No way to add dataset

[jules-o]

Hi,

Using local install via docker, just upgraded and now when I click Edit Datasets, instead of the form to give the elasticsearch index I'm getting a popup to add IGV paths.

Am I doing something wrong or is this a bug?

[hanars]

we've recently made permissions in seqr more granular. To add elasticsearch indices you need to have the is_staff permission set for your user

[jules-o]

Hi Hana, sorry to bother you again but how do I set the is_staff permission for a user? I'm logged in as a Data Manager, looking at the Data Management>Users page, where I can see the user but can't modify anything. I tried to look in Kibana but get:
Error: Unable to connect to Kibana HTTPConnectionPool(host='kibana', port=5601): Max retries exceeded with url: /app/kibana (Caused by NewConnectionError(': Failed to establish a new connection: [Errno -2] Name or service not known'))

I'm also now getting an error when I try to variant search:
relation "reference_data_geneinfo" does not exist LINE 1: ...id", "reference_data_geneinfo"."gene_symbol" FROM "reference... ^
I've run migrations and updated gene-level reference datasets via docker exec, not sure what else to try.

[hanars]

you need to use the /admin page to directly modify the DB

[hanars]

and the second issue you mention is definitely a migration issue. Make sure you run migrate with the
--database=reference_data_db flag to apply migrations to that database

[jules-o]

Thanks Hana, got the user updated now and fixed the migrations. It's the wonderful seqr that I know and love again :)