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Signed-off-by: Ben Sherman <bentshermann@gmail.com>
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This is the only other place where the two-arg constructor is used: /*
* default case, convert the input object to a string and save
* to a local file
*/
def source = input?.toString() ?: ''
def result = Nextflow.tempFile(altName)
result.text = source
return new FileHolder(source, result)This is for when a |
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Folding into #6490 |
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Close #5905
This PR preserves the source path of remote input files in the FileHolder.
Here are the key changes:
TaskProcessor:
if( item instanceof Path || coerceToPath ) { final path = resolvePath(item) final target = executor.isForeignFile(path) ? foreignFiles.addToForeign(path) : path - final holder = new FileHolder(target) + final holder = new FileHolder(path, target) files << holder }FileHolder:
FileHolder( Path path ) { this.sourceObj = path this.storePath = real(path) this.stageName = norm(path.getFileName()) } FileHolder( def origin, Path path ) { this.sourceObj = origin - this.storePath = path + this.storePath = real(path) this.stageName = norm(path.getFileName()) }The two-arg constructor is updated to match the behavior of the one-arg constructor using the
real()method:The
real()method only resolves symlinks for local files, so path resolution should behave the same way as before for both local and remote files.A future improvement would be to forward this information to a less internal data structure in
TaskEvent. But this change is necessary either way to preserve the remote input path in theTaskRun.