biosimulators_rbapy package

biosimulators_rbapy.exec_sed_doc(doc, working_dir, base_out_path, rel_out_path=None, apply_xml_model_changes=False, log=None, indent=0, pretty_print_modified_xml_models=False, log_level=StandardOutputErrorCapturerLevel.c, config=None)[source]

Execute the tasks specified in a SED document and generate the specified outputs

Parameters

  • doc (SedDocument or str) – SED document or a path to SED-ML file which defines a SED document

  • working_dir (str) – working directory of the SED document (path relative to which models are located)

  • base_out_path (str) –

    path to store the outputs

    • CSV: directory in which to save outputs to files {base_out_path}/{rel_out_path}/{report.id}.csv

    • HDF5: directory in which to save a single HDF5 file ({base_out_path}/reports.h5), with reports at keys {rel_out_path}/{report.id} within the HDF5 file

  • rel_out_path (str, optional) – path relative to base_out_path to store the outputs

  • apply_xml_model_changes (bool, optional) – if True, apply any model changes specified in the SED-ML file before calling task_executer.

  • log (SedDocumentLog, optional) – log of the document

  • indent (int, optional) – degree to indent status messages

  • pretty_print_modified_xml_models (bool, optional) – if True, pretty print modified XML models

  • log_level (StandardOutputErrorCapturerLevel, optional) – level at which to log output

  • config (Config, optional) – BioSimulators common configuration

  • simulator_config (SimulatorConfig, optional) – tellurium configuration

Returns

  • ReportResults: results of each report

  • SedDocumentLog: log of the document

Return type

tuple

biosimulators_rbapy.exec_sed_task(task, variables, preprocessed_task=None, log=None, config=None)[source]

Execute a task and save its results

Parameters

  • task (Task) – task

  • variables (list of Variable) – variables that should be recorded

  • preprocessed_task (dict, optional) – preprocessed information about the task, including possible model changes and variables. This can be used to avoid repeatedly executing the same initialization for repeated calls to this method.

  • log (TaskLog, optional) – log for the task

  • config (Config, optional) – BioSimulators common configuration

Returns

VariableResults: results of variables TaskLog: log

Return type

tuple

Raises

NotImplementedError –

  • Task requires a time course that RBApy doesn’t support * Task requires an algorithm that RBApy doesn’t support

biosimulators_rbapy.exec_sedml_docs_in_combine_archive(archive_filename, out_dir, config=None)[source]

Execute the SED tasks defined in a COMBINE/OMEX archive and save the outputs

Parameters

  • archive_filename (str) – path to COMBINE/OMEX archive

  • out_dir (str) –

    path to store the outputs of the archive

    • CSV: directory in which to save outputs to files { out_dir }/{ relative-path-to-SED-ML-file-within-archive }/{ report.id }.csv

    • HDF5: directory in which to save a single HDF5 file ({ out_dir }/reports.h5), with reports at keys { relative-path-to-SED-ML-file-within-archive }/{ report.id } within the HDF5 file

  • config (Config, optional) – BioSimulators common configuration

Returns

  • SedDocumentResults: results

  • CombineArchiveLog: log

Return type

tuple

biosimulators_rbapy.get_simulator_version()[source]

Get the version of RBApy

Returns

version

Return type

str

biosimulators_rbapy.preprocess_sed_task(task, variables, config=None)[source]

Preprocess a SED task, including its possible model changes and variables. This is useful for avoiding repeatedly initializing tasks on repeated calls of exec_sed_task.

Parameters

  • task (Task) – task

  • variables (list of Variable) – variables that should be recorded

  • config (Config, optional) – BioSimulators common configuration

Returns

preprocessed information about the task

Return type

dict

Submodules

biosimulators_rbapy.core module

BioSimulators-compliant command-line interface to the RBApy simulation program.

Author

Jonathan Karr <karr@mssm.edu>

Date

2021-08-12

Copyright

2021, Center for Reproducible Biomedical Modeling

License

MIT

biosimulators_rbapy.core.exec_sed_doc(doc, working_dir, base_out_path, rel_out_path=None, apply_xml_model_changes=False, log=None, indent=0, pretty_print_modified_xml_models=False, log_level=StandardOutputErrorCapturerLevel.c, config=None)[source]

Execute the tasks specified in a SED document and generate the specified outputs

Parameters

  • doc (SedDocument or str) – SED document or a path to SED-ML file which defines a SED document

  • working_dir (str) – working directory of the SED document (path relative to which models are located)

  • base_out_path (str) –

    path to store the outputs

    • CSV: directory in which to save outputs to files {base_out_path}/{rel_out_path}/{report.id}.csv

    • HDF5: directory in which to save a single HDF5 file ({base_out_path}/reports.h5), with reports at keys {rel_out_path}/{report.id} within the HDF5 file

  • rel_out_path (str, optional) – path relative to base_out_path to store the outputs

  • apply_xml_model_changes (bool, optional) – if True, apply any model changes specified in the SED-ML file before calling task_executer.

  • log (SedDocumentLog, optional) – log of the document

  • indent (int, optional) – degree to indent status messages

  • pretty_print_modified_xml_models (bool, optional) – if True, pretty print modified XML models

  • log_level (StandardOutputErrorCapturerLevel, optional) – level at which to log output

  • config (Config, optional) – BioSimulators common configuration

  • simulator_config (SimulatorConfig, optional) – tellurium configuration

Returns

  • ReportResults: results of each report

  • SedDocumentLog: log of the document

Return type

tuple

biosimulators_rbapy.core.exec_sed_task(task, variables, preprocessed_task=None, log=None, config=None)[source]

Execute a task and save its results

Parameters

  • task (Task) – task

  • variables (list of Variable) – variables that should be recorded

  • preprocessed_task (dict, optional) – preprocessed information about the task, including possible model changes and variables. This can be used to avoid repeatedly executing the same initialization for repeated calls to this method.

  • log (TaskLog, optional) – log for the task

  • config (Config, optional) – BioSimulators common configuration

Returns

VariableResults: results of variables TaskLog: log

Return type

tuple

Raises

NotImplementedError –

  • Task requires a time course that RBApy doesn’t support * Task requires an algorithm that RBApy doesn’t support

biosimulators_rbapy.core.exec_sedml_docs_in_combine_archive(archive_filename, out_dir, config=None)[source]

Execute the SED tasks defined in a COMBINE/OMEX archive and save the outputs

Parameters

  • archive_filename (str) – path to COMBINE/OMEX archive

  • out_dir (str) –

    path to store the outputs of the archive

    • CSV: directory in which to save outputs to files { out_dir }/{ relative-path-to-SED-ML-file-within-archive }/{ report.id }.csv

    • HDF5: directory in which to save a single HDF5 file ({ out_dir }/reports.h5), with reports at keys { relative-path-to-SED-ML-file-within-archive }/{ report.id } within the HDF5 file

  • config (Config, optional) – BioSimulators common configuration

Returns

  • SedDocumentResults: results

  • CombineArchiveLog: log

Return type

tuple

biosimulators_rbapy.core.modify_model(model, changes, preprocessed_task)[source]

Modify a model

Parameters

  • model (rba.model.RbaModel) – RBA model

  • changes (list of ModelAttributeChange) – changes to apply to the model

  • preprocessed_task (dict) – preprocessed informationa about the model

biosimulators_rbapy.core.preprocess_sed_task(task, variables, config=None)[source]

Preprocess a SED task, including its possible model changes and variables. This is useful for avoiding repeatedly initializing tasks on repeated calls of exec_sed_task.

Parameters

  • task (Task) – task

  • variables (list of Variable) – variables that should be recorded

  • config (Config, optional) – BioSimulators common configuration

Returns

preprocessed information about the task

Return type

dict