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VS-637 Address a couple of issues in SampleLoadStatus handling in GVSImportGenomes. #8052

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merged 21 commits into from
Oct 19, 2022
Merged

VS-637 Address a couple of issues in SampleLoadStatus handling in GVSImportGenomes. #8052

merged 21 commits into from
Oct 19, 2022

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gbggrant
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@gbggrant gbggrant commented Oct 12, 2022 •
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This PR addresses some issues with tracking of sample loading in GVSImportGenomes.

  1. Due to a bug (unresolved as yet) where the status 'STARTED' can be written to sample_load_status multiple times, the method LoadStatus.getSampleLoadState would NEVER return COMPLETE. This PR fixes the logic to allow for the (unexpected) case of multiple 'STARTED' statuses.
  2. I have modified the SetIsLoadedColumn task in GVSImportGenomes to explicitly look for sample_load_status records with both STARTED and FINISHED to use to update sample_info.is_loaded to true.

@gbggrant
Change the Logic of LoadStatus.getSampleLoadState to allow for mutlip…
538b8dd 
…le STARTED and FINISHED records.

Also, have it run the query NOT in batch mode.
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codecov bot commented Oct 12, 2022 •
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Codecov Report

❗ No coverage uploaded for pull request base (ah_var_store@1c5c486). Click here to learn what that means.
The diff coverage is n/a.

Additional details and impacted files 
@@               Coverage Diff                @@
##             ah_var_store     #8052   +/-   ##
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  Coverage                ?   86.242%           
  Complexity              ?     35201           
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  Files                   ?      2173           
  Lines                   ?    165041           
  Branches                ?     17794           
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  Hits                    ?    142334           
  Misses                  ?     16379           
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@gbggrant gbggrant marked this pull request as ready for review October 13, 2022 13:45
@gbggrant gbggrant requested review from mcovarr and rsasch October 13, 2022 13:45
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gbggrant commented Oct 13, 2022 •
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Successful run at:
https://job-manager.dsde-prod.broadinstitute.org/jobs/d6c68894-312a-4db8-b8d4-3c9d4f19c23d

@gbggrant gbggrant changed the title Change the Logic of LoadStatus.getSampleLoadState to allow for mutlip… VS-637 Address a couple of issues in SampleLoadStatus handling in GVSImportGenomes. Oct 13, 2022
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gatk-bot commented Oct 13, 2022 •
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Github actions tests reported job failures from actions build 3244925651
Failures in the following jobs:

Test Type JDK Job ID Logs
cloud 8 3244925651.10 logs
cloud 11 3244925651.11 logs

@gbggrant gbggrant requested a review from RoriCremer October 13, 2022 19:25
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gatk-bot commented Oct 13, 2022 •
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Github actions tests reported job failures from actions build 3245059454
Failures in the following jobs:

Test Type JDK Job ID Logs
cloud 8 3245059454.10 logs
cloud 11 3245059454.11 logs

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gatk-bot commented Oct 13, 2022 •
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Github actions tests reported job failures from actions build 3245400724
Failures in the following jobs:

Test Type JDK Job ID Logs
cloud 8 3245400724.10 logs
cloud 11 3245400724.11 logs

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gatk-bot commented Oct 13, 2022 •
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Github actions tests reported job failures from actions build 3245510955
Failures in the following jobs:

Test Type JDK Job ID Logs
cloud 8 3245510955.10 logs
cloud 11 3245510955.11 logs

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retest this please

gbggrant
gbggrant commented Oct 18, 2022
View reviewed changes
scripts/variantstore/wdl/GvsImportGenomes.wdl Outdated
@@ -22,7 +22,7 @@ workflow GvsImportGenomes {
Int? load_data_batch_size
Int? load_data_preemptible_override
Int? load_data_maxretries_override
File? load_data_gatk_override = "gs://gvs_quickstart_storage/jars/gatk-package-4.2.0.0-613-g1219576-SNAPSHOT-local.jar"
File? load_data_gatk_override = "gs://gvs_quickstart_storage/jars/VS-637/gatk-package-4.2.0.0-614-g8f8f1691-SNAPSHOT-local.jar"
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Note - will update this (put the jar in the 'standard' location) at merge time.

rsasch
rsasch approved these changes Oct 18, 2022
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LGTM

@gbggrant gbggrant merged commit f2dcc68 into ah_var_store Oct 19, 2022
@gbggrant gbggrant deleted the gg_VS-637_RespectSampleLoadStatusFinishedFlag branch October 19, 2022 00:29
This was referenced Mar 17, 2023
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@rsasch rsasch rsasch approved these changes

@mcovarr mcovarr Awaiting requested review from mcovarr

@RoriCremer RoriCremer Awaiting requested review from RoriCremer

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