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 test_get_phage_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_phage_data(phage_data)
count = mysqldb.get_phage_table_count(self.engine)
self.assertEqual(count, 1)
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 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"