def _auth_arr(user):
''' Get authentication array for BoolQuery for retrieving public and
authenticated documents. '''
auth_arr = [Query.missing_terms("field", "group_name")] # all public documents
try:
auth_arr.append(Query.terms("group_name", # all documents in the user group
[gp.lower() for gp in get_user_groups(user)]).query_wrap())
except Http404:
# not logged in
pass
return auth_arr
def test_elastic_group_name(self):
'''
Testing the workflow defined in: https://killin.cimr.cam.ac.uk/nextgensite/2015/08/05/region-authorization/
Testing various elastic queries
idx doc:
"_source":{"attr": {"region_id": "803", "group_name": "[\"DIL\"]", "Name": "4q27"},
"seqid": "chr4", "source": "immunobase", "type": "region",
"score": ".", "strand": ".", "phase": ".", "start": 122061159, "end": 122684373}
idx_query:
Private(in given group) OR Public
-d '{"query":{"filtered":{"filter":{"bool": {
"should": [
{"terms": {"group_name":["dil"]}},
{ "missing": { "field": "group_name" }}
]
}}}}}'
Private(in given group):
-d '{"query":{"filtered":{"filter":{"terms":{"group_name":["dil"]}}}}}'
Public:
-d {'query': {'filtered': {'filter': {'missing': {'field': 'group_name'}},
- 'query': {'term': {'match_all': '{}'}}}}}
'''
# get the groups for the given user
response = self.client.post('/accounts/login/', {
'username': '******',
'password': '******'
})
self.assertTrue(response.status_code, "200")
logged_in_user = User.objects.get(
id=self.client.session['_auth_user_id'])
if logged_in_user and logged_in_user.is_authenticated():
user_groups = get_user_groups(logged_in_user)
self.assertTrue('READ' in user_groups,
"user present in READ group")
# make sure the user is not yet in DIL group
self.assertFalse('DIL' in user_groups,
"user not present in DIL group")
group_names = get_user_groups(logged_in_user)
if 'READ' in group_names: group_names.remove('READ') # @IgnorePep8
group_names = [x.lower() for x in group_names]
self.assertTrue(len(group_names) == 0, "No group present")
# Match all query, as there is no group we do a match all
query = ElasticQuery(Query.match_all())
expected_query_string = {"query": {"match_all": {}}}
self.assertJSONEqual(json.dumps(query.query),
json.dumps(expected_query_string),
"Query string matched")
Search.index_refresh(self.index_name)
elastic = Search(query, idx=self.index_name)
docs = elastic.search().docs
self.assertTrue(
len(docs) == 12,
"Elastic string query retrieved all public regions")
# Filtered query for group names, add the user to DIL group and get the query string
self.dil_group = Group.objects.create(name='DIL')
logged_in_user.groups.add(self.dil_group)
group_names = get_user_groups(logged_in_user)
if 'READ' in group_names: group_names.remove('READ') # @IgnorePep8
group_names = [x.lower() for x in group_names]
self.assertTrue(len(group_names) > 0, "More than 1 group present")
self.assertTrue("dil" in group_names, "DIL group present")
# retrieves all docs with missing field group_name - 11 docs
terms_filter = TermsFilter.get_missing_terms_filter(
"field", "attr.group_name")
query = ElasticQuery.filtered(Query.match_all(), terms_filter)
elastic = Search(query, idx=self.index_name)
docs = elastic.search().docs
self.assertTrue(
len(docs) == 11,
"Elastic string query retrieved all public regions")
# build filtered boolean query to bring all public docs + private docs 11+1 = 12 docs
query_bool = BoolQuery()
query_bool.should(Query.missing_terms("field", "group_name")) \
.should(Query.terms("group_name", group_names).query_wrap())
query = ElasticQuery.filtered_bool(Query.match_all(), query_bool)
elastic = Search(query, idx=self.index_name)
docs = elastic.search().docs
self.assertTrue(
len(docs) == 12,
"Elastic string query retrieved both public + private regions")
terms_filter = TermsFilter.get_terms_filter("attr.group_name",
group_names)
query = ElasticQuery.filtered(Query.match_all(), terms_filter)
elastic = Search(query, idx=self.index_name)
docs = elastic.search().docs
self.assertTrue(
len(docs) == 1,
"Elastic string query retrieved one private regions")
self.assertEqual(docs[0].attr['Name'], "4q27", "type matched region")
self.assertEqual(docs[0].attr['region_id'], "803",
"type matched region")
self.assertEqual(docs[0].attr['group_name'], "[\"DIL\"]",
"type matched region")
def test_elastic_group_name(self):
'''
Testing the workflow defined in: https://killin.cimr.cam.ac.uk/nextgensite/2015/08/05/region-authorization/
Testing various elastic queries
idx doc:
"_source":{"attr": {"region_id": "803", "group_name": "[\"DIL\"]", "Name": "4q27"},
"seqid": "chr4", "source": "immunobase", "type": "region",
"score": ".", "strand": ".", "phase": ".", "start": 122061159, "end": 122684373}
idx_query:
Private(in given group) OR Public
-d '{"query":{"filtered":{"filter":{"bool": {
"should": [
{"terms": {"group_name":["dil"]}},
{ "missing": { "field": "group_name" }}
]
}}}}}'
Private(in given group):
-d '{"query":{"filtered":{"filter":{"terms":{"group_name":["dil"]}}}}}'
Public:
-d {'query': {'filtered': {'filter': {'missing': {'field': 'group_name'}},
- 'query': {'term': {'match_all': '{}'}}}}}
'''
# get the groups for the given user
response = self.client.post('/accounts/login/', {'username': '******', 'password': '******'})
self.assertTrue(response.status_code, "200")
logged_in_user = User.objects.get(id=self.client.session['_auth_user_id'])
if logged_in_user and logged_in_user.is_authenticated():
user_groups = get_user_groups(logged_in_user)
self.assertTrue('READ' in user_groups, "user present in READ group")
# make sure the user is not yet in DIL group
self.assertFalse('DIL' in user_groups, "user not present in DIL group")
group_names = get_user_groups(logged_in_user)
if 'READ' in group_names : group_names.remove('READ') # @IgnorePep8
group_names = [x.lower() for x in group_names]
self.assertTrue(len(group_names) == 0, "No group present")
# Match all query, as there is no group we do a match all
query = ElasticQuery(Query.match_all())
expected_query_string = {"query": {"match_all": {}}}
self.assertJSONEqual(json.dumps(query.query), json.dumps(expected_query_string), "Query string matched")
Search.index_refresh(self.index_name)
elastic = Search(query, idx=self.index_name)
docs = elastic.search().docs
self.assertTrue(len(docs) == 12, "Elastic string query retrieved all public regions")
# Filtered query for group names, add the user to DIL group and get the query string
self.dil_group = Group.objects.create(name='DIL')
logged_in_user.groups.add(self.dil_group)
group_names = get_user_groups(logged_in_user)
if 'READ' in group_names : group_names.remove('READ') # @IgnorePep8
group_names = [x.lower() for x in group_names]
self.assertTrue(len(group_names) > 0, "More than 1 group present")
self.assertTrue("dil" in group_names, "DIL group present")
# retrieves all docs with missing field group_name - 11 docs
terms_filter = TermsFilter.get_missing_terms_filter("field", "attr.group_name")
query = ElasticQuery.filtered(Query.match_all(), terms_filter)
elastic = Search(query, idx=self.index_name)
docs = elastic.search().docs
self.assertTrue(len(docs) == 11, "Elastic string query retrieved all public regions")
# build filtered boolean query to bring all public docs + private docs 11+1 = 12 docs
query_bool = BoolQuery()
query_bool.should(Query.missing_terms("field", "group_name")) \
.should(Query.terms("group_name", group_names).query_wrap())
query = ElasticQuery.filtered_bool(Query.match_all(), query_bool)
elastic = Search(query, idx=self.index_name)
docs = elastic.search().docs
self.assertTrue(len(docs) == 12, "Elastic string query retrieved both public + private regions")
terms_filter = TermsFilter.get_terms_filter("attr.group_name", group_names)
query = ElasticQuery.filtered(Query.match_all(), terms_filter)
elastic = Search(query, idx=self.index_name)
docs = elastic.search().docs
self.assertTrue(len(docs) == 1, "Elastic string query retrieved one private regions")
self.assertEqual(docs[0].attr['Name'], "4q27", "type matched region")
self.assertEqual(docs[0].attr['region_id'], "803", "type matched region")
self.assertEqual(docs[0].attr['group_name'], "[\"DIL\"]", "type matched region")