biosimulators_utils.log package¶
Submodules¶
biosimulators_utils.log.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.log.data_model.CombineArchiveLog(id=None, status=None, exception=None, skip_reason=None, output=None, duration=None, sed_documents=None, out_dir=None)[source]¶
Bases:
biosimulators_utils.log.data_model.Log
Log of a COMBINE/OMEX archive
- sed_documents[source]¶
execution status of each SED document in the archive
- Type
dict
ofstr
toSedDocumentLog
- class biosimulators_utils.log.data_model.Log(id=None, status=None, exception=None, skip_reason=None, output=None, duration=None, parent=None, out_dir=None)[source]¶
Bases:
object
Log of a COMBINE/OMEX archive or one of its components
- class biosimulators_utils.log.data_model.OutputLog(id=None, status=None, exception=None, skip_reason=None, output=None, duration=None, parent=None, out_dir=None)[source]¶
Bases:
biosimulators_utils.log.data_model.Log
Log of a SED output
- class biosimulators_utils.log.data_model.Plot2DLog(id=None, status=None, exception=None, skip_reason=None, output=None, duration=None, curves=None, parent=None, out_dir=None)[source]¶
Bases:
biosimulators_utils.log.data_model.OutputLog
Log of a 2D SED plot
- class biosimulators_utils.log.data_model.Plot3DLog(id=None, status=None, exception=None, skip_reason=None, output=None, duration=None, surfaces=None, parent=None, out_dir=None)[source]¶
Bases:
biosimulators_utils.log.data_model.OutputLog
Log of a 3D SED plot
- class biosimulators_utils.log.data_model.ReportLog(id=None, status=None, exception=None, skip_reason=None, output=None, duration=None, data_sets=None, parent=None, out_dir=None)[source]¶
Bases:
biosimulators_utils.log.data_model.OutputLog
Log of a SED report
- class biosimulators_utils.log.data_model.SedDocumentLog(location=None, status=None, exception=None, skip_reason=None, output=None, duration=None, tasks=None, outputs=None, parent=None, out_dir=None)[source]¶
Bases:
biosimulators_utils.log.data_model.Log
Log of a SED document
- class biosimulators_utils.log.data_model.StandardOutputErrorCapturerLevel(value)[source]¶
Bases:
int
,enum.Enum
Level at which stdout/stderr should be captured
- class biosimulators_utils.log.data_model.Status(value)[source]¶
Bases:
str
,enum.Enum
Status of COMBINE/OMEX archive or one of its components
- class biosimulators_utils.log.data_model.TaskLog(id=None, status=None, exception=None, skip_reason=None, output=None, duration=None, algorithm=None, simulator_details=None, parent=None, out_dir=None)[source]¶
Bases:
biosimulators_utils.log.data_model.Log
Log of a SED task
biosimulators_utils.log.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
- class biosimulators_utils.log.utils.StandardOutputErrorCapturer(level=StandardOutputErrorCapturerLevel.c, relay=False, termination_delay=0.01, disabled=False)[source]¶
Bases:
contextlib.AbstractContextManager
Context manager for capturing standard output/error. When
capturer
is available (i.e., Linux, MacOS, Unix),capturer
is used to capture standard output/error. Whencapturer
is not available (i.e. Windows), this context manager issues a warn and collects no output. The purpose of this context manager is to encapsulate the handling of whethercapturer
is or isn’t available so that the other modules can work seamless in Linux, as well as Windows (except without the ability to log standard output/error).- level[source]¶
level at which stdout/stderr should be captured
- Type
StandardOutputErrorCapturerLevel
, optional
- relay[source]¶
if
True
, collect the standard output/error streams and continue to pass them along. ifFalse
, collect the stream, squash them, and do not pass them along.- Type
bool
- biosimulators_utils.log.utils.get_summary_combine_archive_log(log)[source]¶
Get a summary of the log of a COMBINE/OMEX archive
- Parameters
log (
CombineArchiveLog
) – log of a COMBINE/OMEX archive- Returns
summary of the log
- Return type
str
- biosimulators_utils.log.utils.init_combine_archive_log(archive, archive_dir, supported_features=(<class 'biosimulators_utils.sedml.data_model.SedDocument'>, <class 'biosimulators_utils.sedml.data_model.Task'>, <class 'biosimulators_utils.sedml.data_model.Report'>, <class 'biosimulators_utils.sedml.data_model.Plot2D'>, <class 'biosimulators_utils.sedml.data_model.Plot3D'>, <class 'biosimulators_utils.sedml.data_model.DataSet'>, <class 'biosimulators_utils.sedml.data_model.Curve'>, <class 'biosimulators_utils.sedml.data_model.Surface'>), logged_features=(<class 'biosimulators_utils.sedml.data_model.SedDocument'>, <class 'biosimulators_utils.sedml.data_model.Task'>, <class 'biosimulators_utils.sedml.data_model.Report'>, <class 'biosimulators_utils.sedml.data_model.Plot2D'>, <class 'biosimulators_utils.sedml.data_model.Plot3D'>, <class 'biosimulators_utils.sedml.data_model.DataSet'>, <class 'biosimulators_utils.sedml.data_model.Curve'>, <class 'biosimulators_utils.sedml.data_model.Surface'>))[source]¶
Initialize a log of 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 elements. Default: COMBINE/OMEX archives and SED documents, tasks, reports, plots, data sets, curves, and surfaces.logged_features (
list
oftype
, optional) – list of elements which will be logged. Default: COMBINE/OMEX archives and SED documents, tasks, reports, plots, data sets, curves, and surfaces.
- Returns
initialized log of a COMBINE/OMEX archive
- Return type
CombineArchiveLog
- biosimulators_utils.log.utils.init_output_log(output, supported_features=(<class 'biosimulators_utils.sedml.data_model.DataSet'>, <class 'biosimulators_utils.sedml.data_model.Curve'>, <class 'biosimulators_utils.sedml.data_model.Surface'>), logged_features=(<class 'biosimulators_utils.sedml.data_model.DataSet'>, <class 'biosimulators_utils.sedml.data_model.Curve'>, <class 'biosimulators_utils.sedml.data_model.Surface'>))[source]¶
Initialize a log of an output
- Parameters
output (
Output
) – a SED outputsupported_features (
list
oftype
, optional) – list of supported elements. Default: data sets, curves, and surfaces.logged_features (
list
oftype
, optional) – list of elements which will be logged. Default: data sets, curves, and surfaces.
- Returns
initialized log of a SED document
- Return type
OutputLog
- biosimulators_utils.log.utils.init_plot2d_log(plot, supported_features=<class 'biosimulators_utils.sedml.data_model.Curve'>, logged_features=<class 'biosimulators_utils.sedml.data_model.Curve'>)[source]¶
Initialize a log of a 2D plot
- Parameters
plot (
Plot2D
) – a SED 2D plotsupported_features (
list
oftype
, optional) – list of supported elements. Default: curves.logged_features (
list
oftype
, optional) – list of elements which will be logged. Default: curves.
- Returns
initialized log of a 2D plot
- Return type
Plot2DLog
- biosimulators_utils.log.utils.init_plot3d_log(plot, supported_features=<class 'biosimulators_utils.sedml.data_model.Surface'>, logged_features=<class 'biosimulators_utils.sedml.data_model.Surface'>)[source]¶
Initialize a log of a 3D plot
- Parameters
plot (
Plot3D
) – a SED 3D plotsupported_features (
list
oftype
, optional) – list of supported elements. Default: surfaces.logged_features (
list
oftype
, optional) – list of elements which will be logged. Default: surfaces.
- Returns
initialized log of a 3D plot
- Return type
Plot3DLog
- biosimulators_utils.log.utils.init_report_log(report, supported_features=(<class 'biosimulators_utils.sedml.data_model.DataSet'>, <class 'biosimulators_utils.sedml.data_model.Curve'>, <class 'biosimulators_utils.sedml.data_model.Surface'>), logged_features=(<class 'biosimulators_utils.sedml.data_model.DataSet'>, <class 'biosimulators_utils.sedml.data_model.Curve'>, <class 'biosimulators_utils.sedml.data_model.Surface'>))[source]¶
Initialize a log of a report
- Parameters
report (
Report
) – a SED reportsupported_features (
list
oftype
, optional) – list of supported elements. Default: data sets.logged_features (
list
oftype
, optional) – list of elements which will be logged. Default: data sets.
- Returns
initialized log of a report
- Return type
ReportLog
- biosimulators_utils.log.utils.init_sed_document_log(doc, supported_features=(<class 'biosimulators_utils.sedml.data_model.Task'>, <class 'biosimulators_utils.sedml.data_model.Report'>, <class 'biosimulators_utils.sedml.data_model.Plot2D'>, <class 'biosimulators_utils.sedml.data_model.Plot3D'>, <class 'biosimulators_utils.sedml.data_model.DataSet'>, <class 'biosimulators_utils.sedml.data_model.Curve'>, <class 'biosimulators_utils.sedml.data_model.Surface'>), logged_features=(<class 'biosimulators_utils.sedml.data_model.Task'>, <class 'biosimulators_utils.sedml.data_model.Report'>, <class 'biosimulators_utils.sedml.data_model.Plot2D'>, <class 'biosimulators_utils.sedml.data_model.Plot3D'>, <class 'biosimulators_utils.sedml.data_model.DataSet'>, <class 'biosimulators_utils.sedml.data_model.Curve'>, <class 'biosimulators_utils.sedml.data_model.Surface'>))[source]¶
Initialize a log of a SED document
- Parameters
doc (
SedDocument
) – SED documentsupported_features (
list
oftype
, optional) – list of supported elements. Default: tasks, reports, plots, data sets, curves, and surfaces.logged_features (
list
oftype
, optional) – list of SED elements which will be logged. Default: tasks, reports, plots, data sets, curves, and surfaces.
- Returns
initialized log of a SED document
- Return type
SedDocumentLog
- biosimulators_utils.log.utils.init_task_log(task, supported_features=(), logged_features=())[source]¶
Initialize a log of a task
- Parameters
output (
Task
) – a SED tasksupported_features (
list
oftype
, optional) – list of supported elements. Default: empty list.logged_features (
list
oftype
, optional) – list of elements which will be logged. Default: empty list.
- Returns
initialized log of a SED document
- Return type
OutputLog
biosimulators_utils.log.warnings module¶
Warnings for logging
- Author
Jonathan Karr <karr@mssm.edu>
- Date
2021-02-04
- Copyright
2021, Center for Reproducible Biomedical Modeling
- License
MIT
- exception biosimulators_utils.log.warnings.StandardOutputNotLoggedWarning[source]¶
Bases:
biosimulators_utils.warnings.BioSimulatorsWarning
Warning that standard output and error could not be logged