def setUpClass(cls):
check_spec_test_env()
# import the results file
results_file = os.path.join(_TEST_DIR, 'djornl', 'results.json')
with open(results_file) as fh:
cls.json_data = json.load(fh)
cls.no_results = {'nodes': [], 'edges': []}
cls.maxDiff = None
# load the DB
root_path = os.path.join(_TEST_DIR, 'djornl', 'test_data')
with modified_environ(RES_ROOT_DATA_PATH=root_path):
parser = DJORNL_Parser()
node_name = parser.config('node_name')
edge_name = parser.config('edge_name')
edge_data = parser.load_edges()
r = create_test_docs(node_name, edge_data['nodes'])
print_db_update(r, node_name)
r = create_test_docs(edge_name, edge_data['edges'])
print_db_update(r, edge_name)
node_metadata = parser.load_nodes()
r = create_test_docs(node_name, node_metadata['nodes'], True)
print_db_update(r, node_name)
cluster_data = parser.load_clusters()
r = create_test_docs(node_name, cluster_data['nodes'], True)
print_db_update(r, node_name)
def _create_delta_test_docs(coll_name, docs, edge=False):
"""Add in delta required fields."""
if edge:
for doc in docs:
# Replicate the time-travel system by just setting 'from' and 'to' to the keys
doc['from'] = doc['_from'].split('/')[1]
doc['to'] = doc['_to'].split('/')[1]
else:
for doc in docs:
doc['id'] = doc['_key']
for doc in docs:
doc['expired'] = 9007199254740991
doc['created'] = 0
create_test_docs(coll_name, docs)
def test_valid(self):
"""Test a valid query."""
docs_created = create_test_docs(
'test_vertex',
[
{
'is_public': True,
'_key': 'a',
'ws_id': 10
}, # public access
{
'is_public': False,
'_key': 'b',
'ws_id': 1
}, # private access
{
'is_public': False,
'_key': 'c',
'ws_id': 99
} # no access
])
self.assertEqual(
docs_created.json(),
{
'created': 3,
'details': [],
'empty': 0,
'error': False,
'errors': 0,
'ignored': 0,
'updated': 0
},
)
resp = requests.post(
_QUERY_URL,
headers={
'Authorization': 'valid_token'
} # gives access to workspaces [1,2,3]
).json()
self.assertEqual(resp['count'], 2)
# 'c' is inaccessible
self.assertEqual({r['_key'] for r in resp['results']}, {'a', 'b'})
def test_no_auth(self):
"""Test with blank auth."""
docs_created = create_test_docs(
'test_vertex',
[
{
'is_public': True,
'_key': 'a',
'ws_id': 10
}, # public access
{
'is_public': False,
'_key': 'b',
'ws_id': 1
}, # private access
{
'is_public': False,
'_key': 'c',
'ws_id': 99
} # no access
])
self.assertEqual(
docs_created.json(),
{
'created': 3,
'details': [],
'empty': 0,
'error': False,
'errors': 0,
'ignored': 0,
'updated': 0
},
)
resp = requests.post(_QUERY_URL).json()
self.assertEqual(resp['count'], 1)
# 'b' and 'c' are inaccessible
self.assertEqual([r['_key'] for r in resp['results']], ['a'])
def setUpClass(cls):
"""Create test documents"""
check_spec_test_env()
taxon_docs = [
{'_key': '1', 'scientific_name': 'Bacteria', 'rank': 'Domain', 'strain': False},
{'_key': '2', 'scientific_name': 'Firmicutes', 'rank': 'Phylum', 'strain': False},
{'_key': '3', 'scientific_name': 'Bacilli', 'rank': 'Class', 'strain': False},
{'_key': '4', 'scientific_name': 'Proteobacteria', 'rank': 'Phylum', 'strain': False},
{'_key': '5', 'scientific_name': 'Alphaproteobacteria', 'rank': 'Class', 'strain': False},
{'_key': '6', 'scientific_name': 'Gammaproteobacteria', 'rank': 'Class', 'strain': False},
{'_key': '7', 'scientific_name': 'Deltaproteobacteria', 'rank': 'Class', 'strain': False},
{'_key': '8', 'scientific_name': 'Bacillus subtilis 168', 'rank': 'no rank', 'strain': True},
]
child_docs = [
{'_from': 'ncbi_taxon/2', '_to': 'ncbi_taxon/1', 'from': '2', 'to': '1', 'id': '2'},
{'_from': 'ncbi_taxon/4', '_to': 'ncbi_taxon/1', 'from': '4', 'to': '1', 'id': '4'},
{'_from': 'ncbi_taxon/3', '_to': 'ncbi_taxon/2', 'from': '3', 'to': '2', 'id': '3'},
{'_from': 'ncbi_taxon/5', '_to': 'ncbi_taxon/4', 'from': '5', 'to': '4', 'id': '5'},
{'_from': 'ncbi_taxon/6', '_to': 'ncbi_taxon/4', 'from': '6', 'to': '4', 'id': '6'},
{'_from': 'ncbi_taxon/7', '_to': 'ncbi_taxon/4', 'from': '7', 'to': '4', 'id': '7'},
# a few levels missing here
{'_from': 'ncbi_taxon/8', '_to': 'ncbi_taxon/3', 'from': '8', 'to': '3', 'id': '8'},
]
obj_ver_docs = [
_construct_ws_obj_ver(1, 1, 1, is_public=True),
_construct_ws_obj_ver(1, 1, 2, is_public=True),
_construct_ws_obj_ver(2, 1, 1, is_public=False),
]
obj_docs = [
_construct_ws_obj(1, 1, is_public=True),
_construct_ws_obj(2, 1, is_public=False),
]
obj_to_taxa_docs = [
{'_from': 'ws_object_version/1:1:1', '_to': 'ncbi_taxon/1', 'assigned_by': 'assn1'},
{'_from': 'ws_object_version/1:1:2', '_to': 'ncbi_taxon/1', 'assigned_by': 'assn2'},
{'_from': 'ws_object_version/2:1:1', '_to': 'ncbi_taxon/1', 'assigned_by': 'assn2'},
]
# Create workspace objects associated to taxa
ws_docs = [
_ws_defaults({'_key': '1', 'is_public': True}),
_ws_defaults({'_key': '2', 'is_public': False}),
]
ws_to_obj = [
{'_from': 'ws_workspace/1', '_to': 'ws_object/1:1'},
{'_from': 'ws_workspace/2', '_to': 'ws_object/2:1'},
]
ws_type_version_docs = [
{'_key': 'KBaseGenomes.Genome-99.77', 'module_name': 'KBaseGenomes',
'type_name': 'Genome', 'maj_ver': 99, 'min_ver': 77}
]
ws_obj_instance_of_type_docs = [
{'_from': 'ws_object_version/1:1:1', '_to': 'ws_type_version/KBaseGenomes.Genome-99.77'},
{'_from': 'ws_object_version/1:1:2', '_to': 'ws_type_version/KBaseGenomes.Genome-99.77'}
]
_create_delta_test_docs('ncbi_taxon', taxon_docs)
_create_delta_test_docs('ncbi_child_of_taxon', child_docs, edge=True)
create_test_docs('ws_obj_version_has_taxon', obj_to_taxa_docs)
create_test_docs('ws_object', obj_docs)
create_test_docs('ws_workspace', ws_docs)
create_test_docs('ws_workspace_contains_obj', ws_to_obj)
create_test_docs('ws_object_version', obj_ver_docs)
create_test_docs('ws_obj_instance_of_type', ws_obj_instance_of_type_docs)
create_test_docs('ws_type_version', ws_type_version_docs)
def setUpClass(cls):
"""
Create all test data.
"""
check_spec_test_env()
ws_object_version = [
_ws_obj(1, 1, 1), # root/origin object
_ws_obj(1, 2, 1), # copy object
_ws_obj(1, 3, 1), # provenance object
_ws_obj(1, 4, 1), # reference object
_ws_obj(1, 5, 1, is_public=False), # private copy obj
_ws_obj(1, 6, 1, is_public=False), # private prov obj
_ws_obj(1, 7, 1, is_public=False), # private ref obj
]
create_test_docs('ws_object_version', ws_object_version)
ws_type_version = [{'_key': 'Module.Type1-1.0'}]
create_test_docs('ws_type_version', ws_type_version)
ws_obj_instance_of_type = [
{
'_from': 'ws_object_version/1:1:1',
'_to': 'ws_type_version/Module.Type1-1.0'
},
{
'_from': 'ws_object_version/1:2:1',
'_to': 'ws_type_version/Module.Type1-1.0'
},
{
'_from': 'ws_object_version/1:3:1',
'_to': 'ws_type_version/Module.Type1-1.0'
},
{
'_from': 'ws_object_version/1:4:1',
'_to': 'ws_type_version/Module.Type1-1.0'
},
]
create_test_docs('ws_obj_instance_of_type', ws_obj_instance_of_type)
ws_prov_descendant_of = [
{
'_from': 'ws_object_version/1:1:1',
'_to': 'ws_object_version/1:3:1'
},
{
'_from': 'ws_object_version/1:1:1',
'_to': 'ws_object_version/1:6:1'
},
]
create_test_docs('ws_prov_descendant_of', ws_prov_descendant_of)
ws_refers_to = [
{
'_from': 'ws_object_version/1:1:1',
'_to': 'ws_object_version/1:4:1'
},
{
'_from': 'ws_object_version/1:1:1',
'_to': 'ws_object_version/1:7:1'
},
]
create_test_docs('ws_refers_to', ws_refers_to)
ws_copied_from = [
{
'_from': 'ws_object_version/1:1:1',
'_to': 'ws_object_version/1:2:1'
},
{
'_from': 'ws_object_version/1:1:1',
'_to': 'ws_object_version/1:5:1'
},
]
create_test_docs('ws_copied_from', ws_copied_from)