def setUpClass(self): test_db_utils.create_filled_test_db() self.test_dir = Path(TEST_DIR) if self.test_dir.is_dir(): shutil.rmtree(TEST_DIR) self.test_dir.mkdir()
def setUp(self): # Create test database that contains data for several phages. test_db_utils.create_filled_test_db() self.alchemist = AlchemyHandler(database=DB, username=USER, password=PWD) self.alchemist.build_engine() self.engine = self.alchemist.engine self.temp_dir = "/tmp/pdm_utils_tests_phamerate"
def setUp(self): test_db_utils.create_filled_test_db() test_db_utils.create_empty_test_db(db=DB2) stmt1 = "UPDATE version SET Version = 1" test_db_utils.execute(stmt1) stmt2 = "UPDATE version SET Version = 0" test_db_utils.execute(stmt2, db=DB2) self.alchemist = AlchemyHandler(database=DB, username=USER, password=PWD) self.alchemist.build_engine() self.engine = self.alchemist.engine
def setUpClass(self): test_db_utils.create_filled_test_db() self.test_dir = Path(TEST_DIR) if self.test_dir.is_dir(): shutil.rmtree(TEST_DIR) self.test_dir.mkdir() self.resubmit_form = self.test_dir.joinpath("resubmit_form.txt") basic.export_data_dict(TEST_DATA, self.resubmit_form, PF_HEADER, include_headers=True)
def test_main_5(self, getpass_mock): """Verify database is installed from file and overwrites existing database.""" getpass_mock.side_effect = [USER, PWD] # First install a database with data. Then delete version table. test_db_utils.create_filled_test_db() test_db_utils.execute("DROP TABLE version") unparsed_args = get_unparsed_args(option="file") run.main(unparsed_args) # Now query for version data. This verifies that it replaced # the first database. version_data = test_db_utils.get_data( test_db_utils.version_table_query) self.assertEqual(len(version_data), 1)
def setUpClass(self): base_dir = Path(TMPDIR_BASE) self.test_dir = base_dir.joinpath(TMPDIR_PREFIX) test_db_utils.create_filled_test_db() if self.test_dir.is_dir(): shutil.rmtree(self.test_dir) self.test_dir.mkdir() self.test_import_table_1 = Path(test_file_dir, "test_import_table_1.csv") self.tkt_dict1 = {"phage_id": "L5", "host_genus": "Mycobacterium"} self.tkt_dict2 = {"phage_id": "Trixie", "host_genus": "Mycobacterium"} self.test_fasta_file_1 = Path(test_file_dir, "test_fasta_file_1.fasta") self.test_fasta_file_2 = Path(test_file_dir, "test_fasta_file_2.fasta") self.test_fa_1_gs_to_ts = {} self.test_fa_2_gs_to_ts = {} with self.test_fasta_file_1.open(mode="r") as filehandle: for record in SeqIO.parse(filehandle, "fasta"): self.test_fa_1_gs_to_ts[record.id] = str(record.seq) self.test_fa_2_gs_to_ts[record.id] = str(record.seq) self.test_fa_1_ts_to_gs = {} for seq_id, trans in self.test_fa_1_gs_to_ts.items(): seq_ids = self.test_fa_1_ts_to_gs.get(trans, []) seq_ids.append(seq_id) self.test_fa_1_ts_to_gs[trans] = seq_ids self.test_fa_2_ts_to_gs = {} for seq_id, trans in self.test_fa_2_gs_to_ts.items(): seq_ids = self.test_fa_2_ts_to_gs.get(trans, []) seq_ids.append(seq_id) self.test_fa_2_ts_to_gs[trans] = seq_ids self.fasta_dict_1 = { "Trixie_CDS_11": ("MASIQGKLIALVLKYGISYLRKHPELLKEI" "SKHIPGKVDDLVLEVLAKLLGV") } self.fasta_dict_2 = { "TRIXIE_CDS_3": ("MSGFDDKIVDQAQAIVPADDYDALPLAGPGR" "WAHVPGGLTLYTNDDTVLFAQGDMSTIESSY" "LFQAMEKLRLAGKTASQAFDILRLEADAISG" "DLSELAEE"), "L5_CDS_3": ("MAQMQATHTIEGFLAVEVAPRAFVAENGHVL" "TRLSATKWGGGEGLEILNYEGPGTVEVSDEK" "LAEAQRASEVEAELRREVGKE") }
def setUpClass(self): base_dir = Path(TMPDIR_BASE) self.test_dir = base_dir.joinpath(TMPDIR_PREFIX) test_db_utils.create_filled_test_db() if self.test_dir.is_dir(): shutil.rmtree(self.test_dir) self.test_dir.mkdir() self.alchemist = AlchemyHandler() self.alchemist.username = USER self.alchemist.password = PWD self.alchemist.database = DB self.alchemist.connect(ask_database=True, login_attempts=0) self.acc_id_dict = get_acc_id_dict(self.alchemist) accession_list = list(self.acc_id_dict.keys()) ncbi_handle = Entrez.efetch(db="nucleotide", rettype="ft", id=",".join(accession_list), retmode="text") copy_gb_ft_files(ncbi_handle, self.acc_id_dict, self.test_dir)
def setUpClass(self): test_db_utils.create_filled_test_db()
def setUpClass(self): test_db_utils.create_filled_test_db() test_db_utils.create_empty_test_db(db=DB2)
def setUp(self): test_db_utils.create_filled_test_db() self.alchemist = AlchemyHandler(username=USER, password=PWD) self.alchemist.build_engine() self.engine = self.alchemist.engine
def setUp(self): self.engine = sqlalchemy.create_engine(engine_string, echo=False) self.temp_dir = "/tmp/pdm_utils_tests_phamerate" # Create test database that contains data for several phages. test_db_utils.create_filled_test_db()
def setUp(self): test_db_utils.create_filled_test_db() self.version_data = test_db_utils.get_data(QUERY) self.current = self.version_data[0]["SchemaVersion"] results_path.mkdir()