work in chunks when verify if class exists and to construct suggestio…

…n graph (#321)

Co-authored-by: Anita Caron <[email protected]>

src/template_generation_tools.py

@@ -94,7 +94,11 @@ def generate_class_graph_template(ccf_tools_df :pd.DataFrame, log_dict: dict):
     terms.add(r['o'])
 
   # ENTITY CHECK
-  no_valid_class = ug.query_uberon(" ".join(terms), ug.select_class)
+  if len(terms) > 90:
+    for chunk in chunks(list(terms), 90):
+      no_valid_class = ug.query_uberon(" ".join(chunk), ug.select_class)
+  else:
+    no_valid_class = ug.query_uberon(" ".join(chunk), ug.select_class)
 
   del_index = []
   for t in no_valid_class:

src/uberongraph_tools.py

@@ -473,10 +473,19 @@ def get_suggestion_graph(self, all_as, terms_as_d, all_ct, terms_ct, terms_ct_d)
 
 
       if len(terms_ct_d) > 20:
-        for chunk in chunks(list(terms_ct_d), 30):
-          sec_graph += self.construct_relation(subject="\n".join(chunk), objects="\n".join(list(all_ct)), property="rdfs:subClassOf")
+        for chunk in chunks(list(terms_ct_d), 20):
+          if len(all_ct) > 90:
+            for chunck in chunks(list(all_ct), 90):
+              sec_graph += self.construct_relation(subject="\n".join(chunk), objects="\n".join(list(chunck)), property="rdfs:subClassOf")
+          else:
+            sec_graph += self.construct_relation(subject="\n".join(chunk), objects="\n".join(list(all_ct)), property="rdfs:subClassOf")
       else:
-        sec_graph += self.construct_relation(subject="\n".join(terms_ct_d), objects="\n".join(list(all_ct)), property="rdfs:subClassOf")
+        if len(all_ct) > 90:
+            for chunck in chunks(list(all_ct), 90):
+              sec_graph += self.construct_relation(subject="\n".join(terms_ct_d), objects="\n".join(list(chunck)), property="rdfs:subClassOf")
+        else:
+          sec_graph += self.construct_relation(subject="\n".join(terms_ct_d), objects="\n".join(list(all_ct)), property="rdfs:subClassOf")
+
 
       return sec_graph