def setUp(self):
self.engine = create_engine(test_db_utils.create_engine_string())
session_maker_obj = sessionmaker(bind=self.engine)
self.session = session_maker_obj()
self.metadata = MetaData(bind=self.engine)
self.metadata.reflect()
self.mapper = automap_base(metadata=self.metadata)
self.mapper.prepare()
self.graph = querying.build_graph(self.metadata)
self.phage = self.metadata.tables["phage"]
self.gene = self.metadata.tables["gene"]
self.trna = self.metadata.tables["trna"]
self.PhageID = self.phage.c.PhageID
self.Cluster = self.phage.c.Cluster
self.Subcluster = self.phage.c.Subcluster
self.GeneID = self.gene.c.GeneID
self.PhamID = self.gene.c.PhamID
self.TrnaID = self.trna.c.GeneID
self.AminoAcid = self.trna.c.AminoAcid
def build_graph(self):
"""Create and store SQLAlchemy MetaData related NetworkX Graph object.
"""
if self._metadata is None:
self.build_metadata()
self._graph = querying.build_graph(self._metadata)
def test_build_onclause_2(self):
"""Verify build_onclause() detects table redundencies
"""
graph = querying.build_graph(self.metadata)
table = querying.build_onclause(graph, "phage", "phage")
self.assertEqual(table, self.phage)
def test_build_onclause_1(self, TranslateTable):
TranslateTable.return_value = "phage"
graph = querying.build_graph(self.metadata)
table = querying.build_onclause(graph, "phage", "phage")
TranslateTable.assert_called_with(self.metadata, "phage")
self.assertEqual(table, self.phage)
def test_build_onclause_1(self, translate_table_mock):
"""Verify translate_table() is called with the correct parameters.
"""
translate_table_mock.return_value = "phage"
graph = querying.build_graph(self.metadata)
table = querying.build_onclause(graph, "phage", "phage")
translate_table_mock.assert_called_with(self.metadata, "phage")
def test_build_graph_2(self):
graph = querying.build_graph(self.metadata)
self.assertTrue("phage" in graph.nodes)
self.assertTrue("gene" in graph.nodes)
self.assertTrue("trna" in graph.nodes)
self.assertEqual(graph.nodes["phage"]["table"], self.phage)
self.assertEqual(graph.nodes["gene"]["table"], self.gene)
self.assertEqual(graph.nodes["trna"]["table"], self.trna)
def test_build_graph_2(self):
"""Verify build_graph() stores Table objects with correct structure.
"""
graph = querying.build_graph(self.metadata)
self.assertTrue("phage" in graph.nodes)
self.assertTrue("gene" in graph.nodes)
self.assertTrue("trna" in graph.nodes)
self.assertEqual(graph.nodes["phage"]["table"], self.phage)
self.assertEqual(graph.nodes["gene"]["table"], self.gene)
self.assertEqual(graph.nodes["trna"]["table"], self.trna)
def test_build_graph_3(self):
graph = querying.build_graph(self.metadata)
phage = graph.nodes["phage"]["table"]
gene = graph.nodes["gene"]["table"]
trna = graph.nodes["trna"]["table"]
phage_gene_edge = graph["gene"]["phage"]
phage_trna_edge = graph["trna"]["phage"]
self.assertEqual(phage_gene_edge["key"], self.PhageGeneKey)
self.assertEqual(phage_trna_edge["key"], self.PhageTrnaKey)
def test_build_graph_3(self):
"""Verify build_graph() stores foreign keys with correct structure.
"""
graph = querying.build_graph(self.metadata)
phage = graph.nodes["phage"]["table"]
gene = graph.nodes["gene"]["table"]
trna = graph.nodes["trna"]["table"]
phage_gene_edge = graph["gene"]["phage"]
phage_trna_edge = graph["trna"]["phage"]
self.assertEqual(phage_gene_edge["key"], self.PhageGeneKey)
self.assertEqual(phage_trna_edge["key"], self.PhageTrnaKey)
def test_build_graph_1(self):
"""Verify build_graph() creates a NetworkX Graph object.
"""
graph = querying.build_graph(self.metadata)
self.assertTrue(isinstance(graph, Graph))
def test_build_onclause_2(self):
graph = querying.build_graph(self.metadata)
querying.build_onclause(graph, "phage", "gene")
def test_build_graph_1(self):
graph = querying.build_graph(self.metadata)
self.assertTrue(isinstance(graph, Graph))