class WOS(object):
""" A little module for exporting Web of Science search results into a txt file """
def __init__(self, **kwargs):
"""
Construct a new WOS object given a query, an export file (without ".isi")
a username and a password for authentication
eg :
WOS(query="TS=(epigenetic*", outfile="epigenetic", user="******", passw="mypassw")
"""
#defining params
self.query = kwargs["query"]
self.outfile = kwargs["outfile"]+".isi"
try:
self.user=kwargs["user"]
self.passw = kwargs["passw"]
except:
self.user, self.passw = private
try:
self.browser_app = kwargs["browser"]
except:
self.browser_app = "splinter"
#using MLV Auth Server
self.auth_url = "https://apps-webofknowledge-com.fennec.u-pem.fr/WOS_AdvancedSearch_input.do?&product=WOS&search_mode=AdvancedSearch"
#Firefox Browser
if self.browser_app == "splinter":
self.browser = Browser("firefox")
else:
self.browser = spynner.Browser()
self.browser.set_html_parser(PyQuery)
#self.browser = Browser('zope.testbrowser', ignore_robots=True)
#Session params
self.session = None
self.cookies = {}
if self.query is None:
sys.exit("No query provided")
if "=" not in self.query:
#or "(" not in self.query
logging.warning("Syntax is not WOS compliant. Check Query Syntax")
sys.exit("Query Syntax Error")
if self.outfile is None:
self.outfile = str(re.sub(re.compile("[^0-9a-zA-Z]+"),"_", self.query))+".isi"
if self.user is None and self.passw is None:
self.user, self.passw = private
logging.info("WOS search parameters:\n\t- query: %s\n\t- outfile: %s\n\t- user: %s\n\t- password: %s" %(self.query, self.outfile, self.user, self.passw))
self.run()
def auth(self):
""" authentification throught auth_url to get the session id SID """
#Loading url
if self.browser_app == "splinter":
self.browser.visit(self.auth_url)
self.browser.fill('username', self.user)
self.browser.fill('password', self.passw)
self.browser.find_by_name("submit").click()
self.cookies = self.browser.cookies.all()
else:
self.browser = self.browser.load(self.url)
self.browser.wk_fill('input[id="username"]',self.username)
self.browser.wk_fill('input[id="password"]',self.password)
self.browser.click('input[name="submit"]')
#~ if self.debug is True:
#~ print "Proceding to authentication..."
if "SessionError" in self.session.url :
self.session.click('a[target="_top"]')
self.session.wait(random.uniform(1, 3))
p_url = urlparse(self.browser.url)
if p_url.netloc == "apps-webofknowledge-com.fennec.u-pem.fr":
#print p_url.scheme+"//"+p_url.netloc+"/WOS_GeneralSearch_input.do?"+p_url.query
match = re.match(re.compile("product\=(?P<product>.*?)\&search_mode\=(?P<search_mode>.*?)\&SID=(?P<ssid>.*?)\&preferencesSaved\="), str(p_url.query))
if match is not None:
self.product = match.group("product")
self.ssid = match.group("ssid")
self.search_mode = re.sub("General", "Advanced", match.group("search_mode"))
#self.search_mode = match.group("search_mode")
self.search_url = "%s://%s/%s_%s_input.do?product=%s&search_mode=%s&SID=%s" %(p_url.scheme, p_url.netloc, self.product,self.search_mode,self.product,self.search_mode,self.ssid)
if self.browser_app == "splinter":
self.browser.visit(self.search_url)
print self.browser.url
else:
self.browser.load(self.search_url)
print self.browser.url
return self
else:
return sys.exit("Session Id could not be found")
else:
logging.info("No redirection to service")
return sys.exit("Invalid credentials")
def launch_search(self):
""" Filling the query form found into advanced search page """
logging.info("Launching search")
if self.browser_app == "splinter":
self.browser.fill("value(input1)", self.query)
self.browser.find_by_xpath("/html/body/div[1]/form/div[1]/table/tbody/tr/td[1]/div[2]/div[1]/table/tbody/tr/td[1]/span[1]/input").click()
bs = BeautifulSoup(self.browser.html)
else:
self.session.wk_fill('textarea[id="value(input1)"]', self.query)
self.session.click('input[title="Search"]')
self.session.wait(random.randint(2,5))
bs = BeautifulSoup(self.browser.html.encode("utf-8"))
query_history = bs.find_all("div", {"class":"historyResults"})
self.nb_search = len(query_history)
try:
self.nb_results = int(re.sub(",", "", query_history[0].text))
except IndexError:
self.nb_results = int(re.sub(",", "", query_history.text))
print self.nb_results
logging.warning("Your search \"%s\" gave %i results"%(self.query, self.nb_results))
logging.info("Your SSID is : %s" %self.ssid)
if self.browser_app == "splinter":
self.browser.click_link_by_partial_href('/summary.do?')
else:
self.session.click('a[title="Click to view the results"]',wait_load=True)
print urlparse(self.browser.url).query
match = re.search(re.compile("product=WOS&doc\=(?P<doc>.*?)\&qid\=(?P<qid>.*?)&SID"), urlparse(self.browser.url).query)
if match is not None:
print match.group()
self.doc, self.qid = match.group("doc"), match.group('qid')
print self.doc, self.qid
return self
else:
self.doc, self.qid = self.parse_params()
return self
def load_results(self, markFrom, markTo, i):
""" Load_results(markFrom, markTo) 500 by 500 given the nb of results """
logging.info("loading results")
#print "exporting"
#p_url0= "http://apps.webofknowledge.com/AutoSave_UA_output.do?action=saveForm&SID=%s&product=UA&search_mode=output" %self.ssid
#r0 = requests.post(p_url0, headers= headers, cookies=self.cookies)
# print p_url0
#print r0
#p_url1= "http://apps.webofknowledge.com/AutoSave_UA_output.do?action=saveForm&SID=%s&product=UA&search_mode=results" %self.ssid
# print p_url1
#r1 = requests.post(p_url1, headers= headers, cookies=self.cookies)
#print r1
r_url = "https://apps-webofknowledge-com.fennec.u-pem.fr/summary.do?product=WOS&doc=1&qid="+self.qid+"&SID="+self.ssid+"&search_mode=AdvancedSearch"
post_url = "https://apps-webofknowledge-com.fennec.u-pem.fr/OutboundService.do?action=go&&"
#r2 = requests.post()
header={
'Host': 'apps-webofknowledge-com.fennec.u-pem.fr',
'User-Agent': 'Mozilla/5.0 (X11; Ubuntu; Linux x86_64; rv:29.0) Gecko/20100101 Firefox/29.0',
'Accept': 'text/html,application/xhtml+xml,application/xml;q=0.9,*/*;q=0.8',
'Accept-Language': 'fr,fr-fr;q=0.8,en-us;q=0.5,en;q=0.3',
'Accept-Encoding': 'gzip, deflate',
'DNT': 1,
'Referer': 'https://apps-webofknowledge-com.fennec.u-pem.fr/summary.do?product=WOS&doc=1&qid=%s&SID=%s&search_mode=AdvancedSearch'%(self.qid, self.ssid),
'Connection': 'keep-alive'
}
# markTo = 500
# markFrom = 1
data = {
'SID': self.ssid,
'colName':'WOS',
'count_new_items_marked':0,
'displayCitedRefs':'true',
'displayTimesCited':'true',
'fields_selection':'USAGEIND AUTHORSIDENTIFIERS ACCESSION_NUM FUNDING SUBJECT_CATEGORY JCR_CATEGORY LANG IDS PAGEC SABBR CITREFC ISSN PUBINFO KEYWORDS CITTIMES ADDRS CONFERENCE_SPONSORS DOCTYPE CITREF ABSTRACT CONFERENCE_INFO SOURCE TITLE AUTHORS',
'filters':'USAGEIND AUTHORSIDENTIFIERS ACCESSION_NUM FUNDING SUBJECT_CATEGORY JCR_CATEGORY LANG IDS PAGEC SABBR CITREFC ISSN PUBINFO KEYWORDS CITTIMES ADDRS CONFERENCE_SPONSORS DOCTYPE CITREF ABSTRACT CONFERENCE_INFO SOURCE TITLE AUTHORS',
'format':'saveToFile',
'locale':'en_US',
'markFrom':1,
'markTo':markTo,
'mark_from':markFrom,
'product':'WOS',
'mark_to':markTo,
'mode':'OpenOutputService',
'product':'WOS',
'qid':self.qid,
'startYear':'2015',
'endYear':'2014',
#rurl:'http%3A%2F%2Fapps.webofknowledge.com%2Fsummary.do%3FSID%3DT1WYtnvIngPkHzI4ShI%26product%3DWOS%26doc%3D1%26qid%3D1%26search_mode%3DAd
'rurl':urllib.quote_plus(r_url),
'save_options':'othersoftware',
'search_mode':'AdvancedSearch',
'selectedIds':'',
'sortBy':'PY.D;LD.D;SO.A;VL.D;PG.A;AU.A',
'value(record_select_type)':'range',
'viewType':'summary',
'view_name':'WOS-summary',
}
r = requests.get(post_url, params=data,headers=header, cookies=self.cookies)
#redirects to #url = "http://ets.webofknowledge.com/ETS/ets.do?"
data_directory = self.outfile.split('.isi')[0]
try:
os.mkdir("exported_data")
print "creating directory exported_data"
except:
print "exported_data already exists"
pass
try:
os.mkdir("exported_data/"+data_directory)
print "creating directory "+data_directory
except:
print data_directory +" already exists"
pass
final_r = requests.get(r.url, cookies=self.cookies, stream=True)
with open( "exported_data/"+data_directory+'/'+data_directory+'_'+str(i) +'.isi' , 'w') as f:
final_r.text
f.write(final_r.text.encode('utf-8'))
return self.outfile
def export(self):
"""Writing results into outfile (defaut is normalized query)"""
start_time = time.time()
#open(self.outfile, 'w').close()
l = list(range(0, self.nb_results, 500))
l.append(self.nb_results)
logging.info("Exporting %s 500 by 500..." %self.nb_results)
for i,n in enumerate(l):
if l[i]+1 < self.nb_results:
self.load_results(l[i]+1, l[i+1],str(l[i]+1)+'-'+str(l[i+1]))
total = time.time() - start_time, "seconds"
# raw_file = open(self.outfile, 'r')
# raw_file_data = raw_file.read().decode("utf-8-sig").encode("utf-8")
# nb_occurence = len(raw_file_data.split("\n\n"))-1
logging.info("Query \"%s\" had %d results: %d has been exported" %(self.query, self.nb_results))
logging.info("Sucessfully stored in directory : %s\n" %(self.outfile))
#logging.info("Execution total time:"+str(" ".join(total)))
return
def run(self):
""" Generic method that encapsulates the WOS extract process """
self.auth()
self.launch_search()
self.export()
self.browser.close()
return
