# AUTOGENERATED FILE! PLEASE DON'T EDIT
"""All tools related to the MGI database. Expected to use behind the "mgi"
module name, like this::
from k1lib.imports import *
["SOD1", "AMPK"] | mgi.batch()
"""
from k1lib import cli
from typing import List
import time
__all__ = ["batch"]
[docs]class batch(cli.BaseCli):
"""Queries MGI database, convert list of genes to MGI ids"""
[docs] def __init__(self, headless=True):
"""
:param headless: whether to run this operation headless, or actually
display the browser"""
super().__init__(); self.headless = headless
[docs] def __ror__(self, it:List[str]):
super().__ror__(it)
import selenium; from selenium import webdriver
query = "\n".join(it | cli.strip() | ~cli.isValue(""))
options = selenium.webdriver.chrome.options.Options()
if self.headless: options.add_argument("--headless")
driver = selenium.webdriver.Chrome(options=options);
print("\r1/4 Going to website... ", end="")
driver.get("http://www.informatics.jax.org/batch")
print("\r2/4 Submitting data... ", end="")
driver.find_element_by_name("ids").send_keys(query)
driver.find_element_by_css_selector("tr.queryControls > td > input.buttonLabel").click()
markerIds = []; terms = []; names = []; features = []
print("\r3/4 Getting data... ", end="")
def getStuff(classEnd:str):
return [elem.get_attribute("textContent") for elem in driver.find_elements_by_css_selector(f".yui-dt-col-{classEnd} > div")]
while len(markerIds) <= 1:
markerIds = getStuff("markerId"); terms = getStuff("term")
names = getStuff("name"); features = getStuff("feature")
time.sleep(1)
print("\r4/4 Data received! ")
driver.close()
return cli.joinColumns([markerIds, terms, features, names])