adding synonyms

beacon/db/extract_filtering_terms.py

@@ -200,10 +200,11 @@ def insert_all_ontology_terms_used():
         collections.remove('filtering_terms')
     print("Collections:", collections)
     for c_name in collections:
-        terms_ids = find_ontology_terms_used(c_name)
-        terms = get_filtering_object(terms_ids, c_name)
-        if len(terms) > 0:
-            client.beacon.filtering_terms.insert_many(terms)
+        if c_name not in ['counts', 'similarities', 'synonyms']:
+            terms_ids = find_ontology_terms_used(c_name)
+            terms = get_filtering_object(terms_ids, c_name)
+            if len(terms) > 0:
+                client.beacon.filtering_terms.insert_many(terms)
 
 def find_ontology_terms_used(collection_name: str) -> List[Dict]:
     print(collection_name)

beacon/db/filters.py

@@ -388,7 +388,27 @@ def apply_filters(query: dict, filters: List[dict], collection: str, query_param
 
 
 def apply_ontology_filter(query: dict, filter: OntologyFilter, collection: str, request_parameters: dict) -> dict:
-    scope = filter.scope
+    query_synonyms={}
+    query_synonyms['id']=filter.id
+    synonyms=get_documents(
+        client.beacon.synonyms,
+        query_synonyms,
+        0,
+        1
+    )
+
+    try:
+        synonym_id=synonyms[0]['synonym']
+    except Exception:
+        synonym_id=None
+    LOG.debug(synonym_id)
+    if synonym_id is not None:
+        filter.id=synonym_id
+
+    try:
+        scope = filter.scope
+    except Exception:
+        scope = collection[0:-1]
     is_filter_id_required = True
     # Search similar
     if filter.similarity != Similarity.EXACT:
@@ -407,6 +427,8 @@ def apply_ontology_filter(query: dict, filter: OntologyFilter, collection: str,
             ontology_dict=client.beacon.similarities.find({"id": filter.id})
             final_term_list = ontology_dict[0]["similarity_low"]
 
+
+
         final_term_list.append(filter.id)
         query_filtering={}
         query_filtering['$and']=[]
@@ -609,7 +631,10 @@ def format_operator(operator: Operator) -> str:
 
 def apply_alphanumeric_filter(query: dict, filter: AlphanumericFilter, collection: str) -> dict:
     #LOG.debug(filter.value)
-    scope = filter.scope
+    try:
+        scope = filter.scope
+    except Exception:
+        scope = collection[0:-1]
     formatted_value = format_value(filter.value)
     formatted_operator = format_operator(filter.operator)
     #LOG.debug(collection)
@@ -768,7 +793,10 @@ def apply_alphanumeric_filter(query: dict, filter: AlphanumericFilter, collectio
 def apply_custom_filter(query: dict, filter: CustomFilter, collection:str) -> dict:
     #LOG.debug(query)
 
-    scope=filter.scope
+    try:
+        scope = filter.scope
+    except Exception:
+        scope = collection[0:-1]
     value_splitted = filter.id.split(':')
     if value_splitted[0] in conf.alphanumeric_terms:
         query_term = value_splitted[0]

beacon/reindex.py

@@ -12,6 +12,14 @@
             conf.database_auth_source,
         )
     )
+try:
+    client.beacon.drop_collection("synonyms")
+except Exception:
+    client.beacon.create_collection(name="synonyms")
+try:
+    client.beacon.validate_collection("synonyms")
+except Exception:
+    db=client.beacon.create_collection(name="synonyms")
 try:
     client.beacon.drop_collection("counts")
 except Exception: