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Move foreign file staging after storeDir evaluation #5759

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Move foreign file staging after storeDir evaluation #5759

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a1ab74a
Move forign file staging after storeDir evaluation
jorgee Feb 6, 2025
5c2dbbe
rename batch by foreignFiles
jorgee Feb 24, 2025
65aa966
Merge branch 'master' into 5468-storedir-does-not-skip-staging-of-inputs
jorgee Feb 24, 2025
2b8f4c1
Merge with master@00a53b97 [ci fast]
pditommaso Mar 15, 2025
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19 changes: 10 additions & 9 deletions modules/nextflow/src/main/groovy/nextflow/processor/TaskProcessor.groovy
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Original file line number Diff line number Diff line change
Expand Up @@ -639,7 +639,7 @@ class TaskProcessor {
// -- map the inputs to a map and use to delegate closure values interpolation
final secondPass = [:]
int count = makeTaskContextStage1(task, secondPass, values)
makeTaskContextStage2(task, secondPass, count)
final foreignFiles = makeTaskContextStage2(task, secondPass, count)

// verify that `when` guard, when specified, is satisfied
if( !checkWhenGuard(task) )
Expand All @@ -653,6 +653,9 @@ class TaskProcessor {
if( checkStoredOutput(task) )
return

// -- download foreign files
session.filePorter.transfer(foreignFiles)

def hash = createTaskHashKey(task)
checkCachedOrLaunchTask(task, hash, resumable)
}
Expand Down Expand Up @@ -1928,7 +1931,7 @@ class TaskProcessor {
throw new ProcessUnrecoverableException("Not a valid path value: '$str'")
}

protected List<FileHolder> normalizeInputToFiles( Object obj, int count, boolean coerceToPath, FilePorter.Batch batch ) {
protected List<FileHolder> normalizeInputToFiles( Object obj, int count, boolean coerceToPath, FilePorter.Batch foreignFiles ) {

Collection allItems = obj instanceof Collection ? obj : [obj]
def len = allItems.size()
Expand All @@ -1939,7 +1942,7 @@ class TaskProcessor {

if( item instanceof Path || coerceToPath ) {
def path = normalizeToPath(item)
def target = executor.isForeignFile(path) ? batch.addToForeign(path) : path
def target = executor.isForeignFile(path) ? foreignFiles.addToForeign(path) : path
def holder = new FileHolder(target)
files << holder
}
Expand Down Expand Up @@ -2139,20 +2142,20 @@ class TaskProcessor {
return count
}

final protected void makeTaskContextStage2( TaskRun task, Map secondPass, int count ) {
final protected FilePorter.Batch makeTaskContextStage2( TaskRun task, Map secondPass, int count ) {

final ctx = task.context
final allNames = new HashMap<String,Integer>()

final FilePorter.Batch batch = session.filePorter.newBatch(executor.getStageDir())
final FilePorter.Batch foreignFiles = session.filePorter.newBatch(executor.getStageDir())

// -- all file parameters are processed in a second pass
// so that we can use resolve the variables that eventually are in the file name
for( Map.Entry<FileInParam,?> entry : secondPass.entrySet() ) {
final param = entry.getKey()
final val = entry.getValue()
final fileParam = param as FileInParam
final normalized = normalizeInputToFiles(val, count, fileParam.isPathQualifier(), batch)
final normalized = normalizeInputToFiles(val, count, fileParam.isPathQualifier(), foreignFiles)
final resolved = expandWildcards( fileParam.getFilePattern(ctx), normalized )

if( !param.isValidArity(resolved.size()) )
Expand Down Expand Up @@ -2180,9 +2183,7 @@ class TaskProcessor {
def message = "Process `$name` input file name collision -- There are multiple input files for each of the following file names: ${conflicts.keySet().join(', ')}"
throw new ProcessUnrecoverableException(message)
}

// -- download foreign files
session.filePorter.transfer(batch)
return foreignFiles
}

protected void makeTaskContextStage3( TaskRun task, HashCode hash, Path folder ) {
Expand Down