def test_get_table_count_2(self):
"""Verify the correct number of phages is returned when
the database contains one genome."""
phage_data = test_data_utils.get_trixie_phage_data()
test_db_utils.insert_data(PHAGE, phage_data)
count = mysqldb_basic.get_table_count(self.engine, TABLE)
self.assertEqual(count, 1)
def test_change_version_3(self):
"""Verify the version is decremented by 5."""
data = {"Version": 10, "SchemaVersion": 1}
test_db_utils.insert_data(VERSION, data)
mysqldb.change_version(self.engine, amount=-5)
result = test_db_utils.get_data(test_db_utils.version_table_query)
output_value = result[0]["Version"]
self.assertEqual(output_value, 5)
def test_scalar_1(self):
"""Verify dictionary is returned when there are two rows of data."""
phage_data1 = test_data_utils.get_trixie_phage_data()
phage_data2 = test_data_utils.get_trixie_phage_data()
phage_data1["PhageID"] = "Trixie"
phage_data2["PhageID"] = "L5"
test_db_utils.insert_data(PHAGE, phage_data1)
test_db_utils.insert_data(PHAGE, phage_data2)
count = mysqldb_basic.scalar(self.engine, COUNT_QUERY)
self.assertEqual(count, 2)
def test_first_1(self):
"""Verify dictionary is returned when there are two rows of data."""
phage_data1 = test_data_utils.get_trixie_phage_data()
phage_data2 = test_data_utils.get_trixie_phage_data()
phage_data1["PhageID"] = "Trixie"
phage_data2["PhageID"] = "L5"
test_db_utils.insert_data(PHAGE, phage_data1)
test_db_utils.insert_data(PHAGE, phage_data2)
data = mysqldb_basic.first(self.engine, PHAGE_QUERY, return_dict=True)
self.assertTrue(COLUMN in data.keys())
def setUp(self):
self.engine = sqlalchemy.create_engine(ENGINE_STRING, echo=False)
phage_data = test_data_utils.get_trixie_phage_data()
phage_data["PhageID"] = "Trixie"
phage_data["HostGenus"] = "Mycobacterium"
phage_data["Accession"] = "ABC123"
phage_data["Cluster"] = "A"
phage_data["Subcluster"] = "A1"
phage_data["Sequence"] = "atcg"
phage_data["Length"] = 6
phage_data["DateLastModified"] = constants.EMPTY_DATE
test_db_utils.insert_data(PHAGE, phage_data)
def test_first_2(self):
"""Verify tuple is returned when there are two rows of data."""
phage_data1 = test_data_utils.get_trixie_phage_data()
phage_data2 = test_data_utils.get_trixie_phage_data()
phage_data1["PhageID"] = "Trixie"
phage_data2["PhageID"] = "L5"
test_db_utils.insert_data(PHAGE, phage_data1)
test_db_utils.insert_data(PHAGE, phage_data2)
data = mysqldb_basic.first(self.engine, PHAGE_QUERY, return_dict=False)
with self.subTest():
self.assertIsInstance(data, tuple)
with self.subTest():
self.assertTrue(len(data) > 1)
def test_get_first_row_data_3(self):
"""Verify dictionary is returned when there are two rows of data."""
phage_data1 = test_data_utils.get_trixie_phage_data()
phage_data2 = test_data_utils.get_trixie_phage_data()
phage_data1["PhageID"] = "Trixie"
phage_data2["PhageID"] = "L5"
test_db_utils.insert_data(PHAGE, phage_data1)
test_db_utils.insert_data(PHAGE, phage_data2)
# Get all data from table just to confirm there is more than one row.
all_data = test_db_utils.get_data(test_db_utils.phage_table_query)
data = mysqldb_basic.get_first_row_data(self.engine, TABLE)
with self.subTest():
self.assertEqual(len(all_data), 2)
with self.subTest():
self.assertTrue(COLUMN in data.keys())
def test_create_update_4(self):
"""Verify Gene table statement is created correctly."""
# First add gene Trixie_1 to the database.
gene_data = test_data_utils.get_trixie_gene_data()
gene_data["PhageID"] = "Trixie"
gene_data["Notes"] = "none"
gene_data["GeneID"] = "Trixie_1"
test_db_utils.insert_data(GENE, gene_data)
# Second run the update statement.
statement = mysqldb.create_update("gene", "Notes", "Repressor",
"GeneID", "Trixie_1")
test_db_utils.execute(statement)
result = test_db_utils.get_data(GENE_QUERY2)
results = result[0]
exp = "UPDATE gene SET Notes = 'Repressor' WHERE GeneID = 'Trixie_1';"
with self.subTest():
self.assertEqual(statement, exp)
with self.subTest():
self.assertEqual(results["Notes"].decode("utf-8"), "Repressor")
def setUpClass(self):
test_db_utils.create_empty_test_db(db=DB2)
test_db_utils.create_empty_test_db()
phage_data1 = test_data_utils.get_trixie_phage_data()
phage_data2 = test_data_utils.get_trixie_phage_data()
phage_data3 = test_data_utils.get_trixie_phage_data()
phage_data1["PhageID"] = "L5"
phage_data2["PhageID"] = "Trixie"
phage_data3["PhageID"] = "D29"
phage_data1["HostGenus"] = "Mycobacterium"
phage_data2["HostGenus"] = "Mycobacterium"
phage_data3["HostGenus"] = "Gordonia"
phage_data1["Accession"] = "ABC123"
phage_data2["Accession"] = "XYZ456"
phage_data3["Accession"] = ""
phage_data1["Cluster"] = "A"
phage_data2["Cluster"] = "B"
phage_data3["Cluster"] = "NULL"
phage_data1["Subcluster"] = "A1"
phage_data2["Subcluster"] = "NULL"
phage_data3["Subcluster"] = "NULL"
phage_data1["Sequence"] = "atcg"
phage_data2["Sequence"] = "AATT"
phage_data3["Sequence"] = "GGCC"
phage_data1["Length"] = 6
phage_data2["Length"] = 4
phage_data3["Length"] = 5
phage_data1["DateLastModified"] = constants.EMPTY_DATE
phage_data2["DateLastModified"] = constants.EMPTY_DATE
phage_data3["DateLastModified"] = constants.EMPTY_DATE
phage_data_list = [phage_data1, phage_data2, phage_data3]
for phage_data in phage_data_list:
test_db_utils.insert_data(PHAGE, phage_data)
gene_data1 = test_data_utils.get_trixie_gene_data()
gene_data2 = test_data_utils.get_trixie_gene_data()
gene_data3 = test_data_utils.get_trixie_gene_data()
gene_data4 = test_data_utils.get_trixie_gene_data()
gene_data1["PhageID"] = "Trixie"
gene_data2["PhageID"] = "Trixie"
gene_data3["PhageID"] = "Trixie"
gene_data4["PhageID"] = "D29"
gene_data1["GeneID"] = "Trixie_1"
gene_data2["GeneID"] = "Trixie_2"
gene_data3["GeneID"] = "Trixie_3"
gene_data4["GeneID"] = "D29_1"
gene_data_list = [gene_data1, gene_data2, gene_data3, gene_data4]
for gene_data in gene_data_list:
test_db_utils.insert_data(GENE, gene_data)
def test_get_first_row_data_2(self):
"""Verify dictionary is returned when there is one row of data."""
phage_data = test_data_utils.get_trixie_phage_data()
test_db_utils.insert_data(PHAGE, phage_data)
data = mysqldb_basic.get_first_row_data(self.engine, TABLE)
self.assertTrue(COLUMN in data.keys())
def setUp(self):
test_db_utils.create_empty_test_db(db=DB2)
self.alchemist2 = AlchemyHandler(database=DB2,
username=USER,
password=PWD)
self.alchemist2.build_engine()
self.engine2 = self.alchemist2.engine
test_db_utils.create_empty_test_db()
self.alchemist1 = AlchemyHandler(database=DB,
username=USER,
password=PWD)
self.alchemist1.build_engine()
self.engine1 = self.alchemist1.engine
phage_data1 = test_data_utils.get_trixie_phage_data()
phage_data2 = test_data_utils.get_trixie_phage_data()
phage_data3 = test_data_utils.get_trixie_phage_data()
phage_data1["PhageID"] = "L5"
phage_data2["PhageID"] = "Trixie"
phage_data3["PhageID"] = "D29"
phage_data1["HostGenus"] = "Mycobacterium"
phage_data2["HostGenus"] = "Mycobacterium"
phage_data3["HostGenus"] = "Gordonia"
phage_data1["Accession"] = "ABC123"
phage_data2["Accession"] = "XYZ456"
phage_data3["Accession"] = ""
phage_data1["Cluster"] = "A"
phage_data2["Cluster"] = "B"
phage_data3["Cluster"] = "NULL"
phage_data1["Subcluster"] = "A1"
phage_data2["Subcluster"] = "NULL"
phage_data3["Subcluster"] = "NULL"
phage_data1["Sequence"] = "atcg"
phage_data2["Sequence"] = "AATT"
phage_data3["Sequence"] = "GGCC"
phage_data1["Length"] = 6
phage_data2["Length"] = 4
phage_data3["Length"] = 5
phage_data1["DateLastModified"] = constants.EMPTY_DATE
phage_data2["DateLastModified"] = constants.EMPTY_DATE
phage_data3["DateLastModified"] = constants.EMPTY_DATE
phage_data_list = [phage_data1, phage_data2, phage_data3]
for phage_data in phage_data_list:
test_db_utils.insert_data(PHAGE, phage_data)
gene_data1 = test_data_utils.get_trixie_gene_data()
gene_data2 = test_data_utils.get_trixie_gene_data()
gene_data3 = test_data_utils.get_trixie_gene_data()
gene_data4 = test_data_utils.get_trixie_gene_data()
gene_data1["PhageID"] = "Trixie"
gene_data2["PhageID"] = "Trixie"
gene_data3["PhageID"] = "Trixie"
gene_data4["PhageID"] = "D29"
gene_data1["GeneID"] = "Trixie_1"
gene_data2["GeneID"] = "Trixie_2"
gene_data3["GeneID"] = "Trixie_3"
gene_data4["GeneID"] = "D29_1"
gene_data_list = [gene_data1, gene_data2, gene_data3, gene_data4]
for gene_data in gene_data_list:
test_db_utils.insert_data(GENE, gene_data)
def setUp(self):
self.engine = sqlalchemy.create_engine(ENGINE_STRING, echo=False)
test_db_utils.create_empty_test_db()
phage_data1 = test_data_utils.get_trixie_phage_data()
phage_data2 = test_data_utils.get_trixie_phage_data()
phage_data3 = test_data_utils.get_trixie_phage_data()
phage_data1["PhageID"] = "L5"
phage_data2["PhageID"] = "Trixie"
phage_data3["PhageID"] = "D29"
phage_data1["HostGenus"] = "Mycobacterium"
phage_data2["HostGenus"] = "Mycobacterium"
phage_data3["HostGenus"] = "Gordonia"
phage_data1["Accession"] = "ABC123"
phage_data2["Accession"] = "XYZ456"
phage_data3["Accession"] = ""
phage_data1["Cluster"] = "A"
phage_data2["Cluster"] = "B"
phage_data3["Cluster"] = "NULL"
phage_data1["Subcluster"] = "A1"
phage_data2["Subcluster"] = "NULL"
phage_data3["Subcluster"] = "NULL"
phage_data1["Sequence"] = "atcg"
phage_data2["Sequence"] = "AATT"
phage_data3["Sequence"] = "GGCC"
phage_data1["Length"] = 6
phage_data2["Length"] = 4
phage_data3["Length"] = 5
phage_data1["DateLastModified"] = constants.EMPTY_DATE
phage_data2["DateLastModified"] = constants.EMPTY_DATE
phage_data3["DateLastModified"] = constants.EMPTY_DATE
phage_data_list = [phage_data1, phage_data2, phage_data3]
for phage_data in phage_data_list:
test_db_utils.insert_data(PHAGE, phage_data)
gene_data1 = test_data_utils.get_trixie_gene_data()
gene_data2 = test_data_utils.get_trixie_gene_data()
gene_data3 = test_data_utils.get_trixie_gene_data()
gene_data4 = test_data_utils.get_trixie_gene_data()
gene_data1["PhageID"] = "Trixie"
gene_data2["PhageID"] = "Trixie"
gene_data3["PhageID"] = "Trixie"
gene_data4["PhageID"] = "D29"
gene_data1["GeneID"] = "Trixie_1"
gene_data2["GeneID"] = "Trixie_2"
gene_data3["GeneID"] = "Trixie_3"
gene_data4["GeneID"] = "D29_1"
gene_data_list = [gene_data1, gene_data2, gene_data3, gene_data4]
for gene_data in gene_data_list:
test_db_utils.insert_data(GENE, gene_data)
trna_data1 = test_data_utils.get_trixie_trna_data()
trna_data2 = test_data_utils.get_trixie_trna_data()
trna_data3 = test_data_utils.get_trixie_trna_data()
trna_data1["PhageID"] = "Trixie"
trna_data2["PhageID"] = "Trixie"
trna_data3["PhageID"] = "D29"
trna_data1["GeneID"] = "Trixie_4"
trna_data2["GeneID"] = "Trixie_5"
trna_data3["GeneID"] = "D29_1"
trna_data_list = [trna_data1, trna_data2, trna_data3]
for trna_data in trna_data_list:
test_db_utils.insert_data(TRNA, trna_data)
tmrna_data1 = test_data_utils.get_trixie_tmrna_data()
tmrna_data2 = test_data_utils.get_trixie_tmrna_data()
tmrna_data1["PhageID"] = "Trixie"
tmrna_data2["PhageID"] = "L5"
tmrna_data1["GeneID"] = "Trixie_6"
tmrna_data2["GeneID"] = "L5_1"
tmrna_data_list = [tmrna_data1, tmrna_data2]
for tmrna_data in tmrna_data_list:
test_db_utils.insert_data(TMRNA, tmrna_data)
