# -*- coding: utf-8 -*- """Tests for data structures in PyBEL.""" import os import random import tempfile import unittest from io import StringIO import pybel import pybel.examples from pybel import BELGraph from pybel.constants import CITATION_TYPE_PUBMED, IDENTIFIER, NAMESPACE from pybel.dsl import hgvs, protein from pybel.io.api import InvalidExtensionError from pybel.language import Entity from pybel.testing.utils import n class TestGraphProperties(unittest.TestCase): """Test setting and access to graph properties.""" def setUp(self): """Make fake metadata for the graphs.""" ( self.name, self.version, self.description, self.authors, self.contact, self.licenses, self.copyrights, self.disclaimer, ) = [n() for _ in range(8)] def _help_test_metadata(self, graph: BELGraph) -> None: """Help test the right metadata got in the graph.""" self.assertEqual(self.name, graph.name) self.assertEqual(self.version, graph.version) self.assertEqual(self.description, graph.description) self.assertEqual(self.authors, graph.authors) self.assertEqual(self.contact, graph.contact) self.assertEqual(self.licenses, graph.license) self.assertEqual(self.copyrights, graph.copyright) self.assertEqual(self.disclaimer, graph.disclaimer) self.assertEqual("{name} v{version}".format(name=self.name, version=self.version), str(graph)) def test_str_kwargs(self): """Test setting of metadata through keyword arguments.""" graph = BELGraph( name=self.name, version=self.version, description=self.description, authors=self.authors, contact=self.contact, license=self.licenses, copyright=self.copyrights, disclaimer=self.disclaimer, ) self._help_test_metadata(graph) def test_name(self): """Test setting of metadata through attributes.""" graph = BELGraph() graph.name = self.name graph.version = self.version graph.description = self.description graph.authors = self.authors graph.contact = self.contact graph.license = self.licenses graph.copyright = self.copyrights graph.disclaimer = self.disclaimer self._help_test_metadata(graph) class TestStruct(unittest.TestCase): """Test the BEL graph data structure.""" def test_add_simple(self): """Test that a simple node can be added, but not duplicated.""" graph = BELGraph() node = protein(namespace="TEST", name="YFG") graph.add_node_from_data(node) self.assertEqual(1, graph.number_of_nodes()) graph.add_node_from_data(node) self.assertEqual(1, graph.number_of_nodes(), msg="should not add same node again") def test_summarize(self): """Test summarizing a graph.""" self.maxDiff = None sio = StringIO() random.seed(5) pybel.examples.sialic_acid_graph.version = "1.0.0" pybel.examples.sialic_acid_graph.summarize(file=sio, examples=False) test_str = """--------------------- ------------------- Name Sialic Acid Graph Version 1.0.0 Authors Charles Tapley Hoyt Number of Nodes 9 Number of Namespaces 3 Number of Edges 11 Number of Annotations 2 Number of Citations 1 Number of Authors 0 Number of Components 1 Number of Warnings 0 Network Density 1.53E-01 --------------------- ------------------- Type (3) Count ---------- ------- Protein 7 Complex 1 Abundance 1 Namespace (3) Count --------------- ------- go 15 hgnc 8 chebi 2 Edge Type (7) Count --------------------------------- ------- Protein increases Protein 3 Protein directlyIncreases Protein 2 Protein directlyDecreases Protein 2 Complex increases Protein 1 Abundance partOf Complex 1 Protein partOf Complex 1 Protein hasVariant Protein 1""" self.assertEqual(test_str.strip(), sio.getvalue().strip()) def test_citation_type_error(self): """Test error handling on adding qualified edges.""" graph = BELGraph() with self.assertRaises(TypeError): graph.add_increases( protein(namespace="TEST", name="YFG1"), protein(namespace="TEST", name="YFG2"), evidence=n(), citation=5, ) class TestGetGraphProperties(unittest.TestCase): """The tests in this class check the getting and setting of node properties.""" def setUp(self): """Set up the test case with a fresh BEL graph.""" self.graph = BELGraph() self.graph.annotation_pattern["Species"] = r"\d+" self.graph.annotation_list["Confidence"] = { "Very Low", "Low", "Medium", "High", "Very High", } def test_get_qualified_edge(self): """Test adding an edge to a graph.""" test_source = protein(namespace="TEST", name="YFG") test_target = protein(namespace="TEST", name="YFG2") self.graph.add_node_from_data(test_source) self.graph.add_node_from_data(test_target) test_evidence = n() test_pmid = n() test_key = self.graph.add_increases( test_source, test_target, citation=test_pmid, evidence=test_evidence, annotations={"Species": "9606", "Confidence": "Very High"}, ) citation = self.graph.get_edge_citation(test_source, test_target, test_key) self.assertIsNotNone(citation) self.assertIsInstance(citation, dict) self.assertIn(NAMESPACE, citation) self.assertEqual(CITATION_TYPE_PUBMED, citation[NAMESPACE]) self.assertIn(IDENTIFIER, citation) self.assertEqual(test_pmid, citation[IDENTIFIER]) evidence = self.graph.get_edge_evidence(test_source, test_target, test_key) self.assertIsNotNone(evidence) self.assertIsInstance(evidence, str) self.assertEqual(test_evidence, evidence) annotations = self.graph.get_edge_annotations(test_source, test_target, test_key) self.assertIsNotNone(annotations) self.assertIsInstance(annotations, dict) self.assertIn("Species", annotations) self.assertIn(Entity(namespace="Species", identifier="9606"), annotations["Species"]) self.assertIn("Confidence", annotations) self.assertIn( Entity(namespace="Confidence", identifier="Very High"), annotations["Confidence"], ) def test_get_unqualified_edge(self): """Test adding an unqualified edge.""" test_source = protein(namespace="TEST", name="YFG") test_target = protein(namespace="TEST", name="YFG2") key = self.graph.add_part_of(test_source, test_target) citation = self.graph.get_edge_citation(test_source, test_target, key) self.assertIsNone(citation) evidence = self.graph.get_edge_evidence(test_source, test_target, key) self.assertIsNone(evidence) annotations = self.graph.get_edge_annotations(test_source, test_target, key) self.assertIsNone(annotations) def test_add_node_with_variant(self): """Test that the identifier is carried through to the child.""" graph = BELGraph() namespace, name, identifier, variant_name = n(), n(), n(), n() node = protein( namespace=namespace, name=name, identifier=identifier, variants=hgvs(variant_name), ) node.get_parent() graph.add_node_from_data(node) self.assertEqual(2, graph.number_of_nodes()) class TestExtensionIO(unittest.TestCase): def test_io(self): with tempfile.TemporaryDirectory() as directory: path = os.path.join(directory, "ampk.bel.nodelink.json") pybel.dump(pybel.examples.ampk_graph, path) self.assertTrue(os.path.exists(path)) new_graph = pybel.load(path) self.assertIsNotNone(new_graph) def test_invalid_io(self): with tempfile.TemporaryDirectory() as directory: path = os.path.join(directory, "ampk.bel.invalid.json") with self.assertRaises(InvalidExtensionError): pybel.dump(pybel.examples.ampk_graph, path) self.assertFalse(os.path.exists(path))