sbmlsim.combine.sedml.io

Template functions to run the example cases.

Module Contents

Classes

SEDMLInputType

Types of SED-ML input.

SEDMLReader

Class for reading SED-ML document from various sources.

Functions

check_sedml_doc(sed_doc)

Check SedDocument for errors.

Attributes

logger

sbmlsim.combine.sedml.io.logger[source]
sbmlsim.combine.sedml.io.check_sedml_doc(sed_doc)[source]

Check SedDocument for errors.

Logs errors and warnings

Parameters:

sed_doc (libsedml.SedDocument) – SedDocument.

Return type:

libsedml.SedErrorLog

:return SedErrorLog.

class sbmlsim.combine.sedml.io.SEDMLInputType[source]

Bases: enum.Enum

Types of SED-ML input.

SED-ML can be read from string, file or a COMBINE archive (or zip archives).

SEDML_STRING = 0[source]
SEDML_FILE = 1[source]
OMEX = 2[source]
class sbmlsim.combine.sedml.io.SEDMLReader(source, working_dir=None)[source]

Class for reading SED-ML document from various sources.

SED-ML can be provided as string, file or as file in a COMBINE archive.

Execution must be performed where the master SED-ML is located.

Parameters:
  • source (Union[pathlib.Path, str]) –

  • working_dir (pathlib.Path) –

__repr__()[source]

Get string representation.

Return type:

None

__str__()[source]

Get string.

Return type:

str

read_sedml()[source]

Read SedMLDocument.

Sets the instance variables as a result.

Return type:

Tuple[libsedml.SedDocument, SEDMLInputType]