{ "cells": [ { "cell_type": "code", "execution_count": 1, "id": "2eea5d12-d4dd-44c7-bc3e-2f8a67473174", "metadata": { "tags": [] }, "outputs": [ { "ename": "KeyboardInterrupt", "evalue": "", "output_type": "error", "traceback": [ "\u001b[0;31m---------------------------------------------------------------------------\u001b[0m", "\u001b[0;31mKeyboardInterrupt\u001b[0m Traceback (most recent call last)", "Input \u001b[0;32mIn [1]\u001b[0m, in \u001b[0;36m\u001b[0;34m()\u001b[0m\n\u001b[1;32m 31\u001b[0m TCGAproject_links\u001b[38;5;241m.\u001b[39mappend(project_link)\n\u001b[1;32m 34\u001b[0m \u001b[38;5;28;01mfor\u001b[39;00m TCGAproject_link \u001b[38;5;129;01min\u001b[39;00m TCGAproject_links:\n\u001b[0;32m---> 35\u001b[0m \u001b[43mdriver\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mget\u001b[49m\u001b[43m(\u001b[49m\u001b[43mTCGAproject_link\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 37\u001b[0m \u001b[38;5;66;03m# Find links to internal download pages on the project page\u001b[39;00m\n\u001b[1;32m 38\u001b[0m download_page_links \u001b[38;5;241m=\u001b[39m driver\u001b[38;5;241m.\u001b[39mfind_elements(By\u001b[38;5;241m.\u001b[39mXPATH, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124m//a[contains(@href, \u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124mdataset\u001b[39m\u001b[38;5;124m'\u001b[39m\u001b[38;5;124m)]\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n", "File \u001b[0;32m~/opt/anaconda3/lib/python3.9/site-packages/selenium/webdriver/remote/webdriver.py:353\u001b[0m, in \u001b[0;36mWebDriver.get\u001b[0;34m(self, url)\u001b[0m\n\u001b[1;32m 351\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21mget\u001b[39m(\u001b[38;5;28mself\u001b[39m, url: \u001b[38;5;28mstr\u001b[39m) \u001b[38;5;241m-\u001b[39m\u001b[38;5;241m>\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m:\n\u001b[1;32m 352\u001b[0m \u001b[38;5;124;03m\"\"\"Loads a web page in the current browser session.\"\"\"\u001b[39;00m\n\u001b[0;32m--> 353\u001b[0m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mexecute\u001b[49m\u001b[43m(\u001b[49m\u001b[43mCommand\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mGET\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43m{\u001b[49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[38;5;124;43murl\u001b[39;49m\u001b[38;5;124;43m\"\u001b[39;49m\u001b[43m:\u001b[49m\u001b[43m \u001b[49m\u001b[43murl\u001b[49m\u001b[43m}\u001b[49m\u001b[43m)\u001b[49m\n", "File \u001b[0;32m~/opt/anaconda3/lib/python3.9/site-packages/selenium/webdriver/remote/webdriver.py:342\u001b[0m, in \u001b[0;36mWebDriver.execute\u001b[0;34m(self, driver_command, params)\u001b[0m\n\u001b[1;32m 339\u001b[0m \u001b[38;5;28;01melif\u001b[39;00m \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124msessionId\u001b[39m\u001b[38;5;124m\"\u001b[39m \u001b[38;5;129;01mnot\u001b[39;00m \u001b[38;5;129;01min\u001b[39;00m params:\n\u001b[1;32m 340\u001b[0m params[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124msessionId\u001b[39m\u001b[38;5;124m\"\u001b[39m] \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39msession_id\n\u001b[0;32m--> 342\u001b[0m response \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mcommand_executor\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mexecute\u001b[49m\u001b[43m(\u001b[49m\u001b[43mdriver_command\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mparams\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 343\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m response:\n\u001b[1;32m 344\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39merror_handler\u001b[38;5;241m.\u001b[39mcheck_response(response)\n", "File \u001b[0;32m~/opt/anaconda3/lib/python3.9/site-packages/selenium/webdriver/remote/remote_connection.py:294\u001b[0m, in \u001b[0;36mRemoteConnection.execute\u001b[0;34m(self, command, params)\u001b[0m\n\u001b[1;32m 292\u001b[0m data \u001b[38;5;241m=\u001b[39m utils\u001b[38;5;241m.\u001b[39mdump_json(params)\n\u001b[1;32m 293\u001b[0m url \u001b[38;5;241m=\u001b[39m \u001b[38;5;124mf\u001b[39m\u001b[38;5;124m\"\u001b[39m\u001b[38;5;132;01m{\u001b[39;00m\u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_url\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;132;01m{\u001b[39;00mpath\u001b[38;5;132;01m}\u001b[39;00m\u001b[38;5;124m\"\u001b[39m\n\u001b[0;32m--> 294\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_request\u001b[49m\u001b[43m(\u001b[49m\u001b[43mcommand_info\u001b[49m\u001b[43m[\u001b[49m\u001b[38;5;241;43m0\u001b[39;49m\u001b[43m]\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43murl\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mbody\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mdata\u001b[49m\u001b[43m)\u001b[49m\n", "File \u001b[0;32m~/opt/anaconda3/lib/python3.9/site-packages/selenium/webdriver/remote/remote_connection.py:315\u001b[0m, in \u001b[0;36mRemoteConnection._request\u001b[0;34m(self, method, url, body)\u001b[0m\n\u001b[1;32m 312\u001b[0m body \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mNone\u001b[39;00m\n\u001b[1;32m 314\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mkeep_alive:\n\u001b[0;32m--> 315\u001b[0m response \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_conn\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mrequest\u001b[49m\u001b[43m(\u001b[49m\u001b[43mmethod\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43murl\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mbody\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mbody\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mheaders\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mheaders\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 316\u001b[0m statuscode \u001b[38;5;241m=\u001b[39m response\u001b[38;5;241m.\u001b[39mstatus\n\u001b[1;32m 317\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n", "File \u001b[0;32m~/opt/anaconda3/lib/python3.9/site-packages/urllib3/request.py:78\u001b[0m, in \u001b[0;36mRequestMethods.request\u001b[0;34m(self, method, url, fields, headers, **urlopen_kw)\u001b[0m\n\u001b[1;32m 74\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mrequest_encode_url(\n\u001b[1;32m 75\u001b[0m method, url, fields\u001b[38;5;241m=\u001b[39mfields, headers\u001b[38;5;241m=\u001b[39mheaders, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39murlopen_kw\n\u001b[1;32m 76\u001b[0m )\n\u001b[1;32m 77\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m---> 78\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mrequest_encode_body\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 79\u001b[0m \u001b[43m \u001b[49m\u001b[43mmethod\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43murl\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mfields\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mfields\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mheaders\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mheaders\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43murlopen_kw\u001b[49m\n\u001b[1;32m 80\u001b[0m \u001b[43m \u001b[49m\u001b[43m)\u001b[49m\n", "File \u001b[0;32m~/opt/anaconda3/lib/python3.9/site-packages/urllib3/request.py:170\u001b[0m, in \u001b[0;36mRequestMethods.request_encode_body\u001b[0;34m(self, method, url, fields, headers, encode_multipart, multipart_boundary, **urlopen_kw)\u001b[0m\n\u001b[1;32m 167\u001b[0m extra_kw[\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mheaders\u001b[39m\u001b[38;5;124m\"\u001b[39m]\u001b[38;5;241m.\u001b[39mupdate(headers)\n\u001b[1;32m 168\u001b[0m extra_kw\u001b[38;5;241m.\u001b[39mupdate(urlopen_kw)\n\u001b[0;32m--> 170\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43murlopen\u001b[49m\u001b[43m(\u001b[49m\u001b[43mmethod\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43murl\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mextra_kw\u001b[49m\u001b[43m)\u001b[49m\n", "File \u001b[0;32m~/opt/anaconda3/lib/python3.9/site-packages/urllib3/poolmanager.py:376\u001b[0m, in \u001b[0;36mPoolManager.urlopen\u001b[0;34m(self, method, url, redirect, **kw)\u001b[0m\n\u001b[1;32m 374\u001b[0m response \u001b[38;5;241m=\u001b[39m conn\u001b[38;5;241m.\u001b[39murlopen(method, url, \u001b[38;5;241m*\u001b[39m\u001b[38;5;241m*\u001b[39mkw)\n\u001b[1;32m 375\u001b[0m \u001b[38;5;28;01melse\u001b[39;00m:\n\u001b[0;32m--> 376\u001b[0m response \u001b[38;5;241m=\u001b[39m \u001b[43mconn\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43murlopen\u001b[49m\u001b[43m(\u001b[49m\u001b[43mmethod\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[43mu\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mrequest_uri\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[38;5;241;43m*\u001b[39;49m\u001b[43mkw\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 378\u001b[0m redirect_location \u001b[38;5;241m=\u001b[39m redirect \u001b[38;5;129;01mand\u001b[39;00m response\u001b[38;5;241m.\u001b[39mget_redirect_location()\n\u001b[1;32m 379\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m redirect_location:\n", "File \u001b[0;32m~/opt/anaconda3/lib/python3.9/site-packages/urllib3/connectionpool.py:703\u001b[0m, in \u001b[0;36mHTTPConnectionPool.urlopen\u001b[0;34m(self, method, url, body, headers, retries, redirect, assert_same_host, timeout, pool_timeout, release_conn, chunked, body_pos, **response_kw)\u001b[0m\n\u001b[1;32m 700\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_prepare_proxy(conn)\n\u001b[1;32m 702\u001b[0m \u001b[38;5;66;03m# Make the request on the httplib connection object.\u001b[39;00m\n\u001b[0;32m--> 703\u001b[0m httplib_response \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_make_request\u001b[49m\u001b[43m(\u001b[49m\n\u001b[1;32m 704\u001b[0m \u001b[43m \u001b[49m\u001b[43mconn\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 705\u001b[0m \u001b[43m \u001b[49m\u001b[43mmethod\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 706\u001b[0m \u001b[43m \u001b[49m\u001b[43murl\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 707\u001b[0m \u001b[43m \u001b[49m\u001b[43mtimeout\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mtimeout_obj\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 708\u001b[0m \u001b[43m \u001b[49m\u001b[43mbody\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mbody\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 709\u001b[0m \u001b[43m \u001b[49m\u001b[43mheaders\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mheaders\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 710\u001b[0m \u001b[43m \u001b[49m\u001b[43mchunked\u001b[49m\u001b[38;5;241;43m=\u001b[39;49m\u001b[43mchunked\u001b[49m\u001b[43m,\u001b[49m\n\u001b[1;32m 711\u001b[0m \u001b[43m\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 713\u001b[0m \u001b[38;5;66;03m# If we're going to release the connection in ``finally:``, then\u001b[39;00m\n\u001b[1;32m 714\u001b[0m \u001b[38;5;66;03m# the response doesn't need to know about the connection. Otherwise\u001b[39;00m\n\u001b[1;32m 715\u001b[0m \u001b[38;5;66;03m# it will also try to release it and we'll have a double-release\u001b[39;00m\n\u001b[1;32m 716\u001b[0m \u001b[38;5;66;03m# mess.\u001b[39;00m\n\u001b[1;32m 717\u001b[0m response_conn \u001b[38;5;241m=\u001b[39m conn \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;129;01mnot\u001b[39;00m release_conn \u001b[38;5;28;01melse\u001b[39;00m \u001b[38;5;28;01mNone\u001b[39;00m\n", "File \u001b[0;32m~/opt/anaconda3/lib/python3.9/site-packages/urllib3/connectionpool.py:449\u001b[0m, in \u001b[0;36mHTTPConnectionPool._make_request\u001b[0;34m(self, conn, method, url, timeout, chunked, **httplib_request_kw)\u001b[0m\n\u001b[1;32m 444\u001b[0m httplib_response \u001b[38;5;241m=\u001b[39m conn\u001b[38;5;241m.\u001b[39mgetresponse()\n\u001b[1;32m 445\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mBaseException\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m e:\n\u001b[1;32m 446\u001b[0m \u001b[38;5;66;03m# Remove the TypeError from the exception chain in\u001b[39;00m\n\u001b[1;32m 447\u001b[0m \u001b[38;5;66;03m# Python 3 (including for exceptions like SystemExit).\u001b[39;00m\n\u001b[1;32m 448\u001b[0m \u001b[38;5;66;03m# Otherwise it looks like a bug in the code.\u001b[39;00m\n\u001b[0;32m--> 449\u001b[0m \u001b[43msix\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mraise_from\u001b[49m\u001b[43m(\u001b[49m\u001b[43me\u001b[49m\u001b[43m,\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;28;43;01mNone\u001b[39;49;00m\u001b[43m)\u001b[49m\n\u001b[1;32m 450\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m (SocketTimeout, BaseSSLError, SocketError) \u001b[38;5;28;01mas\u001b[39;00m e:\n\u001b[1;32m 451\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_raise_timeout(err\u001b[38;5;241m=\u001b[39me, url\u001b[38;5;241m=\u001b[39murl, timeout_value\u001b[38;5;241m=\u001b[39mread_timeout)\n", "File \u001b[0;32m:3\u001b[0m, in \u001b[0;36mraise_from\u001b[0;34m(value, from_value)\u001b[0m\n", "File \u001b[0;32m~/opt/anaconda3/lib/python3.9/site-packages/urllib3/connectionpool.py:444\u001b[0m, in \u001b[0;36mHTTPConnectionPool._make_request\u001b[0;34m(self, conn, method, url, timeout, chunked, **httplib_request_kw)\u001b[0m\n\u001b[1;32m 441\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mTypeError\u001b[39;00m:\n\u001b[1;32m 442\u001b[0m \u001b[38;5;66;03m# Python 3\u001b[39;00m\n\u001b[1;32m 443\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 444\u001b[0m httplib_response \u001b[38;5;241m=\u001b[39m \u001b[43mconn\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mgetresponse\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 445\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mBaseException\u001b[39;00m \u001b[38;5;28;01mas\u001b[39;00m e:\n\u001b[1;32m 446\u001b[0m \u001b[38;5;66;03m# Remove the TypeError from the exception chain in\u001b[39;00m\n\u001b[1;32m 447\u001b[0m \u001b[38;5;66;03m# Python 3 (including for exceptions like SystemExit).\u001b[39;00m\n\u001b[1;32m 448\u001b[0m \u001b[38;5;66;03m# Otherwise it looks like a bug in the code.\u001b[39;00m\n\u001b[1;32m 449\u001b[0m six\u001b[38;5;241m.\u001b[39mraise_from(e, \u001b[38;5;28;01mNone\u001b[39;00m)\n", "File \u001b[0;32m~/opt/anaconda3/lib/python3.9/http/client.py:1377\u001b[0m, in \u001b[0;36mHTTPConnection.getresponse\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 1375\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[1;32m 1376\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m-> 1377\u001b[0m \u001b[43mresponse\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mbegin\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 1378\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m \u001b[38;5;167;01mConnectionError\u001b[39;00m:\n\u001b[1;32m 1379\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39mclose()\n", "File \u001b[0;32m~/opt/anaconda3/lib/python3.9/http/client.py:320\u001b[0m, in \u001b[0;36mHTTPResponse.begin\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 318\u001b[0m \u001b[38;5;66;03m# read until we get a non-100 response\u001b[39;00m\n\u001b[1;32m 319\u001b[0m \u001b[38;5;28;01mwhile\u001b[39;00m \u001b[38;5;28;01mTrue\u001b[39;00m:\n\u001b[0;32m--> 320\u001b[0m version, status, reason \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_read_status\u001b[49m\u001b[43m(\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 321\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m status \u001b[38;5;241m!=\u001b[39m CONTINUE:\n\u001b[1;32m 322\u001b[0m \u001b[38;5;28;01mbreak\u001b[39;00m\n", "File \u001b[0;32m~/opt/anaconda3/lib/python3.9/http/client.py:281\u001b[0m, in \u001b[0;36mHTTPResponse._read_status\u001b[0;34m(self)\u001b[0m\n\u001b[1;32m 280\u001b[0m \u001b[38;5;28;01mdef\u001b[39;00m \u001b[38;5;21m_read_status\u001b[39m(\u001b[38;5;28mself\u001b[39m):\n\u001b[0;32m--> 281\u001b[0m line \u001b[38;5;241m=\u001b[39m \u001b[38;5;28mstr\u001b[39m(\u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mfp\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mreadline\u001b[49m\u001b[43m(\u001b[49m\u001b[43m_MAXLINE\u001b[49m\u001b[43m \u001b[49m\u001b[38;5;241;43m+\u001b[39;49m\u001b[43m \u001b[49m\u001b[38;5;241;43m1\u001b[39;49m\u001b[43m)\u001b[49m, \u001b[38;5;124m\"\u001b[39m\u001b[38;5;124miso-8859-1\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n\u001b[1;32m 282\u001b[0m \u001b[38;5;28;01mif\u001b[39;00m \u001b[38;5;28mlen\u001b[39m(line) \u001b[38;5;241m>\u001b[39m _MAXLINE:\n\u001b[1;32m 283\u001b[0m \u001b[38;5;28;01mraise\u001b[39;00m LineTooLong(\u001b[38;5;124m\"\u001b[39m\u001b[38;5;124mstatus line\u001b[39m\u001b[38;5;124m\"\u001b[39m)\n", "File \u001b[0;32m~/opt/anaconda3/lib/python3.9/socket.py:704\u001b[0m, in \u001b[0;36mSocketIO.readinto\u001b[0;34m(self, b)\u001b[0m\n\u001b[1;32m 702\u001b[0m \u001b[38;5;28;01mwhile\u001b[39;00m \u001b[38;5;28;01mTrue\u001b[39;00m:\n\u001b[1;32m 703\u001b[0m \u001b[38;5;28;01mtry\u001b[39;00m:\n\u001b[0;32m--> 704\u001b[0m \u001b[38;5;28;01mreturn\u001b[39;00m \u001b[38;5;28;43mself\u001b[39;49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43m_sock\u001b[49m\u001b[38;5;241;43m.\u001b[39;49m\u001b[43mrecv_into\u001b[49m\u001b[43m(\u001b[49m\u001b[43mb\u001b[49m\u001b[43m)\u001b[49m\n\u001b[1;32m 705\u001b[0m \u001b[38;5;28;01mexcept\u001b[39;00m timeout:\n\u001b[1;32m 706\u001b[0m \u001b[38;5;28mself\u001b[39m\u001b[38;5;241m.\u001b[39m_timeout_occurred \u001b[38;5;241m=\u001b[39m \u001b[38;5;28;01mTrue\u001b[39;00m\n", "\u001b[0;31mKeyboardInterrupt\u001b[0m: " ] } ], "source": [ "from selenium import webdriver\n", "from selenium.webdriver.common.by import By\n", "from selenium.webdriver.chrome.service import Service\n", "from selenium.common.exceptions import StaleElementReferenceException\n", "import os\n", "import time\n", "\n", "#CHANGE the chromedriver path that matches your chrome\n", "service = Service(executable_path='/Users/guoshuyi/Downloads/chromedriver-mac-arm64/chromedriver')\n", "options = webdriver.ChromeOptions()\n", "driver = webdriver.Chrome(service=service, options=options)\n", "\n", "# Navigate to the web page\n", "driver.get(\"https://xenabrowser.net/datapages/\")\n", "\n", "# Wait for the page to load (you may need to adjust the wait time)\n", "driver.implicitly_wait(10) # Wait for 10 seconds\n", "\n", "# Find all the links on the page using Selenium\n", "links = driver.find_elements(By.XPATH, \"//a\")\n", "\n", "# Extract and print the href attributes of the links, store hrefs in a list\n", "project_links=[]\n", "TCGAproject_links=[]\n", "for link in links:\n", " href = link.get_attribute(\"href\")\n", " if href:\n", " project_links.append(href)\n", "for project_link in project_links:\n", " if \"cohort=TCGA\" in project_link:\n", " TCGAproject_links.append(project_link)\n", " \n", "\n", "for TCGAproject_link in TCGAproject_links:\n", " driver.get(TCGAproject_link)\n", "\n", " # Find links to internal download pages on the project page\n", " download_page_links = driver.find_elements(By.XPATH, \"//a[contains(@href, 'dataset')]\")\n", "\n", " download_page_urls = []\n", " for download_page_link in download_page_links:\n", " # Get the URL of the download page\n", " download_page_url = download_page_link.get_attribute(\"href\")\n", " download_page_urls.append(download_page_url)\n", "\n", " dataset_download_urls= []\n", " for download_page_url in download_page_urls:\n", " #replace'clinicalMatrix'with'PANCAN' to download gene expression data\n", " if 'clinicalMatrix' in download_page_url:\n", " driver.get(download_page_url)\n", " dataset_links = driver.find_elements(By.XPATH, \"//a[contains(@href, '/download/')]\")\n", " for dataset_link in dataset_links:\n", " dataset_download_url = dataset_link.get_attribute(\"href\")\n", " dataset_download_urls.append(dataset_download_url)\n", " \n", " for dataset_download_url in dataset_download_urls:\n", " dataset_name = os.path.basename(dataset_download_url)\n", " #replace'clinicalMatrix'with'PANCAN' to download gene expression data\n", " if 'clinicalMatrix' in dataset_name:\n", " # Click on the download link to initiate the download\n", " driver.get(dataset_download_url)\n", "\n", "\n", " " ] }, { "cell_type": "code", "execution_count": null, "id": "c2eeecd4-8da4-44fa-a6fc-fd47682bb820", "metadata": {}, "outputs": [], "source": [] } ], "metadata": { "kernelspec": { "display_name": "Python 3 (ipykernel)", "language": "python", "name": "python3" }, "language_info": { "codemirror_mode": { "name": "ipython", "version": 3 }, "file_extension": ".py", "mimetype": "text/x-python", "name": "python", "nbconvert_exporter": "python", "pygments_lexer": "ipython3", "version": "3.9.12" } }, "nbformat": 4, "nbformat_minor": 5 }