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Merge pull request #1392 from virtualcell/fix-sedml-repeated-1
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OMEX Execution fails with repeated task of size 1
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@jcschaff
jcschaff authored Nov 21, 2024
2 parents 8333ce3 + 52cd0ec commit adce77c
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Showing 10 changed files with 130 additions and 110 deletions.
24 changes: 16 additions & 8 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 @@ -123,21 +123,19 @@ static Map<String, FAULT> knownFaults() {
FAULT.SEDML_ERRONEOUS_UNIT_SYSTEM);


// faults.put("misc-projects/BIOMD0000000005.omex", null); // works
faults.put("misc-projects/BIOMD0000000302.omex", FAULT.MATH_GENERATION_FAILURE); // | Root(root) | OMEX_EXECUTE(BSTS_OmexFile_8639905465728503850omex) | SIMULATIONS_RUN(runSimulations) | **** Error: Unable to initialize bioModel for the given selection: MappingException occurred: failed to generate math: generated an invalid mathDescription: Initial condition for variable 'h_post' references variable 'V_post'. Initial conditions cannot reference variables.
//faults.put("misc-projects/BIOMD0000000005.omex", null); // works
faults.put("misc-projects/BIOMD0000000175.omex", FAULT.MATH_GENERATION_FAILURE); // | Root(root) | OMEX_EXECUTE(BSTS_OmexFile_6652012719407098827omex) | SIMULATIONS_RUN(runSimulations) | **** Error: Unable to initialize bioModel for the given selection: MappingException occurred: failed to generate math: Unable to sort, unknown identifier I_Net_E44PPI3K_binding
faults.put("misc-projects/BIOMD0000000618.omex", FAULT.SBML_IMPORT_FAILURE); // | Root(root) | OMEX_EXECUTE(BSTS_OmexFile_13012177097014737572omex) | SIMULATIONS_RUN(runSimulations) | **** Error: Error processing model: model2 - couldn't find SBase with sid=null in SBMLSymbolMapping
//faults.put("misc-projects/BIOMD0000000569.omex", null); // works!!
//faults.put("misc-projects/BIOMD0000000973.omex", null); // works!!
faults.put("misc-projects/BIOMD0000000302.omex", FAULT.MATH_GENERATION_FAILURE); // | Root(root) | OMEX_EXECUTE(BSTS_OmexFile_8639905465728503850omex) | SIMULATIONS_RUN(runSimulations) | **** Error: Unable to initialize bioModel for the given selection: MappingException occurred: failed to generate math: generated an invalid mathDescription: Initial condition for variable 'h_post' references variable 'V_post'. Initial conditions cannot reference variables.
//faults.put("misc-projects/BIOMD0000000520.omex", null); // works!!
faults.put("misc-projects/BIOMD0000000731.omex", FAULT.SBML_IMPORT_FAILURE); // | Root(root) | OMEX_EXECUTE(BSTS_OmexFile_7811157837075929926omex) | SIMULATIONS_RUN(runSimulations) | **** Error: Unable to initialize bioModel for the given selection: Failed to translate SBML model into BioModel: 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. Check that you have provided the correct and full name (e.g. Ca_Cytosol).
faults.put("misc-projects/BIOMD0000001061.omex", FAULT.SEDML_NO_SEDMLS_TO_EXECUTE); // | Root(root) | OMEX_EXECUTE(BSTS_OmexFile_6151950245083004772omex) | **** Error: writeErrorList(): BSTS_OmexFile_6151950245083004772omex | java.lang.RuntimeException: There are no SED-MLs in the archive to execute
faults.put("misc-projects/BIOMD0000001064.omex", FAULT.SEDML_NO_SEDMLS_TO_EXECUTE); // | Root(root) | OMEX_EXECUTE(BSTS_OmexFile_855930052238018769omex) | **** Error: writeErrorList(): BSTS_OmexFile_855930052238018769omex | java.lang.RuntimeException: There are no SED-MLs in the archive to execute
faults.put("misc-projects/BIOMD0000000561.omex", FAULT.UNCATETORIZED_FAULT); // (not a dynamic system - can't solve) | Root(root) | OMEX_EXECUTE(BSTS_OmexFile_4023640363466179720omex) | SIMULATIONS_RUN(runSimulations) | BioModel(BSTS_OmexFile_4023640363466179720omex_Martins2013.sedml_model) | SIMULATION_RUN(task1_task1) | **** Error: Failed execution: Model 'BSTS_OmexFile_4023640363466179720omex_Martins2013.sedml_model' Task 'task1'.
//faults.put("misc-projects/BIOMD0000000569.omex", null); // works!!
faults.put("misc-projects/BIOMD0000000618.omex", FAULT.SBML_IMPORT_FAILURE); // | Root(root) | OMEX_EXECUTE(BSTS_OmexFile_13012177097014737572omex) | SIMULATIONS_RUN(runSimulations) | **** Error: Error processing model: model2 - couldn't find SBase with sid=null in SBMLSymbolMapping
//faults.put("misc-projects/BIOMD0000000651.omex", null); // works!!
//faults.put("misc-projects/BIOMD0000000668.omex", null); // works!!
//faults.put("misc-projects/BIOMD0000000669.omex", null); // works!!
//faults.put("misc-projects/BIOMD0000000676.omex", null); // works!!
//faults.put("misc-projects/BIOMD0000000718.omex", null); // works!!
faults.put("misc-projects/BIOMD0000000731.omex", FAULT.SBML_IMPORT_FAILURE); // | Root(root) | OMEX_EXECUTE(BSTS_OmexFile_7811157837075929926omex) | SIMULATIONS_RUN(runSimulations) | **** Error: Unable to initialize bioModel for the given selection: Failed to translate SBML model into BioModel: 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. Check that you have provided the correct and full name (e.g. Ca_Cytosol).
//faults.put("misc-projects/BIOMD0000000842.omex", null); // works!!
//faults.put("misc-projects/BIOMD0000000843.omex", null); // works!!
//faults.put("misc-projects/BIOMD0000000932.omex", null); // works!!
Expand All @@ -146,6 +144,7 @@ static Map<String, FAULT> knownFaults() {
//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/BIOMD0000000973.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!!
Expand All @@ -154,6 +153,8 @@ static Map<String, FAULT> knownFaults() {
//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/BIOMD0000001061.omex", FAULT.SEDML_NO_SEDMLS_TO_EXECUTE); // | Root(root) | OMEX_EXECUTE(BSTS_OmexFile_6151950245083004772omex) | **** Error: writeErrorList(): BSTS_OmexFile_6151950245083004772omex | java.lang.RuntimeException: There are no SED-MLs in the archive to execute
faults.put("misc-projects/BIOMD0000001064.omex", FAULT.SEDML_NO_SEDMLS_TO_EXECUTE); // | Root(root) | OMEX_EXECUTE(BSTS_OmexFile_855930052238018769omex) | **** Error: writeErrorList(): BSTS_OmexFile_855930052238018769omex | java.lang.RuntimeException: There are no SED-MLs in the archive to execute
//faults.put("misc-projects/BIOMD0000001072.omex", null); // works!!
//faults.put("misc-projects/BIOMD0000001077.omex", null); // works!!

Expand All @@ -170,6 +171,13 @@ public static Collection<String> testCases() {

return Arrays.stream(BSTSBasedTestSuiteFiles.getBSTSTestCases()).filter(filter).collect(Collectors.toList());
// return Arrays.asList(
// "misc-projects/BIOMD0000000561.omex",
// "misc-projects/BIOMD0000000679.omex",
// "misc-projects/BIOMD0000000680.omex",
// "misc-projects/BIOMD0000000681.omex",
// "misc-projects/BIOMD0000000684.omex",
// "misc-projects/BIOMD0000000724.omex",
// "misc-projects/BIOMD0000000915.omex"
// "misc-projects/BIOMD0000000302.omex",
// "misc-projects/BIOMD0000000175.omex",
// "misc-projects/BIOMD0000000618.omex",
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