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joiningdata / lollipops

Lollipop-style mutation diagrams for annotating genetic variations.
GNU General Public License v3.0
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Fix various issues related to database changes #68

Closed JamesR-S closed 1 year ago

JamesR-S commented 1 year ago

I've added a temporary fix to get around the pfam legacy certificate expiration. I've also fixed the problems with pulling data from uniprot - both getting the uniprot ID from the gene name and extracting domain information from the API. Given pfam will cease to exist soon I also changed the default behaviour so that the data is being pulled from uniprot by default, with pfam legacy being used when -pfam flag is added. Addresses #67 #45

lhelseth commented 1 year ago

Thanks for sharing these changes. I was able to build a working copy which works great with Uniprot IDs.

pbnjay commented 1 year ago

Thanks for investigation the solution and opening a PR @JamesR-S !

I'm going to merge this as-is so you don't have to go back-and-forth with any changes. But I'm going to make a few minor changes around the http requests (specifically noting the insecure pram request happening to anyone watching, and being more explicit about the workaround you found for uniprot's invalid response headers).

JamesR-S commented 1 year ago

Glad to be of help 🙂