Monarch Gene Mappings not found

[anitacaron]

I'm running make mappings to get the mappings, but I'm getting an error when downloading the gene_mappings.tsv. The folder latest is empty in the URL https://data.monarchinitiative.org/monarch-gene-mapping/index.html

mkdir -p mappings tmp
wget http://data.monarchinitiative.org/monarch-gene-mapping/latest/gene_mappings.tsv -O tmp/gene_mappings.sssom.tsv
--2023-11-15 11:24:57--  http://data.monarchinitiative.org/monarch-gene-mapping/latest/gene_mappings.tsv
Resolving data.monarchinitiative.org (data.monarchinitiative.org)... 35.208.191.193
Connecting to data.monarchinitiative.org (data.monarchinitiative.org)|35.208.191.193|:80... connected.
HTTP request sent, awaiting response... 404 Not Found
2023-11-15 11:24:57 ERROR 404: Not Found.

make[1]: *** [mappings/gene_mappings.sssom.tsv] Error 8

This is needed for #29

[matentzn]

@glass-ships I think we should avoid, during the release process, to create a "latest" directory until all files in it are created. Maybe a better way would be to avoid this level of indirection entirely, migrate gene mappings here #26 and deploy the mappings in mapping commons as the official mappings on data.mi.org?

[glass-ships]

we ran the gene-mapping generation overnight and didn't realize until just now that the Jenkins job doesn't run any indexing afterwards. the new gene mapping file is in the data-public bucket, however it won't be available at that particular url until the indexer gets ran.

i'll look at migrating that code here in a future PR, we just wanted to fix the more pressing issues from #33 first

in the meantime, i have another jenkins job running which does the indexing, it just may take a bit to finish.

if you have access to the GCP buckets, you can find the current gene mapping file at data-public-monarchinitiative/monarch-gene-mapping/latest

[kevinschaper]

We renamed it to gene_mappings.sssom.tsv in a build that ran overnight, so next step is fixing the url in this repo - then #26

[glass-ships]

so next step is fixing the url in this repo

i actually just did that in the latest commit in the sssom-mappings branch of this repo