pl.pipeline

Module Contents

class pl.pipeline.Pipeline(models_folder="Models", working_folder="Results", sim_data_folder="sim_data", sim_plots_folder="sim_plots")

Generic pipeline.

Parameters:

• models_folder – the folder containing the models
• working_folder – the folder to store the results
• sim_data_folder – the folder to store the simulation data
• sim_plots_folder – the folder to store the graphic results

__init__(models_folder="Models", working_folder="Results", sim_data_folder="sim_data", sim_plots_folder="sim_plots")

run(config_file)

Run the pipeline.

Parameters:config_file – a configuration file for this pipeline. Returns:True if the pipeline was executed correctly, False otherwise.

get_models_folder()

Return the folder containing the models.

Returns:the models folder.

get_working_folder()

Return the folder containing the results.

Returns:the working folder.

get_sim_data_folder()

Return the folder containing the in-silico generated data sets.

Returns:the folder of the simulated data sets.

get_sim_plots_folder()

Return the folder containing the in-silico generated plots.

Returns:the folder of the simulated plots.

generate_tarball(output_folder)

Create a gz tarball.

Parameters:

• working_dir – the working directory
• output_folder – the name of the folder to store the tar.gz file

Returns:

True if the generation of the tarball succeeded.

get_simul_obj(simulator)

Return the simulator object if this exists. Otherwise throws an exception. The simulator name starts with an upper case letter. Each simulator is in a package within sbpipe.simulator.

Parameters:simulator – the simulator name Returns:the simulator object.

load(config)

Safely load a YAML configuration file and return its structure as a dictionary object.

Parameters:config – a YAML configuration file Returns:the dictionary structure of the configuration file Raise:yaml.YAMLError if the config cannot be loaded.

parse(config_dict)

Read a dictionary structure containing the pipeline configuration. This method is abstract.

Returns:a tuple containing the configuration