def create_whole_network_json():
"""Generates the whole network json."""
conn, cursor = db.db_open("sbider.db")
json_info = get_whole_network(cursor)
create_json_network("sbider_whole_network.json", *json_info)
db.db_close(conn, cursor)
def test_searcher_indirect_2(self):
"""testing the following query ahl and laci = gfp for the indirect traverse"""
conn, cur = db.db_open("sbider.db")
user_query = "ahl and laci = gfp"
logic_dictionary = parse.parse_logic(cur, user_query)
input_dictionary, output_dictionary = db.make_ope_id_spe_id_dics(cur)
repressor_dictionary = db.make_ope_id_rep_spe_id_dic(cur)
self.operon_path_list = search.get_sbider_path(input_dictionary,
repressor_dictionary,
output_dictionary,
['13', '22'], ['11'],
True)
for operon_path in self.operon_path_list:
current_species = ['13', '22']
input_species_set = set(current_species)
output_species_set = set(current_species)
for operon in operon_path:
input_species = helper.uniquely_merge_list_of_lists(
input_dictionary[operon])
output_species = helper.uniquely_merge_list_of_lists(
output_dictionary[operon])
for species in input_species:
if species in output_species_set:
input_species_set.add(species)
for species in output_species:
output_species_set.add(species)
self.assertEquals(
input_species_set.issubset(output_species_set), True)
db.db_close(conn, cur)
def test_searcher_indirect_2(self):
"""testing the following query ahl and laci = gfp for the indirect traverse"""
conn, cur = db.db_open("sbider.db")
user_query = "ahl and laci = gfp"
logic_dictionary = parse.parse_logic(cur, user_query)
input_dictionary, output_dictionary = db.make_ope_id_spe_id_dics(cur)
repressor_dictionary = db.make_ope_id_rep_spe_id_dic(cur)
self.operon_path_list = search.get_sbider_path(input_dictionary,
repressor_dictionary,
output_dictionary,
['13', '22'],
['11'],
True)
for operon_path in self.operon_path_list:
current_species = ['13', '22']
input_species_set = set(current_species)
output_species_set = set(current_species)
for operon in operon_path:
input_species = helper.uniquely_merge_list_of_lists(input_dictionary[operon])
output_species = helper.uniquely_merge_list_of_lists(output_dictionary[operon])
for species in input_species:
if species in output_species_set:
input_species_set.add(species)
for species in output_species:
output_species_set.add(species)
self.assertEquals(input_species_set.issubset(output_species_set), True)
db.db_close(conn,cur)
def create_subnetwork_json(list_of_operon_paths, starting_species_list_of_lists):
"""Generates the subnetwork json."""
conn, cursor = db.db_open("sbider.db")
operon_input_transition_dictionary = get_input_transition_species_dictionary(cursor)
json_info = get_subnetwork(cursor, list_of_operon_paths, starting_species_list_of_lists)
create_json_network("sbider_subnetwork_hurrah.json", *json_info)
db.db_close(conn, cursor)
def test_fail_parser(self):
"""testing faulty query."""
conn, cur = db.db_open("sbider.db")
try:
self.logic = parse.parse_logic(cur, "A and B = C")
except TypeError:
pass
db.db_close(conn, cur)
def test_fail_parser(self):
"""testing faulty query."""
conn, cur = db.db_open("sbider.db")
try:
self.logic = parse.parse_logic(cur, "A and B = C")
except TypeError:
pass
db.db_close(conn,cur)
def create_subnetwork_json(cursor, list_of_operon_paths, json_file_name = "test.json"):
"""Generates the subnetwork json."""
conn, cursor = db.db_open("sbider.db")
operon_input_transition_dictionary = get_input_transition_species_dictionary(cursor)
json_info = get_subnetwork(cursor, list_of_operon_paths)
create_json_network(json_file_name, *json_info)
db.db_close(conn, cursor)
def test_searcher_direct(self):
"""testing the following query lara and arac to gfp for the direct traverse"""
conn, cur = db.db_open("sbider.db")
user_query = "lara and arac = gfp"
logic_dictionary = parse.parse_logic(cur, user_query)
input_dictionary, output_dictionary = db.make_ope_id_spe_id_dics(cur)
repressor_dictionary = db.make_ope_id_rep_spe_id_dic(cur)
self.operon_path_list = search.get_sbider_path(input_dictionary,repressor_dictionary,\
output_dictionary, ['2', '38'], ['11'], False)
for operon_path in self.operon_path_list:
current_species = ['2', '38']
for operon in operon_path:
self.assertEquals(current_species in input_dictionary[operon], True)
current_species = output_dictionary[operon][0]
db.db_close(conn,cur)
def main():
web_path = sys.argv[1]
database_file = web_path + "sbider.db"
global rootPath
rootPath = web_path
device_info = sys.argv[2::]
conn, cur = db.db_open(database_file)
sbol_files = insert_new_device(conn, cur, device_info, web_path)
db.db_close(conn, cur)
#conn, cur = db.db_open(database_file)
#sg.create_network_json_file(cur, web_path + "whole_network.json")
#db.db_close(conn, cur)
#gn.create_whole_network_sbml()
return sbol_files
def test_searcher_direct(self):
"""testing the following query lara and arac to gfp for the direct traverse"""
conn, cur = db.db_open("sbider.db")
user_query = "lara and arac = gfp"
logic_dictionary = parse.parse_logic(cur, user_query)
input_dictionary, output_dictionary = db.make_ope_id_spe_id_dics(cur)
repressor_dictionary = db.make_ope_id_rep_spe_id_dic(cur)
self.operon_path_list = search.get_sbider_path(input_dictionary,repressor_dictionary,\
output_dictionary, ['2', '38'], ['11'], False)
for operon_path in self.operon_path_list:
current_species = ['2', '38']
for operon in operon_path:
self.assertEquals(current_species in input_dictionary[operon],
True)
current_species = output_dictionary[operon][0]
db.db_close(conn, cur)
def test_successful_parser(self):
"""testing a successful query of the sbider network"""
conn, cur = db.db_open("sbider.db")
self.logic = parse.parse_logic(cur, "lara and arac = gfp")
self.assertEquals(type(self.logic), dict)
db.db_close(conn, cur)
def test_successful_parser(self):
"""testing a successful query of the sbider network"""
conn, cur = db.db_open("sbider.db")
self.logic = parse.parse_logic(cur, "lara and arac = gfp")
self.assertEquals(type(self.logic), dict)
db.db_close(conn,cur)