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fix: iRODS functionality - issue #1510 #1611

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merged 5 commits into from May 16, 2022

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ScottMastro
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@ScottMastro ScottMastro commented Apr 27, 2022

Description

This PR includes my recommended changes suggested on issue #1510

  • This brings the functionality of this remote module in-line with what the documentation says (specifically, that the "zone" is not needed in the path).
  • This also fixes an issue where the module does not work unless an iRODS user has read access to all directories in the path. This fix avoids throwing an error if a user doesn't have read access to one or more superdirectories.

QC

  • [ x ] The PR contains a test case for the changes or the changes are already covered by an existing test case.
  • [ x ] 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).

@ScottMastro ScottMastro changed the title Fixing iRODS functionality - issue #1510 fix: iRODS functionality - issue #1510 Apr 27, 2022
snakemake/remote/iRODS.py Outdated Show resolved Hide resolved
@johanneskoester
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johanneskoester commented May 2, 2022

Also, can you please format with black?

ScottMastro and others added 4 commits May 2, 2022
Co-authored-by: Johannes Köster <johannes.koester@uni-due.de>
allows iRODS _upload function to either create (if missing) or ignore (if user has no access) a subdirectory
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sonarcloud bot commented May 9, 2022

Kudos, SonarCloud Quality Gate passed!    Quality Gate passed

Bug A 0 Bugs
Vulnerability A 0 Vulnerabilities
Security Hotspot A 0 Security Hotspots
Code Smell A 0 Code Smells

No Coverage information No Coverage information
No Duplication information No Duplication information

@ScottMastro
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ScottMastro commented May 9, 2022

The irods test was failing because an exception was being thrown when checking for access to a subdirectory that doesn't exist yet - this should be handled now.

@johanneskoester johanneskoester merged commit 9c3767d into snakemake:main May 16, 2022
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2 participants