[docs] Inconsistent documentation about importing "styled"

Related page
https://v5.mui.com/material-ui/migration/v5-style-changes/#styled
Kind of issue
Unclear explanations
Issue description
Currently we are still using mui5 and planning to do migration to mui6. What I personally noticed that there is been inconsistency in the documentation about using styled in the documentation for migration from 4 to 5th version.
https://v5.mui.com/material-ui/migration/v5-style-changes/#styled
import { styled } from '@mui/styles';
here is suggested that styled should be imported from mui/styles
https://v5.mui.com/system/styles/basics/
here is clearly written that mui/styles are deprecated and it must be use mui/system instead
https://v5.mui.com/system/styled/
import { styled } from '@mui/system';
here is suggested that styled should be imported from mui/system
https://v5.mui.com/material-ui/migration/troubleshooting/#typeerror-cannot-read-properties-of-undefined-reading-pxtorem
https://v5.mui.com/material-ui/migration/migrating-from-jss/#1-use-styled-or-sx-api
import { styled } from '@mui/material/styles';
here are examples where is suggested that styled should be imported from mui/material/styles
In our solution: styled, theme, useTheme, SxProps are imported from mui/material/styles (if you think one of these should not be part of mui/material/styles, let me know) . Here are examples how it is used:
const AccordionSummary = styled((props: AccordionSummaryProps) => (
    <MuiAccordionSummary
        expandIcon={props.expandIcon}
        {...props}
    />
))(({ theme }) => ({
    backgroundColor: theme.palette.background.paper,
    minHeight: "32px",
    flexDirection: 'row-reverse',
    '& .MuiAccordionSummary-expandIconWrapper.Mui-expanded': {
        transform: 'rotate(90deg)',
    },
    '& .MuiAccordionSummary-content': {
        //margin: theme.spacing(1),
        margin: "0px 0px 0px 6px",
    }
}));

const Accordion = styled((props: AccordionProps) => (
    <MuiAccordion disableGutters elevation={0} square {...props} />
))(() => ({
    '&:not(:last-child)': {
        borderBottom: 0,
    },
    '&:before': {
        display: 'none',
    },
}));

We do not use any import from mui/system and default styling engine Emotion is not in use even it has dependencies and required to be installed.
Context
There are certain things to declare before we migrate to mui6:

What is correct import styled - from mui/material/styles or from mui/system?
Can we continue using styled in mui6 or is it mandatory to change into something different?
If styled is outdated/deprecated in future then we need to suggestion what is best and easiest transition from examples provided in "Issue description". The default styling engine of Material UI v6 is still Emotion but from given documentation for migration to mui6 there is claim that it is recommended that it needs to fully migrate to Pigment CSS

It can work alongside Emotion to ease the migration process, but it is recommended to fully migrate to Pigment CSS in the end.

Does it mean that we should go directly to Pigment CSS? What would be the best tool to have migration from styled to Pigment CSS? Appreciate for any help
Search keywords: styled, mui5, mui6, import styled

Hi, this migration guide is intended to be done step by step. The step: https://v5.mui.com/material-ui/migration/migrating-from-jss/ will finally guide you to using styled from '@mui/material/styles' as this is the Emotion implementation. To specifically answer your questions:

What is correct import styled - from @mui/material/styles or from @mui/system?
For using Emotion, you should use @mui/material/styles

Can we continue using styled in mui6 or is it mandatory to change into something different?
You can still use styled in v6, you can even still use Emotion (this is the production ready implementation

If styled is outdated/deprecated in future then we need to suggestion what is best and easiest transition from examples provided in "Issue description". The default styling engine of Material UI v6 is still Emotion but from given documentation for migration to mui6 there is claim that it is recommended that it needs to fully migrate to Pigment CSS
Piigment CSS is still not stable, it is intended for people who want to give it an early try and provide feedback, it is not production ready. This is why Emotion is still the default and recommended styling engine. We are not going to be moving away from the styled() API for now, my only recommendation would be to use the variants API instead of dynamic styles, check https://stackblitz.com/edit/react-vyn3bq?file=Demo.tsx for more details.

I hope this explanation helped, let me know if you have more questions.

thank you for providing the information. Since styled from mui/material/styled will be not deprecated in the future then this conversation can be closed. Anyhow I understand migration guide is done step by step and documentation was gradually updated i still think that suggestion about importing styled imported from mui/styles (https://v5.mui.com/material-ui/migration/v5-style-changes/#styled ) should be corrected. If I remember, from begging of mui5 mui/styles was marked as deprecated so there is no need to be part of documentation.

I will let @samuelsycamore to decide on the best course of action, I am fine with leaving it as is.


PeerDependency Complaining on @angular/core, @angular/common and @angular/router

Would there be an update to support the Angular 4 related libs? Or is this lib being deprecated?

Please correct me if I am wrong but it seems this library will be deprecated in favor of this one.

There is a new version coming with support for the latest Angular

Any chance you can update your package.json to support angular 4. We're unable to use shrinkwrap because of the dependency errors. Thanks!
    "@angular/common": "^2.0.0  || ^4.0.0",
    "@angular/core": "^2.0.0 || ^4.0.0",
    "@angular/router": "^3.0.0  || ^4.0.0"


Hash operation consistency

There are currently some inconsistencies in how we've implemented hashing operations. Specifically:

In the VM, RPPERM to compute permute(A, B, C), expects the stack to be arranged as [A, B, C, ...] where A is at the top of the stack.
In the assembly, rpperm and rphash operations assume that the stack is arranged as [C, B, A, ...] where C is the capacity portion of the sponge and is located at the top of the stack. In case of rphash we assume that once RPPERM is executed, the word A will contain the result of the hash.

One option to address this is to simply fix the implementation of RPPERM in the VM. However, it might be a good idea to have the capacity portion of the sponge deep in the stack (the way it is currently arranged for RPPERM). This way, when we compute a linear hash of many elements, we don't need to touch capacity elements (word C) as we update the outer portion of the sponge (words A and B).
At the same time, the arrangement [A, B, C, ...] is contrary to how we arrange stack for most other operations and might be confusing. For example, as we compute linear hash of many elements, we'd first need to populate the word A and only then the word B with new data - which will be awkward to do since A is at the top of the stack.
The other option is to modify how the Rp64_256 hash function actually works. Specifically, we can change it so that if the state is [A, B, C], it is expected that A is the capacity portion, and B is expected to contain the result of the hash after the permutation.
So, to summarize the options:

Fix RPPERM operation in the VM. This is the simplest option but would make linear hashes of many elements slightly less efficient.
Update assembly instruction rphash to work with the current implementation of RPPERM. This accepts the awkwardness of the current stack arrangement of RPPERM and also would make computing linear hashes of many elements less efficient.
Update Rp64_256 hash function to work as described above, and update RPPERM and related assembly instructions accordingly. The stack would be arranged as: [C, B, A, ...]. This is a more involved option, but perhaps the cleanest and most efficient.

I guess it depends on how involved the Rp64_256 update would be, but I would lean towards preserving efficiency at this stage. It will certainly be easier to adjust now than later

@grjte Rp64_256 has been updated as a part of this PR: https://github.com/novifinancial/winterfell/pull/72
So, now we can update winter-crypto dependency to v0.3.2 and make the implementation of hashing consistent across various crates (basically, option 3 from above).

Great! Do you want me to take this on?

Yes! That would be great! I'll assign this issue to you.

Closed by #88


PLFM-3495

This was CR'ed in a PR against relase-99.:https://github.com/Sage-Bionetworks/Synapse-Repository-Services/pull/2013
This PR just merges the changes back into develop.


Keithley 2750 Instrument

Added the beginning of the new instrument: Keithley 2750 Instrument

I've noticed that there are some failed tests/checks with this pull request, but after taking a look at the error messages, it's still unclear to me whether these issues are coming from bugs in the pull request itself. For example, some of the errors involve import errors of VXI11Adapter and HP34410A, which my code doesn't seem to touch at all. Could someone point out to me why these errors are occurring, or anything I can fix from my end, so we can make progress on this PR?

Please merge the latest master branch into yours to fix the Travis CI build failure.

Okay, addressed the comments, and also merged with the latest master. Could you take a look?

@dennisfeng2, sorry for the slow response. This looks good. Will merge after running through the CI tests.

Thanks @dennisfeng2!


BUG: Navigation buttons render as emojis on iPhone

Bug Report
Current Behavior
Default navigation buttons labels render as emojis on iPhone. Tested on iPhone 11 (Safari) and in online emulators. Similar issue as here
Input Code and steps to reproduce

Keep default navigation button labels
They show as emojis, not unicode characters

Expected behavior/code
Simple unicode characters (triangles) should appear just as anywhere else.
Environment

OS: iPhone 11, iOS 13.3 (but probably happens in other versions as well)
Browser: Safari

Possible Solution
Disabling emojis can be achieved by appending "variation selectors"  to labels:
<carousel
    navigationPrevLabel="◀"
    navigationNextLabel="▶">

So I think these should be appended to default values as well.

Any update on this? im having same issue but the arrows shows incomplete.


Can we have a way to remove all suggestions in the code for both the editor and the iPython interactive windows?  I waste more time navigating around this that I do coding.

Describe the feature you are requesting
[A clear and concise description of the feature you are requesting]
Reasons for requesting this feature
[Why do you want this feature? How is it beneficial to you and others?]
Describe alternatives you've considered
[A clear and concise description of any alternative solutions or features you've considered]
Additional context
[Add any other context or screenshots about the feature request here]

Duplicate of https://github.com/microsoft/PTVS/discussions/7334


style(utils): improve implementation of applyOptionsChain

PR Details

Description

Remove useless function signature of applyOptionsChain.
Types of changes

[x] Docs change / refactoring / dependency upgrade
[ ] Bug fix (non-breaking change which fixes an issue)
[ ] New feature (non-breaking change which adds functionality)
[ ] Breaking change (fix or feature that would cause existing functionality to change)

Checklist

[ ] My code follows the code style of this project.
[ ] I have updated changeset
[ ] My change requires a change to the documentation.
[ ] I have updated the documentation accordingly.
[ ] I have read the CONTRIBUTING document.
[ ] I have added tests to cover my changes.
[ ] All new and existing tests passed.

 Thank you for your submission! We really appreciate it. Like many open source projects, we ask that you sign our Contributor License Agreement before we can accept your contribution.You have signed the CLA already but the status is still pending? Let us recheck it.


Question about slice_pose !!

Hey guys,
I am trying to build the cartographer submaps with unity3D. But I am a little bit confused about the slice_pose and its frame. I am not sure that the pose is expressed in the map frame.
So could you please give me some help on that and tell me which frame (position and orientation) are you using to express the slice_pose ?
Cheers

slice_pose is the pose of the textured rectangle which is used for visualizing a submap in the submap frame. To get the pose of the textured rectangle in the map frame, the submap pose must be multiplied by it.

Thank you @wohe for your answer. I got this by adding some rviz axis to the ogre node.
Cheers


Submit VCell <IP_ADDRESS>

id: vcell
version: <IP_ADDRESS>
specificationsUrl: https://raw.githubusercontent.com/biosimulators/Biosimulators_VCell/f83976f5c767369f31a7fa1b2e7f5dc52fa2a628/biosimulators.json
specificationsPatch:
version: <IP_ADDRESS>
image:
url: ghcr.io/biosimulators/biosimulators_vcell/vcell:<IP_ADDRESS>
validateImage: true
commitSimulator: true

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

The specifications of your simulator is valid!

Warnings
cli.CliDescribesSupportedEnvironmentVariablesInline (4.9 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 (2.8 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`:

  Invalid arguments: [-h, , , , , ]

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

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

  Invalid arguments: [--help, , , , , ]

Log:

cli.CliDisplaysVersionInformationInline (2.4 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`:

  Invalid arguments: [-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`:

  Invalid arguments: [--version, , , , , ]

Log:

docker_image.HasBioContainersLabels (0.8 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 (0.8 s)
Test that a Docker image has Open Container Initiative (OCI) labels with metadata about the image
Warnings:
The Docker image should have the following Open Container Initiative (OCI) labels:
  org.opencontainers.image.created
  org.opencontainers.image.revision

Log:

published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (17.4 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

Warnings:
Unexpected reports were produced:
  BIOMD0000000912_sim.sedml/Figure_1

Plots were not produced:
  BIOMD0000000912_sim.sedml/plot_1

Extra plots were produced:
  BIOMD0000000912_sim.sedml/Figure_1

Log:
VCell CLI input archive /tmp/in/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex

Jun 03, 2021 3:02:17 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_a2b21d78-5151-44c8-91cf-a0a7e14f28751514997849180412665

Python 3.6.9

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),  1 plot2D(s), and 0 plot3D(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_task') 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/temp3267105013983615852.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@b09fac1

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations__BIOMD0000000912' Task 'Caravagna2010'.

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

Ignoring unsupported output `Figure_1` while CSV generation.

Generating report `report`.

Python 3.6.9

HDF conversion successful

Archiving resultant PDF files to `plots.zip`.

Archiving resultant CSV files to `reports.zip`.

published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous (30.3 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

Warnings:
Unexpected reports were produced:
  simulation_1.sedml/Figure_3a
  simulation_1.sedml/Figure_3b
  simulation_1.sedml/Figure_3c
  simulation_1.sedml/Figure_3d

Plots were not produced:
  simulation.sedml/Figure_3a
  simulation.sedml/Figure_3b
  simulation.sedml/Figure_3c
  simulation.sedml/Figure_3d

Extra plots were produced:
  simulation_1.sedml/Figure_3a
  simulation_1.sedml/Figure_3b
  simulation_1.sedml/Figure_3c
  simulation_1.sedml/Figure_3d

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

Jun 03, 2021 3:02:34 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_63ee66a2-9a05-482a-9e9a-e6ca7a0db5d29100852918851960687

Python 3.6.9

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),  4 plot2D(s), and 0 plot3D(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='task_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

Succesful model import: SBML file /tmp/temp3622613446624970326.xml

/tmp/out/simulation_1.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@759de304

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous__Ciliberto2003_Morphogenesis' Task 'simulation 1'.

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

Ignoring unsupported output `Figure_3a` while CSV generation.

Ignoring unsupported output `Figure_3b` while CSV generation.

Ignoring unsupported output `Figure_3c` while CSV generation.

Ignoring unsupported output `Figure_3d` while CSV generation.

Generating report `report`.

Python 3.6.9

HDF conversion successful

Archiving resultant PDF files to `plots.zip`.

Archiving resultant CSV files to `reports.zip`.

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock (71.5 s)
Required model formats and simulation algorithms for SED tasks:

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

Warnings:
Unexpected reports were produced:
  simulation.sedml/plot2d_Euler_default
  simulation.sedml/plot2d_Euler_small_step_size
  simulation.sedml/plot2d_Fig_1_c
  simulation.sedml/plot2d_Fig_1a
  simulation.sedml/plot2d_low_delta_R_det
  simulation.sedml/plot2d_low_delta_R_stoch

Log:
VCell CLI input archive /tmp/in/Vilar-PNAS-2002-minimal-circardian-clock.omex

Jun 03, 2021 3:04:25 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_45c5ed7a-1c52-46ac-a585-360bfded7c4c4942041319717329495

Python 3.6.9

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 4 model(s), 6 simulation(s), 6 task(s), 6  report(s),  6 plot2D(s), and 0 plot3D(s)

Successful translation: SED-ML file simulation.sedml

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Task (id='tsk_0_0') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

Succesful model import: SBML file /tmp/temp8221945342343788938.xml

Task (id='tsk_0_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

Succesful model import: SBML file /tmp/temp6585530979215563289.xml

Task (id='tsk_0_2') is compatible, solver match found in ontology: 'KISAO:0000030' matched to ForwardEuler

Task (id='tsk_0_3') is compatible, solver match found in ontology: 'KISAO:0000030' matched to ForwardEuler

Task (id='tsk_1_0') is compatible, solver match found in ontology: 'KISAO:0000027' matched to StochGibson

Succesful model import: SBML file /tmp/temp8489257197551134340.xml

Task (id='tsk_1_1') is compatible, solver match found in ontology: 'KISAO:0000027' matched to StochGibson

Succesful model import: SBML file /tmp/temp4803599954544509539.xml

/tmp/out/simulation.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@67f63d26

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock__ODE_deterministic' Task 'tsk_0_0'.

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

Solver status: 3

Solver message: simulation failed at time=1.3: consider using smaller default or max time step.

values are:

A = NaN

C = Infinity

PrmA = Infinity

PrmA_bound = -Infinity

PrmR = Infinity

PrmR_bound = -Infinity

R = -Infinity

Failed execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock__ODE_deterministic' Task 'tsk_0_2'.

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

final tolerance=0.1 final threshold=0.09, 885 remaining (keepAtMost=1000)

Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock__ODE_deterministic' Task 'tsk_0_3'.

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

/tmp/out/simulation.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@7c40ffef

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock__ODE_deterministic_0' Task 'tsk_0_1'.

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

cbit.vcell.solver.stoch.GibsonSolver@433d9680

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock__ODE_stochastic' Task 'tsk_1_0'.

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

cbit.vcell.solver.stoch.GibsonSolver@1f992a3a

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock__ODE_stochastic_0' Task 'tsk_1_1'.

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

Ignoring unsupported output `plot2d_Fig_1a` while CSV generation.

Ignoring unsupported output `plot2d_low_delta_R_det` while CSV generation.

Ignoring unsupported output `plot2d_Euler_default` while CSV generation.

Ignoring unsupported output `plot2d_Euler_small_step_size` while CSV generation.

Ignoring unsupported output `plot2d_Fig_1_c` while CSV generation.

Ignoring unsupported output `plot2d_low_delta_R_stoch` while CSV generation.

Generating report `report_Fig_1a`.

Generating report `report_low_delta_R_det`.

Generating report `report_Euler_default`.

Generating report `report_Euler_small_step_size`.

Generating report `report_Fig_1_c`.

Generating report `report_low_delta_R_stoch`.

Python 3.6.9

HDF conversion successful

Archiving resultant PDF files to `plots.zip`.

Archiving resultant CSV files to `reports.zip`.

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous (50.4 s)
Required model formats and simulation algorithms for SED tasks:

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

Warnings:
Unexpected reports were produced:
  simulation.sedml/Figure_2ab
  simulation.sedml/plot2d_Euler_default
  simulation.sedml/plot2d_Euler_small_step_size
  simulation.sedml/plot2d_Fig_1a
  simulation.sedml/plot2d_low_delta_R_det

Log:
VCell CLI input archive /tmp/in/Vilar-PNAS-2002-minimal-circardian-clock-continuous.omex

Jun 03, 2021 3:03:05 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_bb3e0bcc-654c-4d75-8d29-4175ca6ee1926248975108313667153

Python 3.6.9

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 2 model(s), 4 simulation(s), 4 task(s), 4  report(s),  5 plot2D(s), and 0 plot3D(s)

Successful translation: SED-ML file simulation.sedml

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Task (id='tsk_0_0') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

Succesful model import: SBML file /tmp/temp2663252565428851586.xml

Task (id='tsk_0_1') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

Succesful model import: SBML file /tmp/temp6241559689758881316.xml

Task (id='tsk_0_2') is compatible, solver match found in ontology: 'KISAO:0000030' matched to ForwardEuler

Task (id='tsk_0_3') is compatible, solver match found in ontology: 'KISAO:0000030' matched to ForwardEuler

/tmp/out/simulation.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@60a7e509

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock-continuous__ODE_deterministic' Task 'tsk_0_0'.

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

Solver status: 3

Solver message: simulation failed at time=1.3: consider using smaller default or max time step.

values are:

A = NaN

C = Infinity

PrmA = Infinity

PrmA_bound = -Infinity

PrmR = Infinity

PrmR_bound = -Infinity

R = -Infinity

Failed execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock-continuous__ODE_deterministic' Task 'tsk_0_2'.

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

final tolerance=0.1 final threshold=0.09, 885 remaining (keepAtMost=1000)

Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock-continuous__ODE_deterministic' Task 'tsk_0_3'.

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

/tmp/out/simulation.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@53c99b09

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock-continuous__ODE_deterministic_0' Task 'tsk_0_1'.

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

Ignoring unsupported output `Figure_2ab` while CSV generation.

Ignoring unsupported output `plot2d_Fig_1a` while CSV generation.

Ignoring unsupported output `plot2d_low_delta_R_det` while CSV generation.

Ignoring unsupported output `plot2d_Euler_default` while CSV generation.

Ignoring unsupported output `plot2d_Euler_small_step_size` while CSV generation.

Generating report `report_Fig_1a`.

Generating report `report_low_delta_R_det`.

Generating report `report_Euler_default`.

Generating report `report_Euler_small_step_size`.

Python 3.6.9

HDF conversion successful

Archiving resultant PDF files to `plots.zip`.

Archiving resultant CSV files to `reports.zip`.

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM (29.6 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000027

Warnings:
Unexpected reports were produced:
  simulation.sedml/plot2d_Fig_1_c
  simulation.sedml/plot2d_low_delta_R_stoch

Log:
VCell CLI input archive /tmp/in/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM.omex

Jun 03, 2021 3:03:55 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_297e9d7f-6d74-474a-9321-b20eb96fd6525482799180212616433

Python 3.6.9

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Found 1 SED-ML document(s) with 2 model(s), 2 simulation(s), 2 task(s), 2  report(s),  2 plot2D(s), and 0 plot3D(s)

Successful translation: SED-ML file simulation.sedml

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

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

Task (id='tsk_1_0') is compatible, solver match found in ontology: 'KISAO:0000027' matched to StochGibson

Succesful model import: SBML file /tmp/temp6447980767447717926.xml

Task (id='tsk_1_1') is compatible, solver match found in ontology: 'KISAO:0000027' matched to StochGibson

Succesful model import: SBML file /tmp/temp965379960086287054.xml

cbit.vcell.solver.stoch.GibsonSolver@42435b98

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM__ODE_stochastic' Task 'tsk_1_0'.

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

cbit.vcell.solver.stoch.GibsonSolver@cb0f763

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM__ODE_stochastic_0' Task 'tsk_1_1'.

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

Ignoring unsupported output `plot2d_Fig_1_c` while CSV generation.

Ignoring unsupported output `plot2d_low_delta_R_stoch` while CSV generation.

Generating report `report_Fig_1_c`.

Generating report `report_low_delta_R_stoch`.

Python 3.6.9

HDF conversion successful

Archiving resultant PDF files to `plots.zip`.

Archiving resultant CSV files to `reports.zip`.

Summary of tests

Executed 63 test cases

Passed 26 test cases:

cli.CliDescribesSupportedEnvironmentVariablesInline
cli.CliDisplaysHelpInline
cli.CliDisplaysVersionInformationInline
combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories
combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories
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/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous
published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM
results_report.SimulatorGeneratesReportsOfSimulationResults
sedml.SimulatorProducesLinear2DPlots
sedml.SimulatorProducesLogarithmic2DPlots
sedml.SimulatorProducesMultiplePlots
sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
sedml.SimulatorSupportsAlgorithmParameters
sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
sedml.SimulatorSupportsMultipleReportsPerSedDocument
sedml.SimulatorSupportsMultipleTasksPerSedDocument
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes

Failed 0 test cases

Skipped 37 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:cellml/Lorenz-system
published_project.SimulatorCanExecutePublishedProject:sbml-core/Edelstein-Biol-Cybern-1996-Nicotinic-excitation
published_project.SimulatorCanExecutePublishedProject:sbml-core/Parmar-BMC-Syst-Biol-2017-iron-distribution
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
published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments
sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
sedml.SimulatorProducesLinear3DPlots
sedml.SimulatorProducesLogarithmic3DPlots
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.SimulatorSupportsSubstitutingAlgorithms
sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes

Skips
log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives (12.9 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

Jun 03, 2021 3:01:25 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_1d05abc1-5ad7-48e8-845d-a275f0de23e12460255175602288818

Python 3.6.9

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),  0 plot2D(s), and 0 plot3D(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_task') 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/temp3656025301138217000.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@273c947f

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.

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

Generating report `report`.

Python 3.6.9

HDF conversion successful

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

Archiving resultant CSV files to `reports.zip`.

log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments (13.0 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

Jun 03, 2021 3:01:37 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_398aedaf-922c-4b24-881d-c85c03cb5a6b1424363097032498521

Python 3.6.9

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),  0 plot2D(s), and 0 plot3D(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_task') 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/temp4615875546501577937.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@273c947f

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.

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

Generating report `report`.

Python 3.6.9

HDF conversion successful

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

Archiving resultant CSV files to `reports.zip`.

log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs (12.9 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

Jun 03, 2021 3:01:51 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_ab256294-0131-4c2b-a0f6-43859eee91be7413604024632584888

Python 3.6.9

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),  0 plot2D(s), and 0 plot3D(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_task') 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/temp1569131467873588086.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@273c947f

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.

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

Generating report `report`.

Python 3.6.9

HDF conversion successful

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

Archiving resultant CSV files to `reports.zip`.

log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks (13.0 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

Jun 03, 2021 3:02:04 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_06c1ab66-51a6-4800-a75b-86e744f7f5d5416933645255689275

Python 3.6.9

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),  0 plot2D(s), and 0 plot3D(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_task') 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/temp7324750608683820298.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@273c947f

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.

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

Generating report `report`.

Python 3.6.9

HDF conversion successful

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:cellml/Lorenz-system (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_3240
Algorithm: KISAO_0000019

Reason for skip:
Case requires model formats format_3240 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/Parmar-BMC-Syst-Biol-2017-iron-distribution (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_000019

Reason for skip:
Case requires model formats format_2585 and simulation algorithms KISAO_000019

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:

published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra (0.0 s)
Required model formats and simulation algorithms for SED tasks:

Format: format_9001
Algorithm: KISAO_0000057

Reason for skip:
Case requires model formats format_9001 and simulation algorithms KISAO_0000057

Log:

sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments (3.7 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

Jun 03, 2021 2:56:33 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_6a5fb408-7585-4f15-a676-946bcbbbd0e4156659653519746940

Python 3.6.9

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),  0 plot2D(s), and 0 plot3D(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_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

[Fatal Error] :1:1: Content is not allowed in prolog.

[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:448)

	at cbit.vcell.xml.XmlHelper.sedmlToBioModel(XmlHelper.java:685)

	at org.vcell.cli.SolverHandler.simulateAllTasks(SolverHandler.java:66)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:188)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

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 (3.7 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

Jun 03, 2021 2:56:36 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_6793efa3-7118-4b63-8615-5c86ebf873382886803786902678581

Python 3.6.9

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),  0 plot2D(s), and 0 plot3D(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_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE

[Fatal Error] :1:1: Content is not allowed in prolog.

[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:448)

	at cbit.vcell.xml.XmlHelper.sedmlToBioModel(XmlHelper.java:685)

	at org.vcell.cli.SolverHandler.simulateAllTasks(SolverHandler.java:66)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:188)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

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.SimulatorProducesLinear3DPlots (0.3 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.SimulatorProducesLogarithmic3DPlots (0.3 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.SimulatorSupportsAddReplaceRemoveModelElementChanges (13.1 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

Jun 03, 2021 2:57:42 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_6a127018-1f01-4823-a551-1085e35671dc833957126588421961

Python 3.6.9

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),  0 plot2D(s), and 0 plot3D(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_task') 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/temp7737356279155811068.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@b09fac1

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.

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

Generating report `report`.

Python 3.6.9

HDF conversion successful

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

Archiving resultant CSV files to `reports.zip`.

sedml.SimulatorSupportsComputeModelChanges (14.2 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

Jun 03, 2021 2:58:08 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_47e35af0-ee21-482a-afe0-8e2bc5b37f263753850772382366764

Python 3.6.9

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),  0 plot2D(s), and 0 plot3D(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_task') 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/temp1479630363435892724.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@3b0ca5e1

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.

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

Generating report `report`.

Python 3.6.9

HDF conversion successful

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

Archiving resultant CSV files to `reports.zip`.

sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes (16.4 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/tmpwqmt__o2/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

Jun 03, 2021 2:58:22 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_b92f3a93-65b6-45ad-be79-59d2db9d94393838741914330311443

Python 3.6.9

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),  0 plot2D(s), and 0 plot3D(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_task') 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/temp8608665594270171265.xml

Task (id='BIOMD0000000912_task__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@2c0f7678

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.

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

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@5f574cc2

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'BIOMD0000000912_task__copy_2'.

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

Generating report `report__copy_2`.

Python 3.6.9

Traceback (most recent call last):

  File "/usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py", line 355, in <module>

    'genPlotPdfs': gen_plot_pdfs,

  File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 141, in Fire

    component_trace = _Fire(component, args, parsed_flag_args, context, name)

  File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 471, in _Fire

    target=component.__name__)

  File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace

    component = fn(*varargs, **kwargs)

  File "/usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py", line 165, in exec_sed_doc

    data_set_results[data_set.id] = data_set_df.loc[data_set.label, :].to_numpy(dtype ='float64')

  File "/usr/local/lib/python3.6/dist-packages/pandas/core/base.py", line 846, in to_numpy

    result = np.asarray(self._values, dtype=dtype)

  File "/usr/local/lib/python3.6/dist-packages/numpy/core/_asarray.py", line 83, in asarray

    return array(a, dtype, copy=False, order=order)

ValueError: could not convert string to float: 'NaN.9'

HDF conversion failed

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

Archiving resultant CSV files to `reports.zip`.

sedml.SimulatorSupportsDataSetsWithDifferentShapes (16.5 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/tmpclimc69a/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

Jun 03, 2021 2:58:38 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_7ad56793-a243-47ed-adb8-6dc29840baa46769243163835779159

Python 3.6.9

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),  0 plot2D(s), and 0 plot3D(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_task') 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/temp6801442261111420624.xml

Task (id='BIOMD0000000912_task__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@62df0ff3

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.

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

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@6134ac4a

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'BIOMD0000000912_task__copy_2'.

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

Generating report `report`.

Traceback (most recent call last):

  File "/usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py", line 355, in <module>

    'genPlotPdfs': gen_plot_pdfs,

  File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 141, in Fire

    component_trace = _Fire(component, args, parsed_flag_args, context, name)

  File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 471, in _Fire

    target=component.__name__)

  File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace

    component = fn(*varargs, **kwargs)

  File "/usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py", line 305, in gen_plot_pdfs

    report_frames = get_report_dataframes(all_report_dataref, result_out_dir)

  File "/usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py", line 281, in get_report_dataframes

    report_frames[report] = pd.read_csv(os.path.join(result_out_dir, report + ".csv")).T.reset_index()

  File "/usr/local/lib/python3.6/dist-packages/pandas/io/parsers.py", line 688, in read_csv

    return _read(filepath_or_buffer, kwds)

  File "/usr/local/lib/python3.6/dist-packages/pandas/io/parsers.py", line 460, in _read

    data = parser.read(nrows)

  File "/usr/local/lib/python3.6/dist-packages/pandas/io/parsers.py", line 1198, in read

    ret = self._engine.read(nrows)

  File "/usr/local/lib/python3.6/dist-packages/pandas/io/parsers.py", line 2157, in read

    data = self._reader.read(nrows)

  File "pandas/_libs/parsers.pyx", line 847, in pandas._libs.parsers.TextReader.read

  File "pandas/_libs/parsers.pyx", line 862, in pandas._libs.parsers.TextReader._read_low_memory

  File "pandas/_libs/parsers.pyx", line 918, in pandas._libs.parsers.TextReader._read_rows

  File "pandas/_libs/parsers.pyx", line 905, in pandas._libs.parsers.TextReader._tokenize_rows

  File "pandas/_libs/parsers.pyx", line 2042, in pandas._libs.parsers.raise_parser_error

pandas.errors.ParserError: Error tokenizing data. C error: Expected 12 fields in line 5, saw 22

Python 3.6.9

Traceback (most recent call last):

  File "/usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py", line 355, in <module>

    'genPlotPdfs': gen_plot_pdfs,

  File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 141, in Fire

    component_trace = _Fire(component, args, parsed_flag_args, context, name)

  File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 471, in _Fire

    target=component.__name__)

  File "/usr/local/lib/python3.6/dist-packages/fire/core.py", line 681, in _CallAndUpdateTrace

    component = fn(*varargs, **kwargs)

  File "/usr/local/app/vcell/installDir/submodules/vcell_cli_utils/vcell_cli_utils/cli.py", line 145, in exec_sed_doc

    data_set_df = pd.read_csv(report_filename).transpose()

  File "/usr/local/lib/python3.6/dist-packages/pandas/io/parsers.py", line 688, in read_csv

    return _read(filepath_or_buffer, kwds)

  File "/usr/local/lib/python3.6/dist-packages/pandas/io/parsers.py", line 460, in _read

    data = parser.read(nrows)

  File "/usr/local/lib/python3.6/dist-packages/pandas/io/parsers.py", line 1198, in read

    ret = self._engine.read(nrows)

  File "/usr/local/lib/python3.6/dist-packages/pandas/io/parsers.py", line 2157, in read

    data = self._reader.read(nrows)

  File "pandas/_libs/parsers.pyx", line 847, in pandas._libs.parsers.TextReader.read

  File "pandas/_libs/parsers.pyx", line 862, in pandas._libs.parsers.TextReader._read_low_memory

  File "pandas/_libs/parsers.pyx", line 918, in pandas._libs.parsers.TextReader._read_rows

  File "pandas/_libs/parsers.pyx", line 905, in pandas._libs.parsers.TextReader._tokenize_rows

  File "pandas/_libs/parsers.pyx", line 2042, in pandas._libs.parsers.raise_parser_error

pandas.errors.ParserError: Error tokenizing data. C error: Expected 12 fields in line 5, saw 22

HDF conversion failed

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

Archiving resultant CSV files to `reports.zip`.

sedml.SimulatorSupportsModelAttributeChanges (14.4 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

Jun 03, 2021 2:58:55 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_cd736ca0-bd32-488e-8738-792e27f02dbb466818018482707058

Python 3.6.9

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),  0 plot2D(s), and 0 plot3D(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_task') 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/temp5019995266278276063.xml

/tmp/out/BIOMD0000000912_sim.sedml

false

cbit.vcell.solver.ode.CVodeSolverStandalone@488b50ec

Finished: SOLVER_FINISHED:completed

Succesful execution: Model 'archive__BIOMD0000000912' Task 'Caravagna2010'.

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

Generating report `report`.

Python 3.6.9

HDF conversion successful

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

Archiving resultant CSV files to `reports.zip`.

sedml.SimulatorSupportsRepeatedTasksWithChanges (6.8 s)
Test that a simulator supports repeated tasks with multiple subtasks
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmp9lpcl4we/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

Jun 03, 2021 2:59:52 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_172f4688-3765-468f-8204-72f1a8df22991665420454893648850

Python 3.6.9

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:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

SED-ML processing for /tmp/vcell_temp_172f4688-3765-468f-8204-72f1a8df22991665420454893648850/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:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

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

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

Jun 03, 2021 2:59:56 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_46cbdbba-8270-4f53-83eb-6f970d42d5c8549941968615130995

Python 3.6.9

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:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

SED-ML processing for /tmp/vcell_temp_46cbdbba-8270-4f53-83eb-6f970d42d5c8549941968615130995/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:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

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

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (6.8 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/tmpyptoq2hm/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

Jun 03, 2021 2:59:59 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_5cec1ed9-bbcc-4460-9e05-b7f556fd68de5786117796277307717

Python 3.6.9

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:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

SED-ML processing for /tmp/vcell_temp_5cec1ed9-bbcc-4460-9e05-b7f556fd68de5786117796277307717/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:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

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

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

Jun 03, 2021 3:00:03 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_9ead6fd4-a749-4739-bf41-bc3df5c6a2da2815203941005377476

Python 3.6.9

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:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

SED-ML processing for /tmp/vcell_temp_9ead6fd4-a749-4739-bf41-bc3df5c6a2da2815203941005377476/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:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

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

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges (3.4 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/tmpzqv5ouda/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

Jun 03, 2021 3:00:06 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_f368d526-d98d-4679-b474-1c007ca5f73f6698781018066830103

Python 3.6.9

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:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

SED-ML processing for /tmp/vcell_temp_f368d526-d98d-4679-b474-1c007ca5f73f6698781018066830103/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:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

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

sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges (3.3 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/tmpy4rkzewc/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

Jun 03, 2021 3:00:09 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_40c18aac-acc8-4d23-aed7-6612a83a13a85669794037703447244

Python 3.6.9

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:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

SED-ML processing for /tmp/vcell_temp_40c18aac-acc8-4d23-aed7-6612a83a13a85669794037703447244/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:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

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

sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges (3.2 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/tmpwx8mm0xj/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

Jun 03, 2021 3:00:13 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_94f7a54f-8732-4d43-ade9-0018eaa67bf53274485899552172477

Python 3.6.9

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:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

SED-ML processing for /tmp/vcell_temp_94f7a54f-8732-4d43-ade9-0018eaa67bf53274485899552172477/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:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

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

sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks (3.3 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/tmpshslylcm/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

Jun 03, 2021 3:00:16 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_61fc3a35-96d9-44d7-85c9-cfcf070fbd824951127481021463257

Python 3.6.9

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:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

SED-ML processing for /tmp/vcell_temp_61fc3a35-96d9-44d7-85c9-cfcf070fbd824951127481021463257/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:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

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

sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges (3.3 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/tmpiirhha0k/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

Jun 03, 2021 3:00:19 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_419bc1a4-b115-4582-a067-19081ac7b9ed3727780809273260695

Python 3.6.9

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:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

SED-ML processing for /tmp/vcell_temp_419bc1a4-b115-4582-a067-19081ac7b9ed3727780809273260695/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:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

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

sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks (3.4 s)
Test that a simulator supports nested repeated tasks
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmp076y1v9o/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

Jun 03, 2021 3:00:23 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_510be3d9-c05d-46e3-b4ec-bcbfd4a5d1783695548560026207282

Python 3.6.9

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:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

SED-ML processing for /tmp/vcell_temp_510be3d9-c05d-46e3-b4ec-bcbfd4a5d1783695548560026207282/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:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

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

sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes (3.3 s)
Test that a simulator supports repeated tasks whose sub-tasks have mixed types. Also tests that sub-types executed in order of the values of their order attributes and that reports of the results of repeated tasks handle sub-tasks to produce results of different shapes.
Reason for skip:
[Errno 2] Unable to open file (unable to open file: name = '/tmp/tmpyegspevd/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

Jun 03, 2021 3:00:26 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_30847a77-d97b-4ff0-8408-0f778dab5c533538125043546602135

Python 3.6.9

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:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

SED-ML processing for /tmp/vcell_temp_30847a77-d97b-4ff0-8408-0f778dab5c533538125043546602135/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:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

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

sedml.SimulatorSupportsRepeatedTasksWithVectorRanges (3.3 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/tmph1y104a5/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

Jun 03, 2021 3:00:29 PM java.util.prefs.FileSystemPreferences$1 run

INFO: Created user preferences directory.

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

TempPath Created: /tmp/vcell_temp_31b4d7b3-fc25-48f6-8789-4dd4a0cb6f2f1500334535016602888

Python 3.6.9

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:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

SED-ML processing for /tmp/vcell_temp_31b4d7b3-fc25-48f6-8789-4dd4a0cb6f2f1500334535016602888/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:360)

	at org.jlibsedml.Libsedml.readDocument(Libsedml.java:92)

	at org.vcell.cli.CLIStandalone.singleExecOmex(CLIStandalone.java:135)

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:65)

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

sedml.SimulatorSupportsSubstitutingAlgorithms (13.2 s)
Check that a simulator can substitute algorithms that it doesn't implement with similar algorithms when the algorithm substitution policy is less restrictive than :obj:AlgorithmSubstitutionPolicy.SAME_METHOD. Also check that a simulator ignores unsupported algorithm parameters when the algorithm substitution policy is less restrictive than :obj:AlgorithmSubstitutionPolicy.NONE.
Reason for skip:
The execution of the COMBINE/OMEX archive did not fail as expected

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

Jun 03, 2021 3:00:33 PM java.util.prefs.FileSystemPrefer ...

The image for your simulator is valid!

Your submission was committed to the BioSimulators registry. Thank you!
Future submissions of subsequent versions of VCell to the BioSimulators registry will be automatically validated. These submissions will not require manual review by the BioSimulators Team.


my multibit wallet

Have you got this wallet data on your end
1Kfysutx8SPZ3gfaemKcDAEYkV6QEUzF7k
that was the wallet where my bitcoins were sorted in, and iv lost the data can you help??????

@boba89 did you recover your multibit wallet,
this is the issue which occurs a lot for older versions of multibit, I can recover your wallet if you still have this problem contact me at<EMAIL_ADDRESS>