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broadinstitute / seqr

web-based analysis tool for rare disease genomics
GNU Affero General Public License v3.0
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monarch link in gene info page does not work #4036

Open zhanglw05 opened 2 months ago

zhanglw05 commented 2 months ago

Hi, Seqr team

the monarch link at the top of gene info page does not work. if you search AGRN in gene info page, the monarch link is set to "https://monarchinitiative.org/ENSEMBL:ENSG00000188157" and this page cannot be opened. Can you please update the link on your repo https://github.com/broadinstitute/seqr/blob/master/ui/shared/components/panel/genes/GeneDetail.jsx#L333 .

hanars commented 2 months ago

We encourage external groups to provide code fixes to this open source repo whenever possible. If you have already identified exactly where in the code the issue arises and how to fix it, this will be fixed much faster if you provide a pull request with the fix. Otherwise, we will prioritize this fix relative to our other planned seqr work and will get to it in due time

zhanglw05 commented 2 months ago

They are using hgnc id in the url, e.g. https://beta.monarchinitiative.org/HGNC:329. Our fix will be different from yours as we do not have your latest gencc table. you may just change the url to https://beta.monarchinitiative.org/HGNC:{gene.hgnc_id} if hgnc_id is in your gene json.

hanars commented 2 months ago

we only have hgnc Ids for a tiny small percentage of genes so that is not a valid solution for us eithe

hanars commented 6 days ago

Blocked on an inability to generate a working link