import streamlit as st from streamlit_agraph import agraph, Node, Edge, Config import os from sqlalchemy import create_engine, text import pandas as pd from utils import get_all_diseases_name, get_most_similar_diseases_from_uri, get_uri_from_name import json username = 'demo' password = 'demo' hostname = os.getenv('IRIS_HOSTNAME', 'localhost') port = '1972' namespace = 'USER' CONNECTION_STRING = f"iris://{username}:{password}@{hostname}:{port}/{namespace}" engine = create_engine(CONNECTION_STRING) def handle_click_on_analyze_button(): # 1. Embed the textual description that the user entered using the model () # 2. Get 5 diseases with the highest cosine silimarity from the DB # 3. Get the similarities of the embeddings of those diseases (cosine similarity of the embeddings of the nodes of such diseases) # 4. Potentially filter out the diseases that are not similar enough (e.g. similarity < 0.8) # 5. Augment the set of diseases: add new diseases that are similar to the ones that are already in the set, until we get 10-15 diseases # 6. Query the embeddings of the diseases related to each clinical trial (also in the DB), to get the most similar clinical trials to our set of diseases # 7. Use an LLM to get a summary of the clinical trials, in plain text format # 8. Use an LLM to extract numerical data from the clinical trials (e.g. number of patients, number of deaths, etc.). Get summary statistics out of that. # 9. Show the results to the user: graph of the diseases chosen, summary of the clinical trials, summary statistics of the clinical trials, and list of the details of the clinical trials considered pass st.write("# Klìnic") description_input = st.text_input(label="Enter the disease description 👇") st.write(":red[Here should be the graph]") # TODO remove chart_data = pd.DataFrame( np.random.randn(20, 3), columns=["a", "b", "c"] ) # TODO remove st.scatter_chart(chart_data) # TODO remove st.write("## Disease Overview") disease_overview = ":red[lorem ipsum]" # TODO st.write(disease_overview) st.write("## Clinical Trials Details") trials = [] # TODO replace mock data with open("mock_trial.json") as f: d = json.load(f) for i in range(0, 5): trials.append(d) for trial in trials: with st.expander(f"{trial['protocolSection']['identificationModule']['nctId']}"): official_title = trial["protocolSection"]["identificationModule"][ "officialTitle" ] st.write(f"##### {official_title}") brief_summary = trial["protocolSection"]["descriptionModule"]["briefSummary"] st.write(brief_summary) status_module = { "Status": trial["protocolSection"]["statusModule"]["overallStatus"], "Status Date": trial["protocolSection"]["statusModule"][ "statusVerifiedDate" ], } st.write("###### Status") st.table(status_module) design_module = { "Study Type": trial["protocolSection"]["designModule"]["studyType"], # "Phases": trial["protocolSection"]["designModule"]["phases"], # breaks formatting because it is an array "Allocation": trial["protocolSection"]["designModule"]["designInfo"][ "allocation" ], "Participants": trial["protocolSection"]["designModule"]["enrollmentInfo"][ "count" ], } st.write("###### Design") st.table(design_module) # TODO more modules?