def test_insert_double_edge_out(self):
with self.g.session_scope() as s:
case1 = md.Case('case_id_1')
case2 = md.Case('case_id_2')
sample = md.Sample('sample_id_1')
sample.cases = [case1, case2]
s.merge(sample)
with self.g.session_scope() as s:
sample = self.g.nodes(md.Sample).subq_path('cases').one()
assert {c.node_id for c in sample._related_cases} == \
{c.node_id for c in [case1, case2]}
def test_delete_one_parent(self):
with self.g.session_scope() as s:
case1 = md.Case('case_id_1')
case2 = md.Case('case_id_2')
sample = md.Sample('sample_id_1')
sample.cases = [case1, case2]
s.merge(sample)
with self.g.session_scope() as s:
case1 = self.g.nodes(md.Case).ids('case_id_1').one()
s.delete(case1)
with self.g.session_scope() as s:
sample = self.g.nodes(md.Sample).one()
assert sample._related_cases == [case2]
def valid_write_access_fn(g):
with g.session_scope() as s:
s.merge(models.Case('1'))
yield
with g.session_scope() as s:
n = g.nodes().get("1")
s.delete(n)
def test_priv_grant_read(self):
"""Test ability to grant read but not write privs"""
self.create_all_tables()
try:
self.engine.execute("CREATE USER pytest WITH PASSWORD 'pyt3st'")
g = PsqlGraphDriver(self.host, 'pytest', 'pyt3st', self.database)
#: If this failes, this test (not the code) is wrong!
with self.assertRaises(ProgrammingError):
with g.session_scope():
g.nodes().count()
pgadmin.main(pgadmin.get_parser().parse_args([
'graph-grant',
'--read=pytest',
] + self.base_args))
with g.session_scope():
g.nodes().count()
with self.assertRaises(ProgrammingError):
with g.session_scope() as s:
s.merge(models.Case('1'))
finally:
self.engine.execute("DROP OWNED BY pytest; DROP USER pytest")
def test_insert_double_edge_in(self):
with self.g.session_scope() as s:
case = md.Case('case_id_1')
sample1 = md.Sample('sample_id_1')
sample2 = md.Sample('sample_id_2')
case.samples = [sample1, sample2]
s.merge(case)
def test_priv_revoke_write(self):
"""Test ability to revoke read/write privs"""
self.create_all_tables()
try:
self.engine.execute("CREATE USER pytest WITH PASSWORD 'pyt3st'")
g = PsqlGraphDriver(self.host, 'pytest', 'pyt3st', self.database)
pgadmin.main(pgadmin.get_parser().parse_args([
'graph-grant',
'--write=pytest',
] + self.base_args))
pgadmin.main(pgadmin.get_parser().parse_args([
'graph-revoke',
'--write=pytest',
] + self.base_args))
with g.session_scope() as s:
g.nodes().count()
with self.assertRaises(ProgrammingError):
with g.session_scope() as s:
s.merge(models.Case('1'))
finally:
self.engine.execute("DROP OWNED BY pytest; DROP USER pytest")
def test_delete_dst_association_proxy(self):
with self.g.session_scope() as s:
case = md.Case('case_id_1')
aliquot = md.Aliquot('aliquot_id_1')
sample = md.Sample('sample_id_1')
aliquot.samples = [sample]
sample.cases = [case]
s.merge(case)
def test_export_all_node_types_json(client, pg_driver, cgci_blgsp, submitter):
post_example_entities_together(client, submitter)
with pg_driver.session_scope() as s:
case = pg_driver.nodes(md.Case).first()
new_case = md.Case(str(uuid.uuid4()))
new_case.props = case.props
new_case.submitter_id = 'case-2'
s.add(new_case)
case_count = pg_driver.nodes(md.Case).count()
def test_updated_datetime_hook(self):
"""Test setting updated datetime when a node is updated."""
with self.g.session_scope() as s:
s.merge(md.Case('case1'))
with self.g.session_scope():
case = self.g.nodes(md.Case).one()
old_created_datetime = case.created_datetime
old_updated_datetime = case.updated_datetime
case.primary_site = 'Kidney'
def test_insert_update_children(self):
with self.g.session_scope() as s:
aliquot = s.merge(md.Aliquot('aliquot_id_1'))
sample = s.merge(md.Sample('sample_id_1'))
aliquot.samples = [sample]
s.merge(md.Case('case_id_1'))
with self.g.session_scope() as s:
case = self.g.nodes(md.Case).one()
sample = self.g.nodes(md.Sample).one()
sample.cases = [case]
def test_export_all_node_types(client, pg_driver, submitter, dictionary_setup):
dictionary_setup('s3://test.com')
put_cgci_blgsp(client, submitter)
post_example_entities_together(client, pg_driver, submitter)
with pg_driver.session_scope() as s:
case = pg_driver.nodes(md.Case).first()
new_case = md.Case(str(uuid.uuid4()))
new_case.props = case.props
new_case.submitter_id = 'case-2'
s.add(new_case)
case_count = pg_driver.nodes(md.Case).count()
def test_no_datetime_update_for_new_edge(self):
"""Verify new inbound edges do not affect a node's updated datetime."""
with self.g.session_scope() as s:
s.merge(md.Case('case1'))
with self.g.session_scope() as s:
case = self.g.nodes(md.Case).one()
old_created_datetime = case.created_datetime
old_updated_datetime = case.updated_datetime
sample = s.merge(md.Sample('sample1'))
case.samples.append(sample)
def test_insert_multiple_edges(self):
with self.g.session_scope() as s:
case = md.Case('case_id_1')
sample = md.Sample('sample_id_1')
portion = md.Portion('portion_id_1')
analyte = md.Analyte('analyte_id_1')
aliquot = md.Aliquot('aliquot_id_1')
general_file = md.File('file_id_1')
sample.cases = [case]
portion.samples = [sample]
analyte.portions = [portion]
aliquot.analytes = [analyte]
general_file.aliquots = [aliquot]
s.merge(case)
def test_created_datetime_hook(self):
"""Test setting created/updated datetime when a node is created."""
time_before = datetime.now().isoformat()
with self.g.session_scope() as s:
s.add(md.Case('case1'))
time_after = datetime.now().isoformat()
with self.g.session_scope():
case = self.g.nodes(md.Case).one()
# Compare against the time both before and after the write to
# ensure the comparison is fair.
assert time_before < case.created_datetime < time_after
assert time_before < case.updated_datetime < time_after
def test_priv_grant_write(self):
"""Test ability to grant read/write privs"""
self.create_all_tables()
try:
self.engine.execute("CREATE USER pytest WITH PASSWORD 'pyt3st'")
self.engine.execute("GRANT USAGE ON SCHEMA public TO pytest")
g = PsqlGraphDriver(self.host, 'pytest', 'pyt3st', self.database)
pgadmin.main(pgadmin.get_parser().parse_args([
'graph-grant',
'--write=pytest',
] + self.base_args))
with g.session_scope() as s:
g.nodes().count()
s.merge(models.Case('1'))
finally:
self.engine.execute("DROP OWNED BY pytest; DROP USER pytest")
def test_preserve_timestamps(self):
"""Confirm cache changes do not affect the case's timestamps."""
with self.g.session_scope() as s:
s.merge(md.Case('case_id_1'))
with self.g.session_scope():
case = self.g.nodes(md.Case).one()
old_created_datetime = case.created_datetime
old_updated_datetime = case.updated_datetime
# Test addition of cache edges.
sample = md.Sample('sample_id_1')
portion = md.Portion('portion_id_1')
analyte = md.Analyte('analyte_id_1')
aliquot = md.Aliquot('aliquot_id_1')
sample.cases = [case]
portion.samples = [sample]
analyte.portions = [portion]
aliquot.analytes = [analyte]
sample2 = md.Sample('sample_id_2')
sample2.cases = [case]
def blocker():
with self.g.session_scope() as s:
s.merge(models.Case('1'))
q.put(0) # Tell main thread we're ready
q.get() # This get should block until this prcoess is killed
assert False, 'Should not be reachable!'
def blocker():
with self.g.session_scope() as s:
s.merge(models.Case('1'))
q.put(0) # Tell main thread we're ready
q.get() # Wait for main thread to tell us to exit
def invalid_write_access_fn(g):
with pytest.raises(ProgrammingError):
with g.session_scope() as s:
s.add(models.Case('1'))
def test_delete_parent(self):
with self.g.session_scope() as s:
case = md.Case('case_id_1')
sample = md.Sample('sample_id_1')
sample.cases = [case]
s.merge(case)
def test_insert_single_association_proxy(self):
with self.g.session_scope() as s:
case = md.Case('case_id_1')
sample = md.Sample('sample_id_1')
sample.cases = [case]
s.merge(sample)
def test_insert_single_edge(self):
with self.g.session_scope() as s:
case = s.merge(md.Case('case_id_1'))
sample = s.merge(md.Sample('sample_id_1'))
edge = md.SampleDerivedFromCase(sample.node_id, case.node_id)
s.merge(edge)
