projectglow / glow

An open-source toolkit for large-scale genomic analysis
https://projectglow.io
Apache License 2.0
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Iss463 quarantine full ds #469

Closed mah-databricks closed 2 years ago

mah-databricks commented 2 years ago

What changes are proposed in this pull request?

Rework Piper to quarantine only the partitions which fail. This required a small rewrite to the Iterator code which calls the external CLI tooling. Also needed to backfill exceptions to make sure the application gives the appearance of still functioning the same way.

How is this patch tested?

(Details)

codecov[bot] commented 2 years ago

Codecov Report

Merging #469 (ea36ea2) into master (a7db6b6) will decrease coverage by 0.00%. The diff coverage is 95.23%.

Impacted file tree graph

@@            Coverage Diff             @@
##           master     #469      +/-   ##
==========================================
- Coverage   93.66%   93.66%   -0.01%     
==========================================
  Files          95       95              
  Lines        4849     4875      +26     
  Branches      463      457       -6     
==========================================
+ Hits         4542     4566      +24     
- Misses        307      309       +2     
Impacted Files Coverage Δ
...rojectglow/transformers/pipe/PipeTransformer.scala 100.00% <ø> (ø)
...scala/io/projectglow/transformers/pipe/Piper.scala 93.51% <94.44%> (-0.60%) :arrow_down:
...jectglow/transformers/pipe/CSVInputFormatter.scala 100.00% <100.00%> (ø)
...low/transformers/pipe/UTF8TextInputFormatter.scala 100.00% <100.00%> (ø)
...n/scala/io/projectglow/vcf/VCFInputFormatter.scala 100.00% <100.00%> (ø)

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williambrandler commented 2 years ago

thanks @mah-databricks, let me merge in, rebuild the project and then perform an integration test on this new quarantine functionality