Use toUriString for paths in work-dir and FilesEx error messages#7075
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pditommaso merged 1 commit intomasterfrom Apr 25, 2026
Merged
Use toUriString for paths in work-dir and FilesEx error messages#7075pditommaso merged 1 commit intomasterfrom
pditommaso merged 1 commit intomasterfrom
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Paths backed by non-default filesystems (e.g. S3, Azure) render as opaque provider objects when interpolated directly into a GString. Wrap them with toUriString so diagnostic messages show a usable URI in the work-dir abort and in FilesEx permission/modify-time failure logs. Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
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bentsherman
reviewed
Apr 27, 2026
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| if(!workDir.mkdirs()) throw new AbortOperationException("Cannot create work-dir: $workDir -- Make sure you have write permissions or specify a different directory by using the `-w` command line option") | ||
| if(!workDir.mkdirs()) | ||
| throw new AbortOperationException("Cannot create work-dir '${FilesEx.toUriString(workDir)}' -- Make sure you have write permissions or specify a different directory by using the `-w` command line option") |
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Nit, you should be able to use workDir.toUriString() here and eliminate the extra import
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Summary
Paths backed by non-default filesystems (S3, Azure Blob, etc.) render as opaque provider objects when interpolated directly into a GString, producing unhelpful messages like
Cannot get read permission on file: nextflow.file.http.XPath@....Wrap the offending paths with
toUriString(...)in:Session.init— the "Cannot create work-dir" abort message now shows the work-dir URI.FilesEx— themkdirs/canRead/canWrite/canExecute/lastModifieddebug/trace logs now include a usable URI.Also splits the long single-line
if(!workDir.mkdirs()) throw ...inSession.initonto two lines for readability.Test plan
./gradlew :nextflow:compileGroovy :nf-commons:compileGroovypasses