def test_without_path_order(client, submitter, pg_driver_clean, cgci_blgsp):
"""Assert that the ordering is applied after the exception"""
put_example_entities_together(client, pg_driver_clean, submitter)
utils.put_entity_from_file(client, 'case.json', submitter)
utils.put_entity_from_file(client, 'sample.json', submitter)
with pg_driver_clean.session_scope():
c = pg_driver_clean.nodes(models.Case).one()
c.samples = []
r = client.post(path,
headers=submitter,
data=json.dumps({
'query':
"""
query Test {
case (
order_by_desc: "created_datetime",
without_path_to: { type: "sample" })
{ submitter_id }
}"""
}))
assert r.json == {
"data": {
"case": [{
"submitter_id": "BLGSP-71-06-00019"
}]
}
}, r.data
def test_filter_empty_prop_list(client, submitter, pg_driver_clean, cgci_blgsp,
monkeypatch):
post_example_entities_together(client, pg_driver_clean, submitter)
utils.put_entity_from_file(client, 'read_group.json', submitter)
utils.patch_indexclient(monkeypatch)
utils.put_entity_from_file(client, 'submitted_unaligned_reads.json',
submitter)
r = client.post(path,
headers=submitter,
data=json.dumps({
'query':
"""{
a: _case_count(submitter_id: [])
b: _submitted_unaligned_reads_count
c: _submitted_unaligned_reads_count(file_state: [])
}"""
}))
assert r.json == {
'data': {
'a': 1,
'b': 1,
'c': 1,
}
}
def test_transaction_log_entities_errors(client, submitter, pg_driver_clean,
cgci_blgsp):
utils.reset_transactions(pg_driver_clean)
post_example_entities_together(client, pg_driver_clean, submitter)
put_response = utils.put_entity_from_file(client,
"read_group_invalid.json",
submitter=submitter,
validate=False)
transaction_id = put_response.json.get("transaction_id")
# using response
query = """
{{ log: transaction_log( id: {} ) {{
doc: documents {{ resp: response {{ ent: entities {{
err: errors {{ type keys message }} }} }} }} }} }}
"""
query = query.format(transaction_id)
r = client.post(path, headers=submitter, data=json.dumps({"query": query}))
assert r.status_code == 200
error = r.json["data"]["log"][0]["doc"][0]["resp"]["ent"][0]["err"][0]
# using response_json
query = """
{{ log: transaction_log( id: {} ) {{
doc: documents {{ resp: response_json
}} }} }}
"""
query = query.format(transaction_id)
r = client.post(path, headers=submitter, data=json.dumps({"query": query}))
assert r.status_code == 200
resp = json.loads(r.json["data"]["log"][0]["doc"][0]["resp"])
error = resp["entities"][0]["errors"][0]
assert all(key in error for key in ("type", "keys", "message"))
def test_submitted_unaligned_reads_with_path_to_read_group(
client, submitter, pg_driver_clean, cgci_blgsp):
"""Regression for incorrect counts"""
post_example_entities_together(client, pg_driver_clean, submitter)
utils.put_entity_from_file(client, 'read_group.json', submitter)
files = [
models.SubmittedUnalignedReads('file_{}'.format(i),
project_id='CGCI-BLGSP')
for i in range(3)
]
with pg_driver_clean.session_scope() as s:
rg = pg_driver_clean.nodes(models.ReadGroup).one()
rg.submitted_unaligned_reads_files = files
rg = s.merge(rg)
r = client.post(path,
headers=submitter,
data=json.dumps({
'query':
"""{
read_group(id: "%s") {
id
_submitted_unaligned_reads_files_count
}
submitted_unaligned_reads(with_path_to:{type: "read_group"}) {
id
}
}""" % rg.node_id
}))
assert r.json == {
"data": {
"read_group": [{
"_submitted_unaligned_reads_files_count": 3,
"id": rg.node_id
}],
"submitted_unaligned_reads": [{
"id": "file_0"
}, {
"id": "file_1"
}, {
"id": "file_2"
}]
}
}
def test_read_group_with_path_to_case(client, submitter, pg_driver_clean,
cgci_blgsp):
"""Regression for incorrect counts"""
put_example_entities_together(client, pg_driver_clean, submitter)
utils.put_entity_from_file(client, 'read_group.json', submitter)
data = json.dumps({
'query':
"""
{
_read_group_count (with_path_to: {type: "case"})
}
""",
})
r = client.post(path, headers=submitter, data=data)
assert r.json == {
"data": {
"_read_group_count": 1,
}
}
def test_transaction_log_entities_errors(client, submitter, pg_driver,
cgci_blgsp):
utils.reset_transactions(pg_driver)
post_example_entities_together(client, pg_driver, submitter)
put_response = utils.put_entity_from_file(client,
'read_group_invalid.json',
submitter=submitter,
validate=False)
transaction_id = put_response.json.get('transaction_id')
query = """
{{ log: transaction_log( id: {} ) {{
doc: documents {{ resp: response {{ ent: entities {{
err: errors {{ type keys message }} }} }} }} }} }}
"""
query = query.format(transaction_id)
r = client.post(path,
headers=submitter(path, 'post'),
data=json.dumps({'query': query}))
assert r.status_code == 200
error = r.json['data']['log'][0]['doc'][0]['resp']['ent'][0]['err'][0]
assert all(key in error for key in ('type', 'keys', 'message'))