antibodyregistry error and data column update #369
Description
Steps to recreate
- Move/delete the latest cache of antibodyregistry at
$PYSTOW_HOME/pyobo/raw/antibodyregistry/ - Run
python -c "import pyobo; df = pyobo.get_mappings_df('antibodyregistry', names=False)"
Error:
ValueError: Usecols do not match columns, columns expected but not found: [0, 1, 2, 3, 5]
Looking at the downloaded CSV file that now appears in $PYSTOW_HOME/pyobo/raw/antibodyregistry/2025-03-10/results.csv, it appears to be some cloudflare protection:
<!doctype html><html><head><link rel="stylesheet" charset="UTF-8" href="https://cdnjs.cloudflare.com/ajax/libs/slick-carousel/1.6.0/slick.min.css"/><link rel="stylesheet" href="https://cdnjs.cloudflare.com/ajax/libs/slick-carousel/1.6.0/slick-theme.min.css"/><script async src="https://www.googletagmanager.com/gtag/js?id=G-JSRSCQE0R7"></script><script>window.dataLayer = window.dataLayer || [];
function gtag(){dataLayer.push(arguments);}
gtag('js', new Date());
gtag('config', 'G-JSRSCQE0R7');</script><link rel="stylesheet" href="https://use.typekit.net/sxc1glc.css"/><meta charset="UTF-8"/><meta name="description" content="Antibodies: Search, Submit and Trace | Researchers only"><meta name="keywords" content="Antibodies, Antibody Registry, Antibody Research"><title>Antibody Registry</title><link rel="icon" href="/logo.svg"><script defer="defer" src="/main.f4163a98f744c41d9314.js"></script></head><body><div id="root"></div></body></html>Potential solution
By registering and logging in to the antibodyregistry (see button in top right corner "Log in / Register"), a download button appears on the top bar and this takes you to a page where you can download the bulk CSV file.