sbmlsim.combine.sedml.numl

Parser for NuML data.

Module Contents

Classes

NumlParser

Helper class for parsing Numl data files.

Attributes

logger

sbmlsim.combine.sedml.numl.logger

class sbmlsim.combine.sedml.numl.NumlParser

Bases: object

Helper class for parsing Numl data files.

class Library

Bases: enum.Enum

Bugfix helper for managing the library issues.

LIBNUML = 1

LIBSEDML = 2

classmethod read_numl_document(path)

Read NuML document and check for errors.

Parameters:

path (pathlib.Path) – path of file

Returns:

libnuml.NUMLDocument

Return type:

libnuml.NUMLDocument

classmethod load_numl_data(path)

Read NuML data from file.

This loads the complete numl data. For more information see: https://github.com/numl/numl

Parameters:

path – NuML path

Returns:

data

Return type:

pandas.DataFrame

classmethod parse_dimension_description(description, library=Library.LIBNUML)

Parse the given dimension description.

Returns dictionary of { key: dtype }

Parameters:

• description –

• library (Library) –

Returns:

classmethod _parse_description(d, info=None, entry=None, library=Library.LIBNUML)

Parse the recursive DimensionDescription, TupleDescription, AtomicDescription.

This gets the dimension information from NuML.

<dimensionDescription>

<compositeDescription indexType=”double” id=”time” name=”time”>

<compositeDescription indexType=”string” id=”SpeciesIds” name=”SpeciesIds”>

<atomicDescription valueType=”double” id=”Concentrations” name=”Concentrations” />

</compositeDescription>

</compositeDescription>

</dimensionDescription>

Parameters:

• d –

• info –

• library (Library) –

Returns:

classmethod _parse_dimension(d, data=None, entry=None, library=Library.LIBNUML)

Parse the recursive CompositeValue, Tuple, AtomicValue.

This gets the actual data from NuML.

Parameters:

library (Library) –