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410be5e
1
Parent(s):
2a31cee
Enhance UI
Browse files- app.py +55 -4
- llama_integration.py +122 -0
- requirements.txt +3 -0
- search.py +134 -0
app.py
CHANGED
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@@ -13,6 +13,8 @@ from sentence_transformers.util import cos_sim
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from memory import MemoryManager
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from translation import translate_query
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from vlm import process_medical_image
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# ✅ Enable Logging for Debugging
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import logging
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@@ -221,7 +223,7 @@ class RAGMedicalChatbot:
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self.model_name = model_name
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self.retrieve = retrieve_function
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-
def chat(self, user_id: str, user_query: str, lang: str = "EN", image_diagnosis: str = "") -> str:
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# 0. Translate query if not EN, this help our RAG system
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if lang.upper() in {"VI", "ZH"}:
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user_query = translate_query(user_query, lang.lower())
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@@ -232,6 +234,24 @@ class RAGMedicalChatbot:
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knowledge_base = "\n".join(retrieved_info)
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## b. Diagnosis RAG from symptom query
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diagnosis_guides = retrieve_diagnosis_from_symptoms(user_query) # smart matcher
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# 2. Hybrid Context Retrieval: RAG + Recent History + Intelligent Selection
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contextual_chunks = memory.get_contextual_chunks(user_id, user_query, lang)
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@@ -258,16 +278,46 @@ class RAGMedicalChatbot:
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# Symptom-Diagnosis prediction RAG
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if diagnosis_guides:
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parts.append("Symptom-based diagnosis guidance (if applicable):\n" + "\n".join(diagnosis_guides))
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parts.append(f"User's question: {user_query}")
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parts.append(f"Language to generate answer: {lang}")
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prompt = "\n\n".join(parts)
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logger.info(f"[LLM] Question query in `prompt`: {prompt}") # Debug out checking RAG on kb and history
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response = gemini_flash_completion(prompt, model=self.model_name, temperature=0.7)
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# Store exchange + chunking
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if user_id:
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memory.add_exchange(user_id, user_query, response, lang=lang)
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logger.info(f"[LLM] Response on `prompt`: {response.strip()}") # Debug out base response
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return response.strip()
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# ✅ Initialize Chatbot
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chatbot = RAGMedicalChatbot(model_name="gemini-2.5-flash", retrieve_function=retrieve_medical_info)
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@@ -280,23 +330,24 @@ async def chat_endpoint(req: Request):
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query_raw = body.get("query")
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query = query_raw.strip() if isinstance(query_raw, str) else ""
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lang = body.get("lang", "EN")
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image_base64 = body.get("image_base64", None)
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img_desc = body.get("img_desc", "Describe and investigate any clinical findings from this medical image.")
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start = time.time()
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image_diagnosis = ""
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# LLM Only
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if not image_base64:
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-
logger.info("[BOT] LLM scenario.")
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# LLM+VLM
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else:
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# If image is present → diagnose first
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safe_load = len(image_base64.encode("utf-8"))
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if safe_load > 5_000_000: # Img size safe processor
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return JSONResponse({"response": "⚠️ Image too large. Please upload smaller images (<5MB)."})
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logger.info("[BOT] VLM+LLM scenario.")
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logger.info(f"[VLM] Process medical image size: {safe_load}, desc: {img_desc}, {lang}.")
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image_diagnosis = process_medical_image(image_base64, img_desc, lang)
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-
answer = chatbot.chat(user_id, query, lang, image_diagnosis)
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elapsed = time.time() - start
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# Final
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return JSONResponse({"response": f"{answer}\n\n(Response time: {elapsed:.2f}s)"})
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from memory import MemoryManager
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from translation import translate_query
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from vlm import process_medical_image
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from search import search_web
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from llama_integration import process_search_query
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# ✅ Enable Logging for Debugging
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import logging
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self.model_name = model_name
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self.retrieve = retrieve_function
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def chat(self, user_id: str, user_query: str, lang: str = "EN", image_diagnosis: str = "", search_mode: bool = False) -> str:
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# 0. Translate query if not EN, this help our RAG system
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if lang.upper() in {"VI", "ZH"}:
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user_query = translate_query(user_query, lang.lower())
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knowledge_base = "\n".join(retrieved_info)
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## b. Diagnosis RAG from symptom query
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diagnosis_guides = retrieve_diagnosis_from_symptoms(user_query) # smart matcher
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# 1.5. Search mode - web search and Llama processing
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search_context = ""
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url_mapping = {}
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if search_mode:
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logger.info("[SEARCH] Starting web search mode")
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try:
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# Search the web
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search_results = search_web(user_query, num_results=5)
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if search_results:
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# Process with Llama
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search_context, url_mapping = process_search_query(user_query, search_results)
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logger.info(f"[SEARCH] Found {len(search_results)} results, processed with Llama")
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else:
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logger.warning("[SEARCH] No search results found")
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except Exception as e:
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logger.error(f"[SEARCH] Search failed: {e}")
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search_context = ""
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# 2. Hybrid Context Retrieval: RAG + Recent History + Intelligent Selection
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contextual_chunks = memory.get_contextual_chunks(user_id, user_query, lang)
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# Symptom-Diagnosis prediction RAG
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if diagnosis_guides:
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parts.append("Symptom-based diagnosis guidance (if applicable):\n" + "\n".join(diagnosis_guides))
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# 5. Search context with citation instructions
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if search_context:
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parts.append("Additional information from web search:\n" + search_context)
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parts.append("IMPORTANT: When you use information from the web search results above, you MUST add a citation tag <#ID> immediately after the relevant content, where ID is the document number (1, 2, 3, etc.). For example: 'According to recent studies <#1>, this condition affects...'")
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parts.append(f"User's question: {user_query}")
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parts.append(f"Language to generate answer: {lang}")
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prompt = "\n\n".join(parts)
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logger.info(f"[LLM] Question query in `prompt`: {prompt}") # Debug out checking RAG on kb and history
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response = gemini_flash_completion(prompt, model=self.model_name, temperature=0.7)
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# 6. Process citations and replace with URLs
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if search_mode and url_mapping:
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response = self._process_citations(response, url_mapping)
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# Store exchange + chunking
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if user_id:
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memory.add_exchange(user_id, user_query, response, lang=lang)
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logger.info(f"[LLM] Response on `prompt`: {response.strip()}") # Debug out base response
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return response.strip()
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def _process_citations(self, response: str, url_mapping: Dict[int, str]) -> str:
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"""Replace citation tags with actual URLs"""
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import re
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# Find all citation tags like <#1>, <#2>, etc.
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citation_pattern = r'<#(\d+)>'
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def replace_citation(match):
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doc_id = int(match.group(1))
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if doc_id in url_mapping:
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return f'<{url_mapping[doc_id]}>'
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return match.group(0) # Keep original if URL not found
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# Replace citations with URLs
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processed_response = re.sub(citation_pattern, replace_citation, response)
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logger.info(f"[CITATION] Processed citations, found {len(re.findall(citation_pattern, response))} citations")
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return processed_response
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# ✅ Initialize Chatbot
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chatbot = RAGMedicalChatbot(model_name="gemini-2.5-flash", retrieve_function=retrieve_medical_info)
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query_raw = body.get("query")
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query = query_raw.strip() if isinstance(query_raw, str) else ""
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lang = body.get("lang", "EN")
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search_mode = body.get("search", False)
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image_base64 = body.get("image_base64", None)
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img_desc = body.get("img_desc", "Describe and investigate any clinical findings from this medical image.")
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start = time.time()
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image_diagnosis = ""
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# LLM Only
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if not image_base64:
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logger.info(f"[BOT] LLM scenario. Search mode: {search_mode}")
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# LLM+VLM
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else:
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# If image is present → diagnose first
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safe_load = len(image_base64.encode("utf-8"))
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if safe_load > 5_000_000: # Img size safe processor
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return JSONResponse({"response": "⚠️ Image too large. Please upload smaller images (<5MB)."})
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logger.info(f"[BOT] VLM+LLM scenario. Search mode: {search_mode}")
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logger.info(f"[VLM] Process medical image size: {safe_load}, desc: {img_desc}, {lang}.")
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image_diagnosis = process_medical_image(image_base64, img_desc, lang)
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answer = chatbot.chat(user_id, query, lang, image_diagnosis, search_mode)
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elapsed = time.time() - start
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# Final
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return JSONResponse({"response": f"{answer}\n\n(Response time: {elapsed:.2f}s)"})
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llama_integration.py
ADDED
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@@ -0,0 +1,122 @@
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import os
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import requests
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import json
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import logging
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from typing import List, Dict, Tuple
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logger = logging.getLogger(__name__)
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class NVIDIALLamaClient:
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def __init__(self):
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self.api_key = os.getenv("NVIDIA_URI")
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if not self.api_key:
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raise ValueError("NVIDIA_URI environment variable not set")
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self.base_url = "https://api.nvcf.nvidia.com/v2/nvcf/chat/completions"
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self.model = "meta/llama-3.1-8b-instruct"
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def generate_keywords(self, user_query: str) -> List[str]:
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"""Use Llama to generate search keywords from user query"""
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try:
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prompt = f"""Given this medical question: "{user_query}"
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Generate 3-5 specific search keywords that would help find relevant medical information online.
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Focus on medical terms, symptoms, conditions, treatments, or procedures mentioned.
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Return only the keywords separated by commas, no explanations.
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Keywords:"""
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response = self._call_llama(prompt)
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# Extract keywords from response
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keywords = [kw.strip() for kw in response.split(',') if kw.strip()]
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logger.info(f"Generated keywords: {keywords}")
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return keywords[:5] # Limit to 5 keywords
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except Exception as e:
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logger.error(f"Failed to generate keywords: {e}")
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return [user_query] # Fallback to original query
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def summarize_documents(self, documents: List[Dict], user_query: str) -> Tuple[str, Dict[int, str]]:
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"""Use Llama to summarize documents and return summary with URL mapping"""
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try:
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# Create document summaries
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doc_summaries = []
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url_mapping = {}
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for doc in documents:
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doc_id = doc['id']
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url_mapping[doc_id] = doc['url']
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# Create a summary prompt for each document
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summary_prompt = f"""Summarize this medical information in 2-3 sentences, focusing on details relevant to: "{user_query}"
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Document: {doc['title']}
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Content: {doc['content'][:1000]}...
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Summary:"""
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summary = self._call_llama(summary_prompt)
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doc_summaries.append(f"Document {doc_id}: {summary}")
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# Combine all summaries
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combined_summary = "\n\n".join(doc_summaries)
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return combined_summary, url_mapping
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except Exception as e:
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logger.error(f"Failed to summarize documents: {e}")
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return "", {}
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def _call_llama(self, prompt: str) -> str:
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"""Make API call to NVIDIA Llama model"""
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try:
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headers = {
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"Authorization": f"Bearer {self.api_key}",
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"Content-Type": "application/json"
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}
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payload = {
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"model": self.model,
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"messages": [
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{
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"role": "user",
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"content": prompt
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}
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],
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"temperature": 0.7,
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"max_tokens": 1000
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}
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response = requests.post(
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self.base_url,
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headers=headers,
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json=payload,
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timeout=30
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)
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response.raise_for_status()
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result = response.json()
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return result['choices'][0]['message']['content'].strip()
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except Exception as e:
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logger.error(f"Llama API call failed: {e}")
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raise
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def process_search_query(user_query: str, search_results: List[Dict]) -> Tuple[str, Dict[int, str]]:
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"""Process search results using Llama model"""
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try:
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llama_client = NVIDIALLamaClient()
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# Generate search keywords
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keywords = llama_client.generate_keywords(user_query)
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# Summarize documents
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summary, url_mapping = llama_client.summarize_documents(search_results, user_query)
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return summary, url_mapping
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except Exception as e:
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logger.error(f"Failed to process search query: {e}")
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| 122 |
+
return "", {}
|
requirements.txt
CHANGED
|
@@ -21,3 +21,6 @@ uvicorn
|
|
| 21 |
fastapi
|
| 22 |
torch # Reduce model load with half-precision (float16) to reduce RAM usage
|
| 23 |
psutil # CPU/RAM logger
|
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|
| 21 |
fastapi
|
| 22 |
torch # Reduce model load with half-precision (float16) to reduce RAM usage
|
| 23 |
psutil # CPU/RAM logger
|
| 24 |
+
# **Web Search**
|
| 25 |
+
requests
|
| 26 |
+
beautifulsoup4
|
search.py
ADDED
|
@@ -0,0 +1,134 @@
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|
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|
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|
|
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|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
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|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
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|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
|
| 1 |
+
import requests
|
| 2 |
+
from bs4 import BeautifulSoup
|
| 3 |
+
import re
|
| 4 |
+
from urllib.parse import urljoin, urlparse
|
| 5 |
+
import time
|
| 6 |
+
import logging
|
| 7 |
+
from typing import List, Dict, Tuple
|
| 8 |
+
import os
|
| 9 |
+
|
| 10 |
+
logger = logging.getLogger(__name__)
|
| 11 |
+
|
| 12 |
+
class WebSearcher:
|
| 13 |
+
def __init__(self):
|
| 14 |
+
self.session = requests.Session()
|
| 15 |
+
self.session.headers.update({
|
| 16 |
+
'User-Agent': 'Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/91.0.4472.124 Safari/537.36'
|
| 17 |
+
})
|
| 18 |
+
self.max_results = 10
|
| 19 |
+
self.timeout = 10
|
| 20 |
+
|
| 21 |
+
def search_google(self, query: str, num_results: int = 10) -> List[Dict]:
|
| 22 |
+
"""Search Google and return results with URLs and titles"""
|
| 23 |
+
try:
|
| 24 |
+
# Use DuckDuckGo as it's more reliable for scraping
|
| 25 |
+
return self.search_duckduckgo(query, num_results)
|
| 26 |
+
except Exception as e:
|
| 27 |
+
logger.error(f"Google search failed: {e}")
|
| 28 |
+
return []
|
| 29 |
+
|
| 30 |
+
def search_duckduckgo(self, query: str, num_results: int = 10) -> List[Dict]:
|
| 31 |
+
"""Search DuckDuckGo and return results"""
|
| 32 |
+
try:
|
| 33 |
+
url = "https://html.duckduckgo.com/html/"
|
| 34 |
+
params = {
|
| 35 |
+
'q': query,
|
| 36 |
+
'kl': 'us-en'
|
| 37 |
+
}
|
| 38 |
+
|
| 39 |
+
response = self.session.get(url, params=params, timeout=self.timeout)
|
| 40 |
+
response.raise_for_status()
|
| 41 |
+
|
| 42 |
+
soup = BeautifulSoup(response.content, 'html.parser')
|
| 43 |
+
results = []
|
| 44 |
+
|
| 45 |
+
# Find result links
|
| 46 |
+
result_links = soup.find_all('a', class_='result__a')
|
| 47 |
+
|
| 48 |
+
for link in result_links[:num_results]:
|
| 49 |
+
try:
|
| 50 |
+
href = link.get('href')
|
| 51 |
+
if href and href.startswith('http'):
|
| 52 |
+
title = link.get_text(strip=True)
|
| 53 |
+
if title and href:
|
| 54 |
+
results.append({
|
| 55 |
+
'url': href,
|
| 56 |
+
'title': title,
|
| 57 |
+
'content': '' # Will be filled later
|
| 58 |
+
})
|
| 59 |
+
except Exception as e:
|
| 60 |
+
logger.warning(f"Error parsing result: {e}")
|
| 61 |
+
continue
|
| 62 |
+
|
| 63 |
+
return results
|
| 64 |
+
|
| 65 |
+
except Exception as e:
|
| 66 |
+
logger.error(f"DuckDuckGo search failed: {e}")
|
| 67 |
+
return []
|
| 68 |
+
|
| 69 |
+
def extract_content(self, url: str) -> str:
|
| 70 |
+
"""Extract text content from a webpage"""
|
| 71 |
+
try:
|
| 72 |
+
response = self.session.get(url, timeout=self.timeout)
|
| 73 |
+
response.raise_for_status()
|
| 74 |
+
|
| 75 |
+
soup = BeautifulSoup(response.content, 'html.parser')
|
| 76 |
+
|
| 77 |
+
# Remove script and style elements
|
| 78 |
+
for script in soup(["script", "style"]):
|
| 79 |
+
script.decompose()
|
| 80 |
+
|
| 81 |
+
# Get text content
|
| 82 |
+
text = soup.get_text()
|
| 83 |
+
|
| 84 |
+
# Clean up text
|
| 85 |
+
lines = (line.strip() for line in text.splitlines())
|
| 86 |
+
chunks = (phrase.strip() for line in lines for phrase in line.split(" "))
|
| 87 |
+
text = ' '.join(chunk for chunk in chunks if chunk)
|
| 88 |
+
|
| 89 |
+
# Limit content length
|
| 90 |
+
if len(text) > 2000:
|
| 91 |
+
text = text[:2000] + "..."
|
| 92 |
+
|
| 93 |
+
return text
|
| 94 |
+
|
| 95 |
+
except Exception as e:
|
| 96 |
+
logger.warning(f"Failed to extract content from {url}: {e}")
|
| 97 |
+
return ""
|
| 98 |
+
|
| 99 |
+
def search_and_extract(self, query: str, num_results: int = 5) -> List[Dict]:
|
| 100 |
+
"""Search for query and extract content from top results"""
|
| 101 |
+
logger.info(f"Searching for: {query}")
|
| 102 |
+
|
| 103 |
+
# Get search results
|
| 104 |
+
search_results = self.search_duckduckgo(query, num_results)
|
| 105 |
+
|
| 106 |
+
# Extract content from each result
|
| 107 |
+
enriched_results = []
|
| 108 |
+
for i, result in enumerate(search_results):
|
| 109 |
+
try:
|
| 110 |
+
logger.info(f"Extracting content from {result['url']}")
|
| 111 |
+
content = self.extract_content(result['url'])
|
| 112 |
+
|
| 113 |
+
if content:
|
| 114 |
+
enriched_results.append({
|
| 115 |
+
'id': i + 1,
|
| 116 |
+
'url': result['url'],
|
| 117 |
+
'title': result['title'],
|
| 118 |
+
'content': content
|
| 119 |
+
})
|
| 120 |
+
|
| 121 |
+
# Add delay to be respectful
|
| 122 |
+
time.sleep(1)
|
| 123 |
+
|
| 124 |
+
except Exception as e:
|
| 125 |
+
logger.warning(f"Failed to process {result['url']}: {e}")
|
| 126 |
+
continue
|
| 127 |
+
|
| 128 |
+
logger.info(f"Successfully processed {len(enriched_results)} results")
|
| 129 |
+
return enriched_results
|
| 130 |
+
|
| 131 |
+
def search_web(query: str, num_results: int = 5) -> List[Dict]:
|
| 132 |
+
"""Main function to search the web and return enriched results"""
|
| 133 |
+
searcher = WebSearcher()
|
| 134 |
+
return searcher.search_and_extract(query, num_results)
|