def test_copy_db_4(self, pc_mock):
"""Verify no data is copied if en error is encountered during copying."""
# Raise an error instead of calling pipe_commands() so that
# the exception block is entered.
pc_mock.side_effect = ValueError("Error raised")
result = mysqldb_basic.copy_db(self.engine, DB2)
self.assertEqual(result, 1)
def test_copy_db_2(self):
"""Verify no data is copied since databases are the same."""
before_v1 = test_db_utils.get_data(test_db_utils.version_table_query)
result = mysqldb_basic.copy_db(self.engine, DB)
after_v1 = test_db_utils.get_data(test_db_utils.version_table_query)
with self.subTest():
self.assertEqual(before_v1[0]["Version"], after_v1[0]["Version"])
with self.subTest():
self.assertEqual(result, 0)
def test_copy_db_1(self):
"""Verify data from database1 is copied to database2."""
before_v1 = test_db_utils.get_data(test_db_utils.version_table_query)
before_v2 = test_db_utils.get_data(test_db_utils.version_table_query, db=DB2)
result = mysqldb_basic.copy_db(self.engine, DB2)
after_v1 = test_db_utils.get_data(test_db_utils.version_table_query)
after_v2 = test_db_utils.get_data(test_db_utils.version_table_query, db=DB2)
with self.subTest():
self.assertNotEqual(before_v1[0]["Version"], before_v2[0]["Version"])
with self.subTest():
self.assertEqual(result, 0)
with self.subTest():
self.assertEqual(after_v1[0]["Version"], after_v2[0]["Version"])
def test_copy_db_3(self):
"""Verify no data is copied since new database does not exist."""
result = mysqldb_basic.copy_db(self.engine, DB3)
self.assertEqual(result, 1)
def main(unparsed_args_list):
"""Run main freeze database pipeline."""
args = parse_args(unparsed_args_list)
ref_database = args.database
reset = args.reset
new_database = args.new_database_name
prefix = args.prefix
# Filters input: phage.Status=draft AND phage.HostGenus=Mycobacterium
# Args structure: [['phage.Status=draft'], ['phage.HostGenus=Mycobacterium']]
filters = args.filters
# Create config object with data obtained from file and/or defaults.
config = configfile.build_complete_config(args.config_file)
mysql_creds = config["mysql"]
# Verify database connection and schema compatibility.
print("Connecting to the MySQL database...")
alchemist1 = AlchemyHandler(database=ref_database,
username=mysql_creds["user"],
password=mysql_creds["password"])
alchemist1.connect(pipeline=True)
engine1 = alchemist1.engine
mysqldb.check_schema_compatibility(engine1, "the freeze pipeline")
# Get SQLAlchemy metadata Table object
# table_obj.primary_key.columns is a
# SQLAlchemy ColumnCollection iterable object
# Set primary key = 'phage.PhageID'
alchemist1.build_metadata()
table = querying.get_table(alchemist1.metadata, TARGET_TABLE)
for column in table.primary_key.columns:
primary_key = column
# Create filter object and then add command line filter strings
db_filter = Filter(alchemist=alchemist1, key=primary_key)
db_filter.values = []
# Attempt to add filters and exit if needed.
add_filters(db_filter, filters)
# Performs the query
db_filter.update()
# db_filter.values now contains list of PhageIDs that pass the filters.
# Get the number of genomes that will be retained and build the
# MYSQL DELETE statement.
keep_set = set(db_filter.values)
delete_stmt = construct_delete_stmt(TARGET_TABLE, primary_key, keep_set)
count_query = construct_count_query(TARGET_TABLE, primary_key, keep_set)
phage_count = mysqldb_basic.scalar(alchemist1.engine, count_query)
# Determine the name of the new database.
if new_database is None:
if prefix is None:
prefix = get_prefix()
new_database = f"{prefix}_{phage_count}"
# Create the new database, but prevent overwriting of current database.
if engine1.url.database != new_database:
result = mysqldb_basic.drop_create_db(engine1, new_database)
else:
print(
"Error: names of the reference and frozen databases are the same.")
print("No database will be created.")
result = 1
# Copy database.
if result == 0:
print(f"Reference database: {ref_database}")
print(f"New database: {new_database}")
result = mysqldb_basic.copy_db(engine1, new_database)
if result == 0:
print(f"Deleting genomes...")
alchemist2 = AlchemyHandler(database=new_database,
username=engine1.url.username,
password=engine1.url.password)
alchemist2.connect(pipeline=True)
engine2 = alchemist2.engine
engine2.execute(delete_stmt)
if reset:
engine2.execute(RESET_VERSION)
# 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.")
def main(unparsed_args_list):
"""Run main conversion pipeline."""
# Parse command line arguments
args = parse_args(unparsed_args_list)
config = configfile.build_complete_config(args.config_file)
mysql_creds = config["mysql"]
alchemist1 = AlchemyHandler(database=args.database,
username=mysql_creds["user"],
password=mysql_creds["password"])
alchemist1.connect(pipeline=True)
engine1 = alchemist1.engine
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_basic.drop_create_db(engine1, args.new_database_name)
if result == 0:
result = mysqldb_basic.copy_db(engine1, args.new_database_name)
if result == 0:
# Create a new connection to the new database.
alchemist2 = AlchemyHandler(database=args.new_database_name,
username=engine1.url.username,
password=engine1.url.password)
alchemist2.connect(pipeline=True)
engine2 = alchemist2.engine
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()