phyks/bmc
1
0
Fork 0
Code Issues Pull Requests Projects Releases Wiki Activity

Download of papers working

Browse Source 
You should pass the url of the pdf file to the script, along with the
`download` parameter. It will try the proxies in the `params.py` file,
until it finds one that allow him to get the pdf file.

TODO : Use pdfparanoia to remove watermarks
This commit is contained in:
Phyks 2014-04-26 11:52:19 +02:00
parent b9f6e145e9
commit 02e679bc72
4 changed files with 58 additions and 473 deletions
Show Stats Download Patch File Download Diff File Expand all files Collapse all files

19
README.md
View File

@ -23,6 +23,9 @@ BiblioManager will always use standard formats such as BibTeX, so that you can e
## Current status ## Current status
* Able to import a PDF / djvu file, automagically find the DOI / ISBN, get the bibtex entry back and add it to the library. If DOI / ISBN search fails, it will prompt you for it. * Able to import a PDF / djvu file, automagically find the DOI / ISBN, get the bibtex entry back and add it to the library. If DOI / ISBN search fails, it will prompt you for it.
* Able to download a URL, using any specified proxy (you can list many and it will try all of them) and store the pdf file with its metadata.
Should be almost working and usable now, although still to be considered as **experimental**.
**Important note :** I use it for personnal use, but I don't read articles from many journals. If you find any file which is not working, please fill an issue or send me an e-mail with the relevant information. There are alternative ways to get the metadata for example, and I didn't know really which one was the best one as writing this code. **Important note :** I use it for personnal use, but I don't read articles from many journals. If you find any file which is not working, please fill an issue or send me an e-mail with the relevant information. There are alternative ways to get the metadata for example, and I didn't know really which one was the best one as writing this code.
@ -32,29 +35,16 @@ TODO -- To be updated
Install pdfminer, pdfparanoia (via pip) and requesocks. Install pdfminer, pdfparanoia (via pip) and requesocks.
Init the submodules and install Zotero translation server.
Copy params.py.example as params.py and customize it. Copy params.py.example as params.py and customize it.
Install pdftotext. Install pdftotext.
Install djvulibre to use djvu files. Install djvulibre to use djvu files.
Install isbntools with pip. Install isbntools with pip.
## Paperbot
Paperbot is a command line utility that fetches academic papers. When given a URL on stdin or as a CLI argument, it fetches the content and returns a public link on stdout. This seems to help enhance the quality of discussion and make us less ignorant.
All content is scraped using [zotero/translators](https://github.com/zotero/translators). These are javascript scrapers that work on a large number of academic publisher sites and are actively maintained. Paperbot offloads links to [zotero/translation-server](https://github.com/zotero/translation-server), which runs the zotero scrapers headlessly in a gecko and xulrunner environment. The scrapers return metadata and a link to the pdf. Then paperbot fetches that particular pdf. When given a link straight to a pdf, which paperbot is also happy to compulsively archive it.
I kept part of the code to handle pdf downloading, and added a backend behind it.
Paperbot can try multiple instances of translation-server (configured to use different ways to access content) and different SOCKS proxies to retrieve the content.
## Used source codes ## Used source codes
* [zotero/translators](https://github.com/zotero/translators) : Links finder
* [zotero/translation-server](https://github.com/zotero/translation-server) : Links finder
* [pdfparanoia](https://github.com/kanzure/pdfparanoia) : Watermark removal * [pdfparanoia](https://github.com/kanzure/pdfparanoia) : Watermark removal
* [paperbot](https://github.com/kanzure/paperbot) although my fetching of papers is way more basic
## License ## License
@ -71,6 +61,7 @@ TODO
A list of ideas and TODO. Don't hesitate to give feedback on the ones you really want or to propose your owns. A list of ideas and TODO. Don't hesitate to give feedback on the ones you really want or to propose your owns.
* pdfparanoia to remove the watermarks on pdf files
* Webserver interface * Webserver interface
* Various re.compile ? * Various re.compile ?
* check output of subprocesses before it ends * check output of subprocesses before it ends

463
fetcher.py
View File

@ -1,462 +1,25 @@
#!/usr/bin/python2 -u #!/usr/bin/python2 -u
# coding=utf8 # coding=utf8
""" """
Fetches papers. Fetches papers.
""" """
import re
import os
import json
import params
import random
import requesocks as requests import requesocks as requests
import lxml.etree import params
import sys
from time import time
from StringIO import StringIO
import pdfparanoia def download_url(url):
for proxy in params.proxies:
def download_proxy(line, zotero, proxy, verbose=True): r_proxy = {
sys.stderr.write("attempting download of %s through %s and %s\n" % "http": proxy,
(line, zotero, proxy)) "https": proxy,
headers = {
"Content-Type": "application/json",
} }
data = { r = requests.get(url, proxies=r_proxy)
"url": line,
"sessionid": "what"
}
data = json.dumps(data) if r.status_code != 200 or 'pdf' not in r.headers['content-type']:
continue
response = requests.post(zotero, data=data, headers=headers)
if response.status_code != 200 or response.content == "[]":
sys.stderr.write("no valid reply from zotero\n")
sys.stderr.write("status %d\n" % response.status_code)
sys.stderr.write("content %s\n" % response.content)
return -1 # fatal
sys.stderr.write("content %s\n" % response.content)
# see if there are any attachments
content = json.loads(response.content)
item = content[0]
title = item["title"]
if not item.has_key("attachments"):
sys.stderr.write("no attachement with this proxy\n")
return 1 # try another proxy
pdf_url = None
for attachment in item["attachments"]:
if attachment.has_key("mimeType") and "application/pdf" in attachment["mimeType"]:
pdf_url = attachment["url"]
break
if not pdf_url:
sys.stderr.write("no PDF attachement with this proxy\n")
return 1 # try another proxy
user_agent = "Mozilla/5.0 (X11; Linux i686 (x86_64)) AppleWebKit/536.11 (KHTML, like Gecko) Chrome/20.0.1132.57 Safari/536.11"
headers = {
"User-Agent": user_agent,
}
sys.stderr.write("try retrieving " +
str(pdf_url) + " through proxy " + proxy + "\n")
response = None
session = requests.Session()
session.proxies = {
'http': proxy,
'https': proxy}
try:
if pdf_url.startswith("https://"):
response = session.get(pdf_url, headers=headers, verify=False)
else:
response = session.get(pdf_url, headers=headers)
except requests.exceptions.ConnectionError:
sys.stderr.write("network failure on download " +
str(pdf_url) + "\n")
return 1
# detect failure
if response.status_code == 401:
sys.stderr.write("HTTP 401 unauthorized when trying to fetch " +
str(pdf_url) + "\n")
return 1
elif response.status_code != 200:
sys.stderr.write("HTTP " + str(response.status_code)
+ " when trying to fetch " + str(pdf_url) + "\n")
return 1
data = response.content
if "pdf" in response.headers["content-type"]:
try:
data = pdfparanoia.scrub(StringIO(data))
except:
# this is to avoid a PDFNotImplementedError
pass
# grr..
title = title.encode("ascii", "ignore")
title = title.replace(" ", "_")
title = title[:params.maxlen]
path = os.path.join(params.folder, title + ".pdf")
file_handler = open(path, "w")
file_handler.write(data)
file_handler.close()
filename = requests.utils.quote(title)
# Remove an ending period, which sometimes happens when the
# title of the paper has a period at the end.
if filename[-1] == ".":
filename = filename[:-1]
url = params.url + filename + ".pdf"
print(url)
return 0
def download(line, verbose=True):
"""
Downloads a paper.
"""
# don't bother if there's nothing there
if len(line) < 5 or (not "http://" in line and not "https://" in line) or not line.startswith("http"):
return
for line in re.findall('http[s]?://(?:[a-zA-Z]|[0-9]|[$-_@.&+]|[!*\(\),]|(?:%[0-9a-fA-F][0-9a-fA-F]))+', line):
line = filter_fix(line)
# fix for login.jsp links to ieee xplore
line = fix_ieee_login_urls(line)
line = fix_jstor_pdf_urls(line)
ok = False
for (zotero, proxy) in params.servers:
s = download_proxy(line, zotero, proxy, verbose)
if s < 0:
break
if s == 0:
ok = True
break
if not ok:
for (zotero, proxy) in params.servers:
s = download_url(line, proxy)
sys.stderr.write("return code " + str(s) + "\n")
if s == 0:
ok = True
break
if not ok:
s = download_url(line, params.servers[0][1], last_resort=True)
if s != 0:
print "couldn't get it at all :("
return
download.commands = ["fetch", "get", "download"]
download.priority = "high"
download.rule = r'(.*)'
def download_ieee(url):
"""
Downloads an IEEE paper. The Zotero translator requires frames/windows to
be available. Eventually translation-server will be fixed, but until then
it might be nice to have an IEEE workaround.
"""
# url = "http://ieeexplore.ieee.org:80/xpl/freeabs_all.jsp?reload=true&arnumber=901261"
# url = "http://ieeexplore.ieee.org/iel5/27/19498/00901261.pdf?arnumber=901261"
raise NotImplementedError
def download_url(url, proxy, last_resort=False):
sys.stderr.write("attempting direct for %s through %s\n" % (url,
proxy))
session = requests.Session()
session.proxies = {
'http': proxy,
'https': proxy}
try:
response = session.get(url, headers={"User-Agent": "origami-pdf"})
except requests.exceptions.ConnectionError:
sys.stderr.write("network failure on download " +
str(url) + "\n")
return 1
content = response.content
# just make up a default filename
title = "%0.2x" % random.getrandbits(128)
# default extension
extension = ".txt"
if "pdf" in response.headers["content-type"]:
extension = ".pdf"
elif check_if_html(response):
# parse the html string with lxml.etree
tree = parse_html(content)
# extract some metadata with xpaths
citation_pdf_url = find_citation_pdf_url(tree, url)
citation_title = find_citation_title(tree)
# aip.org sucks, citation_pdf_url is wrong
if citation_pdf_url and "link.aip.org/" in citation_pdf_url:
citation_pdf_url = None
if citation_pdf_url and "ieeexplore.ieee.org" in citation_pdf_url:
content = session.get(citation_pdf_url).content
tree = parse_html(content)
# citation_title = ...
# wow, this seriously needs to be cleaned up
if citation_pdf_url and citation_title and not "ieeexplore.ieee.org" in citation_pdf_url:
citation_title = citation_title.encode("ascii", "ignore")
response = session.get(citation_pdf_url, headers={"User-Agent": "pdf-defense-force"})
content = response.content
if "pdf" in response.headers["content-type"]:
extension = ".pdf"
title = citation_title
else:
if "sciencedirect.com" in url and not "ShoppingCart" in url:
try:
title = tree.xpath("//h1[@class='svTitle']")[0].text
pdf_url = tree.xpath("//a[@id='pdfLink']/@href")[0]
new_response = session.get(pdf_url, headers={"User-Agent": "sdf-macross"})
new_content = new_response.content
if "pdf" in new_response.headers["content-type"]:
extension = ".pdf"
except Exception:
pass
else:
content = new_content
response = new_response
elif "jstor.org/" in url:
# clean up the url
if "?" in url:
url = url[0:url.find("?")]
# not all pages have the <input type="hidden" name="ppv-title"> element
try:
title = tree.xpath("//div[@class='hd title']")[0].text
except Exception:
try:
title = tree.xpath("//input[@name='ppv-title']/@value")[0]
except Exception:
pass
# get the document id
document_id = None
if url[-1] != "/":
#if "stable/" in url:
#elif "discover/" in url:
#elif "action/showShelf?candidate=" in url:
#elif "pss/" in url:
document_id = url.split("/")[-1]
if document_id.isdigit():
try:
pdf_url = "http://www.jstor.org/stable/pdfplus/" + document_id + ".pdf?acceptTC=true"
new_response = session.get(pdf_url, headers={"User-Agent": "time-machine/1.1"})
new_content = new_response.content
if "pdf" in new_response.headers["content-type"]:
extension = ".pdf"
except Exception:
pass
else:
content = new_content
response = new_response
elif ".aip.org/" in url:
try:
title = tree.xpath("//title/text()")[0].split(" | ")[0]
pdf_url = [link for link in tree.xpath("//a/@href") if "getpdf" in link][0]
new_response = session.get(pdf_url, headers={"User-Agent": "time-machine/1.0"})
new_content = new_response.content
if "pdf" in new_response.headers["content-type"]:
extension = ".pdf"
except Exception:
pass
else:
content = new_content
response = new_response
elif "ieeexplore.ieee.org" in url:
try:
pdf_url = [url for url in tree.xpath("//frame/@src") if "pdf" in url][0]
new_response = session.get(pdf_url, headers={"User-Agent": "time-machine/2.0"})
new_content = new_response.content
if "pdf" in new_response.headers["content-type"]:
extension = ".pdf"
except Exception:
pass
else:
content = new_content
response = new_response
elif "h1 class=\"articleTitle" in content:
try:
title = tree.xpath("//h1[@class='articleTitle']")[0].text
title = title.encode("ascii", "ignore")
pdf_url = tree.xpath("//a[@title='View the Full Text PDF']/@href")[0]
except:
pass
else:
if pdf_url.startswith("/"):
url_start = url[:url.find("/",8)]
pdf_url = url_start + pdf_url
response = session.get(pdf_url, headers={"User-Agent": "pdf-teapot"})
content = response.content
if "pdf" in response.headers["content-type"]:
extension = ".pdf"
# raise Exception("problem with citation_pdf_url or citation_title")
# well, at least save the contents from the original url
pass
# make the title again just in case
if not title:
title = "%0.2x" % random.getrandbits(128)
# can't create directories
title = title.replace("/", "_")
title = title.replace(" ", "_")
title = title[:params.maxlen]
path = os.path.join(params.folder, title + extension)
if extension in [".pdf", "pdf"]:
try:
sys.stderr.write("got it! " +
str(url) + "\n")
content = pdfparanoia.scrub(StringIO(content))
except:
# this is to avoid a PDFNotImplementedError
pass
file_handler = open(path, "w")
file_handler.write(content)
file_handler.close()
title = title.encode("ascii", "ignore")
url = params.url + requests.utils.quote(title) + extension
if extension in [".pdf", "pdf"]:
print url
return 0
else:
sys.stderr.write("couldn't find it, dump: %s\n" % url)
if last_resort:
print "couldn't find it, dump: %s" % url
else:
return 1
return 0
def parse_html(content):
if not isinstance(content, StringIO):
content = StringIO(content)
parser = lxml.etree.HTMLParser()
tree = lxml.etree.parse(content, parser)
return tree
def check_if_html(response):
return "text/html" in response.headers["content-type"]
def find_citation_pdf_url(tree, url):
"""
Returns the <meta name="citation_pdf_url"> content attribute.
"""
citation_pdf_url = extract_meta_content(tree, "citation_pdf_url")
if citation_pdf_url and not citation_pdf_url.startswith("http"):
if citation_pdf_url.startswith("/"):
url_start = url[:url.find("/",8)]
citation_pdf_url = url_start + citation_pdf_url
else:
raise Exception("unhandled situation (citation_pdf_url)")
return citation_pdf_url
def find_citation_title(tree):
"""
Returns the <meta name="citation_title"> content attribute.
"""
citation_title = extract_meta_content(tree, "citation_title")
return citation_title
def extract_meta_content(tree, meta_name):
try:
content = tree.xpath("//meta[@name='" + meta_name + "']/@content")[0]
except:
return None
else:
return content
def filter_fix(url):
"""
Fixes some common problems in urls.
"""
if ".proxy.lib.pdx.edu" in url:
url = url.replace(".proxy.lib.pdx.edu", "")
return url
def fix_ieee_login_urls(url):
"""
Fixes urls point to login.jsp on IEEE Xplore. When someone browses to the
abstracts page on IEEE Xplore, they are sometimes sent to the login.jsp
page, and then this link is given to paperbot. The actual link is based on
the arnumber.
example:
http://ieeexplore.ieee.org/xpl/login.jsp?tp=&arnumber=806324&url=http%3A%2F%2Fieeexplore.ieee.org%2Fxpls%2Fabs_all.jsp%3Farnumber%3D806324
"""
if "ieeexplore.ieee.org/xpl/login.jsp" in url:
if "arnumber=" in url:
parts = url.split("arnumber=")
# i guess the url might not look like the example in the docstring
if "&" in parts[1]:
arnumber = parts[1].split("&")[0]
else:
arnumber = parts[1]
return "http://ieeexplore.ieee.org/xpl/articleDetails.jsp?arnumber=" + arnumber
# default case when things go wrong
return url
def fix_jstor_pdf_urls(url):
"""
Fixes urls pointing to jstor pdfs.
"""
if "jstor.org/" in url:
if ".pdf" in url and not "?acceptTC=true" in url:
url += "?acceptTC=true"
return url
if __name__ == '__main__':
if len(sys.argv) > 1:
for a in sys.argv[1:]:
download(a)
else:
reqs = []
while True:
l = sys.stdin.readline()
if not l:
break
reqs.append(time())
if len(reqs) > params.thresh:
delay = time() - reqs[len(reqs) - params.thresh + 1]
if params.limit - delay > 0:
print "rate limit exceeded, try again in %d second(s)" % (params.limit - delay)
else:
download(l)
return r.content
return False

46
main.py
View File

@ -3,6 +3,7 @@
from __future__ import print_function from __future__ import print_function
import fetcher
import sys import sys
import shutil import shutil
import requests import requests
@ -298,13 +299,14 @@ def addFile(src, filetype):
try: try:
shutil.copy2(src, new_name) shutil.copy2(src, new_name)
except IOError: except IOError:
new_name = False
sys.exit("Unable to move file to library dir " + params.folder+".") sys.exit("Unable to move file to library dir " + params.folder+".")
bibtexAppend(bibtex) bibtexAppend(bibtex)
print("File " + src + " successfully imported.") return new_name
def delete_id(ident): def deleteId(ident):
""" """
Delete a file based on its id in the bibtex file Delete a file based on its id in the bibtex file
""" """
@ -325,7 +327,7 @@ def delete_id(ident):
return True return True
def delete_file(filename): def deleteFile(filename):
""" """
Delete a file based on its filename Delete a file based on its filename
""" """
@ -348,13 +350,41 @@ def delete_file(filename):
return found return found
def downloadFile(url, filetype):
pdf = fetcher.download_url(url)
if pdf is not False:
with open(params.folder+'tmp.pdf', 'w+') as fh:
fh.write(pdf)
new_name = addFile(params.folder+'tmp.pdf', filetype)
try:
os.remove(params.folder+'tmp.pdf')
except:
warning('Unable to delete temp file '+params.folder+'tmp.pdf')
return new_name
else:
warning("Could not fetch "+url)
return False
if __name__ == '__main__': if __name__ == '__main__':
try: try:
if len(sys.argv) < 2: if len(sys.argv) < 2:
sys.exit("Usage : TODO") sys.exit("Usage : TODO")
if sys.argv[1] == 'download': if sys.argv[1] == 'download':
raise Exception('TODO') if len(sys.argv) < 3:
sys.exit("Usage : " + sys.argv[0] +
" download FILE [article|book]")
filetype = None
if len(sys.argv) > 3 and sys.argv[3] in ["article", "book"]:
filetype = sys.argv[3].lower()
new_name = downloadFile(sys.argv[2], filetype)
if new_name is not False:
print(sys.argv[2]+" successfully imported as "+new_name)
sys.exit()
if sys.argv[1] == 'import': if sys.argv[1] == 'import':
if len(sys.argv) < 3: if len(sys.argv) < 3:
@ -365,15 +395,17 @@ if __name__ == '__main__':
if len(sys.argv) > 3 and sys.argv[3] in ["article", "book"]: if len(sys.argv) > 3 and sys.argv[3] in ["article", "book"]:
filetype = sys.argv[3].lower() filetype = sys.argv[3].lower()
addFile(sys.argv[2], filetype) new_name = addFile(sys.argv[2], filetype)
if new_name is not False:
print("File " + src + " successfully imported as "+new_name+".")
sys.exit() sys.exit()
elif sys.argv[1] == 'delete': elif sys.argv[1] == 'delete':
if len(sys.argv) < 3: if len(sys.argv) < 3:
sys.exit("Usage : " + sys.argv[0] + " delete FILE|ID") sys.exit("Usage : " + sys.argv[0] + " delete FILE|ID")
if not delete_id(sys.argv[2]): if not deleteId(sys.argv[2]):
if not delete_file(sys.argv[2]): if not deleteFile(sys.argv[2]):
warning("Unable to delete "+sys.argv[2]) warning("Unable to delete "+sys.argv[2])
sys.exit(1) sys.exit(1)

1
translation-server

@ -1 +0,0 @@
Subproject commit 4d35648672c1ff2d2b6c61308ac7fcb684d63448