biosimulators_utils.report package

Submodules

biosimulators_utils.report.data_model module

Data model for reports

Author:

Jonathan Karr <karr@mssm.edu>

Date:

2020-12-06

Copyright:

2020, Center for Reproducible Biomedical Modeling

License:

MIT

class biosimulators_utils.report.data_model.DataGeneratorResults

Bases: dict

Dictionary that maps the ids of data generators (DataGenerator) to their results (numpy.ndarray)

• Keys (str): ids of data generators (DataGenerator)

• Values (numpy.ndarray): result of each variable

  • Steady-state tasks of non-spatial models: results should be arrays of shape (1,)

  • One-step tasks of non-spatial models: results should be arrays of shape (2,)

  • Uniform time course tasks of non-spatial models: results should be arrays of shape (number_of_steps + 1,)

class biosimulators_utils.report.data_model.DataSetResults

Bases: dict

Dictionary that maps the ids of data sets to their results (numpy.ndarray)

• Keys (str): ids of data sets

• Values (numpy.ndarray): result of each data set

  • Steady-state tasks of non-spatial models: results should be arrays of shape (number of data sets, 1)

  • One-step tasks of non-spatial models: results should be arrays of shape (number of data sets, 2)

  • Uniform time course tasks of non-spatial models: results should be arrays of shape (number_of_steps + 1,)

class biosimulators_utils.report.data_model.ReportFormat(value)

Bases: str, Enum

Format of a report

csv = 'csv'

h5 = 'h5'

hdf = 'h5'

hdf5 = 'h5'

tsv = 'tsv'

xlsx = 'xlsx'

class biosimulators_utils.report.data_model.ReportResults

Bases: dict

Dictionary that maps the ids of reports (e.g., Report) to their results (DataSetResults)

• Keys (str): ids of reports (e.g., Report)

• Values (DataSetResults): result of each report

class biosimulators_utils.report.data_model.SedDocumentResults

Bases: dict

Dictionary that maps the locations of SED-ML documents (e.g., SedDocument) to their results (ReportResults)

• Keys (str): locations of SED documents (e.g., SedDocument)

• Values (ReportResults): result of each document

class biosimulators_utils.report.data_model.VariableResults

Bases: dict

Dictionary that maps the ids of variables (Variable) to their results (numpy.ndarray)

• Keys (str): ids of variables (Variable)

• Values (numpy.ndarray): result of each variable

  • Steady-state tasks of non-spatial models: results should be arrays of shape (1,)

  • One-step tasks of non-spatial models: results should be arrays of shape (2,)

  • Uniform time course tasks of non-spatial models: results should be arrays of shape (number_of_steps + 1,)

biosimulators_utils.report.io module

Utilities for reading and writing reports

Author:

Jonathan Karr <karr@mssm.edu>

Date:

2020-12-06

Copyright:

2020, Center for Reproducible Biomedical Modeling

License:

MIT

class biosimulators_utils.report.io.ReportReader

Bases: object

Class for reading reports of simulation results

static append_report_id(type, report_ids, name, object)

get_ids(base_path, format=ReportFormat.h5, type=<class 'biosimulators_utils.sedml.data_model.Output'>)

Get the ids of the reports in a file

Parameters:

• base_path (str) –

  path to save results

  • CSV: parent directory to save results

  • HDF5: file to save results

• format (ReportFormat, optional) – report format

• type (type) – type of report to get

Returns:

ids of reports

Return type:

list of str

static parse_dataset_str_list_values(raw_values: list)

static parse_dataset_str_value(raw_value)

run(report, base_path, rel_path, format=ReportFormat.h5)

Read a report for a file

Parameters:

• report (Report) – report

• base_path (str) –

  path to save results

  • CSV: parent directory to save results

  • HDF5: file to save results

• rel_path (str) –

  path to save results relative to base_path

  • CSV: relative path to base_path

  • HDF5: key within HDF5 file

• format (ReportFormat, optional) – report format

Returns:

report results

Return type:

DataSetResults

class biosimulators_utils.report.io.ReportWriter

Bases: object

Class for writing reports of simulation results

run(report, results, base_path, rel_path, format=ReportFormat.h5, type=<class 'biosimulators_utils.sedml.data_model.Report'>)

Save a report

Parameters:

• report (Report) – report

• results (DataSetResults) – results of the data sets

• base_path (str) –

  path to save results

  • CSV: parent directory to save results

  • HDF5: file to save results

• rel_path (str) –

  path to save results relative to base_path

  • CSV: relative path to base_path

  • HDF5: key within HDF5 file

• format (ReportFormat, optional) – report format

• type (type) – type of output (e.g., subclass of Output such as Report, Plot2D)

biosimulators_utils.report.warnings module

Warnings for reports

Author:

Jonathan Karr <karr@mssm.edu>

Date:

2021-01-21

Copyright:

2021, Center for Reproducible Biomedical Modeling

License:

MIT

exception biosimulators_utils.report.warnings.CannotExportMultidimensionalTableWarning

Bases: BioSimulatorsWarning

Warning that a multidimensional report cannot be exported (e.g., to CSV, Excel, or TSV).

exception biosimulators_utils.report.warnings.ExtraDataWarning

Bases: BioSimulatorsWarning

Warning that a file contains additional data that could not be mapped to a data set of a report.

exception biosimulators_utils.report.warnings.MissingDataWarning

Bases: BioSimulatorsWarning

Warning that a file does not contain data for one or more data sets of a report.

exception biosimulators_utils.report.warnings.MissingReportMetadataWarning

Bases: BioSimulatorsWarning

Warning that an exported file of a report will not or does contain comprehensive metadata about the report such as the data type and shape of each data set.

exception biosimulators_utils.report.warnings.RepeatDataSetLabelsWarning

Bases: BioSimulatorsWarning

Warning that multiple data sets with a report have the same label