def test_transaction_log_related_cases_filter(
client, submitter, pg_driver_clean, cgci_blgsp):
utils.reset_transactions(pg_driver_clean)
post_example_entities_together(client, pg_driver_clean, submitter)
data = json.dumps({
'query': """
{a: transaction_log (first: 1) { related_cases { id }}}
"""
})
r = client.post(path, headers=submitter, data=data)
assert r.status_code == 200
print r.data
case_id = r.json['data']['a'][0]['related_cases'][0]['id']
data = json.dumps({
'query': """
query Test($caseId: String) {
a: transaction_log (related_cases: [$caseId]) {
related_cases { id submitter_id }
}
}
""",
"variables": {"caseId": case_id},
})
r = client.post(path, headers=submitter, data=data)
assert r.status_code == 200
print r.data
related_case_doc = r.json['data']['a'][0]['related_cases'][0]
assert related_case_doc['id'] == case_id
assert related_case_doc['submitter_id']
def test_get_projects_anonymous(client, submitter, pg_driver_clean, cgci_blgsp,
public_dataset_api):
post_example_entities_together(client, pg_driver_clean, submitter)
with pg_driver_clean.session_scope() as s:
project = models.Project("other",
name="name",
code="OTHER",
dbgap_accession_number="phsid")
program = pg_driver_clean.nodes(
models.Program).props(name="CGCI").first()
project.programs = [program]
s.add(project)
r = client.get("/datasets/projects")
assert r.json == {
"projects": [{
"dbgap_accession_number": "phs000527",
"code": "BLGSP",
"name": "Burkitt Lymphoma Genome Sequencing Project"
}, {
"dbgap_accession_number": "phsid",
"code": "OTHER",
"name": "name"
}]
}
def test_authorized_call_with_protected_config(client, submitter,
pg_driver_clean, cgci_blgsp):
post_example_entities_together(client, pg_driver_clean, submitter)
#: number of nodes to change project_id on, there should be 5
with pg_driver_clean.session_scope() as s:
cases = pg_driver_clean.nodes(models.Case).all()
case_count = len(cases)
for case in cases[0:-3]:
case.project_id = "OTHER-OTHER"
s.merge(case)
def test_transaction_log_documents(client, submitter, pg_driver_clean, cgci_blgsp):
utils.reset_transactions(pg_driver_clean)
post_example_entities_together(client, pg_driver_clean, submitter)
r = client.post(path, headers=submitter, data=json.dumps({
'query': """{ log: transaction_log {
doc: documents { doc_size name }}}"""}))
doc = r.json['data']['log'][0]['doc'][0]
assert doc['name'] is None
assert isinstance(doc['doc_size'], int)
def test_transaction_log_type(client, submitter, pg_driver_clean, cgci_blgsp):
utils.reset_transactions(pg_driver_clean)
post_example_entities_together(client, pg_driver_clean, submitter)
r = client.post(path, headers=submitter, data=json.dumps({
'query': """{ a: transaction_log { role type }}"""}))
print r.data
type_ = graphql.transaction.TransactionLog.TYPE_MAP['create']
assert r.json['data']['a'][0]['type'] == type_
r = client.post(path, headers=submitter, data=json.dumps({
'query': """{
a: transaction_log(type: "%s") { role type }
}""" % type_}))
print r.data
assert r.json['data']['a']
def test_anonymous_call_with_public_config(client, submitter, pg_driver_clean,
cgci_blgsp, public_dataset_api):
post_example_entities_together(client, pg_driver_clean, submitter)
with pg_driver_clean.session_scope() as s:
project = models.Project("other", code="OTHER")
program = pg_driver_clean.nodes(
models.Program).props(name="CGCI").first()
project.programs = [program]
s.add(project)
aliquot_count = pg_driver_clean.nodes(models.Aliquot).count()
cases = pg_driver_clean.nodes(models.Case).all()
case_count = len(cases)
for case in cases[0:-3]:
case.project_id = "CGCI-OTHER"
s.merge(case)
def test_unauthorized_call_with_protected_config(client, submitter,
pg_driver_clean, cgci_blgsp,
mock_arborist_requests):
post_example_entities_together(client, pg_driver_clean, submitter)
mock_arborist_requests(auth_mapping={})
r = client.get("/datasets?nodes=case,aliquot", headers=submitter)
assert r.status_code == 200
assert r.json == {}
r = client.get("/datasets/projects", headers=submitter)
assert r.status_code == 200
assert r.json == {"projects": []}
def test_transaction_logs_order_desc(client, submitter, pg_driver_clean, cgci_blgsp):
utils.reset_transactions(pg_driver_clean)
post_example_entities_together(client, pg_driver_clean, submitter)
with pg_driver_clean.session_scope():
assert pg_driver_clean.nodes(models.submission.TransactionLog).count() == 1
r = client.post(path, headers=submitter, data=json.dumps({
'query': """{
a: transaction_log (order_by_desc: "id") {
id
project_id
created_datetime
}
}"""}))
print r.data
_original = r.json['data']['a']
_sorted = sorted(_original, cmp=(lambda a, b: cmp(b['id'], a['id'])))
assert _original == _sorted, r.data
def test_transaction_logs_quick_search(
client, submitter, pg_driver_clean, cgci_blgsp):
utils.reset_transactions(pg_driver_clean)
post_example_entities_together(client, pg_driver_clean, submitter)
with pg_driver_clean.session_scope():
id_ = str(pg_driver_clean.nodes(models.submission.TransactionLog).first().id)
r = client.post(path, headers=submitter, data=json.dumps({
'query': """{
a: transaction_log (quick_search: "%s") { id }
b: transaction_log (quick_search: %s) { id }
c: transaction_log (quick_search: "A") { id }
}""" % (id_, id_)}))
assert r.json == {
'data': {
'a': [{'id': id_}],
'b': [{'id': id_}],
'c': [],
}
}, r.data
def test_transaction_log_entities(client, submitter, pg_driver_clean, cgci_blgsp):
utils.reset_transactions(pg_driver_clean)
post_example_entities_together(client, pg_driver_clean, submitter)
# using response
r = client.post(path, headers=submitter, data=json.dumps({
'query': """{ log: transaction_log {
doc: documents { resp: response { ent: entities { type }}}}}"""}))
assert r.status_code == 200
entities = r.json['data']['log'][0]['doc'][0]['resp']['ent']
assert all(e['type'] for e in entities)
# using response_json
r = client.post(path, headers=submitter, data=json.dumps({
'query': """{ log: transaction_log {
doc: documents { resp: response_json }}}"""}))
assert r.status_code == 200
resp = json.loads(r.json['data']['log'][0]['doc'][0]['resp'])
assert all(entity['type'] for entity in resp['entities'])
def test_transaction_log_related_cases(
client, submitter, pg_driver_clean, cgci_blgsp):
utils.reset_transactions(pg_driver_clean)
post_example_entities_together(client, pg_driver_clean, submitter)
r = client.post(path, headers=submitter, data=json.dumps({
'query': """
query Test {
a: transaction_log (first: 1) {
type documents {response { entities {related_cases {
id submitter_id
}}}}}
}"""}))
assert r.status_code == 200
print(r.data)
related_case = (r.json['data']
['a'][0]
['documents'][0]
['response']
['entities'][1]
['related_cases'][0])
assert 'submitter_id' in related_case
assert 'id' in related_case
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_transaction_logs(client, submitter, pg_driver_clean, cgci_blgsp):
utils.reset_transactions(pg_driver_clean)
post_example_entities_together(client, pg_driver_clean, submitter)
with pg_driver_clean.session_scope():
assert pg_driver_clean.nodes(models.submission.TransactionLog).count() == 1