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01_get_retracted_articles.py
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01_get_retracted_articles.py
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from selenium import webdriver
from selenium.webdriver.support.ui import Select
from selenium.webdriver.support.ui import WebDriverWait
from selenium.webdriver.support import expected_conditions as EC
from selenium.webdriver.common.by import By
from selenium.webdriver.remote.command import Command
from selenium.webdriver.chrome.options import Options
from selenium.webdriver.common.keys import Keys
import pandas as pd
import time
import os
import shutil
DOWNLOAD_PATH = os.getcwd() + '/retracted_articles'
WEB_SCIENCE_USERNAME = ""
WEB_SCIENCE_PASSWORD = ""
LOGIN_URL = ('https://ezpa.library.ualberta.ca/ezpAuthen.cgi'
'?url=https://www.webofscience.com/wos/woscc/basic-search')
dt = pd.read_csv('../data/retraction_notices11622_refactored.csv',
usecols=['Source Title', 'new_title'])
start = 0
while True:
if start >= len(dt):
break
try:
# Set the default download folder
chrome_driver = os.path.abspath("chromedriver")
os.environ["webdriver.chrome.driver"] = chrome_driver
options = webdriver.ChromeOptions()
options.add_argument("--disable-extensions")
options.add_argument("--disable-gpu")
options.add_argument("--no-sandbox") # linux only
#options.add_argument("--headless")
options.add_argument("--remote-debugging-port=9222")
#options.add_argument("--window-size=1280,1024")
options.add_argument("--window-size=1024,760")
default_download_path = {"download.default_directory": DOWNLOAD_PATH}
options.add_experimental_option("prefs", default_download_path)
browser = webdriver.Chrome(executable_path=chrome_driver,
options=options)
browser.implicitly_wait(3)
browser.get(LOGIN_URL)
elem = browser.find_element(By.CSS_SELECTOR, "input[name=user]")
elem.send_keys(WEB_SCIENCE_USERNAME)
elem = browser.find_element(By.CSS_SELECTOR, "input[name=pass]")
elem.send_keys(WEB_SCIENCE_PASSWORD)
elem = browser.find_element(By.CSS_SELECTOR, "form[name=loginForm]")
elem.submit()
try:
print('Wait for popup')
loc = (By.XPATH, "//button[@class='_pendo-close-guide']")
wait = WebDriverWait(browser, 30, 2)
wait.until(EC.visibility_of_element_located(loc))
print("Close guide popup")
# close popup guide
xpath = "//button[@class='_pendo-close-guide']"
elem = browser.find_element(By.XPATH, xpath)
elem.click()
print('Click on popup')
except Exception as e:
print(e)
try:
print('Wait for cookie popup')
loc = (By.XPATH, "//button[@id='onetrust-accept-btn-handler']")
wait = WebDriverWait(browser, 30, 2)
wait.until(EC.visibility_of_element_located(loc))
print("Close Cookie popup")
# close cookie popup
xpath = "//button[@id='onetrust-accept-btn-handler']"
elem = browser.find_element(By.XPATH, xpath)
elem.click()
except Exception as e:
print(e)
first_search = True
for i in range(0, 200):
if start >= len(dt):
break
a = dt['new_title'][start]
b = dt['Source Title'][start]
print(start)
ofn = DOWNLOAD_PATH + '/' + str(start + 1) + '.txt'
ofn2 = DOWNLOAD_PATH + '/' + str(start + 1) + '_cites.txt'
if os.path.exists(ofn) and os.path.exists(ofn2):
start += 1
continue
try:
# "Advanced Search" click
elem = browser.find_element(By.LINK_TEXT, "Advanced Search")
elem.click()
# Wait until the `advancedSearchInputArea` element appear
# (up to 5 seconds)
print('Wait for Advance Search input Area')
wait = WebDriverWait(browser, 5, 1)
loc = (By.ID, "advancedSearchInputArea")
wait.until(EC.presence_of_element_located(loc))
# enter the query string in textarea
xpath = "//span[contains(., ' Clear ')]"
elem = browser.find_element(By.XPATH, xpath)
elem.click()
elem = browser.find_element(By.ID, "advancedSearchInputArea")
elem.send_keys('TI=(' + a + ') AND SO=(' + b + ')')
# click 'Search' button
xpath = "//button[contains(., ' Search ')]"
elem = browser.find_element(By.XPATH, xpath)
elem.click()
print('Click on search')
if first_search:
# FIXME: it seems popup randomly
try:
print('Wait for popup')
loc = (By.XPATH, "//button[@class='_pendo-close-guide']")
wait = WebDriverWait(browser, 2, 1)
wait.until(EC.visibility_of_element_located(loc))
# click close popup
xpath = "//button[@class='_pendo-close-guide']"
elem = browser.find_element(By.XPATH, xpath)
elem.click()
print('Click on popup')
first_search = False
except Exception as e:
print(e)
xpath = "//span[text()='Sort by:']/following-sibling::span"
try:
print('Wait for search results')
loc = (By.XPATH, xpath)
wait = WebDriverWait(browser, 2, 1)
wait.until(EC.presence_of_element_located(loc))
except Exception as e:
print('No search results')
try:
txt = "< BACK TO BASIC SEARCHES"
elem = browser.find_element(By.LINK_TEXT, txt)
elem.click()
except Exception as e:
print(e)
start += 1
continue
elem = browser.find_element(By.XPATH, xpath)
if elem.text != 'Date: oldest first':
try:
# click "Sort by:"
xpath = "//span[text()='Sort by:']"
elem = browser.find_element(By.XPATH, xpath)
elem.click()
# select "Date: oldest first"
xpath = "//span[text()='Date: oldest first']"
elem = browser.find_element(By.XPATH, xpath)
elem.click()
except Exception as e:
print(e)
# close popup guide
xpath = "//button[@class='_pendo-close-guide']"
elem = browser.find_element(By.XPATH, xpath)
elem.click()
print('Click on popup')
# click "Sort by:"
xpath = "//span[text()='Sort by:']"
elem = browser.find_element(By.XPATH, xpath)
elem.click()
# select "Date: oldest first"
xpath = "//span[text()='Date: oldest first']"
elem = browser.find_element(By.XPATH, xpath)
elem.click()
# select first record
xpath = "//app-record//mat-checkbox"
elems = browser.find_elements(By.XPATH, xpath)
elems[0].click()
print('Wait for Export')
loc = (By.XPATH, "//button[contains(., 'Export')]")
wait = WebDriverWait(browser, 5, 1)
wait.until(EC.presence_of_element_located(loc))
# click 'Export' dropdown button
xpath = "//button[contains(., 'Export')]"
elem = browser.find_element(By.XPATH, xpath)
elem.click()
print('Click on export')
print('Wait for Tab delimited file')
xpath = "//button[contains(., 'Tab delimited file')]"
loc = (By.XPATH, xpath)
wait = WebDriverWait(browser, 5, 1)
wait.until(EC.presence_of_element_located(loc))
try:
xpath = "//button[contains(., 'Tab delimited file')]"
elem = browser.find_element(By.XPATH, xpath)
elem.click()
print('Click on Tab delimeted file')
except Exception as e:
print(e)
webdriver.ActionChains(browser).send_keys(Keys.ESCAPE).perform()
elem.click()
print('Click on Tab delimted file (again)')
print('Wait for Export option')
xpath = "//button[contains(., 'Author, Title, Source')]"
loc = (By.XPATH, xpath)
wait = WebDriverWait(browser, 5, 1)
wait.until(EC.presence_of_element_located(loc))
xpath = "//button[contains(., 'Author, Title, Source')]"
elem = browser.find_element(By.XPATH, xpath)
elem.click()
print('Click on Export option')
#choose 'Full Record'
xpath = "//span[contains(., 'Full Record')]"
elem = browser.find_element(By.XPATH, xpath)
elem.click()
# export file
xpath = "//span[contains(., 'Export')]"
elem = browser.find_element(By.XPATH, xpath)
elem.click()
dfn = DOWNLOAD_PATH + '/' + 'savedrecs.txt'
r = 0
while (r < 20):
print('Download Article...')
time.sleep(1)
if os.path.exists(dfn):
shutil.move(dfn, ofn)
break
r += 1
if r == 20:
xpath = "//span[contains(., 'Cancel')]"
elem = browser.find_element(By.XPATH, xpath)
elem.click()
print('ERROR: Cannot download', start)
if not os.path.exists(ofn2):
# click 'Citations'
try:
print('Wait for Citations')
xpath = "//div[contains(@class, 'citations')]"
loc = (By.XPATH, xpath)
wait = WebDriverWait(browser, 2, 1)
wait.until(EC.presence_of_element_located(loc))
except Exception as e:
print(e)
print('No citations')
start += 1
continue
try:
xpath = "//div[contains(@class, 'citations')]/a"
elem = browser.find_element(By.XPATH, xpath)
elem.click()
except Exception as e:
print(e)
print('No citations')
start += 1
continue
print('Wait for Export citations')
loc = (By.XPATH, "//button[contains(., 'Export')]")
wait = WebDriverWait(browser, 5, 1)
wait.until(EC.presence_of_element_located(loc))
# click 'Export' dropdown button
xpath = "//button[contains(., 'Export')]"
elem = browser.find_element(By.XPATH, xpath)
elem.click()
print('Click on Export citations')
print('Wait for Tab delimited file')
xpath = "//button[contains(., 'Tab delimited file')]"
loc = (By.XPATH, xpath)
wait = WebDriverWait(browser, 5, 1)
wait.until(EC.presence_of_element_located(loc))
try:
xpath = "//button[contains(., 'Tab delimited file')]"
elem = browser.find_element(By.XPATH, xpath)
elem.click()
print('Click on Tab delimted file')
except Exception as e:
print(e)
webdriver.ActionChains(browser).send_keys(Keys.ESCAPE).perform()
elem.click()
print('Click on Tab delimted file (again)')
# tick to 'Records from:'
xpath = "//span[contains(., 'Records from:')]"
elem = browser.find_element(By.XPATH, xpath)
elem.click()
# export file
xpath = "//span[contains(., 'Export')]"
elem = browser.find_element(By.XPATH, xpath)
elem.click()
dfn = DOWNLOAD_PATH + '/' + 'savedrecs.txt'
r = 0
while (r < 20):
print('Download Citations...')
time.sleep(1)
if os.path.exists(dfn):
shutil.move(dfn, ofn2)
break
r += 1
if r == 20:
xpath = "//span[contains(., 'Cancel')]"
elem = browser.find_element(By.XPATH, xpath)
elem.click()
print('ERROR: Cannot download', start)
except Exception as e:
print(e)
try:
txt = "< BACK TO BASIC SEARCHES"
elem = browser.find_element(By.LINK_TEXT, txt)
elem.click()
print('Wait for popup')
loc = (By.XPATH, "//button[@class='_pendo-close-guide']")
wait = WebDriverWait(browser, 3, 1)
wait.until(EC.visibility_of_element_located(loc))
# close popup guide
xpath = "//button[@class='_pendo-close-guide']"
elem = browser.find_element(By.XPATH, xpath)
elem.click()
print('Click on popup')
except Exception as e:
print(e)
start += 1
except Exception as e:
print(e)
time.sleep(300)
finally:
browser.quit()