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adsbibdesk.py
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adsbibdesk.py
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#!/usr/bin/env python
"""
ADS to BibDesk -- frictionless import of ADS publications into BibDesk
Copyright (C) 2014 Rui Pereira <rui.pereira@gmail.com> and
Jonathan Sick <jonathansick@mac.com>
This program is free software: you can redistribute it and/or modify
it under the terms of the GNU General Public License as published by
the Free Software Foundation, either version 3 of the License, or
(at your option) any later version.
This program is distributed in the hope that it will be useful,
but WITHOUT ANY WARRANTY; without even the implied warranty of
MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
GNU General Public License for more details.
You should have received a copy of the GNU General Public License
along with this program. If not, see <http://www.gnu.org/licenses/>.
Based on ADS to Bibdesk automator action by
Jonathan Sick, jonathansick@mac.com, August 2007
Input may be one of the following:
- ADS abstract page URL
- ADS bibcode
- arXiv abstract page
- arXiv identifier
"""
import datetime
import difflib
import fnmatch
import glob
import logging
import math
import optparse
import os
import pprint
import re
import socket
import sys
import tempfile
import time
import requests
try:
from string import uppercase
except ImportError:
from string import ascii_uppercase as uppercase
# cgi.parse_qs is deprecated since 2.6
# but OS X 10.5 only has 2.5
import cgi
#import urllib2
try:
# Python 2
from urllib2 import urlopen
from urllib2 import URLError
from urllib2 import Request as urlreq
from urlparse import urlparse, urlsplit, urlunsplit
from htmlentitydefs import name2codepoint
from HTMLParser import HTMLParser
from HTMLParser import HTMLParseError
except ImportError:
# Python 3
from urllib.request import urlopen
from urllib.request import URLError
from urllib.request import Request as urlreq
from urllib.parse import urlparse, urlsplit, urlunsplit
from html.entities import name2codepoint
from html.parser import HTMLParser
try:
from html.parser import HTMLParseError
except ImportError: # Python 3.5+
class HTMLParseError(Exception):
pass
basestring = str
unichr = chr
import subprocess as sp
try:
import AppKit
except ImportError:
# is this not the system python?
syspath = eval(sp.Popen('/usr/bin/python -c "import sys; print(sys.path)"',
shell=True, stdout=sp.PIPE).stdout.read())
for p in syspath:
if os.path.isdir(p) and glob.glob(os.path.join(p, '*AppKit*')):
sys.path.insert(0, p)
break
# retry
try:
import AppKit
except ImportError:
import webbrowser
url = 'http://pythonhosted.org/pyobjc/install.html'
msg = 'Please install PyObjC...'
print(msg)
sp.call(r'osascript -e "tell application \"System Events\" to '
'display dialog \"%s\" buttons {\"OK\"} default button \"OK\""'
% msg, shell=True, stdout=open('/dev/null', 'w'))
# open browser in PyObjC install page
webbrowser.open(url)
sys.exit()
# default timeout for url calls
socket.setdefaulttimeout(30)
VERSION = "3.2.0"
def main():
"""Parse options and launch main loop"""
usage = """Usage: %prog [options] [article_token or pdf_directory]
adsbibdesk helps you add astrophysics articles listed on NASA/ADS
and arXiv.org to your BibDesk database. There are three modes
in this command line interface:
1. Article mode, for adding single papers to BibDesk given tokens.
2. PDF Ingest mode, where PDFs in a directory are analyzed and added to
BibDesk with ADS meta data.
3. Pre-print Update mode, for updating arXiv pre-prints automatically
with newer bibcodes.
In article mode, adsbibdesk accepts many kinds of article tokens:
- the URL of an ADS or arXiv article page,
- the ADS bibcode of an article (e.g. 1998ApJ...500..525S), or
- the arXiv identifier of an article (e.g. 0911.4956).
(Example: `adsbibdesk 1998ApJ...500..525S`)
In PDF Ingest mode, you specify a directory containing PDFs instead of
an article token (Example: `adsbibdesk -p pdfs` will ingest PDFs from
the pdfs/ directory).
In Pre-print Update mode, every article with an arXiv bibcode will be
updated if it has a new bibcode."""
epilog = "For more information, visit www.jonathansick.ca/adsbibdesk" \
" email jonathansick at mac.com or tweet @jonathansick"
parser = optparse.OptionParser(usage=usage, version=VERSION,
epilog=epilog)
parser.add_option(
'-d', '--debug',
dest="debug", default=False, action="store_true",
help="Debug mode; prints extra statements")
parser.add_option(
'-o', '--only_pdf',
default=False, action='store_true',
help="Download and open PDF for the selected [article_token].")
pdf_ingest_group = optparse.OptionGroup(parser, "PDF Ingest Mode",
description=None)
pdf_ingest_group.add_option(
'-p', '--ingest_pdfs',
dest="ingest_pdfs", default=False, action="store_true",
help="Ingest a folder of PDFs."
" Positional argument should be directory"
" containing PDFs."
" e.g., `adsbibdesk -p .` for the current directory")
pdf_ingest_group.add_option(
'-r', '--recursive',
dest='recursive', action="store_true",
help="Search for PDFs recursively in the directory tree.")
parser.add_option_group(pdf_ingest_group)
arxiv_update_group = optparse.OptionGroup(parser, "Pre-print Update Mode",
description=None)
arxiv_update_group.add_option(
'-u', '--update_arxiv',
default=False, action="store_true",
help='Check arXiv pre-prints for updated bibcodes')
arxiv_update_group.add_option(
'-f', '--from_date',
help='MM/YY date of publication from which to start updating arXiv')
arxiv_update_group.add_option(
'-t', '--to_date',
help='MM/YY date of publication up to which update arXiv')
parser.add_option_group(arxiv_update_group)
options, args = parser.parse_args()
# Get preferences from (optional) config file
prefs = Preferences()
# inject options into preferences for later reference
prefs['options'] = options.__dict__
if options.debug:
prefs['debug'] = True
# Logging saves to log file on when in DEBUG mode
# Always prints to STDOUT as well
logging.basicConfig(
level=logging.DEBUG,
format='%(asctime)s %(name)s %(levelname)s %(message)s',
filename=prefs['log_path'])
if not prefs['debug']:
logging.getLogger('').setLevel(logging.INFO)
ch = logging.StreamHandler()
ch.setLevel(logging.DEBUG)
logging.getLogger('').addHandler(ch)
logging.info("Starting ADS to BibDesk")
logging.debug("ADS to BibDesk version %s" % VERSION)
logging.debug("Python: %s", sys.version)
# Launch the specific workflow
if options.ingest_pdfs:
ingest_pdfs(options, args, prefs)
elif options.only_pdf:
# short-circuit process_articles
# since BibDesk is not needed
# FIXME smells like a refactor
process_token(args[0], prefs, None)
elif options.update_arxiv:
update_arxiv(options, prefs)
else:
process_articles(args, prefs)
def process_articles(args, prefs, delay=15):
"""Workflow for processing article tokens and running process_token()
to add the article to BibDesk.
"""
# FIXME is there ever actually a case where args is None?
if args:
article_tokens = list(args)
else:
# Try to use standard input
article_tokens = [s.strip() for s in sys.stdin.readlines()
if s.strip()]
# AppKit hook for BibDesk
bibdesk = BibDesk()
for article_token in article_tokens:
print("Processing article {0}".format(article_token))
try:
process_token(article_token, prefs, bibdesk)
except ADSException as err:
logging.debug('%s failed - %s' % (article_token, err))
if len(article_tokens) > 1 and article_token != article_tokens[-1]:
time.sleep(delay)
bibdesk.app.dealloc()
# FIXME this function needs to be refactored
def process_token(article_token, prefs, bibdesk):
"""Process a single article token from the user, adding it to BibDesk.
Parameters
----------
article_token : str
Any user-supplied `str` token.
prefs : :class:`Preferences`
A `Preferences` instance.
bibdesk : :class:`BibDesk`
A `BibDesk` AppKit hook instance.
"""
# Determine what we're dealing with
# The goal is to get a URL into ADS
logging.debug("process_token found article token %s", article_token)
connector = ADSConnector(article_token, prefs)
ads_parser = ADSHTMLParser(prefs=prefs)
if isinstance(connector.ads_read, basestring):
# parse the ADS HTML file
ads_parser.parse(connector.ads_read)
elif connector.ads_read and getattr(connector, 'bibtex') is not None:
# parsed from arXiv - dummy ads info
ads_parser.bibtex = connector.bibtex
ads_parser.arxivid = ads_parser.bibtex.Eprint
ads_parser.author = ads_parser.bibtex.Author.split(' and ')
ads_parser.title = ads_parser.bibtex.Title
ads_parser.abstract = ads_parser.bibtex.Abstract
ads_parser.comment = ads_parser.bibtex.AdsComment
# original URL where we *should* have gotten the info
ads_parser.bibtex.AdsURL = connector.ads_url
# inject arXiv mirror into ArXivURL
if 'arxiv_mirror' in prefs and prefs['arxiv_mirror']:
tmpurl = urlsplit(ads_parser.bibtex.ArXivURL)
ads_parser.bibtex.ArXivURL = urlunsplit(
(tmpurl.scheme,
prefs['arxiv_mirror'],
tmpurl.path, tmpurl.query,
tmpurl.fragment))
# link for PDF download
try:
link = [l.get('href', '') for l in ads_parser.bibtex.info['link']
if l.get('title') == 'pdf'][0]
ads_parser.links = {'preprint': link}
except IndexError:
logging.debug("process_token could not find preprint PDF link")
pass
elif connector.ads_read is None:
logging.debug("process_token skipping %s", article_token)
logging.info("Skipped article {0}".format(article_token))
import ipdb; ipdb.set_trace()
return False
# get PDF first
pdf = ads_parser.get_pdf()
# TODO refactor this out into a 'show_pdf' function
if prefs['options'].get('only_pdf'):
if not pdf.endswith('.pdf'):
return False
# just open PDF
reader = ('pdf_reader' in prefs and
prefs['pdf_reader'] is not None) and \
prefs['pdf_reader'] or 'Finder'
app = AppKit.NSAppleScript.alloc()
app.initWithSource_(
'tell application "%s" '
'to open ("%s" as POSIX file)' % (reader, pdf)).\
executeAndReturnError_(None)
# get name of the used viewer
# (Finder may be defaulted to something else than Preview)
if reader == 'Finder':
reader = app.initWithSource_(
'return name of (info for (path to frontmost application))').\
executeAndReturnError_(None)[0].stringValue()
logging.debug('opening %s with %s' % (pdf, reader))
if 'skim' in reader.lower():
time.sleep(1) # give it time to open
app.initWithSource_(
'tell application "%s" to set view settings '
'of first document to {auto scales:true}'
% reader).executeAndReturnError_(None)
app.dealloc()
return True
# search for already existing publication
# with exactly the same title and first author
# match title and first author using fuzzy string comparison
# FIXME put cutoff into preferences; could be related to problems
# FIXME refactor this out
found = difflib.get_close_matches(
ads_parser.title, bibdesk.titles,
n=1, cutoff=.7)
kept_pdfs = []
kept_fields = {}
kept_groups=[]
# first author is the same
if len(found)>0:
if found and difflib.SequenceMatcher(
None,
bibdesk.authors(bibdesk.pid(found[0]))[0],
ads_parser.author[0]).ratio() > .6:
# further comparison on abstract
abstract = bibdesk('abstract', bibdesk.pid(found[0])).stringValue()
if not abstract or difflib.SequenceMatcher(
None, abstract,
ads_parser.abstract).ratio() > .6:
pid = bibdesk.pid(found[0])
kept_groups=bibdesk.get_groups(pid)
# keep all fields for later comparison
# (especially rating + read bool)
kept_fields = dict((k, v) for k, v in
zip(bibdesk('return name of fields', pid, True),
bibdesk('return value of fields', pid, True))
# Adscomment may be arXiv only
if k != 'Adscomment')
# plus BibDesk annotation
kept_fields['BibDeskAnnotation'] = bibdesk(
'return its note', pid).stringValue()
kept_pdfs += bibdesk.safe_delete(pid)
notify('Duplicate publication removed',
article_token, ads_parser.title)
bibdesk.refresh()
# FIXME refactor out this bibdesk import code?
# add new entry
pub = bibdesk(
'import from "%s"' % ads_parser.bibtex.__str__().
replace('\\', r'\\').replace('"', r'\"'))
# pub id
pub = pub.descriptorAtIndex_(1).descriptorAtIndex_(3).stringValue()
# automatic cite key
bibdesk('set cite key to generated cite key', pub)
# abstract
if ads_parser.abstract.startswith('http://'):
# old scanned articles
bibdesk(
'make new linked URL at end of linked URLs '
'with data "%s"' % ads_parser.abstract, pub)
else:
bibdesk(
'set abstract to "%s"'
% ads_parser.abstract.replace('\\', r'\\').replace('"', r'\"').replace('}', ' ').replace('{', ' '),pub)
doi = bibdesk('value of field "doi"', pub).stringValue()
if pdf.endswith('.pdf'):
# register PDF into BibDesk
bibdesk('add POSIX file "%s" to beginning of linked files' % pdf, pub)
# automatic file name
bibdesk('auto file', pub)
elif 'http' in pdf and not doi:
# URL for electronic version - only add it if no DOI link present
# (they are very probably the same)
bibdesk(
'make new linked URL at end of linked URLs with data "%s"'
% pdf, pub)
# add URLs as linked URL if not there yet
urls = bibdesk(
'value of fields whose name ends with "url"',
pub, strlist=True)
urlspub = bibdesk('linked URLs', pub, strlist=True)
for u in [u for u in urls if u not in urlspub]:
bibdesk(
'make new linked URL at end of linked URLs with data "%s"'
% u, pub)
# add old annotated files
for kept_pdf in kept_pdfs:
bibdesk('add POSIX file "%s" to end of linked files' % kept_pdf, pub)
# re-insert custom fields
bibdesk(
'set its note to "%s"' % kept_fields.pop('BibDeskAnnotation', ''),
pub)
newFields = bibdesk('return name of fields', pub, True)
for k, v in kept_fields.items():
if k not in newFields:
bibdesk('set value of field "%s" to "%s"' % (k, v), pub)
notify('New publication added',
bibdesk('cite key', pub).stringValue(),
ads_parser.title)
# add back the static groups assignment
if kept_groups!=[]:
new_groups=bibdesk.add_groups(pub,kept_groups)
def ingest_pdfs(options, args, prefs):
"""Workflow for attempting to ingest a directory of PDFs into BibDesk.
This workflow attempts to scape DOIs from the PDF text, which are then
added to BibDesk using the usual `process_token` function.
"""
assert len(args) == 1, "Please pass a path to a directory"
pdf_dir = args[0]
assert os.path.exists(pdf_dir) is True, "%s does not exist" % pdf_dir
print("Searching", pdf_dir)
if options.recursive:
# Recursive glob solution from
# http://stackoverflow.com/a/2186565
pdf_paths = []
for root, dirnames, filenames in os.walk(pdf_dir):
for filename in fnmatch.filter(filenames, '*.pdf'):
pdf_paths.append(os.path.join(root, filename))
else:
pdf_paths = glob.glob(os.path.join(pdf_dir, "*.pdf"))
# Process each PDF, looking for a DOI
grabber = PDFDOIGrabber()
found = []
for i, pdf_path in enumerate(pdf_paths):
dois = grabber.search(pdf_path)
if not dois:
logging.info(
"%i of %i: no DOIs for %s"
% (i + 1, len(pdf_paths), pdf_path))
else:
found.extend(dois)
for doi in dois:
logging.info(
"%i of %i: %s = %s"
% (i + 1, len(pdf_paths), os.path.basename(pdf_path), doi))
# let process_articles inject everything
if found:
logging.info('Adding %i articles to BibDesk...' % len(found))
process_articles(found, prefs)
def update_arxiv(options, prefs):
"""
Workflow for updating arXiv pre-prints automatically with newer bibcodes.
"""
assert options.from_date is None or \
re.match('^\d{2}/\d{2}$', options.from_date) is not None, \
'--from_date needs to be in MM/YY format'
assert options.to_date is None or \
re.match('^\d{2}/\d{2}$', options.to_date) is not None, \
'--to_date needs to be in MM/YY format'
def b2d(bibtex):
"""BibTex -> publication date"""
m = re.search('Month = \{?(\w*)\}?', bibtex).group(1)
y = re.search('Year = \{?(\d{4})\}?', bibtex).group(1)
return datetime.datetime.strptime(m + y, '%b%Y')
def recent(added, fdate, tdate):
fromdate = fdate is not None and \
datetime.datetime.strptime(fdate, '%m/%y')\
or datetime.datetime(1900, 1, 1)
todate = tdate is not None and \
datetime.datetime.strptime(tdate, '%m/%y')\
or datetime.datetime(3000, 1, 1)
return fromdate <= added <= todate
# frontmost opened BibDesk document
bibdesk = BibDesk()
ids = []
# check for adsurl containing arxiv or astro.ph bibcodes
arxiv = bibdesk(
'return publications whose '
'(value of field "Adsurl" contains "arXiv") or '
'(value of field "Adsurl" contains "astro.ph")')
if arxiv.numberOfItems():
# extract arxiv id from the ADS url
ids = [u.split('bib_query?')[-1].split('abs/')[-1] for u in
bibdesk(
'tell publications whose '
'(value of field "Adsurl" contains "arXiv") or '
'(value of field "Adsurl" contains "astro.ph") '
'to return value of field "Adsurl"', strlist=True)]
dates = [b2d(b) for b in
bibdesk(
'tell publications whose '
'(value of field "Adsurl" contains "arXiv") or '
'(value of field "Adsurl" contains "astro.ph") '
'to return bibtex string', strlist=True)]
# arxiv ids to search
ids = [b for d, b in zip(dates, ids)
if recent(d, options.from_date, options.to_date)]
bibdesk.app.dealloc()
if not ids:
print('Nothing to update!')
sys.exit()
else:
n = len(ids)
t = math.ceil(n * 15. / 60.)
if t > 1:
time_unit = "minutes"
else:
time_unit = "minute"
logging.info('Checking %i arXiv entries for changes...' % n)
logging.info(
'(to prevent ADS flooding this will take a while, '
'check back in around %i %s)' % (t, time_unit))
changed = []
for n, i in enumerate(ids):
# sleep for 15 seconds, to prevent ADS flooding
time.sleep(15)
logging.debug("arxiv id %s" % i)
# these are ADS bibcodes by default
adsURL = urlunsplit(
('http', prefs['ads_mirror'],
'cgi-bin/bib_query', i, ''))
logging.debug("adsURL %s" % adsURL)
# parse the ADS HTML file
ads_parser = ADSHTMLParser(prefs=prefs)
try:
ads_parser.parse_at_url(adsURL)
except ADSException as err:
logging.debug('%s update failed: %s' % (i, err))
continue
logging.debug("ads.bibtex %s" % ads_parser.bibtex)
if ads_parser.bibtex is None: # ADSHTMLParser failed
logging.debug("FAILURE: ads.bibtex is None!")
continue
if ads_parser.bibtex.bibcode != i:
logging.info(
'%i. %s has become %s'
% (n + 1, i, ads_parser.bibtex.bibcode))
changed.append(i)
else:
logging.info('%i. %s has not changed' % (n + 1, i))
continue
# run changed entries through the main loop
if changed and raw_input(
'Updating %i entries, continue? (y/[n]) '
% len(changed)) in ('Y', 'y'):
logging.info(
'(to prevent ADS flooding, we will wait for a while '
'between each update, so go grab a coffee)')
process_articles(changed, prefs)
elif not changed:
logging.info('Nothing to update!')
def notify(title, subtitle, desc, sticky=False):
"""Publish a notification to Notification Center
Adaptation of original by Moises Aranas
https://github.com/maranas/pyNotificationCenter
"""
try:
import objc
notification = objc.lookUpClass('NSUserNotification').alloc().init()
notification.setTitle_(title)
notification.setInformativeText_(desc)
notification.setSubtitle_(subtitle)
objc.lookUpClass('NSUserNotificationCenter').\
defaultUserNotificationCenter().scheduleNotification_(notification)
notification.dealloc()
# this will be either ImportError or objc.nosuchclass_error
except Exception:
# revert to growl
if subtitle:
desc = subtitle + ': ' + desc
growl_notify(title, desc, sticky)
def growl_notify(title, desc, sticky=False):
title = title.replace('"', r'\"')
desc = desc.replace('"', r'\"')
# http://bylr.net/3/2011/09/applescript-and-growl/
# is growl running?
app = AppKit.NSAppleScript.alloc()
growl = app.initWithSource_(
'tell application "System Events" to return '
'processes whose creator type contains "GRRR"').\
executeAndReturnError_(None)[0]
if growl.numberOfItems():
growlapp = growl.descriptorAtIndex_(1).descriptorAtIndex_(3).\
stringValue()
# register
app.initWithSource_(
'tell application "%s" to register as '
'application "BibDesk" '
'all notifications {"BibDesk notification"} '
'default notifications {"BibDesk notification"}'
% growlapp).executeAndReturnError_(None)
# and notify
app.initWithSource_(
'tell application "%s" to notify with name '
'"BibDesk notification" application name "BibDesk" '
'priority 0 title "%s" description "%s" %s'
% (growlapp, title, desc, "with sticky" if sticky else '')).\
executeAndReturnError_(None)
app.dealloc()
def has_annotationss(f):
return sp.Popen(
"strings %s | grep -E 'Contents[ ]{0,1}\('" % f,
shell=True, stdout=sp.PIPE,
stderr=open('/dev/null', 'w')).stdout.read() != b'' # b''!=u'' in Python 3
def get_redirect(url):
"""Utility function to intercept final URL of HTTP redirection"""
"""
EJOURNAL:
ads-ejournal-link: nature;mnras-tmp;
MNRAS: redirect to the HTML page link + "?error=cookie-not-supported..."
NATURE: redirect to the HTML page link
ads-article-link :
MNRAS w/ Paywall: redirect to the HTML page link + '?redirectedFrom=PDF'
MNRAS w/o Paywall: redirect to PDF
"""
# if 'MNRAS' in url:
# # MNRAS rejects requests from "non-browsers"
# response = requests.get(url,
# headers={'User-Agent':
# 'Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_5) AppleWebKit/537.36 (KHTML, like Gecko) Chrome/61.0.3163.100 Safari/537.36'})
# else:
# response = requests.get(url)
#response.raise_for_status()
#return response.url
try:
out = urlopen(url)
red_url=out.geturl()
except URLError as out:
red_url=out.geturl()
if 'nature.com' in red_url:
red_url=re.split('\?error=',red_url)[0]
return red_url
class PDFDOIGrabber(object):
"""Converts PDFs to text and attempts to match all DOIs"""
def __init__(self):
super(PDFDOIGrabber, self).__init__()
regstr = r'(10[.][0-9]{4,}(?:[.][0-9]+)*/(?:(?!["&\'<>\)\.,])\S)+)'
self.pattern = re.compile(regstr)
def search(self, pdfPath):
"""Return a list of DOIs in the text of the PDF at `pdfPath`"""
json_path = os.path.splitext(pdfPath)[0] + ".json"
if os.path.exists(json_path):
os.remove(json_path)
sp.call('pdf2json -q "%s" "%s"' % (pdfPath, json_path), shell=True)
data = open(json_path, 'r').read()
doi_matches = self.pattern.findall(data)
if os.path.exists(json_path):
os.remove(json_path)
# strings can find some stuff that pdf2json does not
if not doi_matches:
data = sp.Popen(
"strings %s" % pdfPath,
shell=True, stdout=sp.PIPE,
stderr=open('/dev/null', 'w')).stdout.read()
doi_matches = self.pattern.findall(data)
return list(set(doi_matches))
class ADSConnector(object):
"""Receives input (token), derives an ADS url, and attempts to connect
to the corresponding ADS abstract page with urllib2.urlopen().
Tokens are tested in order of:
- arxiv identifiers
- bibcodes / digital object identifier (DOI)
- ADS urls
- arxiv urls
"""
def __init__(self, token, prefs):
super(ADSConnector, self).__init__()
self.token = str(token)
self.prefs = prefs
self.ads_url = None # string URL to ADS
self.ads_read = None # a urllib2.urlopen connection to ADS
self.url_parts = urlsplit(token) # supposing it is a URL
# An arXiv identifier or URL?
if self._is_arxiv():
logging.debug("ADSConnector found arXiv ID %s", self.token)
# Try to open the ADS page
if not self._read(self.ads_url):
# parse arxiv instead:
logging.debug('ADS page (%s) not found for %s' %
(self.ads_url, self.token))
notify('ADS page not found', self.token,
'Parsing the arXiv page...')
arxiv_bib = ArXivParser()
try:
arxiv_bib.parse_at_id(self.arxiv_id)
logging.debug(
"arXiv page (%s) parsed for %s"
% (arxiv_bib.url, self.token))
except ArXivException as err:
logging.debug("ADS and arXiv failed, you're in trouble...")
raise ADSException(err)
# dummy ads_read and bibtex
self.ads_read = True
self.bibtex = arxiv_bib
# A bibcode from ADS?
elif not self.url_parts.scheme and self._is_bibcode():
logging.debug("ADSConnector found bibcode/DOI %s", self.token)
else:
# If the path lacks http://, tack it on because
# the token *must* be a URL now
if not self.token.startswith("http://"):
self.token = 'http://' + self.token
# supposing it is a URL
self.url_parts = urlsplit(self.token)
# An abstract page at any ADS mirror site?
if self.url_parts.netloc in self.prefs.adsmirrors \
and self._is_ads_page():
logging.debug("ADSConnector found ADS page %s", self.token)
else:
logging.debug("ADSConnector found nothing for %s", self.token)
def _is_arxiv(self):
"""Try to classify the token as an arxiv article, either:
- new style (YYMM.NNNN), or
- old style (astro-ph/YYMMNNN)
:return: True if ADS page is recovered
"""
arxiv_pattern = re.compile('(\d{4,6}\.\d{4,6}|astro\-ph/\d{7})')
arxiv_matches = arxiv_pattern.findall(self.token)
if len(arxiv_matches) == 1:
self.arxiv_id = arxiv_matches[0]
self.ads_url = urlunsplit((
'http',
self.prefs['ads_mirror'],
'cgi-bin/bib_query',
'arXiv:%s' % self.arxiv_id, ''))
return True
else:
self.arxiv_id = None
return False
def _is_bibcode(self):
"""Test if the token corresponds to an ADS bibcode or DOI"""
self.ads_url = urlunsplit((
'http', self.prefs['ads_mirror'],
'doi/%s' % self.token, '', ''))
read = self._read(self.ads_url)
if read:
return read
else:
self.ads_url = urlunsplit((
'http',
self.prefs['ads_mirror'], 'abs/%s' % self.token, '', ''))
read = self._read(self.ads_url)
return read
def _is_ads_page(self):
"""Test if the token is a url to an ADS abstract page"""
# use our ADS mirror
url = self.url_parts
self.ads_url = urlunsplit((
url.scheme,
self.prefs['ads_mirror'],
url.path, url.query, url.fragment))
return self._read(self.ads_url)
def _read(self, ads_url):
"""Attempt a connection to ads_url, saving the read to
self.ads_read.
:return: True if successful, False otherwise
"""
try:
# remove <head>...</head> - often broken HTML
response = requests.get(ads_url,
headers={'User-Agent':
'Mozilla/5.0 (Macintosh; Intel Mac OS X 10_9_5) AppleWebKit/537.36 \
(KHTML, like Gecko) Chrome/68.0.3440.106 Safari/537.36'})
response.raise_for_status()
htmldata = response.text
#htmldata = urllib2.urlopen(ads_url).read()
#try:
# htmldata = htmldata.decode('utf-8')
#except AttributeError:
# pass
self.ads_read = re.sub(
r'<head>[\s\S]*</head>', '',
htmldata)
return True
except Exception as ex:
print("Exception is: {0}".format(ex))
return False
class Preferences(object):
"""Manages the preferences on disk and in memory. Preferences are accessed
with by a dictionary-like interface.
"""
def __init__(self):
self.prefs_path = os.path.expanduser('~/.adsbibdesk')
self._adsmirrors = [
'esoads.eso.org',
'adsabs.harvard.edu',
'cdsads.u-strasbg.fr',
'ukads.nottingham.ac.uk',
'ads.ari.uni-heidelberg.de',
'ads.inasan.ru',
'ads.mao.kiev.ua',
'ads.astro.puc.cl',
'ads.on.br',
'ads.nao.ac.jp',
'ads.bao.ac.cn',
'ads.iucaa.ernet.in',
'www.ads.lipi.go.id']
self.prefs = self._get_default_prefs() # Hard coded defaults dict
new_prefs = self._get_prefs() # load user prefs from disk
self.prefs.update(new_prefs) # override defaults with user prefs
self._keys = self.prefs.keys()
self._iter_index = -1
def __getitem__(self, key):
return self.prefs[key]
def __setitem__(self, key, value):
self.prefs[key] = value
self._keys = self.prefs.keys()
def __iter__(self):
return self
def next(self):
if self._iter_index == len(self._keys) - 1:
self._iter_index = -1
raise StopIteration
self._iter_index += 1
return self._keys[self._iter_index]
def _get_default_prefs(self):
""":return: a dictionary of the full set of default preferences. This
is done in case the user's preference file is missing a key-value pair.
"""
return {"ads_mirror": "adsabs.harvard.edu",
"arxiv_mirror": None,
"download_pdf": True,
"pdf_reader": None,
"ssh_user": None,
"ssh_server": None,
"ssh_port": 22,
"debug": False,
"log_path": os.path.expanduser("~/.adsbibdesk.log")}
def _get_prefs(self):
"""Read preferences files from `self.prefs_path`, creates one
otherwise.
"""
prefs = {}
# create a default preference file if non existing
if not os.path.exists(self.prefs_path):
self._write_default_prefs()
for l in open(self.prefs_path):
if l.strip() and not l.strip().startswith('#'):
if '=' not in l:
# badly formed setting
continue
k, v = l.strip().split('=')
if not v:
v = None
elif v.strip().lower() in ('true', 'yes'):
v = True
elif v.strip().lower() in ('false', 'no'):
v = False
elif v.strip().lower() == 'none':
v = None
prefs[k] = v
return prefs
def _write_default_prefs(self):
"""
Set a default preferences file (~/.adsbibdesk)
"""
with open(self.prefs_path, 'w') as prefs:
prefs.write("""# ADS mirror
ads_mirror=%s
# arXiv mirror
# (leave it unset to use the arXiv mirror pointed by your ADS mirror)
arxiv_mirror=%s
# download PDFs?
download_pdf=%s
# set these to use your account on a remote machine for fetching
# (refereed) PDF's you have no access locally
ssh_user=%s
ssh_server=%s
ssh_port=%s""" % (self.prefs['ads_mirror'], self.prefs['arxiv_mirror'],
self.prefs['download_pdf'], self.prefs['ssh_user'],
self.prefs['ssh_server'], self.prefs['ssh_port']))
@property
def adsmirrors(self):
return self._adsmirrors
class BibTex(object):
def __init__(self, url):
"""
Create BibTex instance from ADS BibTex URL
"""
bibresponse = requests.get(url)
bibtex = bibresponse.text.split("\n")
#bibtex_obj = urllib2.urlopen(url)
#charset = bibtex_obj.headers.get_content_charset()
#bibtex = [x.decode(charset) for x in bibtex_obj.readlines()]
bibtex = ' '.join([l.strip() for l in bibtex]).strip()
bibtex = bibtex[re.search('@[A-Z]+\{', bibtex).start():]
self.type, self.bibcode, self.info = self.parsebib(bibtex)
def __str__(self):
return (','.join(
['@' + self.type + '{' + self.bibcode] +
['%s=%s' % (i, j) for i, j in self.info.items()]) + '}')
def parsebib(self, bibtex):
"""
Parse bibtex code into dictionary
"""
r = re.search(
'(?<=^@)(?P<type>[A-Z]+){(?P<bibcode>\S+)(?P<info>,.+)}$',
bibtex)
s = re.split('(,\s\w+\s=\s)', r.group('info'))
info = dict(
[(i[1:].replace('=', '').strip(), j.strip())
for i, j in zip(s[1::2], s[2::2])])
return r.group('type'), r.group('bibcode'), info