How to use the gillespy2.core.log.error function in gillespy2

To help you get started, we’ve selected a few gillespy2 examples, based on popular ways it is used in public projects.

Secure your code as it's written. Use Snyk Code to scan source code in minutes - no build needed - and fix issues immediately.

github StochSS / stochss / stochss / handlers / util / run_workflow.py View on Github external
Attributes
    ----------
    wkfl : StochSS Workflow
        The workflow object being worked with.
    verbose : boolean
        Print progress statements.
    '''
    is_ode = wkfl.settings['simulationSettings']['algorithm'] == "ODE"
    # Get the model data from the file and create the model object
    gillespy2_model, stochss_model = get_models(wkfl.wkfl_mdl_path, wkfl.mdl_file.split('.')[0], wkfl.wkfl_path, is_ode)
    # run the workflow
    try:
        wkfl.run(gillespy2_model, verbose)
    except Exception as error:
        # update workflow status to error if GillesPy2 throws an exception
        log.error("Workflow errors: {0}".format(error))
        open(os.path.join(wkfl.wkfl_path, 'ERROR'), 'w').close()
    else:
        open(os.path.join(wkfl.wkfl_path, 'COMPLETE'), 'w').close() # update status to complete
github StochSS / stochss / stochss / handlers / util / run_workflow.py View on Github external
Attributes
    ----------
    wkfl : StochSS Workflow
        The workflow object being worked with.
    wkfl_type : str
        The type of workflow to be used.
    is_new : boolean
        Represents whether the workflow is new or not.
    '''
    old_model_path = os.path.join(wkfl.wkfl_path, wkfl.mdl_file) # path to the old model
    os.remove(old_model_path) # remove the old model
    try:
        copyfile(wkfl.mdl_path, wkfl.wkfl_mdl_path) # copy the new model into the workflow directory
    except FileNotFoundError as error:
        log.error("Failed to copy the model into the directory: {0}".format(error))
    # Update the workflow info file
    update_info_file(wkfl, wkfl_type, initialize)
    # Update workflow settings file
    wkfl.save()
    if initialize:
        # Update workflow status to running
        open(os.path.join(wkfl.wkfl_path, 'RUNNING'), 'w').close()
    return "Successfully saved the existing workflow: {0}".format(wkfl.wkfl_path)