def test_model_in_database_fail(self):
#Model not in databases for COMBINE to be generated
#Checker is called in beginning of database_to_combine
test_model_name_fail = "TestModel, Dummynot, CellModel, CellularResources, ProteomeAllocation, RibosomeLimitation"
combinegen.database_to_combine(test_model_name_fail, settings_name,
Plot_Variable, outputpath,
KISAO_algorithm)
def test_outputOMEX_fail(self):
#OMEX file does not exist
combinegen.database_to_combine(model_name, settings_name,
Plot_Variable, outputpath,
KISAO_algorithm)
filename = model_name.replace(", ", "_")
filename = 'COMBINE_fail_' + filename + '.omex'
filename = os.path.join(outputpath, filename)
assert os.path.exists(filename) == True, "File did not output properly"
system_type = mh.config_to_database(filename)
lst = mh.list_models()
print(lst)
#Add settings to database and view all the settings in the database
system_types_settings_names = sh.config_to_database(filename)
lst_setting = sh.list_settings()
print(lst_setting)
'''
Use database_to_combine to create a COMBINE archive from an existing model in database.
'''
model_name = "Test_Model, OMEX, Repressilator, Example" #Enter model name
settings_name = "__default__" #usually "__default__" by default
Plot_Variable = [
"X", "Y", "Z"
] #, "rmq"] #Assign which variables you would like to plot
KISAO_algorithm = "0"
#Define which KISAO algorithm to use for tspan, write "0" if to use default CVODE
combinegen.database_to_combine(model_name, settings_name, Plot_Variable,
outputpath, KISAO_algorithm)
'''
Use the following function to execute the COMBINE archive
'''
COMBINEfilelocation = str(
Path.cwd() / 'COMBINE_Test_Model_OMEX_Repressilator_Example.omex')
#Autoexecute omex file from file location. Path set to where this python script is saved.
#Use this to choose which COMBINE Archive to execute
te.convertAndExecuteCombineArchive(COMBINEfilelocation)