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app.py

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+import os
+import requests
+import tellurium as te
+import tempfile
+import ollama
+import streamlit as st
+from langchain_text_splitters import CharacterTextSplitter
+import chromadb
+
+# Constants and global variables
+GITHUB_OWNER = "sys-bio"
+GITHUB_REPO_CACHE = "BiomodelsCache"
+BIOMODELS_JSON_DB_PATH = "src/cached_biomodels.json"
+LOCAL_DOWNLOAD_DIR = tempfile.mkdtemp()
+
+cached_data = None
+db = None
+
+def fetch_github_json():
+    url = f"https://api.github.com/repos/{GITHUB_OWNER}/{GITHUB_REPO_CACHE}/contents/{BIOMODELS_JSON_DB_PATH}"
+    headers = {"Accept": "application/vnd.github+json"}
+    response = requests.get(url, headers=headers)
+    
+    if response.status_code == 200:
+        data = response.json()
+        if "download_url" in data:
+            file_url = data["download_url"]
+            json_response = requests.get(file_url)
+            return json_response.json()
+        else:
+            raise ValueError(f"Unable to fetch model DB from GitHub repository: {GITHUB_OWNER} - {GITHUB_REPO_CACHE}")
+    else:
+        raise ValueError(f"Unable to fetch model DB from GitHub repository: {GITHUB_OWNER} - {GITHUB_REPO_CACHE}")
+
+def search_models(search_str):
+    global cached_data
+    if cached_data is None:
+        cached_data = fetch_github_json()
+    
+    query_text = search_str.strip().lower()
+    models = {}
+    
+    for model_id, model_data in cached_data.items():
+        if 'name' in model_data:
+            name = model_data['name'].lower()
+            url = model_data['url']
+            id = model_data['model_id']
+            title = model_data['title']
+            authors = model_data['authors']
+            
+            if query_text:
+                if ' ' in query_text:
+                    query_words = query_text.split(" ")
+                    if all(word in ' '.join([str(v).lower() for v in model_data.values()]) for word in query_words):
+                        models[model_id] = {
+                            'ID': model_id,
+                            'name': name,
+                            'url': url,
+                            'id': id,
+                            'title': title,
+                            'authors': authors,
+                        }
+                else:
+                    if query_text in ' '.join([str(v).lower() for v in model_data.values()]):
+                        models[model_id] = {
+                            'ID': model_id,
+                            'name': name,
+                            'url': url,
+                            'id': id,
+                            'title': title,
+                            'authors': authors,
+                        }
+    
+    return models
+
+def download_model_file(model_url, model_id):
+    model_url = f"https://raw.githubusercontent.com/konankisa/BiomodelsStore/main/biomodels/{model_id}/{model_id}_url.xml"
+    response = requests.get(model_url)
+    
+    if response.status_code == 200:
+        os.makedirs(LOCAL_DOWNLOAD_DIR, exist_ok=True)
+        file_path = os.path.join(LOCAL_DOWNLOAD_DIR, f"{model_id}.xml")
+        
+        with open(file_path, 'wb') as file:
+            file.write(response.content)
+        
+        print(f"Model {model_id} downloaded successfully: {file_path}")
+        return file_path
+    else:
+        raise ValueError(f"Failed to download the model from {model_url}")
+
+def convert_sbml_to_antimony(sbml_file_path, antimony_file_path):
+    try:
+        r = te.loadSBMLModel(sbml_file_path)
+        antimony_str = r.getCurrentAntimony()
+        
+        with open(antimony_file_path, 'w') as file:
+            file.write(antimony_str)
+        
+        print(f"Successfully converted SBML to Antimony: {antimony_file_path}")
+    
+    except Exception as e:
+        print(f"Error converting SBML to Antimony: {e}")
+
+def split_biomodels(antimony_file_path):
+    text_splitter = CharacterTextSplitter(
+        separator="  // ",
+        chunk_size=1000,
+        chunk_overlap=20,
+        length_function=len,
+        is_separator_regex=False
+    )
+    
+    final_items = []
+    directory_path = os.path.dirname(os.path.abspath(antimony_file_path))
+    if not os.path.isdir(directory_path):
+        print(f"Directory not found: {directory_path}")
+        return final_items
+
+    files = os.listdir(directory_path)
+    for file in files:
+        file_path = os.path.join(directory_path, file)
+        try:
+            with open(file_path, 'r') as f:
+                file_content = f.read()
+                items = text_splitter.create_documents([file_content])
+                for item in items:
+                    final_items.append(item)
+                break
+        except Exception as e:
+            print(f"Error reading file {file_path}: {e}")
+
+    return final_items
+
+def create_vector_db(final_items):
+    global db
+    client = chromadb.Client()
+    db = client.create_collection(
+        name="BioModelsRAG",
+        metadata={"hnsw:space": "cosine"}
+    )
+    documents = []
+    
+    for item in final_items:
+        prompt = f"""
+        Summarize the following segment of Antimony in a clear and concise manner:
+        1. Provide a detailed summary using a limited number of words
+        2. Maintain all original values and include any mathematical expressions or values in full. 
+        3. Ensure that all variable names and their values are clearly presented. 
+        4. Write the summary in paragraph format, putting an emphasis on clarity and completeness. 
+        
+        Here is the antimony segment to summarize: {item}
+        """
+        documents5 = ollama.generate(model="llama3", prompt=prompt)
+        documents2 = documents5['response']
+        documents.append(documents2)
+    
+    if final_items:
+        db.add(
+            documents=documents,
+            ids=[f"id{i}" for i in range(len(final_items))]
+        )
+    return db
+
+def generate_response(db, query_text, previous_context):
+    query_results = db.query(
+        query_texts=query_text,
+        n_results=5,
+    )
+    
+    if not query_results.get('documents'):
+        return "No results found."
+    
+    best_recommendation = query_results['documents']
+    
+    prompt_template = f"""
+    Using the context provided below, answer the following question. If the information is insufficient to answer the question, please state that clearly. 
+    
+    Context:
+    {previous_context} {best_recommendation}
+    
+    Instructions:
+    1. Cross-Reference: Use all provided context to define variables and identify any unknown entities. 
+    2. Mathematical Calculations: Perform any necessary calculations based on the context and available data. 
+    3. Consistency: Remember and incorporate previous responses if the question is related to earlier information. 
+    
+    Question: 
+    {query_text}
+
+    """
+    response = ollama.generate(model="llama3", prompt=prompt_template)
+    final_response = response.get('response', 'No response generated')
+    return final_response
+
+def streamlit_app():
+    st.title("BioModels Chat Interface")
+    
+    search_str = st.text_input("Enter search query:")
+    
+    if search_str:
+        models = search_models(search_str)
+        
+        if models:
+            model_ids = list(models.keys())
+            selected_models = st.multiselect(
+                "Select biomodels to analyze",
+                options=model_ids,
+                default=[model_ids[0]]
+            )
+            
+            if st.button("Analyze Selected Models"):
+                all_final_items = []
+                for model_id in selected_models:
+                    model_data = models[model_id]
+                    
+                    st.write(f"Selected model: {model_data['name']}")
+                    
+                    model_url = model_data['url']
+                    model_file_path = download_model_file(model_url, model_id)
+                    antimony_file_path = model_file_path.replace(".xml", ".antimony")
+                    
+                    convert_sbml_to_antimony(model_file_path, antimony_file_path)
+                    
+                    final_items = split_biomodels(antimony_file_path)
+                    if not final_items:
+                        st.write("No content found in the biomodel.")
+                        continue
+                    
+                    all_final_items.extend(final_items)
+                
+                global db
+                db = create_vector_db(all_final_items)
+                
+                if db:
+                    st.write("Models have been processed and added to the database.")
+                    
+                    user_query = st.text_input("Ask a question about the biomodels:")
+                    
+                    if user_query:
+                        if 'previous_context' not in st.session_state:
+                            st.session_state.previous_context = ""
+                        
+                        response = generate_response(db, user_query, st.session_state.previous_context)
+                        st.write(f"Response: {response}")
+                        
+                        st.session_state.previous_context += f"{response}\n"
+        else:
+            st.write("No models found for the given search query.")
+
+if __name__ == "__main__":
+    streamlit_app()

requirements.txt

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+requests==2.32.2
+tellurium==2.2.10
+ollama==0.3.2
+streamlit==1.23.0
+langchain-text-splitters==0.2.4
+chromadb==0.5.5