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()
