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fix: remote pre-command not installing all required storage plugins#3116

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johanneskoester merged 2 commits intosnakemake:mainfrom
jjjermiah:main
Oct 8, 2024
Merged

fix: remote pre-command not installing all required storage plugins#3116
johanneskoester merged 2 commits intosnakemake:mainfrom
jjjermiah:main

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@jjjermiah
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@jjjermiah jjjermiah commented Oct 4, 2024 •
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Related Issues:
#2501
snakemake/snakemake-executor-plugin-kubernetes#19

When the job spawner prepares the precommand for remote execution, it only registers the default storage provider which fails to acknowledge the presence of a storage provider within the snakefile.

This PR should now register all storage providers that workflow has recognized.

NOTE: unsure how to I could add a test case for this?

QC

  • The PR contains a test case for the changes or the changes are already covered by an existing test case.
  • The documentation (docs/) is updated to reflect the changes or this is not necessary (e.g. if the change does neither modify the language nor the behavior or functionalities of Snakemake).

Summary by CodeRabbit

  • New Features

    • Enhanced package installation logic for storage providers, allowing multiple packages to be installed simultaneously when the auto-deploy feature is enabled.

  • Bug Fixes

    • Improved handling of duplicate package names in the installation process.

@coderabbitai
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coderabbitai bot commented Oct 4, 2024 •
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Walkthrough

The changes in this pull request modify the precommand method of the SpawnedJobArgsFactory class in snakemake/spawn_jobs.py. The primary update involves how packages are determined for installation when the auto_deploy_default_storage_provider setting is enabled. The method now collects package names into a set to eliminate duplicates and constructs a single string from these names for the precommand list, allowing for the installation of multiple storage provider plugins simultaneously.

Changes

File Change Summary
snakemake/spawn_jobs.py Modified the precommand method to collect package names from storage provider settings into a set, ensuring no duplicates, and append them as a single string to the precommand list.

Sequence Diagram(s)

sequenceDiagram
    participant User
    participant SpawnedJobArgsFactory
    participant StorageProvider

    User->>SpawnedJobArgsFactory: Request to prepare command
    SpawnedJobArgsFactory->>StorageProvider: Retrieve package names
    StorageProvider-->>SpawnedJobArgsFactory: Return package names
    SpawnedJobArgsFactory->>SpawnedJobArgsFactory: Remove duplicates
    SpawnedJobArgsFactory->>SpawnedJobArgsFactory: Construct precommand string
    SpawnedJobArgsFactory-->>User: Return precommand with packages
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sonarqubecloud bot commented Oct 7, 2024

Quality Gate Passed Quality Gate passed

Issues
0 New issues
0 Accepted issues

Measures
0 Security Hotspots
0.0% Coverage on New Code
0.0% Duplication on New Code

See analysis details on SonarCloud

@johanneskoester
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johanneskoester commented Oct 8, 2024

Good catch! Indeed, a testcase is tricky, but the code is pretty clear and minimal. I think we can for now live with not having one.

@johanneskoester johanneskoester merged commit d829bb7 into snakemake:main Oct 8, 2024
@github-actions github-actions bot mentioned this pull request Oct 8, 2024
Merged
johanneskoester pushed a commit that referenced this pull request Oct 11, 2024
@github-actions
chore(main): release 8.20.7 (#3125)
f301c59 
🤖 I have created a release *beep* *boop*
---


##
[8.20.7](v8.20.6...v8.20.7)
(2024-10-09)


### Bug Fixes

* install conda in container image
([#3127](#3127))
([afa7bad](afa7bad))
* remote pre-command not installing all required storage plugins
([#3116](#3116))
([d829bb7](d829bb7))

---
This PR was generated with [Release
Please](https://github.com/googleapis/release-please). See
[documentation](https://github.com/googleapis/release-please#release-please).

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
@coderabbitai coderabbitai bot mentioned this pull request Nov 29, 2024
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@coderabbitai coderabbitai bot mentioned this pull request Jun 13, 2025
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@jjjermiah @johanneskoester