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Ingest 10K [VS-344] #7860

Merged
merged 11 commits into from
May 26, 2022
Merged

Ingest 10K [VS-344] #7860

merged 11 commits into from
May 26, 2022

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mcovarr
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@mcovarr mcovarr commented May 18, 2022

Setting a default batch size of 5 since that seemed to work out well in the two Stroke Anderson runs, overridable at the workflow level. Also cleaned up some logging and wrapping exceptions before throwing to avoid confusing stack traces when scanning through logs.

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codecov bot commented May 18, 2022

Codecov Report

❗ No coverage uploaded for pull request base (ah_var_store@e7539d5). Click here to learn what that means.
The diff coverage is n/a.

@@               Coverage Diff                @@
##             ah_var_store     #7860   +/-   ##
================================================
  Coverage                ?   86.296%           
  Complexity              ?     35197           
================================================
  Files                   ?      2170           
  Lines                   ?    164877           
  Branches                ?     17783           
================================================
  Hits                    ?    142282           
  Misses                  ?     16271           
  Partials                ?      6324           

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a couple small nits but, essentially, 👍🏻

scripts/variantstore/wdl/GvsImportGenomes.wdl Outdated Show resolved Hide resolved
scripts/variantstore/wdl/GvsUnified.wdl Outdated Show resolved Hide resolved
@@ -119,7 +119,9 @@ protected void writeJsonArray(int retryCount) throws ExecutionException, Interru
}
logger.warn("Caught exception writing to BigQuery, " + (maxRetries - retryCount - 1) + " retries remaining.", e);
long backOffMillis = backoff.nextBackOffMillis();
logger.warn("Sleeping for {} milliseconds before retrying.", backOffMillis);
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I did not know you could use the {} syntax in logger.

@mcovarr mcovarr merged commit a4ac264 into ah_var_store May 26, 2022
@mcovarr mcovarr deleted the vs_344_ingest_10k branch May 26, 2022 19:10
This was referenced Mar 17, 2023
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3 participants