def scrape(url):
if "?fmt=txt" not in url:
url = url + "?fmt=txt"
urls, response = get_response_chain(url)
abstxt = response.read()
paper = build_paper(abstxt)
paper["source_urls"] = [uri for _, uri in urls] + [url.replace("?fmt=txt", "")]
return paper
def scrape(abstract_url):
req = urllib2.Request(abstract_url, headers=utils.headers)
urls, response = utils.get_response_chain(req)
if response.info().get('Content-Encoding') == 'gzip':
buf = StringIO( response.read())
f = gzip.GzipFile(fileobj=buf)
data = f.read()
else:
data = response.read()
page_text = data.decode('utf-8')
tree = lxml.html.fromstring(page_text)
article = make_blank_article()
article['scraper'] = 'npg'
article['source_urls'] = [uri for _, uri in urls]
article['title'] = get_meta('DC.title',tree)
if article['title'] == None:
article['title'] = get_meta('dc.title',tree)
article['publisher'] = get_meta('DC.publisher',tree)
if article['publisher'] == None:
article['publisher'] = get_meta('dc.publisher',tree)
article['author_names'] = get_meta_list('DC.creator',tree)
if article['author_names'] == None:
article['author_names'] = get_meta_list('dc.creator',tree)
article['abstract'] = get_meta('description', tree)
if not article['abstract']:
try:
article['abstract'] = tree.xpath("//div[@class='content']/p")[0].text_content()
except:
pass
if not article['abstract']:
try:
article['abstract'] = tree.xpath("//div[@id='abs']/p")[0].text_content()
except:
pass
article['citation']['journal'] = get_meta('citation_journal_title', tree)
article['citation']['volume'] = get_meta('prism.volume', tree)
article['citation']['page'] = get_meta('prism.startingPage', tree)
article['journal'] = get_meta('prism.publicationName', tree)
year = get_meta('citation_date', tree)
if year:
article['citation']['year'] = year[0:4]
article['ids'] = dict(zip(['doi'], [tree.xpath("//meta[@name='citation_doi']/@content")[0][4:]]))
pub_date = get_meta('DC.date', tree)
if pub_date == None:
pub_date = get_meta('dc.date', tree)
if pub_date:
split = pub_date.split('-')
article['date_published'] = make_datestamp(split[2], split[1], split[0])
#Specific abstract scrapers for subsidiary journals
if article['journal'] == 'The EMBO Journal':
try:
article['abstract'] = tree.xpath("//p[@class='lead']")[0].text_content()
except:
pass
elif article['journal'] == 'EMBO reports':
try:
article['abstract'] = tree.xpath("//p[@class='lead']")[0].text_content()
except:
pass
elif article['journal'] == 'Oncogene':
try:
article['abstract'] = tree.xpath("//p[@class='abs lead']")[0].text_content()
except:
pass
return article
def scrape(abstract_url):
req = urllib2.Request(abstract_url, headers=headers)
urls, page = utils.get_response_chain(req)
# Parse the HTML into a tree we can query
page_text = page.read().decode('utf-8')
tree = lxml.html.fromstring(page_text, base_url=abstract_url)
# Make XPATH queries for the first H1 and second H2 for the article title and how to cite it
title = tree.xpath('//h1')[0].text_content().strip()
cite_as = tree.xpath('//h2')[1].text.strip()
# Scrub the citation.
cite_as = re.sub('\s{1,}', ' ', cite_as)
cite_as = re.sub(' \[.*?\]', '', cite_as)
# Make our article object
article = {}
article['scraper'] = 'pr'
article['title'] = title
article['cite'] = cite_as
try:
article['citation'] = parse_citation(cite_as)
except:
pass
# Grab all links inside the the <div> with the id='aps-authors' and take their text as the author list.
article['author_names'] = [author.text.strip() for author in tree.xpath("//div[@id='aps-authors']//a")]
try:
article['author_names'].remove('Hide All Authors/Affiliations')
except:
pass
# Find the div with class 'aps-abstractbox' and grab the text of the first <p> within it as the abstract
try:
article['abstract'] = tree.xpath("//div[@class='aps-abstractbox']/p")[0].text_content()
except:
pass
months = {'January':1, 'February':2, 'March':3, 'April':4, 'May':5, 'June':6, 'July':7, 'August':8, 'September':9, 'October':10, 'November':11, 'December':12}
# Received 21 December 2011; revised 18 February 2012; published 9 April 2012
date_received = re.findall('Received\s+([0-9]+)\s+([A-Za-z]+)\s+([0-9]+)', page_text)
date_revised = re.findall('revised\s+([0-9]+)\s+([A-Za-z]+)\s+([0-9]+)', page_text)
date_published = re.findall('published\s+([0-9]+)\s+([A-Za-z]+)\s+([0-9]+)', page_text)
def make_datestamp(date_tuple):
year = int(date_tuple[2])
month = months[date_tuple[1]]
day = int(date_tuple[0])
return time.mktime(datetime.date(year, month, day).timetuple())
if date_received:
article['date_received'] = make_datestamp(date_received[0])
if date_revised:
article['date_revised'] = make_datestamp(date_revised[0])
if date_published:
article['date_published'] = make_datestamp(date_published[0])
# Find the <div> with the id 'aps-article-info' and take the respective columns cell contents as the type of id and id.
article['ids'] = dict(zip([e.text.strip().lower().replace(':','') for e in tree.xpath("//div[@id='aps-article-info']//div[@class='table-cell bold']")],\
[e.text.strip() for e in tree.xpath("//div[@id='aps-article-info']//div[@class='table-cell']")]))
if 'subject areas' in article['ids']:
article['pr_subject_areas'] = article['ids']['subject areas']
del article['ids']['subject areas']
article['journal'] = recognise_journal(page.geturl())
article['source_urls'] = [uri for _, uri in urls]
# PACS will be recognised as an id, even though its actually a list of categories.
# Split them out into their own custom field and delete from ids.
if 'pacs' in article['ids']:
article['categories'] = {'PACS':[c.strip() for c in
article['ids']['pacs'].split(',')]}
del article['ids']['pacs']
return article
