def install_db(database, db_filepath=None, schema_version=None):
"""Install database. If database already exists, it is first removed."""
engine1, msg = mysqldb.get_engine(database="", echo=False)
if engine1 is None:
print("Invalid MySQL credentials.")
else:
result2 = mysqldb.drop_create_db(engine1, database)
if result2 != 0:
print("Unable to create new, empty database.")
else:
engine2, msg = mysqldb.get_engine(database=database,
username=engine1.url.username,
password=engine1.url.password,
echo=False)
if engine2 is None:
print(f"No connection to the {database} database due "
"to invalid credentials or database.")
else:
if db_filepath is not None:
mysqldb.install_db(engine2, db_filepath)
else:
mysqldb.execute_transaction(engine2, db_schema_0.STATEMENTS)
convert_args = ["pdm_utils.run", "convert", database,
"-s", str(schema_version)]
convert_db.main(convert_args, engine2)
# Close up all connections in the connection pool.
engine2.dispose()
# Close up all connections in the connection pool.
engine1.dispose()
def main(unparsed_args_list, engine1=None):
"""Run main conversion pipeline."""
# Parse command line arguments
args = parse_args(unparsed_args_list)
if engine1 is None:
engine1 = mysqldb.connect_to_db(args.database)
target = args.schema_version
actual = mysqldb.get_schema_version(engine1)
steps, dir = get_conversion_direction(actual, target)
# Iterate through list of versions and implement SQL files.
if dir == "none":
if args.verbose == True:
print("No schema conversion is needed.")
convert = False
else:
convert = True
if convert == True:
if (args.new_database_name is not None
and args.new_database_name != args.database):
result = mysqldb.drop_create_db(engine1, args.new_database_name)
if result == 0:
result = mysqldb.copy_db(engine1, args.new_database_name)
if result == 0:
# Create a new connection to the new database.
engine2, msg = mysqldb.get_engine(
database=args.new_database_name,
username=engine1.url.username,
password=engine1.url.password,
echo=False)
else:
print("Error: Unable to copy the database for conversion.")
convert = False
else:
print(
"Error: Unable to create the new database for conversion.")
convert = False
else:
engine2 = engine1
if convert == True:
stop_step, summary = convert_schema(engine2,
actual,
dir,
steps,
verbose=args.verbose)
engine2.dispose()
if stop_step == target:
if args.verbose == True:
print("\n\nThe database schema conversion was successful.")
else:
print("\n\nError: "
"The database schema conversion was not successful. "
f"Unable to proceed past schema version {stop_step}.")
if args.verbose == True:
print_summary(summary)
engine1.dispose()
def test_get_engine_10(self, input_mock):
"""Verify that engine is returned when database is provided and
more than one attempt is needed for database."""
input_mock.side_effect = ["invalid", db2]
engine, msg = mysqldb.get_engine(username=user,
password=pwd,
attempts=3)
with self.subTest():
self.assertIsNotNone(engine)
def test_get_engine_8(self, getpass_mock):
"""Verify that engine is returned when database is provided and
more than one attempt is needed for password."""
getpass_mock.side_effect = [user, "invalid", user, pwd]
engine, msg = mysqldb.get_engine(database=db2, attempts=3)
with self.subTest():
self.assertTrue(getpass_mock.called)
with self.subTest():
self.assertIsNotNone(engine)
def test_get_engine_6(self, getpass_mock):
"""Verify that no engine is returned when database is not provided and
invalid user."""
getpass_mock.side_effect = ["invalid", pwd]
engine, msg = mysqldb.get_engine(database="", attempts=1)
with self.subTest():
self.assertTrue(getpass_mock.called)
with self.subTest():
self.assertIsNone(engine)
def test_get_engine_4(self, getpass_mock):
"""Verify that no engine is returned when database is provided and
invalid password."""
getpass_mock.side_effect = [user, "invalid"]
engine, msg = mysqldb.get_engine(database=db2, attempts=1)
with self.subTest():
self.assertTrue(getpass_mock.called)
with self.subTest():
self.assertIsNone(engine)
def test_get_engine_2(self, getpass_mock):
"""Verify that engine returned with valid info
when database is not provided."""
getpass_mock.side_effect = [user, pwd]
engine, msg = mysqldb.get_engine(database="")
with self.subTest():
self.assertTrue(getpass_mock.called)
with self.subTest():
self.assertIsNotNone(engine)
def test_get_engine_9(self, input_mock):
"""Verify that engine is returned when database is provided by input."""
input_mock.side_effect = [db2]
engine, msg = mysqldb.get_engine(username=user,
password=pwd,
attempts=1)
with self.subTest():
self.assertTrue(input_mock.called)
with self.subTest():
self.assertIsNotNone(engine)
def main(unparsed_args_list):
"""Run main freeze database pipeline."""
args = parse_args(unparsed_args_list)
# engine1, msg = mysqldb.get_engine(database=args.database, echo=False)
# Verify database connection and schema compatibility.
print("Connecting to the MySQL database...")
engine1 = mysqldb.connect_to_db(args.database)
mysqldb.check_schema_compatibility(engine1, "the freeze pipeline")
# Get the number of draft genomes.
query = "SELECT count(*) as count FROM phage WHERE Status != 'draft'"
result = engine1.execute(query).fetchall()
phage_count = result[0]["count"]
# Create the new frozen database folder e.g. Actinobacteriophage_XYZ.
prefix = get_prefix()
new_database = f"{prefix}_{phage_count}"
# Create the new database
result = mysqldb.drop_create_db(engine1, new_database)
# Copy database.
if result == 0:
result = mysqldb.copy_db(engine1, new_database)
if result == 0:
print(f"Deleting 'draft' genomes...")
engine2, msg = mysqldb.get_engine(username=engine1.url.username,
password=engine1.url.password,
database=new_database)
statement3 = "DELETE FROM phage WHERE Status = 'draft'"
engine2.execute(statement3)
statement4 = "UPDATE version SET Version = 0"
engine2.execute(statement4)
# Close up all connections in the connection pool.
engine2.dispose()
else:
print("Unable to copy the database.")
# Close up all connections in the connection pool.
engine1.dispose()
else:
print(f"Error creating new database: {new_database}.")
print("Freeze database script completed.")