biosimulators_copasi package¶
- biosimulators_copasi.exec_sed_doc(doc, working_dir, base_out_path, rel_out_path=None, apply_xml_model_changes=True, 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
orstr
) – SED document or a path to SED-ML file which defines a SED documentworking_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 tobase_out_path
to store the outputsapply_xml_model_changes (
bool
, optional) – ifTrue
, apply any model changes specified in the SED-ML file before callingtask_executer
.log (
SedDocumentLog
, optional) – log of the documentindent (
int
, optional) – degree to indent status messagespretty_print_modified_xml_models (
bool
, optional) – ifTrue
, pretty print modified XML modelslog_level (
StandardOutputErrorCapturerLevel
, optional) – level at which to log outputconfig (
Config
, optional) – BioSimulators common configurationsimulator_config (
SimulatorConfig
, optional) – tellurium configuration
- Returns
ReportResults
: results of each reportSedDocumentLog
: log of the document
- Return type
tuple
- biosimulators_copasi.exec_sed_task(task, variables, preprocessed_task=None, log=None, config=None)[source]¶
Execute a task and save its results
- Parameters
task (
Task
) – taskvariables (
list
ofVariable
) – variables that should be recordedpreprocessed_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 taskconfig (
Config
, optional) – BioSimulators common configuration
- Returns
VariableResults
: results of variablesTaskLog
: log- Return type
tuple
- Raises
ValueError – if the task or an aspect of the task is not valid, or the requested output variables could not be recorded
NotImplementedError – if the task is not of a supported type or involves an unsuported feature
- biosimulators_copasi.exec_sedml_docs_in_combine_archive(archive_filename, out_dir, config=None, fix_copasi_generated_combine_archive=None)[source]¶
Execute the SED tasks defined in a COMBINE/OMEX archive and save the outputs
- Parameters
archive_filename (
str
) – path to COMBINE/OMEX archiveout_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 configurationfix_copasi_generated_combine_archive (
bool
, optional) – Whether to make COPASI-generated COMBINE archives compatible with the specifications of the OMEX manifest and SED-ML standards
- Returns
SedDocumentResults
: resultsCombineArchiveLog
: log
- Return type
tuple
- biosimulators_copasi.get_simulator_version()[source]¶
Get the version of COPASI
- Returns
version
- Return type
str
- biosimulators_copasi.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
) – taskvariables (
list
ofVariable
) – variables that should be recordedconfig (
Config
, optional) – BioSimulators common configuration
- Returns
preprocessed information about the task
- Return type
dict
Submodules¶
biosimulators_copasi.core module¶
Methods for executing SED tasks in COMBINE archives and saving their outputs
- Author
Jonathan Karr <karr@mssm.edu>
- Author
Akhil Marupilla <akhilmteja@gmail.com>
- Date
2020-11-17
- Copyright
2020, Center for Reproducible Biomedical Modeling
- License
MIT
- biosimulators_copasi.core.exec_sed_doc(doc, working_dir, base_out_path, rel_out_path=None, apply_xml_model_changes=True, 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
orstr
) – SED document or a path to SED-ML file which defines a SED documentworking_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 tobase_out_path
to store the outputsapply_xml_model_changes (
bool
, optional) – ifTrue
, apply any model changes specified in the SED-ML file before callingtask_executer
.log (
SedDocumentLog
, optional) – log of the documentindent (
int
, optional) – degree to indent status messagespretty_print_modified_xml_models (
bool
, optional) – ifTrue
, pretty print modified XML modelslog_level (
StandardOutputErrorCapturerLevel
, optional) – level at which to log outputconfig (
Config
, optional) – BioSimulators common configurationsimulator_config (
SimulatorConfig
, optional) – tellurium configuration
- Returns
ReportResults
: results of each reportSedDocumentLog
: log of the document
- Return type
tuple
- biosimulators_copasi.core.exec_sed_task(task, variables, preprocessed_task=None, log=None, config=None)[source]¶
Execute a task and save its results
- Parameters
task (
Task
) – taskvariables (
list
ofVariable
) – variables that should be recordedpreprocessed_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 taskconfig (
Config
, optional) – BioSimulators common configuration
- Returns
VariableResults
: results of variablesTaskLog
: log- Return type
tuple
- Raises
ValueError – if the task or an aspect of the task is not valid, or the requested output variables could not be recorded
NotImplementedError – if the task is not of a supported type or involves an unsuported feature
- biosimulators_copasi.core.exec_sedml_docs_in_combine_archive(archive_filename, out_dir, config=None, fix_copasi_generated_combine_archive=None)[source]¶
Execute the SED tasks defined in a COMBINE/OMEX archive and save the outputs
- Parameters
archive_filename (
str
) – path to COMBINE/OMEX archiveout_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 configurationfix_copasi_generated_combine_archive (
bool
, optional) – Whether to make COPASI-generated COMBINE archives compatible with the specifications of the OMEX manifest and SED-ML standards
- Returns
SedDocumentResults
: resultsCombineArchiveLog
: log
- Return type
tuple
- biosimulators_copasi.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
) – taskvariables (
list
ofVariable
) – variables that should be recordedconfig (
Config
, optional) – BioSimulators common configuration
- Returns
preprocessed information about the task
- Return type
dict
biosimulators_copasi.data_model module¶
Data model for maps from KiSAO terms to COPASI algorithms and their arguments
- Author
Jonathan Karr <karr@mssm.edu>
- Date
2020-12-13
- Copyright
2020, BioSimulators Team
- License
MIT
biosimulators_copasi.utils module¶
Utilities for working with the maps from KiSAO ids to COPASI methods and their arguments
- Author
Jonathan Karr <karr@mssm.edu>
- Date
2020-12-13
- Copyright
2020, BioSimulators Team
- License
MIT
- biosimulators_copasi.utils.fix_copasi_generated_combine_archive(in_filename, out_filename, config=None)[source]¶
Utility function that corrects COMBINE/OMEX archives generated by COPASI so they are compatible with other tools.
All currently released versions of COPASI export COMBINE archive files. However, these archives presently diverge from the specifications of the SED-ML format.
Format in OMEX manifests is not a valid PURL media type URI
SED-ML files lack namespaces for SBML
- Parameters
in_filename (
str
) – path to a COMBINE archive to correctout_filename (
str
) – path to save correctd COMBINE archiveconfig (
Config
, optional) – BioSimulators-utils configuration
- biosimulators_copasi.utils.get_algorithm_id(kisao_id, events=False, config=None)[source]¶
Get the COPASI id for an algorithm
- Parameters
kisao_id (
str
) – KiSAO algorithm idevents (
bool
, optional) – whether an algorithm that supports events is neededconfig (
Config
, optional) – configuration
- Returns
str
: KiSAO id of algorithm to executeint
: COPASI id for algorithm
- Return type
tuple
- biosimulators_copasi.utils.get_copasi_model_obj_sbml_ids(model)[source]¶
Get the SBML id of each object of a COPASI model
- Parameters
model (
COPASI.CModel
) – model- Returns
obj:`str: SBML id of each object of the model
- Return type
list
of
- biosimulators_copasi.utils.get_copasi_model_object_by_sbml_id(model, id, units)[source]¶
Get a COPASI model object by its SBML id
- Parameters
model (
COPASI.CModel
) – modelid (
str
) – SBML idunits (
Units
) – desired units for the object
- Returns
model object
- Return type
COPASI.CCompartment
,COPASI.CMetab
,COPASI.CModelValue
, orCOPASI.CReaction
- biosimulators_copasi.utils.set_algorithm_parameter_value(algorithm_kisao_id, algorithm_function, parameter_kisao_id, value)[source]¶
Set a parameter of a COPASI simulation function
- Parameters
algorithm_kisao_id (
str
) – KiSAO algorithm idalgorithm_function (
types.FunctionType
) – algorithm functionparameter_kisao_id (
str
) – KiSAO parameter idvalue (
string
) – parameter value
- Returns
names of the COPASI parameters that were set and their values
- Return type
dict