def test_execute_transaction_5(self):
"""Verify list of three valid statements and one invalid statement
are NOT inserted. All statements rolled back."""
# Valid
domain_data1 = test_data_utils.get_trixie_domain_data()
statement1 = get_domain_insert_statement(domain_data1)
# Valid
gene_domain_data = test_data_utils.get_trixie_gene_domain_data()
statement2 = get_gene_domain_insert_statement(gene_domain_data)
# Invalid
domain_data2 = test_data_utils.get_trixie_domain_data()
statement3 = get_domain_insert_statement(domain_data2)
statement3 = statement3.replace("HitID", "unique_id")
statement3 = statement3.replace("Name", "Name_invalid")
# Valid - function should exit before executing this though.
update_data = get_trixie_gene_table_domain_status_update_data_1()
statement4 = get_gene_update_statement(update_data)
statements = [statement1, statement2, statement3, statement4]
result = find_domains.execute_transaction(self.connection, statements)
gene_table_results = test_db_utils.get_data(
test_db_utils.gene_table_query)
gene_domain_table_results = test_db_utils.get_data(
test_db_utils.gene_domain_table_query)
domain_table_results = test_db_utils.get_data(
test_db_utils.domain_table_query)
domain_status = gene_table_results[0]["DomainStatus"]
with self.subTest():
self.assertEqual(len(domain_table_results), 0)
with self.subTest():
self.assertEqual(len(gene_domain_table_results), 0)
with self.subTest():
self.assertEqual(result, 1)
with self.subTest():
self.assertEqual(domain_status, 0)
def test_execute_transaction_4(self):
"""Verify list of three statements (including one with
duplicated HitID) are inserted."""
domain_data1 = test_data_utils.get_trixie_domain_data()
test_db_utils.insert_domain_data(domain_data1)
domain_table_results1 = test_db_utils.get_data(
test_db_utils.domain_table_query)
# Duplicate HitID
statement1 = get_domain_insert_statement(domain_data1)
# Valid
gene_domain_data = test_data_utils.get_trixie_gene_domain_data()
statement2 = get_gene_domain_insert_statement(gene_domain_data)
# Valid
update_data = get_trixie_gene_table_domain_status_update_data_1()
statement3 = get_gene_update_statement(update_data)
statements = [statement1, statement2, statement3]
result = find_domains.execute_transaction(self.connection, statements)
gene_table_results = test_db_utils.get_data(
test_db_utils.gene_table_query)
gene_domain_table_results = test_db_utils.get_data(
test_db_utils.gene_domain_table_query)
domain_table_results2 = test_db_utils.get_data(
test_db_utils.domain_table_query)
domain_status = gene_table_results[0]["DomainStatus"]
with self.subTest():
self.assertEqual(len(domain_table_results1), 1)
with self.subTest():
self.assertEqual(len(domain_table_results2), 1)
with self.subTest():
self.assertEqual(len(gene_domain_table_results), 1)
with self.subTest():
self.assertEqual(result, 0)
with self.subTest():
self.assertEqual(domain_status, 1)
def test_execute_statement_10(self):
"""Verify invalid data can be inserted after '% w' is
replaced with '%% w'."""
domain_data = test_data_utils.get_trixie_domain_data()
# "Description": "ParB-like nuclease domain"
description = domain_data["Description"]
description = description.replace("nuclease domain",
"nuclease % wdomain")
domain_data["Description"] = description
statement = get_domain_insert_statement(domain_data)
statement = statement.replace("%", "%%")
results_tup = find_domains.execute_statement(self.connection,
statement)
result = results_tup[0]
type_error = results_tup[1]
value_error = results_tup[2]
msg = results_tup[3]
self.trans.commit()
domain_table_results = test_db_utils.get_data(
test_db_utils.domain_table_query)
with self.subTest():
self.assertEqual(len(domain_table_results), 1)
with self.subTest():
self.assertEqual(result, 0)
with self.subTest():
self.assertFalse(type_error)
with self.subTest():
self.assertFalse(value_error)
def test_execute_statement_6(self):
"""Verify invalid data can NOT be inserted into domain table when
there is an invalid column name."""
domain_data = test_data_utils.get_trixie_domain_data()
statement = get_domain_insert_statement(domain_data)
statement = statement.replace("Name", "Name_invalid")
results_tup = find_domains.execute_statement(self.connection,
statement)
result = results_tup[0]
type_error = results_tup[1]
value_error = results_tup[2]
msg = results_tup[3]
self.trans.commit()
domain_table_results = test_db_utils.get_data(
test_db_utils.domain_table_query)
with self.subTest():
self.assertEqual(len(domain_table_results), 0)
with self.subTest():
self.assertEqual(result, 1)
with self.subTest():
self.assertTrue(error_msg in msg)
with self.subTest():
self.assertFalse(type_error)
with self.subTest():
self.assertFalse(value_error)
def test_execute_transaction_2(self):
"""Verify list of one valid statement can be inserted into domain table."""
domain_data = test_data_utils.get_trixie_domain_data()
statement = get_domain_insert_statement(domain_data)
statements = [statement]
result = find_domains.execute_transaction(self.connection, statements)
domain_table_results = test_db_utils.get_data(
test_db_utils.domain_table_query)
with self.subTest():
self.assertEqual(len(domain_table_results), 1)
with self.subTest():
self.assertEqual(result, 0)
def test_execute_transaction_7(self):
"""Verify list of three valid statements and one invalid statement
(containing '% w') are inserted (since '% w' replaced with '%% w')."""
# Valid
domain_data1 = test_data_utils.get_trixie_domain_data()
statement1 = get_domain_insert_statement(domain_data1)
# Valid
gene_domain_data = test_data_utils.get_trixie_gene_domain_data()
statement2 = get_gene_domain_insert_statement(gene_domain_data)
# Invalid '% w'
domain_data2 = test_data_utils.get_trixie_domain_data()
# "Description": "ParB-like nuclease domain"
description = domain_data2["Description"]
description = description.replace("nuclease domain",
"nuclease % wdomain")
domain_data2["Description"] = description
domain_data2["HitID"] = "unique_id"
statement3 = get_domain_insert_statement(domain_data2)
# Valid
update_data = get_trixie_gene_table_domain_status_update_data_1()
statement4 = get_gene_update_statement(update_data)
statements = [statement1, statement2, statement3, statement4]
result = find_domains.execute_transaction(self.connection, statements)
gene_table_results = test_db_utils.get_data(
test_db_utils.gene_table_query)
gene_domain_table_results = test_db_utils.get_data(
test_db_utils.gene_domain_table_query)
domain_table_results = test_db_utils.get_data(
test_db_utils.domain_table_query)
domain_status = gene_table_results[0]["DomainStatus"]
with self.subTest():
self.assertEqual(len(domain_table_results), 2)
with self.subTest():
self.assertEqual(len(gene_domain_table_results), 1)
with self.subTest():
self.assertEqual(result, 0)
with self.subTest():
self.assertEqual(domain_status, 1)
def test_execute_statement_5(self):
"""Verify invalid data can NOT be inserted into domain table when
there is a duplicated HitID."""
domain_data = test_data_utils.get_trixie_domain_data()
statement = get_domain_insert_statement(domain_data)
results_tup1 = find_domains.execute_statement(self.connection,
statement)
result1 = results_tup1[0]
type_error1 = results_tup1[1]
value_error1 = results_tup1[2]
msg1 = results_tup1[3]
self.trans.commit()
domain_table_results1 = test_db_utils.get_data(
test_db_utils.domain_table_query)
new_trans = self.connection.begin()
results_tup2 = find_domains.execute_statement(self.connection,
statement)
result2 = results_tup2[0]
type_error2 = results_tup2[1]
value_error2 = results_tup2[2]
msg2 = results_tup2[3]
new_trans.commit()
domain_table_results2 = test_db_utils.get_data(
test_db_utils.domain_table_query)
with self.subTest():
self.assertEqual(len(domain_table_results1), 1)
with self.subTest():
self.assertEqual(len(domain_table_results2), 1)
with self.subTest():
self.assertEqual(result1, 0)
with self.subTest():
self.assertEqual(result2, 0)
with self.subTest():
self.assertFalse(type_error1)
with self.subTest():
self.assertFalse(type_error2)
with self.subTest():
self.assertFalse(value_error1)
with self.subTest():
self.assertFalse(value_error2)
with self.subTest():
self.assertFalse(error_msg in msg1)
with self.subTest():
self.assertTrue(error_msg in msg2)
def test_execute_transaction_3(self):
"""Verify list of two valid statements can be inserted into
domain and gene_domain tables"""
domain_data = test_data_utils.get_trixie_domain_data()
statement1 = get_domain_insert_statement(domain_data)
gene_domain_data = test_data_utils.get_trixie_gene_domain_data()
statement2 = get_gene_domain_insert_statement(gene_domain_data)
statements = [statement1, statement2]
result = find_domains.execute_transaction(self.connection, statements)
gene_domain_table_results = test_db_utils.get_data(
test_db_utils.gene_domain_table_query)
domain_table_results = test_db_utils.get_data(
test_db_utils.domain_table_query)
with self.subTest():
self.assertEqual(len(domain_table_results), 1)
with self.subTest():
self.assertEqual(len(gene_domain_table_results), 1)
with self.subTest():
self.assertEqual(result, 0)
def test_execute_statement_2(self):
"""Verify valid data can be inserted into domain table."""
domain_data = test_data_utils.get_trixie_domain_data()
statement = get_domain_insert_statement(domain_data)
results_tup = find_domains.execute_statement(self.connection,
statement)
result = results_tup[0]
type_error = results_tup[1]
value_error = results_tup[2]
msg = results_tup[3]
self.trans.commit()
domain_table_results = test_db_utils.get_data(
test_db_utils.domain_table_query)
with self.subTest():
self.assertEqual(len(domain_table_results), 1)
with self.subTest():
self.assertEqual(result, 0)
with self.subTest():
self.assertFalse(type_error)
with self.subTest():
self.assertFalse(value_error)
def test_execute_transaction_8(self, es_mock):
"""Verify error inside try/except block is executed."""
stmt_result1 = 0
type_error1 = False
# TODO make sure this is set correctly
value_error1 = False
msg1 = "empty"
mock_result1 = (stmt_result1, type_error1, value_error1, msg1)
stmt_result2 = 0
type_error2 = False
# TODO make sure this is set correctly
value_error2 = False
msg2 = 2 # the function expects this to be a string, so this should
# break the code and trigger the except block.
mock_result2 = (stmt_result2, type_error2, value_error2, msg2)
es_mock.side_effect = [mock_result1, mock_result2]
# Valid
domain_data1 = test_data_utils.get_trixie_domain_data()
statement1 = get_domain_insert_statement(domain_data1)
# Valid
gene_domain_data = test_data_utils.get_trixie_gene_domain_data()
statement2 = get_gene_domain_insert_statement(gene_domain_data)
statements = [statement1, statement2]
result = find_domains.execute_transaction(self.connection, statements)
gene_domain_table_results = test_db_utils.get_data(
test_db_utils.gene_domain_table_query)
domain_table_results = test_db_utils.get_data(
test_db_utils.domain_table_query)
with self.subTest():
self.assertEqual(len(domain_table_results), 0)
with self.subTest():
self.assertEqual(len(gene_domain_table_results), 0)
with self.subTest():
self.assertEqual(result, 1)
with self.subTest():
self.assertEqual(es_mock.call_count, 2)
def test_execute_statement_3(self):
"""Verify valid data can be inserted into domain and gene_domain tables."""
domain_data = test_data_utils.get_trixie_domain_data()
statement1 = get_domain_insert_statement(domain_data)
results_tup1 = find_domains.execute_statement(self.connection,
statement1)
result1 = results_tup1[0]
type_error1 = results_tup1[1]
value_error1 = results_tup1[2]
msg1 = results_tup1[3]
gene_domain_data = test_data_utils.get_trixie_gene_domain_data()
statement2 = get_gene_domain_insert_statement(gene_domain_data)
results_tup2 = find_domains.execute_statement(self.connection,
statement2)
result2 = results_tup2[0]
type_error2 = results_tup2[1]
value_error2 = results_tup2[2]
msg2 = results_tup2[3]
self.trans.commit()
gene_domain_table_results = test_db_utils.get_data(
test_db_utils.gene_domain_table_query)
domain_table_results = test_db_utils.get_data(
test_db_utils.domain_table_query)
with self.subTest():
self.assertEqual(len(domain_table_results), 1)
with self.subTest():
self.assertEqual(len(gene_domain_table_results), 1)
with self.subTest():
self.assertEqual(result1, 0)
with self.subTest():
self.assertEqual(result2, 0)
with self.subTest():
self.assertFalse(type_error1)
with self.subTest():
self.assertFalse(type_error2)
with self.subTest():
self.assertFalse(value_error1)
with self.subTest():
self.assertFalse(value_error2)