Use ECS properties instead of container properties

.github/workflows/build.yml

@@ -43,13 +43,13 @@ jobs:
                 COMMIT_MESSAGE="$(curl -s \
                   -H "Authorization: token ${{ secrets.GITHUB_TOKEN }}" \
                   https://api.github.com/repos/${{ github.repository }}/commits/$COMMIT_SHA | jq -r '.commit.message')"
-                echo "Commit message=$(printf "%q" "$COMMIT_MESSAGE")" | head -n 1
-                echo "commit_message=$(printf "%q" "$COMMIT_MESSAGE")" | head -n 1 >> $GITHUB_OUTPUT
+                echo "Commit message=$(printf "%s" "$COMMIT_MESSAGE")" | head -n 1
+                echo "commit_message=$(printf "%s" "$COMMIT_MESSAGE")" | head -n 1 >> $GITHUB_OUTPUT
             else
                 echo "GitHub event=${{ github.event_name }}"
                 COMMIT_MESSAGE="${{ github.event.head_commit.message }}"
-                echo "Commit message=$(printf "%q" "$COMMIT_MESSAGE")" | head -n 1
-                echo "commit_message=$(printf "%q" "$COMMIT_MESSAGE")" | head -n 1 >> $GITHUB_OUTPUT
+                echo "Commit message=$(printf "%s" "$COMMIT_MESSAGE")" | head -n 1
+                echo "commit_message=$(printf "%s" "$COMMIT_MESSAGE")" | head -n 1 >> $GITHUB_OUTPUT
             fi
 
       - name: Setup env

plugins/nf-amazon/src/main/nextflow/cloud/aws/batch/AwsBatchHelper.groovy

@@ -20,6 +20,9 @@ import software.amazon.awssdk.services.batch.BatchClient
 import software.amazon.awssdk.services.batch.model.DescribeComputeEnvironmentsRequest
 import software.amazon.awssdk.services.batch.model.DescribeJobQueuesRequest
 import software.amazon.awssdk.services.batch.model.DescribeJobsRequest
+import software.amazon.awssdk.services.batch.model.EcsTaskDetails
+import software.amazon.awssdk.services.batch.model.JobDetail
+import software.amazon.awssdk.services.batch.model.TaskContainerDetails
 import software.amazon.awssdk.services.ec2.Ec2Client
 import software.amazon.awssdk.services.ec2.model.DescribeInstancesRequest
 import software.amazon.awssdk.services.ec2.model.Instance
@@ -193,14 +196,55 @@ class AwsBatchHelper {
         final response = batchClient.describeJobs(request)
         if( response.jobs() ) {
             final detail = response.jobs()[0]
-            return detail.container().logStreamName()
+            return getTaskContainer(detail)?.logStreamName()
+                ?: detail.container()?.logStreamName()
         }
         else {
             log.debug "Unable to find info for batch job id=$jobId"
             return null
         }
     }
 
+    /**
+     * Retrieve the first EcsTaskDetails from the given JobDetail.
+     *
+     * In combination with {@code getTaskContainer(job)} this is analogous to {@code job.getContainer()}, but
+     * using the multi-container ECSProperties model.
+     *
+     * @param job
+     * @return
+     *      The first EcsTaskDetails of the first TaskProperties, or {@code null}
+     */
+    static EcsTaskDetails getTaskProperties(JobDetail job) {
+        try {
+            return job.ecsProperties().taskProperties().first()
+        } catch (Exception e) {
+            def jobId = job?.jobId() ?: '(unknown)'
+            log.debug "Unable to get container properties for batch job id=$jobId: ${e.getMessage()}"
+            return null
+        }
+    }
+
+    /**
+     * Retrieve the first TaskContainerDetails from the given JobDetail.
+     *
+     * In combination with {@code getTaskProperties(job)} this is analogous to {@code job.getContainer()}, but
+     * using the multi-container ECSProperties model.
+     *
+     * @param job
+     * @return
+     *      The first TaskContainerDetails of the first TaskProperties, or {@code null}
+     */
+    static TaskContainerDetails getTaskContainer(JobDetail job) {
+        try {
+            return getTaskProperties(job).containers().first()
+        } catch (Exception e) {
+            def jobId = job?.jobId() ?: '(unknown)'
+            log.debug "Unable to get container details for batch job id=$jobId: ${e.getMessage()}"
+            return null
+        }
+    }
+
     /**
      * Retrieve the cloudwatch logs for the specified AWS Batch Job ID
      *

plugins/nf-amazon/src/main/nextflow/cloud/aws/batch/AwsBatchTaskHandler.groovy

@@ -16,7 +16,7 @@
 
 package nextflow.cloud.aws.batch
 
-
+import static nextflow.cloud.aws.batch.AwsBatchHelper.*
 import static nextflow.cloud.aws.batch.AwsContainerOptionsMapper.*
 
 import java.nio.file.Path
@@ -51,13 +51,13 @@ import nextflow.util.TestOnly
 import software.amazon.awssdk.services.batch.BatchClient
 import software.amazon.awssdk.services.batch.model.ArrayProperties
 import software.amazon.awssdk.services.batch.model.AssignPublicIp
-import software.amazon.awssdk.services.batch.model.AttemptContainerDetail
+import software.amazon.awssdk.services.batch.model.AttemptDetail
 import software.amazon.awssdk.services.batch.model.BatchException
 import software.amazon.awssdk.services.batch.model.ClientException
-import software.amazon.awssdk.services.batch.model.ContainerOverrides
 import software.amazon.awssdk.services.batch.model.DescribeJobDefinitionsRequest
 import software.amazon.awssdk.services.batch.model.DescribeJobDefinitionsResponse
 import software.amazon.awssdk.services.batch.model.DescribeJobsRequest
+import software.amazon.awssdk.services.batch.model.EcsPropertiesOverride
 import software.amazon.awssdk.services.batch.model.EphemeralStorage
 import software.amazon.awssdk.services.batch.model.EvaluateOnExit
 import software.amazon.awssdk.services.batch.model.Host
@@ -79,6 +79,8 @@ import software.amazon.awssdk.services.batch.model.RetryStrategy
 import software.amazon.awssdk.services.batch.model.RuntimePlatform
 import software.amazon.awssdk.services.batch.model.SubmitJobRequest
 import software.amazon.awssdk.services.batch.model.SubmitJobResponse
+import software.amazon.awssdk.services.batch.model.TaskContainerOverrides
+import software.amazon.awssdk.services.batch.model.TaskPropertiesOverride
 import software.amazon.awssdk.services.batch.model.TerminateJobRequest
 import software.amazon.awssdk.services.batch.model.Volume
 /**
@@ -246,7 +248,8 @@ class AwsBatchTaskHandler extends TaskHandler implements BatchHandler<String,Job
             checkIfUnschedulable(job)
         // fetch the task arn
         if( !taskArn )
-            taskArn = job?.container()?.taskArn()
+            taskArn = getTaskProperties(job)?.taskRoleArn()
+                ?: job?.container()?.taskArn()
         return result
     }
 
@@ -282,12 +285,20 @@ class AwsBatchTaskHandler extends TaskHandler implements BatchHandler<String,Job
         final result = new ArrayList(2)
         if( job.statusReason() )
             result.add(job.statusReason())
-        final AttemptContainerDetail container = job.attempts() ? job.attempts()[-1].container() : null
-        if( container?.reason() )
-            result.add(container.reason())
+        final attemptDetail = job.attempts() ? job.attempts()[-1] : null
+        final reason = errReasonFromAttempt (attemptDetail)
+        if( reason )
+            result.add(reason)
         return result.join(' - ')
     }
 
+    private String errReasonFromAttempt(AttemptDetail attempt){
+        if( !attempt )
+            return null
+        return attempt.taskProperties()?.first()?.containers()?.first()?.reason()
+            ?: attempt.container()?.reason()
+    }
+
     /**
      * {@inheritDoc}
      */
@@ -307,7 +318,9 @@ class AwsBatchTaskHandler extends TaskHandler implements BatchHandler<String,Job
             // take the exit code from the `.exitcode` file create by nextflow
             // the rationale of this is that, in case of error, the exit code return
             // by the batch API is more reliable.
-            task.exitStatus = job.container().exitCode() ?: readExitFile()
+            task.exitStatus = getTaskContainer(job)?.exitCode()
+                ?: job.container()?.exitCode()
+                ?: readExitFile()
             // finalize the task
             task.stdout = outputFile
             if( job?.status() == JobStatus.FAILED || task.exitStatus==Integer.MAX_VALUE ) {
@@ -818,7 +831,7 @@ class AwsBatchTaskHandler extends TaskHandler implements BatchHandler<String,Job
 
         // set the actual command
         final resources = new ArrayList<ResourceRequirement>(5)
-        final container = ContainerOverrides.builder()
+        final container = TaskContainerOverrides.builder()
         container.command(getSubmitCommand())
         // set the task memory
         final cpus = task.config.getCpus()
@@ -849,7 +862,13 @@ class AwsBatchTaskHandler extends TaskHandler implements BatchHandler<String,Job
         if( vars )
             container.environment(vars)
 
-        builder.containerOverrides(container.build())
+        builder.ecsPropertiesOverride(EcsPropertiesOverride.builder()
+            .taskProperties(TaskPropertiesOverride.builder()
+                .containers(container.build())
+                .build()
+            )
+            .build()
+        )
 
         // set the array properties
         if( task instanceof TaskArrayRun ) {

plugins/nf-amazon/src/main/nextflow/cloud/aws/batch/model/ContainerPropertiesModel.groovy

@@ -17,7 +17,7 @@
 package nextflow.cloud.aws.batch.model
 
 import groovy.transform.CompileStatic
-import software.amazon.awssdk.services.batch.model.ContainerProperties
+import software.amazon.awssdk.services.batch.model.EcsTaskProperties
 import software.amazon.awssdk.services.batch.model.EphemeralStorage
 import software.amazon.awssdk.services.batch.model.KeyValuePair
 import software.amazon.awssdk.services.batch.model.LinuxParameters
@@ -27,13 +27,14 @@ import software.amazon.awssdk.services.batch.model.NetworkConfiguration
 import software.amazon.awssdk.services.batch.model.ResourceRequirement
 import software.amazon.awssdk.services.batch.model.RuntimePlatform
 import software.amazon.awssdk.services.batch.model.Secret
+import software.amazon.awssdk.services.batch.model.TaskContainerProperties
 import software.amazon.awssdk.services.batch.model.Ulimit
 import software.amazon.awssdk.services.batch.model.Volume
 
 /**
  * Models the container properties used to configure an AWS Batch job.
  *
- * This is a mutable version of {@link ContainerProperties} required
+ * This is a mutable version of {@link TaskContainerProperties} required
  * to simplify the extension of container settings in the AWS Batch executor
  * and its sub-classes (e.g. nf-xpack).
  *
@@ -236,14 +237,11 @@ class ContainerPropertiesModel {
         return runtimePlatform
     }
 
-    ContainerProperties toBatchContainerProperties() {
-        def builder = ContainerProperties.builder()
-
+    EcsTaskProperties toBatchContainerProperties() {
+        def builder = TaskContainerProperties.builder();
         if (image) builder.image(image)
         if (command) builder.command(command)
         if (resourceRequirements) builder.resourceRequirements(resourceRequirements)
-        if (jobRoleArn) builder.jobRoleArn(jobRoleArn)
-        if (executionRoleArn) builder.executionRoleArn(executionRoleArn)
         if (linuxParameters) builder.linuxParameters(linuxParameters)
         if (environment) builder.environment(environment)
         if (privileged) builder.privileged(privileged)
@@ -252,12 +250,16 @@ class ContainerPropertiesModel {
         if (ulimits) builder.ulimits(ulimits)
         if (logConfiguration) builder.logConfiguration(logConfiguration)
         if (mountPoints) builder.mountPoints(mountPoints)
-        if (volumes) builder.volumes(volumes)
-        if (networkConfiguration) builder.networkConfiguration(networkConfiguration)
-        if (ephemeralStorage) builder.ephemeralStorage(ephemeralStorage)
-        if (runtimePlatform) builder.runtimePlatform(runtimePlatform)
+        def ecsTaskBuilder = EcsTaskProperties.builder()
+        ecsTaskBuilder.containers(builder.build())
+        if (jobRoleArn) ecsTaskBuilder.taskRoleArn(jobRoleArn)
+        if (executionRoleArn) ecsTaskBuilder.executionRoleArn(executionRoleArn)
+        if (volumes) ecsTaskBuilder.volumes(volumes)
+        if (networkConfiguration) ecsTaskBuilder.networkConfiguration(networkConfiguration)
+        if (ephemeralStorage) ecsTaskBuilder.ephemeralStorage(ephemeralStorage)
+        if (runtimePlatform) ecsTaskBuilder.runtimePlatform(runtimePlatform)
 
-        return builder.build()
+        return ecsTaskBuilder.build()
     }
 
     @Override
@@ -280,6 +282,7 @@ class ContainerPropertiesModel {
             ", networkConfiguration=" + networkConfiguration +
             ", ephemeralStorage=" + ephemeralStorage +
             ", runtimePlatform=" + runtimePlatform +
+            ", ecsMode=true" + //Added to generate a different token if the job definition was generated with older containerProperties
             '}';
     }
 }

plugins/nf-amazon/src/main/nextflow/cloud/aws/batch/model/RegisterJobDefinitionModel.groovy

@@ -18,6 +18,7 @@ package nextflow.cloud.aws.batch.model
 
 
 import groovy.transform.CompileStatic
+import software.amazon.awssdk.services.batch.model.EcsProperties
 import software.amazon.awssdk.services.batch.model.JobDefinitionType
 import software.amazon.awssdk.services.batch.model.PlatformCapability
 import software.amazon.awssdk.services.batch.model.RegisterJobDefinitionRequest
@@ -116,7 +117,10 @@ class RegisterJobDefinitionModel {
         if (platformCapabilities)
             builder.platformCapabilities(platformCapabilities)
         if (containerProperties)
-            builder.containerProperties(containerProperties.toBatchContainerProperties())
+            builder.ecsProperties(EcsProperties.builder()
+                .taskProperties(containerProperties.toBatchContainerProperties())
+                .build()
+            )
         if (parameters)
             builder.parameters(parameters)
         if (tags)