def test_CreateFromSeqRecord(self): with GeneSequenceApp.app.test_request_context("/"): GeneSequenceApp.app.preprocess_request() with open(__location__ + "/testfiles/422900759.pickle", 'rb') as f: record = pickle.load(f) GenBankEntry.create_from_seqrecord(record, "") entry = Sequence.create_from_seqrecord(record) self.assertEqual(entry.Sequence, str(record.seq))
def try_add_from_genbank(id, silk_type): get_module_logger().info("Calling entrez for ID {}".format(id)) fasta = entrez_get_fasta_seqrecord(id) success = False if fasta is not None: get_module_logger().info("Data for ID {} found. Trying to add to database.".format(id)) try: get_module_logger().info("Creating GenBankEntry.") GenBankEntry.create_from_seqrecord(fasta, silk_type) get_module_logger().info("Creating Sequence.") Sequence.create_from_seqrecord(fasta) success = True except: raise else: get_module_logger().info("Data for ID {} not found.") return success