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Added code to download pathways CSV #9

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Added code to download pathways CSV #9

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22 changes: 22 additions & 0 deletions scripts/drugInfoScript-FILEOUTPUT.py
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Original file line number Diff line number Diff line change
Expand Up @@ -3,6 +3,24 @@
import random
import csv
import pandas as pd
from selenium import webdriver
from selenium.webdriver.common.by import By
import time

def downloadPathwayCSV(url):
driver = webdriver.Firefox()
driver.get(url)
#download_button = driver.find_element_by_class_name("btn-text")
time.sleep(20)
download_button = driver.find_element_by_xpath("//button[@id='Download']")
time.sleep(20)
download_button.click()
time.sleep(20)
save_button = driver.find_element_by_xpath("//span[.='Save']")
time.sleep(20)
save_button.click()
time.sleep(20)
driver.close()

# base url for pubchem
baseURL = "https://pubchem.ncbi.nlm.nih.gov/rest/pug/compound/cid/"
Expand Down Expand Up @@ -64,6 +82,10 @@
pathwayURL = "https://pubchem.ncbi.nlm.nih.gov/sdq/sdqagent.cgi?infmt=json&outfmt=csv&query={%22download%22:%22*%22,%22collection%22:%22pathway%22,%22where%22:{%22ands%22:[{%22cid%22:%222244%22},{%22core%22:%221%22}]},%22order%22:[%22name,asc%22],%22start%22:1,%22limit%22:10000000,%22downloadfilename%22:%22CID_" + compoundNum + "_pathway%22}"
pathway = requests.get(pathwayURL).text

# This will download the code to the pathway
downloadpathwayURL = "https://pubchem.ncbi.nlm.nih.gov/compound/"+ compoundNum +"#section=Pathways&fullscreen=true"
pathwayCSV = downloadPathwayCSV(downloadPathwayURL)

pathwayData = pd.read_csv(pathwayURL)

# drop duplicate names in list
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