def test_search_with_aggregation_params(self, mock_es):
def side_effect(*args, **kwargs):
if "size" in kwargs:
return self.es_search_response
else:
return self.es_aggregation_response
mock_es.side_effect = side_effect
response = self.app.get(
'/api/search?q=act1&category=gene&go_names=cytoplasm')
es_query = build_search_query(
"act1", self.search_fields, "gene", self.category_filters,
ImmutableMultiDict([("q", "act1"), ("category", "gene"),
("go_names", "cytoplasm")]))
mock_es.assert_has_calls([
mock.call(index=self.index,
body=build_es_search_body_request(
"act1", "gene", es_query, self.json_response_fields,
self.search_fields, ""),
size=10,
from_=0,
preference='p_act1')
])
mock_es.assert_has_calls([
mock.call(index=self.index,
body=build_es_aggregation_body_request(
es_query, "gene", self.category_filters))
])
self.assertEqual(response.status_code, 200)
def test_build_es_aggregation_body_request_should_aggregate_each_subcategory(self):
query = ""
fields = ["name", "symbol"]
category = "genes"
category_filters = {
"genes": ['go_ids', 'go_names'],
"go": ['gene'],
}
args = ImmutableMultiDict([
('go_names', 'A'),
('go_names', 'B'),
('go_names', 'C')
])
es_query = build_search_query(query, fields, category, category_filters, args)
self.assertEqual(build_es_aggregation_body_request(es_query, category, category_filters), {
'query': es_query,
'size': 0,
'aggs': {
'go_ids': {
'terms': {'field': 'go_ids.raw', 'size': 999}
},
'go_names': {
'terms': {'field': 'go_names.raw', 'size': 999}
}
}
})
def test_search_default_params(self, mock_es):
def side_effect(*args, **kwargs):
if "size" in kwargs:
return self.es_search_response
else:
return self.es_aggregation_response
mock_es.side_effect = side_effect
response = self.app.get('/api/search')
es_query = build_search_query('', self.search_fields, '',
self.category_filters, {})
mock_es.assert_has_calls([
mock.call(index=self.index,
body=build_es_search_body_request(
'', '', es_query, self.json_response_fields,
self.search_fields, ''),
size=10,
from_=0,
preference='p_')
])
mock_es.assert_has_calls([
mock.call(index=self.index,
body=build_es_aggregation_body_request(
es_query, '', self.category_filters))
])
self.assertEqual(response.status_code, 200)
def test_build_es_search_body_should_not_randomize_results_if_category_is_defined(self):
query = ""
fields = ["name", "symbol"]
category = "genes"
category_filters = {
"genes": ['go_ids', 'go_names'],
"go": ['gene'],
}
sort_by = "alphabetical"
args = ImmutableMultiDict([
('go_names', 'A'),
('go_names', 'B'),
('go_names', 'C')
])
search_fields = ["name", "symbol"]
json_response_fields = ['name', 'symbol', 'synonym']
es_query = build_search_query(query, fields, category, category_filters, args)
self.assertEqual(build_es_search_body_request(query, category, es_query, json_response_fields, search_fields, sort_by), {
'_source': json_response_fields,
'highlight': {
'fields': {'name': {}, 'symbol': {}}
},
'query': es_query,
'sort': [
{
"name.raw": {
"order": "asc"
}
}
]
})
def test_build_es_search_body_should_add_highlighting(self):
query = ""
fields = ["name", "symbol"]
category = ""
category_filters = {
"genes": ['go_ids', 'go_names'],
"go": ['gene'],
}
sort_by = "relevance"
args = ImmutableMultiDict([
('go_names', 'A'),
('go_names', 'B'),
('go_names', 'C')
])
search_fields = ["name", "symbol"]
json_response_fields = ['name', 'symbol', 'synonym']
es_query = build_search_query(query, fields, category, category_filters, args)
self.assertEqual(build_es_search_body_request(query, category, es_query, json_response_fields, search_fields, sort_by), {
'_source': json_response_fields,
'highlight': {
'fields': {'name': {}, 'symbol': {}}
},
'query': {
"function_score": {
"query": es_query,
"random_score": {"seed": 12345}
}
}
})
def test_build_search_query_should_filter_subcategories_if_passed(self):
query = "act1"
fields = ["name", "symbol"]
category = "genes"
category_filters = {
"genes": ['go_ids', 'go_names'],
"go": ['gene'],
}
args = ImmutableMultiDict([
('go_names', 'A'),
('go_names', 'B'),
('go_names', 'C')
])
es_query = build_search_params(query, fields)
self.assertEqual(build_search_query(query, fields, category, category_filters, args), {
'filtered': {
'query': es_query,
'filter': {
'bool': {
'must': [
{'term': {'category': category}},
{'term': {'go_names.raw': 'A'}},
{'term': {'go_names.raw': 'B'}},
{'term': {'go_names.raw': 'C'}}
]
}
}
}
})
def test_search_with_custom_params(self, mock_es):
def side_effect(*args, **kwargs):
if "size" in kwargs:
return self.es_search_response
else:
return self.es_aggregation_response
mock_es.side_effect = side_effect
response = self.app.get(
'/api/search?q=act1&category=gene&limit=25&offset=10&sort_by=alphabetical'
)
es_query = build_search_query(
"act1", self.search_fields, "gene", self.category_filters,
ImmutableMultiDict([("q", "act1"), ("category", "gene"),
("limit", 25), ("offset", 10),
("sort_by", "alphabetical")]))
mock_es.assert_has_calls([
mock.call(index=self.index,
body=build_es_search_body_request(
"act1", "gene", es_query, self.json_response_fields,
self.search_fields, "alphabetical"),
size=25,
from_=10)
])
mock_es.assert_has_calls([
mock.call(index=self.index,
body=build_es_aggregation_body_request(
es_query, "gene", self.category_filters))
])
self.assertEqual(response.status_code, 200)
def test_build_search_query_should_return_search_params_only_for_no_category(self):
query = "gene"
fields = ["name", "symbol"]
category = ''
category_filters = {
"genes": ['go_ids', 'go_names'],
"go": ['gene'],
}
args = ImmutableMultiDict()
es_query = build_search_params(query, fields)
self.assertEqual(build_search_query(query, fields, category, category_filters, args), es_query)
def test_build_es_aggregation_body_request_should_return_empty_for_invalid_category(self):
query = ""
fields = ["name", "symbol"]
category = "invalid_category"
category_filters = {
"genes": ['go_ids', 'go_names'],
"go": ['gene'],
}
args = ImmutableMultiDict([
('go_names', 'A'),
('go_names', 'B'),
('go_names', 'C')
])
es_query = build_search_query(query, fields, category, category_filters, args)
self.assertEqual(build_es_aggregation_body_request(es_query, category, category_filters), {})
def test_build_search_query_should_filter_by_category(self):
query = "gene"
fields = ["name", "symbol"]
category = 'genes'
category_filters = {
"genes": ['go_ids', 'go_names'],
"go": ['gene']
}
args = ImmutableMultiDict()
es_query = build_search_params(query, fields)
self.assertEqual(build_search_query(query, fields, category, category_filters, args), {
'filtered': {
'query': es_query,
'filter': {
'bool': {
'must': [{'term': {'category': category}}]
}
}
}
})
