2.1.4. biosimulators_utils.exec_status package

2.1.4.1. Submodules

2.1.4.2. biosimulators_utils.exec_status.data_model module

Data model for the execution status of COMBINE/OMEX archives

Author

Jonathan Karr <karr@mssm.edu>

Date

2020-12-06

Copyright

2020, Center for Reproducible Biomedical Modeling

License

MIT

class biosimulators_utils.exec_status.data_model.CombineArchiveExecutionStatus(status=None, sed_documents=None, out_dir=None)[source]

Bases: object

Execution status of a COMBINE/OMEX archive

Attributes

status (ExecutionStatus): execution status of the archive sed_documents (dict of str to SedDocumentExecutionStatus): execution status of each

SED document in the archive

out_dir (str): directory to export status

export()[source]

Write to a file

finalize()[source]

Mark all unexceuted elements as skipped

to_dict()[source]

Generate a JSON-compatible representation

Returns

JSON-compatible representation

Return type

dict

class biosimulators_utils.exec_status.data_model.ExecutionStatus(value)[source]

Bases: str, enum.Enum

Execution status of a component of a COMBINE/OMEX archive

FAILED = 'FAILED'[source]
QUEUED = 'QUEUED'[source]
RUNNING = 'RUNNING'[source]
SKIPPED = 'SKIPPED'[source]
SUCCEEDED = 'SUCCEEDED'[source]
class biosimulators_utils.exec_status.data_model.OutputExecutionStatus(status=None, document_status=None)[source]

Bases: object

Execution status of a SED output

Attributes

status (ExecutionStatus): execution status of the archive document_status (SedDocumentExecutionStatus): execution status of parent SED document

export()[source]

Write to a file

finalize()[source]

Mark all unexceuted elements as skipped

to_dict()[source]

Generate a JSON-compatible representation

Returns

JSON-compatible representation

Return type

dict

class biosimulators_utils.exec_status.data_model.Plot2DExecutionStatus(status=None, curves=None, document_status=None)[source]

Bases: biosimulators_utils.exec_status.data_model.OutputExecutionStatus

Execution status of a 2D SED plot

Attributes

status (ExecutionStatus): execution status of the archive curves (dict of str to ExecutionStatus): execution status of each

curve

document_status (SedDocumentExecutionStatus): execution status of parent SED document

finalize()[source]

Mark all unexceuted elements as skipped

to_dict()[source]

Generate a JSON-compatible representation

Returns

JSON-compatible representation

Return type

dict

class biosimulators_utils.exec_status.data_model.Plot3DExecutionStatus(status=None, surfaces=None, document_status=None)[source]

Bases: biosimulators_utils.exec_status.data_model.OutputExecutionStatus

Execution status of a 3D SED plot

Attributes

status (ExecutionStatus): execution status of the archive surfaces (dict of str to ExecutionStatus): execution status of each

surface

document_status (SedDocumentExecutionStatus): execution status of parent SED document

finalize()[source]

Mark all unexceuted elements as skipped

to_dict()[source]

Generate a JSON-compatible representation

Returns

JSON-compatible representation

Return type

dict

class biosimulators_utils.exec_status.data_model.ReportExecutionStatus(status=None, data_sets=None, document_status=None)[source]

Bases: biosimulators_utils.exec_status.data_model.OutputExecutionStatus

Execution status of a SED report

Attributes

status (ExecutionStatus): execution status of the archive data_sets (dict of str to ExecutionStatus): execution status of each

data set

document_status (SedDocumentExecutionStatus): execution status of parent SED document

finalize()[source]

Mark all unexceuted elements as skipped

to_dict()[source]

Generate a JSON-compatible representation

Returns

JSON-compatible representation

Return type

dict

class biosimulators_utils.exec_status.data_model.SedDocumentExecutionStatus(status=None, tasks=None, outputs=None, combine_archive_status=None)[source]

Bases: object

Execution status of a SED document

Attributes

status (ExecutionStatus): execution status of the archive tasks (dict of str to TaskExecutionStatus): execution status of each

task

outputs (dict of str to OutputExecutionStatus): execution status of each

output

combine_archive_status (CombineArchiveExecutionStatus): execution status of parent COMBINE/OMEX archive

export()[source]

Write to a file

finalize()[source]

Mark all unexceuted elements as skipped

to_dict()[source]

Generate a JSON-compatible representation

Returns

JSON-compatible representation

Return type

dict

class biosimulators_utils.exec_status.data_model.TaskExecutionStatus(status=None, document_status=None)[source]

Bases: object

Execution status of a SED task

Attributes

status (ExecutionStatus): execution status of the task document_status (SedDocumentExecutionStatus): execution status of parent SED document

export()[source]

Write to a file

finalize()[source]

Mark all unexceuted elements as skipped

to_dict()[source]

Generate a JSON-compatible representation

Returns

JSON-compatible representation

Return type

dict

2.1.4.3. biosimulators_utils.exec_status.utils module

Utilities for working with COMBINE/OMEX archives

Author

Jonathan Karr <karr@mssm.edu>

Date

2020-12-06

Copyright

2020, Center for Reproducible Biomedical Modeling

License

MIT

biosimulators_utils.exec_status.utils.init_combine_archive_exec_status(archive, archive_dir, supported_features=(<class 'biosimulators_utils.combine.data_model.CombineArchive'>, <class 'biosimulators_utils.sedml.data_model.SedDocument'>, <class 'biosimulators_utils.sedml.data_model.Task'>, <class 'biosimulators_utils.sedml.data_model.Report'>))[source]

Initialize the execution status of the SED documents in a COMBINE/OMEX archive

Parameters

  • archive (CombineArchive) – COMBINE/OMEX archive

  • archive_dir (str) – path where the content of the archive is located

  • supported_features (list of type, optional) – list of supported SED elements. Default: COMBINE/OMEX archives, SED documents, SED tasks, and SED reports

Returns

initial execution status of the SED documents in an archive

Return type

CombineArchiveExecutionStatus