def test_where_eq(O):
errors = []
setupGraph(O)
count = 0
for i in O.query().V().where(aql.eq("_gid", "vertex3")):
count += 1
if i['gid'] != "vertex3":
errors.append("Wrong vertex returned %s" % (i))
if count != 1:
errors.append(
"Fail: O.query().V().where(aql.eq(\"_gid\", \"vertex3\")) %s != %s"
% (count, 1))
count = 0
for i in O.query().V().where(aql.eq("_label", "person")):
count += 1
if i['label'] != "person":
errors.append("Wrong vertex label %s" % (i['label']))
if count != 4:
errors.append(
"Fail: O.query().V().where(aql.eq(\"_label\", \"person\")) %s != %s"
% (count, 4))
count = 0
for i in O.query().V().where(aql.eq("occupation", "jedi")):
count += 1
if i['gid'] not in ["vertex2", "vertex5"]:
errors.append("Wrong vertex returned %s" % (i))
if count != 2:
errors.append(
"Fail: O.query().V().where(aql.eq(\"occupation\", \"jedi\")) %s != %s"
% (count, 2))
return errors
def run(args):
conn = aql.Connection(args.arachne)
O = conn.graph(args.graph)
ensembl_id = conversions.hugo_ensembl(args.gene)
gid = "gene:" + ensembl_id
sample_mutation_status = {}
query = O.query().V(gid).\
in_("variantIn").mark("variant").\
out("variantCall").where(aql.eq("method", "MUTECT")).mark("callset").\
out("callSetOf").where(aql.eq("sample_type", "Primary Tumor")).mark("sample").\
in_("fileFor").mark("cel")
if args.project is not None:
query = query.where(aql.eq("project", args.project))
query = query.mark("cel").\
select(["variant", "sample", "callset", "cel"])
for res in query:
if res.variant.data.alternateBases != res.variant.data.referenceBases:
if res.cel.data.individual_barcode not in sample_mutation_status:
sample_mutation_status[res.cel.data.individual_barcode] = 2
query = O.query().V().where(aql.eq("_label", "CELFile"))
if args.project is not None:
query = query.where(aql.eq("project", args.project))
for res in query:
if res.data.individual_barcode not in sample_mutation_status:
sample_mutation_status[res.data.individual_barcode] = 1
for k in sample_mutation_status:
print(k, k, sample_mutation_status[k], sep="\t")
return
def test_render(O):
errors = []
O.addVertex("1", "Person", {"name": "marko", "age": "29"})
O.addVertex("2", "Person", {"name": "vadas", "age": "27"})
O.addVertex("3", "Software", {"name": "lop", "lang": "java"})
O.addVertex("4", "Person", {"name": "josh", "age": "32"})
O.addVertex("5", "Software", {"name": "ripple", "lang": "java"})
O.addVertex("6", "Person", {"name": "peter", "age": "35"})
O.addEdge("1", "3", "created", {"weight": 0.4})
O.addEdge("1", "2", "knows", {"weight": 0.5})
O.addEdge("1", "4", "knows", {"weight": 1.0})
O.addEdge("4", "3", "created", {"weight": 0.4})
O.addEdge("6", "3", "created", {"weight": 0.2})
O.addEdge("4", "5", "created", {"weight": 1.0})
query = O.query().V().where(aql.eq("_label", "Person")).render({
"Name": "name",
"Age": "age"
})
for row in query:
if 'Age' not in row or "Name" not in row:
errors.append("Missing fields")
query = O.query().V().where(aql.eq("_label", "Person")).render({
"Name":
"name",
"NonExistent":
"non-existent"
})
for row in query:
if 'NonExistent' not in row or "Name" not in row:
errors.append("Missing fields")
query = O.query().V().where(aql.eq("_label",
"Person")).render(["name", "age"])
for row in query:
if not isinstance(row, list):
errors.append("unexpected output format")
if len(row) != 2:
errors.append("Missing fields")
query = O.query().V().where(aql.eq("_label", "Person")).render(
["name", "non-existent"])
for row in query:
if not isinstance(row, list):
errors.append("unexpected output format")
if len(row) != 2:
errors.append("Missing fields")
return errors
def test_where_not(O):
errors = []
setupGraph(O)
count = 0
for i in O.query().V().where(aql.not_(aql.eq("_label", "person"))):
count += 1
if i['gid'] not in ["vertex3", "vertex4"]:
errors.append("Wrong vertex returned %s" % (i))
if count != 2:
errors.append(
"Fail: O.query().V().where(aql.not_(aql.eq(\"_label\", \"person\"))) %s != %s"
% (count, 2))
count = 0
for i in O.query().V().where(aql.not_(aql.neq("_label", "person"))):
count += 1
if i['gid'] not in ["vertex1", "vertex2", "vertex5", "vertex6"]:
errors.append("Wrong vertex returned %s" % (i))
if count != 4:
errors.append(
"Fail: O.query().V().where(aql.not_(aql.neq(\"_label\", \"person\"))) %s != %s"
% (count, 4))
return errors
def test_distinct(O):
errors = []
O.addVertex("1", "Person", {"name": "marko", "age": 29})
O.addVertex("2", "Person", {"name": "vadas", "age": 25})
O.addVertex("4", "Person", {"name": "josh", "age": 32})
O.addVertex("6", "Person", {"name": "peter", "age": 35})
O.addVertex("7", "Person", {"name": "marko", "age": 41})
O.addVertex("9", "Person", {"name": "alex", "age": 30})
O.addVertex("10", "Person", {"name": "alex", "age": 45})
O.addVertex("11", "Person", {"name": "steve", "age": 26})
O.addVertex("12", "Person", {"name": "alice", "age": 22})
O.addVertex("13", "Person", {"name": "wanda", "age": 36})
O.addVertex("5", "Software", {"name": "ripple", "lang": "java"})
O.addVertex("3", "Software", {"name": "lop", "lang": "java"})
O.addVertex("8", "Software", {"name": "funnel", "lang": "go"})
O.addVertex("14", "Software", {"name": "arachne", "lang": None})
O.addEdge("1", "5", "developer", gid="edge1")
O.addEdge("7", "5", "developer", gid="edge2")
O.addEdge("3", "8", "dependency", gid="edge3")
count = 0
for i in O.query().V().distinct():
count += 1
if count != 14:
errors.append("Distinct %s != %s" % (count, 14))
count = 0
for i in O.query().V().distinct("_gid"):
count += 1
if count != 14:
errors.append("Distinct %s != %s" % (count, 14))
count = 0
for i in O.query().V().distinct("name"):
count += 1
if count != 12:
errors.append("Distinct %s != %s" % (count, 12))
count = 0
for i in O.query().V().distinct("lang"):
count += 1
if count != 3:
errors.append("Distinct %s != %s" % (count, 3))
count = 0
for i in O.query().V().distinct("non-existent-field"):
count += 1
if count != 0:
errors.append("Distinct %s != %s" % (count, 0))
count = 0
for i in O.query().V().where(aql.eq(
"_label", "Person")).mark("person").out().distinct("$person.name"):
count += 1
if count != 1:
errors.append("Distinct %s != %s" % (count, 1))
return errors
def test_where_or(O):
errors = []
setupGraph(O)
count = 0
for i in O.query().V().where(
aql.or_(aql.eq("occupation", "sith"), aql.eq("occupation",
"jedi"))):
count += 1
if i['gid'] not in ["vertex2", "vertex5", "vertex6"]:
errors.append("Wrong vertex returned %s" % (i))
if count != 3:
errors.append(
"Fail: O.query().V().where(aql.or_(aql.eq(\"occupation\", \"sith\"), aql.eq(\"occupation\", \"jedi\"))) %s != %s"
% (count, 3))
return errors
def test_where_and(O):
errors = []
setupGraph(O)
count = 0
for i in O.query().V().where(
aql.and_(aql.eq("_label", "person"), aql.eq("occupation",
"jedi"))):
count += 1
if i['gid'] not in ["vertex2", "vertex5"]:
errors.append("Wrong vertex returned %s" % (i))
if count != 2:
errors.append(
"Fail: O.query().V().where(aql.and_(aql.eq(\"_label\", \"person\"), aql.eq(\"occupation\", \"jedi\"))) %s != %s"
% (count, 2))
return errors
def test_match_count(O):
errors = []
O.addVertex("1", "Person", {"name": "marko", "age": "29"})
O.addVertex("2", "Person", {"name": "vadas", "age": "27"})
O.addVertex("3", "Software", {"name": "lop", "lang": "java"})
O.addVertex("4", "Person", {"name": "josh", "age": "32"})
O.addVertex("5", "Software", {"name": "ripple", "lang": "java"})
O.addVertex("6", "Person", {"name": "peter", "age": "35"})
O.addEdge("1", "3", "created", {"weight": 0.4})
O.addEdge("1", "2", "knows", {"weight": 0.5})
O.addEdge("1", "4", "knows", {"weight": 1.0})
O.addEdge("4", "3", "created", {"weight": 0.4})
O.addEdge("6", "3", "created", {"weight": 0.2})
O.addEdge("4", "5", "created", {"weight": 1.0})
query = O.query().V().match([
O.query().mark('a').out('created').mark('b'),
O.query().mark('b').where(aql.eq('$.name', 'lop')),
O.query().mark('b').in_('created').mark('c'),
O.query().mark('c').where(aql.eq('$.age', "29"))
]).select(['a', 'c'])
count = 0
for row in query.execute(stream=True):
count += 1
if len(row) != 2:
errors.append("Incorrect number of marks returned in row")
continue
if row["c"]['data']['name'] != "marko":
errors.append("Incorrect return")
if count != 3:
errors.append("Incorrect return count: %d != %d" % (count, 3))
return errors
def test_where_complex(O):
errors = []
setupGraph(O)
count = 0
for i in O.query().V().where(
aql.and_(
aql.eq("_label", "person"),
aql.not_(
aql.or_(aql.eq("occupation", "jedi"),
aql.eq("occupation", "sith"))))):
count += 1
if i['gid'] != "vertex1":
errors.append("Wrong vertex returned %s" % (i))
if count != 1:
errors.append(
"Fail: O.query().V().where(aql.and_(aql.eq(\"_label\", \"person\"), aql.not_(aql.or_(aql.eq(\"occupation\", \"jedi\"), aql.eq(\"occupation\", \"sith\"))))) %s != %s"
% (count, 1))
count = 0
for i in O.query().V().where(
aql.not_(
aql.or_(
aql.eq("_label", "robot"),
aql.eq("occupation", "jedi"),
))):
count += 1
if i['gid'] not in ["vertex1", "vertex6"]:
errors.append("Wrong vertex returned %s" % (i))
if count != 2:
errors.append(
"Fail: O.query().V().where(aql.not_(aql.and_(aql.eq(\"_label\", \"robot\"), aql.eq(\"occupation\", \"jedi\")))) %s != %s"
% (count, 2))
count = 0
for i in O.query().V().where(
aql.not_(
aql.or_(
aql.eq("_label", "robot"),
aql.or_(aql.eq("occupation", "jedi"),
aql.contains("starships", "millennium falcon"))))):
count += 1
if i['gid'] != "vertex6":
errors.append("Wrong vertex returned %s" % (i))
if count != 1:
errors.append(
"Fail: O.query().V().where(aql.not_(aql.or_(aql.eq(\"_label\", \"robot\"), aql.or_(aql.eq(\"occupation\", \"jedi\"), aql.contains(\"starships\", \"millennium falcon\"))))) %s != %s"
% (count, 1))
count = 0
for i in O.query().V().where(
aql.not_(
aql.and_(
aql.eq("_label", "robot"),
aql.or_(aql.eq("occupation", "jedi"),
aql.contains("starships", "millennium falcon"))))):
count += 1
if count != 6:
errors.append(
"Fail: O.query().V().where(aql.not_(aql.and_(aql.eq(\"_label\", \"robot\"), aql.or_(aql.eq(\"occupation\", \"jedi\"), aql.contains(\"starships\", \"millennium falcon\"))))) %s != %s"
% (count, 6))
return errors