provide Jupyter notebook

This provides a Jupyter notebook that runs the cam baseline example as defined in the config file.
It also changes the config file to be almost out-of-the-box for users, using default directories provided that they enter their user name at the top. The jupyter notebook has a check for this but we may want to write a check into the code for it, too.
Resolves #56

@bitterbark It looks like there are some failing tests in this PR.  Do you want me to just push the fixes to your branch directly, or would you prefer to fix them yourself?  Just let me know either way.  Thanks!

I’ll be in to look at these tomorrow, or feel free to push fixes if you know what it needs.

On Jul 19, 2022, at 2:06 PM, Jesse Nusbaumer @.***> wrote:

@bitterbark It looks like there are some failing tests in this PR. Do you want me to just push the fixes to your branch directly, or would you prefer to fix them yourself? Just let me know either way. Thanks!
—
Reply to this email directly, view it on GitHub, or unsubscribe.
You are receiving this because you were mentioned.

So the failures look to be because I changed some of the defaults in the config...yaml file.
This fails
self.assertEqual(cam_case_name_val, "/some/where/you/want/to/have/regridded_files")
because I changed the default to
/glade/scratch/${user}/ADF/regrid
I believe these were agreed upon changes, so does that mean I should figure out how to change the test?
It looks like several of the tests that failed ran into this particular variable; I'm not sure if there are other errors also.


i would like generate-report to be affected by the tags option

generate-report should understand and limit output if the tags option is present.
e.g. twine generate-report  -tags ios would out info on strings with the ios tag

generate-report has been removed in lieu of validate-strings-file


headless need to change robots from disallow to allow

Right after switching the live domain cannabis.ca.gov to point to the headless instance we need to change robots from disallow to allow
The code change needs to be made in https://github.com/cagov/cannabis.ca.gov/blob/main/src/rootcopy/robots.txt

@carterm assigning this to you to perform when we go live with headless. Updated launch plans are in https://docs.google.com/document/d/1Smdb0ZS3pt-R_PsIazeEW5cmINge-ipDW6WSo1H-xZA/edit


Update to newest set of Notebook Push API changes

Changes here:
https://github.com/microsoft/vscode/issues/93265#issuecomment-824906339

Validated as kernel execution works in Insiders.


Will you be adding an AssertConfigurationIsValid() equivalent?

Apologies if I have not found it and it exists, but do you have or plan to implement an AssertConfigurationIsValid() equivalent, as found in Automapper? This basically checks all maps are valid and we use from unit tests.

I too am wondering where I can do this sort of thing.
I see the TypeAdapterConfig.GlobalSettings.Compile(failFast: true) but it doesn't seem to do much, at least I can't see if its supposed to throw an error when RequireExplicitMapping and RequireDestinationMemberSource are set to true.

Any news on this issue? I'm experiencing the same problem.

I'm also curious about this one. I tried to upgrade to a prerelease version (7.4.0-pre06), but it still validates neither during compile time nor during startup. It throws exceptions only during runtime


activation list should allow server-side filtering by activation type

When one lists activations today, there is no way to filter on the server side activations that are singleton actions, sequences, or conductor top level invocations. This forces a client to have to scan through many activations to find the ones that it's looking for.
So this issue is to propose and scope filtering activations by some of their annotations on the server side.

@rabbah I would also propose adding the option of filtering by statusCode. I've already done some experimenting on different options for the view key in CouchDB, and perform combined filtering based on several filters like namespace, name, version, kind and status. However, given the nature of CouchDB, this is not an easy task to solve if you want to filter on several attributes at the same time. It becomes almost impossible if you also want to be able to perform the equivalent of a LIKE filter.


Add maintenance note

@danharrin A lot of people are confused by the default 503 error when the demo is refreshing. I added a blade file with a better maintenance note for that.
Can you add this to the deployment and merge this PR afterwards?
# Before
php artisan down --render=maintenance

# After
php artisan up

Done! Thanks


Counter badge shifts panel labels (depending on number length)

In my experience, issues without labels are simply lost and forgotten. Maybe this one is as-designed and should be closed, so ... cc @isidorn

Thanks for filling hits, however this is as designed as we always keep the constant width between items(including their badge).
This is just more flexible as the problems badge in theory could have a large number that takes a lot of width.
Also I do not think th shifting is that bad, thus closing as designed.


Fix Fix that tvf reading empty files in compressed formats.

Proposed changes
Issue Number: close #xxx

Fix the issue with tvf reading empty compressed files.

move two test cases (test_local_tvf_compression and test_s3_tvf_compression) from p2 to p0

docs: https://github.com/apache/doris-website/pull/654

Further comments
If this is a relatively large or complex change, kick off the discussion at<EMAIL_ADDRESS>by explaining why you chose the solution you did and what alternatives you considered, etc...

run buildall

run p0

run buildall

run p0

run buildall


docs: implement module preloading strategy

Hey @rubenperegrina thank you for contribution, can you also add the way we can do it using StandAlone API, this is a great contribution

Hey @santoshyadavdev , I just uploaded it using the StandAlone API, check it out


Compilation fails when deserializing (binary) std::shared_prt<T const>

Hi,
I just discovered cereal and want to transition from Boost. Doing this, I discovered that cereal doesn't seem to be able to handle a special case where Boost did not complain.
I have a std::shared_ptr<T const> amongst my data to save and load. I use binary archives. Everything works fine until saving the data, but when I write the code to load the archive, compilation of my program fails. Here is a minimal example that illustrates the issue:
#include <fstream>
#include <unordered_map>

#include <cereal/access.hpp>
#include <cereal/archives/binary.hpp>
#include <cereal/types/memory.hpp>

class Foo {
public:
    Foo() : foo_{std::make_shared<int>(0)} {}
    int foo() const { return *foo_; }
private:
    friend class cereal::access;
    template <typename Archive>
    void serialize(Archive& archive) {
        archive(foo_);
    }

    std::shared_ptr<int const> foo_;
};

int main() {
    Foo foo;

    {
        std::ofstream os("./foo.cereal", std::ios_base::binary);
        cereal::BinaryOutputArchive oar(os);
        oar(foo);
        os.close();
    }

    {
        std::ifstream is("./foo.cereal", std::ios_base::binary);
        cereal::BinaryInputArchive iar(is);
        iar(bar);
        is.close();
    }
    return 0;
}

Compiling fails with following message:
./lib/cereal/types/memory.hpp:337:7: error: no matching function for call to ‘cereal::BinaryInputArchive::registerSharedPointer(uint32_t&, std::shared_ptr<const int>&)’
       ar.registerSharedPointer( id, ptr );
       ^~
In file included from ./lib/cereal/types/memory.hpp:33,
                 from src/experiment.cpp:14:
./lib/cereal/cereal.hpp:690:19: note: candidate: ‘void cereal::InputArchive<ArchiveType, Flags>::registerSharedPointer(uint32_t, std::shared_ptr<void>) [with ArchiveType = cereal::BinaryInputArchive; unsigned int Flags = 1; uint32_t = unsigned int]’
       inline void registerSharedPointer(std::uint32_t const id, std::shared_ptr<void> ptr)
                   ^~~~~~~~~~~~~~~~~~~~~
./lib/cereal/cereal.hpp:690:19: note:   no known conversion for argument 2 from ‘shared_ptr<const int>’ to ‘shared_ptr<void>’

FYI: I am using cereal v1.2.2 and gcc version 8.2.0 on Ubuntu 18.04
If I change std::shared_ptr<int const> foo_; to std::shared_ptr<int> foo_;, it compiles. However, in my actual project, this is not an option. I actually found a workaround to retain my datastructures:
If I use separate save() and load() functions instead of serialize(), I can load the data to a temporary std::sharet_ptr<T> and then manually copy it to the member:
class Foo {
public:
    Foo() : foo_{std::make_shared<int>(0)} {}
    int foo() const { return *foo_; }
private:
    friend class cereal::access;
    template <typename Archive>
    void save(Archive& archive) const {
        archive(foo_);
    }
    template <typename Archive>
    void load(Archive& archive) {
        std::shared_ptr<int> temp;
        archive(temp);
        foo_ = temp;
    }

    std::shared_ptr<int const> foo_;
};

I applied this workaround in my actual project and it seems to work fine. However, it would be nice if cereal would be able to work with std::shared_ptr<T const> natively.

This is a known issue in the current release of cereal and will be fixed in version 1.2.3 which should be released soon (likely within days of writing this). In the meantime, you can try using the develop branch. See #417 and #423.


WFLY-5970 Plain JMS clients don't fallback

(cherry picked from commit 1f40a86fd7134d8b2211bdad4d7028e24b6003bd)
url: https://issues.jboss.org/browse/WFLY-5970

@bstansberry  let me check it tomorrow ...

retest this please

@bstansberry fixed

@bstansberry please could you merge this PR since it is upstream fix for BZ1258304 and it's included in next EAP 6.4. payload?

@vpakan It needs an equivalent PR against the jboss-eap7/7.x branch. For background I just forwarded a recent thread about this to the SET mailing list.

@bstansberry  this is PR to jboss-eap7/7.x  you asked https://github.com/jbossas/jboss-eap7/pull/748

@vpakan @treblereel Sorry, I should have looked more closely again at the PR before asking for 7.x.
This PR is functionally a no-op. It just does the same thing as the existing code in a slightly less correct way, e.g. not using resolveModelAttribute. I commented previously on one location where that was the case but every other change has no functional effect AFAICT. If I'm missing something please point it out.
@jmesnil is WFLY-5970 a duplicate for some other issue?
Perhaps there is a EAP 6 issue that was dealt with in WildFly/EAP 7 long ago and there is no need for an upstream change?  WFLY-5970 says it's a bug in 10.0.0.Final though and this class was in its current form long before that.

@bstansberry WFLY-5970 is a dup of https://issues.jboss.org/browse/WFLY-5394 that was fixed in WFLY 10.0.0.CR2.
This PR can be closed, I've resolved the WFLY-5970 issue as duplicate.

Thanks @jmesnil.
@treblereel @vpakan I'll close this and the 7.x one. As for the upstream-first requirement for a 6.4.x fix, you can link to this discussion as evidence that this is already handled upstream.


Integrated terminal not working

VSCode Version: v1.22.2
OS Version: Mac OS Sierra v10.12.6

Steps to Reproduce:

Open vscode and click View->"Integrated terminal",  it shows blank screen

I have cross checked the vscode settings and the bash terminal pointing to the right folder path
  // The path of the shell that the terminal uses on OS X.   "terminal.integrated.shell.osx": "/bin/bash",
On Developer tools I am getting the following console message while clicking terminal window
[Violation] Added non-passive event listener to a scroll-blocking 'wheel' event. Consider marking event handler as 'passive' to make the page more responsive. Terminal.ts:2212
[Violation] Added non-passive event listener to a scroll-blocking 'touchstart' event. Consider marking event handler as 'passive' to make the page more responsive. Terminal.ts:2212
[Violation] Added non-passive event listener to a scroll-blocking 'touchmove' event. Consider marking event handler as 'passive' to make the page more responsive.

Can you close all VS Code windows and then launch in a terminal with code --log trace. This will expose some terminal logs that you can get to from the command "Developer: Open Log File..." (F1 opened command palette). Can you get the logs when the issue happens and paste it in here?


undefined method `coverage'

/usr/local/bundle/gems/simplecov-json-0.2/lib/simplecov-json.rb:16:in `block in format': undefined method `coverage' for #<SimpleCov::SourceFile:0x000056089302af48> (NoMethodError)
Did you mean?  coverage_data
	from /usr/local/lib/ruby/2.6.0/forwardable.rb:230:in `each'
	from /usr/local/lib/ruby/2.6.0/forwardable.rb:230:in `each'
	from /usr/local/bundle/gems/simplecov-json-0.2/lib/simplecov-json.rb:11:in `format'
	from /usr/local/bundle/gems/simplecov-0.18.2/lib/simplecov/result.rb:49:in `format!'
	from /usr/local/bundle/gems/simplecov-0.18.2/lib/simplecov/configuration.rb:196:in `block in at_exit'
	from /usr/local/bundle/gems/simplecov-0.18.2/lib/simplecov.rb:201:in `run_exit_tasks!'
	from /usr/local/bundle/gems/simplecov-0.18.2/lib/simplecov/defaults.rb:31:in `block in <top (required)>'

Can you please fix it. I think it is related to a pull request that is already submitted. Can you please release the gem with the fix?
Sonarqube expects this output, it is not accepting the simplecov's default .resultset.json output.

Fixed after https://github.com/vicentllongo/simplecov-json/pull/12


Upgrade to 2.12.8

I have NB published semanticdb-scalac v4.1.0 for 2.12.8

Looks like Travis is unhappy. Other than that, lgtm.


Cross and Dot Product in GD4 Math Tutorial

Hi,
it seems that the last two scentences in the tutorial VECTORS: USING DOT AND CROSS PRODUCT are somewhat switched up.
The .gif in the tutorial shows us that the dot product can be used to identifiy if something ist left or right and cross product can be used to identify if sth. is in front or behind of something.
So:
Dot product: Using the result, we can tell if the object is in front of (> 0) or behind (< 0) us.
Cross product: Using the result, we can tell if the object is to the left (> 0) or right (< 0).

should then be:
Cross product: Using the result, we can tell if the object is in front of (> 0) or behind (< 0) us.
Dot product: Using the result, we can tell if the object is to the left (> 0) or right (< 0).

The text is correct. If you look at the animation:

The red arrow is our forward direction. The green arrow is the direction vector pointing to some other object.

When the green arrow is pointing to the right, the two arrows are more aligned, and the dot product is positive - the object is in front of us.

When the green arrow is pointing to the left, dot product is negative - the object is behind us.
And so on.


Submit VCell <IP_ADDRESS>

id: vcell
version: <IP_ADDRESS>
specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_VCell/fdc426f8c0252b211cf8237a2a4dc42c73722535/biosimulators.json
specificationsPatch:
version: <IP_ADDRESS>
image:
url: ghcr.io/biosimulators/biosimulators_vcell/vcell:<IP_ADDRESS>
validateImage: true
commitSimulator: true

Changelog

@gmarupilla @moraru I'm trying running the test suite as root to address the VCell/Docker permission issue
Debugging

Thank you @jonrkarr 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!

The validation/submission of your simulator failed.
- [Errno 2] No such file or directory: 'singularity': 'singularity'

The complete log of your validation/submission job, including further information about the failure, is available here.
If you chose to validate your Docker image, the results of the validation of your image will 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.
Once you have fixed the problem, edit the first block of this issue to re-initiate this validation.
The BioSimulators Team is happy to help. Questions and feedback can be directed to the BioSimulators Team by posting comments to this issues that reference the GitHub team @biosimulators/biosimulators (without the backticks).

Thank you @jonrkarr 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 60 test cases

Passed 18 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
published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations
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
sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
sedml.SimulatorSupportsAlgorithmParameters
sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
sedml.SimulatorSupportsMultipleReportsPerSedDocument

Failed 6 test cases:

combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories
combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories
published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous
results_report.SimulatorGeneratesReportsOfSimulationResults
sedml.SimulatorSupportsMultipleTasksPerSedDocument
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes

Skipped 36 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.SimulatorSupportsAddReplaceRemoveModelElementChanges
sedml.SimulatorSupportsComputeModelChanges
sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes
sedml.SimulatorSupportsDataSetsWithDifferentShapes
sedml.SimulatorSupportsModelAttributeChanges
sedml.SimulatorSupportsRepeatedTasksWithChanges
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables
sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges
sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges
sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges
sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks
sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges
sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks
sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes
sedml.SimulatorSupportsRepeatedTasksWithVectorRanges
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes

Warnings
cli.CliDescribesSupportedEnvironmentVariablesInline (4.3 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 (2.2 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 (1.6 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 (0.3 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 (0.2 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:

Failures
combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories (3.2 s)
Test that SED documents in nested directories can be executed
Exception:
[Errno 13] Permission denied: 'BIOMD0000000912_sim.sedml'

Log:
VCell CLI input archive /tmp/in/archive.omex

Apr 03, 2021 5:51:39 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_f8db9f12-86ec-4b7b-8e11-a10a4f3145f86195986517608018107

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 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

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

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:66)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:157)

	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 (2.9 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: 'BIOMD0000000912_sim.sedml'

Log:
VCell CLI input archive /tmp/in/archive.omex

Apr 03, 2021 5:51:42 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_b2d36ed7-f4dc-4b5e-83ab-9ade43de8a0f1745644132620645705

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 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

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

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:66)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:157)

	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/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous (26.3 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

Exception:
No reports were generated

Log:
VCell CLI input archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex

Apr 03, 2021 5:56:56 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_f6c3fab0-ec08-4c21-99fb-ac8c3a229bb1449033477108885083

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/temp2532013071451002429.xml

/tmp/out/simulation_1.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@fb0a08c

Finished: SOLVER_FINISHED:completed

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'

No PDF files found, skipping archiving `plots.zip` files

Archiving resultant CSV files to `reports.zip`.

results_report.SimulatorGeneratesReportsOfSimulationResults (10.8 s)
Test that when a COMBINE/OMEX archive defines a (single) master file, the simulator only executes this file.
Exception:
ufunc 'isnan' not supported for the input types, and the inputs could not be safely coerced to any supported types according to the casting rule ''safe''

Log:
VCell CLI input archive /tmp/in/archive.omex

Apr 03, 2021 5:55:44 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_48e8adfb-80d0-462a-9d78-1a2e83fadca24955410705856695243

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 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/temp7679168779559612745.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@49bf29c6

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive_BIOMD0000000912' Task 'Caravagna2010'.

-----------------------------------------------------------------------------------------------------

Generating report `BIOMD0000000912_sim`.

HDF conversion completed in '/tmp/out'

No PDF files found, skipping archiving `plots.zip` files

Archiving resultant CSV files to `reports.zip`.

sedml.SimulatorSupportsMultipleTasksPerSedDocument (4.6 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

Apr 03, 2021 5:54:44 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_8e227d94-9b0c-470d-8c37-4a76864f28a2490563489975195251

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 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/temp8072365346285694061.xml

Task (id='BIOMD0000000912_sim__test_suite_copy') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

java.beans.PropertyVetoException: Simulation with name Caravagna2010 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:66)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:157)

	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 Caravagna2010 already exists

Unable to initialize bioModel for the given selection

Simulation with name Caravagna2010 already exists

sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes (10.8 s)
Test that a simulator supports time courses with non-zero output start times
Exception:
ufunc 'isnan' not supported for the input types, and the inputs could not be safely coerced to any supported types according to the casting rule ''safe''

Log:
VCell CLI input archive /tmp/in/archive.omex

Apr 03, 2021 5:55:33 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_7f678a86-dd04-41a8-baeb-af7d5aa930cf717380718247242246

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 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/temp3836307610847820180.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@49bf29c6

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive_BIOMD0000000912' Task 'Caravagna2010'.

-----------------------------------------------------------------------------------------------------

Generating report `BIOMD0000000912_sim`.

HDF conversion completed in '/tmp/out'

No PDF files found, skipping archiving `plots.zip` files

Archiving resultant CSV files to `reports.zip`.

Skips
log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives (10.9 s)
Test that simulator logs the execution of COMBINE/OMEX archives
Reason for skip:
The simulator did not export information about the status of its execution. Simulators are encouraged to stream information about their execution status.

More information: https://biosimulators.org/conventions/status

Log:
VCell CLI input archive /tmp/in/archive.omex

Apr 03, 2021 5:55:55 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_37992503-39f2-4e81-9666-61685fa05cef6496187820443470416

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 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/temp1577715728485233850.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@49bf29c6

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive_BIOMD0000000912' Task 'Caravagna2010'.

-----------------------------------------------------------------------------------------------------

Generating report `BIOMD0000000912_sim`.

HDF conversion completed in '/tmp/out'

No PDF files found, skipping archiving `plots.zip` files

Archiving resultant CSV files to `reports.zip`.

log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments (11.8 s)
Test that simulator logs the execution of individual SED document in COMBINE/OMEX archives
Reason for skip:
The simulator did not export information about the status of its execution. Simulators are encouraged to stream information about their execution status.

More information: https://biosimulators.org/conventions/status

Log:
VCell CLI input archive /tmp/in/archive.omex

Apr 03, 2021 5:56:07 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_3739d2e4-68e0-4978-b22d-555e4270abea2158733974284178231

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 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/temp5291008536107995414.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@49bf29c6

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive_BIOMD0000000912' Task 'Caravagna2010'.

-----------------------------------------------------------------------------------------------------

Generating report `BIOMD0000000912_sim`.

HDF conversion completed in '/tmp/out'

No PDF files found, skipping archiving `plots.zip` files

Archiving resultant CSV files to `reports.zip`.

log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs (11.7 s)
Test that simulator logs the execution of individual SED outputs in COMBINE/OMEX archives
Reason for skip:
The simulator did not export information about the status of its execution. Simulators are encouraged to stream information about their execution status.

More information: https://biosimulators.org/conventions/status

Log:
VCell CLI input archive /tmp/in/archive.omex

Apr 03, 2021 5:56:19 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_a54bca1c-7a75-4f9c-8d09-241d0e1354b78520778961151656800

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 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/temp3216034860499515733.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@49bf29c6

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive_BIOMD0000000912' Task 'Caravagna2010'.

-----------------------------------------------------------------------------------------------------

Generating report `BIOMD0000000912_sim`.

HDF conversion completed in '/tmp/out'

No PDF files found, skipping archiving `plots.zip` files

Archiving resultant CSV files to `reports.zip`.

log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks (11.7 s)
Test that simulator logs the execution of individual SED tasks in COMBINE/OMEX archives
Reason for skip:
The simulator did not export information about the status of its execution. Simulators are encouraged to stream information about their execution status.

More information: https://biosimulators.org/conventions/status

Log:
VCell CLI input archive /tmp/in/archive.omex

Apr 03, 2021 5:56:30 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_327520cc-59c6-488b-bbe0-ed2addd793522554852378039952591

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 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/temp6072359153320325604.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@49bf29c6

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive_BIOMD0000000912' Task 'Caravagna2010'.

-----------------------------------------------------------------------------------------------------

Generating report `BIOMD0000000912_sim`.

HDF conversion completed in '/tmp/out'

No PDF files found, skipping archiving `plots.zip` files

Archiving resultant CSV files to `reports.zip`.

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 (4.1 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

Apr 03, 2021 5:52:16 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_259fe88f-0dfc-462b-b56a-f6af1c61fcab7605712680729717353

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 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

[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:66)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:157)

	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 (3.8 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

Apr 03, 2021 5:52:20 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_618f12fd-206e-4040-aae6-f0190afb0e523354468570370736365

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 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

[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:66)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:157)

	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 (7.5 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

Apr 03, 2021 5:52:24 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_a2ea7ca4-9ecf-414f-9c4f-2d9eef512cc91403279502810949385

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 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/temp3166207926062859321.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@49bf29c6

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive_BIOMD0000000912' Task 'Caravagna2010'.

-----------------------------------------------------------------------------------------------------

Ignoring unsupported output `plot_0` while CSV generation.

No PDF files found, skipping archiving `plots.zip` files

No CSV files found, skipping archiving `reports.zip` files

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 (7.4 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

Apr 03, 2021 5:52:31 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_eb271acb-bb6d-4a34-bbb5-7ce782ff21f57432845139002579218

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 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/temp628048141422143272.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@49bf29c6

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive_BIOMD0000000912' Task 'Caravagna2010'.

-----------------------------------------------------------------------------------------------------

Ignoring unsupported output `plot_0` while CSV generation.

No PDF files found, skipping archiving `plots.zip` files

No CSV files found, skipping archiving `reports.zip` files

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 (7.3 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

Apr 03, 2021 5:52:39 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_40ef6ad9-92a8-4f95-b552-2e6a337f05b61892006032238428754

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 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/temp5823713822672922321.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@49bf29c6

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive_BIOMD0000000912' Task 'Caravagna2010'.

-----------------------------------------------------------------------------------------------------

Ignoring unsupported output `plot_0` while CSV generation.

Ignoring unsupported output `plot_1` while CSV generation.

No PDF files found, skipping archiving `plots.zip` files

No CSV files found, skipping archiving `reports.zip` files

sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges (12.0 s)
Test that a simulator supports model changes that involve adding, replacing, and removing model elements.
Reason for skip:
The execution of the COMBINE/OMEX archive did not fail as expected

Log:
VCell CLI input archive /tmp/in/archive.omex

Apr 03, 2021 5:52:58 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_bc50e415-b9d3-47bb-89de-2a79381fcf085942986186003647497

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 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/temp3640361568144685037.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@6979efad

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive_BIOMD0000000912' Task 'Caravagna2010'.

-----------------------------------------------------------------------------------------------------

Generating report `BIOMD0000000912_sim`.

HDF conversion completed in '/tmp/out'

No PDF files found, skipping archiving `plots.zip` files

Archiving resultant CSV files to `reports.zip`.

sedml.SimulatorSupportsComputeModelChanges (13.2 s)
Test that a simulator supports compute model changes
Reason for skip:
The execution of the COMBINE/OMEX archive did not fail as expected

Log:
VCell CLI input archive /tmp/in/archive.omex

Apr 03, 2021 5:53:22 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_773fd1da-7f65-4999-b2a6-c300bcda397f7957241927726885987

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 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/temp547590331611676875.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@4303b7f0

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive_BIOMD0000000912' Task 'Caravagna2010'.

-----------------------------------------------------------------------------------------------------

Generating report `BIOMD0000000912_sim`.

HDF conversion completed in '/tmp/out'

No PDF files found, skipping archiving `plots.zip` files

Archiving resultant CSV files to `reports.zip`.

sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes (15.3 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/tmp8f2ra3nh/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

Apr 03, 2021 5:53:36 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_0d2de9c0-a197-45a9-98d4-2b64396355f87332933052173495507

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 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/temp1378017116311770009.xml

Task (id='BIOMD0000000912_sim__copy_2') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@2a415aa9

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive_BIOMD0000000912' Task 'Caravagna2010'.

-----------------------------------------------------------------------------------------------------

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@22fa55b2

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive_BIOMD0000000912' Task 'BIOMD0000000912_sim__copy_2'.

-----------------------------------------------------------------------------------------------------

Generating report `BIOMD0000000912_sim__copy_2`.

HDF conversion completed in '/tmp/out'

No PDF files found, skipping archiving `plots.zip` files

Archiving resultant CSV files to `reports.zip`.

sedml.SimulatorSupportsDataSetsWithDifferentShapes (15.3 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/tmp4_cwr724/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

Apr 03, 2021 5:53:51 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_93815f47-47f5-463b-8619-79904bd6d4fe5280193445392909966

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 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/temp1163643353944752735.xml

Task (id='BIOMD0000000912_sim__copy_2') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@5a6d5a8f

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive_BIOMD0000000912' Task 'Caravagna2010'.

-----------------------------------------------------------------------------------------------------

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@30457e14

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive_BIOMD0000000912' Task 'BIOMD0000000912_sim__copy_2'.

-----------------------------------------------------------------------------------------------------

Generating report `BIOMD0000000912_sim`.

HDF conversion completed in '/tmp/out'

No PDF files found, skipping archiving `plots.zip` files

Archiving resultant CSV files to `reports.zip`.

sedml.SimulatorSupportsModelAttributeChanges (13.0 s)
Test that a simulator supports changes to the attributes of model elements
Reason for skip:
The execution of the COMBINE/OMEX archive did not fail as expected

Log:
VCell CLI input archive /tmp/in/archive.omex

Apr 03, 2021 5:54:06 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_6c3646bd-cacf-476b-a1a3-40f3ea1b619f5736410502698775760

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 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/temp372413565741821570.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@6443b128

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive_BIOMD0000000912' Task 'Caravagna2010'.

-----------------------------------------------------------------------------------------------------

Generating report `BIOMD0000000912_sim`.

HDF conversion completed in '/tmp/out'

No PDF files found, skipping archiving `plots.zip` files

Archiving resultant CSV files to `reports.zip`.

sedml.SimulatorSupportsRepeatedTasksWithChanges (7.3 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/tmpjv2e5ecy/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

Apr 03, 2021 5:54:49 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_2a74dd3f-ed77-4680-959c-73c0060978a43062540567823263974

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:124)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)

SED-ML processing for /tmp/vcell_temp_2a74dd3f-ed77-4680-959c-73c0060978a43062540567823263974/BIOMD0000000912_sim.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:124)

	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

Apr 03, 2021 5:54:52 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_4e9c5e30-bc1c-4687-be5c-867103308cbf7812681818147359459

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:124)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)

SED-ML processing for /tmp/vcell_temp_4e9c5e30-bc1c-4687-be5c-867103308cbf7812681818147359459/BIOMD0000000912_sim.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:124)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)

One or more errors encountered while executing archive /tmp/in/archive.omex

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (7.2 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/tmp6rpsf39o/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

Apr 03, 2021 5:54:56 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_cf774f3f-61b2-45be-a0dc-a3c3b9d513c72726361663810562340

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:124)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)

SED-ML processing for /tmp/vcell_temp_cf774f3f-61b2-45be-a0dc-a3c3b9d513c72726361663810562340/BIOMD0000000912_sim.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:124)

	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

Apr 03, 2021 5:54:59 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_1a3696dc-2e36-4dbf-b93a-15895a8c061d2976619837159997010

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:124)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)

SED-ML processing for /tmp/vcell_temp_1a3696dc-2e36-4dbf-b93a-15895a8c061d2976619837159997010/BIOMD0000000912_sim.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:124)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)

One or more errors encountered while executing archive /tmp/in/archive.omex

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges (2.4 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/tmpb1mj0hrm/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

Apr 03, 2021 5:55:02 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_9d178b64-44e9-477c-9ba3-0cd5d7bb134c1594380649296166618

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:124)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)

SED-ML processing for /tmp/vcell_temp_9d178b64-44e9-477c-9ba3-0cd5d7bb134c1594380649296166618/BIOMD0000000912_sim.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:124)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)

One or more errors encountered while executing archive /tmp/in/archive.omex

sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges (2.6 s)
Test that a simulator supports repeated tasks over uniform ranges
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmp9gjfd9d5/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

Apr 03, 2021 5:55:04 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_c1fa02f1-0d94-4f52-978e-b6e018d2af5f4407148524636076574

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:124)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)

SED-ML processing for /tmp/vcell_temp_c1fa02f1-0d94-4f52-978e-b6e018d2af5f4407148524636076574/BIOMD0000000912_sim.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:124)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)

One or more errors encountered while executing archive /tmp/in/archive.omex

sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges (2.5 s)
Test that a simulator supports repeated tasks over uniform ranges
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmphocivu8g/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

Apr 03, 2021 5:55:07 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_2b192185-df7e-46ba-b621-a7344db84bd31389299508059978347

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:124)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)

SED-ML processing for /tmp/vcell_temp_2b192185-df7e-46ba-b621-a7344db84bd31389299508059978347/BIOMD0000000912_sim.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:124)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)

One or more errors encountered while executing archive /tmp/in/archive.omex

sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks (2.5 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/tmp10i2jcrs/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

Apr 03, 2021 5:55:10 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_5cb5721e-9cb0-4bee-8e17-79f63db8e4314565198881711347049

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:124)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)

SED-ML processing for /tmp/vcell_temp_5cb5721e-9cb0-4bee-8e17-79f63db8e4314565198881711347049/BIOMD0000000912_sim.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:124)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)

One or more errors encountered while executing archive /tmp/in/archive.omex

sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges (2.5 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/tmp2d2z__ew/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

Apr 03, 2021 5:55:12 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_619327b9-41f6-4deb-b411-3978fc9a76e8488438657200552533

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:124)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)

SED-ML processing for /tmp/vcell_temp_619327b9-41f6-4deb-b411-3978fc9a76e8488438657200552533/BIOMD0000000912_sim.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:124)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)

One or more errors encountered while executing archive /tmp/in/archive.omex

sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks (2.5 s)
Test that a simulator supports nested repeated tasks
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmp4q4d3_8d/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

Apr 03, 2021 5:55:15 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_fff1aa07-a040-46f8-856c-b491d4b292731214929334044572273

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:124)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)

SED-ML processing for /tmp/vcell_temp_fff1aa07-a040-46f8-856c-b491d4b292731214929334044572273/BIOMD0000000912_sim.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:124)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)

One or more errors encountered while executing archive /tmp/in/archive.omex

sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes (2.6 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/tmpc9x7_p5r/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

Apr 03, 2021 5:55:17 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_15f8aea3-649c-48f7-9e9f-61bc8f6d44d66313966444453196264

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:124)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)

SED-ML processing for /tmp/vcell_temp_15f8aea3-649c-48f7-9e9f-61bc8f6d44d66313966444453196264/BIOMD0000000912_sim.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:124)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)

One or more errors encountered while executing archive /tmp/in/archive.omex

sedml.SimulatorSupportsRepeatedTasksWithVectorRanges (2.5 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/tmpzxttv8zd/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

Apr 03, 2021 5:55:20 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_e383d353-9f2e-448b-95b6-93752fb94df87380717883710979101

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:124)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)

SED-ML processing for /tmp/vcell_temp_e383d353-9f2e-448b-95b6-93752fb94df87380717883710979101/BIOMD0000000912_sim.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:124)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:63)

One or more errors encountered while executing archive /tmp/in/archive.omex

sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes (10.9 s)
Test that a simulator supports multiple time courses with non-zero initial times
Reason for skip:
ufunc 'isnan' not supported for the input types, and the inputs could not be safely coerced to any supported types according to the casting rule ''safe''

Log:
VCell CLI input archive /tmp/in/archive.omex

Apr 03, 2021 5:55:22 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

-----------------------------------------------------------------------------------------------------

TempPath Created: /tmp/vcell_temp_9d10209f-2afc-4b04-9903-1d258d5afc229107144342334168148

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 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 ...

- 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/714824057). 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/714824057).


Update scoverage contrib module and fixed/reworked test setup

We still face an issue with un-closed files in scoverage. Probably this: https://github.com/scoverage/scalac-scoverage-plugin/issues/371


Feature/sliding window api for spillway

This feature PR introduce a simple sliding window calculation to the Spillway API:tryUpdateAndVerifyLimit
Here, we calculate sliding window count just as described here: https://blog.cloudflare.com/counting-things-a-lot-of-different-things/

@dlafreniere  @lbourdages @MiloszKul @dreisch-coveo

I'll follow up what louis said I see what looks like breaking changes there not sure we can go ahead and do that but I don't have the full picture of how this works.

is anyone planning to take ownership of this? if not i would close it

is anyone planning to take ownership of this? if not i would close it

Not in the near future. I would have closed it but I don't have the rights to do so 😅