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import re
import sys
import urllib.parse
from bs4 import BeautifulSoup
RESEARCHSQUARE_REGEX = re.compile(r'"url":"(https://assets.researchsquare.com/files/.{1,50}/v\d+/Manuscript.pdf)"')
IEEEXPLORE_REGEX = re.compile(r'"pdfPath":"(/.*?\.pdf)"')
OVID_JOURNAL_URL_REGEX = re.compile(r'journalURL = "(http.*)";')
SCIENCEDIRECT_BOUNCE_URL_REGEX = re.compile(r"window.location = '(http.*)';")
def test_regex():
lines = """
blah
var journalURL = "https://journals.lww.com/co-urology/fulltext/10.1097/MOU.0000000000000689";
asdf"""
m = OVID_JOURNAL_URL_REGEX.search(lines)
assert m.group(1) == "https://journals.lww.com/co-urology/fulltext/10.1097/MOU.0000000000000689"
lines = """
window.onload = function () {
window.location = 'https://pdf.sciencedirectassets.com/320270/AIP/1-s2.0-S2590109519300424/main.pdf?X-Amz-Security-Token=IQoJb3JpZ2luX2VjEH0aCXVzLWVhc3QtMSJGMEQCICBF0dnrtKfpcs3T1kOjMS9w9gedqiLBrcbp4aKQSP8fAiAT9G426t6FWXHO2zPSXRFLq2eiqgbew2vkNKbcn87teyq9Awj1%2F%2F%2F%2F%2F%2F%2F%2F%2F%2F8BEAIaDDA1OTAwMzU0Njg2NSIMnZcTRhbvMwF%2F5PA5KpEDdN%2FDI4V%2BNMDWQDFeAdUc99Lyxak%2B6vhAsfCBCf8hhvrRpalz75e74%2FXMAQwMN9m6i98o0Ljv9od7cuQEy8t%2B0DLzjzX5n3%2FxmpttowhMUm1jc8tBniLKBjwhTyiSHwhdeaVZf6x2zCJ0EIOWMNJHp3iFEqpaFvkRZbC1KWK4XPNNKo72HCvXuG7xmGrdHByz91AP7UgIYCy4hT10fnM43gbOE4wW8fqpgnvwCId%2F2u8k4rQoCLBqLYZzqshCRm1DBbsXCQhTwDXiMC2Ek3f63yKgw7rRCAxvs0vqirG%2B4mJ6LADaztAFMtKDPfnd4e%2B7%2FvnKU2NeotrqrkRgOkIAoFumbQXf20ky6mKWyHBk%2FxirVp60vUcLQpUm2Pcp6ythYxUi9IJxRGX8EF6aV4UHuCpUDUE7o8N84KUXIedUpytUZx7Xoxfk9w%2BR3%2FgX4LEHfkrWgiFAS3bVxNGOeV7GTwcXdcAggbdCaiAe46dfv7DDedx0KhVKOPH7obfvShqd6TYc0BjrV4sx61594ZJ3%2FO0ws7Lj8AU67AF17%2B1NZ3Ugu%2BwG9Ys9s7OxG8E4kBJ58vEY1yuBOQK9y2we4%2FTGPuqSxCuezqA%2BseslXYP%2FRc%2FZL9xx%2FUYaSjZhk1p1mhojxgBrckJYU7d8c4ELMPmtVy6R1yd2VDUoawEU8SB7nbNnMKzqQ3RgGgqGJiELys6dt%2FIr%2BVhpqM%2FZT4zadvzs8P%2FLoGzUHJKNZt0f99wLvZilphV92E%2BOUnwC4wbg3i3af3zozULwgEr7T%2FX2VsyREgexlzk76qMALPn0lgnciUyyQXxyUWAilXYQ0mQdXefh9lFfycczvt0UEuarX9p1sMwl8Ve5aw%3D%3D&X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Date=20200110T210936Z&X-Amz-SignedHeaders=host&X-Amz-Expires=300&X-Amz-Credential=ASIAQ3PHCVTY23CMDBNC%2F20200110%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Signature=b43525576e1a0fdbab581481a3fe6db2862cbb2c69f2860b70cc8d444ccd73d5&hash=ccd128dfe597e704224bdfb4b3358de29b2be5d95887c71076bdab1236ba9e42&host=68042c943591013ac2b2430a89b270f6af2c76d8dfd086a07176afe7c76c2c61&pii=S2590109519300424&tid=spdf-74468ebd-6be6-43ac-b294-ced86e8eea58&sid=f9676d658285a749c46b6d081d965bb12aa8gxrqa&type=client';
refreshOriginalWindow();
}
"""
url = "https://pdf.sciencedirectassets.com/320270/AIP/1-s2.0-S2590109519300424/main.pdf?X-Amz-Security-Token=IQoJb3JpZ2luX2VjEH0aCXVzLWVhc3QtMSJGMEQCICBF0dnrtKfpcs3T1kOjMS9w9gedqiLBrcbp4aKQSP8fAiAT9G426t6FWXHO2zPSXRFLq2eiqgbew2vkNKbcn87teyq9Awj1%2F%2F%2F%2F%2F%2F%2F%2F%2F%2F8BEAIaDDA1OTAwMzU0Njg2NSIMnZcTRhbvMwF%2F5PA5KpEDdN%2FDI4V%2BNMDWQDFeAdUc99Lyxak%2B6vhAsfCBCf8hhvrRpalz75e74%2FXMAQwMN9m6i98o0Ljv9od7cuQEy8t%2B0DLzjzX5n3%2FxmpttowhMUm1jc8tBniLKBjwhTyiSHwhdeaVZf6x2zCJ0EIOWMNJHp3iFEqpaFvkRZbC1KWK4XPNNKo72HCvXuG7xmGrdHByz91AP7UgIYCy4hT10fnM43gbOE4wW8fqpgnvwCId%2F2u8k4rQoCLBqLYZzqshCRm1DBbsXCQhTwDXiMC2Ek3f63yKgw7rRCAxvs0vqirG%2B4mJ6LADaztAFMtKDPfnd4e%2B7%2FvnKU2NeotrqrkRgOkIAoFumbQXf20ky6mKWyHBk%2FxirVp60vUcLQpUm2Pcp6ythYxUi9IJxRGX8EF6aV4UHuCpUDUE7o8N84KUXIedUpytUZx7Xoxfk9w%2BR3%2FgX4LEHfkrWgiFAS3bVxNGOeV7GTwcXdcAggbdCaiAe46dfv7DDedx0KhVKOPH7obfvShqd6TYc0BjrV4sx61594ZJ3%2FO0ws7Lj8AU67AF17%2B1NZ3Ugu%2BwG9Ys9s7OxG8E4kBJ58vEY1yuBOQK9y2we4%2FTGPuqSxCuezqA%2BseslXYP%2FRc%2FZL9xx%2FUYaSjZhk1p1mhojxgBrckJYU7d8c4ELMPmtVy6R1yd2VDUoawEU8SB7nbNnMKzqQ3RgGgqGJiELys6dt%2FIr%2BVhpqM%2FZT4zadvzs8P%2FLoGzUHJKNZt0f99wLvZilphV92E%2BOUnwC4wbg3i3af3zozULwgEr7T%2FX2VsyREgexlzk76qMALPn0lgnciUyyQXxyUWAilXYQ0mQdXefh9lFfycczvt0UEuarX9p1sMwl8Ve5aw%3D%3D&X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Date=20200110T210936Z&X-Amz-SignedHeaders=host&X-Amz-Expires=300&X-Amz-Credential=ASIAQ3PHCVTY23CMDBNC%2F20200110%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Signature=b43525576e1a0fdbab581481a3fe6db2862cbb2c69f2860b70cc8d444ccd73d5&hash=ccd128dfe597e704224bdfb4b3358de29b2be5d95887c71076bdab1236ba9e42&host=68042c943591013ac2b2430a89b270f6af2c76d8dfd086a07176afe7c76c2c61&pii=S2590109519300424&tid=spdf-74468ebd-6be6-43ac-b294-ced86e8eea58&sid=f9676d658285a749c46b6d081d965bb12aa8gxrqa&type=client"
m = SCIENCEDIRECT_BOUNCE_URL_REGEX.search(lines)
assert m.group(1) == url
def extract_fulltext_url(html_url, html_body):
"""
Takes an HTML document (and URL), assumed to be a landing page, and tries
to find a fulltext PDF url.
"""
host_prefix = '/'.join(html_url.split('/')[:3])
soup = BeautifulSoup(html_body, 'html.parser')
### General Tricks ###
# highwire-style meta tag
meta = soup.find('meta', attrs={"name":"citation_pdf_url"})
if not meta:
meta = soup.find('meta', attrs={"name":"bepress_citation_pdf_url"})
if not meta:
# researchgate does this; maybe others also?
meta = soup.find('meta', attrs={"property":"citation_pdf_url"})
# wiley has a weird almost-blank page we don't want to loop on
if meta and not "://onlinelibrary.wiley.com/doi/pdf/" in html_url:
url = meta['content'].strip()
if url.startswith('/'):
return dict(pdf_url=host_prefix+url, technique='citation_pdf_url')
elif url.startswith('http'):
return dict(pdf_url=url, technique='citation_pdf_url')
else:
print("malformed citation_pdf_url? {}".format(url), file=sys.stderr)
# sage, and also utpjournals (see below)
# https://journals.sagepub.com/doi/10.1177/2309499019888836
# <a href="http://journals.sagepub.com/doi/pdf/10.1177/2309499019888836" class="show-pdf" target="_self">
# <a href="http://utpjournals.press/doi/pdf/10.3138/cjh.ach.54.1-2.05" class="show-pdf" target="_blank">
href = soup.find('a', attrs={"class":"show-pdf"})
if href:
url = href['href'].strip()
if url.startswith('http'):
return dict(pdf_url=url, technique='href_show-pdf')
# ACS (and probably others) like:
# https://pubs.acs.org/doi/10.1021/acs.estlett.9b00379
# <a href="/doi/pdf/10.1021/acs.estlett.9b00379" title="PDF" target="_blank" class="button_primary"><i class="icon-file-pdf-o"></i><span>PDF (1 MB)</span></a>
href = soup.find('a', attrs={"title":"PDF"})
if href:
url = href['href'].strip()
if url.startswith('http'):
return dict(pdf_url=url, technique='href_title')
elif url.startswith('/'):
return dict(pdf_url=host_prefix+url, technique='href_title')
# http://www.jasstudies.com/DergiTamDetay.aspx?ID=3401
# <embed src="/files/jass_makaleler/1359848334_33-Okt.%20Yasemin%20KARADEM%C4%B0R.pdf" type="application/pdf" />
embed = soup.find('embed', attrs={"type": "application/pdf"})
if embed:
url = embed['src'].strip()
if url.startswith('/'):
url = host_prefix+url
if url.startswith('http'):
return dict(pdf_url=url, technique='embed_type')
### Publisher/Platform Specific ###
# eLife (elifesciences.org)
if '://elifesciences.org/articles/' in html_url:
anchor = soup.find("a", attrs={"data-download-type": "pdf-article"})
if anchor:
url = anchor['href'].strip()
assert '.pdf' in url
return dict(pdf_url=url, technique='publisher')
# research square (researchsquare.com)
if 'researchsquare.com/article/' in html_url:
# JSON in body with a field like:
# "url":"https://assets.researchsquare.com/files/4a57970e-b002-4608-b507-b95967649483/v2/Manuscript.pdf"
m = RESEARCHSQUARE_REGEX.search(html_body.decode('utf-8'))
if m:
url = m.group(1)
assert len(url) < 4096
return dict(release_stage="manuscript", pdf_url=url, technique='publisher')
# elseiver linking hub
# https://linkinghub.elsevier.com/retrieve/pii/S1569199319308975
if '://linkinghub.elsevier.com/retrieve/pii/' in html_url:
# <input type="hidden" name="redirectURL" value="http%3A%2F%2Fcysticfibrosisjournal.com%2Fretrieve%2Fpii%2FS1569199319308975" id="redirectURL"/>
redirect = soup.find("input", attrs={"name": "redirectURL"})
if redirect:
url = redirect['value'].strip()
if 'http' in url:
url = urllib.parse.unquote(url)
# drop any the query parameter
url = url.split('?via')[0]
return dict(next_url=url, technique="elsevier-linkinghub")
# sciencedirect PDF bounce page
# https://www.sciencedirect.com/science/article/pii/S2590109519300424/pdfft?md5=854f43a44de186eb58674b8e20631691&pid=1-s2.0-S2590109519300424-main.pdf
if '://www.sciencedirect.com/' in html_url and html_url.endswith(".pdf"):
# window.location = 'https://pdf.sciencedirectassets.com/320270/AIP/1-s2.0-S2590109519300424/main.pdf?X-Amz-Security-Token=[...]&X-Amz-Algorithm=AWS4-HMAC-SHA256&X-Amz-Date=20200110T210936Z&X-Amz-SignedHeaders=host&X-Amz-Expires=300&X-Amz-Credential=ASIAQ3PHCVTY23CMDBNC%2F20200110%2Fus-east-1%2Fs3%2Faws4_request&X-Amz-Signature=[...]&hash=[...]&host=[...]&pii=S2590109519300424&tid=spdf-74468ebd-6be6-43ac-b294-ced86e8eea58&sid=[...]&type=client';
m = SCIENCEDIRECT_BOUNCE_URL_REGEX.search(html_body.decode('utf-8'))
if m:
url = m.group(1)
assert len(url) < 4000
return dict(pdf_url=url, technique="sciencedirect-bounce")
# ieeexplore.ieee.org
# https://ieeexplore.ieee.org/document/8730316
if '://ieeexplore.ieee.org/document/' in html_url:
# JSON in body with a field like:
# "pdfPath":"/iel7/6287639/8600701/08730316.pdf",
m = IEEEXPLORE_REGEX.search(html_body.decode('utf-8'))
if m:
url = m.group(1)
assert len(url) < 4096
return dict(release_stage="published", pdf_url=host_prefix+url, technique="ieeexplore")
# https://ieeexplore.ieee.org/stamp/stamp.jsp?arnumber=8730313
if '://ieeexplore.ieee.org/stamp/stamp.jsp?arnumber' in html_url:
# HTML iframe like:
# <iframe src="http://web.archive.org/web/20191026011528if_/https://ieeexplore.ieee.org/ielx7/6287639/8600701/08730313.pdf?tp=&arnumber=8730313&isnumber=8600701&ref=" frameborder="0"></iframe>
iframe = soup.find("iframe")
if iframe and '.pdf' in iframe['src']:
return dict(pdf_url=iframe['src'], technique="iframe")
# utpjournals.press
# https://utpjournals.press/doi/10.3138/cjh.ach.54.1-2.05
if '://utpjournals.press/doi/10.' in html_url:
# <a href="http://utpjournals.press/doi/pdf/10.3138/cjh.ach.54.1-2.05" class="show-pdf" target="_blank">
href = soup.find('a', attrs={"class":"show-pdf"})
if href:
url = href['href'].strip()
if url.startswith('http'):
return dict(pdf_url=url, technique='publisher-href')
# https://www.jcancer.org/v10p4038.htm
# simple journal-specific href
if '://www.jcancer.org/' in html_url and html_url.endswith(".htm"):
# <a href='v10p4038.pdf' class='textbutton'>PDF</a>
href = soup.find('a', attrs={"class":"textbutton"})
if href:
url = href['href'].strip()
if url.endswith(".pdf") and not "http" in url:
return dict(pdf_url=host_prefix+"/"+url, technique='journal-href')
# https://insights.ovid.com/crossref?an=00042307-202001000-00013
# Ovid is some kind of landing page bounce portal tracking run-around.
# Can extract actual journal URL from javascript blob in the HTML
if '://insights.ovid.com/crossref' in html_url:
# var journalURL = "https://journals.lww.com/co-urology/fulltext/10.1097/MOU.0000000000000689";
m = OVID_JOURNAL_URL_REGEX.search(html_body.decode('utf-8'))
if m:
url = m.group(1)
assert len(url) < 4096
return dict(next_url=url, technique='ovid')
# osf.io
# https://osf.io/8phvx/
# https://osf.io/preprints/socarxiv/8phvx/
# wow, they ship total javascript crud! going to just guess download URL
# based on URL for now. Maybe content type header would help?
if '://osf.io/' in html_url and not '/download' in html_url:
if not html_url.endswith("/"):
next_url = html_url+"/download"
else:
next_url = html_url+"download"
return dict(next_url=next_url, technique='osf-by-url')
# wiley
# https://onlinelibrary.wiley.com/doi/pdf/10.1111/1467-923X.12787
if "://onlinelibrary.wiley.com/doi/pdf/" in html_url:
if b"/doi/pdfdirect/" in html_body:
next_url = html_url.replace('/doi/pdf/', '/doi/pdfdirect/')
return dict(next_url=next_url, technique='wiley-pdfdirect')
# taylor and frances
# https://www.tandfonline.com/doi/full/10.1080/19491247.2019.1682234
# <a href="/doi/pdf/10.1080/19491247.2019.1682234?needAccess=true" class="show-pdf" target="_blank">
if "://www.tandfonline.com/doi/full/10." in html_url:
href = soup.find('a', attrs={"class":"show-pdf"})
if href:
url = href['href'].strip()
if "/pdf/" in url:
return dict(pdf_url=host_prefix+url, technique='publisher-href')
# arxiv abstract pages
if "://arxiv.org/abs/" in html_url:
url = html_url.replace("/abs/", "/pdf/")
return dict(pdf_url=url, technique='arxiv-url')
# american archivist (OA)
# https://americanarchivist.org/doi/abs/10.17723/aarc.62.2.j475270470145630
if "://americanarchivist.org/doi/abs/" in html_url:
# <a href="/doi/pdf/10.17723/aarc.62.2.j475270470145630" target="_blank">
hrefs = soup.find_all('a', attrs={"target":"_blank"})
for href in hrefs:
url = href['href'].strip()
if "/doi/pdf/" in url:
if url.startswith('http'):
return dict(pdf_url=url, technique='publisher-href')
elif url.startswith('/'):
return dict(pdf_url=host_prefix+url, technique='publisher-href')
# protocols.io
# https://www.protocols.io/view/flow-cytometry-protocol-mgdc3s6
if "://www.protocols.io/view/" in html_url and not html_url.endswith(".pdf"):
url = html_url + ".pdf"
return dict(pdf_url=url, technique='protocolsio-url')
return dict()
|
