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))