From 52cf62cbc3ec76d9f20ced440450b63283b7dde6 Mon Sep 17 00:00:00 2001 From: Jim Schaff Date: Tue, 18 Aug 2026 01:04:14 -0400 Subject: [PATCH] Accept the BMDB baseline after the SBML scope fixes Nightly run 32094317081 reported FAIL: 28 changed, the first run after #1983 (reaction-rate references) and #1985 (UNRESOLVED.initConc / UNRESOLVED.Size) landed. Every shard passed; the gate was refusing a baseline those fixes had made stale. Eighteen archives improved outright -- they now import AND simulate: 256 457 499 589 599 628 632 705 710 739 764 804 832 867 872 908 969 FAIL -> PASS 1065 SOLVER_FAILURE -> PASS Seven more get further than before, failing after import rather than during it: 534 535 536 537 547 1021 SBML_IMPORT_FAILURE -> SOLVER_FAILURE 613 SBML_IMPORT_FAILURE -> DIVIDE_BY_ZERO The remaining three look like a step backwards and are not. Each model has TWO unsupported features, and the reaction-rate check from #1983 now reports first: 63 UNSUPPORTED_NON_INT_STOCH -> SBML_IMPORT_FAILURE 245 UNSUPPORTED_NON_INT_STOCH -> SBML_IMPORT_FAILURE 627 UNSUPPORTED_NON_CONSTANT_COMPARTMENTS -> SBML_IMPORT_FAILURE Verified rather than assumed: 'Vhk' in 63 and 'r2' in 245 are both genuine elements referenced from an assignmentRule, and neither is declared as a species, parameter or compartment, so these are not false positives. Both models also genuinely carry the non-integer stoichiometries the old entries named (0.5; 0.063, 0.127, ...). 627 is the same shape, on reaction 'vSTIM' alongside its non-constant compartment. Both old and new reasons are true; only which is reached first has changed, and the models fail either way. No archive went from PASS to FAIL. Taken verbatim from the run's test_cases.updated.ndjson artifact: 1182 rows before and after, 28 lines changed, no rows added, removed or reordered. Co-Authored-By: Claude Opus 5 (1M context) --- .../src/main/resources/test_cases.ndjson | 56 +++++++++---------- 1 file changed, 28 insertions(+), 28 deletions(-) diff --git a/vcell-cli/src/main/resources/test_cases.ndjson b/vcell-cli/src/main/resources/test_cases.ndjson index 0ce6ebbf86..e3b22456d6 100644 --- a/vcell-cli/src/main/resources/test_cases.ndjson +++ b/vcell-cli/src/main/resources/test_cases.ndjson @@ -170,7 +170,7 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000060.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000061.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000062.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000063.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_NON_INT_STOCH","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('0.5' for reactant 'FDP' in reaction 'Vgol') not handled in VCell at this time."} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000063.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"Unable to initialize bioModel for the given selection: Failed to translate SBML model into BioModel: org.vcell.sbml.vcell.SBMLImportException: Reaction rate reference: reaction 'Vhk' is named in an expression, which in SBML denotes that reaction's rate. Reaction rates cannot be referenced in expressions in VCell at this time. Expression: '(Vhk / (cytoplasm * parameter_7))' org.vcell.sbml.vcell.SBMLImportException: Failed to translate SBML model into BioModel: org.vcell.sbml.vcell.SBMLImportException: Reaction rate reference: reaction 'Vhk' is named in an expression, which in SBML denotes that reaction's rate. Reaction rates cannot be referenced in expressions in VCell at this time. Expression: '(Vhk / (cytoplasm * parameter_7))'"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000064.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000065.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000066.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -352,7 +352,7 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000242.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000243.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000244.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_NON_INT_STOCH","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('0.5' for reactant 'FBP' in reaction 'e_Emp') not handled in VCell at this time."} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000245.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_NON_INT_STOCH","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('0.978' for product 's_pyr' in reaction 'r1') not handled in VCell at this time."} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000245.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"Unable to initialize bioModel for the given selection: Failed to translate SBML model into BioModel: org.vcell.sbml.vcell.SBMLImportException: Reaction rate reference: reaction 'r2' is named in an expression, which in SBML denotes that reaction's rate. Reaction rates cannot be referenced in expressions in VCell at this time. Expression: '(((1000.0 / 32.0) * ((((0.178 * r1) + (0.908 * r2) + (0.363 * r4) + (1.066 * r5)) - (0.363 * r6)) + (0.063 * r7) + (0.214 * r8))) / (x * env))' org.vcell.sbml.vcell.SBMLImportException: Failed to translate SBML model into BioModel: org.vcell.sbml.vcell.SBMLImportException: Reaction rate reference: reaction 'r2' is named in an expression, which in SBML denotes that reaction's rate. Reaction rates cannot be referenced in expressions in VCell at this time. Expression: '(((1000.0 / 32.0) * ((((0.178 * r1) + (0.908 * r2) + (0.363 * r4) + (1.066 * r5)) - (0.363 * r6)) + (0.063 * r7) + (0.214 * r8))) / (x * env))'"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000246.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_NON_INT_STOCH","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('0.001' for product 'Ca_in' in reaction 'vo') not handled in VCell at this time."} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000247.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000248.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Failed to translate SBML model into BioModel: Error binding global parameter 'ATPase_flux_mM' to model: 'ATPase' is either not found in your model or is not allowed to be used in the current context."} @@ -363,7 +363,7 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000253.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000254.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000255.omex","should_fail":false,"known_status":"SKIP","known_failure_type":null,"known_failure_desc":"deliberately excluded by the NightlyBMDB_CLI.yml skip list - too slow or otherwise misbehaved"} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000256.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Failed to translate SBML model into BioModel: Error binding global parameter 'XIAP_ini' 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":"BIOMD0000000256.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000257.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000258.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000259.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -564,7 +564,7 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000454.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000455.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000456.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000457.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"Error binding global parameter 'parameter_1' to model: 'UNRESOLVED.Size' is either not found in your model or is not allowed to be used in the current context."} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000457.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000458.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000459.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_RESULTS_MAPPING_FAILURE","known_failure_desc":"java.lang.RuntimeException: CSV generation failed: failed to find VCell structure size parameter for sbml compartment size: compartment"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000460.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_RESULTS_MAPPING_FAILURE","known_failure_desc":"java.lang.RuntimeException: CSV generation failed: failed to find VCell structure size parameter for sbml compartment size: compartment"} @@ -606,7 +606,7 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000496.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_NON_INT_STOCH","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('1.1358' for reactant 's_0001' in reaction 'r_1812') not handled in VCell at this time."} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000497.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"UNSUPPORTED_NON_INT_STOCH","known_failure_desc":"org.vcell.sbml.vcell.SBMLImportException: Non-integer stoichiometry ('1.1358' for reactant 's_0001' in reaction 'r_1812') not handled in VCell at this time."} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000498.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SEDML_NON_UTC_SIMULATION_FOUND","known_failure_desc":"There are SedML simulations VCell is not capable of running at this time!"} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000499.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"Error binding global parameter 'Metabolite_9' 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":"BIOMD0000000499.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000500.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SEDML_NON_UTC_SIMULATION_FOUND","known_failure_desc":"There are SedML simulations VCell is not capable of running at this time!"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000501.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SEDML_NON_UTC_SIMULATION_FOUND","known_failure_desc":"There are SedML simulations VCell is not capable of running at this time!"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000502.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -641,10 +641,10 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000531.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SOLVER_FAILURE","known_failure_desc":"Failed execution: Model 'BIOMD0000000531_model.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":"BIOMD0000000532.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SOLVER_FAILURE","known_failure_desc":"Failed execution: Model 'BIOMD0000000532_Vazquez2014.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":"BIOMD0000000533.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000534.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"Error binding global parameter 'Metabolite_6' 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":"BIOMD0000000535.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":"BIOMD0000000536.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"Error binding global parameter 'Metabolite_80' 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":"BIOMD0000000537.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"Error binding global parameter 'Metabolite_40' 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":"BIOMD0000000534.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SOLVER_FAILURE","known_failure_desc":"Failed execution:\n\t> Elapsed Time:\t163ms\n\t> Model:\t\tBIOMD0000000534_BIOMD0000000534_url.sedml_BIOMD0000000534_url\n\t> Task:\t\t\ttask1\n\t> Cause:\t\tRuntimeException\n\t> Message:\t\tSolver (CVodeSolverStandalone) status: `Aborted` (Could not execute code: CVODE solver failed : at time 0.1, discontinuity (t >= 0.10000000000000000555) evaluated to TRUE, solver assumed FALSE\n\n\n\n(/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 /tmp/VCell_CLI_1a012e4347f12397638103846920865/BIOMD0000000534/BIOMD0000000534_url.sedml/SimID_1261893409_0_.cvodeInput /tmp/VCell_CLI_1a012e4347f12397638103846920865/BIOMD0000000534/BIOMD0000000534_url.sedml/SimID_1261893409_0_.ida)) java.lang.RuntimeException: Solver (CVodeSolverStandalone) status: `Aborted` (Could not execute code: CVODE solver failed : at time 0.1, discontinuity (t >= 0.10000000000000000555) evaluated to TRUE, solver assumed FALSE\n\n\n\n(/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 /tmp/VCell_CLI_1a012e4347f12397638103846920865/BIOMD0000000534/BIOMD0000000534_url.sedml/SimID_1261893409_0_.cvodeInput /tmp/VCell_CLI_1a012e4347f12397638103846920865/BIOMD0000000534/BIOMD0000000534_url.sedml/SimID_1261893409_0_.ida)) "} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000535.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SOLVER_FAILURE","known_failure_desc":"Failed execution:\n\t> Elapsed Time:\t147ms\n\t> Model:\t\tBIOMD0000000535_BIOMD0000000535_url.sedml_BIOMD0000000535_url\n\t> Task:\t\t\ttask1\n\t> Cause:\t\tRuntimeException\n\t> Message:\t\tSolver (CVodeSolverStandalone) status: `Aborted` (Could not execute code: CVODE solver failed : at time 0.1, discontinuity (t >= 0.10000000000000000555) evaluated to TRUE, solver assumed FALSE\n\n\n\n(/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 /tmp/VCell_CLI_1a012df675e18174365372491545812/BIOMD0000000535/BIOMD0000000535_url.sedml/SimID_1817234605_0_.cvodeInput /tmp/VCell_CLI_1a012df675e18174365372491545812/BIOMD0000000535/BIOMD0000000535_url.sedml/SimID_1817234605_0_.ida)) java.lang.RuntimeException: Solver (CVodeSolverStandalone) status: `Aborted` (Could not execute code: CVODE solver failed : at time 0.1, discontinuity (t >= 0.10000000000000000555) evaluated to TRUE, solver assumed FALSE\n\n\n\n(/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 /tmp/VCell_CLI_1a012df675e18174365372491545812/BIOMD0000000535/BIOMD0000000535_url.sedml/SimID_1817234605_0_.cvodeInput /tmp/VCell_CLI_1a012df675e18174365372491545812/BIOMD0000000535/BIOMD0000000535_url.sedml/SimID_1817234605_0_.ida)) "} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000536.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SOLVER_FAILURE","known_failure_desc":"Failed execution:\n\t> Elapsed Time:\t142ms\n\t> Model:\t\tBIOMD0000000536_BIOMD0000000536_url.sedml_BIOMD0000000536_url\n\t> Task:\t\t\ttask1\n\t> Cause:\t\tRuntimeException\n\t> Message:\t\tSolver (CVodeSolverStandalone) status: `Aborted` (Could not execute code: CVODE solver failed : at time 0.1, discontinuity (t >= 0.10000000000000000555) evaluated to TRUE, solver assumed FALSE\n\n\n\n(/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 /tmp/VCell_CLI_1a012df723d16493013318848509462/BIOMD0000000536/BIOMD0000000536_url.sedml/SimID_2049186196_0_.cvodeInput /tmp/VCell_CLI_1a012df723d16493013318848509462/BIOMD0000000536/BIOMD0000000536_url.sedml/SimID_2049186196_0_.ida)) java.lang.RuntimeException: Solver (CVodeSolverStandalone) status: `Aborted` (Could not execute code: CVODE solver failed : at time 0.1, discontinuity (t >= 0.10000000000000000555) evaluated to TRUE, solver assumed FALSE\n\n\n\n(/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 /tmp/VCell_CLI_1a012df723d16493013318848509462/BIOMD0000000536/BIOMD0000000536_url.sedml/SimID_2049186196_0_.cvodeInput /tmp/VCell_CLI_1a012df723d16493013318848509462/BIOMD0000000536/BIOMD0000000536_url.sedml/SimID_2049186196_0_.ida)) "} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000537.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SOLVER_FAILURE","known_failure_desc":"Failed execution:\n\t> Elapsed Time:\t192ms\n\t> Model:\t\tBIOMD0000000537_BIOMD0000000537_url.sedml_BIOMD0000000537_url\n\t> Task:\t\t\ttask1\n\t> Cause:\t\tRuntimeException\n\t> Message:\t\tSolver (CVodeSolverStandalone) status: `Aborted` (Could not execute code: CVODE solver failed : at time 0.1, discontinuity (t >= 0.10000000000000000555) evaluated to TRUE, solver assumed FALSE\n\n\n\n(/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 /tmp/VCell_CLI_1a012dfa5402500014239244828591/BIOMD0000000537/BIOMD0000000537_url.sedml/SimID_763987299_0_.cvodeInput /tmp/VCell_CLI_1a012dfa5402500014239244828591/BIOMD0000000537/BIOMD0000000537_url.sedml/SimID_763987299_0_.ida)) java.lang.RuntimeException: Solver (CVodeSolverStandalone) status: `Aborted` (Could not execute code: CVODE solver failed : at time 0.1, discontinuity (t >= 0.10000000000000000555) evaluated to TRUE, solver assumed FALSE\n\n\n\n(/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 /tmp/VCell_CLI_1a012dfa5402500014239244828591/BIOMD0000000537/BIOMD0000000537_url.sedml/SimID_763987299_0_.cvodeInput /tmp/VCell_CLI_1a012dfa5402500014239244828591/BIOMD0000000537/BIOMD0000000537_url.sedml/SimID_763987299_0_.ida)) "} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000538.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000539.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000540.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -654,7 +654,7 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000544.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000545.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000546.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000547.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"Error binding global parameter 'Compartment_3' to model: 'UNRESOLVED.Size' is either not found in your model or is not allowed to be used in the current context"} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000547.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SOLVER_FAILURE","known_failure_desc":"Failed execution:\n\t> Elapsed Time:\t144ms\n\t> Model:\t\tBIOMD0000000547_BIOMD0000000547_url.sedml_BIOMD0000000547_url\n\t> Task:\t\t\ttask1\n\t> Cause:\t\tRuntimeException\n\t> Message:\t\tSolver (CVodeSolverStandalone) status: `Aborted` (Could not execute code: \n[CVODE WARNING] CVode\n Internal t = 8.09814e-18 and h = 6.56931e-34 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 8.09814e-18 and h = 6.56931e-34 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 8.09814e-18 and h = 6.56931e-34 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 8.09814e-18 and h = 6.56931e-34 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 8.09814e-18 and h = 6.56931e-34 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 8.09814e-18 and h = 6.56931e-34 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 8.09814e-18 and h = 6.56931e-34 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 8.09814e-18 and h = 6.56931e-34 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 8.09814e-18 and h = 6.56931e-34 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 8.09814e-18 and h = 6.56931e-34 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 = 8.09814e-18, 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.\n\n\n(/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 /tmp/VCell_CLI_1a012df8bf310320975355326824798/BIOMD0000000547/BIOMD0000000547_url.sedml/SimID_1369103932_0_.cvodeInput /tmp/VCell_CLI_1a012df8bf310320975355326824798/BIOMD0000000547/BIOMD0000000547_url.sedml/SimID_1369103932_0_.ida)) java.lang.RuntimeException: Solver (CVodeSolverStandalone) status: `Aborted` (Could not execute code: \n[CVODE WARNING] CVode\n Internal t = 8.09814e-18 and h = 6.56931e-34 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 8.09814e-18 and h = 6.56931e-34 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 8.09814e-18 and h = 6.56931e-34 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 8.09814e-18 and h = 6.56931e-34 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 8.09814e-18 and h = 6.56931e-34 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 8.09814e-18 and h = 6.56931e-34 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 8.09814e-18 and h = 6.56931e-34 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 8.09814e-18 and h = 6.56931e-34 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 8.09814e-18 and h = 6.56931e-34 are such that t + h = t on the next step. The solver will continue anyway.\n\n\n[CVODE WARNING] CVode\n Internal t = 8.09814e-18 and h = 6.56931e-34 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 = 8.09814e-18, 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.\n\n\n(/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 /tmp/VCell_CLI_1a012df8bf310320975355326824798/BIOMD0000000547/BIOMD0000000547_url.sedml/SimID_1369103932_0_.cvodeInput /tmp/VCell_CLI_1a012df8bf310320975355326824798/BIOMD0000000547/BIOMD0000000547_url.sedml/SimID_1369103932_0_.ida)) "} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000548.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000549.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000550.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -696,7 +696,7 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000586.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000587.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000588.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000589.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"Error binding global parameter 'Metabolite_17' 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":"BIOMD0000000589.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000590.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000591.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"Error adding Lambda functionParse Error while parsing expression '\"Boehm2014 - isoform-specific dimerization of pSTAT5A and pSTAT5B\"': Lexical error at line 1, column 1. Encountered: \"\\\"\" (34), after : \"\""} {"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"} @@ -706,7 +706,7 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000596.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"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} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000599.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"Error binding global parameter 'Metabolite_1' 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":"BIOMD0000000599.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000600.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000601.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000602.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -720,7 +720,7 @@ {"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":"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":"BIOMD0000000613.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"DIVIDE_BY_ZERO","known_failure_desc":"Failed execution:\n\t> Elapsed Time:\t215ms\n\t> Model:\t\tBIOMD0000000613_BIOMD0000000613_url.sedml_BIOMD0000000613_url\n\t> Task:\t\t\ttask1\n\t> Cause:\t\tRuntimeException\n\t> Message:\t\tSolver (CVodeSolverStandalone) status: `Aborted` (CVODE solver could not generate input file: divide by zero '(M_initConc / OC_initConc)') java.lang.RuntimeException: Solver (CVodeSolverStandalone) status: `Aborted` (CVODE solver could not generate input file: divide by zero '(M_initConc / OC_initConc)') "} {"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} @@ -734,12 +734,12 @@ {"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":"FAIL","known_failure_type":"UNSUPPORTED_NON_CONSTANT_COMPARTMENTS","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":"BIOMD0000000627.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"Unable to initialize bioModel for the given selection: Failed to translate SBML model into BioModel: Error adding Lambda functionorg.vcell.sbml.vcell.SBMLImportException: Reaction rate reference: reaction 'vSTIM' is named in an expression, which in SBML denotes that reaction's rate. Reaction rates cannot be referenced in expressions in VCell at this time. Expression: '(vSTIM * ratio_Na_GLU * (GLU_n / (GLU_n + Km_GLU)) * Volume)' org.vcell.sbml.vcell.SBMLImportException: Failed to translate SBML model into BioModel: Error adding Lambda functionorg.vcell.sbml.vcell.SBMLImportException: Reaction rate reference: reaction 'vSTIM' is named in an expression, which in SBML denotes that reaction's rate. Reaction rates cannot be referenced in expressions in VCell at this time. Expression: '(vSTIM * ratio_Na_GLU * (GLU_n / (GLU_n + Km_GLU)) * Volume)'"} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000628.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"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":"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":"BIOMD0000000632.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"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} @@ -810,12 +810,12 @@ {"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":"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":"BIOMD0000000705.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"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":"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":"BIOMD0000000710.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000711.omex","should_fail":false,"known_status":"SKIP","known_failure_type":null,"known_failure_desc":"deliberately excluded by the NightlyBMDB_CLI.yml skip list - too slow or otherwise misbehaved"} {"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} @@ -844,7 +844,7 @@ {"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":"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":"BIOMD0000000739.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"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} @@ -869,7 +869,7 @@ {"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":"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":"BIOMD0000000764.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"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} @@ -909,7 +909,7 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000801.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000802.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000803.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SEDML_NON_UTC_SIMULATION_FOUND","known_failure_desc":"There are SedML simulations VCell is not capable of running at this time!"} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000804.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"Error binding global parameter 'Metabolite_1' 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":"BIOMD0000000804.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000805.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000806.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000807.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -937,7 +937,7 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000829.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000830.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000831.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000832.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"Error binding global parameter 'Metabolite_4' 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":"BIOMD0000000832.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000833.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000834.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000835.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -972,12 +972,12 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000864.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000865.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SEDML_NON_UTC_SIMULATION_FOUND","known_failure_desc":"There are SedML simulations VCell is not capable of running at this time!"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000866.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SEDML_NON_UTC_SIMULATION_FOUND","known_failure_desc":"There are SedML simulations VCell is not capable of running at this time!"} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000867.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"Error binding global parameter 'Metabolite_9' 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":"BIOMD0000000867.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000868.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SEDML_NON_UTC_SIMULATION_FOUND","known_failure_desc":"There are SedML simulations VCell is not capable of running at this time!"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000869.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SEDML_NON_UTC_SIMULATION_FOUND","known_failure_desc":"There are SedML simulations VCell is not capable of running at this time!"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000870.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SEDML_NON_UTC_SIMULATION_FOUND","known_failure_desc":"There are SedML simulations VCell is not capable of running at this time!"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000871.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SEDML_NON_UTC_SIMULATION_FOUND","known_failure_desc":"There are SedML simulations VCell is not capable of running at this time!"} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000872.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"Unable to initialize bioModel for the given selection: Failed to translate SBML model into BioModel: Error binding global parameter 'beta' to model: 'UNRESOLVED.initConc' is either not found in your model or is not allowed to be used in the current context. Check that you have provided the correct and full name (e.g. Ca_Cytosol). org.vcell.sbml.vcell.SBMLImportException: Failed to translate SBML model into BioModel: Error binding global parameter 'beta' to model: 'UNRESOLVED.initConc' is either not found in your model or is not allowed to be used in the current context. Check that you have provided the correct and full name (e.g. Ca_Cytosol)."} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000872.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000873.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000874.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000875.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -1013,7 +1013,7 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000905.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000906.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000907.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000908.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"Error binding global parameter 'Metabolite_2' 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":"BIOMD0000000908.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000909.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000910.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000911.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -1074,7 +1074,7 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000966.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000967.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000968.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000969.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SBML_IMPORT_FAILURE","known_failure_desc":"Error binding global parameter 'Metabolite_11' 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":"BIOMD0000000969.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000970.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000971.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000000972.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} @@ -1124,7 +1124,7 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001018.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"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":"BIOMD0000001021.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SOLVER_FAILURE","known_failure_desc":"Failed execution:\n\t> Elapsed Time:\t300074ms\n\t> Model:\t\tBIOMD0000001021_Lavigne2021 - ODE model (paracrine only condition).sedml_model1\n\t> Task:\t\t\ttask1\n\t> Cause:\t\tRuntimeException\n\t> Message:\t\tSolver (CVodeSolverStandalone) status: `Aborted` (Could not execute code: Unexpected error: Process timed out\n\n(/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 \"/tmp/VCell_CLI_1a013247ce35206697111963609227/BIOMD0000001021/Lavigne2021 - ODE model (paracrine only condition).sedml/SimID_934484583_0_.cvodeInput\" \"/tmp/VCell_CLI_1a013247ce35206697111963609227/BIOMD0000001021/Lavigne2021 - ODE model (paracrine only condition).sedml/SimID_934484583_0_.ida\")) java.lang.RuntimeException: Solver (CVodeSolverStandalone) status: `Aborted` (Could not execute code: Unexpected error: Process timed out\n\n(/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 \"/tmp/VCell_CLI_1a013247ce35206697111963609227/BIOMD0000001021/Lavigne2021 - ODE model (paracrine only condition).sedml/SimID_934484583_0_.cvodeInput\" \"/tmp/VCell_CLI_1a013247ce35206697111963609227/BIOMD0000001021/Lavigne2021 - ODE model (paracrine only condition).sedml/SimID_934484583_0_.ida\")) "} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001022.omex","should_fail":false,"known_status":"SKIP","known_failure_type":null,"known_failure_desc":"deliberately excluded by the NightlyBMDB_CLI.yml skip list - too slow or otherwise misbehaved"} {"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} @@ -1165,7 +1165,7 @@ {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001062.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SEDML_NO_SEDMLS_TO_EXECUTE","known_failure_desc":"writeErrorList(): BIOMD0000001062 java.lang.RuntimeException: There are no SED-MLs in the archive to execute"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001063.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SEDML_NO_SEDMLS_TO_EXECUTE","known_failure_desc":"writeErrorList(): BIOMD0000001063 java.lang.RuntimeException: There are no SED-MLs in the archive to execute"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001064.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SEDML_NO_SEDMLS_TO_EXECUTE","known_failure_desc":"writeErrorList(): BIOMD0000001064 java.lang.RuntimeException: There are no SED-MLs in the archive to execute"} -{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001065.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SOLVER_FAILURE","known_failure_desc":"Failed execution: Model 'BIOMD0000001065_vonDassow2000_1x4.timecourse1.sedml_model' Task 'task1'. java.lang.RuntimeException: Could not execute code: \n[CVODE ERROR] CVode\n At t = 660.5repeated recoverable right-hand side function errors.\n\nCVODE solver failed : CV_REPTD_RHSFUNC_ERR: repeated recoverable right-hand side function errors : FunctionDomainException : FunctionDomainException : pow(u,v) and u=-0.000000<0 and v=2.619640 not an integer in \"((0.052821806954783216692 * ((0.00030494421841729539872 / (0.00030494421841729539872 + (EN_0_0 ^ 2.6196399999999999686))) ^ 9.6309500000000003439) / (5.7617237886031359827e-23 + (0.4000000000000000222 * ((0.00030494421841729539872 / (0.00030494421841729539872 + (EN_0_0 ^ 2.6196399999999999686))) ^ 9.6309500000000003439)))) - (0.13205451738695803132 * ci_0_0))\"\n where:\n\tEN_0_0 = -0.000000\n\tci_0_0 = 1.000000\n\n\n\n(/usr/local/app/vcell/installDir/localsolvers/linux64/SundialsSolverStandalone_x64 /tmp/VCell_CLI_193f9f93f2012192791967497390908/BIOMD0000001065/vonDassow2000_1x4.timecourse1.sedml/SimID_1545840175_0_.cvodeInput /tmp/VCell_CLI_193f9f93f2012192791967497390908/BIOMD0000001065/vonDassow2000_1x4.timecourse1.sedml/SimID_1545840175_0_.ida) "} +{"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001065.omex","should_fail":false,"known_status":"PASS","known_failure_type":null,"known_failure_desc":null} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001066.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SEDML_NO_SEDMLS_TO_EXECUTE","known_failure_desc":"writeErrorList(): BIOMD0000001066 java.lang.RuntimeException: There are no SED-MLs in the archive to execute"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001067.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SEDML_NO_SEDMLS_TO_EXECUTE","known_failure_desc":"writeErrorList(): BIOMD0000001067 java.lang.RuntimeException: There are no SED-MLs in the archive to execute"} {"test_collection":"SYSBIO_BIOMD","file_path":"BIOMD0000001068.omex","should_fail":false,"known_status":"FAIL","known_failure_type":"SEDML_NO_SEDMLS_TO_EXECUTE","known_failure_desc":"writeErrorList(): BIOMD0000001068 java.lang.RuntimeException: There are no SED-MLs in the archive to execute"}