bmc/libbmc/fetcher.py

# -*- coding: utf8 -*-
# -----------------------------------------------------------------------------
# "THE NO-ALCOHOL BEER-WARE LICENSE" (Revision 42):
# Phyks (webmaster@phyks.me) wrote this file. As long as you retain this notice
# you can do whatever you want with this stuff (and you can also do whatever
# you want with this stuff without retaining it, but that's not cool...). If we
# meet some day, and you think this stuff is worth it, you can buy me a
# <del>beer</del> soda in return.
#                                                                   Phyks
# -----------------------------------------------------------------------------


import isbnlib
import re
import socket
import socks
import subprocess
import sys
try:
    # For Python 3.0 and later
    from urllib.request import urlopen, Request
    from urllib.error import URLError
except ImportError:
    # Fall back to Python 2's urllib2
    from urllib2 import urlopen, Request, URLError
import arxiv2bib as arxiv_metadata
import libbmc.tools as tools
import bibtexparser
from libbmc.config import Config


config = Config()
default_socket = socket.socket
try:
    stdout_encoding = sys.stdout.encoding
    assert(stdout_encoding is not None)
except (AttributeError, AssertionError):
    stdout_encoding = 'UTF-8'


def download(url):
    """Download url tofile

    Check that it is a valid pdf or djvu file. Tries all the
    available proxies sequentially. Returns the raw content of the file, or
    false if it could not be downloaded.
    """
    for proxy in config.get("proxies"):
        if proxy.startswith('socks'):
            if proxy[5] == '4':
                proxy_type = socks.SOCKS4
            else:
                proxy_type = socks.SOCKS5
            proxy = proxy[proxy.find('://')+3:]
            try:
                proxy, port = proxy.split(':')
            except ValueError:
                port = None
            socks.set_default_proxy(proxy_type, proxy, port)
            socket.socket = socks.socksocket
        elif proxy == '':
            socket.socket = default_socket
        else:
            try:
                proxy, port = proxy.split(':')
            except ValueError:
                port = None
            socks.set_default_proxy(socks.HTTP, proxy, port)
            socket.socket = socks.socksocket
        try:
            r = urlopen(url)
            try:
                size = int(dict(r.info())['content-length'].strip())
            except KeyError:
                try:
                    size = int(dict(r.info())['Content-Length'].strip())
                except KeyError:
                    size = 0
            dl = b""
            dl_size = 0
            while True:
                buf = r.read(1024)
                if buf:
                    dl += buf
                    dl_size += len(buf)
                    if size != 0:
                        done = int(50 * dl_size / size)
                        sys.stdout.write("\r[%s%s]" % ('='*done, ' '*(50-done)))
                        sys.stdout.write(" "+str(int(float(done)/52*100))+"%")
                        sys.stdout.flush()
                else:
                    break
            contenttype = False
            contenttype_req = None
            try:
                contenttype_req = dict(r.info())['content-type']
            except KeyError:
                try:
                    contenttype_req = dict(r.info())['Content-Type']
                except KeyError:
                    continue
            try:
                if 'pdf' in contenttype_req:
                    contenttype = 'pdf'
                elif 'djvu' in contenttype_req:
                    contenttype = 'djvu'
            except KeyError:
                pass

            if r.getcode() != 200 or contenttype is False:
                continue

            return dl, contenttype
        except ValueError:
            tools.warning("Invalid URL")
            return False, None
        except (URLError, socket.error):
            if proxy != "":
                proxy_txt = "using proxy "+proxy
            else:
                proxy_txt = "without using any proxy"
            tools.warning("Unable to get "+url+" "+proxy_txt+". It " +
                          "may not be available at the moment.")
            continue
    return False, None


isbn_re = re.compile(r'isbn[\s]?:?[\s]?((?:[0-9]{3}[ -]?)?[0-9]{1,5}[ -]?[0-9]{1,7}[ -]?[0-9]{1,6}[- ]?[0-9])',
                     re.IGNORECASE)


def findISBN(src):
    """Search for a valid ISBN in src.

    Returns the ISBN or false if not found or an error occurred."""
    if src.endswith(".pdf"):
        totext = subprocess.Popen(["pdftotext", src, "-"],
                                  stdout=subprocess.PIPE,
                                  stderr=subprocess.PIPE,
                                  bufsize=1)
    elif src.endswith(".djvu"):
        totext = subprocess.Popen(["djvutxt", src],
                                  stdout=subprocess.PIPE,
                                  stderr=subprocess.PIPE,
                                  bufsize=1)
    else:
        return False

    while totext.poll() is None:
        extractfull = ' '.join([i.decode(stdout_encoding).strip() for i in totext.stdout.readlines()])
        extractISBN = isbn_re.search(extractfull.lower().replace('&#338;',
                                                                 '-'))
        if extractISBN:
            totext.terminate()
            break

    err = totext.communicate()[1]
    if totext.returncode > 0:
        # Error happened
        tools.warning(err)
        return False

    cleanISBN = False
    # Clean ISBN is the ISBN number without separators
    if extractISBN:
        cleanISBN = extractISBN.group(1).replace('-', '').replace(' ', '')
    return cleanISBN


def isbn2Bib(isbn):
    """Tries to get bibtex entry from an ISBN number"""
    # Default merges results from worldcat.org and google books
    try:
        return isbnlib.registry.bibformatters['bibtex'](isbnlib.meta(isbn,
                                                                     'default'))
    except (isbnlib.ISBNLibException, TypeError):
        return ''


doi_re = re.compile('(?<=doi)/?:?\s?[0-9\.]{7}/\S*[0-9]', re.IGNORECASE)
doi_pnas_re = re.compile('(?<=doi).?10.1073/pnas\.\d+', re.IGNORECASE)
doi_jsb_re = re.compile('10\.1083/jcb\.\d{9}', re.IGNORECASE)
clean_doi_re = re.compile('^/')
clean_doi_fabse_re = re.compile('^10.1096')
clean_doi_jcb_re = re.compile('^10.1083')
clean_doi_len_re = re.compile(r'\d\.\d')
arXiv_re = re.compile(r'arXiv:\s*([\w\.\/\-]+)', re.IGNORECASE)


def findArticleID(src, only=["DOI", "arXiv"]):
    """Search for a valid article ID (DOI or ArXiv) in src.

    Returns a tuple (type, first matching ID) or False if not found
    or an error occurred.
    From : http://en.dogeno.us/2010/02/release-a-python-script-for-organizing-scientific-papers-pyrenamepdf-py/
    and https://github.com/minad/bibsync/blob/3fdf121016f6187a2fffc66a73cd33b45a20e55d/lib/bibsync/utils.rb
    """
    if src.endswith(".pdf"):
        totext = subprocess.Popen(["pdftotext", src, "-"],
                                  stdout=subprocess.PIPE,
                                  stderr=subprocess.PIPE)
    elif src.endswith(".djvu"):
        totext = subprocess.Popen(["djvutxt", src],
                                  stdout=subprocess.PIPE,
                                  stderr=subprocess.PIPE)
    else:
        return (False, False)

    extractfull = ''
    extract_type = False
    extractID = None
    while totext.poll() is None:
        extractfull += ' '.join([i.decode(stdout_encoding).strip() for i in totext.stdout.readlines()])
        # Try to extract DOI
        if "DOI" in only:
            extractID = doi_re.search(extractfull.lower().replace('&#338;', '-'))
            if not extractID:
                # PNAS fix
                extractID = doi_pnas_re.search(extractfull.
                                               lower().
                                               replace('pnas', '/pnas'))
                if not extractID:
                    # JSB fix
                    extractID = doi_jsb_re.search(extractfull.lower())
            if extractID:
                extract_type = "DOI"
                totext.terminate()
        # Try to extract arXiv
        if "arXiv" in only:
            tmp_extractID = arXiv_re.search(extractfull)
            if tmp_extractID:
                if not extractID or extractID.start(0) > tmp_extractID.start(1):
                    # Only use arXiv id if it is before the DOI in the pdf
                    extractID = tmp_extractID
                    extract_type = "arXiv"
                    totext.terminate()
        if extract_type is not False:
            break

    err = totext.communicate()[1]
    if totext.returncode > 0:
        # Error happened
        tools.warning(err)
        return (False, False)

    if extractID is not None and extract_type == "DOI":
        # If DOI extracted, clean it and return it
        cleanDOI = False
        cleanDOI = extractID.group(0).replace(':', '').replace(' ', '')
        if clean_doi_re.search(cleanDOI):
            cleanDOI = cleanDOI[1:]
        # FABSE J fix
        if clean_doi_fabse_re.search(cleanDOI):
            cleanDOI = cleanDOI[:20]
        # Second JCB fix
        if clean_doi_jcb_re.search(cleanDOI):
            cleanDOI = cleanDOI[:21]
        if len(cleanDOI) > 40:
            cleanDOItemp = clean_doi_len_re.sub('000', cleanDOI)
            reps = {'.': 'A', '-': '0'}
            cleanDOItemp = tools.replaceAll(cleanDOItemp[8:], reps)
            digitStart = 0
            for i in range(len(cleanDOItemp)):
                if cleanDOItemp[i].isdigit():
                    digitStart = 1
                    if cleanDOItemp[i].isalpha() and digitStart:
                        break
            cleanDOI = cleanDOI[0:(8+i)]
        return ("DOI", cleanDOI)
    elif extractID is not None and extract_type == "arXiv":
        # If arXiv id is extracted, return it
        return ("arXiv", extractID.group(1))
    return (False, False)


def doi2Bib(doi):
    """Returns a bibTeX string of metadata for a given DOI.

    From : https://gist.github.com/jrsmith3/5513926
    """
    url = "http://dx.doi.org/" + doi
    headers = {"accept": "application/x-bibtex"}
    req = Request(url, headers=headers)
    try:
        r = urlopen(req)

        try:
            if dict(r.info())['content-type'] == 'application/x-bibtex':
                return r.read().decode('utf-8')
            else:
                return ''
        except KeyError:
            try:
                if dict(r.info())['Content-Type'] == 'application/x-bibtex':
                    return r.read().decode('utf-8')
                else:
                    return ''
            except KeyError:
                return ''
    except:
        tools.warning('Unable to contact remote server to get the bibtex ' +
                      'entry for doi '+doi)
        return ''


def arXiv2Bib(arxiv):
    """Returns bibTeX string of metadata for a given arXiv id

    arxiv is an arxiv id
    """
    bibtex = arxiv_metadata.arxiv2bib([arxiv])
    for bib in bibtex:
        if isinstance(bib, arxiv_metadata.ReferenceErrorInfo):
            continue
        else:
            fetched_bibtex = bibtexparser.loads(bib.bibtex())
            fetched_bibtex = fetched_bibtex.entries_dict
            fetched_bibtex = fetched_bibtex[list(fetched_bibtex.keys())[0]]
            try:
                del(fetched_bibtex['file'])
            except KeyError:
                pass
            return tools.parsed2Bibtex(fetched_bibtex)
    return ''


HAL_re = re.compile(r'(hal-\d{8}), version (\d+)')


def findHALId(src):
    """Searches for a valid HAL id in src

    Returns a tuple of the HAL id and the version
    or False if not found or an error occurred.
    """
    if src.endswith(".pdf"):
        totext = subprocess.Popen(["pdftotext", src, "-"],
                                  stdout=subprocess.PIPE,
                                  stderr=subprocess.PIPE)
    elif src.endswith(".djvu"):
        totext = subprocess.Popen(["djvutxt", src],
                                  stdout=subprocess.PIPE,
                                  stderr=subprocess.PIPE)
    else:
        return False

    while totext.poll() is None:
        extractfull = ' '.join([i.decode(stdout_encoding).strip() for i in totext.stdout.readlines()])
        extractID = HAL_re.search(extractfull)
        if extractID:
            totext.terminate()
            break

    err = totext.communicate()[1]
    if totext.returncode > 0:
        # Error happened
        tools.warning(err)
        return False
    else:
        return extractID.group(1), extractID.group(2)