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Add deleteTasksOnCompletion to Azure Batch configuration #4114

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merged 11 commits into from
Jul 25, 2023
Merged

Add deleteTasksOnCompletion to Azure Batch configuration #4114

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778d0f0
Add deleteTasksOnCompletion to Azure Configuration
adamrtalbot Jul 19, 2023
32abc3c
Revert commited Const.groovy file
adamrtalbot Jul 20, 2023
51bf0d9
minor edits
bentsherman Jul 21, 2023
caa2366
Cleanup docs and comments
bentsherman Jul 21, 2023
64307dc
Change default Azure deleteJobsOnCompletion to false
adamrtalbot Jul 21, 2023
a86498a
Be more specific with azure.batch.terminateJobsOnCompletion docs
adamrtalbot Jul 21, 2023
48c59ff
Azure config tests corrected
adamrtalbot Jul 21, 2023
46a4301
Update docs/config.md
adamrtalbot Jul 21, 2023
1e0fa0b
Update docs/config.md
adamrtalbot Jul 21, 2023
c6c9527
Update tests and docs
bentsherman Jul 24, 2023
e363418
Update docs for deleteTasksOnCompletion
bentsherman Jul 24, 2023
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3 changes: 3 additions & 0 deletions docs/config.md
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Expand Up @@ -333,6 +333,9 @@ The following settings are available:
`azure.batch.terminateJobsOnCompletion`
: Enables the Batch Job to automatically terminate a job once all tasks have completed (default: `true`).

`azure.batch.deleteTasksOnCompletion`
: Delete tasks after successful completion. This deletes them on the Azure Batch service but files and resources may persist on the compute nodes (default: `true`).

`azure.batch.deleteJobsOnCompletion`
: Enable the automatic deletion of jobs created by the pipeline execution (default: `true`).

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4 changes: 2 additions & 2 deletions modules/nf-commons/src/main/nextflow/Const.groovy
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Original file line number Diff line number Diff line change
Expand Up @@ -57,12 +57,12 @@ class Const {
/**
* The app build time as linux/unix timestamp
*/
static public final long APP_TIMESTAMP = 1686776566745
static public final long APP_TIMESTAMP = 1689766233402

/**
* The app build number
*/
static public final int APP_BUILDNUM = 5864
static public final int APP_BUILDNUM = 5867

/**
* The app build time string relative to UTC timezone
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4 changes: 2 additions & 2 deletions plugins/nf-azure/src/main/nextflow/cloud/azure/batch/AzBatchTaskHandler.groovy
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Expand Up @@ -130,15 +130,15 @@ class AzBatchTaskHandler extends TaskHandler implements FusionAwareTask {
}

private Boolean shouldDelete() {
executor.config.batch().deleteJobsOnCompletion
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executor.config.batch().deleteTasksOnCompletion
}

protected void deleteTask(AzTaskKey taskKey, TaskRun task) {
if( !taskKey || shouldDelete()==Boolean.FALSE )
return

if( !task.isSuccess() && shouldDelete()==null ) {
// do not delete successfully executed pods for debugging purpose
// do not delete successfully executed tasks for debugging purpose
return
}

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2 changes: 2 additions & 0 deletions plugins/nf-azure/src/main/nextflow/cloud/azure/config/AzBatchOpts.groovy
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Expand Up @@ -48,6 +48,7 @@ class AzBatchOpts implements CloudTransferOptions {
Boolean autoPoolMode
Boolean allowPoolCreation
Boolean terminateJobsOnCompletion
Boolean deleteTasksOnCompletion
Boolean deleteJobsOnCompletion
Boolean deletePoolsOnCompletion
CopyToolInstallMode copyToolInstallMode
Expand All @@ -64,6 +65,7 @@ class AzBatchOpts implements CloudTransferOptions {
autoPoolMode = config.autoPoolMode
allowPoolCreation = config.allowPoolCreation
terminateJobsOnCompletion = config.terminateJobsOnCompletion
deleteTasksOnCompletion = config.deleteTasksOnCompletion
deleteJobsOnCompletion = config.deleteJobsOnCompletion
deletePoolsOnCompletion = config.deletePoolsOnCompletion
pools = parsePools(config.pools instanceof Map ? config.pools as Map<String,Map> : Collections.<String,Map>emptyMap())
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1 change: 0 additions & 1 deletion plugins/nf-azure/src/test/nextflow/cloud/azure/batch/AzBatchServiceTest.groovy
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Expand Up @@ -350,7 +350,6 @@ class AzBatchServiceTest extends Specification {

}


def 'should cleanup jobs by default' () {
given:
def CONFIG = [:]
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7 changes: 6 additions & 1 deletion plugins/nf-azure/src/test/nextflow/cloud/azure/config/AzureConfigTest.groovy
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Expand Up @@ -99,7 +99,10 @@ class AzureConfigTest extends Specification {
endpoint: ENDPOINT,
location: LOCATION,
autoPoolMode: true,
allowPoolCreation: true, deleteJobsOnCompletion: false,
allowPoolCreation: true,
terminateJobsOnCompletion: false,
deleteTasksOnCompletion: false,
deleteJobsOnCompletion: false,
deletePoolsOnCompletion: true,
pools: [ myPool: [
vmType: 'Foo_A1',
Expand All @@ -124,6 +127,8 @@ class AzureConfigTest extends Specification {
cfg.batch().location == LOCATION
cfg.batch().autoPoolMode == true
cfg.batch().allowPoolCreation == true
cfg.batch().terminateJobsOnCompletion == false
cfg.batch().deleteTasksOnCompletion == false
cfg.batch().deleteJobsOnCompletion == false
cfg.batch().deletePoolsOnCompletion == true
cfg.batch().canCreatePool()
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