app.py

import re
import uuid

import pandas as pd
import streamlit as st
import re
import matplotlib.pyplot as plt

import subprocess
import sys
import io

from utils.default_values import get_system_prompt, get_guidelines_dict
from utils.epfl_meditron_utils import get_llm_response, gptq_model_options
from utils.openai_utils import get_available_engines, get_search_query_type_options

from sklearn.metrics import confusion_matrix, ConfusionMatrixDisplay
from sklearn.metrics import classification_report

DATA_FOLDER = "data/"

POC_VERSION = "0.1.0"
MAX_QUESTIONS = 10
AVAILABLE_LANGUAGES = ["DE", "EN", "FR"]

st.set_page_config(page_title='Medgate Whisper PoC', page_icon='public/medgate.png')

# Azure apparently truncates message if longer than 200, see
MAX_SYSTEM_MESSAGE_TOKENS = 200


def format_question(q):
    res = q

    # Remove numerical prefixes, if any, e.g. '1. [...]'
    if re.match(r'^[0-9].\s', q):
        res = res[3:]

    # Replace doc reference by doc name
    if len(st.session_state["citations"]) > 0:
        for source_ref in re.findall(r'\[doc[0-9]+\]', res):
            citation_number = int(re.findall(r'[0-9]+', source_ref)[0])
            citation_index = citation_number - 1 if citation_number > 0 else 0
            citation = st.session_state["citations"][citation_index]
            source_title = citation["title"]
            res = res.replace(source_ref, '[' + source_title + ']')

    return res.strip()


def get_text_from_row(text):
    res = str(text)
    if res == "nan":
        return ""
    return res
def get_questions_from_df(df, lang, test_scenario_name):
    questions = []
    for i, row in df.iterrows():
        questions.append({
            "question": row[lang + ": Fragen"],
            "answer": get_text_from_row(row[test_scenario_name]),
            "question_id": uuid.uuid4()
        })
    return questions


def get_questions(df, lead_symptom, lang, test_scenario_name):
    print(str(st.session_state["lead_symptom"]) + " -> " + lead_symptom)
    print(str(st.session_state["scenario_name"]) + " -> " + test_scenario_name)
    if st.session_state["lead_symptom"] != lead_symptom or st.session_state["scenario_name"] != test_scenario_name:
        st.session_state["lead_symptom"] = lead_symptom
        st.session_state["scenario_name"] = test_scenario_name
        symptom_col_name = st.session_state["language"] + ": Symptome"
        df_questions = df[(df[symptom_col_name] == lead_symptom)]
        st.session_state["questions"] = get_questions_from_df(df_questions, lang, test_scenario_name)

    return st.session_state["questions"]


def display_streamlit_sidebar():
    st.sidebar.title("Local LLM PoC " + str(POC_VERSION))

    st.sidebar.write('**Parameters**')
    form = st.sidebar.form("config_form", clear_on_submit=True)

    model_name_or_path = form.selectbox("Select model", gptq_model_options())
    
    temperature = form.slider(label="Temperature", min_value=0.0, max_value=1.0, step=0.01, value=0.01)
    do_sample = form.checkbox('do_sample')
    top_p = form.slider(label="top_p", min_value=0.0, max_value=1.0, step=0.01, value=0.95)
    top_k = form.slider(label="top_k", min_value=1, max_value=1000, step=1, value=40)
    max_new_tokens = form.slider(label="max_new_tokens", min_value=32, max_value=512, step=1, value=32)
    repetition_penalty = form.slider(label="repetition_penalty", min_value=0.0, max_value=1.0, step=0.01, value=0.95)
    
    temperature = form.slider('Temperature (0 = deterministic, 1 = more freedom)', min_value=0.0,
                              max_value=1.0, value=st.session_state['temperature'], step=0.1)
    
    top_p = form.slider('top_p (0 = focused, 1 = broader answer range)', min_value=0.0,
                        max_value=1.0, value=st.session_state['top_p'], step=0.1)

    form.write('Best practice is to only modify temperature or top_p, not both')

    submitted = form.form_submit_button("Start session")
    if submitted and not st.session_state['session_started']:
        print('Parameters updated...')
        st.session_state['session_started'] = True

        st.session_state["session_events"] = []
        st.session_state["model_name_or_path"] = model_name_or_path
        st.session_state["temperature"] = temperature
        st.session_state["do_sample"] = do_sample
        st.session_state["top_p"] = top_p
        st.session_state["top_k"] = top_k
        st.session_state["max_new_tokens"] = max_new_tokens
        st.session_state["repetition_penalty"] = repetition_penalty

        st.rerun()


def to_str(text):
    res = str(text)
    if res == "nan":
        return " "
    return " " + res


def set_df_prompts(path, sheet_name):
    df_prompts = pd.read_excel(path, sheet_name, header=None)
    for i in range(3, df_prompts.shape[0]):
        df_prompts.iloc[2] += df_prompts.iloc[i].apply(to_str)

    df_prompts = df_prompts.T
    df_prompts = df_prompts[[0, 1, 2]]
    df_prompts[0] = df_prompts[0].astype(str)
    df_prompts[1] = df_prompts[1].astype(str)
    df_prompts[2] = df_prompts[2].astype(str)

    df_prompts.columns = ["Questionnaire", "Used Guideline", "Prompt"]
    df_prompts = df_prompts[1:]
    st.session_state["df_prompts"] = df_prompts


def handle_nbq_click(c):
    question_without_source = re.sub(r'\[.*\]', '', c)
    question_without_source = question_without_source.strip()
    st.session_state['doctor_question'] = question_without_source


def get_doctor_question_value():
    if 'doctor_question' in st.session_state:
        return st.session_state['doctor_question']

    return ''


def update_chat_history(dr_question, patient_reply):
    print("update_chat_history" + str(dr_question) + " - " + str(patient_reply) + '...\n')
    if dr_question is not None:
        dr_msg = {
            "role": "Doctor",
            "content": dr_question
        }
        st.session_state["chat_history_array"].append(dr_msg)

    if patient_reply is not None:
        patient_msg = {
            "role": "Patient",
            "content": patient_reply
        }
        st.session_state["chat_history_array"].append(patient_msg)

    return st.session_state["chat_history_array"]


def get_chat_history_string(chat_history):
    res = ''
    for i in chat_history:
        if i["role"] == "Doctor":
            res += '**Doctor**: ' + str(i["content"].strip()) + "  \n  "
        elif i["role"] == "Patient":
            res += '**Patient**: ' + str(i["content"].strip()) + "  \n\n  "
        else:
            raise Exception('Unknown role: ' + str(i["role"]))

    return res
      

def init_session_state():
    print('init_session_state()')
    st.session_state['session_started'] = False
    st.session_state["session_events"] = []
    st.session_state["model_name_or_path"] = "TheBloke/meditron-7B-GPTQ"
    st.session_state["temperature"] = 0.01
    st.session_state["do_sample"] = True
    st.session_state["top_p"] = 0.95
    st.session_state["top_k"] = 40
    st.session_state["max_new_tokens"] = 512
    st.session_state["repetition_penalty"] = 1.1
    st.session_state["system_message"] = "You are a medical expert that provides answers for a medically trained audience"  

def get_genders():
    return ['Male', 'Female']





def display_session_overview():
    st.subheader('History of LLM queries')
    st.write(st.session_state["llm_messages"])
    st.subheader("Session costs overview")

    df_session_overview = pd.DataFrame.from_dict(st.session_state["session_events"])
    st.write(df_session_overview)

    if "prompt_tokens" in df_session_overview:
        prompt_tokens = df_session_overview["prompt_tokens"].sum()
        st.write("Prompt tokens: " + str(prompt_tokens))

        prompt_cost = df_session_overview["prompt_cost_chf"].sum()
        st.write("Prompt CHF: " + str(prompt_cost))

        completion_tokens = df_session_overview["completion_tokens"].sum()
        st.write("Completion tokens: " + str(completion_tokens))

        completion_cost = df_session_overview["completion_cost_chf"].sum()
        st.write("Completion CHF: " + str(completion_cost))

        completion_cost = df_session_overview["total_cost_chf"].sum()
        st.write("Total costs CHF: " + str(completion_cost))

        total_time = df_session_overview["response_time"].sum()
        st.write("Total compute time (ms): " + str(total_time))


def remove_question(question_id):
    st.session_state["questions"] = [value for value in st.session_state["questions"] if
                                     str(value["question_id"]) != str(question_id)]
    st.rerun()


def get_prompt_from_lead_symptom(df_config, df_prompt, lead_symptom, lang, fallback=True):
    de_lead_symptom = lead_symptom

    if lang != "DE":
        df_lead_symptom = df_config[df_config[lang + ": Symptome"] == lead_symptom]
        de_lead_symptom = df_lead_symptom["DE: Symptome"].iloc[0]
        print("DE lead symptom: " + de_lead_symptom)

    for i, row in df_prompt.iterrows():
        if de_lead_symptom in row["Questionnaire"]:
            return row["Prompt"]

    warning_text = "No guidelines found for lead symptom " + lead_symptom + " (" + de_lead_symptom + ")"
    if fallback:
        st.toast(warning_text + ", using generic prompt", icon='🚨')
        return st.session_state["system_prompt"]
    st.toast(warning_text, icon='🚨')

    return ""


def get_scenarios(df):
    return [v for v in df.columns.values if v.startswith('TLC') or v.startswith('GP')]


def get_gender_age_from_test_scenario(test_scenario):
    try:
        result = re.search(r"([FM])(\d+)", test_scenario)
        res_age = int(result.group(2))
        gender = result.group(1)
        res_gender = None
        if gender == "M":
            res_gender = "Male"
        elif gender == "F":
            res_gender = "Female"
        else:
            raise Exception('Unexpected gender')

        return res_gender, res_age

    except:
        st.error("Unable to extract name, gender; using 30M as default")
        return "Male", 30

def get_freetext_to_reco(reco_freetext_cased, emg_class_enabled=False):
    reco_freetext = ""
    if reco_freetext_cased:
        reco_freetext = reco_freetext_cased.lower()

    if reco_freetext.startswith('treat remotely') or reco_freetext.startswith('telecare'):
        return 'TELECARE'
    if reco_freetext.startswith('treat ad-real') or reco_freetext.startswith('gp') \
            or reco_freetext.startswith('general practitioner'):
        return 'GP'
    if reco_freetext.startswith('emergency') or reco_freetext.startswith('emg') \
            or reco_freetext.startswith('urgent'):
        if emg_class_enabled:
            return 'EMERGENCY'
        return 'GP'

    if "gp" in reco_freetext or 'general practitioner' in reco_freetext \
            or "nicht über tele" in reco_freetext or 'durch einen arzt erford' in reco_freetext \
            or "persönliche untersuchung erfordert" in reco_freetext:
        return 'GP'

    if ("telecare" in reco_freetext or 'telemed' in reco_freetext or
            'can be treated remotely' in reco_freetext):
        return 'TELECARE'

    if ('emergency' in reco_freetext or 'urgent' in reco_freetext or
            'not be treated remotely' in reco_freetext or "nicht tele" in reco_freetext):
        return 'GP'

    warning_msg = 'Cannot extract reco from LLM text: ' + reco_freetext
    st.toast(warning_msg)
    print(warning_msg)
    return 'TRIAGE_IMPOSSIBLE'


def get_structured_reco(row, index, emg_class_enabled):
    freetext_reco_col_name = "llm_reco_freetext_" + str(index)
    freetext_reco = row[freetext_reco_col_name].lower()
    return get_freetext_to_reco(freetext_reco, emg_class_enabled)


def add_expected_dispo(row, emg_class_enabled):
    disposition = row["disposition"]
    if disposition == "GP" or disposition == "TELECARE":
        return disposition
    if disposition == "EMERGENCY":
        if emg_class_enabled:
            return "EMERGENCY"
        return "GP"

    raise Exception("Missing disposition for row " + str(row.name) + " with summary " + row["case_summary"])


def get_test_scenarios(df):
    res = []
    for col in df.columns.values:
        if str(col).startswith('GP') or str(col).startswith('TLC'):
            res.append(col)
    return res


def get_transcript(df, test_scenario, lang):
    transcript = ""
    for i, row in df.iterrows():
        transcript += "\nDoctor: " + row[lang + ": Fragen"]
        transcript += ", Patient: " + str(row[test_scenario])
    return transcript


def get_expected_from_scenario(test_scenario):
    reco = test_scenario.split('_')[0]
    if reco == "GP":
        return "GP"
    elif reco == "TLC":
        return "TELECARE"
    else:
        raise Exception('Unexpected reco: ' + reco)


def plot_report(title, expected, predicted, display_labels):
    st.markdown('#### ' + title)
    conf_matrix = confusion_matrix(expected, predicted, labels=display_labels)
    conf_matrix_plot = ConfusionMatrixDisplay(confusion_matrix=conf_matrix, display_labels=display_labels)
    conf_matrix_plot.plot()
    st.pyplot(plt.gcf())

    report = classification_report(expected, predicted, output_dict=True)
    df_report = pd.DataFrame(report).transpose()
    st.write(df_report)

    df_rp = df_report
    df_rp = df_rp.drop('support', axis=1)
    df_rp = df_rp.drop(['accuracy', 'macro avg', 'weighted avg'])

    try:
        ax = df_rp.plot(kind="bar", legend=True)
        for container in ax.containers:
            ax.bar_label(container, fontsize=7)
        plt.xticks(rotation=45)
        plt.legend(loc=(1.04, 0))
        st.pyplot(plt.gcf())
    except Exception as e:
        # Out of bounds
        pass


def get_complete_prompt(generic_prompt, guidelines_prompt):
    complete_prompt = ""
    if generic_prompt:
        complete_prompt += generic_prompt

    if generic_prompt and guidelines_prompt:
        complete_prompt += ".\n\n"

    if guidelines_prompt:
        complete_prompt += guidelines_prompt

    return complete_prompt


def run_command(args):
    """Run command, transfer stdout/stderr back into Streamlit and manage error"""
    cmd = ' '.join(args)
    result = subprocess.run(cmd, capture_output=True, text=True)
    print(result)

def get_diarized_f_path(audio_f_name):
    # TODO p2: Quick hack, cleaner with os or regexes
    base_name = audio_f_name.split('.')[0]
    return DATA_FOLDER + base_name + ".txt"


def get_prompt_format(model_name):
    if model_name == "TheBloke/Llama-2-13B-chat-GPTQ":
        return '''[INST] <<SYS>>
        You are a helpful, respectful and honest assistant. Always answer as helpfully as possible, while being safe.  Your answers should not include any harmful, unethical, racist, sexist, toxic, dangerous, or illegal content. Please ensure that your responses are socially unbiased and positive in nature. If a question does not make any sense, or is not factually coherent, explain why instead of answering something not correct. If you don't know the answer to a question, please don't share false information.
        <</SYS>>
        {prompt}[/INST]

        '''
    if model_name == "TheBloke/Llama-2-7B-Chat-GPTQ":
        return "[INST] <<SYS>>＼nYou are a helpful, respectful and honest assistant. Always answer as helpfully as possible, while being safe.  Your answers should not include any harmful, unethical, racist, sexist, toxic, dangerous, or illegal content. Please ensure that your responses are socially unbiased and positive in nature. If a question does not make any sense, or is not factually coherent, explain why instead of answering something not correct. If you don't know the answer to a question, please don't share false information.＼n<</SYS>>＼n{prompt}[/INST]"
    
    if model_name == "TheBloke/meditron-7B-GPTQ" or model_name == "TheBloke/meditron-70B-GPTQ":
        return '''<|im_start|>system
        {system_message}<|im_end|>
        <|im_start|>user
        {prompt}<|im_end|>
        <|im_start|>assistant'''
    
    return ""

def format_prompt(template, system_message, prompt):
    if template == "":
        return f"{system_message} {prompt}"
    return template.format(system_message=system_message, prompt=prompt)

def display_llm_output():
    st.header("LLM")

    form = st.form('llm')

    prompt_format_str = get_prompt_format(st.session_state["model_name_or_path"])
    prompt_format = form.text_area('Prompt format', value=prompt_format_str)
    system_prompt = form.text_area('System prompt', value=st.session_state["system_prompt"])
    prompt = form.text_area('Prompt', value=st.session_state["prompt"])

    submitted = form.form_submit_button('Submit')

    if submitted:
        formatted_prompt = format_prompt(prompt_format, system_prompt, prompt)
        print(f"Formatted prompt: {format_prompt}")
        llm_response = get_llm_response(
            st.session_state["model_name"],
            st.session_state["temperature"],
            st.session_state["do_sample"],
            st.session_state["top_p"],
            st.session_state["top_k"],
            st.session_state["max_new_tokens"],
            st.session_state["repetition_penalty"],
            formatted_prompt)
        st.write(llm_response)
        st.write('Done displaying LLM response')

def main():
    print('Running Local LLM PoC Streamlit app...')
    session_inactive_info = st.empty()
    if "session_started" not in st.session_state or not st.session_state["session_started"]:
        init_session_state()
        display_streamlit_sidebar()
    else:
        display_streamlit_sidebar()
        session_inactive_info.empty()
        display_llm_output()
        display_session_overview()


if __name__ == '__main__':
    main()