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Move insertions out of metadata #372

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fengelniederhammer opened this issue Mar 27, 2024 · 0 comments · Fixed by #429
Closed

Move insertions out of metadata #372

fengelniederhammer opened this issue Mar 27, 2024 · 0 comments · Fixed by #429
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@Taepper

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@fengelniederhammer
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  • There should not be a metadata type for insertions
  • In the tsv/fasta preprocessing format: Currently, insertions are provided to SILO in the metadata.tsv file. Think of how else insertions should be provided
  • In NDJSON format, insertions can be provided separately from metadata already.
  • This solves a couple of issues:
@Taepper Taepper mentioned this issue May 17, 2024
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@fengelniederhammer fengelniederhammer mentioned this issue May 21, 2024
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fengelniederhammer pushed a commit that referenced this issue May 23, 2024
@Taepper @fengelniederhammer
feat: insertions no longer in metadata or databaseConfig, instead exp…
4e29220 
…ected for all aligned sequences #372

BREAKING CHANGE: old database_config files might be invalid if they contained insertion columns. Also, we are more prohibitive for ndjson input files, which now MUST contain nucleotide/amino acid insertions for all respective sequences. The insertions action and filter do no longer require a column field.
fengelniederhammer pushed a commit that referenced this issue May 23, 2024
@Taepper @fengelniederhammer
feat: insertions no longer in metadata or databaseConfig, instead exp…
1f3680c 
…ected for all aligned sequences #372

BREAKING CHANGE: old database_config files might be invalid if they contained insertion columns. Also, we are more prohibitive for ndjson input files, which now MUST contain nucleotide/amino acid insertions for all respective sequences. The insertions action and filter do no longer require a column field.
@fengelniederhammer fengelniederhammer mentioned this issue May 23, 2024
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@github-actions github-actions bot mentioned this issue May 23, 2024
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fengelniederhammer added a commit to loculus-project/loculus that referenced this issue May 27, 2024
@fengelniederhammer
chore(kubernetes): update LAPIS and SILO
fb60752 
GenSpectrum/LAPIS-SILO#372 introduced a breaking change in the database config schema
@fengelniederhammer fengelniederhammer mentioned this issue May 27, 2024
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fengelniederhammer added a commit to loculus-project/loculus that referenced this issue May 27, 2024
@fengelniederhammer
chore(kubernetes): update LAPIS and SILO
57b2e2a 
GenSpectrum/LAPIS-SILO#372 introduced a breaking change in the database config schema
@corneliusroemer corneliusroemer mentioned this issue May 27, 2024
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corneliusroemer pushed a commit to loculus-project/loculus that referenced this issue May 28, 2024
@fengelniederhammer @corneliusroemer
chore(kubernetes): update LAPIS and SILO
24bc771 
GenSpectrum/LAPIS-SILO#372 introduced a breaking change in the database config schema
(cherry picked from commit 57b2e2a)
corneliusroemer added a commit to loculus-project/loculus that referenced this issue May 28, 2024
@corneliusroemer @fengelniederhammer
chore(kubernetes): bump LAPIS and SILO to 0.2.x (#2039)
d62c6ef 
* chore(kubernetes): update LAPIS and SILO

GenSpectrum/LAPIS-SILO#372 introduced a breaking change in the database config schema
(cherry picked from commit 57b2e2a)

* chore(kubernetes): update SILO to 0.2.1 

---------

Co-authored-by: Fabian Engelniederhammer <fabian.engelniederhammer@tngtech.com>
@github-actions github-actions bot mentioned this issue Jul 9, 2024
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@github-actions github-actions bot mentioned this issue Aug 30, 2024
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This was referenced Sep 12, 2024
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@github-actions github-actions bot mentioned this issue Oct 1, 2024
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Insertions out of metadata GenSpectrum/LAPIS-SILO
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@Taepper @fengelniederhammer