Submit: VCell 7.6.0.40

Question

Submit: VCell 7.6.0.40

Closed this issue 4 months ago · 108 comments

Answer 1 · 2024-08-29T20:39:33.000Z

Thank you @CodeByDrescher 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 for 90 days 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 for 90 days from the "Artifacts" section at the bottom of this page.

Answer 2 · 2024-08-29T20:39:39.000Z

The specifications of your simulator is valid!

Answer 3 · 2024-08-29T20:39:40.000Z

The validation/submission of your simulator failed.

- Error while fetching server API version: Not supported URL scheme http+docker

The complete log of your validation/submission job, including further information about the failure, is available for 90 days here.

If you chose to validate your Docker image, the results of the validation of your image will be available shortly as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.

Once you have fixed the problem, edit the first block of this issue to re-initiate this validation.

The BioSimulators Team is happy to help. Questions and feedback can be directed to the BioSimulators Team by posting comments to this issues that reference the GitHub team @biosimulators/biosimulators (without the backticks).

Answer 4 · 2024-08-30T17:17:55.000Z

Thank you @CodeByDrescher 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 for 90 days 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 for 90 days from the "Artifacts" section at the bottom of this page.

Answer 5 · 2024-08-30T17:18:02.000Z

The specifications of your simulator is valid!

Answer 6 · 2024-08-30T17:18:03.000Z

The validation/submission of your simulator failed.

- Error while fetching server API version: HTTPConnection.request() got an unexpected keyword argument 'chunked'

The complete log of your validation/submission job, including further information about the failure, is available for 90 days here.

If you chose to validate your Docker image, the results of the validation of your image will be available shortly as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.

Once you have fixed the problem, edit the first block of this issue to re-initiate this validation.

The BioSimulators Team is happy to help. Questions and feedback can be directed to the BioSimulators Team by posting comments to this issues that reference the GitHub team @biosimulators/biosimulators (without the backticks).

Answer 7 · 2024-08-30T17:26:44.000Z

Thank you @CodeByDrescher 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 for 90 days 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 for 90 days from the "Artifacts" section at the bottom of this page.

Answer 8 · 2024-08-30T17:26:50.000Z

The specifications of your simulator is valid!

Answer 9 · 2024-08-30T17:26:51.000Z

The validation/submission of your simulator failed.

- Error while fetching server API version: Not supported URL scheme http+docker

The complete log of your validation/submission job, including further information about the failure, is available for 90 days here.

If you chose to validate your Docker image, the results of the validation of your image will be available shortly as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.

Once you have fixed the problem, edit the first block of this issue to re-initiate this validation.

The BioSimulators Team is happy to help. Questions and feedback can be directed to the BioSimulators Team by posting comments to this issues that reference the GitHub team @biosimulators/biosimulators (without the backticks).

Answer 10 · 2024-08-30T17:33:16.000Z

Thank you @CodeByDrescher 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 for 90 days 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 for 90 days from the "Artifacts" section at the bottom of this page.

Answer 11 · 2024-08-30T17:33:21.000Z

The specifications of your simulator is valid!

Answer 12 · 2024-08-30T17:33:23.000Z

The validation/submission of your simulator failed.

- Error while fetching server API version: HTTPConnection.request() got an unexpected keyword argument 'chunked'

The complete log of your validation/submission job, including further information about the failure, is available for 90 days here.

If you chose to validate your Docker image, the results of the validation of your image will be available shortly as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.

Once you have fixed the problem, edit the first block of this issue to re-initiate this validation.

The BioSimulators Team is happy to help. Questions and feedback can be directed to the BioSimulators Team by posting comments to this issues that reference the GitHub team @biosimulators/biosimulators (without the backticks).

Answer 13 · 2024-08-30T17:49:40.000Z

Thank you @CodeByDrescher 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 for 90 days 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 for 90 days from the "Artifacts" section at the bottom of this page.

Answer 14 · 2024-08-30T17:49:45.000Z

The specifications of your simulator is valid!

Answer 15 · 2024-08-30T17:50:07.000Z

The validation/submission of your simulator failed.

- Command '['singularity', 'build', '/home/runner/.biosimulators-test-suite/singularity/ghcr.io_virtualcell_biosimulators_vcell_7.6.0.27.sif', 'docker-daemon://ghcr.io/virtualcell/biosimulators_vcell:7.6.0.27']' returned non-zero exit status 255.

The complete log of your validation/submission job, including further information about the failure, is available for 90 days here.

If you chose to validate your Docker image, the results of the validation of your image will be available shortly as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.

Once you have fixed the problem, edit the first block of this issue to re-initiate this validation.

The BioSimulators Team is happy to help. Questions and feedback can be directed to the BioSimulators Team by posting comments to this issues that reference the GitHub team @biosimulators/biosimulators (without the backticks).

Answer 16 · 2024-08-30T18:03:42.000Z

Thank you @CodeByDrescher 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 for 90 days 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 for 90 days from the "Artifacts" section at the bottom of this page.

Answer 17 · 2024-08-30T18:03:48.000Z

The specifications of your simulator is valid!

Answer 18 · 2024-08-30T18:04:07.000Z

The validation/submission of your simulator failed.

- Command '['singularity', 'build', '/home/runner/.biosimulators-test-suite/singularity/ghcr.io_virtualcell_biosimulators_vcell_7.6.0.27.sif', 'docker-daemon://ghcr.io/virtualcell/biosimulators_vcell:7.6.0.27']' returned non-zero exit status 255.

The complete log of your validation/submission job, including further information about the failure, is available for 90 days here.

If you chose to validate your Docker image, the results of the validation of your image will be available shortly as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.

Once you have fixed the problem, edit the first block of this issue to re-initiate this validation.

The BioSimulators Team is happy to help. Questions and feedback can be directed to the BioSimulators Team by posting comments to this issues that reference the GitHub team @biosimulators/biosimulators (without the backticks).

Answer 19 · 2024-08-30T18:19:09.000Z

Thank you @CodeByDrescher 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 for 90 days 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 for 90 days from the "Artifacts" section at the bottom of this page.

Answer 20 · 2024-08-30T18:19:16.000Z

The specifications of your simulator is valid!

Answer 21 · 2024-08-30T18:19:38.000Z

The validation/submission of your simulator failed.

- Command '['singularity', 'build', '/home/runner/.biosimulators-test-suite/singularity/ghcr.io_virtualcell_biosimulators_vcell_7.6.0.27.sif', 'docker-daemon://ghcr.io/virtualcell/biosimulators_vcell:7.6.0.27']' returned non-zero exit status 255.

The complete log of your validation/submission job, including further information about the failure, is available for 90 days here.

If you chose to validate your Docker image, the results of the validation of your image will be available shortly as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.

Once you have fixed the problem, edit the first block of this issue to re-initiate this validation.

The BioSimulators Team is happy to help. Questions and feedback can be directed to the BioSimulators Team by posting comments to this issues that reference the GitHub team @biosimulators/biosimulators (without the backticks).

Answer 22 · 2024-08-30T18:26:14.000Z

Thank you @CodeByDrescher 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 for 90 days 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 for 90 days from the "Artifacts" section at the bottom of this page.

Answer 23 · 2024-08-30T18:26:20.000Z

The specifications of your simulator is valid!

Answer 24 · 2024-08-30T18:26:43.000Z

The validation/submission of your simulator failed.

- Command '['singularity', 'build', '/home/runner/.biosimulators-test-suite/singularity/ghcr.io_virtualcell_biosimulators_vcell_7.6.0.27.sif', 'docker-daemon://ghcr.io/virtualcell/biosimulators_vcell:7.6.0.27']' returned non-zero exit status 255.

The complete log of your validation/submission job, including further information about the failure, is available for 90 days here.

If you chose to validate your Docker image, the results of the validation of your image will be available shortly as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.

Once you have fixed the problem, edit the first block of this issue to re-initiate this validation.

The BioSimulators Team is happy to help. Questions and feedback can be directed to the BioSimulators Team by posting comments to this issues that reference the GitHub team @biosimulators/biosimulators (without the backticks).

Answer 25 · 2024-08-31T19:43:22.000Z

Thank you @CodeByDrescher 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 for 90 days 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 for 90 days from the "Artifacts" section at the bottom of this page.

Answer 26 · 2024-08-31T19:43:27.000Z

The specifications of your simulator is valid!

Answer 27 · 2024-08-31T19:43:48.000Z

The validation/submission of your simulator failed.

- Command '['singularity', 'build', '/home/runner/.biosimulators-test-suite/singularity/ghcr.io_virtualcell_biosimulators_vcell_7.6.0.27.sif', 'docker-daemon://ghcr.io/virtualcell/biosimulators_vcell:7.6.0.27']' returned non-zero exit status 255.

The complete log of your validation/submission job, including further information about the failure, is available for 90 days here.

If you chose to validate your Docker image, the results of the validation of your image will be available shortly as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.

Once you have fixed the problem, edit the first block of this issue to re-initiate this validation.

The BioSimulators Team is happy to help. Questions and feedback can be directed to the BioSimulators Team by posting comments to this issues that reference the GitHub team @biosimulators/biosimulators (without the backticks).

Answer 28 · 2024-08-31T20:03:31.000Z

Thank you @CodeByDrescher 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 for 90 days 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 for 90 days from the "Artifacts" section at the bottom of this page.

Answer 29 · 2024-08-31T20:03:38.000Z

The specifications of your simulator is valid!

Answer 30 · 2024-08-31T20:03:59.000Z

The validation/submission of your simulator failed.

- Command '['singularity', 'build', '/home/runner/.biosimulators-test-suite/singularity/ghcr.io_virtualcell_biosimulators_vcell_7.6.0.27.sif', 'docker-daemon://ghcr.io/virtualcell/biosimulators_vcell:7.6.0.27']' returned non-zero exit status 255.

The complete log of your validation/submission job, including further information about the failure, is available for 90 days here.

If you chose to validate your Docker image, the results of the validation of your image will be available shortly as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.

Once you have fixed the problem, edit the first block of this issue to re-initiate this validation.

The BioSimulators Team is happy to help. Questions and feedback can be directed to the BioSimulators Team by posting comments to this issues that reference the GitHub team @biosimulators/biosimulators (without the backticks).

Answer 31 · 2024-08-31T20:33:42.000Z

Thank you @CodeByDrescher 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 for 90 days 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 for 90 days from the "Artifacts" section at the bottom of this page.

Answer 32 · 2024-08-31T20:33:46.000Z

The specifications of your simulator is valid!

Answer 33 · 2024-08-31T20:34:06.000Z

The validation/submission of your simulator failed.

- Command '['singularity', 'build', '/home/runner/.biosimulators-test-suite/singularity/ghcr.io_virtualcell_biosimulators_vcell_7.6.0.27.sif', 'docker-daemon://ghcr.io/virtualcell/biosimulators_vcell:7.6.0.27']' returned non-zero exit status 255.

The complete log of your validation/submission job, including further information about the failure, is available for 90 days here.

If you chose to validate your Docker image, the results of the validation of your image will be available shortly as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.

Once you have fixed the problem, edit the first block of this issue to re-initiate this validation.

The BioSimulators Team is happy to help. Questions and feedback can be directed to the BioSimulators Team by posting comments to this issues that reference the GitHub team @biosimulators/biosimulators (without the backticks).

Answer 34 · 2024-08-31T20:53:41.000Z

Thank you @CodeByDrescher 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 for 90 days 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 for 90 days from the "Artifacts" section at the bottom of this page.

Answer 35 · 2024-08-31T20:53:45.000Z

The specifications of your simulator is valid!

Answer 36 · 2024-08-31T20:54:06.000Z

The validation/submission of your simulator failed.

- Command '['singularity', 'build', '/home/runner/.biosimulators-test-suite/singularity/ghcr.io_virtualcell_biosimulators_vcell_7.6.0.27.sif', 'docker-daemon://ghcr.io/virtualcell/biosimulators_vcell:7.6.0.27']' returned non-zero exit status 255.

The complete log of your validation/submission job, including further information about the failure, is available for 90 days here.

If you chose to validate your Docker image, the results of the validation of your image will be available shortly as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.

Once you have fixed the problem, edit the first block of this issue to re-initiate this validation.

The BioSimulators Team is happy to help. Questions and feedback can be directed to the BioSimulators Team by posting comments to this issues that reference the GitHub team @biosimulators/biosimulators (without the backticks).

Answer 37 · 2024-09-01T13:35:25.000Z

Thank you @CodeByDrescher 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 for 90 days 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 for 90 days from the "Artifacts" section at the bottom of this page.

Answer 38 · 2024-09-01T13:35:32.000Z

The specifications of your simulator is valid!

Answer 39 · 2024-09-01T13:35:51.000Z

The validation/submission of your simulator failed.

- Command '['singularity', 'build', '/home/runner/.biosimulators-test-suite/singularity/ghcr.io_virtualcell_biosimulators_vcell_7.6.0.27.sif', 'docker-daemon://ghcr.io/virtualcell/biosimulators_vcell:7.6.0.27']' returned non-zero exit status 255.

The complete log of your validation/submission job, including further information about the failure, is available for 90 days here.

If you chose to validate your Docker image, the results of the validation of your image will be available shortly as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.

Once you have fixed the problem, edit the first block of this issue to re-initiate this validation.

The BioSimulators Team is happy to help. Questions and feedback can be directed to the BioSimulators Team by posting comments to this issues that reference the GitHub team @biosimulators/biosimulators (without the backticks).

Answer 40 · 2024-09-01T16:45:33.000Z

Thank you @CodeByDrescher 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 for 90 days 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 for 90 days from the "Artifacts" section at the bottom of this page.

Answer 41 · 2024-09-01T16:45:39.000Z

The specifications of your simulator is valid!

Answer 42 · 2024-09-01T16:46:02.000Z

The validation/submission of your simulator failed.

- Command '['singularity', 'build', '/home/runner/.biosimulators-test-suite/singularity/ghcr.io_virtualcell_biosimulators_vcell_7.6.0.27.sif', 'docker-daemon://ghcr.io/virtualcell/biosimulators_vcell:7.6.0.27']' returned non-zero exit status 255.

The complete log of your validation/submission job, including further information about the failure, is available for 90 days here.

If you chose to validate your Docker image, the results of the validation of your image will be available shortly as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.

Once you have fixed the problem, edit the first block of this issue to re-initiate this validation.

The BioSimulators Team is happy to help. Questions and feedback can be directed to the BioSimulators Team by posting comments to this issues that reference the GitHub team @biosimulators/biosimulators (without the backticks).

Answer 43 · 2024-09-01T18:51:23.000Z

Thank you @CodeByDrescher 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 for 90 days 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 for 90 days from the "Artifacts" section at the bottom of this page.

Answer 44 · 2024-09-01T18:51:28.000Z

The specifications of your simulator is valid!

Answer 45 · 2024-09-01T18:51:49.000Z

The validation/submission of your simulator failed.

- Command '['singularity', 'build', '/home/runner/.biosimulators-test-suite/singularity/ghcr.io_virtualcell_biosimulators_vcell_7.6.0.27.sif', 'docker-daemon://ghcr.io/virtualcell/biosimulators_vcell:7.6.0.27']' returned non-zero exit status 255.

The complete log of your validation/submission job, including further information about the failure, is available for 90 days here.

If you chose to validate your Docker image, the results of the validation of your image will be available shortly as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.

Once you have fixed the problem, edit the first block of this issue to re-initiate this validation.

The BioSimulators Team is happy to help. Questions and feedback can be directed to the BioSimulators Team by posting comments to this issues that reference the GitHub team @biosimulators/biosimulators (without the backticks).

Answer 46 · 2024-09-01T19:40:32.000Z

Thank you @CodeByDrescher 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 for 90 days 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 for 90 days from the "Artifacts" section at the bottom of this page.

Answer 47 · 2024-09-01T19:40:39.000Z

The specifications of your simulator is valid!

Answer 48 · 2024-09-01T20:42:28.000Z

Thank you @CodeByDrescher 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 for 90 days 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 for 90 days from the "Artifacts" section at the bottom of this page.

Answer 49 · 2024-09-01T20:42:33.000Z

The specifications of your simulator is valid!

Answer 50 · 2024-09-04T16:13:45.000Z

Thank you @CodeByDrescher 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 for 90 days 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 for 90 days from the "Artifacts" section at the bottom of this page.

Answer 51 · 2024-09-04T16:13:50.000Z

The specifications of your simulator is valid!

Answer 52 · 2024-09-04T16:14:12.000Z

The validation/submission of your simulator failed.

- Command '['singularity', 'build', '/home/runner/.biosimulators-test-suite/singularity/ghcr.io_virtualcell_biosimulators_vcell_7.6.0.27.sif', 'docker-daemon://ghcr.io/virtualcell/biosimulators_vcell:7.6.0.27']' returned non-zero exit status 255.

The complete log of your validation/submission job, including further information about the failure, is available for 90 days here.

If you chose to validate your Docker image, the results of the validation of your image will be available shortly as a JSON file. A link to this file will be available for 90 days from the "Artifacts" section at the bottom of this page.

Once you have fixed the problem, edit the first block of this issue to re-initiate this validation.

The BioSimulators Team is happy to help. Questions and feedback can be directed to the BioSimulators Team by posting comments to this issues that reference the GitHub team @biosimulators/biosimulators (without the backticks).

Answer 53 · 2024-09-04T16:20:03.000Z

Thank you @CodeByDrescher 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 for 90 days 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 for 90 days from the "Artifacts" section at the bottom of this page.

Answer 54 · 2024-09-04T16:20:07.000Z

The specifications of your simulator is valid!

Answer 55 · 2024-09-04T16:22:55.000Z

Summary of tests

Executed 74 test cases
Passed 7 test cases:
- cli.CliDescribesSupportedEnvironmentVariablesInline
- cli.CliDisplaysHelpInline
- cli.CliDisplaysVersionInformationInline
- docker_image.DeclaresSupportedEnvironmentVariables
- docker_image.DefaultUserIsRoot
- docker_image.HasBioContainersLabels
- docker_image.HasOciLabels
Failed 29 test cases:
- combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories
- combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories
- combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
- combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
- docker_image.SingularityImageExecutesSimulationsSuccessfully
- log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
- log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
- log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
- log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks
- 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-Fehlberg
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator
- 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
- published_project.SimulatorCanExecutePublishedProject:vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength
- results_report.SimulatorGeneratesReportsOfSimulationResults
- sedml.SimulatorProducesLinear2DPlots
- sedml.SimulatorProducesLinear3DPlots
- sedml.SimulatorProducesLogarithmic2DPlots
- sedml.SimulatorProducesLogarithmic3DPlots
- sedml.SimulatorProducesMultiplePlots
- sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
- sedml.SimulatorSupportsAlgorithmParameters
- sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
- sedml.SimulatorSupportsMultipleReportsPerSedDocument
- sedml.SimulatorSupportsMultipleTasksPerSedDocument
- sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes
Skipped 38 test cases:
- published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
- published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
- published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator
- published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system
- published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism
- published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE
- published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler
- published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT
- 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:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle
- published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra
- published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells
- sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments
- sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
- 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

Answer 56 · 2024-09-04T16:22:55.000Z

Failures

combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories (0.0 s)

Test that SED documents in nested directories can be executed

Exception:

No module named 'libsbml'

Log: None

combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories (0.0 s)

Test that SED documents with the same names in nested directories can be executed and their outputs are saved to distinct paths

Exception:

No module named 'libsbml'

Log: None

combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile (0.0 s)

Test that when a COMBINE/OMEX archive defines a (single) master file, the simulator only executes this file.

Exception:

No module named 'libsbml'

Log: None

combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments (0.0 s)

Test that when a COMBINE/OMEX archive does not have a defined master file, the simulator executes all SED-ML files.

Exception:

No module named 'libsbml'

Log: None

docker_image.SingularityImageExecutesSimulationsSuccessfully (0.0 s)

Test that the Singularity version of a Docker image can sucessfully execute COMBINE archives

Exception:

No module named 'libsbml'

Log: None

log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives (0.0 s)

Test that simulator logs the execution of COMBINE/OMEX archives

Exception:

No module named 'libsbml'

Log: None

log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments (0.0 s)

Test that simulator logs the execution of individual SED document in COMBINE/OMEX archives

Exception:

No module named 'libsbml'

Log: None

log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs (0.0 s)

Test that simulator logs the execution of individual SED outputs in COMBINE/OMEX archives

Exception:

No module named 'libsbml'

Log: None

log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks (0.0 s)

Test that simulator logs the execution of individual SED tasks in COMBINE/OMEX archives

Exception:

No module named 'libsbml'

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (6.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.6.0.27' could not execute the archive:

  Unknown error

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg (6.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000086

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.6.0.27' could not execute the archive:

  Unknown error

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous (6.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.6.0.27' could not execute the archive:

  Unknown error

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator (5.8 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.6.0.27' could not execute the archive:

  Unknown error

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock (6.1 s)

Required model formats and simulation algorithms for SED tasks:

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

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.6.0.27' could not execute the archive:

  Unknown error

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-continuous (5.8 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.6.0.27' could not execute the archive:

  Unknown error

Log: None

published_project.SimulatorCanExecutePublishedProject:sbml-core/Vilar-PNAS-2002-minimal-circardian-clock-discrete-NRM (6.1 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000027

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.6.0.27' could not execute the archive:

  Unknown error

Log: None

published_project.SimulatorCanExecutePublishedProject:vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength (5.9 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9000
Algorithm: KISAO_0000019

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.6.0.27' could not execute the archive:

  Unknown error

Log: None

results_report.SimulatorGeneratesReportsOfSimulationResults (0.0 s)

Test that when a COMBINE/OMEX archive defines a (single) master file, the simulator only executes this file.

Exception:

No module named 'libsbml'

Log: None

sedml.SimulatorProducesLinear2DPlots (0.0 s)

Test that a simulator produces linear 2D plots

Exception:

No module named 'libsbml'

Log: None

sedml.SimulatorProducesLinear3DPlots (0.0 s)

Test that a simulator produces linear 3D plots

Exception:

No module named 'libsbml'

Log: None

sedml.SimulatorProducesLogarithmic2DPlots (0.0 s)

Test that a simulator produces logarithmic 2D plots

Exception:

No module named 'libsbml'

Log: None

sedml.SimulatorProducesLogarithmic3DPlots (0.0 s)

Test that a simulator produces logarithmic 3D plots

Exception:

No module named 'libsbml'

Log: None

sedml.SimulatorProducesMultiplePlots (0.0 s)

Test that a simulator produces multiple plots

Exception:

No module named 'libsbml'

Log: None

sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions (0.0 s)

Test that that the curated number of output dimensions matches the actual number of output dimensions

Exception:

No module named 'libsbml'

Log: None

sedml.SimulatorSupportsAlgorithmParameters (0.0 s)

Test that a simulator supports setting the values of parameters of algorithms

Exception:

No module named 'libsbml'

Log: None

sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports (0.0 s)

Test that a simulator supports the core elements of SED: models, simulations, tasks, data generators for individual variables, and reports

Exception:

No module named 'libsbml'

Log: None

sedml.SimulatorSupportsMultipleReportsPerSedDocument (0.0 s)

Test that a simulator supports multiple reports per SED document

Exception:

No module named 'libsbml'

Log: None

sedml.SimulatorSupportsMultipleTasksPerSedDocument (0.0 s)

Test that a simulator supports multiple tasks per SED document

Exception:

No module named 'libsbml'

Log: None

sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes (0.0 s)

Test that a simulator supports time courses with non-zero output start times

Exception:

No module named 'libsbml'

Log: None

Answer 57 · 2024-09-04T16:22:56.000Z

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (3.3 s)

Test that the inline help for a command-line interface describes the environment variables that the simulator supports.

Warnings:

The inline help for a command-line interface for a simulation tool should describe the environment variables that the simulation tool supports.

The command-line interface does not describe the following standard environment variables recognized by BioSimulators:
  - 'ALGORITHM_SUBSTITUTION_POLICY'
  - 'BUNDLE_OUTPUTS'
  - 'COLLECT_COMBINE_ARCHIVE_RESULTS'
  - 'COLLECT_SED_DOCUMENT_RESULTS'
  - 'DEBUG'
  - 'H5_REPORTS_PATH'
  - 'KEEP_INDIVIDUAL_OUTPUTS'
  - 'LOG_PATH'
  - 'OMEX_METADATA_INPUT_FORMAT'
  - 'OMEX_METADATA_OUTPUT_FORMAT'
  - 'OMEX_METADATA_SCHEMA'
  - 'PLOTS_PATH'
  - 'REPORTS_PATH'
  - 'REPORT_FORMATS'
  - 'SAVE_PLOT_DATA'
  - 'VALIDATE_IMAGES'
  - 'VALIDATE_IMPORTED_MODEL_FILES'
  - 'VALIDATE_OMEX_MANIFESTS'
  - 'VALIDATE_OMEX_METADATA'
  - 'VALIDATE_RESULTS'
  - 'VALIDATE_SEDML'
  - 'VALIDATE_SEDML_MODELS'
  - 'VERBOSE'
  - 'VIZ_FORMATS'

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: None

cli.CliDisplaysHelpInline (4.3 s)

Test that a command-line interface provides inline help.

Warnings:

Command-line interfaces should display basic help when no arguments are provided.

The command-line interface displayed the following when no argument was provided:

  docker: Command recieved::<>
  <>
  Default case selected
  VCell shall execute <biosimulations >
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
   INFO (CLIStandalone:36) - Starting Vcell... []{}
  ERROR (BiosimulationsCommand:116) - Cannot invoke "java.io.File.getAbsolutePath()" because "outputDirectory" is null []{}
  java.lang.NullPointerException: Cannot invoke "java.io.File.getAbsolutePath()" because "outputDirectory" is null
  	at org.vcell.cli.CLIRecorder.<init>(CLIRecorder.java:70) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.CLIRecorder.<init>(CLIRecorder.java:59) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.CLIRecorder.<init>(CLIRecorder.java:48) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:50) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]
  	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

  docker: Command recieved::<-h>
  <-h>
  Default case selected
  VCell shall execute <biosimulations -h>
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
   INFO (CLIStandalone:36) - Starting Vcell... []{}
  Usage: �[1mCLIStandalone biosimulations�[21m�[0m [�[33m-dhqv�[39m�[0m] [�[33m-i�[39m�[0m=�[3m<ARCHIVE>�[23m�[0m] [�[33m-o�[39m�[0m=�[3m<OUT_DIR>�[23m�[0m]
  BioSimulators-compliant command-line interface to the vcell simulation program
  <https://vcell.org>.
    �[33m-d�[39m�[0m, �[33m--debug�[39m�[0m               full application debug mode
    �[33m-h�[39m�[0m, �[33m--help�[39m�[0m                show this help message and exit
    �[33m-i�[39m�[0m, �[33m--archive�[39m�[0m=�[3m<ARCHIVE>�[23m�[0m   Path to a COMBINE/OMEX archive file which contains
                                one or more SED-ML-encoded simulation experiments
    �[33m-o�[39m�[0m, �[33m--out-dir�[39m�[0m=�[3m<OUT_DIR>�[23m�[0m   Directory to save outputs
    �[33m-q�[39m�[0m, �[33m--quiet�[39m�[0m               suppress all console output
    �[33m-v�[39m�[0m, �[33m--version�[39m�[0m             show program's version number and exit

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

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

  docker: Command recieved::<--help>
  <--help>
  Default case selected
  VCell shall execute <biosimulations --help>
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
   INFO (CLIStandalone:36) - Starting Vcell... []{}
  Usage: �[1mCLIStandalone biosimulations�[21m�[0m [�[33m-dhqv�[39m�[0m] [�[33m-i�[39m�[0m=�[3m<ARCHIVE>�[23m�[0m] [�[33m-o�[39m�[0m=�[3m<OUT_DIR>�[23m�[0m]
  BioSimulators-compliant command-line interface to the vcell simulation program
  <https://vcell.org>.
    �[33m-d�[39m�[0m, �[33m--debug�[39m�[0m               full application debug mode
    �[33m-h�[39m�[0m, �[33m--help�[39m�[0m                show this help message and exit
    �[33m-i�[39m�[0m, �[33m--archive�[39m�[0m=�[3m<ARCHIVE>�[23m�[0m   Path to a COMBINE/OMEX archive file which contains
                                one or more SED-ML-encoded simulation experiments
    �[33m-o�[39m�[0m, �[33m--out-dir�[39m�[0m=�[3m<OUT_DIR>�[23m�[0m   Directory to save outputs
    �[33m-q�[39m�[0m, �[33m--quiet�[39m�[0m               suppress all console output
    �[33m-v�[39m�[0m, �[33m--version�[39m�[0m             show program's version number and exit

Log: None

docker_image.DeclaresSupportedEnvironmentVariables (0.2 s)

Test if a Docker image declares the environment variables that is supports

Warnings:

Docker images for simulation tools should declare the environment variables that they support.

The Docker image does not declare the following standard environment variables recognized by BioSimulators:
  - 'BUNDLE_OUTPUTS'
  - 'COLLECT_COMBINE_ARCHIVE_RESULTS'
  - 'COLLECT_SED_DOCUMENT_RESULTS'
  - 'DEBUG'
  - 'H5_REPORTS_PATH'
  - 'KEEP_INDIVIDUAL_OUTPUTS'
  - 'LOG_PATH'
  - 'OMEX_METADATA_INPUT_FORMAT'
  - 'OMEX_METADATA_OUTPUT_FORMAT'
  - 'OMEX_METADATA_SCHEMA'
  - 'PLOTS_PATH'
  - 'REPORTS_PATH'
  - 'REPORT_FORMATS'
  - 'SAVE_PLOT_DATA'
  - 'VALIDATE_IMAGES'
  - 'VALIDATE_IMPORTED_MODEL_FILES'
  - 'VALIDATE_OMEX_MANIFESTS'
  - 'VALIDATE_OMEX_METADATA'
  - 'VALIDATE_RESULTS'
  - 'VALIDATE_SEDML'
  - 'VALIDATE_SEDML_MODELS'
  - 'VERBOSE'
  - 'VIZ_FORMATS'

If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator.

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

Log: None

docker_image.HasBioContainersLabels (0.2 s)

Test that a Docker image has BioContainers labels with metadata about the image

Warnings:

Docker images are encouraged to have the following BioContainers labels:
  extra.identifiers.biotools

Log: None

Answer 58 · 2024-09-04T16:22:56.000Z

Skips

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: None

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: None

published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator (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: None

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: None

published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9004
Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_9004 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9004
Algorithm: KISAO_0000030

Reason for skip:

Case requires model formats format_9004 and simulation algorithms KISAO_0000030

Log: None

published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9012
Algorithm: KISAO_0000669

Reason for skip:

Case requires model formats format_9012 and simulation algorithms KISAO_0000669

Log: None

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: None

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: None

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: None

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: None

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: None

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: None

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: None

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: None

published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle (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: None

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: None

published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9010
Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_9010 and simulation algorithms KISAO_0000019

Log: None

sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments (0.0 s)

Test that a simulator can resolve model sources defined by URI fragments (e.g., #model1).

Reason for skip:

No module named 'libsbml'

Log: None

sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges (0.0 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:

No module named 'libsbml'

Log: None

sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges (0.0 s)

Test that a simulator supports model changes that involve adding, replacing, and removing model elements.

Reason for skip:

No module named 'libsbml'

Log: None

sedml.SimulatorSupportsComputeModelChanges (0.0 s)

Test that a simulator supports compute model changes

Reason for skip:

No module named 'libsbml'

Log: None

sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes (0.0 s)

Test that a simulator supports data generators with different shapes

Reason for skip:

No module named 'libsbml'

Log: None

sedml.SimulatorSupportsDataSetsWithDifferentShapes (0.0 s)

Test that a simulator supports data generators with different shapes

Reason for skip:

No module named 'libsbml'

Log: None

sedml.SimulatorSupportsModelAttributeChanges (0.0 s)

Test that a simulator supports changes to the attributes of model elements

Reason for skip:

No module named 'libsbml'

Log: None

sedml.SimulatorSupportsRepeatedTasksWithChanges (0.0 s)

Test that a simulator supports repeated tasks with multiple subtasks

Reason for skip:

No module named 'libsbml'

Log: None

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRangeVariables (0.0 s)

Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables

Reason for skip:

No module named 'libsbml'

Log: None

sedml.SimulatorSupportsRepeatedTasksWithFunctionalRanges (0.0 s)

Test that a simulator supports repeated tasks over functional ranges

Reason for skip:

No module named 'libsbml'

Log: None

sedml.SimulatorSupportsRepeatedTasksWithLinearUniformRanges (0.0 s)

Test that a simulator supports repeated tasks over uniform ranges

Reason for skip:

No module named 'libsbml'

Log: None

sedml.SimulatorSupportsRepeatedTasksWithLogarithmicUniformRanges (0.0 s)

Test that a simulator supports repeated tasks over uniform ranges

Reason for skip:

No module named 'libsbml'

Log: None

sedml.SimulatorSupportsRepeatedTasksWithMultipleSubTasks (0.0 s)

Test that a simulator supports repeated tasks with multiple subtasks

Reason for skip:

No module named 'libsbml'

Log: None

sedml.SimulatorSupportsRepeatedTasksWithNestedFunctionalRanges (0.0 s)

Test that a simulator supports repeated tasks over nested functional ranges based on model (specification) variables

Reason for skip:

No module named 'libsbml'

Log: None

sedml.SimulatorSupportsRepeatedTasksWithNestedRepeatedTasks (0.0 s)

Test that a simulator supports nested repeated tasks

Reason for skip:

No module named 'libsbml'

Log: None

sedml.SimulatorSupportsRepeatedTasksWithSubTasksOfMixedTypes (0.0 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:

No module named 'libsbml'

Log: None

sedml.SimulatorSupportsRepeatedTasksWithVectorRanges (0.0 s)

Test that a simulator supports repeated tasks over vector ranges

Reason for skip:

No module named 'libsbml'

Log: None

sedml.SimulatorSupportsSubstitutingAlgorithms (0.0 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:

No module named 'libsbml'

Log: None

sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroInitialTimes (0.0 s)

Test that a simulator supports multiple time courses with non-zero initial times

Reason for skip:

No module named 'libsbml'

Log: None

Answer 59 · 2024-09-04T16:22:57.000Z

- After correcting your simulator, please edit the first block of this issue to re-initiate this validation.
- 
- The complete log of your validation/submission job, including further information about the failure, is available for 90 days [here](https://github.com/biosimulators/Biosimulators/actions/runs/10705553862). The results of the validation of your image will also be available shortly as a JSON file. A link to this file will be available from the "Artifacts" section at the bottom of [this page](https://github.com/biosimulators/Biosimulators/actions/runs/10705553862).

Answer 60 · 2024-09-06T18:57:07.000Z

Thank you @CodeByDrescher 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 for 90 days 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 for 90 days from the "Artifacts" section at the bottom of this page.

Answer 61 · 2024-09-06T18:57:12.000Z

The specifications of your simulator is valid!

Answer 62 · 2024-09-06T19:04:18.000Z

Summary of tests

Executed 74 test cases
Passed 7 test cases:
- cli.CliDescribesSupportedEnvironmentVariablesInline
- cli.CliDisplaysHelpInline
- cli.CliDisplaysVersionInformationInline
- docker_image.DeclaresSupportedEnvironmentVariables
- docker_image.DefaultUserIsRoot
- docker_image.HasBioContainersLabels
- docker_image.HasOciLabels
Failed 26 test cases:
- combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories
- combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories
- combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
- combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
- docker_image.SingularityImageExecutesSimulationsSuccessfully
- log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
- log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
- log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
- log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks
- 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-Fehlberg
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator
- 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
- published_project.SimulatorCanExecutePublishedProject:vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength
- results_report.SimulatorGeneratesReportsOfSimulationResults
- sedml.SimulatorProducesLinear2DPlots
- sedml.SimulatorProducesLogarithmic2DPlots
- sedml.SimulatorProducesMultiplePlots
- sedml.SimulatorSupportsAlgorithmParameters
- sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
- sedml.SimulatorSupportsMultipleReportsPerSedDocument
- sedml.SimulatorSupportsMultipleTasksPerSedDocument
- sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes
Skipped 41 test cases:
- published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
- published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
- published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator
- published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system
- published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism
- published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE
- published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler
- published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT
- 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:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle
- published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra
- published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells
- sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments
- sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
- sedml.SimulatorProducesLinear3DPlots
- sedml.SimulatorProducesLogarithmic3DPlots
- sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
- 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

Answer 63 · 2024-09-06T19:04:19.000Z

Failures

combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories (5.6 s)

Test that SED documents in nested directories can be executed

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.6.0.37' could not execute the archive:

  Unknown error

Log:

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:92) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}

ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_86a9e5dd-7675-4863-8bef-9b7b5e576b8f4381790082999841445 []{}

ERROR (ExecutionJob:101) - null, error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:116) - null, error for archive /tmp/in/archive.omex []{}

java.lang.RuntimeException: null, error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.nio.file.ReadOnlyFileSystemException

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?]

	at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$2(OmexHandler.java:76) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:64) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:44) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more

combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories (5.7 s)

Test that SED documents with the same names in nested directories can be executed and their outputs are saved to distinct paths

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.6.0.37' could not execute the archive:

  Unknown error

Log:

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:92) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}

ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_0eaf2710-3a71-49ae-91cf-ce71fa4ddf3417404771232365202264 []{}

ERROR (ExecutionJob:101) - null, error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:116) - null, error for archive /tmp/in/archive.omex []{}

java.lang.RuntimeException: null, error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.nio.file.ReadOnlyFileSystemException

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?]

	at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$2(OmexHandler.java:76) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:64) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:44) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more

combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile (5.6 s)

Test that when a COMBINE/OMEX archive defines a (single) master file, the simulator only executes this file.

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.6.0.37' could not execute the archive:

  Unknown error

Log:

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:92) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}

ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_4761abe5-14d7-4899-b4c9-6968b3f9b12a14986782074410191294 []{}

ERROR (ExecutionJob:101) - null, error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:116) - null, error for archive /tmp/in/archive.omex []{}

java.lang.RuntimeException: null, error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.nio.file.ReadOnlyFileSystemException

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?]

	at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$2(OmexHandler.java:76) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:64) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:44) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more

combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments (5.6 s)

Test that when a COMBINE/OMEX archive does not have a defined master file, the simulator executes all SED-ML files.

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.6.0.37' could not execute the archive:

  Unknown error

Log:

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:92) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}

ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_dbfdace8-ecac-40b3-ab32-77ccb29e321a13676160696900306029 []{}

ERROR (ExecutionJob:101) - null, error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:116) - null, error for archive /tmp/in/archive.omex []{}

java.lang.RuntimeException: null, error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.nio.file.ReadOnlyFileSystemException

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?]

	at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$2(OmexHandler.java:76) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:64) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:44) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more

docker_image.SingularityImageExecutesSimulationsSuccessfully (19.2 s)

Test that the Singularity version of a Docker image can sucessfully execute COMBINE archives

Exception:

The Docker image could not be successfully executed as a Singularity image (error code 1:
  docker: Command recieved::<-i /root/archive.omex -o /root>
  <-i>
  Default case selected
  VCell shall execute <biosimulations -i /root/archive.omex -o /root>
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
   INFO (CLIStandalone:36) - Starting Vcell... []{}
   INFO (BiosimulationsCommand:92) - Beginning execution []{}
   INFO (CLIPythonManager:116) - Initializing Python... []{}
  ERROR (BiosimulationsCommand:116) - Python error caught: <
  Traceback (most recent call last):
    File "<stdin>", line 1, in <module>
    File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/wrapper.py", line 5, in <module>
      from deprecated import deprecated
  ModuleNotFoundError: No module named 'deprecated'
  
  >
  
   []{}
  org.vcell.cli.PythonStreamException: Python error caught: <
  Traceback (most recent call last):
    File "<stdin>", line 1, in <module>
    File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/wrapper.py", line 5, in <module>
      from deprecated import deprecated
  ModuleNotFoundError: No module named 'deprecated'
  
  >
  
  
  	at org.vcell.cli.CLIPythonManager.parsePythonReturn(CLIPythonManager.java:287) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.CLIPythonManager.parsePythonReturn(CLIPythonManager.java:263) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.CLIPythonManager.executeThroughPython(CLIPythonManager.java:192) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.CLIPythonManager.instantiatePythonProcess(CLIPythonManager.java:135) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:94) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]
  	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Log: None

log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives (5.6 s)

Test that simulator logs the execution of COMBINE/OMEX archives

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.6.0.37' could not execute the archive:

  Unknown error

Log:

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:92) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}

ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_f0488b91-9b4d-4071-a12a-86ed73cbb624140695129786205724 []{}

ERROR (ExecutionJob:101) - null, error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:116) - null, error for archive /tmp/in/archive.omex []{}

java.lang.RuntimeException: null, error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.nio.file.ReadOnlyFileSystemException

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?]

	at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$2(OmexHandler.java:76) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:64) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:44) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more

log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments (5.6 s)

Test that simulator logs the execution of individual SED document in COMBINE/OMEX archives

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.6.0.37' could not execute the archive:

  Unknown error

Log:

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:92) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}

ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_b69354c9-5fbd-4eac-9d30-ed6f9b317ce914036025890690575373 []{}

ERROR (ExecutionJob:101) - null, error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:116) - null, error for archive /tmp/in/archive.omex []{}

java.lang.RuntimeException: null, error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.nio.file.ReadOnlyFileSystemException

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?]

	at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$2(OmexHandler.java:76) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:64) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:44) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more

log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs (5.6 s)

Test that simulator logs the execution of individual SED outputs in COMBINE/OMEX archives

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.6.0.37' could not execute the archive:

  Unknown error

Log:

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:92) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}

ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_263b9252-0bd7-4c06-8182-9284f5d3f6fe15149837849000779509 []{}

ERROR (ExecutionJob:101) - null, error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:116) - null, error for archive /tmp/in/archive.omex []{}

java.lang.RuntimeException: null, error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.nio.file.ReadOnlyFileSystemException

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?]

	at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$2(OmexHandler.java:76) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:64) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:44) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more

log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks (5.7 s)

Test that simulator logs the execution of individual SED tasks in COMBINE/OMEX archives

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.6.0.37' could not execute the archive:

  Unknown error

Log:

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:92) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}

ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_c26deb7f-21a7-4ba1-9bb0-dca9505052b616424584102683010756 []{}

ERROR (ExecutionJob:101) - null, error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:116) - null, error for archive /tmp/in/archive.omex []{}

java.lang.RuntimeException: null, error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.nio.file.ReadOnlyFileSystemException

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?]

	at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$2(OmexHandler.java:76) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:64) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:44) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more

published_project.SimulatorCanExecutePublishedProject:sbml-core/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations (5.6 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.6.0.37' could not execute the archive:

  Unknown error

Log:

docker: Command recieved::<-i /tmp/in/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:92) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}

ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_c88210fa-8c88-49d1-be88-ab343bb8cd1a302601716540320092 []{}

ERROR (ExecutionJob:101) - null, error for archive /tmp/in/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex []{}

 | Root(root) | OMEX_EXECUTE(Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex) | **** Error: error message

ERROR (BiosimulationsCommand:116) - null, error for archive /tmp/in/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex []{}

java.lang.RuntimeException: null, error for archive /tmp/in/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.nio.file.ReadOnlyFileSystemException

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?]

	at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$2(OmexHandler.java:76) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:64) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:44) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more

published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg (5.6 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000086

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.6.0.37' could not execute the archive:

  Unknown error

Log:

docker: Command recieved::<-i /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:92) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}

ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_8e07fa38-9ec7-436a-95d0-6175ca952cbb2951944841419183816 []{}

ERROR (ExecutionJob:101) - null, error for archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex []{}

 | Root(root) | OMEX_EXECUTE(Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex) | **** Error: error message

ERROR (BiosimulationsCommand:116) - null, error for archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex []{}

java.lang.RuntimeException: null, error for archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-Fehlberg.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.nio.file.ReadOnlyFileSystemException

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?]

	at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$2(OmexHandler.java:76) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:64) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:44) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more

published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous (5.6 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.6.0.37' could not execute the archive:

  Unknown error

Log:

docker: Command recieved::<-i /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:92) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}

ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous.omex []{}

-------- ...

Answer 64 · 2024-09-06T19:04:19.000Z

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (1.4 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'
  - 'BUNDLE_OUTPUTS'
  - 'COLLECT_COMBINE_ARCHIVE_RESULTS'
  - 'COLLECT_SED_DOCUMENT_RESULTS'
  - 'DEBUG'
  - 'H5_REPORTS_PATH'
  - 'KEEP_INDIVIDUAL_OUTPUTS'
  - 'LOG_PATH'
  - 'OMEX_METADATA_INPUT_FORMAT'
  - 'OMEX_METADATA_OUTPUT_FORMAT'
  - 'OMEX_METADATA_SCHEMA'
  - 'PLOTS_PATH'
  - 'REPORTS_PATH'
  - 'REPORT_FORMATS'
  - 'SAVE_PLOT_DATA'
  - 'VALIDATE_IMAGES'
  - 'VALIDATE_IMPORTED_MODEL_FILES'
  - 'VALIDATE_OMEX_MANIFESTS'
  - 'VALIDATE_OMEX_METADATA'
  - 'VALIDATE_RESULTS'
  - 'VALIDATE_SEDML'
  - 'VALIDATE_SEDML_MODELS'
  - 'VERBOSE'
  - 'VIZ_FORMATS'

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: None

cli.CliDisplaysHelpInline (4.0 s)

Test that a command-line interface provides inline help.

Warnings:

Command-line interfaces should display basic help when no arguments are provided.

The command-line interface displayed the following when no argument was provided:

  docker: Command recieved::<>
  <>
  Default case selected
  VCell shall execute <biosimulations >
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
   INFO (CLIStandalone:36) - Starting Vcell... []{}
  ERROR (BiosimulationsCommand:116) - Cannot invoke "java.io.File.getAbsolutePath()" because "outputDirectory" is null []{}
  java.lang.NullPointerException: Cannot invoke "java.io.File.getAbsolutePath()" because "outputDirectory" is null
  	at org.vcell.cli.CLIRecorder.<init>(CLIRecorder.java:70) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.CLIRecorder.<init>(CLIRecorder.java:59) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.CLIRecorder.<init>(CLIRecorder.java:48) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:50) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]
  	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

  docker: Command recieved::<-h>
  <-h>
  Default case selected
  VCell shall execute <biosimulations -h>
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
   INFO (CLIStandalone:36) - Starting Vcell... []{}
  Usage: �[1mCLIStandalone biosimulations�[21m�[0m [�[33m-dhqv�[39m�[0m] [�[33m-i�[39m�[0m=�[3m<ARCHIVE>�[23m�[0m] [�[33m-o�[39m�[0m=�[3m<OUT_DIR>�[23m�[0m]
  BioSimulators-compliant command-line interface to the vcell simulation program
  <https://vcell.org>.
    �[33m-d�[39m�[0m, �[33m--debug�[39m�[0m               full application debug mode
    �[33m-h�[39m�[0m, �[33m--help�[39m�[0m                show this help message and exit
    �[33m-i�[39m�[0m, �[33m--archive�[39m�[0m=�[3m<ARCHIVE>�[23m�[0m   Path to a COMBINE/OMEX archive file which contains
                                one or more SED-ML-encoded simulation experiments
    �[33m-o�[39m�[0m, �[33m--out-dir�[39m�[0m=�[3m<OUT_DIR>�[23m�[0m   Directory to save outputs
    �[33m-q�[39m�[0m, �[33m--quiet�[39m�[0m               suppress all console output
    �[33m-v�[39m�[0m, �[33m--version�[39m�[0m             show program's version number and exit

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

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

  docker: Command recieved::<--help>
  <--help>
  Default case selected
  VCell shall execute <biosimulations --help>
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
   INFO (CLIStandalone:36) - Starting Vcell... []{}
  Usage: �[1mCLIStandalone biosimulations�[21m�[0m [�[33m-dhqv�[39m�[0m] [�[33m-i�[39m�[0m=�[3m<ARCHIVE>�[23m�[0m] [�[33m-o�[39m�[0m=�[3m<OUT_DIR>�[23m�[0m]
  BioSimulators-compliant command-line interface to the vcell simulation program
  <https://vcell.org>.
    �[33m-d�[39m�[0m, �[33m--debug�[39m�[0m               full application debug mode
    �[33m-h�[39m�[0m, �[33m--help�[39m�[0m                show this help message and exit
    �[33m-i�[39m�[0m, �[33m--archive�[39m�[0m=�[3m<ARCHIVE>�[23m�[0m   Path to a COMBINE/OMEX archive file which contains
                                one or more SED-ML-encoded simulation experiments
    �[33m-o�[39m�[0m, �[33m--out-dir�[39m�[0m=�[3m<OUT_DIR>�[23m�[0m   Directory to save outputs
    �[33m-q�[39m�[0m, �[33m--quiet�[39m�[0m               suppress all console output
    �[33m-v�[39m�[0m, �[33m--version�[39m�[0m             show program's version number and exit

Log: None

docker_image.DeclaresSupportedEnvironmentVariables (0.2 s)

Test if a Docker image declares the environment variables that is supports

Warnings:

Docker images for simulation tools should declare the environment variables that they support.

The Docker image does not declare the following standard environment variables recognized by BioSimulators:
  - 'BUNDLE_OUTPUTS'
  - 'COLLECT_COMBINE_ARCHIVE_RESULTS'
  - 'COLLECT_SED_DOCUMENT_RESULTS'
  - 'DEBUG'
  - 'H5_REPORTS_PATH'
  - 'KEEP_INDIVIDUAL_OUTPUTS'
  - 'LOG_PATH'
  - 'OMEX_METADATA_INPUT_FORMAT'
  - 'OMEX_METADATA_OUTPUT_FORMAT'
  - 'OMEX_METADATA_SCHEMA'
  - 'PLOTS_PATH'
  - 'REPORTS_PATH'
  - 'REPORT_FORMATS'
  - 'SAVE_PLOT_DATA'
  - 'VALIDATE_IMAGES'
  - 'VALIDATE_IMPORTED_MODEL_FILES'
  - 'VALIDATE_OMEX_MANIFESTS'
  - 'VALIDATE_OMEX_METADATA'
  - 'VALIDATE_RESULTS'
  - 'VALIDATE_SEDML'
  - 'VALIDATE_SEDML_MODELS'
  - 'VERBOSE'
  - 'VIZ_FORMATS'

If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator.

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

Log: None

docker_image.HasBioContainersLabels (0.2 s)

Test that a Docker image has BioContainers labels with metadata about the image

Warnings:

Docker images are encouraged to have the following BioContainers labels:
  extra.identifiers.biotools

Log: None

Answer 65 · 2024-09-06T19:04:20.000Z

Skips

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: None

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: None

published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator (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: None

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: None

published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9004
Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_9004 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9004
Algorithm: KISAO_0000030

Reason for skip:

Case requires model formats format_9004 and simulation algorithms KISAO_0000030

Log: None

published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9012
Algorithm: KISAO_0000669

Reason for skip:

Case requires model formats format_9012 and simulation algorithms KISAO_0000669

Log: None

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: None

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: None

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: None

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: None

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: None

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: None

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: None

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: None

published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle (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: None

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: None

published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9010
Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_9010 and simulation algorithms KISAO_0000019

Log: None

sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments (5.7 s)

Test that a simulator can resolve model sources defined by URI fragments (e.g., #model1).

Reason for skip:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.6.0.37' could not execute the archive:

  Unknown error

Log:

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:92) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}

ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_73e329f3-9b45-43ff-95ed-f1654b4283f116035373411407420403 []{}

ERROR (ExecutionJob:101) - null, error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:116) - null, error for archive /tmp/in/archive.omex []{}

java.lang.RuntimeException: null, error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.nio.file.ReadOnlyFileSystemException

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?]

	at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$2(OmexHandler.java:76) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:64) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:44) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more

sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges (6.1 s)

Test that a simulator can resolve model sources defined by URI fragments (e.g., #model1) and inherit the changes of the model.

Reason for skip:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.6.0.37' could not execute the archive:

  Unknown error

Log:

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:92) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}

ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_79e133fb-508d-4d07-ba4a-23c32440e5801763761980137004688 []{}

ERROR (ExecutionJob:101) - null, error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:116) - null, error for archive /tmp/in/archive.omex []{}

java.lang.RuntimeException: null, error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.nio.file.ReadOnlyFileSystemException

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?]

	at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$2(OmexHandler.java:76) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:64) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:44) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more

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: None

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: None

sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions (0.3 s)

Test that that the curated number of output dimensions matches the actual number of output dimensions

Reason for skip:

No curated COMBINE/OMEX archives are available to generate archives for testing

Log: None

sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges (11.2 s)

Test that a simulator supports model changes that involve adding, replacing, and removing model elements.

Reason for skip:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.6.0.37' could not execute the archive:

  Unknown error

Log:

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:92) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}

ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_04383606-ed57-4fc1-9bf5-e0db83fb3148991420147039966606 []{}

ERROR (ExecutionJob:101) - null, error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:116) - null, error for archive /tmp/in/archive.omex []{}

java.lang.RuntimeException: null, error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.nio.file.ReadOnlyFileSystemException

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?]

	at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$2(OmexHandler.java:76) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:64) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:44) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:92) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}

ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_5be530b3-f42b-4362-bf11-2f5be7d709f69931242586256111630 []{}

ERROR (ExecutionJob:101) - null, error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:116) - null, error for archive /tmp/in/archive.omex []{}

java.lang.RuntimeException: null, error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.nio.file.ReadOnlyFileSystemException

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?]

	at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$2(OmexHandler.java:76) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:64) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:44) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more

sedml.SimulatorSupportsComputeModelChanges (11.3 s)

Test that a simulator supports compute model changes

Reason for skip:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.6.0.37' could not execute the archive:

  Unknown error

Log:

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:92) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}

ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_02135631-dad2-471b-8e18-e738514eb89216289184989564879759 []{}

ERROR (ExecutionJob:101) - null, error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:116) - null, error for archive /tmp/in/archive.omex []{}

java.lang.RuntimeException: null, error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.nio.file.ReadOnlyFileSystemException

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?]

	at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$2(OmexHandler.java:76) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:64) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:44) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:92) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}

ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_519eaae6-62ac-4151-bef9-8e5f00b2c37c15578150331501444709 []{}

ERROR (ExecutionJob:101) - null, error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:116) - null, error for archive /tmp/in/archive.omex []{}

java.lang.RuntimeException: null, error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.nio.file.ReadOnlyFileSystemException

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?]

	at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$2(OmexHandler.java:76) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:64) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:44) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more

sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes (5.7 s)

Test that a simulator supports data generators with different shapes

Reason for skip:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.6.0.37' could not execute the archive:

  Unknown error

Log:

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:92) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}

ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_89e467d7-6b58-4323-a159-7496f88ff50b6573029331628960498 []{}

ERROR (ExecutionJob:101) - null, error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:116) - null, error for archive /tmp/in/archive.omex []{}

java.lang.RuntimeException: null, error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.nio.file.ReadOnlyFileSystemException

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?]

	at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$2(OmexHandler.java:76) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:64) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:44) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more

sedml.SimulatorSupportsDataSetsWithDifferentShapes (5.7 s)

Test that a simulator supports data generators with different shapes

Reason for skip:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.6.0.37' could not execute the archive:

  Unknown error

Log:

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:92) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}

ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_2c546259-1a6f-42b1-b5a1-5d57f3c329534188079018959764620 []{}

ERROR (ExecutionJob:101) - null, error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:116) - null, error for archive /tmp/in/archive.omex []{}

java.lang.RuntimeException: null, error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.nio.file.ReadOnlyFileSystemException

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?]

	at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$2(OmexHandler.java:76) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:64) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:44) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more

sedml.SimulatorSupportsModelAttributeChanges (11.3 s)

Test that a simulator supports changes to the attributes of model elements

Reason for skip:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.6.0.37' could not execute the archive:

  Unknown error

Log:

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:92) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}

ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_6423b384-4100-44e9-843e-0f7cb044e0e32495022958145274362 []{}

ERROR (ExecutionJob:101) - null, error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:116) - null, error for archive /tmp/in/archive.omex []{}

java.lang.RuntimeException: null, error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.nio.file.ReadOnlyFileSystemException

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?]

	at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$2(OmexHandler.java:76) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:64) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:44) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugi ...

Answer 66 · 2024-09-06T19:04:20.000Z

- After correcting your simulator, please edit the first block of this issue to re-initiate this validation.
- 
- The complete log of your validation/submission job, including further information about the failure, is available for 90 days [here](https://github.com/biosimulators/Biosimulators/actions/runs/10743688818). The results of the validation of your image will also be available shortly as a JSON file. A link to this file will be available from the "Artifacts" section at the bottom of [this page](https://github.com/biosimulators/Biosimulators/actions/runs/10743688818).

Answer 67 · 2024-09-11T13:44:49.000Z

Thank you @CodeByDrescher 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 for 90 days 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 for 90 days from the "Artifacts" section at the bottom of this page.

Answer 68 · 2024-09-11T13:44:55.000Z

The specifications of your simulator is valid!

Answer 69 · 2024-09-11T13:52:00.000Z

Summary of tests

Executed 74 test cases
Passed 7 test cases:
- cli.CliDescribesSupportedEnvironmentVariablesInline
- cli.CliDisplaysHelpInline
- cli.CliDisplaysVersionInformationInline
- docker_image.DeclaresSupportedEnvironmentVariables
- docker_image.DefaultUserIsRoot
- docker_image.HasBioContainersLabels
- docker_image.HasOciLabels
Failed 26 test cases:
- combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories
- combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories
- combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile
- combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments
- docker_image.SingularityImageExecutesSimulationsSuccessfully
- log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
- log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
- log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
- log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks
- 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-Fehlberg
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator
- 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
- published_project.SimulatorCanExecutePublishedProject:vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength
- results_report.SimulatorGeneratesReportsOfSimulationResults
- sedml.SimulatorProducesLinear2DPlots
- sedml.SimulatorProducesLogarithmic2DPlots
- sedml.SimulatorProducesMultiplePlots
- sedml.SimulatorSupportsAlgorithmParameters
- sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
- sedml.SimulatorSupportsMultipleReportsPerSedDocument
- sedml.SimulatorSupportsMultipleTasksPerSedDocument
- sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes
Skipped 41 test cases:
- published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
- published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
- published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator
- published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system
- published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism
- published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE
- published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler
- published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT
- 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:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle
- published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra
- published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells
- sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments
- sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
- sedml.SimulatorProducesLinear3DPlots
- sedml.SimulatorProducesLogarithmic3DPlots
- sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
- 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

Answer 70 · 2024-09-11T13:52:00.000Z

Failures

combine_archive.CombineArchiveHasSedDocumentsInNestedDirectories (5.8 s)

Test that SED documents in nested directories can be executed

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.6.0.39' could not execute the archive:

  Unknown error

Log:

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:92) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}

ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_9b9cdbbd-3b7b-416a-8af9-da72a8ea47ef2371831271469457351 []{}

11.09 13:47:16 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@200: found no entry for description 0 in /subdir/metadata.rdf (about=/http:/omex-library.org/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex).

11.09 13:47:16 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@200: found no entry for description 1 in /subdir/metadata.rdf (about=/http:/omex-library.org/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex/BIOMD0000000912_sim.sedml/Figure_1_bottom_left).

11.09 13:47:16 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 2 in /subdir/metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:16 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 3 in /subdir/metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:16 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 4 in /subdir/metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:16 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 5 in /subdir/metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:16 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 6 in /subdir/metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:16 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 7 in /subdir/metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:16 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 8 in /subdir/metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:16 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 9 in /subdir/metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:16 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 10 in /subdir/metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:16 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 11 in /subdir/metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:16 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 12 in /subdir/metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:16 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 13 in /subdir/metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:16 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 14 in /subdir/metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:16 WARNS de.unirostock.sems.cbarchive.CombineArchive@1536: couldn't look into directory / (throwing java.nio.file.ReadOnlyFileSystemException: null)

ERROR (ExecutionJob:101) - Error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:116) - Unexpected Error in BioSimulations execution: []{}

java.lang.RuntimeException: Error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.RuntimeException: Unable to delete metadata.rdf file from OMEX archive: 

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:118) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:55) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more

Caused by: java.nio.file.ReadOnlyFileSystemException

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?]

	at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$5(OmexHandler.java:108) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:96) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:55) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more

combine_archive.CombineArchiveHasSedDocumentsWithSameNamesInDifferentInNestedDirectories (5.9 s)

Test that SED documents with the same names in nested directories can be executed and their outputs are saved to distinct paths

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.6.0.39' could not execute the archive:

  Unknown error

Log:

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:92) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}

ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_35c42ff7-8a0e-48b8-985b-611bf940a35a1125556806065559124 []{}

11.09 13:47:22 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@200: found no entry for description 0 in /subdir/metadata.rdf (about=/http:/omex-library.org/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex).

11.09 13:47:22 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@200: found no entry for description 1 in /subdir/metadata.rdf (about=/http:/omex-library.org/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex/BIOMD0000000912_sim.sedml/Figure_1_bottom_left).

11.09 13:47:22 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 2 in /subdir/metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:22 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 3 in /subdir/metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:22 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 4 in /subdir/metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:22 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 5 in /subdir/metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:22 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 6 in /subdir/metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:22 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 7 in /subdir/metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:22 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 8 in /subdir/metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:22 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 9 in /subdir/metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:22 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 10 in /subdir/metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:22 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 11 in /subdir/metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:22 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 12 in /subdir/metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:22 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 13 in /subdir/metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:22 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 14 in /subdir/metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:22 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@200: found no entry for description 0 in /subdir__copy/metadata.rdf (about=/http:/omex-library.org/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex).

11.09 13:47:22 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@200: found no entry for description 1 in /subdir__copy/metadata.rdf (about=/http:/omex-library.org/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex/BIOMD0000000912_sim.sedml/Figure_1_bottom_left).

11.09 13:47:22 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 2 in /subdir__copy/metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:22 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 3 in /subdir__copy/metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:22 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 4 in /subdir__copy/metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:22 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 5 in /subdir__copy/metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:22 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 6 in /subdir__copy/metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:22 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 7 in /subdir__copy/metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:22 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 8 in /subdir__copy/metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:22 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 9 in /subdir__copy/metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:22 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 10 in /subdir__copy/metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:22 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 11 in /subdir__copy/metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:22 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 12 in /subdir__copy/metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:22 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 13 in /subdir__copy/metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:22 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 14 in /subdir__copy/metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:22 WARNS de.unirostock.sems.cbarchive.CombineArchive@1536: couldn't look into directory / (throwing java.nio.file.ReadOnlyFileSystemException: null)

ERROR (ExecutionJob:101) - Error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:116) - Unexpected Error in BioSimulations execution: []{}

java.lang.RuntimeException: Error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.RuntimeException: Unable to delete metadata.rdf file from OMEX archive: 

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:118) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:55) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more

Caused by: java.nio.file.ReadOnlyFileSystemException

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?]

	at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$5(OmexHandler.java:108) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:96) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:55) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more

combine_archive.WhenACombineArchiveHasAMasterFileSimulatorOnlyExecutesThisFile (5.8 s)

Test that when a COMBINE/OMEX archive defines a (single) master file, the simulator only executes this file.

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.6.0.39' could not execute the archive:

  Unknown error

Log:

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:92) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}

ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_349d0536-41c5-421c-acbf-dd8955297521637779142836508798 []{}

11.09 13:47:28 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@200: found no entry for description 0 in /metadata.rdf (about=/http:/omex-library.org/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex).

11.09 13:47:28 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@200: found no entry for description 1 in /metadata.rdf (about=/http:/omex-library.org/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex/BIOMD0000000912_sim.sedml/Figure_1_bottom_left).

11.09 13:47:28 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 2 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:28 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 3 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:28 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 4 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:28 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 5 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:28 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 6 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:28 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 7 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:28 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 8 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:28 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 9 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:28 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 10 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:28 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 11 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:28 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 12 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:28 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 13 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:28 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 14 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

ERROR (ExecutionJob:101) - Error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:116) - Unexpected Error in BioSimulations execution: []{}

java.lang.RuntimeException: Error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.RuntimeException: Unable to delete metadata.rdf file from OMEX archive: 

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:118) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:55) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more

Caused by: java.nio.file.ReadOnlyFileSystemException

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?]

	at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$5(OmexHandler.java:108) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:96) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:55) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more

combine_archive.WhenACombineArchiveHasNoMasterFileSimulatorExecutesAllSedDocuments (5.7 s)

Test that when a COMBINE/OMEX archive does not have a defined master file, the simulator executes all SED-ML files.

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.6.0.39' could not execute the archive:

  Unknown error

Log:

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:92) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}

ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_9e0acd41-d79a-4093-8059-da6ba602a6d96414648084295226730 []{}

11.09 13:47:33 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@200: found no entry for description 0 in /metadata.rdf (about=/http:/omex-library.org/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex).

11.09 13:47:33 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@200: found no entry for description 1 in /metadata.rdf (about=/http:/omex-library.org/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex/BIOMD0000000912_sim.sedml/Figure_1_bottom_left).

11.09 13:47:33 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 2 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:33 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 3 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:33 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 4 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:33 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 5 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:33 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 6 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:33 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 7 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:33 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 8 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:33 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 9 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:33 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 10 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:33 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 11 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:33 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 12 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:33 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 13 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:33 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 14 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

ERROR (ExecutionJob:101) - Error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:116) - Unexpected Error in BioSimulations execution: []{}

java.lang.RuntimeException: Error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.RuntimeException: Unable to delete metadata.rdf file from OMEX archive: 

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:118) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:55) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more

Caused by: java.nio.file.ReadOnlyFileSystemException

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?]

	at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$5(OmexHandler.java:108) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:96) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:55) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more

docker_image.SingularityImageExecutesSimulationsSuccessfully (19.1 s)

Test that the Singularity version of a Docker image can sucessfully execute COMBINE archives

Exception:

The Docker image could not be successfully executed as a Singularity image (error code 1:
  docker: Command recieved::<-i /root/archive.omex -o /root>
  <-i>
  Default case selected
  VCell shall execute <biosimulations -i /root/archive.omex -o /root>
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
   INFO (CLIStandalone:36) - Starting Vcell... []{}
   INFO (BiosimulationsCommand:92) - Beginning execution []{}
   INFO (CLIPythonManager:116) - Initializing Python... []{}
  ERROR (BiosimulationsCommand:116) - Unexpected Error in BioSimulations execution: []{}
  org.vcell.cli.PythonStreamException: Python error caught: <
  Traceback (most recent call last):
    File "<stdin>", line 1, in <module>
    File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/wrapper.py", line 5, in <module>
      from deprecated import deprecated
  ModuleNotFoundError: No module named 'deprecated'
  
  >
  
  
  	at org.vcell.cli.CLIPythonManager.parsePythonReturn(CLIPythonManager.java:287) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.CLIPythonManager.parsePythonReturn(CLIPythonManager.java:263) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.CLIPythonManager.executeThroughPython(CLIPythonManager.java:192) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.CLIPythonManager.instantiatePythonProcess(CLIPythonManager.java:135) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:94) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]
  	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Log: None

log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives (5.7 s)

Test that simulator logs the execution of COMBINE/OMEX archives

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.6.0.39' could not execute the archive:

  Unknown error

Log:

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:92) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}

ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_65a41b01-fbc0-43a4-8b06-25fe61f452f76023235200864128597 []{}

11.09 13:50:55 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@200: found no entry for description 0 in /metadata.rdf (about=/http:/omex-library.org/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex).

11.09 13:50:55 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@200: found no entry for description 1 in /metadata.rdf (about=/http:/omex-library.org/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex/BIOMD0000000912_sim.sedml/Figure_1_bottom_left).

11.09 13:50:55 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 2 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:50:55 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 3 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:50:55 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 4 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:50:55 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 5 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:50:55 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 6 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:50:55 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 7 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:50:55 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 8 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:50:55 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 9 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:50:55 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 10 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:50:55 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 11 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:50:55 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 12 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:50:55 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 13 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:50:55 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 14 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

ERROR (ExecutionJob:101) - Error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:116) - Unexpected Error in BioSimulations execution: []{}

java.lang.RuntimeException: Error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.RuntimeException: Unable to delete metadata.rdf file from OMEX archive: 

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:118) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:55) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more

Caused by: java.nio.file.ReadOnlyFileSystemException

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?]

	at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$5(OmexHandler.java:108) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:96) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:55) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more

log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments (5.7 s)

Test that simulator logs the execution of individual SED document in COMBINE/OMEX archives

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.6.0.39' could not execute the archive:

  Unknown error

Log:

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:92) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}

ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_ead21a80-1cc0-4f38-aaa5-70c2de8ece1d12308824378913054284 []{}

11.09 13:51:01 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@200: found no entry for description 0 in /metadata.rdf (about=/http:/omex-library.org/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex).

11.09 13:51:01 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@200: found no entry for description 1 in /metadata.rdf (about=/http:/omex-library.org/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex/BIOMD0000000912_sim.sedml/Figure_1_bottom_left).

11.09 13:51:01 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 2 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:51:01 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 3 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:51:01 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 4 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:51:01 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 5 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:51:01 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 6 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:51:01 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 7 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:51:01 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 8 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:51:01 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 9 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:51:01 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 10 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:51:01 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 11 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:51:01 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 12 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:51:01 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 13 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:51:01 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 14 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

ERROR (ExecutionJob:101) - Error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:116) - Unexpected Error in BioSimulations execution: []{}

java.lang.RuntimeException: Error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.RuntimeException: Unable to delete metadata.rdf file from OMEX archive: 

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:118) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:55) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more

Caused by: java.nio.file.ReadOnlyFileSystemException

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?]

	at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$5(OmexHandler.java:108) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:96) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:55) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more

log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs (5.7 s)

Test that simulator logs the execution of individual SED outputs in COMBINE/OMEX archives

Exception:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.6.0.39' could not execute the archive:

  Unknown error

Log:

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:92) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}

ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_f49a1243-6827-44ce-8bd5-e0941dc078166080963819574298542 []{}

11.09 13:51:07 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@200: found no entry for description 0 in /metadata.rdf (about=/http:/omex-library.org/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex).

11.09 13:51:07 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@200: found no entry for description 1 in /metadata.rdf (about=/http:/omex-library.org/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex/BIOMD0000000912_sim.sedml/Figure_1_bottom_left).

11.09 13:51:07 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 2 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:51:07 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 3 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:51:07 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 4 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:51:07 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 5 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:51:07 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 6 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:51:07 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 7 in /metadata.rdf does not contain an  ...

Answer 71 · 2024-09-11T13:52:01.000Z

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (1.5 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'
  - 'BUNDLE_OUTPUTS'
  - 'COLLECT_COMBINE_ARCHIVE_RESULTS'
  - 'COLLECT_SED_DOCUMENT_RESULTS'
  - 'DEBUG'
  - 'H5_REPORTS_PATH'
  - 'KEEP_INDIVIDUAL_OUTPUTS'
  - 'LOG_PATH'
  - 'OMEX_METADATA_INPUT_FORMAT'
  - 'OMEX_METADATA_OUTPUT_FORMAT'
  - 'OMEX_METADATA_SCHEMA'
  - 'PLOTS_PATH'
  - 'REPORTS_PATH'
  - 'REPORT_FORMATS'
  - 'SAVE_PLOT_DATA'
  - 'VALIDATE_IMAGES'
  - 'VALIDATE_IMPORTED_MODEL_FILES'
  - 'VALIDATE_OMEX_MANIFESTS'
  - 'VALIDATE_OMEX_METADATA'
  - 'VALIDATE_RESULTS'
  - 'VALIDATE_SEDML'
  - 'VALIDATE_SEDML_MODELS'
  - 'VERBOSE'
  - 'VIZ_FORMATS'

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: None

cli.CliDisplaysHelpInline (4.2 s)

Test that a command-line interface provides inline help.

Warnings:

Command-line interfaces should display basic help when no arguments are provided.

The command-line interface displayed the following when no argument was provided:

  docker: Command recieved::<>
  <>
  Default case selected
  VCell shall execute <biosimulations >
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
   INFO (CLIStandalone:36) - Starting Vcell... []{}
  ERROR (BiosimulationsCommand:116) - Unexpected Error in BioSimulations execution: []{}
  java.lang.NullPointerException: Cannot invoke "java.io.File.getAbsolutePath()" because "outputDirectory" is null
  	at org.vcell.cli.CLIRecorder.<init>(CLIRecorder.java:70) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.CLIRecorder.<init>(CLIRecorder.java:59) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.CLIRecorder.<init>(CLIRecorder.java:48) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:50) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]
  	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

  docker: Command recieved::<-h>
  <-h>
  Default case selected
  VCell shall execute <biosimulations -h>
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
   INFO (CLIStandalone:36) - Starting Vcell... []{}
  Usage: �[1mCLIStandalone biosimulations�[21m�[0m [�[33m-dhqv�[39m�[0m] [�[33m-i�[39m�[0m=�[3m<ARCHIVE>�[23m�[0m] [�[33m-o�[39m�[0m=�[3m<OUT_DIR>�[23m�[0m]
  BioSimulators-compliant command-line interface to the vcell simulation program
  <https://vcell.org>.
    �[33m-d�[39m�[0m, �[33m--debug�[39m�[0m               full application debug mode
    �[33m-h�[39m�[0m, �[33m--help�[39m�[0m                show this help message and exit
    �[33m-i�[39m�[0m, �[33m--archive�[39m�[0m=�[3m<ARCHIVE>�[23m�[0m   Path to a COMBINE/OMEX archive file which contains
                                one or more SED-ML-encoded simulation experiments
    �[33m-o�[39m�[0m, �[33m--out-dir�[39m�[0m=�[3m<OUT_DIR>�[23m�[0m   Directory to save outputs
    �[33m-q�[39m�[0m, �[33m--quiet�[39m�[0m               suppress all console output
    �[33m-v�[39m�[0m, �[33m--version�[39m�[0m             show program's version number and exit

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

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

  docker: Command recieved::<--help>
  <--help>
  Default case selected
  VCell shall execute <biosimulations --help>
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
   INFO (CLIStandalone:36) - Starting Vcell... []{}
  Usage: �[1mCLIStandalone biosimulations�[21m�[0m [�[33m-dhqv�[39m�[0m] [�[33m-i�[39m�[0m=�[3m<ARCHIVE>�[23m�[0m] [�[33m-o�[39m�[0m=�[3m<OUT_DIR>�[23m�[0m]
  BioSimulators-compliant command-line interface to the vcell simulation program
  <https://vcell.org>.
    �[33m-d�[39m�[0m, �[33m--debug�[39m�[0m               full application debug mode
    �[33m-h�[39m�[0m, �[33m--help�[39m�[0m                show this help message and exit
    �[33m-i�[39m�[0m, �[33m--archive�[39m�[0m=�[3m<ARCHIVE>�[23m�[0m   Path to a COMBINE/OMEX archive file which contains
                                one or more SED-ML-encoded simulation experiments
    �[33m-o�[39m�[0m, �[33m--out-dir�[39m�[0m=�[3m<OUT_DIR>�[23m�[0m   Directory to save outputs
    �[33m-q�[39m�[0m, �[33m--quiet�[39m�[0m               suppress all console output
    �[33m-v�[39m�[0m, �[33m--version�[39m�[0m             show program's version number and exit

Log: None

docker_image.DeclaresSupportedEnvironmentVariables (0.2 s)

Test if a Docker image declares the environment variables that is supports

Warnings:

Docker images for simulation tools should declare the environment variables that they support.

The Docker image does not declare the following standard environment variables recognized by BioSimulators:
  - 'BUNDLE_OUTPUTS'
  - 'COLLECT_COMBINE_ARCHIVE_RESULTS'
  - 'COLLECT_SED_DOCUMENT_RESULTS'
  - 'DEBUG'
  - 'H5_REPORTS_PATH'
  - 'KEEP_INDIVIDUAL_OUTPUTS'
  - 'LOG_PATH'
  - 'OMEX_METADATA_INPUT_FORMAT'
  - 'OMEX_METADATA_OUTPUT_FORMAT'
  - 'OMEX_METADATA_SCHEMA'
  - 'PLOTS_PATH'
  - 'REPORTS_PATH'
  - 'REPORT_FORMATS'
  - 'SAVE_PLOT_DATA'
  - 'VALIDATE_IMAGES'
  - 'VALIDATE_IMPORTED_MODEL_FILES'
  - 'VALIDATE_OMEX_MANIFESTS'
  - 'VALIDATE_OMEX_METADATA'
  - 'VALIDATE_RESULTS'
  - 'VALIDATE_SEDML'
  - 'VALIDATE_SEDML_MODELS'
  - 'VERBOSE'
  - 'VIZ_FORMATS'

If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator.

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

Log: None

docker_image.HasBioContainersLabels (0.2 s)

Test that a Docker image has BioContainers labels with metadata about the image

Warnings:

Docker images are encouraged to have the following BioContainers labels:
  extra.identifiers.biotools

Log: None

Answer 72 · 2024-09-11T13:52:01.000Z

Skips

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: None

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: None

published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator (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: None

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: None

published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9004
Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_9004 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9004
Algorithm: KISAO_0000030

Reason for skip:

Case requires model formats format_9004 and simulation algorithms KISAO_0000030

Log: None

published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9012
Algorithm: KISAO_0000669

Reason for skip:

Case requires model formats format_9012 and simulation algorithms KISAO_0000669

Log: None

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: None

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: None

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: None

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: None

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: None

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: None

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: None

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: None

published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle (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: None

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: None

published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9010
Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_9010 and simulation algorithms KISAO_0000019

Log: None

sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments (5.8 s)

Test that a simulator can resolve model sources defined by URI fragments (e.g., #model1).

Reason for skip:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.6.0.39' could not execute the archive:

  Unknown error

Log:

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:92) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}

ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_7c0ee0e7-99b8-4c2d-b14a-7bbda198eff68087810596559368451 []{}

11.09 13:47:39 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@200: found no entry for description 0 in /metadata.rdf (about=/http:/omex-library.org/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex).

11.09 13:47:39 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@200: found no entry for description 1 in /metadata.rdf (about=/http:/omex-library.org/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex/BIOMD0000000912_sim.sedml/Figure_1_bottom_left).

11.09 13:47:39 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 2 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:39 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 3 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:39 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 4 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:39 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 5 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:39 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 6 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:39 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 7 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:39 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 8 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:39 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 9 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:39 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 10 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:39 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 11 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:39 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 12 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:39 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 13 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:39 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 14 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

ERROR (ExecutionJob:101) - Error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:116) - Unexpected Error in BioSimulations execution: []{}

java.lang.RuntimeException: Error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.RuntimeException: Unable to delete metadata.rdf file from OMEX archive: 

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:118) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:55) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more

Caused by: java.nio.file.ReadOnlyFileSystemException

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?]

	at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$5(OmexHandler.java:108) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:96) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:55) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more

sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges (5.7 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/virtualcell/biosimulators_vcell:7.6.0.39' could not execute the archive:

  Unknown error

Log:

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:92) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}

ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_91435a56-1a58-49eb-8732-1cbcee07210c14312703251139517793 []{}

11.09 13:47:45 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@200: found no entry for description 0 in /metadata.rdf (about=/http:/omex-library.org/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex).

11.09 13:47:45 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@200: found no entry for description 1 in /metadata.rdf (about=/http:/omex-library.org/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex/BIOMD0000000912_sim.sedml/Figure_1_bottom_left).

11.09 13:47:45 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 2 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:45 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 3 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:45 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 4 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:45 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 5 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:45 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 6 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:45 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 7 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:45 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 8 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:45 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 9 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:45 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 10 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:45 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 11 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:45 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 12 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:45 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 13 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:47:45 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 14 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

ERROR (ExecutionJob:101) - Error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:116) - Unexpected Error in BioSimulations execution: []{}

java.lang.RuntimeException: Error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.RuntimeException: Unable to delete metadata.rdf file from OMEX archive: 

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:118) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:55) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more

Caused by: java.nio.file.ReadOnlyFileSystemException

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?]

	at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$5(OmexHandler.java:108) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:96) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:55) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more

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: None

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: None

sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions (0.3 s)

Test that that the curated number of output dimensions matches the actual number of output dimensions

Reason for skip:

No curated COMBINE/OMEX archives are available to generate archives for testing

Log: None

sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges (11.5 s)

Test that a simulator supports model changes that involve adding, replacing, and removing model elements.

Reason for skip:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.6.0.39' could not execute the archive:

  Unknown error

Log:

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:92) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}

ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_d7df9c48-e211-4a3a-8223-e83f7addd8029384675044900882096 []{}

11.09 13:48:09 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@200: found no entry for description 0 in /metadata.rdf (about=/http:/omex-library.org/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex).

11.09 13:48:09 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@200: found no entry for description 1 in /metadata.rdf (about=/http:/omex-library.org/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex/BIOMD0000000912_sim.sedml/Figure_1_bottom_left).

11.09 13:48:09 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 2 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:48:09 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 3 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:48:09 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 4 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:48:09 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 5 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:48:09 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 6 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:48:09 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 7 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:48:09 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 8 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:48:09 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 9 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:48:09 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 10 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:48:09 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 11 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:48:09 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 12 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:48:09 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 13 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:48:09 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 14 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

ERROR (ExecutionJob:101) - Error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:116) - Unexpected Error in BioSimulations execution: []{}

java.lang.RuntimeException: Error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.RuntimeException: Unable to delete metadata.rdf file from OMEX archive: 

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:118) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:55) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more

Caused by: java.nio.file.ReadOnlyFileSystemException

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?]

	at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$5(OmexHandler.java:108) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:96) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:55) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:92) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}

ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_eaa43c04-6af3-45cb-966a-c2832ecc6e9510793499441033713959 []{}

11.09 13:48:15 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@200: found no entry for description 0 in /metadata.rdf (about=/http:/omex-library.org/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex).

11.09 13:48:15 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@200: found no entry for description 1 in /metadata.rdf (about=/http:/omex-library.org/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex/BIOMD0000000912_sim.sedml/Figure_1_bottom_left).

11.09 13:48:15 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 2 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:48:15 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 3 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:48:15 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 4 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:48:15 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 5 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:48:15 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 6 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:48:15 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 7 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:48:15 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 8 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:48:15 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 9 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:48:15 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 10 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:48:15 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 11 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:48:15 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 12 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:48:15 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 13 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:48:15 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 14 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

ERROR (ExecutionJob:101) - Error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:116) - Unexpected Error in BioSimulations execution: []{}

java.lang.RuntimeException: Error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.RuntimeException: Unable to delete metadata.rdf file from OMEX archive: 

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:118) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:55) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more

Caused by: java.nio.file.ReadOnlyFileSystemException

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?]

	at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$5(OmexHandler.java:108) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:96) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:55) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more

sedml.SimulatorSupportsComputeModelChanges (11.8 s)

Test that a simulator supports compute model changes

Reason for skip:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.6.0.39' could not execute the archive:

  Unknown error

Log:

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:92) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}

ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_246290e8-a6c5-4370-aa95-5e807a084fff14695625839570597861 []{}

11.09 13:48:26 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@200: found no entry for description 0 in /metadata.rdf (about=/http:/omex-library.org/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex).

11.09 13:48:26 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@200: found no entry for description 1 in /metadata.rdf (about=/http:/omex-library.org/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex/BIOMD0000000912_sim.sedml/Figure_1_bottom_left).

11.09 13:48:26 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 2 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:48:26 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 3 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:48:26 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 4 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:48:26 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 5 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:48:26 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 6 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:48:26 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 7 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:48:26 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 8 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:48:26 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 9 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:48:26 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 10 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:48:26 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 11 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:48:26 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 12 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:48:26 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 13 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:48:26 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 14 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

ERROR (ExecutionJob:101) - Error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:116) - Unexpected Error in BioSimulations execution: []{}

java.lang.RuntimeException: Error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.RuntimeException: Unable to delete metadata.rdf file from OMEX archive: 

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:118) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:55) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more

Caused by: java.nio.file.ReadOnlyFileSystemException

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystem.checkWritable(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystem.deleteFile(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipPath.delete(Unknown Source) ~[jdk.zipfs:?]

	at jdk.zipfs@17.0.12/jdk.nio.zipfs.ZipFileSystemProvider.delete(Unknown Source) ~[jdk.zipfs:?]

	at java.base/java.nio.file.Files.delete(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.lambda$replaceMetadataRdfFiles$5(OmexHandler.java:108) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$2$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline$3$1.accept(Unknown Source) ~[?:?]

	at java.base/java.util.Iterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.Spliterators$IteratorSpliterator.forEachRemaining(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.copyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.wrapAndCopyInto(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ForEachOps$ForEachOp$OfRef.evaluateSequential(Unknown Source) ~[?:?]

	at java.base/java.util.stream.AbstractPipeline.evaluate(Unknown Source) ~[?:?]

	at java.base/java.util.stream.ReferencePipeline.forEach(Unknown Source) ~[?:?]

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:96) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:55) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:92) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:134) - Preparing output directory... []{}

ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}

ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/in/archive.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_177b5599-fa5e-43db-b0d3-537e68518a6117520338152926912490 []{}

11.09 13:48:32 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@200: found no entry for description 0 in /metadata.rdf (about=/http:/omex-library.org/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex).

11.09 13:48:32 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@200: found no entry for description 1 in /metadata.rdf (about=/http:/omex-library.org/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex/BIOMD0000000912_sim.sedml/Figure_1_bottom_left).

11.09 13:48:32 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 2 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:48:32 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 3 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:48:32 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 4 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:48:32 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 5 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:48:32 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 6 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:48:32 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 7 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:48:32 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 8 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:48:32 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 9 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:48:32 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 10 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:48:32 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 11 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:48:32 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 12 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:48:32 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 13 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 13:48:32 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 14 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

ERROR (ExecutionJob:101) - Error for archive /tmp/in/archive.omex []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | **** Error: error message

ERROR (BiosimulationsCommand:116) - Unexpected Error in BioSimulations execution: []{}

java.lang.RuntimeException: Error for archive /tmp/in/archive.omex

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:106) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:238) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:142) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:159) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.RuntimeException: Unable to delete metadata.rdf file from OMEX archive: 

	at org.vcell.cli.run.OmexHandler.replaceMetadataRdfFiles(OmexHandler.java:118) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.OmexHandler.<init>(OmexHandler.java:55) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.preprocessArchive(ExecutionJob.java:90) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	... 14 more

Caused by: java.nio.file.ReadOnlyFileSystemException

	at jdk.zipfs@17.0.12/ ...

Answer 73 · 2024-09-11T13:52:02.000Z

- After correcting your simulator, please edit the first block of this issue to re-initiate this validation.
- 
- The complete log of your validation/submission job, including further information about the failure, is available for 90 days [here](https://github.com/biosimulators/Biosimulators/actions/runs/10812896718). The results of the validation of your image will also be available shortly as a JSON file. A link to this file will be available from the "Artifacts" section at the bottom of [this page](https://github.com/biosimulators/Biosimulators/actions/runs/10812896718).

Answer 74 · 2024-09-11T17:00:37.000Z

Thank you @CodeByDrescher 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 for 90 days 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 for 90 days from the "Artifacts" section at the bottom of this page.

Answer 75 · 2024-09-11T17:00:43.000Z

The specifications of your simulator is valid!

Answer 76 · 2024-09-11T17:15:43.000Z

Summary of tests

Executed 74 test cases
Passed 37 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
- log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
- log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
- log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
- log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks
- 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-Fehlberg
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator
- 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
- published_project.SimulatorCanExecutePublishedProject:vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength
- results_report.SimulatorGeneratesReportsOfSimulationResults
- sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments
- sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
- sedml.SimulatorProducesLinear2DPlots
- sedml.SimulatorProducesLogarithmic2DPlots
- sedml.SimulatorProducesMultiplePlots
- sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges
- sedml.SimulatorSupportsAlgorithmParameters
- sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes
- sedml.SimulatorSupportsDataSetsWithDifferentShapes
- sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
- sedml.SimulatorSupportsMultipleReportsPerSedDocument
- sedml.SimulatorSupportsMultipleTasksPerSedDocument
- sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes
Failed 1 test cases:
- docker_image.SingularityImageExecutesSimulationsSuccessfully
Skipped 36 test cases:
- published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
- published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
- published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator
- published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system
- published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism
- published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE
- published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler
- published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT
- 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:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle
- published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra
- published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells
- sedml.SimulatorProducesLinear3DPlots
- sedml.SimulatorProducesLogarithmic3DPlots
- sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
- sedml.SimulatorSupportsComputeModelChanges
- 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

Answer 77 · 2024-09-11T17:15:44.000Z

Failures

docker_image.SingularityImageExecutesSimulationsSuccessfully (19.5 s)

Test that the Singularity version of a Docker image can sucessfully execute COMBINE archives

Exception:

The Docker image could not be successfully executed as a Singularity image (error code 1:
  docker: Command recieved::<-i /root/archive.omex -o /root>
  <-i>
  Default case selected
  VCell shall execute <biosimulations -i /root/archive.omex -o /root>
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
   INFO (CLIStandalone:36) - Starting Vcell... []{}
   INFO (BiosimulationsCommand:92) - Beginning execution []{}
   INFO (CLIPythonManager:116) - Initializing Python... []{}
  ERROR (BiosimulationsCommand:116) - Unexpected Error in BioSimulations execution: []{}
  org.vcell.cli.PythonStreamException: Python error caught: <
  Traceback (most recent call last):
    File "<stdin>", line 1, in <module>
    File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/wrapper.py", line 5, in <module>
      from deprecated import deprecated
  ModuleNotFoundError: No module named 'deprecated'
  
  >
  
  
  	at org.vcell.cli.CLIPythonManager.parsePythonReturn(CLIPythonManager.java:287) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.CLIPythonManager.parsePythonReturn(CLIPythonManager.java:263) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.CLIPythonManager.executeThroughPython(CLIPythonManager.java:192) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.CLIPythonManager.instantiatePythonProcess(CLIPythonManager.java:135) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:94) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]
  	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Log: None

Answer 78 · 2024-09-11T17:15:44.000Z

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (1.8 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'
  - 'BUNDLE_OUTPUTS'
  - 'COLLECT_COMBINE_ARCHIVE_RESULTS'
  - 'COLLECT_SED_DOCUMENT_RESULTS'
  - 'DEBUG'
  - 'H5_REPORTS_PATH'
  - 'KEEP_INDIVIDUAL_OUTPUTS'
  - 'LOG_PATH'
  - 'OMEX_METADATA_INPUT_FORMAT'
  - 'OMEX_METADATA_OUTPUT_FORMAT'
  - 'OMEX_METADATA_SCHEMA'
  - 'PLOTS_PATH'
  - 'REPORTS_PATH'
  - 'REPORT_FORMATS'
  - 'SAVE_PLOT_DATA'
  - 'VALIDATE_IMAGES'
  - 'VALIDATE_IMPORTED_MODEL_FILES'
  - 'VALIDATE_OMEX_MANIFESTS'
  - 'VALIDATE_OMEX_METADATA'
  - 'VALIDATE_RESULTS'
  - 'VALIDATE_SEDML'
  - 'VALIDATE_SEDML_MODELS'
  - 'VERBOSE'
  - 'VIZ_FORMATS'

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: None

cli.CliDisplaysHelpInline (4.5 s)

Test that a command-line interface provides inline help.

Warnings:

Command-line interfaces should display basic help when no arguments are provided.

The command-line interface displayed the following when no argument was provided:

  docker: Command recieved::<>
  <>
  Default case selected
  VCell shall execute <biosimulations >
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
   INFO (CLIStandalone:36) - Starting Vcell... []{}
  ERROR (BiosimulationsCommand:116) - Unexpected Error in BioSimulations execution: []{}
  java.lang.NullPointerException: Cannot invoke "java.io.File.getAbsolutePath()" because "outputDirectory" is null
  	at org.vcell.cli.CLIRecorder.<init>(CLIRecorder.java:70) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.CLIRecorder.<init>(CLIRecorder.java:59) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.CLIRecorder.<init>(CLIRecorder.java:48) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:50) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]
  	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

  docker: Command recieved::<-h>
  <-h>
  Default case selected
  VCell shall execute <biosimulations -h>
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
   INFO (CLIStandalone:36) - Starting Vcell... []{}
  Usage: �[1mCLIStandalone biosimulations�[21m�[0m [�[33m-dhqv�[39m�[0m] [�[33m-i�[39m�[0m=�[3m<ARCHIVE>�[23m�[0m] [�[33m-o�[39m�[0m=�[3m<OUT_DIR>�[23m�[0m]
  BioSimulators-compliant command-line interface to the vcell simulation program
  <https://vcell.org>.
    �[33m-d�[39m�[0m, �[33m--debug�[39m�[0m               full application debug mode
    �[33m-h�[39m�[0m, �[33m--help�[39m�[0m                show this help message and exit
    �[33m-i�[39m�[0m, �[33m--archive�[39m�[0m=�[3m<ARCHIVE>�[23m�[0m   Path to a COMBINE/OMEX archive file which contains
                                one or more SED-ML-encoded simulation experiments
    �[33m-o�[39m�[0m, �[33m--out-dir�[39m�[0m=�[3m<OUT_DIR>�[23m�[0m   Directory to save outputs
    �[33m-q�[39m�[0m, �[33m--quiet�[39m�[0m               suppress all console output
    �[33m-v�[39m�[0m, �[33m--version�[39m�[0m             show program's version number and exit

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

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

  docker: Command recieved::<--help>
  <--help>
  Default case selected
  VCell shall execute <biosimulations --help>
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
   INFO (CLIStandalone:36) - Starting Vcell... []{}
  Usage: �[1mCLIStandalone biosimulations�[21m�[0m [�[33m-dhqv�[39m�[0m] [�[33m-i�[39m�[0m=�[3m<ARCHIVE>�[23m�[0m] [�[33m-o�[39m�[0m=�[3m<OUT_DIR>�[23m�[0m]
  BioSimulators-compliant command-line interface to the vcell simulation program
  <https://vcell.org>.
    �[33m-d�[39m�[0m, �[33m--debug�[39m�[0m               full application debug mode
    �[33m-h�[39m�[0m, �[33m--help�[39m�[0m                show this help message and exit
    �[33m-i�[39m�[0m, �[33m--archive�[39m�[0m=�[3m<ARCHIVE>�[23m�[0m   Path to a COMBINE/OMEX archive file which contains
                                one or more SED-ML-encoded simulation experiments
    �[33m-o�[39m�[0m, �[33m--out-dir�[39m�[0m=�[3m<OUT_DIR>�[23m�[0m   Directory to save outputs
    �[33m-q�[39m�[0m, �[33m--quiet�[39m�[0m               suppress all console output
    �[33m-v�[39m�[0m, �[33m--version�[39m�[0m             show program's version number and exit

Log: None

docker_image.DeclaresSupportedEnvironmentVariables (0.5 s)

Test if a Docker image declares the environment variables that is supports

Warnings:

Docker images for simulation tools should declare the environment variables that they support.

The Docker image does not declare the following standard environment variables recognized by BioSimulators:
  - 'BUNDLE_OUTPUTS'
  - 'COLLECT_COMBINE_ARCHIVE_RESULTS'
  - 'COLLECT_SED_DOCUMENT_RESULTS'
  - 'DEBUG'
  - 'H5_REPORTS_PATH'
  - 'KEEP_INDIVIDUAL_OUTPUTS'
  - 'LOG_PATH'
  - 'OMEX_METADATA_INPUT_FORMAT'
  - 'OMEX_METADATA_OUTPUT_FORMAT'
  - 'OMEX_METADATA_SCHEMA'
  - 'PLOTS_PATH'
  - 'REPORTS_PATH'
  - 'REPORT_FORMATS'
  - 'SAVE_PLOT_DATA'
  - 'VALIDATE_IMAGES'
  - 'VALIDATE_IMPORTED_MODEL_FILES'
  - 'VALIDATE_OMEX_MANIFESTS'
  - 'VALIDATE_OMEX_METADATA'
  - 'VALIDATE_RESULTS'
  - 'VALIDATE_SEDML'
  - 'VALIDATE_SEDML_MODELS'
  - 'VERBOSE'
  - 'VIZ_FORMATS'

If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator.

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

Log: None

docker_image.HasBioContainersLabels (0.5 s)

Test that a Docker image has BioContainers labels with metadata about the image

Warnings:

Docker images are encouraged to have the following BioContainers labels:
  extra.identifiers.biotools

Log: None

Answer 79 · 2024-09-11T17:15:45.000Z

Skips

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: None

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: None

published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator (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: None

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: None

published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9004
Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_9004 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9004
Algorithm: KISAO_0000030

Reason for skip:

Case requires model formats format_9004 and simulation algorithms KISAO_0000030

Log: None

published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9012
Algorithm: KISAO_0000669

Reason for skip:

Case requires model formats format_9012 and simulation algorithms KISAO_0000669

Log: None

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: None

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: None

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: None

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: None

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: None

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: None

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: None

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: None

published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle (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: None

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: None

published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9010
Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_9010 and simulation algorithms KISAO_0000019

Log: None

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: None

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: None

sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions (0.3 s)

Test that that the curated number of output dimensions matches the actual number of output dimensions

Reason for skip:

No curated COMBINE/OMEX archives are available to generate archives for testing

Log: None

sedml.SimulatorSupportsComputeModelChanges (19.8 s)

Test that a simulator supports compute model changes

Reason for skip:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.6.0.40' could not execute the archive:

  Unknown error

Log:

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:92) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:133) - Preparing output directory... []{}

ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}

ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/archive11351539017678566110.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_dee25dc0-7de1-494f-9be8-a9077873443f10498822019629189837 []{}

11.09 17:08:15 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@200: found no entry for description 0 in /metadata.rdf (about=/http:/omex-library.org/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex).

11.09 17:08:15 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@200: found no entry for description 1 in /metadata.rdf (about=/http:/omex-library.org/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex/BIOMD0000000912_sim.sedml/Figure_1_bottom_left).

11.09 17:08:15 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 2 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 17:08:15 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 3 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 17:08:15 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 4 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 17:08:15 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 5 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 17:08:15 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 6 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 17:08:15 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 7 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 17:08:15 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 8 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 17:08:15 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 9 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 17:08:15 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 10 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 17:08:15 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 11 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 17:08:15 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 12 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 17:08:15 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 13 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 17:08:15 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 14 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

 INFO (OmexHandler:65) - Successfully Repaired `archive11351539017678566110.omex` []{}

 INFO (SedmlJob:110) - Initializing SED-ML document... []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:125) - Processing SED-ML: BIOMD0000000912_sim.sedml []{}

 INFO (SedmlJob:161) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

 []{}

 INFO (SedmlJob:166) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{}

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

 INFO (SedmlJob:170) - Creating pseudo SED-ML for HDF5 conversion... []{}

 INFO (SedmlJob:182) - Creating Biomodel from pseudo SED-ML []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:257) - Building solvers and starting simulation of all tasks...  []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 INFO (SEDMLImporter:182) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{}

ERROR (SolverHandler:332) - Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:253) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:156) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:173) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:897) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:309) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	... 18 more

ERROR (SedmlJob:273) - Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:253) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:156) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:173) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:897) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:309) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	... 18 more

 INFO (SedmlJob:298) - Generating outputs...  []{}

 INFO (SedmlJob:388) - Generating HDF5 file...  []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:146) - We did not get any entries in the final data set. This may mean a problem has been encountered. []{}

ERROR (SedmlJob:462) - Failure executing the sed document.  []{}

java.lang.RuntimeException: Failure executing the sed document. 

	at org.vcell.cli.run.SedmlJob.evaluateResults(SedmlJob.java:323) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:244) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:253) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:156) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:173) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

 WARN (SedmlJob:332) - Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importFailure executing the sed document.  []{}

ERROR (ExecutionJob:146) - Processing of SedML has failed.

org.vcell.cli.run.SedmlStatistics@3f866f50 []{}

 INFO (NativeLib:32) - Loading jhdf5 []{}

 INFO (BiosimulationsHdf5Writer:52) - Creating hdf5 file `reports.h5` in/tmp/out []{}

 INFO (BiosimulationsHdf5Writer:130) - HDF5 file successfully written to. []{}

 INFO (ExecutionJob:174) - Omex archive11351539017678566110.omex processing completed (4s) []{}

ERROR (BiosimulationsCommand:98) - Errors occurred during execution []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | SIMULATIONS_RUN(runSimulations) | **** Error: 

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:92) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:133) - Preparing output directory... []{}

ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}

ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/archive11685860763479932377.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_2e25bea8-6690-4724-a2e1-69eeefadba7f2945355592176180919 []{}

11.09 17:08:25 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@200: found no entry for description 0 in /metadata.rdf (about=/http:/omex-library.org/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex).

11.09 17:08:25 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@200: found no entry for description 1 in /metadata.rdf (about=/http:/omex-library.org/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex/BIOMD0000000912_sim.sedml/Figure_1_bottom_left).

11.09 17:08:25 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 2 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 17:08:25 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 3 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 17:08:25 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 4 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 17:08:25 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 5 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 17:08:25 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 6 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 17:08:25 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 7 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 17:08:25 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 8 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 17:08:25 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 9 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 17:08:25 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 10 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 17:08:25 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 11 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 17:08:25 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 12 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 17:08:25 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 13 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 17:08:25 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 14 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

 INFO (OmexHandler:65) - Successfully Repaired `archive11685860763479932377.omex` []{}

 INFO (SedmlJob:110) - Initializing SED-ML document... []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:125) - Processing SED-ML: BIOMD0000000912_sim.sedml []{}

 INFO (SedmlJob:161) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

 []{}

 INFO (SedmlJob:166) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{}

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

 INFO (SedmlJob:170) - Creating pseudo SED-ML for HDF5 conversion... []{}

 INFO (SedmlJob:182) - Creating Biomodel from pseudo SED-ML []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:257) - Building solvers and starting simulation of all tasks...  []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 INFO (SEDMLImporter:182) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{}

ERROR (SolverHandler:332) - Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:253) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:156) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:173) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:897) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:309) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	... 18 more

ERROR (SedmlJob:273) - Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:253) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:156) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:173) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:897) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:309) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	... 18 more

 INFO (SedmlJob:298) - Generating outputs...  []{}

 INFO (SedmlJob:388) - Generating HDF5 file...  []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:146) - We did not get any entries in the final data set. This may mean a problem has been encountered. []{}

ERROR (SedmlJob:462) - Failure executing the sed document.  []{}

java.lang.RuntimeException: Failure executing the sed document. 

	at org.vcell.cli.run.SedmlJob.evaluateResults(SedmlJob.java:323) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:244) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:253) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:156) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:173) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

 WARN (SedmlJob:332) - Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importFailure executing the sed document.  []{}

ERROR (ExecutionJob:146) - Processing of SedML has failed.

org.vcell.cli.run.SedmlStatistics@5b44318 []{}

 INFO (NativeLib:32) - Loading jhdf5 []{}

 INFO (BiosimulationsHdf5Writer:52) - Creating hdf5 file `reports.h5` in/tmp/out []{}

 INFO (BiosimulationsHdf5Writer:130) - HDF5 file successfully written to. []{}

 INFO (ExecutionJob:174) - Omex archive11685860763479932377.omex processing completed (4s) []{}

ERROR (BiosimulationsCommand:98) - Errors occurred during execution []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | SIMULATIONS_RUN(runSimulations) | **** Error:

sedml.SimulatorSupportsModelAttributeChanges (19.1 s)

Test that a simulator supports changes to the attributes of model elements

Reason for skip:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.6.0.40' could not execute the archive:

  Unknown error

Log:

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:92) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:133) - Preparing output directory... []{}

ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}

ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/archive10341339354377231852.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_e081377c-7402-4d44-8003-0cf1a7795ee51761398310988880416 []{}

11.09 17:08:56 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@200: found no entry for description 0 in /metadata.rdf (about=/http:/omex-library.org/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex).

11.09 17:08:56 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@200: found no entry for description 1 in /metadata.rdf (about=/http:/omex-library.org/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex/BIOMD0000000912_sim.sedml/Figure_1_bottom_left).

11.09 17:08:56 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 2 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 17:08:56 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 3 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 17:08:56 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 4 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 17:08:56 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 5 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 17:08:56 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 6 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 17:08:56 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 7 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 17:08:56 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 8 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 17:08:56 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 9 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 17:08:56 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 10 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 17:08:56 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 11 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 17:08:56 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 12 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 17:08:56 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 13 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 17:08:56 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 14 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

 INFO (OmexHandler:65) - Successfully Repaired `archive10341339354377231852.omex` []{}

 INFO (SedmlJob:110) - Initializing SED-ML document... []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:125) - Processing SED-ML: BIOMD0000000912_sim.sedml []{}

 INFO (SedmlJob:161) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

 []{}

 INFO (SedmlJob:166) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{}

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

 INFO (SedmlJob:170) - Creating pseudo SED-ML for HDF5 conversion... []{}

 INFO (SedmlJob:182) - Creating Biomodel from pseudo SED-ML []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:257) - Building solvers and starting simulation of all tasks...  []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 WARN (StringTools:486) - Could not create an integer from the string x []{}

ERROR (SolverHandler:332) - Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection

Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references. []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:253) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:156) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:173) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.RuntimeException: Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.

	at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:845) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:144) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	... 18 more

Caused by: java.lang.Exception: Errors reported:

IllegalArgumentException occurred: Must be of type int!



	at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:844) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:144) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	... 18 more

ERROR (SedmlJob:273) - Unable to initialize bioModel for the given selection

Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.Errors reported:

IllegalArgumentException occurred: Must be of type int!

 []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:253) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:156) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:173) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.RuntimeException: Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.

	at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:845) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:144) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	... 18 more

Caused by: java.lang.Exception: Errors reported:

IllegalArgumentException occurred: Must be of type int!



	at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:844) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:144) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	... 18 more

 INFO (SedmlJob:298) - Generating outputs...  []{}

 INFO (SedmlJob:388) - Generating HDF5 file...  []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:146) - We did not get any entries in the final data set. This may mean a problem has been encountered. []{}

ERROR (SedmlJob:462) - Failure executing the sed document.  []{}

java.lang.RuntimeException: Failure executing the sed document. 

	at org.vcell.cli.run.SedmlJob.evaluateResults(SedmlJob.java:323) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:244) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:253) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:156) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:173) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

 WARN (SedmlJob:332) - Unable to initialize bioModel for the given selection

Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.Errors reported:

IllegalArgumentException occurred: Must be of type int!

Failure executing the sed document.  []{}

ERROR (ExecutionJob:146) - Processing of SedML has failed.

org.vcell.cli.run.SedmlStatistics@177c41d7 []{}

 INFO (NativeLib:32) - Loading jhdf5 []{}

 INFO (BiosimulationsHdf5Writer:52) - Creating hdf5 file `reports.h5` in/tmp/out []{}

 INFO (BiosimulationsHdf5Writer:130) - HDF5 file successfully written to. []{}

 INFO (ExecutionJob:174) - Omex archive10341339354377231852.omex processing completed (3s) []{}

ERROR (BiosimulationsCommand:98) - Errors occurred during execution []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | SIMULATIONS_RUN(runSimulations) | **** Error: 

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:92) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:133) - Preparing output directory... []{}

ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}

ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/archive2539664152018376043.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_00de0662-a145-4b51-8260-46651f49f75d15573536586052999301 []{}

11.09 17:09:05 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@200: found no entry for description 0 in /metadata.rdf (about=/http:/omex-library.org/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex).

11.09 17:09:05 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@200: found no entry for description 1 in /metadata.rdf (about=/http:/omex-library.org/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex/BIOMD0000000912_sim.sedml/Figure_1_bottom_left).

11.09 17:09:05 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 2 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 17:09:05 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 3 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 17:09:05 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 4 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 17:09:05 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 5 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 17:09:05 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 6 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 17:09:05 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 7 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 17:09:05 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 8 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 17:09:05 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 9 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 17:09:05 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 10 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 17:09:05 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 11 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 17:09:05 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 12 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 17:09:05 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 13 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

11.09 17:09:05 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 14 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

 INFO (OmexHandler:65) - Successfully Repaired `archive2539664152018376043.omex` []{}

 INFO (SedmlJob:110) - Initializing SED-ML ...

Answer 80 · 2024-09-11T17:15:46.000Z

- After correcting your simulator, please edit the first block of this issue to re-initiate this validation.
- 
- The complete log of your validation/submission job, including further information about the failure, is available for 90 days [here](https://github.com/biosimulators/Biosimulators/actions/runs/10816135513). The results of the validation of your image will also be available shortly as a JSON file. A link to this file will be available from the "Artifacts" section at the bottom of [this page](https://github.com/biosimulators/Biosimulators/actions/runs/10816135513).

Answer 81 · 2024-09-13T18:23:05.000Z

Thank you @CodeByDrescher 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 for 90 days 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 for 90 days from the "Artifacts" section at the bottom of this page.

Answer 82 · 2024-09-13T18:23:11.000Z

The specifications of your simulator is valid!

Answer 83 · 2024-09-13T18:35:23.000Z

Summary of tests

Executed 74 test cases
Passed 37 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
- log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
- log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
- log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
- log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks
- 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-Fehlberg
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator
- 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
- published_project.SimulatorCanExecutePublishedProject:vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength
- results_report.SimulatorGeneratesReportsOfSimulationResults
- sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments
- sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
- sedml.SimulatorProducesLinear2DPlots
- sedml.SimulatorProducesLogarithmic2DPlots
- sedml.SimulatorProducesMultiplePlots
- sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges
- sedml.SimulatorSupportsAlgorithmParameters
- sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes
- sedml.SimulatorSupportsDataSetsWithDifferentShapes
- sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
- sedml.SimulatorSupportsMultipleReportsPerSedDocument
- sedml.SimulatorSupportsMultipleTasksPerSedDocument
- sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes
Failed 1 test cases:
- docker_image.SingularityImageExecutesSimulationsSuccessfully
Skipped 36 test cases:
- published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
- published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
- published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator
- published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system
- published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism
- published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE
- published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler
- published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT
- 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:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle
- published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra
- published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells
- sedml.SimulatorProducesLinear3DPlots
- sedml.SimulatorProducesLogarithmic3DPlots
- sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
- sedml.SimulatorSupportsComputeModelChanges
- 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

Answer 84 · 2024-09-13T18:35:24.000Z

Failures

docker_image.SingularityImageExecutesSimulationsSuccessfully (19.4 s)

Test that the Singularity version of a Docker image can sucessfully execute COMBINE archives

Exception:

The Docker image could not be successfully executed as a Singularity image (error code 1:
  docker: Command recieved::<-i /root/archive.omex -o /root>
  <-i>
  Default case selected
  VCell shall execute <biosimulations -i /root/archive.omex -o /root>
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
   INFO (CLIStandalone:36) - Starting Vcell... []{}
   INFO (BiosimulationsCommand:92) - Beginning execution []{}
   INFO (CLIPythonManager:116) - Initializing Python... []{}
  ERROR (BiosimulationsCommand:116) - Unexpected Error in BioSimulations execution: []{}
  org.vcell.cli.PythonStreamException: Python error caught: <
  Traceback (most recent call last):
    File "<stdin>", line 1, in <module>
    File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/wrapper.py", line 5, in <module>
      from deprecated import deprecated
  ModuleNotFoundError: No module named 'deprecated'
  
  >
  
  
  	at org.vcell.cli.CLIPythonManager.parsePythonReturn(CLIPythonManager.java:287) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.CLIPythonManager.parsePythonReturn(CLIPythonManager.java:263) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.CLIPythonManager.executeThroughPython(CLIPythonManager.java:192) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.CLIPythonManager.instantiatePythonProcess(CLIPythonManager.java:135) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:94) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]
  	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Log: None

Answer 85 · 2024-09-13T18:35:24.000Z

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (1.6 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'
  - 'BUNDLE_OUTPUTS'
  - 'COLLECT_COMBINE_ARCHIVE_RESULTS'
  - 'COLLECT_SED_DOCUMENT_RESULTS'
  - 'DEBUG'
  - 'H5_REPORTS_PATH'
  - 'KEEP_INDIVIDUAL_OUTPUTS'
  - 'LOG_PATH'
  - 'OMEX_METADATA_INPUT_FORMAT'
  - 'OMEX_METADATA_OUTPUT_FORMAT'
  - 'OMEX_METADATA_SCHEMA'
  - 'PLOTS_PATH'
  - 'REPORTS_PATH'
  - 'REPORT_FORMATS'
  - 'SAVE_PLOT_DATA'
  - 'VALIDATE_IMAGES'
  - 'VALIDATE_IMPORTED_MODEL_FILES'
  - 'VALIDATE_OMEX_MANIFESTS'
  - 'VALIDATE_OMEX_METADATA'
  - 'VALIDATE_RESULTS'
  - 'VALIDATE_SEDML'
  - 'VALIDATE_SEDML_MODELS'
  - 'VERBOSE'
  - 'VIZ_FORMATS'

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: None

cli.CliDisplaysHelpInline (4.0 s)

Test that a command-line interface provides inline help.

Warnings:

Command-line interfaces should display basic help when no arguments are provided.

The command-line interface displayed the following when no argument was provided:

  docker: Command recieved::<>
  <>
  Default case selected
  VCell shall execute <biosimulations >
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
   INFO (CLIStandalone:36) - Starting Vcell... []{}
  ERROR (BiosimulationsCommand:116) - Unexpected Error in BioSimulations execution: []{}
  java.lang.NullPointerException: Cannot invoke "java.io.File.getAbsolutePath()" because "outputDirectory" is null
  	at org.vcell.cli.CLIRecorder.<init>(CLIRecorder.java:70) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.CLIRecorder.<init>(CLIRecorder.java:59) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.CLIRecorder.<init>(CLIRecorder.java:48) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:50) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]
  	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

  docker: Command recieved::<-h>
  <-h>
  Default case selected
  VCell shall execute <biosimulations -h>
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
   INFO (CLIStandalone:36) - Starting Vcell... []{}
  Usage: �[1mCLIStandalone biosimulations�[21m�[0m [�[33m-dhqv�[39m�[0m] [�[33m-i�[39m�[0m=�[3m<ARCHIVE>�[23m�[0m] [�[33m-o�[39m�[0m=�[3m<OUT_DIR>�[23m�[0m]
  BioSimulators-compliant command-line interface to the vcell simulation program
  <https://vcell.org>.
    �[33m-d�[39m�[0m, �[33m--debug�[39m�[0m               full application debug mode
    �[33m-h�[39m�[0m, �[33m--help�[39m�[0m                show this help message and exit
    �[33m-i�[39m�[0m, �[33m--archive�[39m�[0m=�[3m<ARCHIVE>�[23m�[0m   Path to a COMBINE/OMEX archive file which contains
                                one or more SED-ML-encoded simulation experiments
    �[33m-o�[39m�[0m, �[33m--out-dir�[39m�[0m=�[3m<OUT_DIR>�[23m�[0m   Directory to save outputs
    �[33m-q�[39m�[0m, �[33m--quiet�[39m�[0m               suppress all console output
    �[33m-v�[39m�[0m, �[33m--version�[39m�[0m             show program's version number and exit

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

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

  docker: Command recieved::<--help>
  <--help>
  Default case selected
  VCell shall execute <biosimulations --help>
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
   INFO (CLIStandalone:36) - Starting Vcell... []{}
  Usage: �[1mCLIStandalone biosimulations�[21m�[0m [�[33m-dhqv�[39m�[0m] [�[33m-i�[39m�[0m=�[3m<ARCHIVE>�[23m�[0m] [�[33m-o�[39m�[0m=�[3m<OUT_DIR>�[23m�[0m]
  BioSimulators-compliant command-line interface to the vcell simulation program
  <https://vcell.org>.
    �[33m-d�[39m�[0m, �[33m--debug�[39m�[0m               full application debug mode
    �[33m-h�[39m�[0m, �[33m--help�[39m�[0m                show this help message and exit
    �[33m-i�[39m�[0m, �[33m--archive�[39m�[0m=�[3m<ARCHIVE>�[23m�[0m   Path to a COMBINE/OMEX archive file which contains
                                one or more SED-ML-encoded simulation experiments
    �[33m-o�[39m�[0m, �[33m--out-dir�[39m�[0m=�[3m<OUT_DIR>�[23m�[0m   Directory to save outputs
    �[33m-q�[39m�[0m, �[33m--quiet�[39m�[0m               suppress all console output
    �[33m-v�[39m�[0m, �[33m--version�[39m�[0m             show program's version number and exit

Log: None

docker_image.DeclaresSupportedEnvironmentVariables (0.1 s)

Test if a Docker image declares the environment variables that is supports

Warnings:

Docker images for simulation tools should declare the environment variables that they support.

The Docker image does not declare the following standard environment variables recognized by BioSimulators:
  - 'BUNDLE_OUTPUTS'
  - 'COLLECT_COMBINE_ARCHIVE_RESULTS'
  - 'COLLECT_SED_DOCUMENT_RESULTS'
  - 'DEBUG'
  - 'H5_REPORTS_PATH'
  - 'KEEP_INDIVIDUAL_OUTPUTS'
  - 'LOG_PATH'
  - 'OMEX_METADATA_INPUT_FORMAT'
  - 'OMEX_METADATA_OUTPUT_FORMAT'
  - 'OMEX_METADATA_SCHEMA'
  - 'PLOTS_PATH'
  - 'REPORTS_PATH'
  - 'REPORT_FORMATS'
  - 'SAVE_PLOT_DATA'
  - 'VALIDATE_IMAGES'
  - 'VALIDATE_IMPORTED_MODEL_FILES'
  - 'VALIDATE_OMEX_MANIFESTS'
  - 'VALIDATE_OMEX_METADATA'
  - 'VALIDATE_RESULTS'
  - 'VALIDATE_SEDML'
  - 'VALIDATE_SEDML_MODELS'
  - 'VERBOSE'
  - 'VIZ_FORMATS'

If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator.

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

Log: None

docker_image.HasBioContainersLabels (0.2 s)

Test that a Docker image has BioContainers labels with metadata about the image

Warnings:

Docker images are encouraged to have the following BioContainers labels:
  extra.identifiers.biotools

Log: None

Answer 86 · 2024-09-13T18:35:25.000Z

Skips

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: None

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: None

published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator (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: None

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: None

published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9004
Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_9004 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9004
Algorithm: KISAO_0000030

Reason for skip:

Case requires model formats format_9004 and simulation algorithms KISAO_0000030

Log: None

published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9012
Algorithm: KISAO_0000669

Reason for skip:

Case requires model formats format_9012 and simulation algorithms KISAO_0000669

Log: None

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: None

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: None

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: None

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: None

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: None

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: None

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: None

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: None

published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle (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: None

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: None

published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9010
Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_9010 and simulation algorithms KISAO_0000019

Log: None

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: None

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: None

sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions (0.3 s)

Test that that the curated number of output dimensions matches the actual number of output dimensions

Reason for skip:

No curated COMBINE/OMEX archives are available to generate archives for testing

Log: None

sedml.SimulatorSupportsComputeModelChanges (18.6 s)

Test that a simulator supports compute model changes

Reason for skip:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.6.0.40' could not execute the archive:

  Unknown error

Log:

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:92) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:133) - Preparing output directory... []{}

ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}

ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/archive2827456694391609397.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_209b3562-6cdd-4a77-86c2-58b5d980a4106619877305317157694 []{}

13.09 18:28:24 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@200: found no entry for description 0 in /metadata.rdf (about=/http:/omex-library.org/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex).

13.09 18:28:24 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@200: found no entry for description 1 in /metadata.rdf (about=/http:/omex-library.org/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex/BIOMD0000000912_sim.sedml/Figure_1_bottom_left).

13.09 18:28:24 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 2 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

13.09 18:28:24 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 3 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

13.09 18:28:24 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 4 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

13.09 18:28:24 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 5 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

13.09 18:28:24 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 6 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

13.09 18:28:24 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 7 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

13.09 18:28:24 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 8 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

13.09 18:28:24 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 9 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

13.09 18:28:24 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 10 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

13.09 18:28:24 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 11 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

13.09 18:28:24 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 12 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

13.09 18:28:24 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 13 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

13.09 18:28:24 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 14 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

 INFO (OmexHandler:65) - Successfully Repaired `archive2827456694391609397.omex` []{}

 INFO (SedmlJob:110) - Initializing SED-ML document... []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:125) - Processing SED-ML: BIOMD0000000912_sim.sedml []{}

 INFO (SedmlJob:161) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

 []{}

 INFO (SedmlJob:166) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{}

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

 INFO (SedmlJob:170) - Creating pseudo SED-ML for HDF5 conversion... []{}

 INFO (SedmlJob:182) - Creating Biomodel from pseudo SED-ML []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:257) - Building solvers and starting simulation of all tasks...  []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 INFO (SEDMLImporter:182) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{}

ERROR (SolverHandler:332) - Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:253) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:156) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:173) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:897) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:309) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	... 18 more

ERROR (SedmlJob:273) - Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:253) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:156) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:173) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:897) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:309) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	... 18 more

 INFO (SedmlJob:298) - Generating outputs...  []{}

 INFO (SedmlJob:388) - Generating HDF5 file...  []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:146) - We did not get any entries in the final data set. This may mean a problem has been encountered. []{}

ERROR (SedmlJob:462) - Failure executing the sed document.  []{}

java.lang.RuntimeException: Failure executing the sed document. 

	at org.vcell.cli.run.SedmlJob.evaluateResults(SedmlJob.java:323) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:244) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:253) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:156) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:173) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

 WARN (SedmlJob:332) - Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importFailure executing the sed document.  []{}

ERROR (ExecutionJob:146) - Processing of SedML has failed.

org.vcell.cli.run.SedmlStatistics@3f866f50 []{}

 INFO (NativeLib:32) - Loading jhdf5 []{}

 INFO (BiosimulationsHdf5Writer:52) - Creating hdf5 file `reports.h5` in/tmp/out []{}

 INFO (BiosimulationsHdf5Writer:130) - HDF5 file successfully written to. []{}

 INFO (ExecutionJob:174) - Omex archive2827456694391609397.omex processing completed (4s) []{}

ERROR (BiosimulationsCommand:98) - Errors occurred during execution []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | SIMULATIONS_RUN(runSimulations) | **** Error: 

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:92) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:133) - Preparing output directory... []{}

ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}

ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/archive9997559220677172916.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_fa47a54e-acbd-445c-9232-160241f8d7e83143535161176115989 []{}

13.09 18:28:34 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@200: found no entry for description 0 in /metadata.rdf (about=/http:/omex-library.org/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex).

13.09 18:28:34 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@200: found no entry for description 1 in /metadata.rdf (about=/http:/omex-library.org/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex/BIOMD0000000912_sim.sedml/Figure_1_bottom_left).

13.09 18:28:34 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 2 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

13.09 18:28:34 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 3 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

13.09 18:28:34 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 4 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

13.09 18:28:34 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 5 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

13.09 18:28:34 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 6 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

13.09 18:28:34 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 7 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

13.09 18:28:34 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 8 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

13.09 18:28:34 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 9 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

13.09 18:28:34 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 10 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

13.09 18:28:34 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 11 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

13.09 18:28:34 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 12 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

13.09 18:28:34 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 13 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

13.09 18:28:34 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 14 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

 INFO (OmexHandler:65) - Successfully Repaired `archive9997559220677172916.omex` []{}

 INFO (SedmlJob:110) - Initializing SED-ML document... []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:125) - Processing SED-ML: BIOMD0000000912_sim.sedml []{}

 INFO (SedmlJob:161) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

 []{}

 INFO (SedmlJob:166) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{}

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

 INFO (SedmlJob:170) - Creating pseudo SED-ML for HDF5 conversion... []{}

 INFO (SedmlJob:182) - Creating Biomodel from pseudo SED-ML []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:257) - Building solvers and starting simulation of all tasks...  []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 INFO (SEDMLImporter:182) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{}

ERROR (SolverHandler:332) - Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:253) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:156) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:173) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:897) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:309) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	... 18 more

ERROR (SedmlJob:273) - Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:253) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:156) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:173) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:897) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:309) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	... 18 more

 INFO (SedmlJob:298) - Generating outputs...  []{}

 INFO (SedmlJob:388) - Generating HDF5 file...  []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:146) - We did not get any entries in the final data set. This may mean a problem has been encountered. []{}

ERROR (SedmlJob:462) - Failure executing the sed document.  []{}

java.lang.RuntimeException: Failure executing the sed document. 

	at org.vcell.cli.run.SedmlJob.evaluateResults(SedmlJob.java:323) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:244) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:253) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:156) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:173) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

 WARN (SedmlJob:332) - Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importFailure executing the sed document.  []{}

ERROR (ExecutionJob:146) - Processing of SedML has failed.

org.vcell.cli.run.SedmlStatistics@6c995c5d []{}

 INFO (NativeLib:32) - Loading jhdf5 []{}

 INFO (BiosimulationsHdf5Writer:52) - Creating hdf5 file `reports.h5` in/tmp/out []{}

 INFO (BiosimulationsHdf5Writer:130) - HDF5 file successfully written to. []{}

 INFO (ExecutionJob:174) - Omex archive9997559220677172916.omex processing completed (4s) []{}

ERROR (BiosimulationsCommand:98) - Errors occurred during execution []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | SIMULATIONS_RUN(runSimulations) | **** Error:

sedml.SimulatorSupportsModelAttributeChanges (17.8 s)

Test that a simulator supports changes to the attributes of model elements

Reason for skip:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.6.0.40' could not execute the archive:

  Unknown error

Log:

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:92) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:133) - Preparing output directory... []{}

ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}

ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/archive3166483272677238518.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_87797262-4f04-4668-a519-3efe397e67d612916954534715144471 []{}

13.09 18:29:03 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@200: found no entry for description 0 in /metadata.rdf (about=/http:/omex-library.org/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex).

13.09 18:29:03 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@200: found no entry for description 1 in /metadata.rdf (about=/http:/omex-library.org/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex/BIOMD0000000912_sim.sedml/Figure_1_bottom_left).

13.09 18:29:03 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 2 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

13.09 18:29:03 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 3 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

13.09 18:29:03 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 4 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

13.09 18:29:03 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 5 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

13.09 18:29:03 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 6 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

13.09 18:29:03 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 7 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

13.09 18:29:03 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 8 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

13.09 18:29:03 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 9 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

13.09 18:29:03 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 10 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

13.09 18:29:03 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 11 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

13.09 18:29:03 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 12 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

13.09 18:29:03 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 13 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

13.09 18:29:03 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 14 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

 INFO (OmexHandler:65) - Successfully Repaired `archive3166483272677238518.omex` []{}

 INFO (SedmlJob:110) - Initializing SED-ML document... []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:125) - Processing SED-ML: BIOMD0000000912_sim.sedml []{}

 INFO (SedmlJob:161) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

 []{}

 INFO (SedmlJob:166) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{}

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

 INFO (SedmlJob:170) - Creating pseudo SED-ML for HDF5 conversion... []{}

 INFO (SedmlJob:182) - Creating Biomodel from pseudo SED-ML []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:257) - Building solvers and starting simulation of all tasks...  []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 WARN (StringTools:486) - Could not create an integer from the string x []{}

ERROR (SolverHandler:332) - Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection

Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references. []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:253) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:156) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:173) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.RuntimeException: Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.

	at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:845) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:144) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	... 18 more

Caused by: java.lang.Exception: Errors reported:

IllegalArgumentException occurred: Must be of type int!



	at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:844) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:144) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	... 18 more

ERROR (SedmlJob:273) - Unable to initialize bioModel for the given selection

Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.Errors reported:

IllegalArgumentException occurred: Must be of type int!

 []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:253) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:156) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:173) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.RuntimeException: Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.

	at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:845) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:144) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	... 18 more

Caused by: java.lang.Exception: Errors reported:

IllegalArgumentException occurred: Must be of type int!



	at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:844) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:144) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	... 18 more

 INFO (SedmlJob:298) - Generating outputs...  []{}

 INFO (SedmlJob:388) - Generating HDF5 file...  []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:146) - We did not get any entries in the final data set. This may mean a problem has been encountered. []{}

ERROR (SedmlJob:462) - Failure executing the sed document.  []{}

java.lang.RuntimeException: Failure executing the sed document. 

	at org.vcell.cli.run.SedmlJob.evaluateResults(SedmlJob.java:323) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:244) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:253) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:156) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:173) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

 WARN (SedmlJob:332) - Unable to initialize bioModel for the given selection

Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.Errors reported:

IllegalArgumentException occurred: Must be of type int!

Failure executing the sed document.  []{}

ERROR (ExecutionJob:146) - Processing of SedML has failed.

org.vcell.cli.run.SedmlStatistics@177c41d7 []{}

 INFO (NativeLib:32) - Loading jhdf5 []{}

 INFO (BiosimulationsHdf5Writer:52) - Creating hdf5 file `reports.h5` in/tmp/out []{}

 INFO (BiosimulationsHdf5Writer:130) - HDF5 file successfully written to. []{}

 INFO (ExecutionJob:174) - Omex archive3166483272677238518.omex processing completed (3s) []{}

ERROR (BiosimulationsCommand:98) - Errors occurred during execution []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | SIMULATIONS_RUN(runSimulations) | **** Error: 

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:92) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:133) - Preparing output directory... []{}

ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}

ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/archive4649540337449123481.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_54136c49-0b2c-4420-b15a-383ef92e23f914699721384346226606 []{}

13.09 18:29:11 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@200: found no entry for description 0 in /metadata.rdf (about=/http:/omex-library.org/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex).

13.09 18:29:11 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@200: found no entry for description 1 in /metadata.rdf (about=/http:/omex-library.org/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex/BIOMD0000000912_sim.sedml/Figure_1_bottom_left).

13.09 18:29:11 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 2 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

13.09 18:29:11 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 3 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

13.09 18:29:11 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 4 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

13.09 18:29:11 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 5 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

13.09 18:29:11 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 6 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

13.09 18:29:11 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 7 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

13.09 18:29:11 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 8 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

13.09 18:29:11 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 9 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

13.09 18:29:11 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 10 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

13.09 18:29:11 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 11 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

13.09 18:29:11 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 12 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

13.09 18:29:11 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 13 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

13.09 18:29:11 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 14 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

 INFO (OmexHandler:65) - Successfully Repaired `archive4649540337449123481.omex` []{}

 INFO (SedmlJob:110) - Initializing SED-ML documen ...

Answer 87 · 2024-09-13T18:35:25.000Z

- After correcting your simulator, please edit the first block of this issue to re-initiate this validation.
- 
- The complete log of your validation/submission job, including further information about the failure, is available for 90 days [here](https://github.com/biosimulators/Biosimulators/actions/runs/10854125878). The results of the validation of your image will also be available shortly as a JSON file. A link to this file will be available from the "Artifacts" section at the bottom of [this page](https://github.com/biosimulators/Biosimulators/actions/runs/10854125878).

Answer 88 · 2024-09-17T14:15:20.000Z

Thank you @CodeByDrescher 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 for 90 days 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 for 90 days from the "Artifacts" section at the bottom of this page.

Answer 89 · 2024-09-17T14:15:28.000Z

The specifications of your simulator is valid!

Answer 90 · 2024-09-17T14:28:16.000Z

Summary of tests

Executed 74 test cases
Passed 37 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
- log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
- log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
- log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
- log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks
- 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-Fehlberg
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator
- 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
- published_project.SimulatorCanExecutePublishedProject:vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength
- results_report.SimulatorGeneratesReportsOfSimulationResults
- sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments
- sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
- sedml.SimulatorProducesLinear2DPlots
- sedml.SimulatorProducesLogarithmic2DPlots
- sedml.SimulatorProducesMultiplePlots
- sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges
- sedml.SimulatorSupportsAlgorithmParameters
- sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes
- sedml.SimulatorSupportsDataSetsWithDifferentShapes
- sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
- sedml.SimulatorSupportsMultipleReportsPerSedDocument
- sedml.SimulatorSupportsMultipleTasksPerSedDocument
- sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes
Failed 1 test cases:
- docker_image.SingularityImageExecutesSimulationsSuccessfully
Skipped 36 test cases:
- published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
- published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
- published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator
- published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system
- published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism
- published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE
- published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler
- published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT
- 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:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle
- published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra
- published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells
- sedml.SimulatorProducesLinear3DPlots
- sedml.SimulatorProducesLogarithmic3DPlots
- sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
- sedml.SimulatorSupportsComputeModelChanges
- 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

Answer 91 · 2024-09-17T14:28:16.000Z

Failures

docker_image.SingularityImageExecutesSimulationsSuccessfully (18.1 s)

Test that the Singularity version of a Docker image can sucessfully execute COMBINE archives

Exception:

The Docker image could not be successfully executed as a Singularity image (error code 1:
  docker: Command recieved::<-i /root/archive.omex -o /root>
  <-i>
  Default case selected
  VCell shall execute <biosimulations -i /root/archive.omex -o /root>
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
   INFO (CLIStandalone:36) - Starting Vcell... []{}
   INFO (BiosimulationsCommand:92) - Beginning execution []{}
   INFO (CLIPythonManager:116) - Initializing Python... []{}
  ERROR (BiosimulationsCommand:116) - Unexpected Error in BioSimulations execution: []{}
  org.vcell.cli.PythonStreamException: Python error caught: <
  Traceback (most recent call last):
    File "<stdin>", line 1, in <module>
    File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/wrapper.py", line 5, in <module>
      from deprecated import deprecated
  ModuleNotFoundError: No module named 'deprecated'
  
  >
  
  
  	at org.vcell.cli.CLIPythonManager.parsePythonReturn(CLIPythonManager.java:287) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.CLIPythonManager.parsePythonReturn(CLIPythonManager.java:263) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.CLIPythonManager.executeThroughPython(CLIPythonManager.java:192) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.CLIPythonManager.instantiatePythonProcess(CLIPythonManager.java:135) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:94) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]
  	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Log: None

Answer 92 · 2024-09-17T14:28:17.000Z

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (1.6 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'
  - 'BUNDLE_OUTPUTS'
  - 'COLLECT_COMBINE_ARCHIVE_RESULTS'
  - 'COLLECT_SED_DOCUMENT_RESULTS'
  - 'DEBUG'
  - 'H5_REPORTS_PATH'
  - 'KEEP_INDIVIDUAL_OUTPUTS'
  - 'LOG_PATH'
  - 'OMEX_METADATA_INPUT_FORMAT'
  - 'OMEX_METADATA_OUTPUT_FORMAT'
  - 'OMEX_METADATA_SCHEMA'
  - 'PLOTS_PATH'
  - 'REPORTS_PATH'
  - 'REPORT_FORMATS'
  - 'SAVE_PLOT_DATA'
  - 'VALIDATE_IMAGES'
  - 'VALIDATE_IMPORTED_MODEL_FILES'
  - 'VALIDATE_OMEX_MANIFESTS'
  - 'VALIDATE_OMEX_METADATA'
  - 'VALIDATE_RESULTS'
  - 'VALIDATE_SEDML'
  - 'VALIDATE_SEDML_MODELS'
  - 'VERBOSE'
  - 'VIZ_FORMATS'

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: None

cli.CliDisplaysHelpInline (4.2 s)

Test that a command-line interface provides inline help.

Warnings:

Command-line interfaces should display basic help when no arguments are provided.

The command-line interface displayed the following when no argument was provided:

  docker: Command recieved::<>
  <>
  Default case selected
  VCell shall execute <biosimulations >
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
   INFO (CLIStandalone:36) - Starting Vcell... []{}
  ERROR (BiosimulationsCommand:116) - Unexpected Error in BioSimulations execution: []{}
  java.lang.NullPointerException: Cannot invoke "java.io.File.getAbsolutePath()" because "outputDirectory" is null
  	at org.vcell.cli.CLIRecorder.<init>(CLIRecorder.java:70) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.CLIRecorder.<init>(CLIRecorder.java:59) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.CLIRecorder.<init>(CLIRecorder.java:48) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:50) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]
  	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

  docker: Command recieved::<-h>
  <-h>
  Default case selected
  VCell shall execute <biosimulations -h>
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
   INFO (CLIStandalone:36) - Starting Vcell... []{}
  Usage: �[1mCLIStandalone biosimulations�[21m�[0m [�[33m-dhqv�[39m�[0m] [�[33m-i�[39m�[0m=�[3m<ARCHIVE>�[23m�[0m] [�[33m-o�[39m�[0m=�[3m<OUT_DIR>�[23m�[0m]
  BioSimulators-compliant command-line interface to the vcell simulation program
  <https://vcell.org>.
    �[33m-d�[39m�[0m, �[33m--debug�[39m�[0m               full application debug mode
    �[33m-h�[39m�[0m, �[33m--help�[39m�[0m                show this help message and exit
    �[33m-i�[39m�[0m, �[33m--archive�[39m�[0m=�[3m<ARCHIVE>�[23m�[0m   Path to a COMBINE/OMEX archive file which contains
                                one or more SED-ML-encoded simulation experiments
    �[33m-o�[39m�[0m, �[33m--out-dir�[39m�[0m=�[3m<OUT_DIR>�[23m�[0m   Directory to save outputs
    �[33m-q�[39m�[0m, �[33m--quiet�[39m�[0m               suppress all console output
    �[33m-v�[39m�[0m, �[33m--version�[39m�[0m             show program's version number and exit

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

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

  docker: Command recieved::<--help>
  <--help>
  Default case selected
  VCell shall execute <biosimulations --help>
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
   INFO (CLIStandalone:36) - Starting Vcell... []{}
  Usage: �[1mCLIStandalone biosimulations�[21m�[0m [�[33m-dhqv�[39m�[0m] [�[33m-i�[39m�[0m=�[3m<ARCHIVE>�[23m�[0m] [�[33m-o�[39m�[0m=�[3m<OUT_DIR>�[23m�[0m]
  BioSimulators-compliant command-line interface to the vcell simulation program
  <https://vcell.org>.
    �[33m-d�[39m�[0m, �[33m--debug�[39m�[0m               full application debug mode
    �[33m-h�[39m�[0m, �[33m--help�[39m�[0m                show this help message and exit
    �[33m-i�[39m�[0m, �[33m--archive�[39m�[0m=�[3m<ARCHIVE>�[23m�[0m   Path to a COMBINE/OMEX archive file which contains
                                one or more SED-ML-encoded simulation experiments
    �[33m-o�[39m�[0m, �[33m--out-dir�[39m�[0m=�[3m<OUT_DIR>�[23m�[0m   Directory to save outputs
    �[33m-q�[39m�[0m, �[33m--quiet�[39m�[0m               suppress all console output
    �[33m-v�[39m�[0m, �[33m--version�[39m�[0m             show program's version number and exit

Log: None

docker_image.DeclaresSupportedEnvironmentVariables (0.4 s)

Test if a Docker image declares the environment variables that is supports

Warnings:

Docker images for simulation tools should declare the environment variables that they support.

The Docker image does not declare the following standard environment variables recognized by BioSimulators:
  - 'BUNDLE_OUTPUTS'
  - 'COLLECT_COMBINE_ARCHIVE_RESULTS'
  - 'COLLECT_SED_DOCUMENT_RESULTS'
  - 'DEBUG'
  - 'H5_REPORTS_PATH'
  - 'KEEP_INDIVIDUAL_OUTPUTS'
  - 'LOG_PATH'
  - 'OMEX_METADATA_INPUT_FORMAT'
  - 'OMEX_METADATA_OUTPUT_FORMAT'
  - 'OMEX_METADATA_SCHEMA'
  - 'PLOTS_PATH'
  - 'REPORTS_PATH'
  - 'REPORT_FORMATS'
  - 'SAVE_PLOT_DATA'
  - 'VALIDATE_IMAGES'
  - 'VALIDATE_IMPORTED_MODEL_FILES'
  - 'VALIDATE_OMEX_MANIFESTS'
  - 'VALIDATE_OMEX_METADATA'
  - 'VALIDATE_RESULTS'
  - 'VALIDATE_SEDML'
  - 'VALIDATE_SEDML_MODELS'
  - 'VERBOSE'
  - 'VIZ_FORMATS'

If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator.

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

Log: None

docker_image.HasBioContainersLabels (0.3 s)

Test that a Docker image has BioContainers labels with metadata about the image

Warnings:

Docker images are encouraged to have the following BioContainers labels:
  extra.identifiers.biotools

Log: None

Answer 93 · 2024-09-17T14:28:18.000Z

Skips

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: None

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: None

published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator (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: None

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: None

published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9004
Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_9004 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9004
Algorithm: KISAO_0000030

Reason for skip:

Case requires model formats format_9004 and simulation algorithms KISAO_0000030

Log: None

published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9012
Algorithm: KISAO_0000669

Reason for skip:

Case requires model formats format_9012 and simulation algorithms KISAO_0000669

Log: None

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: None

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: None

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: None

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: None

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: None

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: None

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: None

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: None

published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle (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: None

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: None

published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9010
Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_9010 and simulation algorithms KISAO_0000019

Log: None

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: None

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: None

sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions (0.3 s)

Test that that the curated number of output dimensions matches the actual number of output dimensions

Reason for skip:

No curated COMBINE/OMEX archives are available to generate archives for testing

Log: None

sedml.SimulatorSupportsComputeModelChanges (19.7 s)

Test that a simulator supports compute model changes

Reason for skip:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.6.0.40' could not execute the archive:

  Unknown error

Log:

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:92) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:133) - Preparing output directory... []{}

ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}

ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/archive10583932312392682480.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_4682709c-529b-4fcf-8ea5-a2e310fdcf036068961793620595705 []{}

17.09 14:20:55 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@200: found no entry for description 0 in /metadata.rdf (about=/http:/omex-library.org/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex).

17.09 14:20:55 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@200: found no entry for description 1 in /metadata.rdf (about=/http:/omex-library.org/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex/BIOMD0000000912_sim.sedml/Figure_1_bottom_left).

17.09 14:20:55 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 2 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:20:55 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 3 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:20:55 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 4 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:20:55 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 5 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:20:55 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 6 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:20:55 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 7 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:20:55 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 8 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:20:55 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 9 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:20:55 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 10 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:20:55 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 11 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:20:55 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 12 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:20:55 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 13 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:20:55 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 14 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

 INFO (OmexHandler:65) - Successfully Repaired `archive10583932312392682480.omex` []{}

 INFO (SedmlJob:110) - Initializing SED-ML document... []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:125) - Processing SED-ML: BIOMD0000000912_sim.sedml []{}

 INFO (SedmlJob:161) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

 []{}

 INFO (SedmlJob:166) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{}

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

 INFO (SedmlJob:170) - Creating pseudo SED-ML for HDF5 conversion... []{}

 INFO (SedmlJob:182) - Creating Biomodel from pseudo SED-ML []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:257) - Building solvers and starting simulation of all tasks...  []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 INFO (SEDMLImporter:182) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{}

ERROR (SolverHandler:332) - Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:253) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:156) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:173) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:897) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:309) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	... 18 more

ERROR (SedmlJob:273) - Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:253) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:156) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:173) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:897) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:309) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	... 18 more

 INFO (SedmlJob:298) - Generating outputs...  []{}

 INFO (SedmlJob:388) - Generating HDF5 file...  []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:146) - We did not get any entries in the final data set. This may mean a problem has been encountered. []{}

ERROR (SedmlJob:462) - Failure executing the sed document.  []{}

java.lang.RuntimeException: Failure executing the sed document. 

	at org.vcell.cli.run.SedmlJob.evaluateResults(SedmlJob.java:323) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:244) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:253) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:156) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:173) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

 WARN (SedmlJob:332) - Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importFailure executing the sed document.  []{}

ERROR (ExecutionJob:146) - Processing of SedML has failed.

org.vcell.cli.run.SedmlStatistics@7b95bdb0 []{}

 INFO (NativeLib:32) - Loading jhdf5 []{}

 INFO (BiosimulationsHdf5Writer:52) - Creating hdf5 file `reports.h5` in/tmp/out []{}

 INFO (BiosimulationsHdf5Writer:130) - HDF5 file successfully written to. []{}

 INFO (ExecutionJob:174) - Omex archive10583932312392682480.omex processing completed (4s) []{}

ERROR (BiosimulationsCommand:98) - Errors occurred during execution []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | SIMULATIONS_RUN(runSimulations) | **** Error: 

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:92) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:133) - Preparing output directory... []{}

ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}

ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/archive5066959645889893311.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_55808345-8121-4d50-b31a-607649d68d289694746617688289025 []{}

17.09 14:21:05 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@200: found no entry for description 0 in /metadata.rdf (about=/http:/omex-library.org/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex).

17.09 14:21:05 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@200: found no entry for description 1 in /metadata.rdf (about=/http:/omex-library.org/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex/BIOMD0000000912_sim.sedml/Figure_1_bottom_left).

17.09 14:21:05 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 2 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:21:05 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 3 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:21:05 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 4 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:21:05 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 5 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:21:05 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 6 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:21:05 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 7 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:21:05 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 8 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:21:05 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 9 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:21:05 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 10 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:21:05 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 11 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:21:05 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 12 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:21:05 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 13 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:21:05 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 14 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

 INFO (OmexHandler:65) - Successfully Repaired `archive5066959645889893311.omex` []{}

 INFO (SedmlJob:110) - Initializing SED-ML document... []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:125) - Processing SED-ML: BIOMD0000000912_sim.sedml []{}

 INFO (SedmlJob:161) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

 []{}

 INFO (SedmlJob:166) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{}

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

 INFO (SedmlJob:170) - Creating pseudo SED-ML for HDF5 conversion... []{}

 INFO (SedmlJob:182) - Creating Biomodel from pseudo SED-ML []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:257) - Building solvers and starting simulation of all tasks...  []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 INFO (SEDMLImporter:182) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{}

ERROR (SolverHandler:332) - Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:253) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:156) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:173) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:897) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:309) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	... 18 more

ERROR (SedmlJob:273) - Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:253) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:156) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:173) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:897) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:309) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	... 18 more

 INFO (SedmlJob:298) - Generating outputs...  []{}

 INFO (SedmlJob:388) - Generating HDF5 file...  []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:146) - We did not get any entries in the final data set. This may mean a problem has been encountered. []{}

ERROR (SedmlJob:462) - Failure executing the sed document.  []{}

java.lang.RuntimeException: Failure executing the sed document. 

	at org.vcell.cli.run.SedmlJob.evaluateResults(SedmlJob.java:323) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:244) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:253) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:156) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:173) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

 WARN (SedmlJob:332) - Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importFailure executing the sed document.  []{}

ERROR (ExecutionJob:146) - Processing of SedML has failed.

org.vcell.cli.run.SedmlStatistics@4217bce6 []{}

 INFO (NativeLib:32) - Loading jhdf5 []{}

 INFO (BiosimulationsHdf5Writer:52) - Creating hdf5 file `reports.h5` in/tmp/out []{}

 INFO (BiosimulationsHdf5Writer:130) - HDF5 file successfully written to. []{}

 INFO (ExecutionJob:174) - Omex archive5066959645889893311.omex processing completed (5s) []{}

ERROR (BiosimulationsCommand:98) - Errors occurred during execution []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | SIMULATIONS_RUN(runSimulations) | **** Error:

sedml.SimulatorSupportsModelAttributeChanges (18.4 s)

Test that a simulator supports changes to the attributes of model elements

Reason for skip:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.6.0.40' could not execute the archive:

  Unknown error

Log:

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:92) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:133) - Preparing output directory... []{}

ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}

ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/archive5524167257504830800.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_f3d0e290-014f-40e0-a924-53adc95a6cce3784753288549684610 []{}

17.09 14:21:36 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@200: found no entry for description 0 in /metadata.rdf (about=/http:/omex-library.org/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex).

17.09 14:21:36 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@200: found no entry for description 1 in /metadata.rdf (about=/http:/omex-library.org/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex/BIOMD0000000912_sim.sedml/Figure_1_bottom_left).

17.09 14:21:36 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 2 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:21:36 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 3 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:21:36 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 4 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:21:36 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 5 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:21:36 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 6 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:21:36 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 7 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:21:36 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 8 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:21:36 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 9 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:21:36 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 10 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:21:36 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 11 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:21:36 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 12 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:21:36 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 13 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:21:36 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 14 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

 INFO (OmexHandler:65) - Successfully Repaired `archive5524167257504830800.omex` []{}

 INFO (SedmlJob:110) - Initializing SED-ML document... []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:125) - Processing SED-ML: BIOMD0000000912_sim.sedml []{}

 INFO (SedmlJob:161) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

 []{}

 INFO (SedmlJob:166) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{}

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

 INFO (SedmlJob:170) - Creating pseudo SED-ML for HDF5 conversion... []{}

 INFO (SedmlJob:182) - Creating Biomodel from pseudo SED-ML []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:257) - Building solvers and starting simulation of all tasks...  []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 WARN (StringTools:486) - Could not create an integer from the string x []{}

ERROR (SolverHandler:332) - Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection

Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references. []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:253) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:156) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:173) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.RuntimeException: Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.

	at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:845) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:144) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	... 18 more

Caused by: java.lang.Exception: Errors reported:

IllegalArgumentException occurred: Must be of type int!



	at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:844) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:144) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	... 18 more

ERROR (SedmlJob:273) - Unable to initialize bioModel for the given selection

Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.Errors reported:

IllegalArgumentException occurred: Must be of type int!

 []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:253) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:156) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:173) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.RuntimeException: Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.

	at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:845) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:144) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	... 18 more

Caused by: java.lang.Exception: Errors reported:

IllegalArgumentException occurred: Must be of type int!



	at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:844) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:144) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	... 18 more

 INFO (SedmlJob:298) - Generating outputs...  []{}

 INFO (SedmlJob:388) - Generating HDF5 file...  []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:146) - We did not get any entries in the final data set. This may mean a problem has been encountered. []{}

ERROR (SedmlJob:462) - Failure executing the sed document.  []{}

java.lang.RuntimeException: Failure executing the sed document. 

	at org.vcell.cli.run.SedmlJob.evaluateResults(SedmlJob.java:323) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:244) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:253) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:156) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:173) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

 WARN (SedmlJob:332) - Unable to initialize bioModel for the given selection

Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.Errors reported:

IllegalArgumentException occurred: Must be of type int!

Failure executing the sed document.  []{}

ERROR (ExecutionJob:146) - Processing of SedML has failed.

org.vcell.cli.run.SedmlStatistics@28f4f300 []{}

 INFO (NativeLib:32) - Loading jhdf5 []{}

 INFO (BiosimulationsHdf5Writer:52) - Creating hdf5 file `reports.h5` in/tmp/out []{}

 INFO (BiosimulationsHdf5Writer:130) - HDF5 file successfully written to. []{}

 INFO (ExecutionJob:174) - Omex archive5524167257504830800.omex processing completed (3s) []{}

ERROR (BiosimulationsCommand:98) - Errors occurred during execution []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | SIMULATIONS_RUN(runSimulations) | **** Error: 

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:92) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:133) - Preparing output directory... []{}

ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}

ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/archive1110781233513319211.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_3fd1b9da-2666-4fc0-9a38-d3f6828a82997915658821503643507 []{}

17.09 14:21:44 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@200: found no entry for description 0 in /metadata.rdf (about=/http:/omex-library.org/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex).

17.09 14:21:44 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@200: found no entry for description 1 in /metadata.rdf (about=/http:/omex-library.org/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex/BIOMD0000000912_sim.sedml/Figure_1_bottom_left).

17.09 14:21:44 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 2 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:21:44 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 3 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:21:44 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 4 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:21:44 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 5 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:21:44 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 6 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:21:44 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 7 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:21:44 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 8 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:21:44 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 9 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:21:44 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 10 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:21:44 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 11 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:21:44 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 12 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:21:44 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 13 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:21:44 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 14 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

 INFO (OmexHandler:65) - Successfully Repaired `archive1110781233513319211.omex` []{}

 INFO (SedmlJob:110) - Initializing SED-ML docume ...

Answer 94 · 2024-09-17T14:28:18.000Z

- After correcting your simulator, please edit the first block of this issue to re-initiate this validation.
- 
- The complete log of your validation/submission job, including further information about the failure, is available for 90 days [here](https://github.com/biosimulators/Biosimulators/actions/runs/10854125878). The results of the validation of your image will also be available shortly as a JSON file. A link to this file will be available from the "Artifacts" section at the bottom of [this page](https://github.com/biosimulators/Biosimulators/actions/runs/10854125878).

Answer 95 · 2024-09-17T14:37:30.000Z

Thank you @CodeByDrescher 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 for 90 days 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 for 90 days from the "Artifacts" section at the bottom of this page.

Answer 96 · 2024-09-17T14:37:36.000Z

The specifications of your simulator is valid!

Answer 97 · 2024-09-17T14:50:41.000Z

Summary of tests

Executed 74 test cases
Passed 37 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
- log.SimulatorReportsTheStatusOfTheExecutionOfCombineArchives
- log.SimulatorReportsTheStatusOfTheExecutionOfSedDocuments
- log.SimulatorReportsTheStatusOfTheExecutionOfSedOutputs
- log.SimulatorReportsTheStatusOfTheExecutionOfSedTasks
- 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-Fehlberg
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Ciliberto-J-Cell-Biol-2003-morphogenesis-checkpoint-continuous
- published_project.SimulatorCanExecutePublishedProject:sbml-core/Elowitz-Nature-2000-Repressilator
- 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
- published_project.SimulatorCanExecutePublishedProject:vcml/Powers-Pflugers-Arch-2016-Drosophila-synaptic-strength
- results_report.SimulatorGeneratesReportsOfSimulationResults
- sedml.SimulatorCanResolveModelSourcesDefinedByUriFragments
- sedml.SimulatorCanResolveModelSourcesDefinedByUriFragmentsAndInheritChanges
- sedml.SimulatorProducesLinear2DPlots
- sedml.SimulatorProducesLogarithmic2DPlots
- sedml.SimulatorProducesMultiplePlots
- sedml.SimulatorSupportsAddReplaceRemoveModelElementChanges
- sedml.SimulatorSupportsAlgorithmParameters
- sedml.SimulatorSupportsDataGeneratorsWithDifferentShapes
- sedml.SimulatorSupportsDataSetsWithDifferentShapes
- sedml.SimulatorSupportsModelsSimulationsTasksDataGeneratorsAndReports
- sedml.SimulatorSupportsMultipleReportsPerSedDocument
- sedml.SimulatorSupportsMultipleTasksPerSedDocument
- sedml.SimulatorSupportsUniformTimeCoursesWithNonZeroOutputStartTimes
Failed 1 test cases:
- docker_image.SingularityImageExecutesSimulationsSuccessfully
Skipped 36 test cases:
- published_project.SimulatorCanExecutePublishedProject:bngl/Dolan-PLoS-Comput-Biol-2015-NHEJ
- published_project.SimulatorCanExecutePublishedProject:bngl/test-bngl
- published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator
- published_project.SimulatorCanExecutePublishedProject:cellml/Lorenz-system
- published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism
- published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE
- published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler
- published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT
- 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:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle
- published_project.SimulatorCanExecutePublishedProject:smoldyn/Lotka-Volterra
- published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells
- sedml.SimulatorProducesLinear3DPlots
- sedml.SimulatorProducesLogarithmic3DPlots
- sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions
- sedml.SimulatorSupportsComputeModelChanges
- 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

Answer 98 · 2024-09-17T14:50:42.000Z

Failures

docker_image.SingularityImageExecutesSimulationsSuccessfully (19.7 s)

Test that the Singularity version of a Docker image can sucessfully execute COMBINE archives

Exception:

The Docker image could not be successfully executed as a Singularity image (error code 1:
  docker: Command recieved::<-i /root/archive.omex -o /root>
  <-i>
  Default case selected
  VCell shall execute <biosimulations -i /root/archive.omex -o /root>
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
   INFO (CLIStandalone:36) - Starting Vcell... []{}
   INFO (BiosimulationsCommand:92) - Beginning execution []{}
   INFO (CLIPythonManager:116) - Initializing Python... []{}
  ERROR (BiosimulationsCommand:116) - Unexpected Error in BioSimulations execution: []{}
  org.vcell.cli.PythonStreamException: Python error caught: <
  Traceback (most recent call last):
    File "<stdin>", line 1, in <module>
    File "/usr/local/app/vcell/installDir/python/vcell_cli_utils/vcell_cli_utils/wrapper.py", line 5, in <module>
      from deprecated import deprecated
  ModuleNotFoundError: No module named 'deprecated'
  
  >
  
  
  	at org.vcell.cli.CLIPythonManager.parsePythonReturn(CLIPythonManager.java:287) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.CLIPythonManager.parsePythonReturn(CLIPythonManager.java:263) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.CLIPythonManager.executeThroughPython(CLIPythonManager.java:192) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.CLIPythonManager.instantiatePythonProcess(CLIPythonManager.java:135) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:94) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]
  	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Log: None

Answer 99 · 2024-09-17T14:50:43.000Z

Warnings

cli.CliDescribesSupportedEnvironmentVariablesInline (2.0 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'
  - 'BUNDLE_OUTPUTS'
  - 'COLLECT_COMBINE_ARCHIVE_RESULTS'
  - 'COLLECT_SED_DOCUMENT_RESULTS'
  - 'DEBUG'
  - 'H5_REPORTS_PATH'
  - 'KEEP_INDIVIDUAL_OUTPUTS'
  - 'LOG_PATH'
  - 'OMEX_METADATA_INPUT_FORMAT'
  - 'OMEX_METADATA_OUTPUT_FORMAT'
  - 'OMEX_METADATA_SCHEMA'
  - 'PLOTS_PATH'
  - 'REPORTS_PATH'
  - 'REPORT_FORMATS'
  - 'SAVE_PLOT_DATA'
  - 'VALIDATE_IMAGES'
  - 'VALIDATE_IMPORTED_MODEL_FILES'
  - 'VALIDATE_OMEX_MANIFESTS'
  - 'VALIDATE_OMEX_METADATA'
  - 'VALIDATE_RESULTS'
  - 'VALIDATE_SEDML'
  - 'VALIDATE_SEDML_MODELS'
  - 'VERBOSE'
  - 'VIZ_FORMATS'

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: None

cli.CliDisplaysHelpInline (4.6 s)

Test that a command-line interface provides inline help.

Warnings:

Command-line interfaces should display basic help when no arguments are provided.

The command-line interface displayed the following when no argument was provided:

  docker: Command recieved::<>
  <>
  Default case selected
  VCell shall execute <biosimulations >
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
   INFO (CLIStandalone:36) - Starting Vcell... []{}
  ERROR (BiosimulationsCommand:116) - Unexpected Error in BioSimulations execution: []{}
  java.lang.NullPointerException: Cannot invoke "java.io.File.getAbsolutePath()" because "outputDirectory" is null
  	at org.vcell.cli.CLIRecorder.<init>(CLIRecorder.java:70) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.CLIRecorder.<init>(CLIRecorder.java:59) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.CLIRecorder.<init>(CLIRecorder.java:48) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:50) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]
  	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]
  	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]
  	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

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

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

  docker: Command recieved::<-h>
  <-h>
  Default case selected
  VCell shall execute <biosimulations -h>
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
   INFO (CLIStandalone:36) - Starting Vcell... []{}
  Usage: �[1mCLIStandalone biosimulations�[21m�[0m [�[33m-dhqv�[39m�[0m] [�[33m-i�[39m�[0m=�[3m<ARCHIVE>�[23m�[0m] [�[33m-o�[39m�[0m=�[3m<OUT_DIR>�[23m�[0m]
  BioSimulators-compliant command-line interface to the vcell simulation program
  <https://vcell.org>.
    �[33m-d�[39m�[0m, �[33m--debug�[39m�[0m               full application debug mode
    �[33m-h�[39m�[0m, �[33m--help�[39m�[0m                show this help message and exit
    �[33m-i�[39m�[0m, �[33m--archive�[39m�[0m=�[3m<ARCHIVE>�[23m�[0m   Path to a COMBINE/OMEX archive file which contains
                                one or more SED-ML-encoded simulation experiments
    �[33m-o�[39m�[0m, �[33m--out-dir�[39m�[0m=�[3m<OUT_DIR>�[23m�[0m   Directory to save outputs
    �[33m-q�[39m�[0m, �[33m--quiet�[39m�[0m               suppress all console output
    �[33m-v�[39m�[0m, �[33m--version�[39m�[0m             show program's version number and exit

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

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

  docker: Command recieved::<--help>
  <--help>
  Default case selected
  VCell shall execute <biosimulations --help>
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
  WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release
   INFO (CLIStandalone:36) - Starting Vcell... []{}
  Usage: �[1mCLIStandalone biosimulations�[21m�[0m [�[33m-dhqv�[39m�[0m] [�[33m-i�[39m�[0m=�[3m<ARCHIVE>�[23m�[0m] [�[33m-o�[39m�[0m=�[3m<OUT_DIR>�[23m�[0m]
  BioSimulators-compliant command-line interface to the vcell simulation program
  <https://vcell.org>.
    �[33m-d�[39m�[0m, �[33m--debug�[39m�[0m               full application debug mode
    �[33m-h�[39m�[0m, �[33m--help�[39m�[0m                show this help message and exit
    �[33m-i�[39m�[0m, �[33m--archive�[39m�[0m=�[3m<ARCHIVE>�[23m�[0m   Path to a COMBINE/OMEX archive file which contains
                                one or more SED-ML-encoded simulation experiments
    �[33m-o�[39m�[0m, �[33m--out-dir�[39m�[0m=�[3m<OUT_DIR>�[23m�[0m   Directory to save outputs
    �[33m-q�[39m�[0m, �[33m--quiet�[39m�[0m               suppress all console output
    �[33m-v�[39m�[0m, �[33m--version�[39m�[0m             show program's version number and exit

Log: None

docker_image.DeclaresSupportedEnvironmentVariables (0.7 s)

Test if a Docker image declares the environment variables that is supports

Warnings:

Docker images for simulation tools should declare the environment variables that they support.

The Docker image does not declare the following standard environment variables recognized by BioSimulators:
  - 'BUNDLE_OUTPUTS'
  - 'COLLECT_COMBINE_ARCHIVE_RESULTS'
  - 'COLLECT_SED_DOCUMENT_RESULTS'
  - 'DEBUG'
  - 'H5_REPORTS_PATH'
  - 'KEEP_INDIVIDUAL_OUTPUTS'
  - 'LOG_PATH'
  - 'OMEX_METADATA_INPUT_FORMAT'
  - 'OMEX_METADATA_OUTPUT_FORMAT'
  - 'OMEX_METADATA_SCHEMA'
  - 'PLOTS_PATH'
  - 'REPORTS_PATH'
  - 'REPORT_FORMATS'
  - 'SAVE_PLOT_DATA'
  - 'VALIDATE_IMAGES'
  - 'VALIDATE_IMPORTED_MODEL_FILES'
  - 'VALIDATE_OMEX_MANIFESTS'
  - 'VALIDATE_OMEX_METADATA'
  - 'VALIDATE_RESULTS'
  - 'VALIDATE_SEDML'
  - 'VALIDATE_SEDML_MODELS'
  - 'VERBOSE'
  - 'VIZ_FORMATS'

If the simulation tool implements these variables, they should be declared in the Dockerfile for the Docker image for the simulator.

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

Log: None

docker_image.HasBioContainersLabels (0.7 s)

Test that a Docker image has BioContainers labels with metadata about the image

Warnings:

Docker images are encouraged to have the following BioContainers labels:
  extra.identifiers.biotools

Log: None

Answer 100 · 2024-09-17T14:50:43.000Z

Skips

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: None

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: None

published_project.SimulatorCanExecutePublishedProject:cellml/Elowitz-Nature-2000-Repressilator (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: None

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: None

published_project.SimulatorCanExecutePublishedProject:mass/Bordbar-Cell-Syst-2015-RBC-metabolism (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_2585
Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_2585 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-CVODE (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9004
Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_9004 and simulation algorithms KISAO_0000019

Log: None

published_project.SimulatorCanExecutePublishedProject:neuroml-lems/Hodgkin-Huxley-cell-Euler (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9004
Algorithm: KISAO_0000030

Reason for skip:

Case requires model formats format_9004 and simulation algorithms KISAO_0000030

Log: None

published_project.SimulatorCanExecutePublishedProject:rba/Escherichia-coli-K12-WT (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9012
Algorithm: KISAO_0000669

Reason for skip:

Case requires model formats format_9012 and simulation algorithms KISAO_0000669

Log: None

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: None

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: None

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: None

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: None

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: None

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: None

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: None

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: None

published_project.SimulatorCanExecutePublishedProject:sbml-qual/Irons-J-Theor-Biol-2009-yeast-cell-cycle (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: None

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: None

published_project.SimulatorCanExecutePublishedProject:xpp/Wu-Biochem-Pharmacol-2006-pituitary-GH3-cells (0.0 s)

Required model formats and simulation algorithms for SED tasks:

Format: format_9010
Algorithm: KISAO_0000019

Reason for skip:

Case requires model formats format_9010 and simulation algorithms KISAO_0000019

Log: None

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: None

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: None

sedml.SimulatorProducesReportsWithCuratedNumberOfDimensions (0.3 s)

Test that that the curated number of output dimensions matches the actual number of output dimensions

Reason for skip:

No curated COMBINE/OMEX archives are available to generate archives for testing

Log: None

sedml.SimulatorSupportsComputeModelChanges (20.0 s)

Test that a simulator supports compute model changes

Reason for skip:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.6.0.40' could not execute the archive:

  Unknown error

Log:

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:92) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:133) - Preparing output directory... []{}

ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}

ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/archive8686264288986387036.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_e2c8a3f0-e90e-459a-b2c8-78f43b1de5df15048698128389417129 []{}

17.09 14:43:08 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@200: found no entry for description 0 in /metadata.rdf (about=/http:/omex-library.org/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex).

17.09 14:43:08 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@200: found no entry for description 1 in /metadata.rdf (about=/http:/omex-library.org/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex/BIOMD0000000912_sim.sedml/Figure_1_bottom_left).

17.09 14:43:08 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 2 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:43:08 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 3 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:43:08 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 4 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:43:08 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 5 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:43:08 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 6 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:43:08 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 7 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:43:08 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 8 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:43:08 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 9 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:43:08 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 10 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:43:08 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 11 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:43:08 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 12 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:43:08 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 13 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:43:08 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 14 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

 INFO (OmexHandler:65) - Successfully Repaired `archive8686264288986387036.omex` []{}

 INFO (SedmlJob:110) - Initializing SED-ML document... []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:125) - Processing SED-ML: BIOMD0000000912_sim.sedml []{}

 INFO (SedmlJob:161) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

 []{}

 INFO (SedmlJob:166) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{}

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

 INFO (SedmlJob:170) - Creating pseudo SED-ML for HDF5 conversion... []{}

 INFO (SedmlJob:182) - Creating Biomodel from pseudo SED-ML []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:257) - Building solvers and starting simulation of all tasks...  []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 INFO (SEDMLImporter:182) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{}

ERROR (SolverHandler:332) - Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:253) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:156) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:173) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:897) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:309) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	... 18 more

ERROR (SedmlJob:273) - Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:253) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:156) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:173) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:897) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:309) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	... 18 more

 INFO (SedmlJob:298) - Generating outputs...  []{}

 INFO (SedmlJob:388) - Generating HDF5 file...  []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:146) - We did not get any entries in the final data set. This may mean a problem has been encountered. []{}

ERROR (SedmlJob:462) - Failure executing the sed document.  []{}

java.lang.RuntimeException: Failure executing the sed document. 

	at org.vcell.cli.run.SedmlJob.evaluateResults(SedmlJob.java:323) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:244) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:253) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:156) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:173) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

 WARN (SedmlJob:332) - Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importFailure executing the sed document.  []{}

ERROR (ExecutionJob:146) - Processing of SedML has failed.

org.vcell.cli.run.SedmlStatistics@350ff014 []{}

 INFO (NativeLib:32) - Loading jhdf5 []{}

 INFO (BiosimulationsHdf5Writer:52) - Creating hdf5 file `reports.h5` in/tmp/out []{}

 INFO (BiosimulationsHdf5Writer:130) - HDF5 file successfully written to. []{}

 INFO (ExecutionJob:174) - Omex archive8686264288986387036.omex processing completed (4s) []{}

ERROR (BiosimulationsCommand:98) - Errors occurred during execution []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | SIMULATIONS_RUN(runSimulations) | **** Error: 

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:92) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:133) - Preparing output directory... []{}

ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}

ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/archive11608050985932717507.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_27f603fb-a68f-4651-980b-1765b43e4d0017220770121999592381 []{}

17.09 14:43:18 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@200: found no entry for description 0 in /metadata.rdf (about=/http:/omex-library.org/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex).

17.09 14:43:18 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@200: found no entry for description 1 in /metadata.rdf (about=/http:/omex-library.org/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex/BIOMD0000000912_sim.sedml/Figure_1_bottom_left).

17.09 14:43:18 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 2 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:43:18 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 3 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:43:18 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 4 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:43:18 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 5 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:43:18 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 6 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:43:18 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 7 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:43:18 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 8 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:43:18 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 9 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:43:18 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 10 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:43:18 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 11 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:43:18 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 12 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:43:18 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 13 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:43:18 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 14 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

 INFO (OmexHandler:65) - Successfully Repaired `archive11608050985932717507.omex` []{}

 INFO (SedmlJob:110) - Initializing SED-ML document... []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:125) - Processing SED-ML: BIOMD0000000912_sim.sedml []{}

 INFO (SedmlJob:161) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

 []{}

 INFO (SedmlJob:166) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{}

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

 INFO (SedmlJob:170) - Creating pseudo SED-ML for HDF5 conversion... []{}

 INFO (SedmlJob:182) - Creating Biomodel from pseudo SED-ML []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:257) - Building solvers and starting simulation of all tasks...  []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 WARN (SolverUtilities:168) - KISAO - bad format, skipping []{}

 INFO (SEDMLImporter:182) - Task (id='BIOMD0000000912_task') is compatible, solver match found in ontology: 'KISAO:0000019' matched to CVODE []{}

ERROR (SolverHandler:332) - Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:253) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:156) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:173) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:897) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:309) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	... 18 more

ERROR (SedmlJob:273) - Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:253) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:156) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:173) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.RuntimeException: Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML import

	at org.jlibsedml.modelsupport.SBMLSupport.getIdFromXPathIdentifer(SBMLSupport.java:121) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.canTranslateToOverrides(SEDMLImporter.java:897) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:309) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	... 18 more

 INFO (SedmlJob:298) - Generating outputs...  []{}

 INFO (SedmlJob:388) - Generating HDF5 file...  []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:146) - We did not get any entries in the final data set. This may mean a problem has been encountered. []{}

ERROR (SedmlJob:462) - Failure executing the sed document.  []{}

java.lang.RuntimeException: Failure executing the sed document. 

	at org.vcell.cli.run.SedmlJob.evaluateResults(SedmlJob.java:323) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:244) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:253) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:156) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:173) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

 WARN (SedmlJob:332) - Unable to initialize bioModel for the given selection

Xpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importXpath for SBML Level (/sbml:sbml[1]/@level) not supported for vcell SEDML importFailure executing the sed document.  []{}

ERROR (ExecutionJob:146) - Processing of SedML has failed.

org.vcell.cli.run.SedmlStatistics@6c995c5d []{}

 INFO (NativeLib:32) - Loading jhdf5 []{}

 INFO (BiosimulationsHdf5Writer:52) - Creating hdf5 file `reports.h5` in/tmp/out []{}

 INFO (BiosimulationsHdf5Writer:130) - HDF5 file successfully written to. []{}

 INFO (ExecutionJob:174) - Omex archive11608050985932717507.omex processing completed (4s) []{}

ERROR (BiosimulationsCommand:98) - Errors occurred during execution []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | SIMULATIONS_RUN(runSimulations) | **** Error:

sedml.SimulatorSupportsModelAttributeChanges (19.3 s)

Test that a simulator supports changes to the attributes of model elements

Reason for skip:

The image 'ghcr.io/virtualcell/biosimulators_vcell:7.6.0.40' could not execute the archive:

  Unknown error

Log:

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:92) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:133) - Preparing output directory... []{}

ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}

ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/archive7772474308547968071.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_639a527e-996d-4d15-88ed-73e3ed4d8df26899727930573115470 []{}

17.09 14:43:50 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@200: found no entry for description 0 in /metadata.rdf (about=/http:/omex-library.org/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex).

17.09 14:43:50 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@200: found no entry for description 1 in /metadata.rdf (about=/http:/omex-library.org/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex/BIOMD0000000912_sim.sedml/Figure_1_bottom_left).

17.09 14:43:50 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 2 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:43:50 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 3 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:43:50 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 4 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:43:50 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 5 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:43:50 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 6 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:43:50 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 7 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:43:50 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 8 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:43:50 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 9 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:43:50 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 10 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:43:50 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 11 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:43:50 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 12 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:43:50 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 13 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:43:50 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 14 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

 INFO (OmexHandler:65) - Successfully Repaired `archive7772474308547968071.omex` []{}

 INFO (SedmlJob:110) - Initializing SED-ML document... []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:125) - Processing SED-ML: BIOMD0000000912_sim.sedml []{}

 INFO (SedmlJob:161) - Found one SED-ML document with 1 model(s), 1 simulation(s), 1 task(s), 1  report(s),  0 plot2D(s), and 0 plot3D(s)

 []{}

 INFO (SedmlJob:166) - Successful translation of SED-ML file : BIOMD0000000912_sim.sedml []{}

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

 INFO (SedmlJob:170) - Creating pseudo SED-ML for HDF5 conversion... []{}

 INFO (SedmlJob:182) - Creating Biomodel from pseudo SED-ML []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 INFO (SedmlJob:257) - Building solvers and starting simulation of all tasks...  []{}

SED-ML version level not supported, import may fail

SED-ML version level not supported, import may fail

Unsupported version, import may fail

 WARN (StringTools:486) - Could not create an integer from the string x []{}

ERROR (SolverHandler:332) - Unable to Parse SED-ML into Bio-Model, failed with err: Unable to initialize bioModel for the given selection

Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references. []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:253) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:156) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:173) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.RuntimeException: Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.

	at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:845) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:144) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	... 18 more

Caused by: java.lang.Exception: Errors reported:

IllegalArgumentException occurred: Must be of type int!



	at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:844) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:144) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	... 18 more

ERROR (SedmlJob:273) - Unable to initialize bioModel for the given selection

Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.Errors reported:

IllegalArgumentException occurred: Must be of type int!

 []{}

java.lang.RuntimeException: Unable to initialize bioModel for the given selection

Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:364) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SolverHandler.simulateAllTasks(SolverHandler.java:330) ~[vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.runSimulations(SedmlJob.java:259) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:230) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:253) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:156) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:173) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

Caused by: java.lang.RuntimeException: Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.

	at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:845) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:144) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	... 18 more

Caused by: java.lang.Exception: Errors reported:

IllegalArgumentException occurred: Must be of type int!



	at org.vcell.sedml.SEDMLImporter.createBioModels(SEDMLImporter.java:844) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.sedml.SEDMLImporter.getBioModels(SEDMLImporter.java:144) ~[vcell-core-0.0.1-SNAPSHOT.jar:?]

	... 18 more

 INFO (SedmlJob:298) - Generating outputs...  []{}

 INFO (SedmlJob:388) - Generating HDF5 file...  []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:59) - Was not able to find simulation data for task with ID: BIOMD0000000912_task []{}

 WARN (NonspatialResultsConverter:146) - We did not get any entries in the final data set. This may mean a problem has been encountered. []{}

ERROR (SedmlJob:462) - Failure executing the sed document.  []{}

java.lang.RuntimeException: Failure executing the sed document. 

	at org.vcell.cli.run.SedmlJob.evaluateResults(SedmlJob.java:323) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.SedmlJob.simulateSedml(SedmlJob.java:244) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecutionJob.executeArchive(ExecutionJob.java:139) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleExecOmex(ExecuteImpl.java:253) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:156) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.run.ExecuteImpl.singleMode(ExecuteImpl.java:173) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:95) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at org.vcell.cli.biosimulation.BiosimulationsCommand.call(BiosimulationsCommand.java:19) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

	at picocli.CommandLine.executeUserObject(CommandLine.java:1953) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.access$1300(CommandLine.java:145) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.executeUserObjectOfLastSubcommandWithSameParent(CommandLine.java:2358) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2352) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.handle(CommandLine.java:2314) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$AbstractParseResultHandler.execute(CommandLine.java:2179) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine$RunLast.execute(CommandLine.java:2316) [picocli-4.6.3.jar:4.6.3]

	at picocli.CommandLine.execute(CommandLine.java:2078) [picocli-4.6.3.jar:4.6.3]

	at org.vcell.cli.CLIStandalone.main(CLIStandalone.java:43) [vcell-cli-0.0.1-SNAPSHOT.jar:?]

 WARN (SedmlJob:332) - Unable to initialize bioModel for the given selection

Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.Unresolvable Model(s) encountered. Either there is incompatible / unsupported SED-ML features, or there are unresolvable references.Errors reported:

IllegalArgumentException occurred: Must be of type int!

Failure executing the sed document.  []{}

ERROR (ExecutionJob:146) - Processing of SedML has failed.

org.vcell.cli.run.SedmlStatistics@1d61a348 []{}

 INFO (NativeLib:32) - Loading jhdf5 []{}

 INFO (BiosimulationsHdf5Writer:52) - Creating hdf5 file `reports.h5` in/tmp/out []{}

 INFO (BiosimulationsHdf5Writer:130) - HDF5 file successfully written to. []{}

 INFO (ExecutionJob:174) - Omex archive7772474308547968071.omex processing completed (3s) []{}

ERROR (BiosimulationsCommand:98) - Errors occurred during execution []{}

 | Root(root) | OMEX_EXECUTE(archive.omex) | SIMULATIONS_RUN(runSimulations) | **** Error: 

docker: Command recieved::<-i /tmp/in/archive.omex -o /tmp/out>

<-i>

Default case selected

VCell shall execute <biosimulations -i /tmp/in/archive.omex -o /tmp/out>

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

WARN StatusConsoleListener The use of package scanning to locate plugins is deprecated and will be removed in a future release

 INFO (CLIStandalone:36) - Starting Vcell... []{}

 INFO (BiosimulationsCommand:92) - Beginning execution []{}

 INFO (CLIPythonManager:116) - Initializing Python... []{}

 INFO (CLIPythonManager:136) - Python initialization success! []{}

 INFO (ExecuteImpl:133) - Preparing output directory... []{}

ERROR (CLIUtils:37) - Failed to delete the file: /tmp/out []{}

ERROR (RunUtils:508) - java.lang.Exception: File '/tmp/out' could not be deleted! []{}

 INFO (ExecutionJob:84) - Executing OMEX archive /tmp/archive17874462645847002722.omex []{}

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

 INFO (RunUtils:476) - TempPath Created: /tmp/vcell_temp_6f4df73c-e564-4a5f-9339-d904006e79117539994246758202697 []{}

17.09 14:43:59 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@200: found no entry for description 0 in /metadata.rdf (about=/http:/omex-library.org/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex).

17.09 14:43:59 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@200: found no entry for description 1 in /metadata.rdf (about=/http:/omex-library.org/Caravagna-J-Theor-Biol-2010-tumor-suppressive-oscillations.omex/BIOMD0000000912_sim.sedml/Figure_1_bottom_left).

17.09 14:43:59 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 2 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:43:59 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 3 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:43:59 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 4 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:43:59 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 5 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:43:59 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 6 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:43:59 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 7 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:43:59 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 8 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:43:59 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 9 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:43:59 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 10 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:43:59 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 11 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:43:59 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 12 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:43:59 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 13 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

17.09 14:43:59 ERROR de.unirostock.sems.cbarchive.meta.MetaDataFile@136: meta description 14 in /metadata.rdf does not contain an `about` value. so we cannot assign it to an entity.

 INFO (OmexHandler:65) - Successfully Repaired `archive17874462645847002722.omex` []{}

 INFO (SedmlJob:110) - Initializing SED-ML do ...

Simulation tool

Support for BioSimulators' conventions

Summary of tests

Failures

Warnings

Skips

Summary of tests

Failures

Warnings

Skips

Summary of tests

Failures

Warnings

Skips

Summary of tests

Failures

Warnings

Skips

Summary of tests

Failures

Warnings

Skips

Summary of tests

Failures

Warnings

Skips

Summary of tests

Failures

Warnings

Skips