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Fix Fusion symlink resolution with nested files #4726

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bentsherman wants to merge 3 commits into from
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Fix Fusion symlink resolution with nested files #4726

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a269ec4
Fix Fusion symlink resolution with nested files
bentsherman Feb 8, 2024
d4de81d
Merge branch 'master' into fix-fusion-symlink-with-stageas
bentsherman Apr 22, 2024
b9429c0
Merge branch 'master' into fix-fusion-symlink-with-stageas
bentsherman Apr 24, 2024
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5 changes: 3 additions & 2 deletions modules/nextflow/src/main/groovy/nextflow/processor/PublishDir.groovy
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Original file line number Diff line number Diff line change
Expand Up @@ -406,9 +406,10 @@ class PublishDir {

// resolve Fusion symlink if applicable
if( FusionHelper.isFusionEnabled(session) ) {
final sourceName = sourceDir.relativize(source).toString()
final inputs = getTaskInputs()
if( source.name in inputs )
source = resolveFusionLink(inputs[source.name])
if( sourceName in inputs )
source = resolveFusionLink(inputs[sourceName])
}

// create target dirs if required
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9 changes: 5 additions & 4 deletions plugins/nf-amazon/src/test/nextflow/processor/PublishDirS3Test.groovy
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Expand Up @@ -80,12 +80,13 @@ class PublishDirS3Test extends Specification {
}
and:
def prev = FileHelper.asPath('s3://bucket/work/0/foo.txt')
def file = FileHelper.asPath('s3://bucket/work/1/foo.txt')
def taskInputs = ['foo.txt': file]
def sourceDir = FileHelper.asPath('s3://bucket/work/1/')
def file = sourceDir.resolve('bar/foo.txt')
def taskInputs = ['bar/foo.txt': file]
and:
def targetDir = FileHelper.asPath('s3://bucket/results')
def target = targetDir.resolve('foo.txt')
def publisher = Spy(new PublishDir(path: targetDir)) { getTaskInputs()>>taskInputs }
def target = targetDir.resolve('bar/foo.txt')
def publisher = Spy(new PublishDir(sourceDir: sourceDir, path: targetDir)) { getTaskInputs()>>taskInputs }

when:
publisher.processFile(file, target)
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