fix: issue #1882 WorkflowError: Metadata can't be created as it already exists (Windows) #1971
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Fixes issue #1882: WorkflowError: Metadata can't be created as it already exists (Windows) Cause: os.rename fails with an exception on Windows if the target exists Fix: os.replace is a cross-platform way to achieve the same (cf. https://stackoverflow.com/q/8107352)
Run a simple rule twice. Used to fail on Windows.
stanmart
changed the title
johanneskoester
approved these changes
Nov 18, 2022
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May I ask you to update to the latest upstream version of the main branch? |
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Sure! Though it seems to me that this branch is up to date with main unless I'm missing something. |
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Kudos, SonarCloud Quality Gate passed!
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johanneskoester
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that referenced
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Dec 13, 2022
🤖 I have created a release *beep* *boop* --- ## [7.19.0](v7.18.2...v7.19.0) (2022-12-13) ### Features * add keyword to gridftp remote provide to specify the number or disable usage of multiple data stream ([#1974](#1974)) ([3e6675d](3e6675d)) * provide information about temp, pipe, and service files in --summary ([#1977](#1977)) ([c7c7776](c7c7776)) * native SLURM support (--slurm, see docs) ([#1015](#1015)) ([c7ea059](c7ea059)) ### Bug Fixes * avoid logfile writing in case of dryrun; better hints in case of incomplete checkpoints ([#1994](#1994)) ([a022705](a022705)) * handle case where zenodo deposition does not return files ([#2004](#2004)) ([b63c4a7](b63c4a7)) * issue [#1882](#1882) WorkflowError: Metadata can't be created as it already exists (Windows) ([#1971](#1971)) ([d4484e6](d4484e6)) * json validation error with markdown cells ([#1986](#1986)) ([6c26f75](6c26f75)) --- 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> Co-authored-by: Johannes Köster <johannes.koester@tu-dortmund.de>
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Description
Fixes issue #1882: WorkflowError: Metadata can't be created as it already exists (Windows)
The underlying cause of the problem is that
os.renamewas used to overwrite the target file. Unfortunately, it has a different behavior under Unix/Linux (overwrites target) and Windows (fails).os.replaceis an alternative toos.renamethat simulates the Unix behavior.The required change is extremely small (commit 4ad1ab1) and I have also added a test case covering it (commit e12955f).
QC
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).