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Empty input #433

Merged
merged 2 commits into from
May 31, 2024
Merged

Empty input #433

merged 2 commits into from
May 31, 2024

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Taepper
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@Taepper Taepper commented May 17, 2024

resolves #244

Summary

We want to be able to start without data, such that downstream packages do not need extra logic.

In particular the ingest with an empty ndjson (which does not have keys anymore) should not fail. This was challenging, because we never want to read the ndjson files into a table as a whole, but only the non-sequence columns of it, and the sequence columns should be compressed while reading them

PR Checklist

- [ ] All necessary documentation has been adapted or there is an issue to do so.

  • The implemented feature is covered by an appropriate test.

@Taepper Taepper force-pushed the insertions-out-of-metadata branch from c86ed18 to e8680f0 Compare May 21, 2024 08:04
@Taepper Taepper force-pushed the insertions-out-of-metadata branch 2 times, most recently from 8c6a42f to d2ecf3a Compare May 23, 2024 12:18
@fengelniederhammer fengelniederhammer force-pushed the insertions-out-of-metadata branch from d2ecf3a to 4e29220 Compare May 23, 2024 13:01
Base automatically changed from insertions-out-of-metadata to main May 23, 2024 13:18
@Taepper Taepper force-pushed the empty-input branch 4 times, most recently from 3116e01 to d6898ca Compare May 27, 2024 07:53
@Taepper Taepper requested a review from JonasKellerer May 27, 2024 07:57
@fengelniederhammer fengelniederhammer linked an issue May 27, 2024 that may be closed by this pull request
@Taepper Taepper force-pushed the empty-input branch 2 times, most recently from ff7715e to dd5cd6c Compare May 27, 2024 19:09
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@fengelniederhammer fengelniederhammer left a comment

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Actually looks good, but IMO the code needs a little clean up.

src/silo/common/string_utils.cpp Outdated Show resolved Hide resolved
src/silo/preprocessing/preprocessor.cpp Outdated Show resolved Hide resolved
src/silo/preprocessing/preprocessor.cpp Outdated Show resolved Hide resolved
src/silo/preprocessing/preprocessor.cpp Outdated Show resolved Hide resolved
src/silo/preprocessing/preprocessor.cpp Outdated Show resolved Hide resolved
include/silo/preprocessing/metadata_info.h Outdated Show resolved Hide resolved
src/silo/preprocessing/metadata_info.cpp Show resolved Hide resolved
src/silo/preprocessing/metadata_info.cpp Outdated Show resolved Hide resolved
src/silo/config/database_config.cpp Outdated Show resolved Hide resolved
testBaseData/emptyInputTsv/small_metadata_set.tsv Outdated Show resolved Hide resolved
@Taepper Taepper force-pushed the empty-input branch 3 times, most recently from 4ea4eea to d996531 Compare May 29, 2024 16:24
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@fengelniederhammer fengelniederhammer left a comment

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LGTM

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@corneliusroemer
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Can I already test this works? Are there any breaking changes or can I just use the docker image as is?

@Taepper Taepper merged commit d407b92 into main May 31, 2024
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@Taepper Taepper deleted the empty-input branch May 31, 2024 13:37
corneliusroemer added a commit to loculus-project/loculus that referenced this pull request Jun 2, 2024
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Start without data
3 participants