def test_str_has_name(self):
namespace, name = n(), n()
node = abundance(namespace=namespace, name=name)
self.assertEqual(
'a({namespace}:{name})'.format(namespace=namespace,
name=ensure_quotes(name)),
str(node))
def test_str_has_both(self):
namespace, identifier = n(), n()
node = abundance(namespace=namespace, identifier=identifier)
self.assertEqual(
'a({namespace}:{identifier})'.format(
namespace=namespace, identifier=ensure_quotes(identifier)),
str(node))
def test_as_tuple(self):
namespace, name = n(), n()
node_tuple = ABUNDANCE, namespace, name
node = abundance(namespace=namespace, name=name)
self.assertEqual(node_tuple, node.as_tuple())
self.assertEqual(hash(node_tuple), hash(node))
def test_add_simple(self):
g = BELGraph()
namespace, name = n(), n()
g.add_node_from_data(protein(namespace=namespace, name=name))
self.assertEqual(1, g.number_of_nodes())
g.add_node_from_data(protein(namespace=namespace, name=name))
self.assertEqual(1, g.number_of_nodes())
def test_citation(self):
ref = n()
model = Citation(type=CITATION_TYPE_PUBMED, reference=ref)
expected = {
CITATION_TYPE: CITATION_TYPE_PUBMED,
CITATION_REFERENCE: ref
}
self.assertEqual(expected, model.to_json())
expected[CITATION_TITLE] = model.title = n()
def test_get_node_properties(self):
test_name = n()
test_identifier = n()
node = self.graph.add_node_from_data(protein(namespace='TEST', name=test_name, identifier=test_identifier))
self.assertEqual(test_name, self.graph.get_node_name(node))
self.assertEqual(test_identifier, self.graph.get_node_identifier(node))
self.assertIsNone(self.graph.get_node_description(node))
test_description = n()
self.graph.set_node_description(node, test_description)
self.assertEqual(test_description, self.graph.get_node_description(node))
def test_network(self):
name = n()
version = n()
model = Network(name=name, version=version)
expected = {
METADATA_NAME: name,
METADATA_VERSION: version,
'created': None,
}
self.assertEqual(expected, model.to_json())
expected[METADATA_AUTHORS] = model.authors = n()
self.assertEqual(expected, model.to_json())
expected[METADATA_CONTACT] = model.contact = n()
self.assertEqual(expected, model.to_json())
expected[METADATA_DESCRIPTION] = model.description = n()
self.assertEqual(expected, model.to_json())
expected[METADATA_COPYRIGHT] = model.copyright = n()
self.assertEqual(expected, model.to_json())
expected[METADATA_DISCLAIMER] = model.disclaimer = n()
self.assertEqual(expected, model.to_json())
expected[METADATA_LICENSES] = model.licenses = n()
self.assertEqual(expected, model.to_json())
expected['id'] = None
self.assertEqual(expected, model.to_json(include_id=True))
def test_name(self):
(
name,
version,
description,
authors,
contact,
licenses,
copyrights,
disclaimer
) = [n() for _ in range(8)]
g = BELGraph()
g.name = name
g.version = version
g.description = description
g.authors = authors
g.contact = contact
g.license = licenses
g.copyright = copyrights
g.disclaimer = disclaimer
self.assertEqual(name, g.name)
self.assertEqual(version, g.version)
self.assertEqual(description, g.description)
self.assertEqual(authors, g.authors)
self.assertEqual(contact, g.contact)
self.assertEqual(licenses, g.license)
self.assertEqual(copyrights, g.copyright)
self.assertEqual(disclaimer, g.disclaimer)
self.assertEqual('{name} v{version}'.format(name=name, version=version), str(g))
def add_edge(self, subject_modifier=None, object_modifier=None, annotations=None):
self.key += 1
self.g.add_qualified_edge(
self.u,
self.v,
relation=INCREASES,
evidence=n(),
citation=n(),
subject_modifier=subject_modifier,
object_modifier=object_modifier,
annotations=annotations,
key=self.key
)
return canonicalize_edge(self.get_data(self.key))
def test_multiple_annotations(self):
a1, v1, v2 = map(lambda _: n(), range(3))
v1, v2 = sorted([v1, v2])
self.graph.add_qualified_edge(protein(namespace='HGNC', name='YFG1'),
protein(namespace='HGNC', name='YFG'),
relation=INCREASES,
citation=self.citation,
evidence=self.evidence,
annotations={a1: {v1, v2}})
self.assertEqual(2, self.graph.number_of_nodes())
self.assertEqual(1, self.graph.number_of_edges())
expected_lines = [
'#' * 80,
'SET Citation = {{"PubMed", "{}"}}'.format(self.citation),
'SET SupportingText = "{}"'.format(self.evidence),
'SET {} = {{"{}", "{}"}}'.format(a1, v1, v2),
'p(HGNC:YFG1) increases p(HGNC:YFG)',
'UNSET {}'.format(a1),
'UNSET SupportingText',
'UNSET Citation',
]
self.help_check_lines(expected_lines)
def setUp(self):
super(TestCascades, self).setUp()
self.n1 = Node(type=PROTEIN, bel='p(HGNC:A)')
self.n2 = Node(type=PROTEIN, bel='p(HGNC:B)')
self.n3 = Node(type=PROTEIN, bel='p(HGNC:C)')
self.e1 = Edge(source=self.n1, target=self.n2, relation=INCREASES, bel='p(HGNC:A) increases p(HGNC:B)')
self.e2 = Edge(source=self.n2, target=self.n3, relation=INCREASES, bel='p(HGNC:B) increases p(HGNC:C)')
self.e3 = Edge(source=self.n1, target=self.n3, relation=INCREASES, bel='p(HGNC:A) increases p(HGNC:C)')
self.g1 = Network(name=n(), version=n(), edges=[self.e1, self.e2, self.e3])
self.g2 = Network(name=n(), version=n(), edges=[self.e1])
self.manager.session.add_all([self.n1, self.n2, self.n3, self.e1, self.e2, self.e3, self.g1, self.g2])
self.manager.session.commit()
self.assertEqual(3, self.manager.count_nodes())
self.assertEqual(3, self.manager.count_edges())
self.assertEqual(2, self.manager.count_networks())
def test_get_qualified_edge(self):
test_source = self.graph.add_node_from_data(protein(namespace='TEST', name='YFG'))
test_target = self.graph.add_node_from_data(protein(namespace='TEST', name='YFG2'))
test_key = n()
test_evidence = n()
test_pmid = n()
self.graph.add_qualified_edge(
test_source,
test_target,
relation=INCREASES,
citation=test_pmid,
evidence=test_evidence,
annotations={
'Species': '9606',
'Confidence': 'Very High'
},
key=test_key
)
citation = self.graph.get_edge_citation(test_source, test_target, test_key)
self.assertIsNotNone(citation)
self.assertIsInstance(citation, dict)
self.assertIn(CITATION_TYPE, citation)
self.assertEqual(CITATION_TYPE_PUBMED, citation[CITATION_TYPE])
self.assertIn(CITATION_REFERENCE, citation)
self.assertEqual(test_pmid, citation[CITATION_REFERENCE])
evidence = self.graph.get_edge_evidence(test_source, test_target, test_key)
self.assertIsNotNone(evidence)
self.assertIsInstance(evidence, string_types)
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('9606', annotations['Species'])
self.assertTrue(annotations['Species']['9606'])
self.assertIn('Confidence', annotations)
self.assertIn('Very High', annotations['Confidence'])
self.assertTrue(annotations['Confidence']['Very High'])
def test_citation_type_error(self):
g = BELGraph()
with self.assertRaises(TypeError):
g.add_qualified_edge(
protein(namespace='TEST', name='YFG1'),
protein(namespace='TEST', name='YFG2'),
relation=INCREASES,
evidence=n(),
citation=5
)
def test_drop_namespace(self):
keyword, url = n(), n()
namespace = Namespace(keyword=keyword, url=url)
self.manager.session.add(namespace)
n_entries = 5
for _ in range(n_entries):
entry = NamespaceEntry(name=n(), namespace=namespace)
self.manager.session.add(entry)
self.manager.session.commit()
self.assertEqual(1, self.manager.count_namespaces(), msg='Should have one namespace')
self.assertEqual(n_entries, self.manager.count_namespace_entries(),
msg='Should have {} entries'.format(n_entries))
self.manager.drop_namespace_by_url(url)
self.assertEqual(0, self.manager.count_namespaces(), msg='Should have no namespaces')
self.assertEqual(0, self.manager.count_namespace_entries(), msg='Entries should have been dropped')
def test_single_annotation(self):
"""Tests a scenario with a qualified edge, but no annotaitons"""
a1, v1 = map(lambda _: n(), range(2))
self.graph.add_qualified_edge(protein(namespace='HGNC', name='YFG1'),
protein(namespace='HGNC', name='YFG'),
relation=INCREASES,
citation=self.citation,
evidence=self.evidence,
annotations={a1: {v1}})
self.assertEqual(2, self.graph.number_of_nodes())
self.assertEqual(1, self.graph.number_of_edges())
expected_lines = [
'#' * 80,
'SET Citation = {{"PubMed", "{}"}}'.format(self.citation),
'SET SupportingText = "{}"'.format(self.evidence),
'SET {} = "{}"'.format(a1,
v1), 'p(HGNC:YFG1) increases p(HGNC:YFG)',
'UNSET {}'.format(a1), 'UNSET SupportingText', 'UNSET Citation'
]
self.help_check_lines(expected_lines)
def setUp(self):
self.citation = n()
self.evidence = n()
self.url = n()
self.graph = BELGraph()
self.graph.namespace_url['HGNC'] = self.url
def test_get_node_identifier(self):
test_name = n()
node = self.graph.add_node_from_data(protein(namespace='TEST', name=test_name))
self.assertIsNotNone(self.graph.get_node_name(node))
self.assertIsNone(self.graph.get_node_identifier(node))