app.py

import os
import re
import time
import logging
import zipfile
import requests
import bibtexparser
from tqdm import tqdm
from urllib.parse import quote, urlencode
import gradio as gr
from bs4 import BeautifulSoup
import io
import asyncio
import aiohttp

# Configure logging
logging.basicConfig(level=logging.INFO,
                    format='%(asctime)s - %(levelname)s: %(message)s')
logger = logging.getLogger(__name__)


class PaperDownloader:
    def __init__(self, output_dir='papers'):
        self.output_dir = output_dir
        os.makedirs(output_dir, exist_ok=True)

        # Updated download sources
        self.download_sources = [
            'https://sci-hub.ee/',
            'https://sci-hub.st/',
            'https://sci-hub.ru/',
            'https://sci-hub.ren/',
            'https://sci-hub.mksa.top/',
            'https://sci-hub.se/',
            'https://libgen.rs/scimag/'
        ]

        # Request headers
        self.headers = {
            'User-Agent': 'Mozilla/5.0 (Windows NT 10.0; Win64; x64) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/114.0.0.0 Safari/537.36',
            'Accept': 'text/html,application/xhtml+xml,application/xml;q=0.9,image/avif,image/webp,*/*;q=0.8',
            'Accept-Language': 'en-US,en;q=0.9',
        }

    def clean_doi(self, doi):
        """Clean and encode DOI for URL"""
        if not isinstance(doi, str):
            return None
        return quote(doi.strip()) if doi else None

    async def fetch_with_headers(self, session, url, timeout=10):
        """Utility method to fetch an URL with headers and timeout"""
        try:
            async with session.get(url, headers=self.headers, timeout=timeout, allow_redirects=True) as response:
                response.raise_for_status()
                return await response.text(), response.headers
        except Exception as e:
            logger.debug(f"Error fetching {url}: {e}")
            return None, None
    
    
    async def download_paper_direct_doi_async(self, session, doi):
      """Attempt to download the pdf from the landing page of the doi"""
      if not doi:
         return None
      
      try:
         doi_url = f"https://doi.org/{self.clean_doi(doi)}"
         text, headers = await self.fetch_with_headers(session, doi_url, timeout=15)
         if not text:
            return None

         pdf_patterns = [
           r'(https?://[^\s<>"]+?\.pdf)',
           r'(https?://[^\s<>"]+?download/[^\s<>"]+)',
           r'(https?://[^\s<>"]+?\/pdf\/[^\s<>"]+)',
         ]
            
         pdf_urls = []
         for pattern in pdf_patterns:
            pdf_urls.extend(re.findall(pattern, text))

         for pdf_url in pdf_urls:
           try:
               pdf_response = await session.get(pdf_url, headers=self.headers, timeout=10)
               if 'application/pdf' in pdf_response.headers.get('Content-Type', ''):
                    logger.debug(f"Found PDF from: {pdf_url}")
                    return await pdf_response.read()
           except Exception as e:
               logger.debug(f"Error downloading PDF from {pdf_url}: {e}")


      except Exception as e:
           logger.debug(f"Error trying to get the PDF from {doi}: {e}")
      
      return None

    async def download_paper_scihub_async(self, session, doi):
        """Improved method to download paper from Sci-Hub using async requests"""
        if not doi:
            logger.warning("DOI not provided")
            return None

        for base_url in self.download_sources:
            try:
                scihub_url = f"{base_url}{self.clean_doi(doi)}"
                text, headers = await self.fetch_with_headers(session, scihub_url, timeout=15)
                if not text:
                    continue

                # Search for multiple PDF URL patterns
                pdf_patterns = [
                    r'(https?://[^\s<>"]+?\.pdf)',
                    r'(https?://[^\s<>"]+?download/[^\s<>"]+)',
                    r'(https?://[^\s<>"]+?\/pdf\/[^\s<>"]+)',
                ]

                pdf_urls = []
                for pattern in pdf_patterns:
                    pdf_urls.extend(re.findall(pattern, text))

                # Try downloading from found URLs
                for pdf_url in pdf_urls:
                    try:
                        pdf_response = await session.get(pdf_url, headers=self.headers, timeout=10)
                        # Verify if it's a PDF
                        if 'application/pdf' in pdf_response.headers.get('Content-Type', ''):
                            logger.debug(f"Found PDF from: {pdf_url}")
                            return await pdf_response.read()
                    except Exception as e:
                        logger.debug(f"Error downloading PDF from {pdf_url}: {e}")

            except Exception as e:
                logger.debug(f"Error trying to download {doi} from {base_url}: {e}")

        return None

    async def download_paper_libgen_async(self, session, doi):
        """Download from Libgen, handles the query and the redirection"""
        if not doi:
            return None

        base_url = 'https://libgen.rs/scimag/'
        try:
            search_url = f"{base_url}?q={self.clean_doi(doi)}"
            text, headers = await self.fetch_with_headers(session, search_url, timeout=10)

            if not text or "No results" in text:
                logger.debug(f"No results for DOI: {doi} on libgen")
                return None

            soup = BeautifulSoup(text, 'html.parser')

            links = soup.select('table.c > tbody > tr:nth-child(2) > td:nth-child(1) > a')

            if links:
                link = links[0]
                pdf_url = link['href']
                pdf_response = await session.get(pdf_url, headers=self.headers, allow_redirects=True, timeout=10)
                if 'application/pdf' in pdf_response.headers.get('Content-Type', ''):
                    logger.debug(f"Found PDF from: {pdf_url}")
                    return await pdf_response.read()
        except Exception as e:
            logger.debug(f"Error trying to download {doi} from libgen: {e}")
        return None

    async def download_paper_google_scholar_async(self, session, doi):
        """Search google scholar to find an article with the given doi, try to get the pdf"""
        if not doi:
            return None

        try:
            query = f'doi:"{doi}"'
            params = {'q': query}
            url = f'https://scholar.google.com/scholar?{urlencode(params)}'

            text, headers = await self.fetch_with_headers(session, url, timeout=10)
            if not text:
                return None

            soup = BeautifulSoup(text, 'html.parser')

            # Find any links with [PDF]
            links = soup.find_all('a', string=re.compile(r'\[PDF\]', re.IGNORECASE))

            if links:
                pdf_url = links[0]['href']
                pdf_response = await session.get(pdf_url, headers=self.headers, timeout=10)
                if 'application/pdf' in pdf_response.headers.get('Content-Type', ''):
                    logger.debug(f"Found PDF from: {pdf_url}")
                    return await pdf_response.read()
        except Exception as e:
            logger.debug(f"Google Scholar error for {doi}: {e}")

        return None

    async def download_paper_crossref_async(self, session, doi):
        """Alternative search method using Crossref"""
        if not doi:
            return None

        try:
            # Search for open access link
            url = f"https://api.crossref.org/works/{doi}"
            response = await session.get(url, headers=self.headers, timeout=10)

            if response.status == 200:
                data = await response.json()
                work = data.get('message', {})

                # Search for open access links
                links = work.get('link', [])
                for link in links:
                    if link.get('content-type') == 'application/pdf':
                        pdf_url = link.get('URL')
                        if pdf_url:
                            pdf_response = await session.get(pdf_url, headers=self.headers)
                            if 'application/pdf' in pdf_response.headers.get('Content-Type', ''):
                                logger.debug(f"Found PDF from: {pdf_url}")
                                return await pdf_response.read()

        except Exception as e:
            logger.debug(f"Crossref error for {doi}: {e}")

        return None

    async def download_with_retry_async(self, doi, max_retries=3, initial_delay=2):
        """Downloads a paper using multiple strategies with exponential backoff and async requests"""
        pdf_content = None
        retries = 0
        delay = initial_delay

        async with aiohttp.ClientSession() as session:
            while retries < max_retries and not pdf_content:
                try:
                    pdf_content = (
                        await self.download_paper_direct_doi_async(session, doi) or
                        await self.download_paper_scihub_async(session, doi) or
                        await self.download_paper_libgen_async(session, doi) or
                        await self.download_paper_google_scholar_async(session, doi) or
                        await self.download_paper_crossref_async(session, doi)

                    )
                    if pdf_content:
                        return pdf_content
                except Exception as e:
                    logger.error(f"Error in download attempt {retries + 1} for DOI {doi}: {e}")

                if not pdf_content:
                    retries += 1
                    logger.warning(f"Retry attempt {retries} for DOI: {doi} after {delay} seconds")
                    await asyncio.sleep(delay)
                    delay *= 2  # Exponential backoff

        return None

    def download_paper_scihub(self, doi):
        """Improved method to download paper from Sci-Hub"""
        if not doi:
            logger.warning("DOI not provided")
            return None

        for base_url in self.download_sources:
            try:
                scihub_url = f"{base_url}{self.clean_doi(doi)}"

                # Request with more tolerance
                response = requests.get(scihub_url,
                                        headers=self.headers,
                                        allow_redirects=True,
                                        timeout=15)

                # Search for multiple PDF URL patterns
                pdf_patterns = [
                    r'(https?://[^\s<>"]+?\.pdf)',
                    r'(https?://[^\s<>"]+?download/[^\s<>"]+)',
                    r'(https?://[^\s<>"]+?\/pdf\/[^\s<>"]+)',
                ]

                pdf_urls = []
                for pattern in pdf_patterns:
                    pdf_urls.extend(re.findall(pattern, response.text))

                # Try downloading from found URLs
                for pdf_url in pdf_urls:
                    try:
                        pdf_response = requests.get(pdf_url,
                                                    headers=self.headers,
                                                    timeout=10)

                        # Verify if it's a PDF
                        if 'application/pdf' in pdf_response.headers.get('Content-Type', ''):
                            logger.debug(f"Found PDF from: {pdf_url}")
                            return pdf_response.content
                    except Exception as e:
                        logger.debug(f"Error downloading PDF from {pdf_url}: {e}")

            except Exception as e:
                logger.debug(f"Error trying to download {doi} from {base_url}: {e}")

        return None

    def download_paper_libgen(self, doi):
        """Download from Libgen, handles the query and the redirection"""
        if not doi:
            return None

        base_url = 'https://libgen.rs/scimag/'
        try:
            search_url = f"{base_url}?q={self.clean_doi(doi)}"
            response = requests.get(search_url, headers=self.headers, allow_redirects=True, timeout=10)
            response.raise_for_status()

            if "No results" in response.text:
                logger.debug(f"No results for DOI: {doi} on libgen")
                return None

            soup = BeautifulSoup(response.text, 'html.parser')

            # Find the link using a specific selector
            links = soup.select('table.c > tbody > tr:nth-child(2) > td:nth-child(1) > a')

            if links:
                link = links[0]
                pdf_url = link['href']
                pdf_response = requests.get(pdf_url, headers=self.headers, allow_redirects=True, timeout=10)
                if 'application/pdf' in pdf_response.headers.get('Content-Type', ''):
                    logger.debug(f"Found PDF from: {pdf_url}")
                    return pdf_response.content

        except Exception as e:
            logger.debug(f"Error trying to download {doi} from libgen: {e}")
        return None

    def download_paper_google_scholar(self, doi):
        """Search google scholar to find an article with the given doi, try to get the pdf"""
        if not doi:
            return None

        try:
            query = f'doi:"{doi}"'
            params = {'q': query}
            url = f'https://scholar.google.com/scholar?{urlencode(params)}'

            response = requests.get(url, headers=self.headers, timeout=10)
            response.raise_for_status()

            soup = BeautifulSoup(response.text, 'html.parser')

            # Find any links with [PDF]
            links = soup.find_all('a', string=re.compile(r'\[PDF\]', re.IGNORECASE))

            if links:
                pdf_url = links[0]['href']
                pdf_response = requests.get(pdf_url, headers=self.headers, timeout=10)
                if 'application/pdf' in pdf_response.headers.get('Content-Type', ''):
                    logger.debug(f"Found PDF from: {pdf_url}")
                    return pdf_response.content
        except Exception as e:
            logger.debug(f"Google Scholar error for {doi}: {e}")

        return None

    def download_paper_crossref(self, doi):
        """Alternative search method using Crossref"""
        if not doi:
            return None

        try:
            # Search for open access link
            url = f"https://api.crossref.org/works/{doi}"
            response = requests.get(url, headers=self.headers, timeout=10)

            if response.status_code == 200:
                data = response.json()
                work = data.get('message', {})

                # Search for open access links
                links = work.get('link', [])
                for link in links:
                    if link.get('content-type') == 'application/pdf':
                        pdf_url = link.get('URL')
                        if pdf_url:
                            pdf_response = requests.get(pdf_url, headers=self.headers)
                            if 'application/pdf' in pdf_response.headers.get('Content-Type', ''):
                                logger.debug(f"Found PDF from: {pdf_url}")
                                return pdf_response.content

        except Exception as e:
            logger.debug(f"Crossref error for {doi}: {e}")

        return None

    def download_with_retry(self, doi, max_retries=3, initial_delay=2):
        """Downloads a paper using multiple strategies with exponential backoff"""
        pdf_content = None
        retries = 0
        delay = initial_delay

        while retries < max_retries and not pdf_content:
            try:
                 pdf_content = (
                     self.download_paper_scihub(doi) or
                     self.download_paper_libgen(doi) or
                     self.download_paper_google_scholar(doi) or
                     self.download_paper_crossref(doi)

                  )

                 if pdf_content:
                     return pdf_content
            except Exception as e:
                logger.error(f"Error in download attempt {retries + 1} for DOI {doi}: {e}")

            if not pdf_content:
                retries += 1
                logger.warning(f"Retry attempt {retries} for DOI: {doi} after {delay} seconds")
                time.sleep(delay)
                delay *= 2  # Exponential backoff

        return None

    def download_single_doi(self, doi):
        """Downloads a single paper using a DOI"""
        if not doi:
            return None, "Error: DOI not provided", "Error: DOI not provided"

        try:
            pdf_content = self.download_with_retry(doi)

            if pdf_content:
                if doi is None:
                    return None, "Error: DOI not provided", "Error: DOI not provided"
                filename = f"{str(doi).replace('/', '_').replace('.', '_')}.pdf"
                filepath = os.path.join(self.output_dir, filename)
                with open(filepath, 'wb') as f:
                    f.write(pdf_content)
                logger.info(f"Successfully downloaded: {filename}")
                return filepath, f'<a href="https://doi.org/{doi}">{doi}</a>', ""
            else:
                logger.warning(f"Could not download: {doi}")
                return None, f"Could not download {doi}", f'<a href="https://doi.org/{doi}">{doi}</a>'

        except Exception as e:
            logger.error(f"Error processing {doi}: {e}")
            return None, f"Error processing {doi}: {e}", f"Error processing {doi}: {e}"

    def download_multiple_dois(self, dois_text):
        """Downloads multiple papers from a list of DOIs"""
        if not dois_text:
            return None, "Error: No DOIs provided", "Error: No DOIs provided"

        dois = [doi.strip() for doi in dois_text.split('\n') if doi.strip()]
        if not dois:
            return None, "Error: No valid DOIs provided", "Error: No valid DOIs provided"

        downloaded_files = []
        failed_dois = []
        downloaded_links = []
        for i, doi in enumerate(tqdm(dois, desc="Downloading papers")):
            filepath, success_message, fail_message = self.download_single_doi(doi)
            if filepath:
                # Unique filename for zip
                filename = f"{str(doi).replace('/', '_').replace('.', '_')}_{i}.pdf"
                filepath_unique = os.path.join(self.output_dir, filename)
                os.rename(filepath, filepath_unique)
                downloaded_files.append(filepath_unique)
                downloaded_links.append(f'<a href="https://doi.org/{doi}">{doi}</a>')

            else:
                failed_dois.append(f'<a href="https://doi.org/{doi}">{doi}</a>')

        if downloaded_files:
            zip_filename = 'papers.zip'
            with zipfile.ZipFile(zip_filename, 'w') as zipf:
                for file_path in downloaded_files:
                    zipf.write(file_path, arcname=os.path.basename(file_path))
            logger.info(f"ZIP file created: {zip_filename}")

        return zip_filename if downloaded_files else None, "\n".join(downloaded_links), "\n".join(failed_dois)

    def process_bibtex(self, bib_file):
        """Process BibTeX file and download papers with multiple strategies"""
        # Read BibTeX file content from the uploaded object
        try:
            with open(bib_file.name, 'r', encoding='utf-8') as f:
                bib_content = f.read()
        except Exception as e:
            logger.error(f"Error reading uploaded file {bib_file.name}: {e}")
            return None, f"Error reading uploaded file {bib_file.name}: {e}", f"Error reading uploaded file {bib_file.name}: {e}", None

        # Parse BibTeX data
        try:
            bib_database = bibtexparser.loads(bib_content)
        except Exception as e:
            logger.error(f"Error parsing BibTeX data: {e}")
            return None, f"Error parsing BibTeX data: {e}", f"Error parsing BibTeX data: {e}", None

        # Extract DOIs
        dois = [entry.get('doi') for entry in bib_database.entries if entry.get('doi')]
        logger.info(f"Found {len(dois)} DOIs to download")

        # Result lists
        downloaded_files = []
        failed_dois = []
        downloaded_links = []

        # Download PDFs
        for doi in tqdm(dois, desc="Downloading papers"):
            try:
                # Try to download with multiple methods with retries
                pdf_content = self.download_with_retry(doi)

                # Save PDF
                if pdf_content:
                    if doi is None:
                        return None, "Error: DOI not provided", "Error: DOI not provided", None
                    filename = f"{str(doi).replace('/', '_').replace('.', '_')}.pdf"
                    filepath = os.path.join(self.output_dir, filename)

                    with open(filepath, 'wb') as f:
                        f.write(pdf_content)

                    downloaded_files.append(filepath)
                    downloaded_links.append(f'<a href="https://doi.org/{doi}">{doi}</a>')
                    logger.info(f"Successfully downloaded: {filename}")
                else:
                    failed_dois.append(f'<a href="https://doi.org/{doi}">{doi}</a>')

            except Exception as e:
                failed_dois.append(f'<a href="https://doi.org/{doi}">{doi}</a>')
                logger.error(f"Error processing {doi}: {e}")

        # Create ZIP of downloaded papers
        if downloaded_files:
            zip_filename = 'papers.zip'
            with zipfile.ZipFile(zip_filename, 'w') as zipf:
                for file_path in downloaded_files:
                    zipf.write(file_path, arcname=os.path.basename(file_path))
            logger.info(f"ZIP file created: {zip_filename}")

        return zip_filename, "\n".join(downloaded_links), "\n".join(failed_dois), None

    async def process_bibtex_async(self, bib_file):
        """Process BibTeX file and download papers with multiple strategies"""
        # Read BibTeX file content from the uploaded object
        try:
            with open(bib_file.name, 'r', encoding='utf-8') as f:
                bib_content = f.read()
        except Exception as e:
            logger.error(f"Error reading uploaded file {bib_file.name}: {e}")
            return None, f"Error reading uploaded file {bib_file.name}: {e}", f"Error reading uploaded file {bib_file.name}: {e}", None

        # Parse BibTeX data
        try:
            bib_database = bibtexparser.loads(bib_content)
        except Exception as e:
            logger.error(f"Error parsing BibTeX data: {e}")
            return None, f"Error parsing BibTeX data: {e}", f"Error parsing BibTeX data: {e}", None

        # Extract DOIs
        dois = [entry.get('doi') for entry in bib_database.entries if entry.get('doi')]
        logger.info(f"Found {len(dois)} DOIs to download")

        # Result lists
        downloaded_files = []
        failed_dois = []
        downloaded_links = []

        # Download PDFs
        for doi in tqdm(dois, desc="Downloading papers"):
            try:
                # Try to download with multiple methods with retries
                pdf_content = await self.download_with_retry_async(doi)

                # Save PDF
                if pdf_content:
                    if doi is None:
                        return None, "Error: DOI not provided", "Error: DOI not provided", None
                    filename = f"{str(doi).replace('/', '_').replace('.', '_')}.pdf"
                    filepath = os.path.join(self.output_dir, filename)

                    with open(filepath, 'wb') as f:
                        f.write(pdf_content)

                    downloaded_files.append(filepath)
                    downloaded_links.append(f'<a href="https://doi.org/{doi}">{doi}</a>')
                    logger.info(f"Successfully downloaded: {filename}")
                else:
                    failed_dois.append(f'<a href="https://doi.org/{doi}">{doi}</a>')

            except Exception as e:
                failed_dois.append(f'<a href="https://doi.org/{doi}">{doi}</a>')
                logger.error(f"Error processing {doi}: {e}")

        # Create ZIP of downloaded papers
        if downloaded_files:
            zip_filename = 'papers.zip'
            with zipfile.ZipFile(zip_filename, 'w') as zipf:
                for file_path in downloaded_files:
                    zipf.write(file_path, arcname=os.path.basename(file_path))
            logger.info(f"ZIP file created: {zip_filename}")

        return zip_filename, "\n".join(downloaded_links), "\n".join(failed_dois), None

def create_gradio_interface():
    """Create Gradio interface for Paper Downloader"""
    downloader = PaperDownloader()

    async def download_papers(bib_file, doi_input, dois_input):
        if bib_file:
            # Check file type
            if not bib_file.name.lower().endswith('.bib'):
                return None, "Error: Please upload a .bib file", "Error: Please upload a .bib file", None

            zip_path, downloaded_dois, failed_dois, _ = await downloader.process_bibtex_async(bib_file)
            return zip_path, downloaded_dois, failed_dois, None
        elif doi_input:
            filepath, message, failed_doi = downloader.download_single_doi(doi_input)
            return None, message, failed_doi, filepath
        elif dois_input:
            zip_path, downloaded_dois, failed_dois = downloader.download_multiple_dois(dois_input)
            return zip_path, downloaded_dois, failed_dois, None
        else:
            return None, "Please provide a .bib file, a single DOI, or a list of DOIs", "Please provide a .bib file, a single DOI, or a list of DOIs", None

    # Gradio Interface
    interface = gr.Interface(
        fn=download_papers,
        inputs=[
            gr.File(file_types=['.bib'], label="Upload BibTeX File"),
            gr.Textbox(label="Enter Single DOI", placeholder="10.xxxx/xxxx"),
            gr.Textbox(label="Enter Multiple DOIs (one per line)", placeholder="10.xxxx/xxxx\n10.yyyy/yyyy\n...")
        ],
        outputs=[
            gr.File(label="Download Papers (ZIP) or Single PDF"),
            gr.HTML(label="""
                <div style='padding-bottom: 5px; font-weight: bold;'>
                    Found DOIs
                </div>
                <div style='border: 1px solid #ddd; padding: 5px; border-radius: 5px;'>
                    <div id="downloaded-dois"></div>
                </div>
            """),
            gr.HTML(label="""
                <div style='padding-bottom: 5px; font-weight: bold;'>
                    Missed DOIs
                </div>
                <div style='border: 1px solid #ddd; padding: 5px; border-radius: 5px;'>
                    <div id="failed-dois"></div>
                </div>
            """),
            gr.File(label="Downloaded Single PDF")
        ],
        title="🔬 Academic Paper Batch Downloader",
        description="Upload a BibTeX file or enter DOIs to download PDFs. We'll attempt to fetch PDFs from multiple sources like Sci-Hub, Libgen, Google Scholar and Crossref. You can use any of the three inputs at any moment.",
        theme="Hev832/Applio",
        examples=[
            ["example.bib", None, None],  # Bibtex File
            [None, "10.1038/nature12373", None],  # Single DOI
            [None, None, "10.1109/5.771073\n10.3390/horticulturae8080677"],  # Multiple DOIs
        ],
        css="""
        .gradio-container {
            background-color: black;
        }
        .gr-interface {
            max-width: 800px;
            margin: 0 auto;
        }
        .gr-box {
            background-color: black;
            border-radius: 10px;
            box-shadow: 0 4px 6px rgba(0, 0, 0, 0.1);
        }
           .output-text a {
               color: #007bff; /* Blue color for hyperlinks */
            }
        """,
        cache_examples=False,
    )

    # Add Javascript to update HTML
    interface.load = """
        function(downloaded_dois, failed_dois){
             let downloaded_html = '';
             downloaded_dois.split('\\n').filter(Boolean).forEach(doi => {
                downloaded_html +=  '[' + doi + ']<br>';
            });
            document.querySelector("#downloaded-dois").innerHTML = downloaded_html;

             let failed_html = '';
             failed_dois.split('\\n').filter(Boolean).forEach(doi => {
                failed_html += '[' + doi + ']<br>';
            });
            document.querySelector("#failed-dois").innerHTML = failed_html;
            return [downloaded_html, failed_html];
        }
    """
    return interface


def main():
    interface = create_gradio_interface()
    interface.launch(share=True)


if __name__ == "__main__":
    main()