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authorBryan Newbold <bnewbold@archive.org>2020-11-08 21:54:24 -0800
committerBryan Newbold <bnewbold@archive.org>2020-11-08 21:54:24 -0800
commita68aadc4107fc68dc2748c52dab8a4bd92cca022 (patch)
treeda3da0a847d5c10dee873e8bce8198a39c12ce1f /python
parent6a701f966b8bc760bf904c0569562b0159e13559 (diff)
downloadsandcrawler-a68aadc4107fc68dc2748c52dab8a4bd92cca022.tar.gz
sandcrawler-a68aadc4107fc68dc2748c52dab8a4bd92cca022.zip
move some PDF URL extraction into declarative format
Diffstat (limited to 'python')
-rw-r--r--python/sandcrawler/html.py134
-rw-r--r--python/sandcrawler/html_metadata.py158
-rw-r--r--python/sandcrawler/ingest.py16
-rw-r--r--python/tests/test_html.py8
-rw-r--r--python/tests/test_html_metadata.py4
5 files changed, 177 insertions, 143 deletions
diff --git a/python/sandcrawler/html.py b/python/sandcrawler/html.py
index 70761a3..14561bf 100644
--- a/python/sandcrawler/html.py
+++ b/python/sandcrawler/html.py
@@ -11,24 +11,6 @@ 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):
"""
@@ -87,56 +69,8 @@ def extract_fulltext_url(html_url, html_body):
if meta and meta.get('content'):
meta_generator = meta['content'].strip()
- # 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 and href.get('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.revistas.unam.mx/index.php/rep/article/view/35503/32336
- href = soup.find('a', attrs={"id":"pdfDownloadLink"})
- if href and href.get('href'):
- url = href['href'].strip()
- if url.startswith('http'):
- return dict(pdf_url=url, technique='href_pdfDownloadLink')
- elif url.startswith('/'):
- return dict(pdf_url=host_prefix+url, technique='href_pdfDownloadLink')
-
- # 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 and embed.get('src'):
- 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:
@@ -188,26 +122,6 @@ def extract_fulltext_url(html_url, html_body):
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
@@ -238,16 +152,6 @@ def extract_fulltext_url(html_url, 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/")
@@ -313,15 +217,6 @@ def extract_fulltext_url(html_url, html_body):
url = html_url.replace('/doi/full/10.', '/doi/pdf/10.').replace('/doi/10.', '/doi/pdf/10.')
return dict(pdf_url=url, technique='ehp.niehs.nigh.gov-url')
- # journals.tsu.ru (and maybe others)
- # http://journals.tsu.ru/psychology/&journal_page=archive&id=1815&article_id=40405
- # <a class='file pdf' href='http://journals.tsu.ru/engine/download.php?id=150921&area=files'>Скачать электронную версию публикации</a>
- href = soup.find('a', attrs={"class":"file pdf"})
- if href:
- url = href['href'].strip()
- if url.startswith('http'):
- return dict(pdf_url=url, technique='href_file_pdf-pdf')
-
# cogentoa.com
# https://www.cogentoa.com/article/10.1080/23311975.2017.1412873
if "://www.cogentoa.com/article/" in html_url and not ".pdf" in html_url:
@@ -342,17 +237,6 @@ def extract_fulltext_url(html_url, html_body):
if url and url.startswith('http'):
return dict(pdf_url=url, technique='figshare-json')
- # eurosurveillance
- # https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2020.25.11.2000230
- if "://www.eurosurveillance.org/content/" in html_url:
- # <a href="/deliver/fulltext/eurosurveillance/25/11/eurosurv-25-11-3.pdf?itemId=/content/10.2807/1560-7917.ES.2020.25.11.2000230&mimeType=pdf&containerItemId=content/eurosurveillance" class="pdf " title="Download" rel="http://instance.metastore.ingenta.com/content/10.2807/1560-7917.ES.2020.25.11.2000230" target="/content/10.2807/1560-7917.ES.2020.25.11.2000230-pdf" >
- href = soup.find('a', attrs={"class":"pdf", "title": "Download"})
- if href:
- url = href['href'].strip()
- if not url.startswith('http'):
- url = host_prefix + url
- return dict(pdf_url=url, technique='eurosurveillance-href')
-
# CNKI COVID-19 landing pages
# http://en.gzbd.cnki.net/gzbt/detail/detail.aspx?FileName=HBGF202002003&DbName=GZBJ7920&DbCode=GZBJ
if '://en.gzbd.cnki.net/KCMS/detail/detail.aspx' in html_url:
@@ -410,3 +294,21 @@ def extract_fulltext_url(html_url, html_body):
return dict(pdf_url=url, technique='guess-url-plus-pdf')
return dict()
+
+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
diff --git a/python/sandcrawler/html_metadata.py b/python/sandcrawler/html_metadata.py
index eb89a01..15f44f4 100644
--- a/python/sandcrawler/html_metadata.py
+++ b/python/sandcrawler/html_metadata.py
@@ -1,4 +1,5 @@
+import sys
import datetime
from typing import List, Optional, Any, Tuple, Dict
import urllib.parse
@@ -212,6 +213,13 @@ XML_FULLTEXT_PATTERNS: List[dict] = [
"attr": "href",
"technique": "OJS Gallery XML link",
},
+ {
+ "in_fulltext_url": "/download/xml/",
+ "selector": "a[title='XML']",
+ "attr": "href",
+ "technique": "ARPHA XML link",
+ "example_page": "https://zookeys.pensoft.net/article/26391",
+ },
]
HTML_FULLTEXT_PATTERNS: List[dict] = [
@@ -241,17 +249,137 @@ HTML_FULLTEXT_PATTERNS: List[dict] = [
},
]
+# This is a database of matching patterns. Most of these discovered by hand,
+# looking at OA journal content that failed to craw/ingest.
PDF_FULLTEXT_PATTERNS: List[dict] = [
{
- "selector": "meta[name='citation_pdf_url']",
+ "selector": "head meta[name='citation_pdf_url']",
+ "attr": "content",
+ "technique": "citation_pdf_url",
+ },
+ {
+ "selector": "head meta[name='bepress_citation_pdf_url']",
"attr": "content",
"technique": "citation_pdf_url",
},
{
- "selector": "meta[name='bepress_citation_pdf_url']",
+ "in_doc_url": "journals.lww.com",
+ "selector": "head meta[name='wkhealth_pdf_url']",
+ "attr": "content",
+ "technique": "wkhealth_pdf_url",
+ "example_page": "https://journals.lww.com/otainternational/Fulltext/2019/03011/Trauma_systems_in_North_America.2.aspx",
+ },
+ {
+ "selector": "head meta[propery='citation_pdf_url']",
"attr": "content",
"technique": "citation_pdf_url",
+ # eg, researchgate
+ },
+ {
+ "selector": "head meta[name='eprints.document_url']",
+ "attr": "content",
+ "technique": "citation_pdf_url (property)",
+ },
+ {
+ "in_doc_url": "/doi/10.",
+ "in_fulltext_url": "/doi/pdf/",
+ "selector": "a.show-pdf",
+ "attr": "href",
+ "technique": "SAGE/UTP show-pdflink",
+ "example_page": "https://journals.sagepub.com/doi/10.1177/2309499019888836",
+ # also http://utpjournals.press/doi/10.3138/cjh.ach.54.1-2.05
+ },
+ {
+ "in_doc_url": "/doi/10.",
+ "in_fulltext_url": "/doi/pdf/",
+ "selector": "a[title='PDF']",
+ "attr": "href",
+ "technique": "title=PDF link",
+ "example_page": "https://pubs.acs.org/doi/10.1021/acs.estlett.9b00379",
+ },
+ {
+ "in_doc_url": "/article/view/",
+ "selector": "a#pdfDownloadLink",
+ "attr": "href",
+ "technique": "pdfDownloadLink link",
+ "example_page": "http://www.revistas.unam.mx/index.php/rep/article/view/35503/32336",
+ },
+ {
+ "in_fulltext_url": "/pdf/",
+ "selector": "a.show-pdf",
+ "attr": "href",
+ "technique": "SAGE PDF link",
+ "example_page": "http://journals.sagepub.com/doi/pdf/10.1177/2309499019888836",
+ },
+ {
+ "in_doc_url": "://elifesciences.org/articles/",
+ "in_fulltext_url": "/download/",
+ "selector": "a[data-download-type='pdf-article']",
+ "attr": "href",
+ "technique": "eLife PDF link",
+ "example_page": "https://elifesciences.org/articles/59841",
+ },
+ {
+ "in_doc_url": "://www.jcancer.org/",
+ "in_fulltext_url": ".pdf",
+ "selector": ".divboxright a.text-button",
+ "attr": "href",
+ "technique": "jcancer PDF link",
+ "example_page": "https://www.jcancer.org/v10p4038.htm",
+ },
+ {
+ "in_doc_url": "://www.tandfonline.com/doi/full/10.",
+ "in_fulltext_url": "/pdf/",
+ "selector": "a.show-pdf",
+ "attr": "href",
+ "technique": "t+f show-pdf link",
+ "example_page": "https://www.tandfonline.com/doi/full/10.1080/19491247.2019.1682234",
+ },
+ {
+ "in_doc_url": "article_id=",
+ "in_fulltext_url": "download.php",
+ "selector": "a.file.pdf",
+ "attr": "href",
+ "technique": "pdf file link",
+ "example_page": "http://journals.tsu.ru/psychology/&journal_page=archive&id=1815&article_id=40405",
+ },
+ {
+ "in_doc_url": "/content/10.",
+ "in_fulltext_url": "pdf",
+ "selector": "a.pdf[title='Download']",
+ "attr": "href",
+ "technique": "pdf file link",
+ "example_page": "https://www.eurosurveillance.org/content/10.2807/1560-7917.ES.2020.25.11.2000230",
},
+ {
+ "selector": "embed[type='application/pdf']",
+ "attr": "src",
+ "technique": "PDF embed",
+ "example_page": "http://www.jasstudies.com/DergiTamDetay.aspx?ID=3401",
+ },
+ {
+ "in_doc_url": "/html/",
+ "in_fulltext_url": "create_pdf",
+ "selector": ".AbsPdfFigTab img[src='images/pdf-icon.jpg'] + a",
+ "attr": "href",
+ "technique": "PDF URL link",
+ "example_page": "http://www.aed.org.cn/nyzyyhjxb/html/2018/4/20180408.htm",
+ },
+ {
+ "in_doc_url": "/archive-detail/",
+ "in_fulltext_url": ".pdf",
+ "selector": ".contact-list a.download-pdf",
+ "attr": "href",
+ "technique": "PDF URL link",
+ "example_page": "http://www.bezmialemscience.org/archives/archive-detail/article-preview/editorial/20439",
+ },
+]
+
+FULLTEXT_URL_PATTERNS_SKIP = [
+ # wiley has a weird almost-blank page we don't want to loop on
+ "://onlinelibrary.wiley.com/doi/pdf/"
+ "://doi.org/"
+ "://dx.doi.org/"
]
RELEASE_TYPE_MAP = {
@@ -310,6 +438,7 @@ def html_extract_fulltext_url(doc_url: str, doc: HTMLParser, patterns: List[dict
Returns null or a tuple of (url, technique)
"""
+ self_doc_url: Optional[Tuple[str, str]] = None
for pattern in patterns:
if not 'selector' in pattern:
continue
@@ -321,13 +450,24 @@ def html_extract_fulltext_url(doc_url: str, doc: HTMLParser, patterns: List[dict
continue
if 'attr' in pattern:
val = elem.attrs[pattern['attr']]
- if val:
- val = urllib.parse.urljoin(doc_url, val)
- assert val
- if 'in_fulltext_url' in pattern:
- if not pattern['in_fulltext_url'] in val:
- continue
- return (val, pattern.get('technique', 'unknown'))
+ if not val:
+ continue
+ val = urllib.parse.urljoin(doc_url, val)
+ assert val
+ if 'in_fulltext_url' in pattern:
+ if not pattern['in_fulltext_url'] in val:
+ continue
+ for skip_pattern in FULLTEXT_URL_PATTERNS_SKIP:
+ if skip_pattern in val.lower():
+ continue
+ if url_fuzzy_equal(doc_url, val):
+ # don't link to self, unless no other options
+ self_doc_url = (val, pattern.get('technique', 'unknown'))
+ continue
+ return (val, pattern.get('technique', 'unknown'))
+ if self_doc_url:
+ print(f" WARN: returning fulltext URL pointing to self", file=sys.stderr)
+ return self_doc_url
return None
def html_extract_biblio(doc_url: str, doc: HTMLParser) -> Optional[BiblioMetadata]:
diff --git a/python/sandcrawler/ingest.py b/python/sandcrawler/ingest.py
index 2f6be05..602f9c5 100644
--- a/python/sandcrawler/ingest.py
+++ b/python/sandcrawler/ingest.py
@@ -605,16 +605,14 @@ class IngestFileWorker(SandcrawlerWorker):
if ingest_type == "pdf" and html_ish_resource:
- fulltext_url = extract_fulltext_url(resource.terminal_url, resource.body)
-
# the new style of URL extraction (already computed)
- # we aren't quite ready to adopt this for the PDF path (which
- # has more complex logic to avoid loops, etc)
- #if not fulltext_url and html_biblio and html_biblio.pdf_fulltext_url:
- # fulltext_url = dict(
- # pdf_url=html_biblio.pdf_fulltext_url,
- # technique="html_biblio",
- # )
+ if html_biblio and html_biblio.pdf_fulltext_url:
+ fulltext_url = dict(
+ pdf_url=html_biblio.pdf_fulltext_url,
+ technique="html_biblio",
+ )
+ else:
+ fulltext_url = extract_fulltext_url(resource.terminal_url, resource.body)
result['extract_next_hop'] = fulltext_url
if not fulltext_url:
diff --git a/python/tests/test_html.py b/python/tests/test_html.py
index 7d58a39..9a81852 100644
--- a/python/tests/test_html.py
+++ b/python/tests/test_html.py
@@ -31,11 +31,3 @@ def test_extract_fulltext_url():
f.read(),
)
assert resp['pdf_url'] == "https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0213978&type=printable"
-
- with open('tests/files/elife_article.html', 'rb') as f:
- resp = extract_fulltext_url(
- "https://elifesciences.org/articles/44753",
- f.read(),
- )
- assert resp['pdf_url'] == "https://elifesciences.org/download/aHR0cHM6Ly9jZG4uZWxpZmVzY2llbmNlcy5vcmcvYXJ0aWNsZXMvNDQ3NTMvZWxpZmUtNDQ3NTMtdjIucGRm/elife-44753-v2.pdf?_hash=CfyqOqVryCR4OjcMTfcdpeIWAGZznmh9jXksYKYChCw%3D"
-
diff --git a/python/tests/test_html_metadata.py b/python/tests/test_html_metadata.py
index b428b0d..bf26a98 100644
--- a/python/tests/test_html_metadata.py
+++ b/python/tests/test_html_metadata.py
@@ -39,6 +39,7 @@ def test_html_metadata_plos() -> None:
assert meta.publisher == "Public Library of Science"
assert meta.raw_references and "citation_title=Reticuloendotheliosis virus sequences within the genomes of field strains of fowlpox virus display variability;citation_author=P Singh;citation_author=W. M. Schnitzlein;citation_author=D. N. Tripathy;citation_journal_title=J. Virol;citation_volume=77;citation_number=77;citation_first_page=5855;citation_last_page=5862;citation_publication_date=2003;" in meta.raw_references
assert meta.release_type == "article-journal"
+ assert meta.pdf_fulltext_url == "https://journals.plos.org/plosone/article/file?id=10.1371/journal.pone.0213978&type=printable"
def test_html_metadata_elife() -> None:
@@ -46,7 +47,7 @@ def test_html_metadata_elife() -> None:
with open('tests/files/elife_article.html', 'r') as f:
elife_html = f.read()
- meta = html_extract_biblio("http://example.org", HTMLParser(elife_html))
+ meta = html_extract_biblio("https://elifesciences.org/articles/44753", HTMLParser(elife_html))
assert meta is not None
assert meta.title == "Parallel visual circuitry in a basal chordate"
assert meta.doi == "10.7554/eLife.44753"
@@ -63,6 +64,7 @@ def test_html_metadata_elife() -> None:
# 2019-04-18
assert meta.release_date == datetime.date(year=2019, month=4, day=18)
assert meta.publisher == "eLife Sciences Publications Limited"
+ assert meta.pdf_fulltext_url == "https://elifesciences.org/download/aHR0cHM6Ly9jZG4uZWxpZmVzY2llbmNlcy5vcmcvYXJ0aWNsZXMvNDQ3NTMvZWxpZmUtNDQ3NTMtdjIucGRm/elife-44753-v2.pdf?_hash=CfyqOqVryCR4OjcMTfcdpeIWAGZznmh9jXksYKYChCw%3D"
def test_html_metadata_peerj() -> None: