def test_failing_query(rosetta):
"""IN the current set of edges, there is no gene->anatomy service. If we add one this teset will fail"""
disease_name = 'test_name'
did = 'DOID:123'
disease_identifiers = [did]
name_node = KNode('{}:{}'.format(node_types.DISEASE_NAME, disease_name),
node_types.DISEASE_NAME)
qd = UserQuery(disease_identifiers, node_types.DISEASE, name_node)
qd.add_transition(node_types.GENE)
qd.add_transition(node_types.ANATOMY)
assert not qd.compile_query(rosetta)
def generate_query(pathway,
start_identifiers,
start_name=None,
end_identifiers=None,
end_name=None):
start, middle, end = pathway[0], pathway[1:-1], pathway[-1]
query = UserQuery(start_identifiers, start.nodetype, start_name)
for transition in middle:
print(transition)
query.add_transition(transition.nodetype, transition.min_path_length,
transition.max_path_length)
query.add_transition(end.nodetype,
end.min_path_length,
end.max_path_length,
end_values=end_identifiers,
end_name=end_name)
return query
def test_query_set_different_valid_ids(rosetta):
disease_name = 'test_name'
disease_identifiers = ['DOID:123', 'EFO:456']
name_node = KNode('{}:{}'.format(node_types.DISEASE_NAME, disease_name),
node_types.DISEASE_NAME)
qd = UserQuery(disease_identifiers, node_types.DISEASE, name_node)
qd.add_transition(node_types.GENE)
qd.add_transition(node_types.GENETIC_CONDITION)
assert qd.compile_query(rosetta)
cyphers = qd.generate_cypher()
assert len(cyphers) == 2
start_nodes = qd.get_start_node()
assert len(start_nodes) == 2
assert start_nodes[0][0] == disease_identifiers[0]
assert start_nodes[1][0] == disease_identifiers[1]
lookups = qd.get_lookups()
assert len(lookups) == 2
assert lookups[0].identifier == '{}:{}'.format(node_types.DISEASE_NAME,
disease_name)
assert lookups[1].identifier == '{}:{}'.format(node_types.DISEASE_NAME,
disease_name)
reverse = qd.get_reversed()
assert len(reverse) == 2
assert not reverse[0]
assert not reverse[1]
def build_question2(drug_name, disease_name, drug_ids, disease_ids):
drug_name_node = KNode('{}.{}'.format(node_types.DRUG_NAME, drug_name),
node_types.DRUG_NAME)
disease_name_node = KNode(
'{}.{}'.format(node_types.DISEASE_NAME, disease_name),
node_types.DISEASE_NAME)
query = UserQuery(drug_ids, node_types.DRUG, drug_name_node)
query.add_transition(node_types.GENE)
query.add_transition(node_types.PROCESS)
query.add_transition(node_types.CELL)
query.add_transition(node_types.ANATOMY)
query.add_transition(node_types.PHENOTYPE)
query.add_transition(node_types.DISEASE, end_values=disease_ids)
return query
def test_query_two(rosetta):
drug_name = 'test_drug'
drug_name_node = KNode('{}.{}'.format(node_types.DRUG_NAME, drug_name),
node_types.DRUG_NAME)
drug_identifiers = ['CTD:Adapalene', 'PHAROS.DRUG:95769', 'PUBCHEM:60164']
disease_name = 'test_disease'
disease_name_node = KNode(
'{}.{}'.format(node_types.DISEASE_NAME, disease_name),
node_types.DISEASE_NAME)
disease_identifiers = ['DOID:123']
query = UserQuery(drug_identifiers, node_types.DRUG, drug_name_node)
query.add_transition(node_types.GENE)
query.add_transition(node_types.PROCESS)
query.add_transition(node_types.CELL)
query.add_transition(node_types.ANATOMY)
query.add_transition(node_types.PHENOTYPE)
query.add_transition(node_types.DISEASE, end_values=disease_identifiers)
query.add_end_lookup_node(disease_name_node)
assert query.compile_query(rosetta)
def test_generate_set(rosetta):
drug_name = 'test_drug'
drug_name_node = KNode('{}.{}'.format(node_types.DRUG_NAME, drug_name),
node_types.DRUG_NAME)
drug_identifiers = ['CTD:123']
disease_name = 'test_disease'
disease_name_node = KNode(
'{}.{}'.format(node_types.DISEASE_NAME, disease_name),
node_types.DISEASE_NAME)
disease_identifiers = ['DOID:123']
query = UserQuery(drug_identifiers, node_types.DRUG, drug_name_node)
query.add_transition(node_types.GENE)
query.add_transition(node_types.PROCESS)
query.add_transition(node_types.CELL)
query.add_transition(node_types.ANATOMY)
query.add_transition(node_types.PHENOTYPE)
query.add_transition(node_types.DISEASE, end_values=disease_identifiers)
query.add_end_lookup_node(disease_name_node)
d = query.definition
l, r = d.generate_paired_query(4)
assert len(l.transitions) == 4
assert len(r.transitions) == 2
lq = OneSidedLinearUserQuerySet(l)
rq = OneSidedLinearUserQuerySet(r)
#print(lq.generate_cypher()[0])
#print()
#print(rq.generate_cypher()[0])
print(rq.generate_cypher()[0])
assert lq.compile_query(rosetta)
assert rq.compile_query(rosetta)
def test_two_sided_query_compose(rosetta):
"""Create a 2sided query, composing it by hand.Mimics what should happen
automatically in a 2 sided user query"""
drug_name = 'test_drug'
drug_name_node = KNode('{}.{}'.format(node_types.DRUG_NAME, drug_name),
node_types.DRUG_NAME)
drug_identifiers = ['CTD:123']
disease_name = 'test_disease'
disease_name_node = KNode(
'{}.{}'.format(node_types.DISEASE_NAME, disease_name),
node_types.DISEASE_NAME)
disease_identifiers = ['DOID:123']
#This will create a OneSidedQuerySet
queryl = UserQuery(drug_identifiers, node_types.DRUG, drug_name_node)
queryl.add_transition(node_types.GENE)
queryl.add_transition(node_types.PROCESS)
queryl.add_transition(node_types.CELL)
queryl.add_transition(node_types.ANATOMY)
#this is another
queryr = UserQuery(disease_identifiers, node_types.DISEASE,
disease_name_node)
queryr.add_transition(node_types.PHENOTYPE)
queryr.add_transition(node_types.ANATOMY)
#The individual queries check out
assert queryl.compile_query(rosetta)
assert queryr.compile_query(rosetta)
#The two sided checks out
twolq = TwoSidedLinearUserQuery(queryl.query, queryr.query)
assert twolq.compile_query(rosetta)
twolqs = TwoSidedLinearUserQuerySet()
twolqs.add_query(twolq, rosetta)
#the two sided set checks out
assert twolqs.compile_query(rosetta)
def test_simple_query(rosetta):
disease_name = 'test_name'
did = 'DOID:123'
disease_identifiers = [did]
name_node = KNode('{}:{}'.format(node_types.DISEASE_NAME, disease_name),
node_types.DISEASE_NAME)
qd = UserQuery(disease_identifiers, node_types.DISEASE, name_node)
qd.add_transition(node_types.GENE)
qd.add_transition(node_types.GENETIC_CONDITION)
assert qd.compile_query(rosetta)
cyphers = qd.generate_cypher()
assert len(cyphers) == 1
start_nodes = qd.get_start_node()
assert len(start_nodes) == 1
assert start_nodes[0][0] == did
lookups = qd.get_lookups()
assert len(lookups) == 1
assert lookups[0].identifier == '{}:{}'.format(node_types.DISEASE_NAME,
disease_name)
reverse = qd.get_reversed()
assert len(reverse) == 1
assert not reverse[0]