Entities Join: allow to include previous hash to encode it in state

app/blueprints/entities_join/controllers/entities_join_controller.py

@@ -26,6 +26,7 @@ def get_link_to_related_items():
     entity_to = request_parameters.sanitise_parameter(form_data.get('entity_to'))
     es_query = request_parameters.sanitise_parameter(form_data.get('es_query'))
     selection_description = request_parameters.sanitise_parameter(form_data.get('selection_description'))
+    previous_hash = request_parameters.sanitise_parameter(form_data.get('previous_hash'))
 
     app_logging.debug(f'destination_entity_browser_state_template: {destination_entity_browser_state_template}')
     app_logging.debug(f'entity_from: {entity_from}')
@@ -34,9 +35,9 @@ def get_link_to_related_items():
     app_logging.debug(f'selection_description: {selection_description}')
 
     try:
-        json_response = entities_join_service.get_link_to_related_items(destination_entity_browser_state_template,
+        json_response = entities_join_service.get_tiny_hash_to_related_items(destination_entity_browser_state_template,
                                                                         entity_from, entity_to, es_query,
-                                                                        selection_description)
+                                                                        selection_description, previous_hash)
         return jsonify(json_response)
     except entities_join_service.EntitiesJoinServiceError as error:
 

app/blueprints/entities_join/controllers/marshmallow_schemas.py

@@ -13,3 +13,4 @@ class EntitiesJoinQuery(Schema):
     entity_to = fields.String(required=True)
     es_query = fields.String(required=True)
     selection_description = fields.String(required=True)
+    previous_hash = fields.String()

app/blueprints/entities_join/services/entities_join_service.py

@@ -8,22 +8,23 @@ class EntitiesJoinServiceError(Exception):
     """Base class for exceptions in this file."""
 
 
-def get_link_to_related_items(destination_entity_browser_state_template,
-                              entity_from, entity_to, es_query,
-                              selection_description):
+def get_tiny_hash_to_related_items(destination_entity_browser_state_template,
+                                   entity_from, entity_to, es_query,
+                                   selection_description, previous_hash):
     """
     :param destination_entity_browser_state_template: template for building the resulting browser url
     :param entity_from: source entity of the items
     :param entity_to: destination entity of the join
     :param es_query: query in elasticsearch for the dataset
     :param selection_description: stringifyed javascript object describing de selection of items in the dataset
+    :param previous_hash: hash of the state that originated this join of entities
     :return: a dict with the tiny url to the link with the generated state
     """
 
     try:
         tiny_hash = entities_joiner.get_tiny_hash_to_related_items(destination_entity_browser_state_template,
                                                                    entity_from, entity_to, es_query,
-                                                                   selection_description)
+                                                                   selection_description, previous_hash)
 
         return {
             'tiny_hash': tiny_hash

app/entities_joiner/entities_joiner.py

@@ -15,13 +15,14 @@ class EntitiesJoinerError(Exception):
 
 def get_tiny_hash_to_related_items(destination_entity_browser_state_template,
                                    entity_from, entity_to, raw_es_query,
-                                   raw_selection_description):
+                                   raw_selection_description, previous_hash):
     """
     :param destination_entity_browser_state_template: template for building the resulting browser url
     :param entity_from: source entity of the items
     :param entity_to: destination entity of the join
     :param raw_es_query: stringifyed query in elasticsearch for the dataset
     :param raw_selection_description: stringifyed javascript object describing de selection of items in the dataset
+    :param previous_hash: hash of the state that originated this join of entities
     :return: the hash to the link with the generated state
     """
     parsed_from_entity = None
@@ -52,16 +53,12 @@ def get_tiny_hash_to_related_items(destination_entity_browser_state_template,
     if entity_to == entity_from:
         raise EntitiesJoinerError(f'entity_to ({entity_to}) and entity_from ({entity_from}) cannot be the same!')
 
-    print('load ids:')
-
     index_name = standardisation.get_index_name_for_from_entity(parsed_from_entity)
     fail_if_null(index_name, 'index name', parsed_from_entity, parsed_to_entity)
 
-    print('index_name: ', index_name)
     from_property = standardisation.get_from_property(parsed_from_entity, parsed_to_entity)
     fail_if_null(from_property, 'from property', parsed_from_entity, parsed_to_entity)
 
-    print('from_property: ', from_property)
     selection_description = json.loads(raw_selection_description)
     es_query = json.loads(raw_es_query)
     ids = ids_loader.load_ids_for_query(es_query, selection_description, from_property, index_name)
@@ -76,9 +73,8 @@ def get_tiny_hash_to_related_items(destination_entity_browser_state_template,
     fail_if_null(browser_name, 'browser name', parsed_from_entity, parsed_to_entity)
 
     join_state_hash = get_join_state_hash(ids, to_property, settings_path, browser_name,
-                                          destination_entity_browser_state_template)
-    print('join_state_hash: ')
-    print(join_state_hash)
+                                          destination_entity_browser_state_template,
+                                          previous_hash)
 
     return join_state_hash
 
@@ -96,23 +92,23 @@ def fail_if_null(value, value_name, parsed_from_entity, parsed_to_entity):
                                   f'to {parsed_to_entity.value}')
 
 
-def get_join_state_hash(ids, to_property, settings_path, browser_name, destination_entity_browser_state_template):
+def get_join_state_hash(ids, to_property, settings_path, browser_name, destination_entity_browser_state_template,
+                        previous_hash):
     """
     :param ids: list of its for the join
     :param to_property: entity to which to do the join
     :param settings_path: settings path to be used by the user interface
     :param browser_name: name of the destination browser used to build the desired url
     :param destination_entity_browser_state_template: template to build the url for the destination entity browser
+    :param previous_hash: hash of the state that originated this join of entities
     :return: the hash for the query state used for the join
     """
-    print('get_join_query')
-    print('ids: ')
-    print(ids)
-    print('to_property: ')
-    print(to_property)
-
     ids_clauses = " OR ".join([f'"{item_id}"' for item_id in ids])
     desired_state = {
+        'origin': {
+            'type': 'ENTITIES_JOIN',
+            'previous_hash': previous_hash,
+        },
         'list': {
             'settings_path': settings_path,
             'custom_query': f'{to_property}({ids_clauses})',
@@ -121,10 +117,7 @@ def get_join_state_hash(ids, to_property, settings_path, browser_name, destinati
             'at_least_one_facet_is_selected': False,
         }
     }
-    print('desired_state: ', desired_state)
     b64_desired_state = base64.b64encode(json.dumps(desired_state).encode())
-    print('b64_desired_state: ', b64_desired_state)
-    print('destination_entity_browser_state_template: ', destination_entity_browser_state_template)
     destination_entity_browser_state_url = destination_entity_browser_state_template.replace(
         '<BROWSER_NAME>',
         browser_name
@@ -134,10 +127,7 @@ def get_join_state_hash(ids, to_property, settings_path, browser_name, destinati
         b64_desired_state.decode()
     )
 
-    print('destination_entity_browser_state_url: ', destination_entity_browser_state_url)
     hashable_part = f'#{destination_entity_browser_state_url.split("#")[1]}'
-    print('hashable_part: ', hashable_part)
-
     return get_destination_url_hash(hashable_part)
 
 

app/entities_joiner/standardisation.py

@@ -69,6 +69,10 @@ JOIN_PROPERTIES = {
                 PossibleEntitiesTo.CHEMBL_ACTIVITIES: {
                     'from_property': 'drug_warning.molecule_chembl_id',
                     'to_property': 'molecule_chembl_id'
+                },
+                PossibleEntitiesTo.CHEMBL_COMPOUNDS: {
+                    'from_property': 'drug_warning.molecule_chembl_id',
+                    'to_property': 'molecule_chembl_id'
                 }
             }
         }
@@ -78,10 +82,12 @@ JOIN_PROPERTIES = {
 # This is used by the frontend to know which settings use to load the page, should be discarded in the future
 SETTINGS_PATHS_FOR_TO_ENTITIES = {
     PossibleEntitiesTo.CHEMBL_ACTIVITIES: 'ES_INDEXES_NO_MAIN_SEARCH.ACTIVITY',
+    PossibleEntitiesTo.CHEMBL_COMPOUNDS: 'ES_INDEXES_NO_MAIN_SEARCH.COMPOUND_COOL_CARDS'
 }
 
 BROWSER_NAMES_FOR_TO_ENTITIES = {
     PossibleEntitiesTo.CHEMBL_ACTIVITIES: 'activities',
+    PossibleEntitiesTo.CHEMBL_COMPOUNDS: 'compounds'
 }
 
 

app/swagger/swagger.yaml

@@ -535,6 +535,11 @@ paths:
           description: 'stringifyied version of the description of the selection parameters of the dataset. //selectionMode options: ["allItemsExcept", "noItemsExcept"]'
           type: 'string'
           default: '{"selectionMode": "allItemsExcept","exceptions": ["CHEMBL3989861", "CHEMBL3989724", "CHEMBL64"]}'
+        - name: 'previous_hash'
+          in: 'formData'
+          description: 'hash of the state that is making the call'
+          type: 'string'
+          default: 'sQseUMn43BEG1hQ-doPggw=='
       responses:
         '200':
           description: "success"

functional_tests/specific_tests/entities_join/fun_test_entities_join_0.py

@@ -17,4 +17,5 @@ def run_test(server_base_url, delayed_jobs_server_base_path):
 
     dataset_query = utils.load_json_data('functional_tests/specific_tests/data/entities_join_query_0.json')
     selection_description = {"selectionMode": "allItemsExcept", "exceptions": []}
-    entities_join_utils.test_entities_join(dataset_query, selection_description, server_base_url)
+    entities_join_utils.test_entities_join(dataset_query, selection_description, server_base_url,
+                                           entity_from='CHEMBL_DRUG_WARNINGS', entity_to='CHEMBL_ACTIVITIES')

functional_tests/specific_tests/entities_join/fun_test_entities_join_1.py

@@ -18,4 +18,6 @@ def run_test(server_base_url, delayed_jobs_server_base_path):
     print('-------------------------------------------')
     dataset_query = utils.load_json_data('functional_tests/specific_tests/data/entities_join_query_0.json')
     selection_description = {"selectionMode": "allItemsExcept", "exceptions": ['CHEMBL2107495', 'CHEMBL340978']}
-    entities_join_utils.test_entities_join(dataset_query, selection_description, server_base_url)
+    entities_join_utils.test_entities_join(dataset_query, selection_description, server_base_url,
+                                           entity_from='CHEMBL_DRUG_WARNINGS',
+                                           entity_to='CHEMBL_ACTIVITIES')

functional_tests/specific_tests/entities_join/fun_test_entities_join_2.py

+# pylint: disable=import-error
+"""
+Module that tests the endpoints to do joins among entities selecting no ids except some
+"""
+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 selecting no ids except some
+    :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_0.json')
+    selection_description = {"selectionMode": "noItemsExcept", "exceptions": ['CHEMBL2107495', 'CHEMBL340978']}
+    entities_join_utils.test_entities_join(dataset_query, selection_description, server_base_url,
+                                           entity_from='CHEMBL_DRUG_WARNINGS', entity_to='CHEMBL_ACTIVITIES')

functional_tests/specific_tests/entities_join/fun_test_entities_join_3.py

+# pylint: disable=import-error
+"""
+Module that tests the endpoints to do joins among entities selecting no ids except some
+"""
+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 selecting no ids except some
+    :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_0.json')
+    selection_description = {"selectionMode": "allItemsExcept", "exceptions": []}
+    entities_join_utils.test_entities_join(dataset_query, selection_description, server_base_url,
+                                           entity_from='CHEMBL_DRUG_WARNINGS', entity_to='CHEMBL_COMPOUNDS')

functional_tests/specific_tests/entities_join/fun_test_entities_join_all_tests.py

 """
 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
+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
 
 
 def run_test(server_base_url, delayed_jobs_server_base_path):
@@ -10,5 +11,6 @@ def run_test(server_base_url, delayed_jobs_server_base_path):
     :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
     """
-    for test_module in [fun_test_entities_join_0, fun_test_entities_join_1]:
+    for test_module in [fun_test_entities_join_0, fun_test_entities_join_1, fun_test_entities_join_2,
+                        fun_test_entities_join_3]:
         test_module.run_test(server_base_url, delayed_jobs_server_base_path)

functional_tests/specific_tests/entities_join/utils.py

@@ -7,21 +7,23 @@ import requests
 from specific_tests import utils
 
 
-def test_entities_join(dataset_query, selection_description, server_base_url):
+def test_entities_join(dataset_query, selection_description, server_base_url, entity_from, entity_to):
     """
     Performs the testing of the entities join endpoint given the parameters
     :param dataset_query: query of the current dataset
     :param selection_description: dict describing the selection
     :param server_base_url: base url of the server being used for the tests
+    :param entity_from: entity from which to do the join
     """
 
     join_params = {
         'destination_entity_browser_state_template':
             'wwwdev.ebi.ac.uk/chembl/g/#browse/<BROWSER_NAME>/full_state/<GENERATED_STATE>',
-        'entity_from': 'CHEMBL_DRUG_WARNINGS',
-        'entity_to': 'CHEMBL_ACTIVITIES',
+        'entity_from': entity_from,
+        'entity_to': entity_to,
         'es_query': json.dumps(dataset_query),
-        'selection_description': json.dumps(selection_description)
+        'selection_description': json.dumps(selection_description),
+        'previous_hash': 'sQseUMn43BEG1hQ-doPggw=='
     }
 
     url = f'{server_base_url}/entities_join/get_link_to_related_items'