Related Entities: add tests for links from drug warnings

app/entities_joiner/entities_joiner.py

@@ -3,10 +3,13 @@ Module with functions to make joins of entities
 """
 import json
 import base64
+from datetime import datetime
 
 from app.entities_joiner import standardisation
 from app.entities_joiner import ids_loader
 from app.url_shortening import url_shortener
+from app.config import RUN_CONFIG
+from app.usage_statistics import statistics_saver
 
 
 class EntitiesJoinerError(Exception):
@@ -76,6 +79,7 @@ def get_tiny_hash_to_related_items(destination_entity_browser_state_template,
                                           destination_entity_browser_state_template,
                                           previous_hash)
 
+    save_statistics(entity_from, entity_to, len(ids))
     return join_state_hash
 
 
@@ -139,3 +143,20 @@ def get_destination_url_hash(hashable_part):
     shortening_response = url_shortener.shorten_url(hashable_part)
     return shortening_response['hash']
 
+
+def save_statistics(raw_entity_from, raw_entity_to, num_ids):
+    """
+    :param raw_entity_from: source entity of the items
+    :param raw_entity_to: destination entity of the join
+    :param num_ids: number of ids joined
+    """
+
+    statistics_document = {
+        'entity_from': raw_entity_from,
+        'entity_to': raw_entity_to,
+        'num_ids': num_ids,
+        'request_date': datetime.utcnow().timestamp() * 1000,
+    }
+
+    index_name = RUN_CONFIG.get('usage_statistics').get('entities_join_statistics_index')
+    statistics_saver.save_record_to_elasticsearch(statistics_document, index_name)

app/entities_joiner/standardisation.py

@@ -30,6 +30,9 @@ class PossibleEntitiesTo(Enum):
     CHEMBL_CELL_LINES = 'CHEMBL_CELL_LINES'
     CHEMBL_TISSUES = 'CHEMBL_TISSUES'
     CHEMBL_DRUG_WARNINGS = 'CHEMBL_DRUG_WARNINGS'
+    CHEMBL_DRUGS = 'CHEMBL_DRUGS'
+    CHEMBL_DRUG_MECHANISMS = 'CHEMBL_DRUG_MECHANISMS'
+    CHEMBL_DRUG_INDICATIONS = 'CHEMBL_DRUG_INDICATIONS'
 
 
 class SelectionModes(Enum):
@@ -73,6 +76,18 @@ JOIN_PROPERTIES = {
                 PossibleEntitiesTo.CHEMBL_COMPOUNDS: {
                     'from_property': 'drug_warning.molecule_chembl_id',
                     'to_property': 'molecule_chembl_id'
+                },
+                PossibleEntitiesTo.CHEMBL_DRUGS: {
+                    'from_property': 'drug_warning.parent_molecule_chembl_id',
+                    'to_property': 'molecule_chembl_id'
+                },
+                PossibleEntitiesTo.CHEMBL_DRUG_MECHANISMS: {
+                    'from_property': 'drug_warning.parent_molecule_chembl_id',
+                    'to_property': 'molecule_chembl_id'
+                },
+                PossibleEntitiesTo.CHEMBL_DRUG_INDICATIONS: {
+                    'from_property': 'drug_warning.parent_molecule_chembl_id',
+                    'to_property': 'molecule_chembl_id'
                 }
             }
         }
@@ -82,12 +97,18 @@ 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'
+    PossibleEntitiesTo.CHEMBL_COMPOUNDS: 'ES_INDEXES_NO_MAIN_SEARCH.COMPOUND_COOL_CARDS',
+    PossibleEntitiesTo.CHEMBL_DRUGS: 'ES_INDEXES_NO_MAIN_SEARCH.DRUGS_LIST',
+    PossibleEntitiesTo.CHEMBL_DRUG_MECHANISMS: 'ES_INDEXES_NO_MAIN_SEARCH.MECHANISMS_OF_ACTION',
+    PossibleEntitiesTo.CHEMBL_DRUG_INDICATIONS: 'ES_INDEXES_NO_MAIN_SEARCH.DRUG_INDICATIONS'
 }
 
 BROWSER_NAMES_FOR_TO_ENTITIES = {
     PossibleEntitiesTo.CHEMBL_ACTIVITIES: 'activities',
-    PossibleEntitiesTo.CHEMBL_COMPOUNDS: 'compounds'
+    PossibleEntitiesTo.CHEMBL_COMPOUNDS: 'compounds',
+    PossibleEntitiesTo.CHEMBL_DRUGS: 'drugs',
+    PossibleEntitiesTo.CHEMBL_DRUG_MECHANISMS: 'mechanisms_of_action',
+    PossibleEntitiesTo.CHEMBL_DRUG_INDICATIONS: 'drug_indications'
 }
 
 

app/swagger/swagger.yaml

@@ -515,14 +515,14 @@ paths:
           description: 'Source entity for the join.'
           required: true
           type: 'string'
-          enum: [ 'CHEMBL_ACTIVITIES', 'CHEMBL_COMPOUNDS', 'CHEMBL_TARGETS', 'CHEMBL_ASSAYS', 'CHEMBL_DOCUMENTS', 'CHEMBL_CELL_LINES', 'CHEMBL_TISSUES', 'CHEMBL_DRUG_WARNINGS' ]
+          enum: [ 'CHEMBL_ACTIVITIES', 'CHEMBL_COMPOUNDS', 'CHEMBL_TARGETS', 'CHEMBL_ASSAYS', 'CHEMBL_DOCUMENTS', 'CHEMBL_CELL_LINES', 'CHEMBL_TISSUES', 'CHEMBL_DRUG_WARNINGS', 'CHEMBL_DRUGS' ]
           default: 'CHEMBL_COMPOUNDS'
         - name: 'entity_to'
           in: 'formData'
           description: 'The entity in ChEMBL to do the join with.'
           required: true
           type: 'string'
-          enum: [ 'CHEMBL_ACTIVITIES', 'CHEMBL_COMPOUNDS', 'CHEMBL_TARGETS', 'CHEMBL_ASSAYS', 'CHEMBL_DOCUMENTS', 'CHEMBL_CELL_LINES', 'CHEMBL_TISSUES', 'CHEMBL_DRUG_WARNINGS' ]
+          enum: [ 'CHEMBL_ACTIVITIES', 'CHEMBL_COMPOUNDS', 'CHEMBL_TARGETS', 'CHEMBL_ASSAYS', 'CHEMBL_DOCUMENTS', 'CHEMBL_CELL_LINES', 'CHEMBL_TISSUES', 'CHEMBL_DRUG_WARNINGS', 'CHEMBL_DRUGS', 'CHEMBL_DRUG_MECHANISMS', 'CHEMBL_DRUG_INDICATIONS' ]
           default: 'CHEMBL_COMPOUNDS'
         - name: 'es_query'
           in: 'formData'

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
+Module that tests the endpoints to do joins among entities from drug warnings to compounds
 """
 from specific_tests import utils
 from specific_tests.entities_join import utils as entities_join_utils
@@ -8,7 +8,7 @@ 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
+    Tests doing a join among different entities from drug warnings to compounds
     :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
     """

functional_tests/specific_tests/entities_join/fun_test_entities_join_4.py

+# pylint: disable=import-error
+"""
+Module that tests the endpoints to do joins among entities from drug warnings to compounds
+"""
+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 compounds
+    :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_DRUGS')

functional_tests/specific_tests/entities_join/fun_test_entities_join_5.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 indications
+    :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_DRUG_INDICATIONS')

functional_tests/specific_tests/entities_join/fun_test_entities_join_6.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_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_DRUG_MECHANISMS')

functional_tests/specific_tests/entities_join/fun_test_entities_join_all_tests.py

@@ -2,7 +2,7 @@
 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_3, fun_test_entities_join_4, fun_test_entities_join_5
 
 
 def run_test(server_base_url, delayed_jobs_server_base_path):
@@ -12,5 +12,5 @@ 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_3, fun_test_entities_join_4, fun_test_entities_join_5]:
         test_module.run_test(server_base_url, delayed_jobs_server_base_path)

functional_tests/specific_tests/entities_join/utils.py

@@ -30,20 +30,16 @@ def test_entities_join(dataset_query, selection_description, server_base_url, en
     request = requests.post(url, data=join_params)
 
     status_code = request.status_code
-    print(f'status_code: {status_code}')
     response_text = request.text
     utils.print_es_response(response_text)
     assert status_code == 200, 'The request failed!'
 
     url_hash_got = request.json()['tiny_hash']
-    print('url_hash_got: ', url_hash_got)
 
     expansion_url = f'{server_base_url}/url_shortening/expand_url/{url_hash_got}'
-    print(f'Checking tiny hash: {expansion_url}')
     request = requests.get(expansion_url)
 
     status_code = request.status_code
-    print(f'status_code: {status_code}')
     response_text = request.text
     utils.print_es_response(response_text)
     assert status_code == 200, 'The request failed!'