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
ofstr
toSedDocumentExecutionStatus
): execution status of eachSED document in the archive
out_dir (
str
): directory to export status
-
class
biosimulators_utils.exec_status.data_model.
ExecutionStatus
(value)[source]¶ Bases:
str
,enum.Enum
Execution status of a component of a COMBINE/OMEX archive
-
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
-
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
ofstr
toExecutionStatus
): execution status of eachcurve
document_status (
SedDocumentExecutionStatus
): execution status of parent SED document
-
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
ofstr
toExecutionStatus
): execution status of eachsurface
document_status (
SedDocumentExecutionStatus
): execution status of parent SED document
-
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
ofstr
toExecutionStatus
): execution status of eachdata set
document_status (
SedDocumentExecutionStatus
): execution status of parent SED document
-
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
ofstr
toTaskExecutionStatus
): execution status of eachtask
- outputs (
dict
ofstr
toOutputExecutionStatus
): execution status of each output
combine_archive_status (
CombineArchiveExecutionStatus
): execution status of parent COMBINE/OMEX archive- outputs (
-
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
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 archivearchive_dir (
str
) – path where the content of the archive is locatedsupported_features (
list
oftype
, 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