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_data1["PhageID"] = "Trixie"
phage_data1["HostGenus"] = "Mycobacterium"
phage_data1["Accession"] = "ABC123"
phage_data1["Cluster"] = "A"
phage_data1["Subcluster"] = "A1"
phage_data1["Sequence"] = "atcg"
phage_data1["Length"] = 6
phage_data1["DateLastModified"] = constants.EMPTY_DATE
test_db_utils.insert_data(PHAGE, phage_data1)
gene_data1 = test_data_utils.get_trixie_gene_data()
gene_data2 = test_data_utils.get_trixie_gene_data()
gene_data1["PhageID"] = "Trixie"
gene_data2["PhageID"] = "Trixie"
gene_data1["GeneID"] = "Trixie_1"
gene_data2["GeneID"] = "Trixie_2"
test_db_utils.insert_data(GENE, gene_data1)
test_db_utils.insert_data(GENE, gene_data2)
def setUp(self):
self.engine = sqlalchemy.create_engine(engine_string1, echo=False)
test_db_utils.create_empty_test_db()
phage_data1 = test_data_utils.get_trixie_phage_data()
phage_data1["PhageID"] = "Trixie"
phage_data1["HostGenus"] = "Mycobacterium"
phage_data1["Accession"] = "ABC123"
phage_data1["Cluster"] = "A"
phage_data1["Subcluster"] = "A1"
phage_data1["Sequence"] = "atcg"
phage_data1["Length"] = 6
phage_data1["DateLastModified"] = constants.EMPTY_DATE
test_db_utils.insert_phage_data(phage_data1)
gene_data1 = test_data_utils.get_trixie_gene_data()
gene_data2 = test_data_utils.get_trixie_gene_data()
gene_data1["PhageID"] = "Trixie"
gene_data2["PhageID"] = "Trixie"
gene_data1["GeneID"] = "Trixie_1"
gene_data2["GeneID"] = "Trixie_2"
test_db_utils.insert_gene_data(gene_data1)
test_db_utils.insert_gene_data(gene_data2)
self.phage_query = "SELECT * FROM phage where PhageID = 'Trixie'"
self.gene_query = "SELECT * FROM gene where PhageID = 'Trixie'"
def setUp(self):
test_db_utils.create_empty_test_db()
test_db_utils.insert_phage_data(
test_data_utils.get_trixie_phage_data())
test_db_utils.insert_gene_data(test_data_utils.get_trixie_gene_data())
self.engine = sqlalchemy.create_engine(engine_string, echo=False)
self.connection = self.engine.connect()
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_gene_data(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(self.gene_query)
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 setUp(self):
self.engine = sqlalchemy.create_engine(engine_string1, 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_phage_data(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_gene_data(gene_data)
self.phage_query = "SELECT * FROM phage"
self.gene_query = "SELECT * FROM gene"
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)