source_code_plant_search_gui.py

import PySimpleGUI as sg
from Bio import Entrez
import datetime
import os
import time
import sys
import re
from http.client import IncompleteRead

# Change Search choice to listbox
   

def program_run():

    # directory settings

    
    cwd = os.getcwd()
    original_dir = os.getcwd()
    drive_letter = '1'
    drive_let = 'D'
   
    
    # Read the contents of the text file
    try:
        folderpathGoogle = os.path.join(cwd, 'plant_search_text_files', 'drive.txt')
    except:
        pass
    try:
        with open(folderpathGoogle, 'r') as file:
            contents = file.read()
            
        contents = contents.replace(" ", "")
        
        if ':' in contents:
            drive_let = contents[0].upper()
            drive_letter = contents[0].upper() + ':\\My Drive'
    except:
            pass
    
    # set which save radio button is checked by default
    if drive_letter == '1':
        radio_button1_default= True
        radio_button2_default= False
    else:
        radio_button1_default= False
        radio_button2_default= True    
    

    

    # Construct the full path to the default email file
    folderpath1 = os.path.join(cwd, 'plant_search_text_files', 'email.txt')

    try:
        # open plant_search_text_files/email.txt and read the email address
        with open(folderpath1, 'r') as f:
            previous_value = f.read().strip()
            
    except FileNotFoundError:
        previous_value = ''

    #Set theme to light green
    sg.theme('LightGreen3')

    # Set default fontsize to 32
    sg.set_options(font=("Helvecta", 32))

    # Set listbox search choices
    choices = ['plant genera', 'phytochemicals', 'both', 'human genes (non plant search)']

    # Set layout of the GUI
    layout = [
        [sg.Listbox(choices, size=(30, 4), key='-CHOICE-', enable_events=True, default_values=['plant genera']),
        sg.Text('What is your email address?'), sg.InputText(default_text=previous_value, key='-EMAIL-')],
        [sg.Text('Enter additional non-plant search terms:'), sg.InputText(key='-USER_QUERY-')],
        # add checkbox
        [sg.Checkbox('Open saved_search txt output folder when finished', default=True, key='-OPENFI-', font=('Helvetica 16')), 
         sg.Radio('Save output locally', "RADIO1", default=radio_button1_default, key='-LOCAL-', font=('Helvetica 16')), 
         sg.Radio('Save output in Google Drive', "RADIO1", default=radio_button2_default, key='-CLOUD-', font=('Helvetica 16')), 
         sg.InputText(default_text=drive_let, size=(2,2), key='-DRIV-', font=('Helvetica 16')), 
         sg.Text('<-Google Drive Letter (ex. F)', font=('Helvetica 16'))],
        [sg.Button('Search', bind_return_key=True), sg.Output(size=(300, 3), key='-OUTPUT-', font=('Helvetica 10')) ],
        # add multiline
        [sg.Multiline(size=(80, 5), key='-OUTPUT2-', auto_refresh=True,reroute_stdout=True, autoscroll=True)],
        
    ]



    window = sg.Window('EntrezPlantSearch', layout, size=(None, None), resizable=True)

    
    drive1 = None 
    email = None
    choice = None
    user_query = None
    checkedfi = None

    while True:
        event, values = window.read()
        if event == sg.WIN_CLOSED:
            # Exit the program
            sys.exit()

        if event == 'Search':
            selected_choice = values['-CHOICE-'][0]
            index = choices.index(selected_choice)
            choice = index + 1 
            email = values['-EMAIL-']
            user_query = values['-USER_QUERY-']
            checkedfi = values['-OPENFI-']
            drive1 = values['-DRIV-']
            local1 = values['-LOCAL-']
            cloud1 = values['-CLOUD-']
            break

    
            
    # Set Google Drive directory if chosen:
    try:
        os.chdir(drive_letter)
    except:
        pass
    if local1 == True:
        os.chdir(original_dir)
    if cloud1 == True:
        drive_letter = drive1 + ':\\My Drive'
        os.chdir(drive_letter)

    window['-OUTPUT-'].update(value='Working Directory: ' + os.getcwd())
    
    # # Email address is required by NCBI
    Entrez.email = email

    # Load correct text file
    if choice == 1:
        with open('plant_search_text_files/genus_names2.txt', 'r') as f:
            genus_names = f.read().split('@')
    if choice == 2:
        with open('plant_search_text_files/phytochem3.txt', 'r') as f:
            genus_names = f.read().split('\t')
        
    if choice == 3:
        with open('plant_search_text_files/genus_names2.txt', 'r') as f:
            genus_names = f.read().split('@')
        with open('plant_search_text_files/phytochem3.txt', 'r') as f:
            phyt_names = f.read().split('\t')

    if choice == 4:
        with open('plant_search_text_files/gene1.txt', 'r') as f:
            genus_names = f.read().split('@')


    # User-defined search term
    #user_query = input('Enter additional non-plant search terms: ')

    # Set counter in case choice == 3. This allows first 38 searches to include "plant" as a key word
    gen_phyt_counter = 1

    # Create directory for input files if it doesn't exist
    if not os.path.exists('input_files'):
        os.makedirs('input_files')

    # Split the genus names into groups of 1000 or less, to stay under the PubMed search limit
    genus_groups = [genus_names[i:i+1000] for i in range(0, len(genus_names), 1000)]

    if choice == 3:
        genus_groups = [genus_names[i:i+1000] for i in range(0, len(genus_names), 1000)]
        phyt_groups = [phyt_names[i:i+1000] for i in range(0, len(phyt_names), 1000)]

        genus_groups = genus_groups + phyt_groups
    



    # List to store abstracts and their associated date information
    abstracts_with_info = []
    article_title = []

    # Set to keep track of seen Pubmed IDs
    seen_pmids = set()

    for i, genus_group in enumerate(genus_groups):
        # Construct query string
        if choice == 1: 
            query_terms = '(' + ' OR '.join(genus_group) + ') + AND "plant" AND ' + user_query
        if choice == 3: 
            if gen_phyt_counter <= 38:
                query_terms = '(' + ' OR '.join(genus_group) + ') + AND "plant" AND ' + user_query
            if gen_phyt_counter > 38:
                query_terms = '(' + ' OR '.join(genus_group) + ') + AND ' + user_query 
        if choice == 2: 
            query_terms = '(' + ' OR '.join(genus_group) + ') + AND ' + user_query 
        if choice == 4: 
            query_terms = '(' + ' OR '.join(genus_group) + ') + AND "gene" AND ' + user_query
        
        gen_phyt_counter += 1
        
        # # # testing line, remove
        # if gen_phyt_counter == 38:
        #     print(query_terms)
        # if gen_phyt_counter == 39:
        #     print(query_terms)
        # if gen_phyt_counter == 40:
        #     print(query_terms)


        # Print search query
        print(f'Searching group {i+1}/{len(genus_groups)}')

        
        # Perform search
        herror = 0
        error_number = 0
        while herror == 0:
            try:
                handle = Entrez.esearch(db='pubmed', term=query_terms, retmax=100000)
                record = Entrez.read(handle)
                handle.close()
                herror = 1
            except Exception as err:
                error_number += 1
                if error_number == 5:
                    raise err
                print(f"Error: {str(err)}. Retrying in 5 seconds...")
                time.sleep(5)
                herror = 0
            

        # Fetch abstracts for all search results
        id_list = record['IdList']
        
        query_numb = 1
        exc = 1
        
        if id_list:
            while exc == 1:
                try:
                    print(f'Fetching {len(id_list)} abstracts...')
                    handle = Entrez.efetch(db='pubmed', id=id_list, retmode='xml')
                    records = Entrez.read(handle)
                    handle.close()
                    exc = 0

                # commented out lines below still allow for http error
                # except IncompleteRead: 
                #   query_numb += 1
                #   if query_numb == 5:
                #     raise Exception('Failed to fetch abstracts after 5 attempts.')
                #   print(f'Error fetching abstracts, retrying ({query_numb}/5)...')
                #   time.sleep(5) # Wait 5 seconds before retrying
                #   exc = 1
                
                except Exception as err:
                    query_numb += 1
                    if query_numb == 5:
                        raise err
                    print(f"Error: {str(err)}. Retrying in 5 seconds...")
                    time.sleep(5)
                    exc = 1
            
            
            

        # def fetch_abstracts(id_list):
        #   for i in range(5): # Try up to 5 times
        #       try:
        #           print(f'Fetching {len(id_list)} abstracts...')
        #           handle = Entrez.efetch(db='pubmed', id=id_list, retmode='xml')
        #           records = Entrez.read(handle)
        #           handle.close()
        #           return records
        #       except IncompleteRead:
        #           print(f'Error fetching abstracts, retrying ({i+1}/5)...')
        #           time.sleep(5) # Wait 5 seconds before retrying
        #           raise Exception('Failed to fetch abstracts after 5 attempts.')

        # fetch_abstracts(id_list)

            # Extract abstracts and date information for each record
            for record in records['PubmedArticle']:
                try:
                    abstract = record['MedlineCitation']['Article']['Abstract']['AbstractText'][0]
                except (KeyError, IndexError):
                    abstract = 'Not available'
                #EntrezDate
                try:
                    pub_date = record['MedlineCitation']['DateRevised']
                    pub_date_str = f"{pub_date.get('Year', 'Not available')}-{pub_date.get('Month', 'Not available')}-{pub_date.get('Day', 'Not available')}"
                except KeyError:
                    pub_date_str = 'Not available'
                #PubDate
                try:
                    pub_date1 = record['MedlineCitation']['Article']['Journal']['JournalIssue']['PubDate']
                    pub_date_str1 = f"{pub_date1.get('Year', 'Not available')} {pub_date1.get('Month', 'Not available')}"
                except KeyError:
                    pub_date_str1 = 'Not available'
                try:
                    journal = record['MedlineCitation']['Article']['Journal']['Title']
                except KeyError:
                    journal = 'Not available'
                try:
                    authors = record['MedlineCitation']['Article']['AuthorList']
                    author_names = [f"{author.get('LastName', 'Not available')}, {author.get('ForeName', '')}" for author in authors]
                    authors_str = ', '.join(author_names)
                except KeyError:
                    authors_str = 'Not available'
                try:
                    pmid = record['MedlineCitation']['PMID']
                except KeyError:
                    pmid = 'Not available'
                
                #Add new PubMed ID to set
                skipme=1
                if pmid not in seen_pmids:
                    seen_pmids.add(pmid)
                    skipme=0

                

                Date1 = pub_date_str1[0:4]
                Date0 = pub_date_str[0:4]

                

                if Date1 != Date0:
                    if "Not" in Date1:
                        out_string = f"{pub_date_str}  -DateCatalogued\n{pub_date_str1} -DatePublished\nAuthors: {authors_str}\nJournal: {journal}\nTitle: {record['MedlineCitation']['Article']['ArticleTitle']}\nPMID: {pmid}\nAbstract: {abstract}\n\n"
                        out_string2 = f"{pub_date_str}  -DateCatalogued\n{pub_date_str1} -DatePublished\nTitle: {record['MedlineCitation']['Article']['ArticleTitle']}"
                    else:
                        if Date1 < Date0:
                            out_string = f"{pub_date_str1} -DatePublished\n{pub_date_str}  -DateCatalogued\nAuthors: {authors_str}\nJournal: {journal}\nTitle: {record['MedlineCitation']['Article']['ArticleTitle']}\nPMID: {pmid}\nAbstract: {abstract}\n\n"    
                            out_string2 = f"{pub_date_str1} -DatePublished\n{pub_date_str}  -DateCatalogued\nTitle: {record['MedlineCitation']['Article']['ArticleTitle']}"
                        if Date1 > Date0:
                            out_string = f"{pub_date_str}  -DateCatalogued\n{pub_date_str1} -DatePublished\nAuthors: {authors_str}\nJournal: {journal}\nTitle: {record['MedlineCitation']['Article']['ArticleTitle']}\nPMID: {pmid}\nAbstract: {abstract}\n\n"
                            out_string2 = f"{pub_date_str}  -DateCatalogued\n{pub_date_str1} -DatePublished\nTitle: {record['MedlineCitation']['Article']['ArticleTitle']}"
                else:
                    out_string = f"{pub_date_str}  -DateCatalogued\n{pub_date_str1} -DatePublished\nAuthors: {authors_str}\nJournal: {journal}\nTitle: {record['MedlineCitation']['Article']['ArticleTitle']}\nPMID: {pmid}\nAbstract: {abstract}\n\n"
                    out_string2 = f"{pub_date_str}  -DateCatalogued\n{pub_date_str1} -DatePublished\nTitle: {record['MedlineCitation']['Article']['ArticleTitle']}"
                if skipme==0:
                    abstracts_with_info.append(out_string)
                    article_title.append(out_string2)


            time.sleep(1) # Add a delay of 1 second
        else:
            print('No results found for this group.')



    # Sort abstracts by date
    abstracts_with_info.sort(reverse=True)
    article_title.sort(reverse=True)

    # Create subfolder if it doesn't exist
    #if not os.path.exists("phyto_results"):
        #os.mkdir("phyto_results")

    # Get current time to name output file
    user_query = re.sub(r'[^a-zA-Z0-9]+', '_', user_query)
    now = datetime.datetime.now()

    #output_file_name = f"phyto_results/{user_query}_{now.strftime('%Y%m%d_%H%M%S')}.txt"

    output_file_name = f"plant_search_text_files/saved_searches/{choice}_{user_query}_{now.strftime('%Y%m%d_%H%M%S')}.txt"
    title_file_name = f"plant_search_text_files/titles_only/Titles_only_{choice}_{user_query}_{now.strftime('%Y%m%d_%H%M%S')}.txt"
    pubmed_query = f"plant_search_text_files/query_files/query_file_{choice}_{user_query}_{now.strftime('%Y%m%d_%H%M%S')}.txt"

    # Merge all abstracts into one file, sorted by date
    with open(output_file_name, 'w', encoding='utf-8') as out_file, \
        open(pubmed_query, 'w', encoding='utf-8') as query_file, \
        open(title_file_name, 'w', encoding='utf-8') as title_file:
        query_file.write(query_terms + '\n')
        count_papers = 1
        total_length = len(abstracts_with_info)
        out_file.write(str(total_length) + ' papers are in this text file \n' )
        for abstract in abstracts_with_info:
            out_file.write('Paper #' + str(count_papers) + ' - ')
            count_papers += 1
            out_file.write(abstract)
            

        count_titles = 1
        title_file.write(str(total_length) + ' papers are in this text file \n' )
        for title in article_title:
            title_file.write('\n\nPaper #' + str(count_titles) + ' - ')
            count_titles += 1
            title_file.write(title)

            

    # Empty the input_files folder
    for file_name in os.listdir('input_files'):
        file_path = os.path.join('input_files', file_name)
        try:
            os.remove(file_path)
        except:
            print(f'Error deleting {file_path}')




    # print search complete message
    #print('\n\nSearch complete. \n\n Results (abstracts, journal, PMID, authors, etc.) are in the subfolder called saved_searches in the plant_text_search_files folder \n\n To only browse titles, view the file in the titles_only folder. \n\n To see a small sample of your search query terms, view the file in the query_files folder. \n\n Have a nice day!')

    # Exit the program


    #sg.popup_ok('Search complete. \n\n Results (abstracts, journal, PMID, authors, etc.) are in the subfolder called saved_searches in the plant_text_search_files folder \n\n To only browse titles, view the file in the titles_only folder. \n\n To see a small sample of your search query terms, view the file in the query_files folder. \n\n Have a nice day!') 
    #sg.PrintClose()


    # if checkbox is checked, open the folder with the results

    if checkedfi == True:
        
        # Get the path to the current working directory
        cwd = os.getcwd()

        # Construct the full path to the folder
        folder_path = os.path.join(cwd, 'plant_search_text_files', 'saved_searches')

        # Open the folder in Windows File Explorer
        os.startfile(folder_path)
        
    os.chdir(original_dir)
        
    window.close()
    

program_run()

# Ask user if they want to run the program again

def try_again():
    response = sg.popup_yes_no('Search complete. \n\n Results (abstracts, journal, PMID, authors, etc.) are in the subfolder called saved_searches in the plant_text_search_files folder \n\n To only browse titles, view the file in the titles_only folder. \n\n To see a small sample of your search query terms, view the file in the query_files folder. \n\n Have a nice day! \n\n Search Again?')    
    if response == 'Yes':
        program_run()
    else:
        sys.exit()

try_again()
try_again()
try_again()
try_again()
try_again()

sg.popup_ok('Thank you for using the Plant Text Search Program. \n\n In order to give the NCBI server a break, we will exit now. \n\n Have a nice day!')

# End of program
sys.exit()