.toFile(), cliRecorder);
Path computedH5File = outdirPath.resolve("report.h5");

assertFalse(Tracer.hasErrors(), "failure: '" + Tracer.getErrors().get(0).message.replace("\n", " | "));
String errorMessage = (Tracer.hasErrors()) ? "failure: '" + Tracer.getErrors().get(0).message.replace("\n", " | ") : "";
assertFalse(Tracer.hasErrors(), errorMessage);
if (knownFault != null){
throw new RuntimeException("test case passed, but expected " + knownFault.name() + ", remove "
+ testCaseProjectID + " from known faults");
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