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Add CID H2 plugin #5889

Merged
merged 5 commits into from
Mar 20, 2025
Merged

Add CID H2 plugin #5889

merged 5 commits into from
Mar 20, 2025

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pditommaso
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@pditommaso pditommaso commented Mar 16, 2025

Summary

This PR adds a new CID implementation that uses H2 to store CID data.

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Add the following settings in your nextflow.config file

plugins {
  id 'nf-cid-h2'
}

workflow.data.store.location = "jdbc:h2:file:./.data/h2;AUTO_SERVER=TRUE"
workflow.data.enabled = true

@pditommaso pditommaso requested a review from jorgee March 16, 2025 17:48
@pditommaso pditommaso changed the base branch from master to cid-store March 16, 2025 17:48
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Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
Signed-off-by: jorgee <jorge.ejarque@seqera.io>
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jorgee commented Mar 18, 2025

I have tested with rnaseq-nf and working with h2 and default when using local disk. Defautl with s3 locations were not supported. I have pushed some changes in DefaultCidStoreFactory to allow s3, gs and az schemes

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@jorgee is this ready to go in your side?

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jorgee commented Mar 20, 2025

Yes, it is

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jorgee commented Mar 20, 2025

Sorry, I forgot to rename the plugin, just a commit missing

Signed-off-by: jorgee <jorge.ejarque@seqera.io>
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jorgee commented Mar 20, 2025

Now renamed plugin is pushed

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
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Ok, I've also replace the Service loader in the cid command with classic plugin

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
@pditommaso pditommaso merged commit eb14d4b into cid-store Mar 20, 2025
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@pditommaso pditommaso deleted the cid-h2 branch March 20, 2025 11:58
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3 participants