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Move BigQuery classes [VS-971] #8375

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merged 5 commits into from
Jun 30, 2023
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mcovarr
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@mcovarr mcovarr commented Jun 22, 2023

Move BigQuery classes that are only used by GVS into a gvs package. This should facilitate the alignment of GVS with GATK master by making it clear that these classes were created specifically for GVS and are not necessarily more generally usable in their current forms.

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LGTM. Appear to just be moving packages and a bit of formatting.

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Looks good to me.

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codecov bot commented Jun 22, 2023

Codecov Report

❗ No coverage uploaded for pull request base (ah_var_store@90aa0fd). Click here to learn what that means.
The diff coverage is n/a.

❗ Current head 96b13ac differs from pull request most recent head 16fbf89. Consider uploading reports for the commit 16fbf89 to get more accurate results

Additional details and impacted files
@@               Coverage Diff                @@
##             ah_var_store     #8375   +/-   ##
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  Coverage                ?   86.155%           
  Complexity              ?     35517           
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  Files                   ?      2194           
  Lines                   ?    166538           
  Branches                ?     17926           
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  Hits                    ?    143481           
  Misses                  ?     16674           
  Partials                ?      6383           

@mcovarr mcovarr force-pushed the vs_971_move_bigquery_classes branch from 96b13ac to 4655993 Compare June 22, 2023 21:24
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droazen commented Jun 23, 2023

@mcovarr Does the GVS traversal artifact destined to remain in GATK depend on the BigQueryUtils? I'm guessing that it does? Is the intention that BigQueryUtils would remain in gatk/master, then, just in a different package?

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mcovarr commented Jun 23, 2023

@droazen exactly, the artifact will depend on BigQueryUtils which would be in a gvs package to hopefully make clear that the contents are currently fairly specific to GVS and probably not ideal for more general use in their present form.

@mcovarr mcovarr force-pushed the vs_971_move_bigquery_classes branch from 4655993 to 6470418 Compare June 28, 2023 19:58
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Github actions tests reported job failures from actions build 5405305229
Failures in the following jobs:

Test Type JDK Job ID Logs
conda 8 5405305229.3 logs

@mcovarr mcovarr force-pushed the vs_971_move_bigquery_classes branch from 6470418 to 16fbf89 Compare June 29, 2023 17:11
@mcovarr mcovarr merged commit 09989de into ah_var_store Jun 30, 2023
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@mcovarr mcovarr deleted the vs_971_move_bigquery_classes branch June 30, 2023 16:27
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6 participants