def autogenerate_sbml_from_folder(folderpath):
'''To automatically generate the corresponding SBML files from the given
folder containing all the configuration files.
:param folderpath: the path to the folder containing all the configuration files.
:type folderpath: str
'''
files = [
f for f in glob.glob(os.path.join(folderpath, "**/*.ini"),
recursive=True)
]
for f in files:
print('\n', f)
sbmlfilelist = []
number_scenario = 0
for f in files: #Add ini files to database
system_type = mh.config_to_database(f)
system_types_settings_names = sh.config_to_database(f)
system_type, settings_name = system_types_settings_names[0]
search_result_model = mh.quick_search(system_type)
search_result_settings = sh.quick_search(system_type=system_type,
settings_name=settings_name)
core_model = search_result_model
settings = search_result_settings
addparam = settings['parameters']
number_init = len(settings['init'])
number_parameters = len(settings['parameters'])
unit_model = unitlookup(settings)
for j in range(number_init): #Cycle through number of init values
for k in range(
number_parameters): #Cycle through number of parameters
sbmlstr = SBMLcreation(core_model, settings, unit_model,
addparam, j, k)
number_scenario = number_scenario + 1
placeholder = os.path.splitext(os.path.basename(f))[0]
sbmlfilename = os.path.join(
folderpath, 'DatabasetoSBML_' + placeholder + '.xml')
f = open(
sbmlfilename,
'w') #creates SBML file in same folder as python script
f.write(sbmlstr)
f.close()
del sbmlstr
sbmlfilelist.append(sbmlfilename)
#Function that creates SBML file and returns the number of files outputed and the file list.
print()
print('Number of Files Printed =', number_scenario)
print('SBML files outputed: ', sbmlfilelist)
def config_to_sbml(inifileslist, output_path):
'''Read in list of configuration files and generate the corresponding SBML
files.
:param inifileslist: a list of input configuration files in strings.
:type inifileslist: list
'''
sbmlfilelist = []
number_scenario = 0
for f in inifileslist:
print('\n', f)
for f in inifileslist: #Add ini files to database
print('filename', f)
system_type = mh.config_to_database(f)
system_types_settings_names = sh.config_to_database(f)
system_type, settings_name = system_types_settings_names[0]
search_result_model = mh.quick_search(system_type)
search_result_settings = sh.quick_search(system_type=system_type,
settings_name=settings_name)
core_model = search_result_model
settings = search_result_settings
addparam = settings['parameters']
number_init = len(settings['init'])
number_parameters = len(settings['parameters'])
unit_model = unitlookup(settings)
for j in range(number_init): #Cycle through number of init values
for k in range(
number_parameters): #Cycle through number of parameters
sbmlstr = SBMLcreation(core_model, settings, unit_model,
addparam, j, k)
#Function that creates SBML file and returns the number of files outputed and the file list.
number_scenario = number_scenario + 1
placeholder = os.path.splitext(f)[0]
sbmlfilename = os.path.join(
output_path, 'DatabasetoSBML_' + placeholder + '.xml')
f = open(
sbmlfilename,
'w') #creates SBML file in same folder as python script
f.write(sbmlstr)
f.close()
del sbmlstr
sbmlfilelist.append(sbmlfilename)
print()
print('Number of Files Printed =', number_scenario)
print('SBML files outputed: ', sbmlfilelist)
system_types_settings_names = sh.config_to_database(filename)
system_type, settings_name = system_types_settings_names[0]
#View the database
#Get all system_types as a list
lst = sh.list_settings()
#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 = sh.to_df()
r = df[df['system_type'] == system_type]
#Retrieve param ensemble
search_result1 = sh.quick_search(system_type=system_type,
settings_name=settings_name)
#Print search result
for key in search_result1:
print(key)
print(search_result1[key])
print()
#Create a template
sh.make_settings_template(system_types_settings_names,
filename='settings_template.ini')
#Deactivate a settings and remove it from searches.
sh.delete(system_type=system_type, settings_name=settings_name)
#Check if it is still visible in the list view and search results
import os
import glob
import add_BMSS_to_path as lab
import BMSS.standardfiles_generators.sbmlgen as sbmlgen
import BMSS.models.model_handler as mh
import BMSS.models.settings_handler as sh
import tempfile
import BMSS.standardfiles_generators.simplesbml as simplesbml
import pytest
system_type = 'TestModel, BMSS, LogicGate, gate, DelayActivationInput2'
settings_name = '__default__'
core_model_1 = mh.quick_search(system_type)
settings = sh.quick_search(system_type=system_type, settings_name=settings_name)
addparam = settings['parameters']
number_init = len(settings['init'])
number_parameters = len(settings['parameters'])
unit_model = sbmlgen.unitlookup(settings)
init_scenario = 0
param_scenario = 0
output_path = tempfile.gettempdir()
model_2 = simplesbml.SbmlModel()
model_2.addSpecies('Inde', 0)
model_2.addSpecies('Indi', 0)
model_2.addSpecies('mRNA1', 0)
model_2.addSpecies('Pep1', 0)
model_2.addSpecies('mRNA2', 0)
model_2.addSpecies('Pep2', 0)