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Load experiment design data into our local environment #181

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ke4 opened this issue Mar 25, 2024 · 0 comments
Open
2 tasks

Load experiment design data into our local environment #181

ke4 opened this issue Mar 25, 2024 · 0 comments
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bulk Improvement Improve/refactor existing code

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@ke4
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ke4 commented Mar 25, 2024

We need to able to load the experiment design data for each experiments to the PostgreSQL database.
For that purpose we can use a script from the db-scxa repository: https://github.com/ebi-gene-expression-group/db-scxa/blob/develop/bin/load_exp_design.sh.
We have a tested example in our single cell repo: https://github.com/ebi-gene-expression-group/atlas-web-single-cell/blob/092fea1d41f4075fc66225d3359f23173fc7141a/docker/prepare-dev-environment/postgres/docker-compose.yml#L55
We could reuse that.

In bulk we are handling database population differently than in scxa. We are doing that via our application's admin endpoint:
We are using this endpoint for DB operations:
http://$TOMCAT_HOST/gxa/admin/experiments/${expAcc}/${WEB_APP_CALL}
where

  • expAcc: the Experiment accession ID
  • WEB_APP_CALL: import_public or coexpression_update

Tasks:

  • Add load_exp_design.sh shell script into the relevant docker compose file
    Add experiment design table(s) population into that above endpoint
  • Execute the postgres step from the env creation steps and check whether the DB tables (exp_design_column and exp_design) has been populated
@ke4 ke4 added bulk Improvement Improve/refactor existing code high priority labels Mar 25, 2024
@ke4 ke4 removed the high priority label Apr 25, 2024
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Labels
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