def get_acc_id_dict(alchemist):
"""Test helper function to retrieve accessions of database entries.
"""
db_filter = Filter(alchemist=alchemist)
db_filter.key = "phage.PhageID"
db_filter.values = db_filter.build_values()
groups = db_filter.group("phage.Accession")
return groups
class TestFilter(unittest.TestCase):
@classmethod
def setUpClass(self):
setup_test_db()
def setUp(self):
alchemist = AlchemyHandler()
alchemist.username = "******"
alchemist.password = "******"
alchemist.database = "test_db"
alchemist.connect()
alchemist.build_graph()
self.alchemist = alchemist
self.db_filter = Filter(alchemist=self.alchemist)
phageid = self.alchemist.get_column("phage.PhageID")
self.phageid = phageid
def test_constructor_1(self):
db_filter = Filter(alchemist=self.alchemist)
def test_constructor_2(self):
self.assertTrue(isinstance(self.db_filter.graph, Graph))
self.assertTrue(isinstance(self.db_filter.engine, Engine))
def test_add_1(self):
self.db_filter.add("phage.PhageID=Myrna")
self.assertTrue("phage.PhageID=" in self.db_filter.filters.keys())
def test_add_2(self):
self.db_filter.add("phage.PhageID=Myrna")
where_clauses = self.db_filter.filters["phage.PhageID="]
self.assertTrue(isinstance(where_clauses, list))
self.assertTrue(isinstance(where_clauses[0], BinaryExpression))
def test_add_3(self):
self.db_filter.add("phage.PhageID=Myrna")
self.db_filter.add("phage.PhageID=D29")
where_clauses = self.db_filter.filters["phage.PhageID="]
self.assertEqual(len(where_clauses), 2)
def test_remove_1(self):
self.db_filter.add("phage.PhageID=Myrna")
self.db_filter.remove("phage.PhageID=Myrna")
self.assertEqual(self.db_filter.filters, {})
def test_remove_2(self):
self.db_filter.add("phage.PhageID=Myrna")
self.db_filter.add("phage.PhageID=D29")
self.db_filter.remove("phage.PhageID=Myrna")
where_clauses = self.db_filter.filters["phage.PhageID="]
self.assertTrue(len(where_clauses) == 1)
self.assertEqual(where_clauses[0].right.value, "D29")
def test_build_where_clauses_1(self):
self.db_filter.add("phage.PhageID=Myrna")
self.db_filter.add("phage.PhageID=D29")
queries = self.db_filter.build_where_clauses()
self.assertEqual(len(queries), 2)
def test_build_where_clauses_2(self):
self.db_filter.add("phage.PhageID=Myrna")
self.db_filter.add("phage.PhageID=D29")
queries = self.db_filter.build_where_clauses()
for query in queries:
self.assertTrue(isinstance(query, BinaryExpression))
def test_build_values_1(self):
self.db_filter.key = self.phageid
self.db_filter.values = ["Myrna", "D29"]
values = self.db_filter.build_values()
self.assertTrue("Myrna" in values)
self.assertTrue("D29" in values)
def test_transpose_1(self):
self.db_filter.values = ["Myrna"]
self.db_filter.key = self.phageid
self.db_filter.refresh()
host_genera = self.db_filter.transpose("phage.HostGenus")
self.assertEqual(host_genera, ["Mycobacterium"])
def test_retrieve_1(self):
self.db_filter.values = ["Myrna"]
self.db_filter.key = self.phageid
self.db_filter.refresh()
myrna_data = self.db_filter.retrieve(
["phage.HostGenus", "phage.Cluster", "gene.Notes"])
self.assertTrue(len(myrna_data) == 3)
self.assertTrue(isinstance(myrna_data, dict))
self.assertEqual(myrna_data["HostGenus"], ["Mycobacterium"])
self.assertEqual(myrna_data["Cluster"], ["C"])
def test_refresh_2(self):
self.db_filter.key = self.phageid
self.db_filter.values = ["Myrna", "D29", "Sheetz"]
self.db_filter.refresh()
self.assertTrue("Myrna" in self.db_filter.values)
self.assertTrue("D29" in self.db_filter.values)
self.assertFalse("Sheetz" in self.db_filter.values)
def test_update_1(self):
self.db_filter.key = self.phageid
self.db_filter.values = ["Myrna", "D29"]
self.db_filter.add("phage.PhageID=Myrna")
self.db_filter.update()
self.assertTrue("Myrna" in self.db_filter.values)
self.assertFalse("D29" in self.db_filter.values)
def test_sort_1(self):
self.db_filter.key = self.phageid
self.db_filter.values = ["Myrna", "D29"]
self.db_filter.sort(self.phageid)
self.assertTrue("Myrna" in self.db_filter.values)
self.assertTrue("D29" in self.db_filter.values)
self.assertEqual(self.db_filter.values[0], "D29")
def test_group_1(self):
self.db_filter.key = self.phageid
self.db_filter.values = ["Myrna", "D29"]
group_results = self.db_filter.group(self.phageid)
self.assertTrue("Myrna" in group_results.keys())
self.assertTrue("Myrna" in group_results["Myrna"])
self.assertTrue("D29" in group_results.keys())
self.assertTrue("D29" in group_results.keys())
def test_group_2(self):
self.db_filter.key = self.phageid
self.db_filter.values = ["Myrna", "D29"]
group_results = self.db_filter.group("phage.HostGenus")
self.assertTrue("Mycobacterium" in group_results.keys())
self.assertTrue("Myrna" in group_results["Mycobacterium"])
self.assertTrue("D29" in group_results["Mycobacterium"])
@classmethod
def tearDownClass(self):
teardown_test_db()
class TestFilter(unittest.TestCase):
@classmethod
def setUpClass(self):
test_db_utils.create_filled_test_db()
@classmethod
def tearDownClass(self):
test_db_utils.remove_db()
def setUp(self):
alchemist = AlchemyHandler()
alchemist.username=user
alchemist.password=pwd
alchemist.database=db
alchemist.connect()
self.alchemist = alchemist
self.db_filter = Filter(alchemist=self.alchemist)
self.phage = self.alchemist.metadata.tables["phage"]
self.gene = self.alchemist.metadata.tables["gene"]
self.trna = self.alchemist.metadata.tables["trna"]
self.PhageID = self.phage.c.PhageID
self.Cluster = self.phage.c.Cluster
self.Subcluster = self.phage.c.Subcluster
self.Notes = self.gene.c.Notes
def tearDown(self):
self.alchemist.clear()
def test_and__1(self):
"""Verify that and_() creates a dictionary key as expected.
"""
self.db_filter.and_("phage.PhageID=Myrna")
or_block = self.db_filter.filters[0]
self.assertTrue("phage.PhageID=Myrna" in or_block.keys())
def test_and__2(self):
"""Verify that and_() stores BinaryExpression data as expected.
"""
self.db_filter.and_("phage.PhageID=Myrna")
or_block = self.db_filter.filters[0]
self.assertTrue(isinstance(or_block, dict))
where_clauses = or_block["phage.PhageID=Myrna"]
self.assertTrue(isinstance(where_clauses, BinaryExpression))
def test_and_3(self):
"""Verify that and_() recognizes previous and_() data.
"""
self.db_filter.and_("phage.PhageID = Myrna")
self.db_filter.and_("phage.PhageID=Myrna")
self.db_filter.and_("phage.PhageID=D29")
or_block = self.db_filter.filters[0]
self.assertEqual(len(or_block), 2)
def test_remove_1(self):
"""Verify that remove() removes dictionary entry after depleted.
"""
self.db_filter.and_("phage.PhageID=Myrna")
self.db_filter.remove("phage.PhageID=Myrna")
self.assertEqual(self.db_filter.filters, [{}])
def test_remove_2(self):
"""Verify that remove() conserves dictionary entry if not depleted.
"""
self.db_filter.and_("phage.PhageID=Myrna")
self.db_filter.and_("phage.PhageID=D29")
self.db_filter.remove("phage.PhageID=Myrna")
or_block = self.db_filter.filters[0]
where_clauses = or_block["phage.PhageID=D29"]
self.assertEqual(where_clauses.right.value, "D29")
def test_add_1(self):
"""Verify that add() creates a dictionary key as expected.
"""
self.db_filter.add("phage.PhageID=Myrna")
or_block = self.db_filter.filters[0]
self.assertTrue("phage.PhageID=Myrna" in or_block.keys())
def test_add_2(self):
"""Verify that add() creates multiple keys as expected.
"""
self.db_filter.add("phage.PhageID=Myrna AND phage.PhageID = Trixie")
or_block = self.db_filter.filters[0]
self.assertTrue(len(or_block) == 2)
self.assertTrue("phage.PhageID=Myrna" in or_block.keys())
self.assertTrue("phage.PhageID=Trixie" in or_block.keys())
def test_add_3(self):
"""Verify that add() creates multiple or blocks as expected.
"""
self.db_filter.add("phage.PhageID=Myrna OR phage.PhageID = Trixie")
self.assertTrue(len(self.db_filter.filters) == 2)
first_or_block = self.db_filter.filters[0]
second_or_block = self.db_filter.filters[1]
self.assertTrue("phage.PhageID=Myrna" in first_or_block.keys())
self.assertFalse("phage.PhageID=Trixie" in first_or_block.keys())
self.assertFalse("phage.PhageID=Myrna" in second_or_block.keys())
self.assertTrue("phage.PhageID=Trixie" in second_or_block.keys())
def test_get_column_1(self):
"""Verify that get_column() converts string column input.
"""
self.db_filter.key = self.Cluster
column = self.db_filter.get_column("phage.PhageID")
self.assertEqual(column, self.PhageID)
def test_get_column_2(self):
"""Verify that get_column() conserves Column input.
"""
self.db_filter.key = self.Cluster
column = self.db_filter.get_column(self.PhageID)
self.assertEqual(column, self.PhageID)
def test_get_column_3(self):
"""Verify that get_column() raises TypeError.
get_column() should raise TypeError when column input is
neither a string or a Column.
"""
self.db_filter.key = self.Cluster
with self.assertRaises(TypeError):
self.db_filter.get_column(None)
def test_build_where_clauses_1(self):
"""Verify that build_where_clauses() forms list of expected length.
"""
self.db_filter.and_("phage.PhageID=Myrna")
self.db_filter.and_("phage.PhageID=D29")
queries = self.db_filter.build_where_clauses()
self.assertEqual(len(queries[0]), 2)
def test_build_where_clauses_2(self):
"""Verify that build_where_clauses() forms list of BinaryExpressions.
"""
self.db_filter.and_("phage.PhageID=Myrna")
self.db_filter.and_("phage.PhageID=D29")
queries = self.db_filter.build_where_clauses()
for query in queries:
self.assertTrue(isinstance(query, BooleanClauseList))
def test_build_values_1(self):
"""Verify that build_values() does not exclude values as expected.
"""
self.db_filter.key = self.PhageID
values = self.db_filter.build_values()
self.assertTrue("Myrna" in values)
self.assertTrue("D29" in values)
self.assertTrue("Alice" in values)
self.assertTrue("Trixie" in values)
def test_build_values_2(self):
"""Verify that build_values() utilizes WHERE clauses as expected.
"""
self.db_filter.key = self.PhageID
where_clause = (self.Cluster == "A")
values = self.db_filter.build_values(where=where_clause)
self.assertTrue("D29" in values)
self.assertTrue("Trixie" in values)
self.assertFalse("Myrna" in values)
self.assertFalse("Alice" in values)
def test_build_values_3(self):
"""Verify that build_values() creates DISTINCT values as expected.
"""
self.db_filter.key = self.Cluster
where_clause = (self.Subcluster == "A2")
values = self.db_filter.build_values(where=where_clause)
self.assertEqual(len(values), 1)
self.assertEqual(values, ["A"])
def test_build_values_4(self):
"""Verify that build_values() recognizes bytes-type column data.
"""
self.db_filter.key = self.Notes
values = self.db_filter.build_values()
self.assertTrue(isinstance(values[0], str))
def test_query_1(self):
"""Verify that query() creates instances as expected.
"""
self.db_filter.key = "phage.PhageID"
self.db_filter.values = ["Trixie", "D29"]
self.db_filter.refresh()
instances = self.db_filter.query("phage")
instance_ids = []
for instance in instances:
instance_ids.append(instance.PhageID)
self.assertTrue("Trixie" in instance_ids)
self.assertTrue("D29" in instance_ids)
self.assertFalse("Myrna" in instance_ids)
def test_query_2(self):
"""Verify that query() creates instances as expected.
"""
self.db_filter.key = "phage.PhageID"
self.db_filter.values = ["Trixie", "D29"]
self.db_filter.refresh()
instances = self.db_filter.query("gene")
instance_ids = set()
for instance in instances:
instance_ids.add(instance.phage.PhageID)
instance_ids = list(instance_ids)
self.assertTrue("Trixie" in instance_ids)
self.assertTrue("D29" in instance_ids)
self.assertFalse("Myrna" in instance_ids)
def test_transpose_1(self):
"""Verify that transpose() utilizes Filter values as expected.
"""
self.db_filter.values = ["Myrna"]
self.db_filter.key = self.PhageID
self.db_filter.refresh()
clusters = self.db_filter.transpose("phage.Cluster")
self.assertEqual(clusters, ["C"])
def test_transpose_2(self):
"""Verify that transpose() can optionally create dict return value.
"""
self.db_filter.values = ["Myrna"]
self.db_filter.key = self.PhageID
self.db_filter.refresh()
clusters_dict = self.db_filter.transpose(self.Cluster, return_dict=True)
self.assertEqual(clusters_dict["Cluster"], ["C"])
def test_transpose_3(self):
"""Verify that transpose() can alter Filter properties as expected.
"""
self.db_filter.values = ["Myrna"]
self.db_filter.key = self.PhageID
self.db_filter.refresh()
self.db_filter.transpose("phage.Cluster", set_values=True)
self.assertEqual(self.db_filter.key, self.Cluster)
self.assertEqual(self.db_filter.values, ["C"])
def test_transpose_4(self):
"""Verify that transpose() filter parameter functions as expected.
"""
self.db_filter.values = ["Myrna", "D29"]
self.db_filter.key = self.PhageID
self.db_filter.add("gene.GeneID = Myrna_CDS_28")
values = self.db_filter.transpose("gene.GeneID", filter=True)
self.assertEqual(len(values), 1)
self.assertEqual(values[0], "Myrna_CDS_28")
def test_mass_transpose_1(self):
"""Verify that mass_tranpose() returns DISTINCT values as expected.
"""
self.db_filter.values = ["Myrna"]
self.db_filter.key = self.PhageID
self.db_filter.refresh()
myrna_data = self.db_filter.mass_transpose(["phage.HostGenus",
"phage.Cluster",
"gene.Notes"])
self.assertTrue(len(myrna_data) == 3 )
self.assertTrue(isinstance(myrna_data, dict))
self.assertEqual(myrna_data["HostGenus"], ["Mycobacterium"])
self.assertEqual(myrna_data["Cluster"], ["C"])
def test_mass_transpose_2(self):
"""Verify that mass_tranpose() utilizes all values as expected.
"""
self.db_filter.values = ["Myrna", "Trixie"]
self.db_filter.key = self.PhageID
self.db_filter.refresh()
data = self.db_filter.mass_transpose(["phage.HostGenus",
"phage.Cluster",
"gene.Notes"])
self.assertTrue(len(data) == 3)
self.assertTrue(isinstance(data, dict))
self.assertEqual(data["HostGenus"], ["Mycobacterium"])
self.assertEqual(data["Cluster"], ["C", "A"])
def test_retrieve_1(self):
"""Verify that retrieve() separates data as expected.
"""
self.db_filter.values = ["Myrna", "Trixie"]
self.db_filter.key = self.PhageID
self.db_filter.refresh()
data = self.db_filter.retrieve(["phage.HostGenus",
"phage.Cluster"])
myrna_data = data["Myrna"]
self.assertEqual(myrna_data["HostGenus"], ["Mycobacterium"])
self.assertEqual(myrna_data["Cluster"], ["C"])
trixie_data = data["Trixie"]
self.assertEqual(trixie_data["HostGenus"], ["Mycobacterium"])
self.assertEqual(trixie_data["Cluster"], ["A"])
def test_retrieve_2(self):
"""Verify that retrieve() separates data as expected.
"""
self.db_filter.values = ["A", "C"]
self.db_filter.key = self.Cluster
self.db_filter.refresh()
data = self.db_filter.retrieve(["phage.Cluster", "phage.PhageID"])
a_data = data["A"]
self.assertEqual(a_data["Cluster"], ["A"])
self.assertTrue("Trixie" in a_data["PhageID"])
self.assertFalse("Myrna" in a_data["PhageID"])
c_data = data["C"]
self.assertEqual(c_data["Cluster"], ["C"])
self.assertFalse("Trixie" in c_data["PhageID"])
self.assertTrue("Myrna" in c_data["PhageID"])
def test_refresh_1(self):
"""Verify that refresh() eliminates invalid data.
"""
self.db_filter.key = self.PhageID
self.db_filter.values = ["Myrna", "D29", "Sheetz"]
self.db_filter.refresh()
self.assertTrue("Myrna" in self.db_filter.values)
self.assertTrue("D29" in self.db_filter.values)
self.assertFalse("Sheetz" in self.db_filter.values)
def test_update_1(self):
"""Verify that update() filters out values.
"""
self.db_filter.key = self.PhageID
self.db_filter.values = ["Myrna", "D29"]
self.db_filter.and_("phage.PhageID=Myrna")
self.db_filter.update()
self.assertTrue("Myrna" in self.db_filter.values)
self.assertFalse("D29" in self.db_filter.values)
def test_sort_1(self):
"""Verify that sort() orders values as expected.
"""
self.db_filter.key = self.PhageID
self.db_filter.values = ["Myrna", "D29"]
self.db_filter.sort(self.PhageID)
self.assertTrue("Myrna" in self.db_filter.values)
self.assertTrue("D29" in self.db_filter.values)
self.assertEqual(self.db_filter.values[0], "D29")
def test_sort_2(self):
"""Verify that sort() orders values with multiple sort columns.
"""
self.db_filter.key = self.PhageID
self.db_filter.values = ["Myrna", "D29", "Alice"]
self.db_filter.sort([self.Cluster, self.PhageID])
self.assertTrue("Myrna" in self.db_filter.values)
self.assertTrue("D29" in self.db_filter.values)
self.assertTrue("Alice" in self.db_filter.values)
self.assertEqual(self.db_filter.values[0], "D29")
self.assertEqual(self.db_filter.values[1], "Alice")
def test_group_1(self):
"""Verify that group() creates separate groups as expected.
"""
self.db_filter.key = self.PhageID
self.db_filter.values = ["Myrna", "D29"]
group_results = self.db_filter.group(self.PhageID)
self.assertTrue("Myrna" in group_results.keys())
self.assertTrue("Myrna" in group_results["Myrna"])
self.assertTrue("D29" in group_results.keys())
self.assertTrue("D29" in group_results["D29"])
def test_group_2(self):
"""Verify that group() recognizes similarities in values as expected.
"""
self.db_filter.key = self.PhageID
self.db_filter.values = ["Myrna", "D29"]
group_results = self.db_filter.group("phage.HostGenus")
self.assertTrue("Mycobacterium" in group_results.keys())
self.assertTrue("Myrna" in group_results["Mycobacterium"])
self.assertTrue("D29" in group_results["Mycobacterium"])
def test_group_3(self):
"""Verify that group() recognizes differences in values as expected.
"""
self.db_filter.key = self.PhageID
self.db_filter.values = ["Myrna", "D29", "Trixie"]
group_results = self.db_filter.group("phage.Cluster")
self.assertTrue("A" in group_results.keys())
self.assertTrue("C" in group_results.keys())
self.assertTrue("Myrna" in group_results["C"])
self.assertTrue("D29" in group_results["A"])
self.assertTrue("Trixie" in group_results["A"])