Create app.py

app.py

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+import gradio as gr
+import spacy
+import medspacy
+from medspacy.visualization import visualize_dep, visualize_ent
+from spacy import displacy
+
+med_ner = medspacy.load(r"./ner_models//ner_model_v2//training//model-best")
+def merge_tokens(tokens):
+    merged_tokens = []
+    for token in tokens:
+        if merged_tokens and token['entity'].startswith('I-') and merged_tokens[-1]['entity'].endswith(token['entity'][2:]):
+             # If current token continues the entity of the last one, merge them
+            last_token = merged_tokens[-1]
+            last_token['word'] += token['word'].replace('##', '')
+            last_token['end'] = token['end']
+#             last_token['score'] = (last_token['score'] + token['score']) / 2
+        else:
+            # Otherwise, add the token to the list
+            merged_tokens.append(token)
+            
+    return merged_tokens
+
+def ner(inp):
+    output = med_ner(inp)
+    formatted_ents = []
+    for i in output.ents:
+        ent = {}
+        ent['entity']= i.label_
+        ent['word']= i.text
+        ent['start']= int(i.start_char)
+        ent['end']= int(i.end_char)
+        print(i.label_,"->",i.text,"->",i.start_char,"->",i.end_char,"->",type(i.start_char))
+        formatted_ents.append(ent)
+    print(formatted_ents)
+    
+    merged_tokens = merge_tokens(formatted_ents)
+#     return {"text": str(inp), "entities": formatted_ents}
+    return {"text": str(inp), "entities": merged_tokens}
+
+demo = gr.Interface(fn=ner,
+                   inputs=[gr.Textbox(label="Text to find entities", lines=2)],
+                   outputs=[gr.HighlightedText(label="Text with entites")],
+                   title="Custom-NER with Spacy3 and MedSpacy",
+                   description="Find medical entities using the NER model under the hood!",
+                   allow_flagging = True,
+                   examples=["Patient has hx of stroke. Mother diagnosed with diabetes. No evidence of pna.", "I have fever and cough since 2 days."]
+                   )
+
+demo.launch()