Update app.py

app.py

@@ -14,6 +14,7 @@ from transformers import pipeline, AutoTokenizer
 from transformers.pipelines.pt_utils import KeyDataset
 
 from concurrent.futures import ThreadPoolExecutor, as_completed
+from collections import Counter
 
 ##os.environ["PYTORCH_CUDA_ALLOC_CONF"] = "max_split_size_mb:512"
 #os.environ['PYTORCH_CUDA_ALLOC_CONF'] = 'expandable_segments:True'
@@ -2012,7 +2013,24 @@ def nerBio(text, ModelsSelection, CategoriesSelection, ScoreFilt, EntityLinking,
     parser.add_argument("--virtuosokey_filename", type=str, default="", help="file location where it is stored the virtuoso endpoint dba pwd")
     parser.add_argument("--bioportalkey_filename", type=str, default="", help="file location where it is stored the NCBO  BioPortal api key")
 
+    # consose 20250205:
+    # KGchoices = None
+    # KGchoices = ['SNOMED', 'LOINC', 'ICD10', 'NCIT']
+    # KGchoices = ['SNOMED', 'LOINC', 'ICD10', 'MESH', 'NCIT']  # restricts the input to these values only
+    if KGchoices:
+        KGchoices.sort()
+    parser.add_argument("--KG_restriction", nargs='+', choices=KGchoices, default=KGchoices,
+                        help="List of ontologies to which restrict the entity linking task.")
+    # # consose 20250502:
+    # if Counter(KGchoices) == Counter(POSSIBLE_KGchoices_List):
+    #     parser.add_argument("--USE_CACHE", type=str, default="True",
+    #                         help="whether to use cache for the NER and NEL tasks or not")
+    # else:
+    #     # print("Lists do not have the same elements")
+    #     parser.add_argument("--USE_CACHE", type=str, default="False",
+    #                         help="whether to use cache for the NER and NEL tasks or not")
     parser.add_argument("--USE_CACHE", type=str, default="False", help="whether to use cache for the NER and NEL tasks or not")
+    
     parser.add_argument("--num_cores_eLinking", type=int, default=1, help="parallel processing for the entity linking process")
 
     parser.add_argument("--computeEntityContext", type=str, default="False",
@@ -2026,15 +2044,6 @@ def nerBio(text, ModelsSelection, CategoriesSelection, ScoreFilt, EntityLinking,
 
     parser.add_argument("--temperature", type=int, default=0.01)
 
-    #consose 20250205:
-    #KGchoices = None
-    # KGchoices = ['SNOMED', 'LOINC', 'ICD10', 'NCIT']
-    #KGchoices = ['SNOMED', 'LOINC', 'ICD10', 'MESH', 'NCIT']  # restricts the input to these values only
-    if KGchoices:
-        KGchoices.sort()
-    parser.add_argument("--KG_restriction", nargs='+', choices=KGchoices, default=KGchoices,
-                        help="List of ontologies to which restrict the entity linking task.")
-
     args = parser.parse_args()
 
 
@@ -2348,6 +2357,8 @@ demo = gr.Interface(
         gr.CheckboxGroup(categories_List, label="CategoriesSelection", value=categories_List),
         gr.Slider(minimum=0, maximum=1.0, step=0.1, label="Score", value=0.5),
         gr.Checkbox(label="Enable Named-Entity Linking (NEL)", value=False), #True False
+        #gr.CheckboxGroup(POSSIBLE_KGchoices_List, label="KGchoices Selection", value=POSSIBLE_KGchoices_List, visible=True),
+        gr.Dropdown(POSSIBLE_KGchoices_List, multiselect=True, label="KGchoices Selection", value=POSSIBLE_KGchoices_List),
         gr.State(value={})
     ],
     outputs=[