app.py

import streamlit as st
import time
import json
from gensim.models import Word2Vec
import pandas as pd
import matplotlib.pyplot as plt
import squarify
import numpy as np
import re
import urllib.request
import random

st.set_page_config(
    page_title="FATA4 Science",
                page_icon=":microscope:",
                layout="wide",
                initial_sidebar_state="auto",
                menu_items={
                    'About': "FATA4 Science is a Natural Language Processing (NLP) that ...."
                }
                )

# Define the HTML and CSS styles
st.markdown("""
<style>
    [data-testid=stSidebar] {
        background-color: #99CCFF;
    }
</style>
""", unsafe_allow_html=True)
st.markdown("""
    <style>
    body {
        background-color: #CCFFFF;
        # color: #ffffff;
    }
    .stApp {
        background-color: #CCFFFF;
        # color: #ffffff;
    }
    </style>
    """, unsafe_allow_html=True)

opt=st.sidebar.radio("Select a PubMed Corpus", options=('Clotting corpus', 'Neuroblastoma corpus'))
if opt == "Clotting corpus":
    model_used = ("pubmed_model_clotting")
    num_abstracts = 45493
    database_name = "Clotting"
if opt == "Neuroblastoma corpus":
    model_used = ("pubmed_model_neuroblastoma")
    num_abstracts = 29032
    database_name = "Neuroblastoma"

st.title(":red[Fast Acting Text Analysis (FATA) 4 Science]")
st.markdown("---")
st.subheader("Uncovering knowledge through Natural Language Processing (NLP)")

st.header(f"{database_name} Pubmed corpus.")
text_input_value = st.text_input(f"Enter one term to search within the {database_name} corpus")
query = text_input_value
query = query.lower()
query = re.sub("[,.?!&*;:]", "", query)
matches = [" "]
if any([x in query for x in matches]):
    st.write("Please only enter one term or a term without spaces")
# query = input ("Enter your keyword(s):")
if query:
    bar = st.progress(0)
    time.sleep(.05)
    st.caption(f":LightSkyBlue[searching {num_abstracts} {database_name} PubMed abstracts] covering 1990-2022")

    for i in range(10):
        bar.progress((i + 1) * 10)
        time.sleep(.1)

    try:
        model = Word2Vec.load(model_used)  # you can continue training with the loaded model!
        words = list(model.wv.key_to_index)
        X = model.wv[model.wv.key_to_index]
        model2 = model.wv[query]
        df = pd.DataFrame(X)

    except:
        st.error("Term occurrence is too low - please try another term")
        st.stop()

    # def findRelationships(query, df):
    table = model.wv.most_similar_cosmul(query, topn=10000)
    table = (pd.DataFrame(table))
    table.index.name = 'Rank'
    table.columns = ['Word', 'SIMILARITY']
    print()
    print("Similarity to " + str(query))
    pd.set_option('display.max_rows', None)
    print(table.head(50))
    # table.head(10).to_csv("clotting_sim1.csv", index=True)
    # short_table = table.head(50)
    # print(table)
    st.subheader(f"Top 10 Words closely related to {query}")

    # calculate the sizes of the squares in the treemap
    short_table = table.head(10)
    short_table.index += 1
    short_table.index = 1 / short_table.index
    sizes = short_table.index.tolist()

    cmap = plt.cm.Greens(np.linspace(0.05, .5, len(sizes)))
    color = [cmap[i] for i in range(len(sizes))]

    short_table.set_index('Word', inplace=True)
    squarify.plot(sizes=sizes, label=short_table.index.tolist(), color=color, edgecolor="#EBF5FB",
                  text_kwargs={'fontsize': 10})
    # # plot the treemap using matplotlib
    plt.axis('off')
    fig = plt.gcf()
    fig.patch.set_facecolor('#CCFFFF')
    # # display the treemap in Streamlit
    st.pyplot(fig)
    plt.clf()

    csv = table.head(100).to_csv().encode('utf-8')
    st.download_button(label="download top 100 words (csv)", data=csv, file_name=f'{database_name}_words.csv', mime='text/csv')

    # st.write(short_table)
    #

    print()
    print("Human genes similar to " + str(query))
    df1 = table
    df2 = pd.read_csv('Human_Genes.csv')
    m = df1.Word.isin(df2.symbol)
    df1 = df1[m]
    df1.rename(columns={'Word': 'Human Gene'}, inplace=True)
    df1["Human Gene"] = df1["Human Gene"].str.upper()
    print(df1.head(50))
    print()
    # df1.head(50).to_csv("clotting_sim2.csv", index=True, header=False)
    # time.sleep(2)
    st.subheader(f"Top 10 Genes closely related to {query}")

    df10 = df1.head(10)
    df10.index = 1 / df10.index
    sizes = df10.index.tolist()

    cmap2 = plt.cm.Blues(np.linspace(0.05, .5, len(sizes)))
    color2 = [cmap2[i] for i in range(len(sizes))]

    df10.set_index('Human Gene', inplace=True)
    squarify.plot(sizes=sizes, label=df10.index.tolist(), color=color2, edgecolor="#EBF5FB",
                  text_kwargs={'fontsize': 12})
    #
    # # plot the treemap using matplotlib

    plt.axis('off')
    fig2 = plt.gcf()
    fig2.patch.set_facecolor('#CCFFFF')
    # plt.show()
    #
    # # display the treemap in Streamlit
    st.pyplot(fig2)

    csv = df1.head(100).to_csv().encode('utf-8')
    st.download_button(label="download top 100 genes (csv)", data=csv, file_name=f'{database_name}_genes.csv',
                       mime='text/csv')

    if query:
        idlist=[]
        search_keyword = {query}
        html = urllib.request.urlopen("https://www.youtube.com/@NCIgov/search?query=cancer")
        html2 = urllib.request.urlopen("https://www.youtube.com/@CancerCenter/search?query=cancer")
        html3 = urllib.request.urlopen("https://www.youtube.com/@NorthwesternMedicine/search?query=cancer")
        html4 = urllib.request.urlopen("https://www.youtube.com/@TEDEd/search?query=cancer")
        html5 = urllib.request.urlopen("https://www.youtube.com/@CancerResearchUK/search?query=cancer")
        video_ids = re.findall(r"watch\?v=(\S{11})", html.read().decode())
        video_ids2 = re.findall(r"watch\?v=(\S{11})", html2.read().decode())
        video_ids3 = re.findall(r"watch\?v=(\S{11})", html3.read().decode())
        video_ids4 = re.findall(r"watch\?v=(\S{11})", html4.read().decode())
        video_ids5 = re.findall(r"watch\?v=(\S{11})", html5.read().decode())

        for i in video_ids2:
            video_ids.append(i)
        for i in video_ids3:
            video_ids.append(i)
        for i in video_ids4:
            video_ids.append(i)
        for i in video_ids5:
            video_ids.append(i)

        random.shuffle(video_ids)

        c1, c2, c3 = st.columns(3)
        with c1:
           st.video("https://www.youtube.com/watch?v=" + video_ids[0])
        with c2:
           st.video("https://www.youtube.com/watch?v=" + video_ids[1])
        with c3:
           st.video("https://www.youtube.com/watch?v=" + video_ids[2])
            # width = 40
            # side = 30  # (100-width)/2
            # _, container, _ = st.columns([side, width, side])
            # container.video(data=VIDEO_DATA)

            # VIDEO_DATA = "https://www.youtube.com/watch?v=" + video_ids[1]
            # width = 40
            # side = 30  # (100-width)/2
            # _, container, _ = st.columns([side, width, side])
            # container.video(data=VIDEO_DATA)

            # VIDEO_DATA = "https://www.youtube.com/watch?v=" + video_ids[2]
            # width = 40
            # side = 30  # (100-width)/2
            # _, container, _ = st.columns([side, width, side])
            # container.video(data=VIDEO_DATA)