def create_new_token(self):
config = self.check_config_file_API()
if config != None:
self.load_data_from_ini()
else:
self.get_informations()
self.create_ini_api_data()
authentication_obj = AuthenticationAPI(username = self.username, password=self.password, endpoint=self.endpoint)
token = authentication_obj.createAutenthicationToken()
if token != None:
os.environ["token_api"] = token
self.token = token
def createBacterium(acc_number, person_responsible, source_data, fk_strain):
bacteriumObjJson = BacteriumJson(acc_number=acc_number,
person_responsible=person_responsible,
source_data=source_data,
strain=fk_strain)
bacteriumObjJson = bacteriumObjJson.setBacterium()
return bacteriumObjJson.id
#Token connection
conf_obj = ConfigurationAPI()
conf_obj.load_data_from_ini()
AuthenticationAPI().createAutenthicationToken()
#End token connection
dir_path = os.path.dirname(os.path.realpath(__file__))
print(dir_path)
path = dir_path + '/NCBI/organisms/NZ_ABYX00000000.wd.fasta'
#print(path)
path_proteins = dir_path + '/NCBI/organisms/NZ_ABYX00000000.prot_aa.fasta'
#path_proteins_CDS = dir_path + '/NCBI/organisms/NZ_CP016896.1.prot_csd.fasta'
fasta_protein_obj_dict = Fasta_protein_NCBI(path_proteins, 'protein_id')
#fasta_protein_CDS_obj_dict = Fasta_nucleotid_NCBI(path_proteins_CDS, 'db_xref')
#fasta_protein_csd_id = fasta_protein_CDS_obj_dict.get_list_nucleotid_name()
