Mar 25, 2021 9:53:34 PM java.util.prefs.FileSystemPreferences$1 run
WARNING: java.io.IOException: No such file or directory
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_cf54dc0d-c526-40b2-97c0-53e65dffd6475244217697203173006
Installing the required PIP packages..
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s), and 0 plot(s)

Successful translation: SED-ML file simulation_1.sedml
-----------------------------------------------------------------------------------------------------
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='simulation_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
Succesful model import: SBML file /tmp/temp1741056770863835652.xml
java.io.FileNotFoundException: /tmp/out/simulation_1.sedml/SimID_808405030_0_.ida (No such file or directory)
	at java.io.FileInputStream.open0(Native Method)
	at java.io.FileInputStream.open(FileInputStream.java:195)
	at java.io.FileInputStream.<init>(FileInputStream.java:138)
	at java.io.FileInputStream.<init>(FileInputStream.java:93)
	at cbit.vcell.solver.ode.SundialsSolver.getStateVariableResultSet(SundialsSolver.java:299)
	at cbit.vcell.solver.ode.SundialsSolver.getODESolverResultSet(SundialsSolver.java:187)
	at org.vcell.cli.SolverHandler.simulateAllTasks(SolverHandler.java:94)
	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:160)
	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)
Solver status: 3
Solver message: ./.vcell/simdata/temp/808405030_link/SundialsSolverStandalone_x64
Failed execution: Model 'archive_Ciliberto2003_Morphogenesis' Task 'simulation 1'.
-----------------------------------------------------------------------------------------------------
HDF conversion completed in '/tmp/out'

Generating zip Archive for reports
One or more errors encountered while executing archive /tmp/in/archive.omex

sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes (22.3 s)
Test that a simulator supports data generators with different shapes
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpjtj5o1v4/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:
VCell CLI input archive /tmp/in/archive.omex
Mar 25, 2021 9:54:00 PM java.util.prefs.FileSystemPreferences$1 run
WARNING: Couldn't create user preferences directory. User preferences are unusable.
Mar 25, 2021 9:54:00 PM java.util.prefs.FileSystemPreferences$1 run
WARNING: java.io.IOException: No such file or directory
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_92e79e19-4064-4f9a-9ef5-8925f7549fe66151596096731122462
Installing the required PIP packages..
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 1 model(s), 2 simulation(s), 2 task(s), 1  report(s), and 0 plot(s)

Successful translation: SED-ML file simulation_1.sedml
-----------------------------------------------------------------------------------------------------
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='simulation_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
Succesful model import: SBML file /tmp/temp6846700379593445403.xml
Task (id='simulation_1__copy_2') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
java.io.FileNotFoundException: /tmp/out/simulation_1.sedml/SimID_1853208066_0_.ida (No such file or directory)
	at java.io.FileInputStream.open0(Native Method)
	at java.io.FileInputStream.open(FileInputStream.java:195)
	at java.io.FileInputStream.<init>(FileInputStream.java:138)
	at java.io.FileInputStream.<init>(FileInputStream.java:93)
	at cbit.vcell.solver.ode.SundialsSolver.getStateVariableResultSet(SundialsSolver.java:299)
	at cbit.vcell.solver.ode.SundialsSolver.getODESolverResultSet(SundialsSolver.java:187)
	at org.vcell.cli.SolverHandler.simulateAllTasks(SolverHandler.java:94)
	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:160)
	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)
Solver status: 3
Solver message: ./.vcell/simdata/temp/1853208066_link/SundialsSolverStandalone_x64
Failed execution: Model 'archive_Ciliberto2003_Morphogenesis' Task 'simulation 1'.
-----------------------------------------------------------------------------------------------------
java.io.FileNotFoundException: /tmp/out/simulation_1.sedml/SimID_617551990_0_.ida (No such file or directory)
	at java.io.FileInputStream.open0(Native Method)
	at java.io.FileInputStream.open(FileInputStream.java:195)
	at java.io.FileInputStream.<init>(FileInputStream.java:138)
	at java.io.FileInputStream.<init>(FileInputStream.java:93)
	at cbit.vcell.solver.ode.SundialsSolver.getStateVariableResultSet(SundialsSolver.java:299)
	at cbit.vcell.solver.ode.SundialsSolver.getODESolverResultSet(SundialsSolver.java:187)
	at org.vcell.cli.SolverHandler.simulateAllTasks(SolverHandler.java:94)
	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:160)
	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)
Solver status: 3
Solver message: ./.vcell/simdata/temp/617551990_link/SundialsSolverStandalone_x64
Failed execution: Model 'archive_Ciliberto2003_Morphogenesis' Task 'simulation_1__copy_2'.
-----------------------------------------------------------------------------------------------------
HDF conversion completed in '/tmp/out'

Generating zip Archive for reports
One or more errors encountered while executing archive /tmp/in/archive.omex

sedml.SimulatorSupportsDataSetsWithDifferentShapes (22.7 s)
Test that a simulator supports data generators with different shapes
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmp_ejiwtxz/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:
VCell CLI input archive /tmp/in/archive.omex
Mar 25, 2021 9:54:22 PM java.util.prefs.FileSystemPreferences$1 run
WARNING: Couldn't create user preferences directory. User preferences are unusable.
Mar 25, 2021 9:54:22 PM java.util.prefs.FileSystemPreferences$1 run
WARNING: java.io.IOException: No such file or directory
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_0db3d2f2-d121-45fd-95ae-1f57805a2d7a8604472472238131134
Installing the required PIP packages..
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 1 model(s), 2 simulation(s), 2 task(s), 1  report(s), and 0 plot(s)

Successful translation: SED-ML file simulation_1.sedml
-----------------------------------------------------------------------------------------------------
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='simulation_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
Succesful model import: SBML file /tmp/temp8661243011919103232.xml
Task (id='simulation_1__copy_2') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
java.io.FileNotFoundException: /tmp/out/simulation_1.sedml/SimID_1279524785_0_.ida (No such file or directory)
	at java.io.FileInputStream.open0(Native Method)
	at java.io.FileInputStream.open(FileInputStream.java:195)
	at java.io.FileInputStream.<init>(FileInputStream.java:138)
	at java.io.FileInputStream.<init>(FileInputStream.java:93)
	at cbit.vcell.solver.ode.SundialsSolver.getStateVariableResultSet(SundialsSolver.java:299)
	at cbit.vcell.solver.ode.SundialsSolver.getODESolverResultSet(SundialsSolver.java:187)
	at org.vcell.cli.SolverHandler.simulateAllTasks(SolverHandler.java:94)
	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:160)
	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)
Solver status: 3
Solver message: ./.vcell/simdata/temp/1279524785_link/SundialsSolverStandalone_x64
Failed execution: Model 'archive_Ciliberto2003_Morphogenesis' Task 'simulation 1'.
-----------------------------------------------------------------------------------------------------
java.io.FileNotFoundException: /tmp/out/simulation_1.sedml/SimID_1658495322_0_.ida (No such file or directory)
	at java.io.FileInputStream.open0(Native Method)
	at java.io.FileInputStream.open(FileInputStream.java:195)
	at java.io.FileInputStream.<init>(FileInputStream.java:138)
	at java.io.FileInputStream.<init>(FileInputStream.java:93)
	at cbit.vcell.solver.ode.SundialsSolver.getStateVariableResultSet(SundialsSolver.java:299)
	at cbit.vcell.solver.ode.SundialsSolver.getODESolverResultSet(SundialsSolver.java:187)
	at org.vcell.cli.SolverHandler.simulateAllTasks(SolverHandler.java:94)
	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:160)
	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)
Solver status: 3
Solver message: ./.vcell/simdata/temp/1658495322_link/SundialsSolverStandalone_x64
Failed execution: Model 'archive_Ciliberto2003_Morphogenesis' Task 'simulation_1__copy_2'.
-----------------------------------------------------------------------------------------------------
HDF conversion completed in '/tmp/out'

Generating zip Archive for reports
One or more errors encountered while executing archive /tmp/in/archive.omex

sedml.SimulatorSupportsModelAttributeChanges (57.2 s)
Test that a simulator supports changes to the attributes of model elements
Reason for skip:
Simulator did not produce the following reports:
  - `simulation_1.sedml/simulation_1`

Log:
VCell CLI input archive /tmp/in/archive.omex
Mar 25, 2021 9:54:44 PM java.util.prefs.FileSystemPreferences$1 run
WARNING: Couldn't create user preferences directory. User preferences are unusable.
Mar 25, 2021 9:54:44 PM java.util.prefs.FileSystemPreferences$1 run
WARNING: java.io.IOException: No such file or directory
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_fc825fd2-49ff-4035-83bb-2e4caaaacc616732704673533517021
Installing the required PIP packages..
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s), and 0 plot(s)

Successful translation: SED-ML file simulation_1.sedml
-----------------------------------------------------------------------------------------------------
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='simulation_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
Succesful model import: SBML file /tmp/temp1863559737613972841.xml
java.io.FileNotFoundException: /tmp/out/simulation_1.sedml/SimID_99727277_0_.ida (No such file or directory)
	at java.io.FileInputStream.open0(Native Method)
	at java.io.FileInputStream.open(FileInputStream.java:195)
	at java.io.FileInputStream.<init>(FileInputStream.java:138)
	at java.io.FileInputStream.<init>(FileInputStream.java:93)
	at cbit.vcell.solver.ode.SundialsSolver.getStateVariableResultSet(SundialsSolver.java:299)
	at cbit.vcell.solver.ode.SundialsSolver.getODESolverResultSet(SundialsSolver.java:187)
	at org.vcell.cli.SolverHandler.simulateAllTasks(SolverHandler.java:94)
	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:160)
	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)
Solver status: 3
Solver message: ./.vcell/simdata/temp/99727277_link/SundialsSolverStandalone_x64
Failed execution: Model 'archive_Ciliberto2003_Morphogenesis' Task 'simulation 1'.
-----------------------------------------------------------------------------------------------------
HDF conversion completed in '/tmp/out'

Generating zip Archive for reports
One or more errors encountered while executing archive /tmp/in/archive.omex
VCell CLI input archive /tmp/in/archive.omex
Mar 25, 2021 9:55:11 PM java.util.prefs.FileSystemPreferences$1 run
WARNING: Couldn't create user preferences directory. User preferences are unusable.
Mar 25, 2021 9:55:11 PM java.util.prefs.FileSystemPreferences$1 run
WARNING: java.io.IOException: No such file or directory
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_1a3b6cb6-04bb-4214-a4cc-019ca5600253339854510474904207
Installing the required PIP packages..
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s), and 0 plot(s)

Successful translation: SED-ML file simulation_1.sedml
-----------------------------------------------------------------------------------------------------
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='simulation_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
Succesful model import: SBML file /tmp/temp7362775766727535847.xml
java.io.FileNotFoundException: /tmp/out/simulation_1.sedml/SimID_572698027_0_.ida (No such file or directory)
	at java.io.FileInputStream.open0(Native Method)
	at java.io.FileInputStream.open(FileInputStream.java:195)
	at java.io.FileInputStream.<init>(FileInputStream.java:138)
	at java.io.FileInputStream.<init>(FileInputStream.java:93)
	at cbit.vcell.solver.ode.SundialsSolver.getStateVariableResultSet(SundialsSolver.java:299)
	at cbit.vcell.solver.ode.SundialsSolver.getODESolverResultSet(SundialsSolver.java:187)
	at org.vcell.cli.SolverHandler.simulateAllTasks(SolverHandler.java:94)
	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:160)
	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)
Solver status: 3
Solver message: ./.vcell/simdata/temp/572698027_link/SundialsSolverStandalone_x64
Failed execution: Model 'archive_Ciliberto2003_Morphogenesis' Task 'simulation 1'.
-----------------------------------------------------------------------------------------------------
HDF conversion completed in '/tmp/out'

Generating zip Archive for reports
One or more errors encountered while executing archive /tmp/in/archive.omex

sedml.SimulatorSupportsRepeatedTasksWithChanges (36.9 s)
Test that a simulator supports repeated tasks with multiple subtasks
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpgsupxnzs/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:
VCell CLI input archive /tmp/in/archive.omex
Mar 25, 2021 9:56:47 PM java.util.prefs.FileSystemPreferences$1 run
WARNING: Couldn't create user preferences directory. User preferences are unusable.
Mar 25, 2021 9:56:47 PM java.util.prefs.FileSystemPreferences$1 run
WARNING: java.io.IOException: No such file or directory
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_c9c4a982-3f32-4430-aa54-f38181813d01977500807198568701
Installing the required PIP packages..
SED-ML version level not supported, import may fail
java.lang.NullPointerException
	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)
	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)
	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:354)
	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:127)
	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)
SED-ML processing for /tmp/vcell_temp_c9c4a982-3f32-4430-aa54-f38181813d01977500807198568701/simulation_1.sedml failed with error: null
org.jlibsedml.XMLException
	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)
	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:354)
	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:127)
	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)
One or more errors encountered while executing archive /tmp/in/archive.omex
VCell CLI input archive /tmp/in/archive.omex
Mar 25, 2021 9:57:06 PM java.util.prefs.FileSystemPreferences$1 run
WARNING: Couldn't create user preferences directory. User preferences are unusable.
Mar 25, 2021 9:57:06 PM java.util.prefs.FileSystemPreferences$1 run
WARNING: java.io.IOException: No such file or directory
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_7348424b-d85d-4215-966d-d302bd23ba292304653338740234584
Installing the required PIP packages..
SED-ML version level not supported, import may fail
java.lang.NullPointerException
	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)
	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)
	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:354)
	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:127)
	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)
SED-ML processing for /tmp/vcell_temp_7348424b-d85d-4215-966d-d302bd23ba292304653338740234584/simulation_1.sedml failed with error: null
org.jlibsedml.XMLException
	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)
	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:354)
	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:127)
	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)
One or more errors encountered while executing archive /tmp/in/archive.omex

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (37.9 s)
Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpqll9ljpi/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:
VCell CLI input archive /tmp/in/archive.omex
Mar 25, 2021 9:57:25 PM java.util.prefs.FileSystemPreferences$1 run
WARNING: Couldn't create user preferences directory. User preferences are unusable.
Mar 25, 2021 9:57:25 PM java.util.prefs.FileSystemPreferences$1 run
WARNING: java.io.IOException: No such file or directory
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_daa7db2c-e7e0-407c-862f-1471a6872e546452690335249168430
Installing the required PIP packages..
SED-ML version level not supported, import may fail
java.lang.NullPointerException
	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)
	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)
	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:354)
	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:127)
	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)
SED-ML processing for /tmp/vcell_temp_daa7db2c-e7e0-407c-862f-1471a6872e546452690335249168430/simulation_1.sedml failed with error: null
org.jlibsedml.XMLException
	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)
	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:354)
	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:127)
	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)
One or more errors encountered while executing archive /tmp/in/archive.omex
VCell CLI input archive /tmp/in/archive.omex
Mar 25, 2021 9:57:44 PM java.util.prefs.FileSystemPreferences$1 run
WARNING: Couldn't create user preferences directory. User preferences are unusable.
Mar 25, 2021 9:57:44 PM java.util.prefs.FileSystemPreferences$1 run
WARNING: java.io.IOException: No such file or directory
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_03aee7e4-4c8f-40d3-bd3c-984cbdea47427759847000129321631
Installing the required PIP packages..
SED-ML version level not supported, import may fail
java.lang.NullPointerException
	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)
	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)
	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:354)
	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:127)
	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)
SED-ML processing for /tmp/vcell_temp_03aee7e4-4c8f-40d3-bd3c-984cbdea47427759847000129321631/simulation_1.sedml failed with error: null
org.jlibsedml.XMLException
	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)
	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:354)
	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:127)
	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)
One or more errors encountered while executing archive /tmp/in/archive.omex

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges (18.8 s)
Test that a simulator supports repeated tasks over functional ranges
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpvlo3yt4h/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:
VCell CLI input archive /tmp/in/archive.omex
Mar 25, 2021 9:58:03 PM java.util.prefs.FileSystemPreferences$1 run
WARNING: Couldn't create user preferences directory. User preferences are unusable.
Mar 25, 2021 9:58:03 PM java.util.prefs.FileSystemPreferences$1 run
WARNING: java.io.IOException: No such file or directory
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_bfc7d324-1fe9-4dad-a90d-6253ee8887e44968273219279645565
Installing the required PIP packages..
SED-ML version level not supported, import may fail
java.lang.NullPointerException
	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)
	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)
	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:354)
	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:127)
	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)
SED-ML processing for /tmp/vcell_temp_bfc7d324-1fe9-4dad-a90d-6253ee8887e44968273219279645565/simulation_1.sedml failed with error: null
org.jlibsedml.XMLException
	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)
	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:354)
	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:127)
	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)
One or more errors encountered while executing archive /tmp/in/archive.omex

sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks (18.8 s)
Test that a simulator supports repeated tasks with multiple subtasks
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpghmablqu/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:
VCell CLI input archive /tmp/in/archive.omex
Mar 25, 2021 9:58:21 PM java.util.prefs.FileSystemPreferences$1 run
WARNING: Couldn't create user preferences directory. User preferences are unusable.
Mar 25, 2021 9:58:21 PM java.util.prefs.FileSystemPreferences$1 run
WARNING: java.io.IOException: No such file or directory
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_cfa96c9a-30f8-4df6-991e-abfedcf9a1a44844388664865552761
Installing the required PIP packages..
SED-ML version level not supported, import may fail
java.lang.NullPointerException
	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)
	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)
	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:354)
	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:127)
	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)
SED-ML processing for /tmp/vcell_temp_cfa96c9a-30f8-4df6-991e-abfedcf9a1a44844388664865552761/simulation_1.sedml failed with error: null
org.jlibsedml.XMLException
	at org.jlibsedml.SE ...

- After correcting your simulator, please edit the first block of this issue to re-initiate this validation.

@moraru @gmarupilla
I fixed the bug with GitHub that was occurring with some earlier actions. The problem was that messages are limited to 64k characters. Note, the error summaries are now truncated to 64k characters. The full log is available from the associated GitHub action.

Thank you @biosimulators-daemon for your submission to the BioSimulators simulator validation/submission system!
The BioSimulators validator bot is validating the specifications of your simulator, validating your Docker image and committing your simulator to the BioSimulators registry.
We will discuss any concerns with your submission in this issue.
A complete log of your simulator submission job will be available here. The results of the validation of your tool will also be saved as a JSON file.A link to this file will be available from the "Artifacts" section at the bottom of this page.

The specifications of your simulator is valid!

Summary of tests

Executed 58 test cases

Passed 14 test cases:

cli.CliDescribesSupportedEnvironmentVariablesInline
cli.CliDisplaysHelpInline
cli.CliDisplaysVersionInformationInline
combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
docker_image.DeclaresSupportedEnvironmentVariables
docker_image.DefaultUserIsRoot
docker_image.HasBioContainersLabels
docker_image.HasOciLabels
sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges
sedml.SimulatorSupportsAlgorithmParameters
sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
sedml.SimulatorSupportsMultipleReportsPerSedDocument

Failed 11 test cases:

combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories
combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories
published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous
published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM
results_report.SimulatorGeneratesReportsOfSimulationResults
sedml.SimulatorSupportsMultipleTasksPerSedDocument
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes

Skipped 33 test cases:

log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks
published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation
published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis
published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation
published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA
published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism
published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
sedml.SimulatorProducesLinear2DPlots
sedml.SimulatorProducesLinear3DPlots
sedml.SimulatorProducesLogarithmic2DPlots
sedml.SimulatorProducesLogarithmic3DPlots
sedml.SimulatorProducesMultiplePlots
sedml.SimulatorSupportsComputeModelChanges
sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes
sedml.SimulatorSupportsDataSetsWithDifferentShapes
sedml.SimulatorSupportsModelAttributeChanges
sedml.SimulatorSupportsRepeatedTasksWithChanges
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges
sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks
sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges
sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks
sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes
sedml.SimulatorSupportsRepeatedTasksWithVectorRanges
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes

Failures
combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories (7.8 s)
Test that SED documents in nested directories can be executed
Exception:
[Errno 13] Permission denied: 'simulation_1.sedml'

Log:
VCell CLI input archive /tmp/in/archive.omex
Mar 25, 2021 11:32:12 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_d7901ad7-6cdb-4756-a292-d7468fe92d107619447875322828948
Installing the required PIP packages..
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s), and 0 plot(s)

Successful translation: SED-ML file simulation_1.sedml
-----------------------------------------------------------------------------------------------------
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='simulation_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
java.lang.RuntimeException: Error importing from SBML : no SBML source.
	at cbit.vcell.xml.XmlHelper.importSBML(XmlHelper.java:447)
	at cbit.vcell.xml.XmlHelper.sedmlToBioModel(XmlHelper.java:680)
	at org.vcell.cli.SolverHandler.simulateAllTasks(SolverHandler.java:65)
	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:160)
	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)
Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection
Error importing from SBML : no SBML source.
Unable to initialize bioModel for the given selection
Error importing from SBML : no SBML source.

combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories (7.4 s)
Test that SED documents with the same names in nested directories can be executed and their outputs are saved to distinct paths
Exception:
[Errno 13] Permission denied: 'simulation_1.sedml'

Log:
VCell CLI input archive /tmp/in/archive.omex
Mar 25, 2021 11:32:19 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_fb11d8b9-e585-4727-8f59-ef5c9c1b84916792226622487253101
Installing the required PIP packages..
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 2 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s), and 0 plot(s)

Successful translation: SED-ML file simulation_1.sedml
-----------------------------------------------------------------------------------------------------
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='simulation_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
java.lang.RuntimeException: Error importing from SBML : no SBML source.
	at cbit.vcell.xml.XmlHelper.importSBML(XmlHelper.java:447)
	at cbit.vcell.xml.XmlHelper.sedmlToBioModel(XmlHelper.java:680)
	at org.vcell.cli.SolverHandler.simulateAllTasks(SolverHandler.java:65)
	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:160)
	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)
Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection
Error importing from SBML : no SBML source.
Unable to initialize bioModel for the given selection
Error importing from SBML : no SBML source.

published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (13.4 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

Exception:
[Errno 13] Permission denied: 'BIOMD0000000912_sim.csv'

Log:
VCell CLI input archive /tmp/in/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex
Mar 25, 2021 11:44:39 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_c9ac46d3-c1d6-4e56-890e-5adfa56e39e74186348887822183133
Installing the required PIP packages..
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s), and 1 plot(s)

Successful translation: SED-ML file BIOMD0000000912_sim.sedml
-----------------------------------------------------------------------------------------------------
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='BIOMD0000000912_sim') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
SBML Import: no assignment rules.
SBML Import: no assignment rules.
LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import:
- WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters.

User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in.

Succesful model import: SBML file /tmp/temp7570203149968075872.xml
Succesful execution: Model 'Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations_BIOMD0000000912' Task 'Caravagna2010'.
-----------------------------------------------------------------------------------------------------
Ignoring unsupported output plot_1
Generating report BIOMD0000000912_sim
HDF conversion completed in '/tmp/out'

Generating zip Archive for reports

published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous (27.7 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

Exception:
[Errno 13] Permission denied: 'simulation_1.csv'

Log:
VCell CLI input archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex
Mar 25, 2021 11:44:11 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_c762925e-3d21-4023-a1b3-cc69b2859fe67032208062147629323
Installing the required PIP packages..
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s), and 0 plot(s)

Successful translation: SED-ML file simulation_1.sedml
-----------------------------------------------------------------------------------------------------
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='simulation_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
Succesful model import: SBML file /tmp/temp8044022725742099116.xml
Succesful execution: Model 'Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous_Ciliberto2003_Morphogenesis' Task 'simulation 1'.
-----------------------------------------------------------------------------------------------------
Generating report simulation_1
HDF conversion completed in '/tmp/out'

Generating zip Archive for reports

published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution (12.5 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

Exception:
[Errno 13] Permission denied: 'simulation_1.csv'

Log:
VCell CLI input archive /tmp/in/Parmar-BMC-Syst-Biol-2017-iron-distribution.omex
Mar 25, 2021 11:44:52 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_a822ee3f-5561-4163-bf7c-363bab84b0671852393437511652730
Installing the required PIP packages..
Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s), and 0 plot(s)

Successful translation: SED-ML file Parmar2017_Deficient_Rich_tracer.sedml
-----------------------------------------------------------------------------------------------------
Task (id='simulation_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
error binding expression 'v': 'v' 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).
error binding expression '(k1 * Hepcidin)': 'k1' 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).
Succesful model import: SBML file /tmp/temp8225146310779141269.xml
Succesful execution: Model 'Parmar-BMC-Syst-Biol-2017-iron-distribution_model' Task 'simulation_1'.
-----------------------------------------------------------------------------------------------------
Generating report simulation_1
HDF conversion completed in '/tmp/out'

Generating zip Archive for reports

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock (63.7 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019
Format: format_2585
Algorithm: KISAO_0000027
Format: format_2585
Algorithm: KISAO_0000030

Exception:
[Errno 13] Permission denied: 'report_Euler_small_step_size.csv'

Log:
VCell CLI input archive /tmp/in/Vilar-PNAS-2002-minimal-circardian-clock.omex
Mar 25, 2021 11:45:32 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_6d086e53-a8ae-4de1-b104-04dd629989e78111395056132571926
Installing the required PIP packages..
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 4 model(s), 6 simulation(s), 6 task(s), 6  report(s), and 6 plot(s)

Successful translation: SED-ML file simulation.sedml
-----------------------------------------------------------------------------------------------------
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='tsk_0_0') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
Succesful model import: SBML file /tmp/temp5701243383689861769.xml
Task (id='tsk_0_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
Succesful model import: SBML file /tmp/temp301996441887564858.xml
Task (id='tsk_0_2') is compatible, solver match found in ontology: 'KISAO:0000030' matched to ForwardEuler
Task (id='tsk_0_3') is compatible, solver match found in ontology: 'KISAO:0000030' matched to ForwardEuler
Task (id='tsk_1_0') is compatible, solver match found in ontology: 'KISAO:0000027' matched to StochGibson
Succesful model import: SBML file /tmp/temp1566563084042598346.xml
Task (id='tsk_1_1') is compatible, solver match found in ontology: 'KISAO:0000027' matched to StochGibson
Succesful model import: SBML file /tmp/temp5658125350376965802.xml
Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock_ODE_deterministic' Task 'tsk_0_0'.
-----------------------------------------------------------------------------------------------------
Solver status: 3
Solver message: simulation failed at time=1.3: consider using smaller default or max time step.
values are:
A = NaN
C = Infinity
PrmA = Infinity
PrmA_bound = -Infinity
PrmR = Infinity
PrmR_bound = -Infinity
R = -Infinity

Failed execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock_ODE_deterministic' Task 'tsk_0_2'.
-----------------------------------------------------------------------------------------------------
final tolerance=0.1 final threshold=0.09, 885 remaining (keepAtMost=1000)
Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock_ODE_deterministic' Task 'tsk_0_3'.
-----------------------------------------------------------------------------------------------------
Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock_ODE_deterministic_0' Task 'tsk_0_1'.
-----------------------------------------------------------------------------------------------------
Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock_ODE_stochastic' Task 'tsk_1_0'.
-----------------------------------------------------------------------------------------------------
Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock_ODE_stochastic_0' Task 'tsk_1_1'.
-----------------------------------------------------------------------------------------------------
Ignoring unsupported output plot2d_Fig_1a
Ignoring unsupported output plot2d_low_delta_R_det
Ignoring unsupported output plot2d_Euler_default
Ignoring unsupported output plot2d_Euler_small_step_size
Ignoring unsupported output plot2d_Fig_1_c
Ignoring unsupported output plot2d_low_delta_R_stoch
Generating report report_Fig_1a
Generating report report_low_delta_R_det
Generating report report_Euler_default
Generating report report_Euler_small_step_size
Generating report report_Fig_1_c
Generating report report_low_delta_R_stoch
HDF conversion completed in '/tmp/out'

Generating zip Archive for reports

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous (44.3 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019
Format: format_2585
Algorithm: KISAO_0000030

Exception:
[Errno 13] Permission denied: 'report_Euler_small_step_size.csv'

Log:
VCell CLI input archive /tmp/in/Vilar-PNAS-2002-minimal-circardian-clock-continuous.omex
Mar 25, 2021 11:46:36 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_a38b42ff-b5a7-4ef9-8139-099874e5bd7c3443551550534234302
Installing the required PIP packages..
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 2 model(s), 4 simulation(s), 4 task(s), 4  report(s), and 4 plot(s)

Successful translation: SED-ML file simulation.sedml
-----------------------------------------------------------------------------------------------------
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='tsk_0_0') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
Succesful model import: SBML file /tmp/temp202388772933109601.xml
Task (id='tsk_0_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
Succesful model import: SBML file /tmp/temp2229421494439811456.xml
Task (id='tsk_0_2') is compatible, solver match found in ontology: 'KISAO:0000030' matched to ForwardEuler
Task (id='tsk_0_3') is compatible, solver match found in ontology: 'KISAO:0000030' matched to ForwardEuler
Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock-continuous_ODE_deterministic' Task 'tsk_0_0'.
-----------------------------------------------------------------------------------------------------
Solver status: 3
Solver message: simulation failed at time=1.3: consider using smaller default or max time step.
values are:
A = NaN
C = Infinity
PrmA = Infinity
PrmA_bound = -Infinity
PrmR = Infinity
PrmR_bound = -Infinity
R = -Infinity

Failed execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock-continuous_ODE_deterministic' Task 'tsk_0_2'.
-----------------------------------------------------------------------------------------------------
final tolerance=0.1 final threshold=0.09, 885 remaining (keepAtMost=1000)
Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock-continuous_ODE_deterministic' Task 'tsk_0_3'.
-----------------------------------------------------------------------------------------------------
Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock-continuous_ODE_deterministic_0' Task 'tsk_0_1'.
-----------------------------------------------------------------------------------------------------
Ignoring unsupported output plot2d_Fig_1a
Ignoring unsupported output plot2d_low_delta_R_det
Ignoring unsupported output plot2d_Euler_default
Ignoring unsupported output plot2d_Euler_small_step_size
Generating report report_Fig_1a
Generating report report_low_delta_R_det
Generating report report_Euler_default
Generating report report_Euler_small_step_size
HDF conversion completed in '/tmp/out'

Generating zip Archive for reports

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM (27.1 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000027

Exception:
[Errno 13] Permission denied: 'report_Fig_1_c.csv'

Log:
VCell CLI input archive /tmp/in/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM.omex
Mar 25, 2021 11:45:05 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_b29fcece-6cef-4656-95ee-4e91d33b28a48428386973826321104
Installing the required PIP packages..
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 2 model(s), 2 simulation(s), 2 task(s), 2  report(s), and 2 plot(s)

Successful translation: SED-ML file simulation.sedml
-----------------------------------------------------------------------------------------------------
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='tsk_1_0') is compatible, solver match found in ontology: 'KISAO:0000027' matched to StochGibson
Succesful model import: SBML file /tmp/temp4003754950538942809.xml
Task (id='tsk_1_1') is compatible, solver match found in ontology: 'KISAO:0000027' matched to StochGibson
Succesful model import: SBML file /tmp/temp7917875721553052305.xml
Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM_ODE_stochastic' Task 'tsk_1_0'.
-----------------------------------------------------------------------------------------------------
Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM_ODE_stochastic_0' Task 'tsk_1_1'.
-----------------------------------------------------------------------------------------------------
Ignoring unsupported output plot2d_Fig_1_c
Ignoring unsupported output plot2d_low_delta_R_stoch
Generating report report_Fig_1_c
Generating report report_low_delta_R_stoch
HDF conversion completed in '/tmp/out'

Generating zip Archive for reports

results_report.SimulatorGeneratesReportsOfSimulationResults (27.8 s)
Test that when a COMBINE/OMEX archive defines a (single) master file, the simulator only executes this file.
Exception:
[Errno 13] Permission denied: 'simulation_1.csv'

Log:
VCell CLI input archive /tmp/in/archive.omex
Mar 25, 2021 11:41:52 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_7599c18d-80d1-44d9-8b92-08863191aad6525890785988271835
Installing the required PIP packages..
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s), and 0 plot(s)

Successful translation: SED-ML file simulation_1.sedml
-----------------------------------------------------------------------------------------------------
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='simulation_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
Succesful model import: SBML file /tmp/temp6506059311141192340.xml
Succesful execution: Model 'archive_Ciliberto2003_Morphogenesis' Task 'simulation 1'.
-----------------------------------------------------------------------------------------------------
Generating report simulation_1
HDF conversion completed in '/tmp/out'

Generating zip Archive for reports

sedml.SimulatorSupportsMultipleTasksPerSedDocument (9.1 s)
Test that a simulator supports multiple tasks per SED document
Exception:
The image 'ghcr.io/biosimulators/biosimulators_vcell/vcell:<IP_ADDRESS>' could not execute the archive:

  Unknown error

Log:
VCell CLI input archive /tmp/in/archive.omex
Mar 25, 2021 11:39:42 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_115b3a17-f0ff-414f-8477-e9d8bdd34dd67838472855483724416
Installing the required PIP packages..
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 2 task(s), 2  report(s), and 0 plot(s)

Successful translation: SED-ML file simulation_1.sedml
-----------------------------------------------------------------------------------------------------
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='simulation_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
Succesful model import: SBML file /tmp/temp4558664459650601085.xml
Task (id='simulation_1__test_suite_copy') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
java.beans.PropertyVetoException: Simulation with name simulation 1 already exists
	at cbit.vcell.biomodel.BioModel.vetoableChange(BioModel.java:1005)
	at java.beans.VetoableChangeSupport.fireVetoableChange(VetoableChangeSupport.java:375)
	at java.beans.VetoableChangeSupport.fireVetoableChange(VetoableChangeSupport.java:271)
	at cbit.vcell.biomodel.BioModel.fireVetoableChange(BioModel.java:330)
	at cbit.vcell.biomodel.BioModel.setSimulations(BioModel.java:899)
	at cbit.vcell.biomodel.BioModel.addSimulation(BioModel.java:154)
	at cbit.vcell.xml.XmlHelper.sedmlToBioModel(XmlHelper.java:814)
	at org.vcell.cli.SolverHandler.simulateAllTasks(SolverHandler.java:65)
	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:160)
	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)
Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection
Simulation with name simulation 1 already exists
Unable to initialize bioModel for the given selection
Simulation with name simulation 1 already exists

sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes (27.7 s)
Test that a simulator supports time courses with non-zero output start times
Exception:
[Errno 13] Permission denied: 'simulation_1.csv'

Log:
VCell CLI input archive /tmp/in/archive.omex
Mar 25, 2021 11:41:24 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_760f3cae-92ce-4d01-8529-ec52febc9eeb81393996770959010
Installing the required PIP packages..
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s), and 0 plot(s)

Successful translation: SED-ML file simulation_1.sedml
-----------------------------------------------------------------------------------------------------
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='simulation_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
Succesful model import: SBML file /tmp/temp4355047014739413304.xml
Succesful execution: Model 'archive_Ciliberto2003_Morphogenesis' Task 'simulation 1'.
-----------------------------------------------------------------------------------------------------
Generating report simulation_1
HDF conversion completed in '/tmp/out'

Generating zip Archive for reports

Warnings
cli.CliDescribesSupportedEnvironmentVariablesInline (10.7 s)
Test that the inline help for a command-line interface describes the environment variables that the simulator supports.
Warnings:
The inline help for a command-line interface for a simulation tool should describe the environment variables that the simulation tool supports.

The command-line interface does not describe the following standard environment variables recognized by BioSimulators:
  - 'ALGORITHM_SUBSTITUTION_POLICY'

If the simulation tool implements these variables, they should be described in the inline help for its command-line interface.

Note, support for these environment variables is optional. Simulation tools are not required to support these variables.

Log:

cli.CliDisplaysHelpInline (2.4 s)
Test that a command-line interface provides inline help.
Warnings:
Command-line interface should support the `-h` option for displaying help inline.

The command-line interface displayed the following when executed with `-h`:

Command-line interface should support the `--help` option for displaying help inline.

The command-line interface displayed the following when executed with `--help`:

Log:

cli.CliDisplaysVersionInformationInline (1.9 s)
Test that a command-line interface provides version information inline.
Warnings:
Command-line interface should support the `-v` option for displaying version information inline.

The command-line interface displayed the following when executed with `-v`:

Command-line interface should support the `--version` option for displaying version information inline.

The command-line interface displayed the following when executed with `--version`:

Log:

docker_image.HasBioContainersLabels (0.5 s)
Test that a Docker image has BioContainers labels with metadata about the image
Warnings:
The Docker image should have the following BioContainers labels:
  extra.identifiers.biotools

Log:

docker_image.HasOciLabels (0.5 s)
Test that a Docker image has Open Container Initiative (OCI) labels with metadata about the image
Warnings:
The Docker image should have the following Open Container Initiative (OCI) labels:
  org.opencontainers.image.created
  org.opencontainers.image.revision

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (13.4 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

Warnings:
Plots were not produced:
  BIOMD0000000912_sim.sedml/plot_1

Log:
VCell CLI input archive /tmp/in/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex
Mar 25, 2021 11:44:39 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_c9ac46d3-c1d6-4e56-890e-5adfa56e39e74186348887822183133
Installing the required PIP packages..
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s), and 1 plot(s)

Successful translation: SED-ML file BIOMD0000000912_sim.sedml
-----------------------------------------------------------------------------------------------------
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='BIOMD0000000912_sim') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
SBML Import: no assignment rules.
SBML Import: no assignment rules.
LOGGER: msgLevel=MediumPriority, msgType=OverallWarning, Issues encountered during SBML Import:
- WARNING: The imported model has one or more reactions that have ids/names that are longer than 64 characters.

User is STRONGLY recommeded to shorten the names to avoid problems with the length of expressions these names might be used in.

Succesful model import: SBML file /tmp/temp7570203149968075872.xml
Succesful execution: Model 'Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations_BIOMD0000000912' Task 'Caravagna2010'.
-----------------------------------------------------------------------------------------------------
Ignoring unsupported output plot_1
Generating report BIOMD0000000912_sim
HDF conversion completed in '/tmp/out'

Generating zip Archive for reports

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock (63.7 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019
Format: format_2585
Algorithm: KISAO_0000027
Format: format_2585
Algorithm: KISAO_0000030

Warnings:
Plots were not produced:
  simulation.sedml/plot2d_Euler_default
  simulation.sedml/plot2d_Euler_small_step_size
  simulation.sedml/plot2d_Fig_1_c
  simulation.sedml/plot2d_Fig_1a
  simulation.sedml/plot2d_low_delta_R_det
  simulation.sedml/plot2d_low_delta_R_stoch

Log:
VCell CLI input archive /tmp/in/Vilar-PNAS-2002-minimal-circardian-clock.omex
Mar 25, 2021 11:45:32 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_6d086e53-a8ae-4de1-b104-04dd629989e78111395056132571926
Installing the required PIP packages..
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 4 model(s), 6 simulation(s), 6 task(s), 6  report(s), and 6 plot(s)

Successful translation: SED-ML file simulation.sedml
-----------------------------------------------------------------------------------------------------
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='tsk_0_0') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
Succesful model import: SBML file /tmp/temp5701243383689861769.xml
Task (id='tsk_0_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
Succesful model import: SBML file /tmp/temp301996441887564858.xml
Task (id='tsk_0_2') is compatible, solver match found in ontology: 'KISAO:0000030' matched to ForwardEuler
Task (id='tsk_0_3') is compatible, solver match found in ontology: 'KISAO:0000030' matched to ForwardEuler
Task (id='tsk_1_0') is compatible, solver match found in ontology: 'KISAO:0000027' matched to StochGibson
Succesful model import: SBML file /tmp/temp1566563084042598346.xml
Task (id='tsk_1_1') is compatible, solver match found in ontology: 'KISAO:0000027' matched to StochGibson
Succesful model import: SBML file /tmp/temp5658125350376965802.xml
Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock_ODE_deterministic' Task 'tsk_0_0'.
-----------------------------------------------------------------------------------------------------
Solver status: 3
Solver message: simulation failed at time=1.3: consider using smaller default or max time step.
values are:
A = NaN
C = Infinity
PrmA = Infinity
PrmA_bound = -Infinity
PrmR = Infinity
PrmR_bound = -Infinity
R = -Infinity

Failed execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock_ODE_deterministic' Task 'tsk_0_2'.
-----------------------------------------------------------------------------------------------------
final tolerance=0.1 final threshold=0.09, 885 remaining (keepAtMost=1000)
Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock_ODE_deterministic' Task 'tsk_0_3'.
-----------------------------------------------------------------------------------------------------
Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock_ODE_deterministic_0' Task 'tsk_0_1'.
-----------------------------------------------------------------------------------------------------
Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock_ODE_stochastic' Task 'tsk_1_0'.
-----------------------------------------------------------------------------------------------------
Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock_ODE_stochastic_0' Task 'tsk_1_1'.
-----------------------------------------------------------------------------------------------------
Ignoring unsupported output plot2d_Fig_1a
Ignoring unsupported output plot2d_low_delta_R_det
Ignoring unsupported output plot2d_Euler_default
Ignoring unsupported output plot2d_Euler_small_step_size
Ignoring unsupported output plot2d_Fig_1_c
Ignoring unsupported output plot2d_low_delta_R_stoch
Generating report report_Fig_1a
Generating report report_low_delta_R_det
Generating report report_Euler_default
Generating report report_Euler_small_step_size
Generating report report_Fig_1_c
Generating report report_low_delta_R_stoch
HDF conversion completed in '/tmp/out'

Generating zip Archive for reports

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous (44.3 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019
Format: format_2585
Algorithm: KISAO_0000030

Warnings:
Plots were not produced:
  simulation.sedml/plot2d_Euler_default
  simulation.sedml/plot2d_Euler_small_step_size
  simulation.sedml/plot2d_Fig_1a
  simulation.sedml/plot2d_low_delta_R_det

Log:
VCell CLI input archive /tmp/in/Vilar-PNAS-2002-minimal-circardian-clock-continuous.omex
Mar 25, 2021 11:46:36 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_a38b42ff-b5a7-4ef9-8139-099874e5bd7c3443551550534234302
Installing the required PIP packages..
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 2 model(s), 4 simulation(s), 4 task(s), 4  report(s), and 4 plot(s)

Successful translation: SED-ML file simulation.sedml
-----------------------------------------------------------------------------------------------------
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='tsk_0_0') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
Succesful model import: SBML file /tmp/temp202388772933109601.xml
Task (id='tsk_0_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
Succesful model import: SBML file /tmp/temp2229421494439811456.xml
Task (id='tsk_0_2') is compatible, solver match found in ontology: 'KISAO:0000030' matched to ForwardEuler
Task (id='tsk_0_3') is compatible, solver match found in ontology: 'KISAO:0000030' matched to ForwardEuler
Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock-continuous_ODE_deterministic' Task 'tsk_0_0'.
-----------------------------------------------------------------------------------------------------
Solver status: 3
Solver message: simulation failed at time=1.3: consider using smaller default or max time step.
values are:
A = NaN
C = Infinity
PrmA = Infinity
PrmA_bound = -Infinity
PrmR = Infinity
PrmR_bound = -Infinity
R = -Infinity

Failed execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock-continuous_ODE_deterministic' Task 'tsk_0_2'.
-----------------------------------------------------------------------------------------------------
final tolerance=0.1 final threshold=0.09, 885 remaining (keepAtMost=1000)
Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock-continuous_ODE_deterministic' Task 'tsk_0_3'.
-----------------------------------------------------------------------------------------------------
Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock-continuous_ODE_deterministic_0' Task 'tsk_0_1'.
-----------------------------------------------------------------------------------------------------
Ignoring unsupported output plot2d_Fig_1a
Ignoring unsupported output plot2d_low_delta_R_det
Ignoring unsupported output plot2d_Euler_default
Ignoring unsupported output plot2d_Euler_small_step_size
Generating report report_Fig_1a
Generating report report_low_delta_R_det
Generating report report_Euler_default
Generating report report_Euler_small_step_size
HDF conversion completed in '/tmp/out'

Generating zip Archive for reports

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM (27.1 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000027

Warnings:
Plots were not produced:
  simulation.sedml/plot2d_Fig_1_c
  simulation.sedml/plot2d_low_delta_R_stoch

Log:
VCell CLI input archive /tmp/in/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM.omex
Mar 25, 2021 11:45:05 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_b29fcece-6cef-4656-95ee-4e91d33b28a48428386973826321104
Installing the required PIP packages..
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 2 model(s), 2 simulation(s), 2 task(s), 2  report(s), and 2 plot(s)

Successful translation: SED-ML file simulation.sedml
-----------------------------------------------------------------------------------------------------
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='tsk_1_0') is compatible, solver match found in ontology: 'KISAO:0000027' matched to StochGibson
Succesful model import: SBML file /tmp/temp4003754950538942809.xml
Task (id='tsk_1_1') is compatible, solver match found in ontology: 'KISAO:0000027' matched to StochGibson
Succesful model import: SBML file /tmp/temp7917875721553052305.xml
Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM_ODE_stochastic' Task 'tsk_1_0'.
-----------------------------------------------------------------------------------------------------
Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM_ODE_stochastic_0' Task 'tsk_1_1'.
-----------------------------------------------------------------------------------------------------
Ignoring unsupported output plot2d_Fig_1_c
Ignoring unsupported output plot2d_low_delta_R_stoch
Generating report report_Fig_1_c
Generating report report_low_delta_R_stoch
HDF conversion completed in '/tmp/out'

Generating zip Archive for reports

Skips
log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives (27.5 s)
Test that simulator logs the execution of COMBINE/OMEX archives
Reason for skip:
[Errno 13] Permission denied: 'simulation_1.csv'

Log:
VCell CLI input archive /tmp/in/archive.omex
Mar 25, 2021 11:42:19 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_351cb13a-1584-46f5-8d34-6524bb17b2124360272811660941376
Installing the required PIP packages..
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s), and 0 plot(s)

Successful translation: SED-ML file simulation_1.sedml
-----------------------------------------------------------------------------------------------------
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='simulation_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
Succesful model import: SBML file /tmp/temp646887013607090960.xml
Succesful execution: Model 'archive_Ciliberto2003_Morphogenesis' Task 'simulation 1'.
-----------------------------------------------------------------------------------------------------
Generating report simulation_1
HDF conversion completed in '/tmp/out'

Generating zip Archive for reports

log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments (28.0 s)
Test that simulator logs the execution of individual SED document in COMBINE/OMEX archives
Reason for skip:
[Errno 13] Permission denied: 'simulation_1.csv'

Log:
VCell CLI input archive /tmp/in/archive.omex
Mar 25, 2021 11:42:47 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_1d1f34ed-e959-41f8-a99d-5e4e132d02b12641518502801798773
Installing the required PIP packages..
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s), and 0 plot(s)

Successful translation: SED-ML file simulation_1.sedml
-----------------------------------------------------------------------------------------------------
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='simulation_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
Succesful model import: SBML file /tmp/temp7829337330494655083.xml
Succesful execution: Model 'archive_Ciliberto2003_Morphogenesis' Task 'simulation 1'.
-----------------------------------------------------------------------------------------------------
Generating report simulation_1
HDF conversion completed in '/tmp/out'

Generating zip Archive for reports

log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs (27.7 s)
Test that simulator logs the execution of individual SED outputs in COMBINE/OMEX archives
Reason for skip:
[Errno 13] Permission denied: 'simulation_1.csv'

Log:
VCell CLI input archive /tmp/in/archive.omex
Mar 25, 2021 11:43:15 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_112abcbe-a117-4f02-b72b-460dd94f9d34894481377313096701
Installing the required PIP packages..
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s), and 0 plot(s)

Successful translation: SED-ML file simulation_1.sedml
-----------------------------------------------------------------------------------------------------
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='simulation_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
Succesful model import: SBML file /tmp/temp2110437685053586243.xml
Succesful execution: Model 'archive_Ciliberto2003_Morphogenesis' Task 'simulation 1'.
-----------------------------------------------------------------------------------------------------
Generating report simulation_1
HDF conversion completed in '/tmp/out'

Generating zip Archive for reports

log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks (28.1 s)
Test that simulator logs the execution of individual SED tasks in COMBINE/OMEX archives
Reason for skip:
[Errno 13] Permission denied: 'simulation_1.csv'

Log:
VCell CLI input archive /tmp/in/archive.omex
Mar 25, 2021 11:43:43 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_9b940075-b40a-4c91-8fd8-8f7447142ffa5743884979833069156
Installing the required PIP packages..
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s), and 0 plot(s)

Successful translation: SED-ML file simulation_1.sedml
-----------------------------------------------------------------------------------------------------
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='simulation_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
Succesful model import: SBML file /tmp/temp3538547992706037139.xml
Succesful execution: Model 'archive_Ciliberto2003_Morphogenesis' Task 'simulation 1'.
-----------------------------------------------------------------------------------------------------
Generating report simulation_1
HDF conversion completed in '/tmp/out'

Generating zip Archive for reports

published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_3972
Algorithm: KISAO_0000263

Reason for skip:
Case requires model formats format_3972 and simulation algorithms KISAO_0000263

Log:

published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_3972
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_3972 and simulation algorithms KISAO_0000019

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000088

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000088

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Szymanska-J-Theor-Biol-2009-HSP-synthesis (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000496

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000496

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Tomida-EMBO-J-2003-NFAT-translocation (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000560

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000560

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Varusai-Sci-Rep-2018-mTOR-signaling-LSODA-LSODAR-SBML (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000560

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000560

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-SSA (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000029

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000029

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-fbc/Escherichia-coli-core-metabolism (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000437

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000437

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-qual/Chaouiya-BMC-Syst-Biol-2013-EGF-TNFa-signaling (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000449

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_0000449

Log:

sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments (6.8 s)
Test that a simulator can resolve model sources defined by URI fragments (e.g., #model1).
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_vcell/vcell:<IP_ADDRESS>' could not execute the archive:

  Unknown error

Log:
VCell CLI input archive /tmp/in/archive.omex
Mar 25, 2021 11:33:43 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_ea56c9ed-1498-476b-8811-b559b03d9a6f1063326063307057291
Installing the required PIP packages..
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 2 model(s), 1 simulation(s), 1 task(s), 1  report(s), and 0 plot(s)

Successful translation: SED-ML file simulation_1.sedml
-----------------------------------------------------------------------------------------------------
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='simulation_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
[Fatal Error] :1:1: Content is not allowed in prolog.
java.lang.RuntimeException: Error importing from SBML : no SBML source.
	at cbit.vcell.xml.XmlHelper.importSBML(XmlHelper.java:447)
	at cbit.vcell.xml.XmlHelper.sedmlToBioModel(XmlHelper.java:680)
	at org.vcell.cli.SolverHandler.simulateAllTasks(SolverHandler.java:65)
	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:160)
	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)
Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection
Error importing from SBML : no SBML source.
Unable to initialize bioModel for the given selection
Error importing from SBML : no SBML source.

sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges (7.1 s)
Test that a simulator can resolve model sources defined by URI fragments (e.g., #model1) and inherit the changes of the model.
Reason for skip:
The image 'ghcr.io/biosimulators/biosimulators_vcell/vcell:<IP_ADDRESS>' could not execute the archive:

  Unknown error

Log:
VCell CLI input archive /tmp/in/archive.omex
Mar 25, 2021 11:33:50 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_f61aeadd-0cfa-4960-a610-cea7559295945368808162922414012
Installing the required PIP packages..
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 2 model(s), 1 simulation(s), 1 task(s), 1  report(s), and 0 plot(s)

Successful translation: SED-ML file simulation_1.sedml
-----------------------------------------------------------------------------------------------------
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='simulation_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
[Fatal Error] :1:1: Content is not allowed in prolog.
java.lang.RuntimeException: Error importing from SBML : no SBML source.
	at cbit.vcell.xml.XmlHelper.importSBML(XmlHelper.java:447)
	at cbit.vcell.xml.XmlHelper.sedmlToBioModel(XmlHelper.java:680)
	at org.vcell.cli.SolverHandler.simulateAllTasks(SolverHandler.java:65)
	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:160)
	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)
Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection
Error importing from SBML : no SBML source.
Unable to initialize bioModel for the given selection
Error importing from SBML : no SBML source.

sedml.SimulatorProducesLinear2DPlots (9.6 s)
Test that a simulator produces linear 2D plots
Reason for skip:
Simulator did not produce plots

Log:
VCell CLI input archive /tmp/in/archive.omex
Mar 25, 2021 11:33:57 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_3f067d97-fa71-48ef-879b-92d989708ea23550704561551508610
Installing the required PIP packages..
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 0  report(s), and 1 plot(s)

Successful translation: SED-ML file simulation_1.sedml
-----------------------------------------------------------------------------------------------------
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='simulation_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
Succesful model import: SBML file /tmp/temp8170873424294835560.xml
Succesful execution: Model 'archive_Ciliberto2003_Morphogenesis' Task 'simulation 1'.
-----------------------------------------------------------------------------------------------------
Ignoring unsupported output plot_0
Generating zip Archive for reports

sedml.SimulatorProducesLinear3DPlots (0.1 s)
Test that a simulator produces linear 3D plots
Reason for skip:
No curated COMBINE/OMEX archives are available to generate archives for testing

Log:

sedml.SimulatorProducesLogarithmic2DPlots (9.5 s)
Test that a simulator produces logarithmic 2D plots
Reason for skip:
Simulator did not produce plots

Log:
VCell CLI input archive /tmp/in/archive.omex
Mar 25, 2021 11:34:07 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_2a980c4d-310b-497d-8b0b-3d14e518af5f5217689484852784610
Installing the required PIP packages..
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 0  report(s), and 1 plot(s)

Successful translation: SED-ML file simulation_1.sedml
-----------------------------------------------------------------------------------------------------
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='simulation_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
Succesful model import: SBML file /tmp/temp8702983489515503071.xml
Succesful execution: Model 'archive_Ciliberto2003_Morphogenesis' Task 'simulation 1'.
-----------------------------------------------------------------------------------------------------
Ignoring unsupported output plot_0
Generating zip Archive for reports

sedml.SimulatorProducesLogarithmic3DPlots (0.1 s)
Test that a simulator produces logarithmic 3D plots
Reason for skip:
No curated COMBINE/OMEX archives are available to generate archives for testing

Log:

sedml.SimulatorProducesMultiplePlots (9.6 s)
Test that a simulator produces multiple plots
Reason for skip:
Simulator did not produce plots

Log:
VCell CLI input archive /tmp/in/archive.omex
Mar 25, 2021 11:34:17 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_60008cdf-645a-411d-b59e-3731fd6a321a678986298742970092
Installing the required PIP packages..
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 0  report(s), and 2 plot(s)

Successful translation: SED-ML file simulation_1.sedml
-----------------------------------------------------------------------------------------------------
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='simulation_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
Succesful model import: SBML file /tmp/temp3736906631870909535.xml
Succesful execution: Model 'archive_Ciliberto2003_Morphogenesis' Task 'simulation 1'.
-----------------------------------------------------------------------------------------------------
Ignoring unsupported output plot_0
Ignoring unsupported output plot_1
Generating zip Archive for reports

sedml.SimulatorSupportsComputeModelChanges (31.0 s)
Test that a simulator supports compute model changes
Reason for skip:
[Errno 13] Permission denied: 'simulation_1.csv'

Log:
VCell CLI input archive /tmp/in/archive.omex
Mar 25, 2021 11:36:09 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_51c82d9c-25da-4933-89f0-372f2e8855064093203008997892572
Installing the required PIP packages..
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s), and 0 plot(s)

Successful translation: SED-ML file simulation_1.sedml
-----------------------------------------------------------------------------------------------------
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='simulation_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
Succesful model import: SBML file /tmp/temp1556513329573271406.xml
Succesful execution: Model 'archive_Ciliberto2003_Morphogenesis' Task 'simulation 1'.
-----------------------------------------------------------------------------------------------------
Generating report simulation_1
HDF conversion completed in '/tmp/out'

Generating zip Archive for reports

sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes (45.9 s)
Test that a simulator supports data generators with different shapes
Reason for skip:
[Errno 13] Permission denied: 'simulation_1__copy_2.csv'

Log:
VCell CLI input archive /tmp/in/archive.omex
Mar 25, 2021 11:36:40 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_c0a325b6-9b62-440c-bb12-74c40bb519df388384920706170830
Installing the required PIP packages..
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 1 model(s), 2 simulation(s), 2 task(s), 1  report(s), and 0 plot(s)

Successful translation: SED-ML file simulation_1.sedml
-----------------------------------------------------------------------------------------------------
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='simulation_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
Succesful model import: SBML file /tmp/temp20117286537866859.xml
Task (id='simulation_1__copy_2') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
Succesful execution: Model 'archive_Ciliberto2003_Morphogenesis' Task 'simulation 1'.
-----------------------------------------------------------------------------------------------------
Succesful execution: Model 'archive_Ciliberto2003_Morphogenesis' Task 'simulation_1__copy_2'.
-----------------------------------------------------------------------------------------------------
Generating report simulation_1__copy_2
HDF conversion completed in '/tmp/out'

Generating zip Archive for reports

sedml.SimulatorSupportsDataSetsWithDifferentShapes (46.4 s)
Test that a simulator supports data generators with different shapes
Reason for skip:
[Errno 13] Permission denied: 'simulation_1.csv'

Log:
VCell CLI input archive /tmp/in/archive.omex
Mar 25, 2021 11:37:26 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_17681d5a-5b90-4247-984d-ba4bdb1039635678522836663947190
Installing the required PIP packages..
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 1 model(s), 2 simulation(s), 2 task(s), 1  report(s), and 0 plot(s)

Successful translation: SED-ML file simulation_1.sedml
-----------------------------------------------------------------------------------------------------
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='simulation_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
Succesful model import: SBML file /tmp/temp2969464126910298404.xml
Task (id='simulation_1__copy_2') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
Succesful execution: Model 'archive_Ciliberto2003_Morphogenesis' Task 'simulation 1'.
-----------------------------------------------------------------------------------------------------
Succesful execution: Model 'archive_Ciliberto2003_Morphogenesis' Task 'simulation_1__copy_2'.
-----------------------------------------------------------------------------------------------------
Generating report simulation_1
HDF conversion completed in '/tmp/out'

Generating zip Archive for reports

sedml.SimulatorSupportsModelAttributeChanges (33.1 s)
Test that a simulator supports changes to the attributes of model elements
Reason for skip:
[Errno 13] Permission denied: 'simulation_1.csv'

Log:
VCell CLI input archive /tmp/in/archive.omex
Mar 25, 2021 11:38:12 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_a6448c6a-b7d1-4cb7-9d43-e7ab82d974083680359030983035449
Installing the required PIP packages..
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s), and 0 plot(s)

Successful translation: SED-ML file simulation_1.sedml
-----------------------------------------------------------------------------------------------------
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='simulation_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
Succesful model import: SBML file /tmp/temp3811250720785350254.xml
Succesful execution: Model 'archive_Ciliberto2003_Morphogenesis' Task 'simulation 1'.
-----------------------------------------------------------------------------------------------------
Generating report simulation_1
HDF conversion completed in '/tmp/out'

Generating zip Archive for reports

sedml.SimulatorSupportsRepeatedTasksWithChanges (13.1 s)
Test that a simulator supports repeated tasks with multiple subtasks
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpemvk_ux2/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:
VCell CLI input archive /tmp/in/archive.omex
Mar 25, 2021 11:39:52 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_cfab7db8-99e1-4772-9989-3b74a69d635e7211406581403576117
Installing the required PIP packages..
SED-ML version level not supported, import may fail
java.lang.NullPointerException
	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)
	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)
	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:354)
	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:127)
	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)
SED-ML processing for /tmp/vcell_temp_cfab7db8-99e1-4772-9989-3b74a69d635e7211406581403576117/simulation_1.sedml failed with error: null
org.jlibsedml.XMLException
	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)
	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:354)
	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:127)
	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)
One or more errors encountered while executing archive /tmp/in/archive.omex
VCell CLI input archive /tmp/in/archive.omex
Mar 25, 2021 11:39:58 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_655e0c3d-fa08-41a3-ace1-42ba57eed9d41363218518632949829
Installing the required PIP packages..
SED-ML version level not supported, import may fail
java.lang.NullPointerException
	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)
	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)
	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:354)
	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:127)
	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)
SED-ML processing for /tmp/vcell_temp_655e0c3d-fa08-41a3-ace1-42ba57eed9d41363218518632949829/simulation_1.sedml failed with error: null
org.jlibsedml.XMLException
	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)
	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:354)
	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:127)
	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)
One or more errors encountered while executing archive /tmp/in/archive.omex

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (13.2 s)
Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpkt1w49a5/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:
VCell CLI input archive /tmp/in/archive.omex
Mar 25, 2021 11:40:05 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_4aba31bd-9e82-450c-84f8-3b40a69bf0c04421799622500902723
Installing the required PIP packages..
SED-ML version level not supported, import may fail
java.lang.NullPointerException
	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)
	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)
	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:354)
	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:127)
	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)
SED-ML processing for /tmp/vcell_temp_4aba31bd-9e82-450c-84f8-3b40a69bf0c04421799622500902723/simulation_1.sedml failed with error: null
org.jlibsedml.XMLException
	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)
	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:354)
	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:127)
	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)
One or more errors encountered while executing archive /tmp/in/archive.omex
VCell CLI input archive /tmp/in/archive.omex
Mar 25, 2021 11:40:11 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_962616fc-1119-49e5-ab28-572c2f01e3465689438272979672094
Installing the required PIP packages..
SED-ML version level not supported, import may fail
java.lang.NullPointerException
	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)
	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)
	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:354)
	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:127)
	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)
SED-ML processing for /tmp/vcell_temp_962616fc-1119-49e5-ab28-572c2f01e3465689438272979672094/simulation_1.sedml failed with error: null
org.jlibsedml.XMLException
	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)
	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:354)
	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:127)
	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)
One or more errors encountered while executing archive /tmp/in/archive.omex

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges (6.4 s)
Test that a simulator supports repeated tasks over functional ranges
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpoc2pzg4m/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:
VCell CLI input archive /tmp/in/archive.omex
Mar 25, 2021 11:40:18 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_6111483b-a451-4672-aca4-46387c3226e47107795879058385413
Installing the required PIP packages..
SED-ML version level not supported, import may fail
java.lang.NullPointerException
	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)
	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)
	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:354)
	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:127)
	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)
SED-ML processing for /tmp/vcell_temp_6111483b-a451-4672-aca4-46387c3226e47107795879058385413/simulation_1.sedml failed with error: null
org.jlibsedml.XMLException
	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)
	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:354)
	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:127)
	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)
One or more errors encountered while executing archive /tmp/in/archive.omex

sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks (6.5 s)
Test that a simulator supports repeated tasks with multiple subtasks
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpgaehli92/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:
VCell CLI input archive /tmp/in/archive.omex
Mar 25, 2021 11:40:24 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_fdf326e5-6997-40fd-8f7a-d590c96627f96895474866945338306
Installing the required PIP packages..
SED-ML version level not supported, import may fail
java.lang.NullPointerException
	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)
	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)
	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:354)
	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:127)
	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)
SED-ML processing for /tmp/vcell_temp_fdf326e5-6997-40fd-8f7a-d590c96627f96895474866945338306/simulation_1.sedml failed with error: null
org.jlibsedml.XMLException
	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)
	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:354)
	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:127)
	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)
One or more errors encountered while executing archive /tmp/in/archive.omex

sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges (6.5 s)
Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpesb47is0/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:
VCell CLI input archive /tmp/in/archive.omex
Mar 25, 2021 11:40:31 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_cf97ecb7-1469-4528-a393-d6f87edde5292203345337780488648
Installing the required PIP packages..
SED-ML version level not supported, import may fail
java.lang.NullPointerException
	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)
	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)
	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:354)
	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:127)
	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)
SED-ML processing for /tmp/vcell_temp_cf97ecb7-1469-4528-a393-d6f87edde5292203345337780488648/simulation_1.sedml failed with error: null
org.jlibsedml.XMLException
	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)
	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:354)
	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:127)
	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)
One or more errors encountered while executing archive /tmp/in/archive.omex

sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks (6.2 s)
Test that a simulator supports nested repeated tasks
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmp8ivb0ywd/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:
VCell CLI input archive /tmp/in/archive.omex
Mar 25, 2021 11:40:37 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_29fb92d6-2ce9-4e7e-94b5-7bdcdb892e434525630816748327325
Installing the required PIP packages..
SED-ML version level not supported, import may fail
java.lang.NullPointerException
	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)
	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)
	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:354)
	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:127)
	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)
SED-ML processing for /tmp/vcell_temp_29fb92d6-2ce9-4e7e-94b5-7bdcdb892e434525630816748327325/simulation_1.sedml failed with error: null
org.jlibsedml.XMLException
	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)
	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:354)
	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:127)
	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)
One or more errors encountered while executing archive /tmp/in/archive.omex

sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes (6.3 s)
Test that a simulator supports repeated tasks whose sub-tasks have mixed types. Also tests that sub-types executed in order of the values of their order attributes and that reports of the results of repeated tasks handle sub-tasks to produce results of different shapes.
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpvjb4_5ou/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:
VCell CLI input archive /tmp/in/archive.omex
Mar 25, 2021 11:40:44 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_df567fbf-e421-4894-88a7-1b1c87f49f3e4150671573671989461
Installing the required PIP packages..
SED-ML version level not supported, import may fail
java.lang.NullPointerException
	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)
	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)
	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:354)
	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:127)
	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)
SED-ML processing for /tmp/vcell_temp_df567fbf-e421-4894-88a7-1b1c87f49f3e4150671573671989461/simulation_1.sedml failed with error: null
org.jlibsedml.XMLException
	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)
	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:354)
	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:127)
	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)
One or more errors encountered while executing archive /tmp/in/archive.omex

sedml.SimulatorSupportsRepeatedTasksWithVectorRanges (6.4 s)
Test that a simulator supports repeated tasks over vector ranges
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmp8ziz7kjs/outputs/reports.h5', errno = 2, error message = 'No such file or directory', flags = 0, o_flags = 0)

Log:
VCell CLI input archive /tmp/in/archive.omex
Mar 25, 2021 11:40:50 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_0dd37eed-af45-4111-bef4-3d4cb2ccc2585080467128654635030
Installing the required PIP packages..
SED-ML version level not supported, import may fail
java.lang.NullPointerException
	at org.jlibsedml.SEDMLReader.getRepeatedTask(SEDMLReader.java:284)
	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:781)
	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:354)
	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:127)
	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)
SED-ML processing for /tmp/vcell_temp_0dd37eed-af45-4111-bef4-3d4cb2ccc2585080467128654635030/simulation_1.sedml failed with error: null
org.jlibsedml.XMLException
	at org.jlibsedml.SEDMLReader.getSedDocument(SEDMLReader.java:815)
	at org.jlibsedml.Libsedml.buildDocumentFromXMLTree(Libsedml.java:200)
	at org.jlibsedml.Libsedml.readDocumentFromString(Libsedml.java:354)
	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)
	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:127)
	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)
One or more errors encountered while executing archive /tmp/in/archive.omex

sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes (27.7 s)
Test that a simulator supports multiple time courses with non-zero initial times
Reason for skip:
[Errno 13] Permission denied: 'simulation_1.csv'

Log:
VCell CLI input archive /tmp/in/archive.omex
Mar 25, 2021 11:40:56 PM java.util.prefs.FileSystemPreferences$1 run
INFO: Created user preferences directory.
-----------------------------------------------------------------------------------------------------
TempPath Created: /tmp/vcell_temp_198d3483-28f8-4920-adc5-8b414078d3ee8871530074229793028
Installing the required PIP packages..
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Found 1 SED-ML document(s) with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s), and 0 plot(s)

Successful translation: SED-ML file simulation_1.sedml
-----------------------------------------------------------------------------------------------------
SED-ML version level not supported, import may fail
SED-ML version level not supported, import may fail
Unsupported version, import may fail
Task (id='simulation_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE
Succesful model import: SBML file /tmp/temp6748200421601619389.xml
Succesful execution: Model 'archive_Ciliberto2003_Morphogenesis' Task 'simulation 1'.
-----------------------------------------------------------------------------------------------------
Generating report simulation_1
HDF conversion completed in '/tmp/out'

Generating zip Archive for reports

- After correcting your simulator, please edit the first block of this issue to re-initiate this validation.
-
- The complete log of your validation/submission job, including further information about the failure, is available [here](https://github.com/biosimulators/Biosimulators/actions/runs/688233707). The results of the validation of your image will also be available shortly as a JSON file. A link to this file will be available from the "Artifacts" section at the bottom of [this page](https://github.com/biosimulators/Biosimulators/actions/runs/688233707).