Entities join: Add more cases to the joins

app/blueprints/entities_join/controllers/entities_join_controller.py

@@ -40,4 +40,5 @@ def get_link_to_related_items():
                                                                         selection_description, previous_hash)
         return jsonify(json_response)
     except entities_join_service.EntitiesJoinServiceError as error:
+        app_logging.debug(str(error))
         abort(500, f'Internal server error: {str(error)}')

app/entities_joiner/standardisation.py

@@ -70,6 +70,7 @@ def create_simple_query_generator(destination_property):
     :param destination_property: property to use to build the query
     :return: a function to be used to build the join query
     """
+
     def join_function(ids):
         """
         :param ids: ids of the items matches
@@ -77,11 +78,20 @@ def create_simple_query_generator(destination_property):
         """
         ids_clauses = " OR ".join([f'"{item_id}"' for item_id in ids])
         return f'{destination_property}({ids_clauses})'
+
     return join_function
 
 
 JOIN_PROPERTIES = {
     'from': {
+        PossibleDestinationEntities.CHEMBL_COMPOUNDS: {
+            'to': {
+                PossibleDestinationEntities.CHEMBL_ACTIVITIES: {
+                    'origin_property': 'molecule_chembl_id',
+                    'destination_query_generator': create_simple_query_generator('molecule_chembl_id')
+                }
+            }
+        },
         PossibleOriginEntities.CHEMBL_DRUG_WARNINGS: {
             'to': {
                 PossibleDestinationEntities.CHEMBL_ACTIVITIES: {

functional_tests/specific_tests/data/entities_join_query_1.json

+ {
+  "query": {
+    "bool": {
+      "must": [
+        {
+          "query_string": {
+            "analyze_wildcard": true,
+            "query": "*"
+          }
+        }
+      ],
+      "filter": [
+        [
+          {
+            "bool": {
+              "should": [
+                {
+                  "term": {
+                    "molecule_type": "Oligosaccharide"
+                  }
+                }
+              ]
+            }
+          }
+        ]
+      ]
+    }
+  }
+}
\ No newline at end of file

functional_tests/specific_tests/entities_join/fun_test_entities_join_7.py

+# pylint: disable=import-error
+"""
+Module that tests the endpoints to do joins among entities from drug warnings to drug indications
+"""
+from specific_tests import utils
+from specific_tests.entities_join import utils as entities_join_utils
+
+
+def run_test(server_base_url, delayed_jobs_server_base_path):
+    """
+    Tests doing a join among different entities from drug warnings to drug mechanisms
+    :param server_base_url: base url of the running server. E.g. http://127.0.0.1:5000
+    :param delayed_jobs_server_base_path: base path for the delayed_jobs
+    """
+
+    print('-------------------------------------------')
+    print('Testing joins among entities selecting all none except')
+    print('-------------------------------------------')
+    dataset_query = utils.load_json_data('functional_tests/specific_tests/data/entities_join_query_1.json')
+    selection_description = {"selectionMode": "allItemsExcept", "exceptions": []}
+    entities_join_utils.test_entities_join(dataset_query, selection_description, server_base_url,
+                                           entity_from='CHEMBL_COMPOUNDS', entity_to='CHEMBL_ACTIVITIES')

functional_tests/specific_tests/entities_join/fun_test_entities_join_all_tests.py

@@ -2,7 +2,8 @@
 Module that runs all the tests related to the entities join
 """
 from specific_tests.entities_join import fun_test_entities_join_0, fun_test_entities_join_1, fun_test_entities_join_2, \
-    fun_test_entities_join_3, fun_test_entities_join_4, fun_test_entities_join_5
+    fun_test_entities_join_3, fun_test_entities_join_4, fun_test_entities_join_5, fun_test_entities_join_6, \
+    fun_test_entities_join_7
 
 
 def run_test(server_base_url, delayed_jobs_server_base_path):
@@ -12,5 +13,6 @@ def run_test(server_base_url, delayed_jobs_server_base_path):
     :param delayed_jobs_server_base_path: base path for the delayed_jobs
     """
     for test_module in [fun_test_entities_join_0, fun_test_entities_join_1, fun_test_entities_join_2,
-                        fun_test_entities_join_3, fun_test_entities_join_4, fun_test_entities_join_5]:
+                        fun_test_entities_join_3, fun_test_entities_join_4, fun_test_entities_join_5,
+                        fun_test_entities_join_6, fun_test_entities_join_7]:
         test_module.run_test(server_base_url, delayed_jobs_server_base_path)