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Add flag for cost_observability table writing to support sub-cohort use case [VS-521] #8093

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merged 16 commits into from
Nov 21, 2022

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rsasch
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@rsasch rsasch commented Nov 14, 2022

This PR adds documentation for the GvsExtractCohortFromSampleNames workflow and tweaks the handling of the cost_observability table to allow it to be disabled for prepare/extract if using different Google project IDs for GVS source and sub-cohort tables (an AoU use case).

Successful run: https://app.terra.bio/#workspaces/gvs-dev/RSA%20-%20GVS%20Quickstart%20V2%20/job_history/a8db0d7d-86db-48eb-8bd9-df58abd4ba3a

@rsasch rsasch self-assigned this Nov 14, 2022
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codecov bot commented Nov 14, 2022

Codecov Report

❗ No coverage uploaded for pull request base (ah_var_store@dfe7b7e). Click here to learn what that means.
The diff coverage is n/a.

Additional details and impacted files
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##             ah_var_store     #8093   +/-   ##
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@rsasch rsasch marked this pull request as ready for review November 15, 2022 23:19
}

Boolean write_cost_to_db = if ((gvs_project != destination_project_id) || (gvs_project != query_project)) then false else true
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@mcovarr mcovarr Nov 16, 2022

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TOL can this be simplified (actual question, I don't know)?

Suggested change
Boolean write_cost_to_db = if ((gvs_project != destination_project_id) || (gvs_project != query_project)) then false else true
Boolean write_cost_to_db = (gvs_project == destination_project_id) && (gvs_project == query_project)

scripts/variantstore/wdl/SUB_COHORT_WORKFLOW.md Outdated Show resolved Hide resolved
@rsasch rsasch requested a review from mcovarr November 16, 2022 18:57
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@gbggrant gbggrant left a comment

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Looks good to me.

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gatk-bot commented Nov 21, 2022

Github actions tests reported job failures from actions build 3516053178
Failures in the following jobs:

Test Type JDK Job ID Logs
unit 11 3516053178.13 logs
cloud 11 3516053178.11 logs
integration 11 3516053178.12 logs
cloud 11 3516053178.11 logs
cloud 11 3516053178.11 logs

@rsasch rsasch merged commit 08048f1 into ah_var_store Nov 21, 2022
@rsasch rsasch deleted the rsa_vs_521_subcohort_cost branch November 21, 2022 17:58
This was referenced Mar 17, 2023
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4 participants