def test_delete(self):
global core_model_1
system_type = core_model_1['system_type']
lst = mh.list_models()
assert core_model_1['system_type'] in lst
mh.delete(system_type)
#Check if in database
lst = mh.list_models()
assert system_type not in lst
def database_to_combine(system_type, settings_name, Plot_Variable, outputpath, KISAO_algorithm):
'''Select model stored in database and generate the SBML file.
:param system_type: system type of model in string format
:param settings_name: settings name of model in string format
:param Plot_Variable: Variables to be plotted in list format
:param outputpath: filepath to output OMEX file in OS path format
:param KISAO_algorithm: Kinetic Simulation Algorithm Ontology number in string format
'''
combinefilelist=[]
number_scenario = 0
search_result_settings = sh.search_database(system_type, settings_name)
core_model = mh.quick_search(system_type)
settings = search_result_settings[0]
#-- Checkers --
plotvariablechecker(Plot_Variable, core_model)
KISAOchecker(KISAO_algorithm)
if system_type not in mh.list_models():
raise Exception("Model is not in database")
combinefilename, number_scenario = Combinecreator(core_model, settings, Plot_Variable, outputpath, KISAO_algorithm)
combinefilelist.append(combinefilename)
print()
print('Number of Scenarios in COMBINE File=', number_scenario)
print('COMBINE files outputed: ', combinefilelist)
def test_autogenerate_sbml_from_folder(self):
#Test if the function is correctly taking in Config files from folder
#and outputting to Tempdir
inputpath = (Path.cwd()/'ConfigSBML')
output_path_auto = os.path.join(output_path, 'ConfigSBML')
files = [f for f in glob.glob(os.path.join(inputpath,"**/*.ini"), recursive=True)]
for file in files:
core_model_test = mh.from_config(file)
system_type = core_model_test['system_type']
settings_name = 'Setting_test1'
mh.delete(system_type)
sh.delete(system_type=system_type, settings_name=settings_name)
assert system_type not in (mh.list_models()), 'Model was not deleted'
assert system_type not in (sh.list_settings()), 'settings was not deleted'
sbmlgen.autogenerate_sbml_from_folder(inputpath, output_path_auto)
for outputfile in files:
placeholder = outputfile.replace(str(inputpath), '')
placeholder = placeholder.replace('.ini', '')
placeholder = placeholder.replace('\\', '')
filename = os.path.join(output_path_auto, 'DatabasetoSBML_' + placeholder +'.xml')
print('This is the file name:', filename)
print()
assert os.path.exists(filename) == True, "File did not output properly"
def test_restore(self):
global core_model_1
system_type = core_model_1['system_type']
mh.restore(system_type)
#Check if in database
lst = mh.list_models()
assert system_type in lst
def test_add_to_database(self):
'''
Note: add_to_database already makes calls to search/quick_search
'''
global core_model_1
core_model = core_model_1
mh.add_to_database(core_model, dialog=False)
#Check if in database
lst = mh.list_models()
assert core_model['system_type'] in lst
def test_config_to_sbml(self):
#Test if files are output correctly
filelist = ['TestModel_LogicGate_ORgate_DelayActivation_DelayActivation.ini',
'TestModel_CellModel_CellularResources_ProteomeAllocation_RibosomeLimitation.ini']
for file in filelist:
core_model_test = mh.from_config(file)
system_type = core_model_test['system_type']
settings_name = 'Setting_test1'
mh.delete(system_type)
sh.delete(system_type=system_type, settings_name=settings_name)
assert system_type not in (mh.list_models()), 'Model was not deleted'
assert system_type not in (sh.list_settings()), 'settings was not deleted'
sbmlgen.config_to_sbml(filelist, output_path)
for outputfile in filelist:
placeholder = outputfile.replace('.ini', '')
filename = os.path.join(output_path, 'DatabasetoSBML_' + placeholder +'.xml')
assert os.path.exists(filename) == True, "File did not output properly"
plt.close('all')
if __name__ == '__main__':
outputpath = (Path.cwd())
#Where the COMBINE file will be outputed to, working directory by default
print(outputpath)
'''
Use the following section to add model to database from config file.
'''
filename = "TestModel_Repressilator_OMEX_example.ini"
#Add model to database and view all the models in the database
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"
def test_database_to_sbml_fail(self):
#Test if model declared is in database
system_type_fail = "TestModel_fail"
assert system_type_fail in mh.list_models(), 'Model not in database'
sbmlgen.database_to_sbml(system_type, settings_name, output_path)
- Add, edit and retrieve models.
- Delete and restore models.
'''
if __name__ == '__main__':
#Fill in the filenames here
filename = 'TestModel_Dummy.ini'
#Add new core model/Replace existing core model
#Note that this assigns a unique id to the core model that is then printed to the console.
system_type = mh.config_to_database(filename)
#View the database
#Get all system_types as a list
lst = mh.list_models()
#Optional: Export a copy of the entire database as a DataFrame
#Note that changes to the DataFrame do not affect the database.
#Refer to the Pandas documentation for DataFrame operations.
df = mh.to_df()
r = df[df['system_type'] == system_type]
#Search the database
#This returns a list of core_models with system_types containing the keyword
#Try searching using the core model's id
search_result_1 = mh.search_database('TestModel',
search_type='system_type')
core_model_1 = search_result_1[0]
model_id = core_model_1['id']
search_result_2 = mh.search_database(model_id, search_type='id')