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Refresh the workDir if not empty. #58

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merged 1 commit into from
Aug 21, 2023
Merged

Refresh the workDir if not empty. #58

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6 changes: 5 additions & 1 deletion plugins/nf-float/src/main/com/memverge/nextflow/FloatGridExecutor.groovy
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Original file line number Diff line number Diff line change
Expand Up @@ -509,7 +509,11 @@ class FloatGridExecutor extends AbstractGridExecutor {
log.debug "[float] task id: $taskId, nf-job-id: $job.nfJobID, " +
"float-job-id: $job.floatJobID, " +
"float status: $job.status, nf status: $st"
return st == QueueStatus.DONE || st == QueueStatus.ERROR
boolean finished = st == QueueStatus.DONE || st == QueueStatus.ERROR
if (finished) {
floatJobs.refreshWorkDir(job.nfJobID)
}
return finished
}

static private Map<String, QueueStatus> STATUS_MAP = [
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11 changes: 9 additions & 2 deletions plugins/nf-float/src/main/com/memverge/nextflow/FloatJobs.groovy
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Original file line number Diff line number Diff line change
Expand Up @@ -84,6 +84,14 @@ class FloatJobs {
return job.status
}

def refreshWorkDir(String nfJobID) {
def workDir = nfJobID2workDir.get(nfJobID)
if (workDir) {
// call list files to update the folder cache
FileHelper.listDirectory(workDir)
}
}

@WithWriteLock
def updateOcStatus(String oc, String text) {
def stMap = FloatJob.parseJobMap(text)
Expand All @@ -96,8 +104,7 @@ class FloatJobs {
def workDir = nfJobID2workDir.get(job.nfJobID)
if (workDir) {
// check the availability of result files
// call list files to update the folder cache
FileHelper.listDirectory(workDir)
refreshWorkDir(job.nfJobID)
def files = ['.command.out', '.command.err', '.exitcode']
if (currentSt != Completed && job.status == Completed) {
for (filename in files) {
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