class TestIntAct(unittest.TestCase):
def setUp(self) -> None:
self.intact = IntAct()
def test_intact_instance(self):
self.assertEqual(self.intact.node_header,
['id', 'name', 'category', 'ncbi_taxid', 'provided_by'])
self.assertEqual(self.intact.edge_header,
['subject', 'edge_label', 'object', 'relation', 'provided_by', 'type',
'publication', 'num_participants', 'association_type',
'detection_method', 'subj_exp_role', 'obj_exp_role'])
def test_struct_parse_xml_to_nodes_edges(self):
parsed = self.intact.parse_xml_to_nodes_edges('tests/resources/intact_test.xml')
self.assertTrue(isinstance(parsed, dict))
self.assertTrue(isinstance(parsed['nodes'], list))
self.assertTrue(isinstance(parsed['edges'], list))
@parameterized.expand([
('tests/resources/intact_test.xml',
5, 8, # node and edge count, respectively
# nodes and edges given here are checked against the first values in
# parsed['nodes'] and parsed['edges']. Extra items in parsed['nodes'] and
# parsed['edges'] are ignored
{'nodes': [['UniProtKB:P20290', 'btf3_human', 'biolink:Protein', '9606', 'intact'],
['UniProtKB:P0C6X7-PRO_0000037317', 'nsp10_cvhsa', 'biolink:RNA',
'694009', 'intact']],
'edges': [['UniProtKB:P20290', 'biolink:interacts_with',
'UniProtKB:P0C6X7-PRO_0000037317', 'RO:0002437', 'intact', 'biolink:Association',
'PMID:16157265', '2', 'physical association', '2 hybrid', 'prey',
'bait']]
}),
('tests/resources/intact_3_participants.xml', # test interactions with 3 participants
3, 3, # interaction with 3 participants yields 3 edges (1<->2, 2<->3, 1<->3)
{'nodes': [],
'edges': [['UniProtKB:Q3T133',
'biolink:interacts_with',
'UniProtKB:P41811',
'RO:0002437',
'intact',
'biolink:Association',
'PMID:23481256',
'3',
'physical association',
'itc', 'neutral component', 'bait']]
})
])
def test_nodes_parse_xml_to_nodes_edges(self, xml_file, node_count, edge_count,
expect_nodes_edges):
parsed = self.intact.parse_xml_to_nodes_edges(xml_file)
self.assertEqual(node_count, len(parsed['nodes']),
"Didn't get the expected number of nodes")
self.assertEqual(edge_count, len(parsed['edges']),
"Didn't get the expected number of edges")
self.assertEqual(expect_nodes_edges['nodes'],
parsed['nodes'][:len(expect_nodes_edges['nodes'])])
self.assertEqual(expect_nodes_edges['edges'],
parsed['edges'][:len(expect_nodes_edges['edges'])])
@parameterized.expand([
('tests/resources/intact_test.xml', '3674925', {'publication': 'PMID:16157265', 'detection_method': '2 hybrid'}),
('tests/resources/intact_test.xml', '3674926', {'publication': 'PMID:16157265', 'detection_method': '2 hybrid'})
])
def test_parse_experiment_info(self, xml_file, exp_id, correct_data):
xmldoc = minidom.parse(xml_file)
parsed = self.intact.parse_experiment_info(xmldoc)
self.assertTrue(isinstance(parsed, dict))
self.assertTrue(exp_id in parsed)
for key, _ in correct_data.items():
self.assertTrue(key in parsed[exp_id])
self.assertEqual(parsed[exp_id][key], correct_data[key])
def test_fix_for_chebi_id(self):
chebi_test_xml = 'tests/resources/31315999_weird_chebi_id.xml' # weird CHEBI id
parsed = self.intact.parse_xml_to_nodes_edges(chebi_test_xml)
self.assertEqual(parsed['nodes'][0][0], 'CHEBI:28304')
self.assertEqual(parsed['edges'][0][0], 'CHEBI:28304')
def setUp(self) -> None:
self.intact = IntAct()