Scout: "scout update omim" not working

[bjhall]

Worked a few weeks ago... I don't have time to debug this at the moment. If no one else cares about this I will take a look at it next week!

$ scout update omim --institute CMD --api-key xxxxxxxxxxxxxxxxxxxxx

2019-11-21 15:17:13 cmdscout2 scout.commands.base[16298] INFO Running scout version 4.8.3
2019-11-21 15:17:13 cmdscout2 scout.commands.base[16298] DEBUG Debug logging enabled.
2019-11-21 15:17:13 cmdscout2 scout.commands.update.omim[16298] INFO Running scout update omim
2019-11-21 15:17:13 cmdscout2 scout.adapter.mongo.institute[16298] DEBUG Fetch institute CMD
2019-11-21 15:17:13 cmdscout2 scout.adapter.mongo.panel[16298] INFO Fetching gene panels OMIM-AUTO from database
2019-11-21 15:17:13 cmdscout2 scout.adapter.mongo.panel[16298] INFO Setting version to 3.0
2019-11-21 15:17:13 cmdscout2 scout.utils.requests[16298] INFO Fetching OMIM files from https://omim.org/
2019-11-21 15:17:13 cmdscout2 scout.utils.requests[16298] INFO Requesting https://omim.org/static/omim/data/mim2gene.txt
2019-11-21 15:17:14 cmdscout2 scout.utils.requests[16298] INFO Requesting https://data.omim.org/downloads/xxxxxxxxxxxxxxxxx/genemap2.txt
2019-11-21 15:17:15 cmdscout2 scout.adapter.mongo.hgnc[16298] INFO Fetching all genes by alias
2019-11-21 15:17:16 cmdscout2 scout.parse.omim[16298] INFO Get the mim genes
2019-11-21 15:17:16 cmdscout2 scout.parse.omim[16298] INFO Parsing mim2gene
2019-11-21 15:17:16 cmdscout2 scout.parse.omim[16298] INFO Number of genes without hgnc symbol 175
2019-11-21 15:17:16 cmdscout2 scout.parse.omim[16298] INFO Parsing the omim genemap2
2019-11-21 15:17:16 cmdscout2 scout.commands.update.omim[16298] ERROR 'Mim Number'
Aborted!

[northwestwitch]

I can confirm the bug. I've tested the command on our stage environment and on a local instance and I get exactly the same error.
We'll try to fix it ASAP! Thanks @bjhall!

[northwestwitch]

I'll try to fix this today!

[northwestwitch]

It might actually take some more time, because after some attempts my omim key has been blocked, and instead of the definitions I get this message This data account exceeded its download cap, please contact us at https://omim.org/contact if this is an issue

[dnil]

We should keep a backup key...

[northwestwitch]

We should keep a backup key...

Why should I have a backup one when I can get one from Måns or yours? ;)

[dnil]

Mine is expired - I need to renew, but why should I when I can just use Måns’. X-)

[northwestwitch]

Mine is expired - I need to renew, but why should I when I can just use Måns’. X-)

@moonso you should ask for 10 Kr for each time someone uses it!

[moonso]

Haha yes you can always hire mine, just swish me

[northwestwitch]

@bjhall the problem is that they changed a column header in the genemap2 file. "Mim Number" was changed to "MIM Number"