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Add nextflow tags to AWS Batch job def
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Signed-off-by: Paolo Di Tommaso <[email protected]>
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pditommaso committed Feb 6, 2023
1 parent 954cd92 commit b465ac5
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Showing 2 changed files with 14 additions and 2 deletions.
Original file line number Diff line number Diff line change
Expand Up @@ -21,6 +21,7 @@ import static nextflow.cloud.aws.batch.AwsContainerOptionsMapper.*

import java.nio.file.Path
import java.nio.file.Paths
import java.time.Instant

import com.amazonaws.services.batch.AWSBatch
import com.amazonaws.services.batch.model.AWSBatchException
Expand Down Expand Up @@ -53,13 +54,14 @@ import com.amazonaws.services.batch.model.Volume
import groovy.transform.CompileStatic
import groovy.transform.Memoized
import groovy.util.logging.Slf4j
import nextflow.Const
import nextflow.cloud.types.CloudMachineInfo
import nextflow.container.ContainerNameValidator
import nextflow.exception.ProcessSubmitException
import nextflow.exception.ProcessUnrecoverableException
import nextflow.executor.BashWrapperBuilder
import nextflow.fusion.FusionAwareTask
import nextflow.executor.res.AcceleratorResource
import nextflow.fusion.FusionAwareTask
import nextflow.processor.BatchContext
import nextflow.processor.BatchHandler
import nextflow.processor.TaskHandler
Expand Down Expand Up @@ -593,6 +595,10 @@ class AwsBatchTaskHandler extends TaskHandler implements BatchHandler<String,Job
* @return The fully qualified Batch job definition name eg {@code my-job-definition:3}
*/
protected String createJobDef(RegisterJobDefinitionRequest req) {
// add nextflow tags
req.addTagsEntry('nextflow.io/createdAt', Instant.now().toString())
req.addTagsEntry('nextflow.io/version', Const.APP_VER)
// create the job def
final res = createJobDef0(bypassProxy(client), req) // bypass the client proxy! see #1024
return "${res.jobDefinitionName}:$res.revision"
}
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Expand Up @@ -18,6 +18,7 @@
package nextflow.cloud.aws.batch

import java.nio.file.Paths
import java.time.Instant

import com.amazonaws.services.batch.AWSBatch
import com.amazonaws.services.batch.model.ContainerProperties
Expand All @@ -35,6 +36,7 @@ import com.amazonaws.services.batch.model.RetryStrategy
import com.amazonaws.services.batch.model.SubmitJobRequest
import com.amazonaws.services.batch.model.SubmitJobResult
import com.amazonaws.services.batch.model.TerminateJobRequest
import nextflow.Const
import nextflow.cloud.aws.util.S3PathFactory
import nextflow.cloud.types.CloudMachineInfo
import nextflow.cloud.types.PriceModel
Expand Down Expand Up @@ -484,7 +486,7 @@ class AwsBatchTaskHandlerTest extends Specification {
def handler = Spy(AwsBatchTaskHandler)
handler.@client = client

def req = Mock(RegisterJobDefinitionRequest)
def req = new RegisterJobDefinitionRequest()
def res = Mock(RegisterJobDefinitionResult)

when:
Expand All @@ -493,7 +495,11 @@ class AwsBatchTaskHandlerTest extends Specification {
1 * client.registerJobDefinition(req) >> res
1 * res.getJobDefinitionName() >> JOB_NAME
1 * res.getRevision() >> 10
and:
result == "$JOB_NAME:10"
and:
req.getTags().get('nextflow.io/version') == Const.APP_VER
Instant.parse(req.getTags().get('nextflow.io/createdAt'))

}

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