semantic

beacon/db/filters.py

@@ -6,7 +6,7 @@
 
 from beacon.request import ontologies
 from beacon.request.model import AlphanumericFilter, CustomFilter, OntologyFilter, Operator, Similarity
-from beacon.semantic_similarity import semantic_similarity
+#from beacon.semantic_similarity import semantic_similarity
 
 import logging
 
@@ -91,7 +91,7 @@ def apply_ontology_filter(query: dict, filter: OntologyFilter) -> dict:
             cutoff = 0.7
         elif filter.similarity == Similarity.LOW:
             cutoff = 0.5
-        similar_terms = semantic_similarity(filter.id, cutoff)
+        similar_terms = 'semantic_similarity(filter.id, cutoff)'
         LOG.debug("Similar: {}".format(similar_terms))
         for term in similar_terms:
             if query["$text"]["$search"]:

beacon/semantic_similarity.py

@@ -1,3 +1,4 @@
+'''
 #from sentence_transformers import SentenceTransformer
 from scipy.spatial import distance
 import networkx as nx
@@ -192,6 +193,6 @@ def semantic_similarity(term:str, x:float):
 print(list_neighbours)
 
 
-
+'''
 
 

deploy/extract_filtering_terms_oriol.py

@@ -182,19 +182,20 @@ def insert_all_alphanumeric_terms_used():
     collections = client.beacon.list_collection_names()
     if 'filtering_terms' in collections:
         collections.remove('filtering_terms')
+    collections = ['runs']
     print("Collections:", collections)
     for c_name in collections:
         terms = find_alphanumeric_terms_used(c_name)
         print(terms)
-        #if len(terms) > 0:
-            #client.beacon.filtering_terms.insert_many(terms)
+        if len(terms) > 0:
+            client.beacon.filtering_terms.insert_many(terms)
 
 
-#insert_all_ontology_terms_used()
+insert_all_ontology_terms_used()
 #insert_all_alphanumeric_terms_used()
 #terms=find_ontology_terms_used("individuals")
 #print(terms)
 #hola = get_ontology_term_label('NCIT','C173381')
 #print(hola)
-find_alphanumeric_terms_used('analyses')
-
+#hola = find_alphanumeric_terms_used('analyses')
+#print(hola)