def test_validator_good():
"""
A fake test to establish a success condition for validation.
"""
G = NxGraph()
G.add_node(
"UniProtKB:P123456", id="UniProtKB:P123456", name="fake", category=["Protein"]
)
G.add_node(
"UBERON:0000001", id="UBERON:0000001", name="fake", category=["NamedThing"]
)
G.add_node(
"UBERON:0000002", id="UBERON:0000002", name="fake", category=["NamedThing"]
)
G.add_edge(
"UBERON:0000001",
"UBERON:0000002",
id="UBERON:0000001-part_of-UBERON:0000002",
relation="RO:1",
predicate="part_of",
subject="UBERON:0000001",
object="UBERON:0000002",
category=["biolink:Association"],
)
validator = Validator(verbose=True)
validator.validate(G)
print(validator.get_errors())
assert len(validator.get_errors()) == 0
def test_validator_good():
"""
A fake test to establish a success condition for validation.
"""
G = NxGraph()
G.add_node('UniProtKB:P123456',
id='UniProtKB:P123456',
name='fake',
category=['Protein'])
G.add_node('UBERON:0000001',
id='UBERON:0000001',
name='fake',
category=['NamedThing'])
G.add_node('UBERON:0000002',
id='UBERON:0000002',
name='fake',
category=['NamedThing'])
G.add_edge(
'UBERON:0000001',
'UBERON:0000002',
id='UBERON:0000001-part_of-UBERON:0000002',
relation='RO:1',
predicate='part_of',
subject='UBERON:0000001',
object='UBERON:0000002',
category=['biolink:Association'],
)
validator = Validator(verbose=True)
e = validator.validate(G)
print(validator.report(e))
assert len(e) == 0
def test_add_edge():
"""
Test adding an edge to an NxGraph.
"""
g = NxGraph()
g.add_node('A')
g.add_node('B')
g.add_edge('A', 'B', predicate='biolink:related_to', provided_by='test')
assert g.has_edge('A', 'B')
g.add_edge('B', 'C', edge_key='B-biolink:related_to-C', provided_by='test')
assert g.has_edge('B', 'C')
def test_add_edge():
"""
Test adding an edge to an NxGraph.
"""
g = NxGraph()
g.add_node("A")
g.add_node("B")
g.add_edge("A", "B", predicate="biolink:related_to", provided_by="test")
assert g.has_edge("A", "B")
g.add_edge("B", "C", edge_key="B-biolink:related_to-C", provided_by="test")
assert g.has_edge("B", "C")
def test_relabel_nodes():
"""
Test relabelling of nodes in an NxGraph.
"""
g = get_graphs()[1]
m = {'A': 'A:1', 'E': 'E:1'}
NxGraph.relabel_nodes(g, m)
assert not g.has_node('A')
assert g.has_node('A:1')
assert not g.has_node('E')
assert g.has_node('E:1')
assert len(g.in_edges('A:1')) == 3
def test_relabel_nodes():
"""
Test relabelling of nodes in an NxGraph.
"""
g = get_graphs()[1]
m = {"A": "A:1", "E": "E:1"}
NxGraph.relabel_nodes(g, m)
assert not g.has_node("A")
assert g.has_node("A:1")
assert not g.has_node("E")
assert g.has_node("E:1")
assert len(g.in_edges("A:1")) == 3
def test_validator_explicit_biolink_version():
"""
A fake test to establish a success condition for validation.
"""
G = NxGraph()
G.add_node(
"CHEMBL.COMPOUND:1222250",
id="CHEMBL.COMPOUND:1222250",
name="Dextrose",
category=["Carbohydrate"],
)
G.add_node(
"UBERON:0000001", id="UBERON:0000001", name="fake", category=["NamedThing"]
)
G.add_edge(
"CHEMBL.COMPOUND:1222250",
"UBERON:0000001",
id="CHEMBL.COMPOUND:1222250-part_of-UBERON:0000001",
relation="RO:1",
predicate="part_of",
subject="CHEMBL.COMPOUND:1222250",
object="UBERON:0000001",
category=["biolink:Association"],
)
Validator.set_biolink_model(version="1.8.2")
validator = Validator(verbose=True)
validator.validate(G)
print(validator.get_errors())
assert len(validator.get_errors()) == 0
def test_set_edge_attributes():
"""
Test setting edge attributes in bulk.
"""
g = NxGraph()
g.add_node("X:1", alias="A:1")
g.add_node("X:2", alias="B:2")
g.add_edge("X:2", 'X:1', edge_key='edge1', source="Source 1")
d = {('X:2', 'X:1', 'edge1'): {'source': 'Modified Source 1'}}
NxGraph.set_edge_attributes(g, d)
e = list(g.edges(keys=True, data=True))[0]
assert e[3]['source'] == 'Modified Source 1'
def test_set_edge_attributes():
"""
Test setting edge attributes in bulk.
"""
g = NxGraph()
g.add_node("X:1", alias="A:1")
g.add_node("X:2", alias="B:2")
g.add_edge("X:2", "X:1", edge_key="edge1", source="Source 1")
d = {("X:2", "X:1", "edge1"): {"source": "Modified Source 1"}}
NxGraph.set_edge_attributes(g, d)
e = list(g.edges(keys=True, data=True))[0]
assert e[3]["source"] == "Modified Source 1"
def test_clique_merge():
"""
Test for clique merge.
"""
input_args = {
'filename': [
os.path.join(RESOURCE_DIR, 'cm_nodes.csv'),
os.path.join(RESOURCE_DIR, 'cm_edges.csv'),
],
'format':
'csv',
}
t = Transformer()
t.transform(input_args)
updated_graph, clique_graph = clique_merge(
target_graph=t.store.graph,
prefix_prioritization_map=prefix_prioritization_map)
leaders = NxGraph.get_node_attributes(updated_graph, 'clique_leader')
leader_list = list(leaders.keys())
leader_list.sort()
assert len(leader_list) == 2
n1 = updated_graph.nodes()[leader_list[0]]
assert n1['election_strategy'] == 'PREFIX_PRIORITIZATION'
assert 'NCBIGene:100302240' in n1['same_as']
assert 'ENSEMBL:ENSG00000284458' in n1['same_as']
n2 = updated_graph.nodes()[leader_list[1]]
assert n2['election_strategy'] == 'PREFIX_PRIORITIZATION'
assert 'NCBIGene:8202' in n2['same_as']
assert 'OMIM:601937' in n2['same_as']
assert 'ENSEMBL:ENSG00000124151' not in n2['same_as']
def test_clique_merge():
"""
Test for clique merge.
"""
input_args = {
"filename": [
os.path.join(RESOURCE_DIR, "cm_nodes.csv"),
os.path.join(RESOURCE_DIR, "cm_edges.csv"),
],
"format": "csv",
}
t = Transformer()
t.transform(input_args)
updated_graph, clique_graph = clique_merge(
target_graph=t.store.graph, prefix_prioritization_map=prefix_prioritization_map
)
leaders = NxGraph.get_node_attributes(updated_graph, "clique_leader")
leader_list = list(leaders.keys())
leader_list.sort()
assert len(leader_list) == 2
n1 = updated_graph.nodes()[leader_list[0]]
assert n1["election_strategy"] == "PREFIX_PRIORITIZATION"
assert "NCBIGene:100302240" in n1["same_as"]
assert "ENSEMBL:ENSG00000284458" in n1["same_as"]
n2 = updated_graph.nodes()[leader_list[1]]
assert n2["election_strategy"] == "PREFIX_PRIORITIZATION"
assert "NCBIGene:8202" in n2["same_as"]
assert "OMIM:601937" in n2["same_as"]
assert "ENSEMBL:ENSG00000124151" not in n2["same_as"]
def test_get_edge_attributes():
"""
Test getting edge attributes in bulk.
"""
g = get_graphs()[1]
d = NxGraph.get_edge_attributes(g, 'relation')
assert ('B', 'A', 'B-biolink:related_to-A') in d
assert d[('B', 'A', 'B-biolink:related_to-A')] == 'biolink:related_to'
def test_get_node_attributes():
"""
Test getting node attributes in bulk.
"""
g = get_graphs()[1]
d = NxGraph.get_node_attributes(g, 'name')
assert 'A' in d and d['A'] == 'Node A'
assert 'E' in d and d['E'] == 'Node E'
def test_get_node_attributes():
"""
Test getting node attributes in bulk.
"""
g = get_graphs()[1]
d = NxGraph.get_node_attributes(g, "name")
assert "A" in d and d["A"] == "Node A"
assert "E" in d and d["E"] == "Node E"
def test_get_edge_attributes():
"""
Test getting edge attributes in bulk.
"""
g = get_graphs()[1]
d = NxGraph.get_edge_attributes(g, "relation")
assert ("B", "A", "B-biolink:related_to-A") in d
assert d[("B", "A", "B-biolink:related_to-A")] == "biolink:related_to"
def test_validator_bad():
"""
A fake test to establish a fail condition for validation.
"""
G = NxGraph()
G.add_node("x", foo=3)
G.add_node("ZZZ:3", **{"nosuch": 1})
G.add_edge("x", "y", **{"baz": 6})
validator = Validator(verbose=True)
validator.validate(G)
assert len(validator.get_errors()) > 0
def test_validator_bad():
"""
A fake test to establish a fail condition for validation.
"""
G = NxGraph()
G.add_node('x', foo=3)
G.add_node('ZZZ:3', **{'nosuch': 1})
G.add_edge('x', 'y', **{'baz': 6})
validator = Validator(verbose=True)
e = validator.validate(G)
assert len(e) > 0
def test_add_node():
"""
Test adding a node to an NxGraph.
"""
g = NxGraph()
g.add_node("A")
g.add_node("A", name="Node A", description="Node A")
assert g.has_node("A")
def test_add_node():
"""
Test adding a node to an NxGraph.
"""
g = NxGraph()
g.add_node('A')
g.add_node('A', name='Node A', description='Node A')
assert g.has_node('A')
def test_merge_graphs():
"""
Test for merging 3 graphs into one,
while not preserving conflicting node and edge properties.
"""
graphs = get_graphs()
merged_graph = merge_graphs(NxGraph(), graphs)
assert merged_graph.number_of_nodes() == 6
assert merged_graph.number_of_edges() == 6
assert merged_graph.name not in [x.name for x in graphs]
def test_add_node_attribute():
"""
Test adding a node attribute to an NxGraph.
"""
g = NxGraph()
g.add_node('A')
g.add_node_attribute('A', 'provided_by', 'test')
n = g.get_node('A')
assert 'provided_by' in n and n['provided_by'] == 'test'
def test_update_edge_attribute():
"""
Test updating an edge attribute for an edge in an NxGraph.
"""
g = NxGraph()
g.add_edge('A', 'B', 'edge_ab')
g.update_edge_attribute('A', 'B', 'edge_ab', 'source', 'test')
e = g.get_edge('A', 'B', 'edge_ab')
assert 'source' in e and e['source'] == 'test'
def test_update_edge_attribute():
"""
Test updating an edge attribute for an edge in an NxGraph.
"""
g = NxGraph()
g.add_edge("A", "B", "edge_ab")
g.update_edge_attribute("A", "B", "edge_ab", "source", "test")
e = g.get_edge("A", "B", "edge_ab")
assert "source" in e and e["source"] == "test"
def test_add_node_attribute():
"""
Test adding a node attribute to an NxGraph.
"""
g = NxGraph()
g.add_node("A")
g.add_node_attribute("A", "provided_by", "test")
n = g.get_node("A")
assert "provided_by" in n and n["provided_by"] == "test"
def test_update_node_attribute():
"""
Test updating a node attribute for a node in an NxGraph.
"""
g = NxGraph()
g.add_node('A', name='A', description='Node A')
g.update_node_attribute('A', 'description', 'Modified description')
n = g.get_node('A')
assert 'name' in n and n['name'] == 'A'
assert 'description' in n and n['description'] == 'Modified description'
def test_update_node_attribute():
"""
Test updating a node attribute for a node in an NxGraph.
"""
g = NxGraph()
g.add_node("A", name="A", description="Node A")
g.update_node_attribute("A", "description", "Modified description")
n = g.get_node("A")
assert "name" in n and n["name"] == "A"
assert "description" in n and n["description"] == "Modified description"
def test_add_edge_attribute():
"""
Test adding an edge attribute to an NxGraph.
"""
g = NxGraph()
g.add_edge('A', 'B')
g.add_edge_attribute('A', 'B', 'edge_ab', 'predicate',
'biolink:related_to')
def test_add_edge_attribute():
"""
Test adding an edge attribute to an NxGraph.
"""
g = NxGraph()
g.add_edge("A", "B")
g.add_edge_attribute("A", "B", "edge_ab", "predicate",
"biolink:related_to")
def test_set_node_attributes():
"""
Test setting node attributes in bulk.
"""
g = NxGraph()
g.add_node("X:1", alias="A:1")
g.add_node("X:2", alias="B:2")
d = {'X:1': {'alias': 'ABC:1'}, 'X:2': {'alias': 'DEF:2'}}
NxGraph.set_node_attributes(g, d)
def test_set_node_attributes():
"""
Test setting node attributes in bulk.
"""
g = NxGraph()
g.add_node("X:1", alias="A:1")
g.add_node("X:2", alias="B:2")
d = {"X:1": {"alias": "ABC:1"}, "X:2": {"alias": "DEF:2"}}
NxGraph.set_node_attributes(g, d)