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from selenium import webdriver
from selenium.webdriver.firefox.firefox_binary import FirefoxBinary
from bs4 import BeautifulSoup
import os
import sys
import pypandoc
from time import sleep
import subprocess
import requests
import json
import tempfile
_publishers = list()
_publisher_domains = dict()
_publisher_names = list()
class Publisher(object):
"""General class for scientific article publishers"""
def __init__(self, url, doi=None, out_format='epub'):
self.url = url
self.doi = doi
def get_final_url(self):
pass
def check_fulltext(self):
pass
def soupify(self):
"""Get HTML from article's page"""
self.get_final_url()
os.environ['MOZ_HEADLESS'] = '1'
print('Starting headless browser...',end='',flush=True)
if(os.name == "posix"):
binary = FirefoxBinary('/usr/bin/firefox')
elif(os.name == "nt"):
binary = FirefoxBinary('C:/Program Files/Mozilla Firefox/firefox.exe')
else:
sys.exit("Error: Unknown OS")
try:
driver = webdriver.Firefox(firefox_binary=binary,
log_path=os.path.join(tempfile.gettempdir(), 'gecko_log'))
print('done')
except:
sys.exit('Failed to load Firefox; is it installed?')
print('Loading page................',end="",flush=True)
try:
driver.get(self.url)
except:
sys.exit('Failed to load URL')
if self.doi != None:
sleep(5) #To allow redirects
sleep(5)
print('done')
self.url = driver.current_url
self.soup = BeautifulSoup(driver.page_source,'html.parser')
driver.quit()
def doi2json(self):
"""Get a dictionary of metadata for a given DOI."""
url = "http://dx.doi.org/" + self.doi
headers = {"accept": "application/json"}
r = requests.get(url, headers = headers)
self.meta = r.json()
def get_metadata(self):
"""Extract metadata from DOI"""
self.doi2json()
self.title = self.meta['title']
self.author_surnames = []
self.author_givennames = []
for i in self.meta['author']:
self.author_surnames.append(i['family'])
self.author_givennames.append(i['given'])
self.journal = self.meta['container-title']
if 'published-print' in self.meta.keys():
self.year = str(self.meta['published-print']['date-parts'][0][0])
else:
self.year = str(self.meta['published-online']['date-parts'][0][0])
try:
self.volume = str(self.meta['volume'])
except:
self.volume = ''
try:
self.pages = str(self.meta['page'])
except:
self.pages = ''
def get_citation(self,link=False):
"""Generate a formatted citation from metadata"""
all_authors = ''
for i in range(0,len(self.author_surnames)):
all_authors += self.author_surnames[i] + ', '
all_authors += self.author_givennames[i]
if(i != (len(self.author_surnames) - 1)):
all_authors += '; '
if all_authors[-1] == '.':
cap = ' '
else:
cap = '. '
if link:
doi = '<a href="https://dx.doi.org/'+self.doi+'">'+self.doi+'</a>'
else:
doi = self.doi
if self.volume != '':
return(all_authors+cap+self.year+'. '+self.title+'. ' \
+self.journal+' '+self.volume+': '+self.pages+'.' \
+' doi: '+doi)
else:
return(all_authors+cap+self.year+'. '+self.title+'. ' \
+self.journal+'. '+' doi: '+doi)
def extract_data(self):
self.check_fulltext()
print('Extracting data from HTML...',end='',flush=True)
self.get_doi()
self.get_metadata()
self.get_abstract()
self.get_keywords()
self.get_body()
self.get_references()
print('done')
def epubify(self,output=None):
"""Convert data into epub format"""
all_authors = ''
for i in range(0,len(self.author_surnames)):
all_authors += self.author_givennames[i] + ' '
all_authors += self.author_surnames[i]
if(i != (len(self.author_surnames) - 1)):
all_authors += ', '
self.get_citation()
args = []
args.append('-M')
args.append('title="'+self.title+'"')
args.append('-M')
args.append('author="'+all_authors+'"')
#args.append('--parse-raw')
args.append('--webtex')
if output == None:
self.output = self.author_surnames[0]+'_'+self.year+'.epub'
else:
self.output = output
output_raw = os.path.join(tempfile.gettempdir(), 'raw.epub')
combined = ''
combined += str(self.get_citation(link=True))
combined += str(self.abstract)
combined += str(self.body)
combined += str(self.references)
print('Generating epub.............',end='',flush=True)
epubout = pypandoc.convert_text(combined,format='html',to='epub+raw_html',
extra_args=args,
outputfile=output_raw)
subprocess.check_output(['ebook-convert',output_raw,self.output,
'--no-default-epub-cover'])
print('done')
def register_publisher(publisher):
_publishers.append(publisher)
_publisher_names.append(publisher.name)
for d in publisher.domains:
_publisher_domains[d] = publisher
def get_publishers():
return _publisher_domains
def list_publishers():
return _publisher_names
def match_publisher(url,doi):
"""Match a URL to a publisher class"""
domain = ".".join(url.split("//")[-1].split("/")[0] \
.split('?')[0].split('.')[-2:])
if domain == 'doi.org':
sys.exit('DOI not found; is it correct?')
try:
art = get_publishers()[domain](url=url,doi=doi)
print('Matched URL to publisher: '+art.name)
return(art)
except:
sys.exit('Publisher ['+domain+'] not supported.')
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