Get exit code from google API

Signed-off-by: jorgee <jorge.ejarque@seqera.io>

Author: jorgee

plugins/nf-google/src/main/nextflow/cloud/google/batch/GoogleBatchTaskHandler.groovy

@@ -545,7 +545,7 @@ class GoogleBatchTaskHandler extends TaskHandler implements FusionAwareTask {
         if( state in COMPLETED ) {
             log.debug "[GOOGLE BATCH] Process `${task.lazyName()}` - terminated job=$jobId; task=$taskId; state=$state"
             // finalize the task
-            task.exitStatus = readExitFile()
+            task.exitStatus = getExitCode()
             if( state == 'FAILED' ) {
                 if( task.exitStatus == Integer.MAX_VALUE )
                     task.error = getJobError()
@@ -565,6 +565,29 @@ class GoogleBatchTaskHandler extends TaskHandler implements FusionAwareTask {
         return false
     }
 
+    /**
+     * Try to get the latest exit code form the task status events list.
+     * Fallback to read .exitcode file generated by Nextflow if not found (null).
+     * The rationale of this is that, in case of error, the exit code return by the batch API is more reliable.
+     *
+     * @return exit code if found, otherwise Integer.MAX_VALUE
+     */
+    private Integer getExitCode(){
+        final events = client.getTaskStatus(jobId, taskId)?.getStatusEventsList()
+        if( events ) {
+            log.debug("[GOOGLE BATCH] Getting exit code from events: $events")
+            final batchExitCode = events.stream().filter(ev -> ev.hasTaskExecution())
+                .max( (ev1, ev2) -> Long.compare(ev1.getEventTime().seconds, ev2.getEventTime().seconds) )
+                .map(ev -> ev.getTaskExecution().getExitCode())
+                .orElse(null)
+            if( batchExitCode != null && batchExitCode < 50000) // Ignore 500XX codes, they will be managed later.
+                return batchExitCode
+        }
+        // fallback to read
+        log.debug("[GOOGLE BATCH] Exit code not found from API. Checking .exitcode file...")
+        return readExitFile()
+    }
+
     protected Throwable getJobError() {
         try {
             final events = noTaskJobfailure
@@ -574,7 +597,7 @@ class GoogleBatchTaskHandler extends TaskHandler implements FusionAwareTask {
             log.debug "[GOOGLE BATCH] Process `${task.lazyName()}` - last event: ${lastEvent}; exit code: ${lastEvent?.taskExecution?.exitCode}"
 
             final error = lastEvent?.description
-            if( error && (EXIT_CODE_REGEX.matcher(error).find() || BATCH_ERROR_REGEX.matcher(error).find()) ) {
+            if( error && (EXIT_CODE_REGEX.matcher(error).find() || BATCH_ERROR_REGEX.matcher(error).find()) || lastEvent?.taskExecution?.exitCode > 50000) {
                 return new ProcessException(error)
             }
         }

plugins/nf-google/src/test/nextflow/cloud/google/batch/GoogleBatchTaskHandlerTest.groovy

@@ -21,7 +21,10 @@ import com.google.api.gax.grpc.GrpcStatusCode
 import com.google.api.gax.rpc.NotFoundException
 import com.google.cloud.batch.v1.JobStatus
 import com.google.cloud.batch.v1.Task
+import com.google.cloud.batch.v1.TaskExecution
 import io.grpc.Status
+import nextflow.cloud.google.batch.logging.BatchLogging
+import nextflow.exception.ProcessException
 
 import java.nio.file.Path
 
@@ -473,15 +476,18 @@ class GoogleBatchTaskHandlerTest extends Specification {
 
     }
 
-    TaskStatus makeTaskStatus(TaskStatus.State state, String desc) {
+    TaskStatus makeTaskStatus(TaskStatus.State state, String desc, Integer exitCode = null) {
         def builder = TaskStatus.newBuilder()
         if (state)
             builder.setState(state)
-        if (desc)
-            builder.addStatusEvents(
-                StatusEvent.newBuilder()
-                    .setDescription(desc)
-            )
+        if (desc || exitCode != null) {
+            def statusBuilder = StatusEvent.newBuilder()
+            if (desc)
+                statusBuilder.setDescription(desc)
+            if (exitCode != null)
+                statusBuilder.setTaskExecution(TaskExecution.newBuilder().setExitCode(exitCode).build())
+            builder.addStatusEvents(statusBuilder.build())
+        }
         builder.build()
     }
 
@@ -665,4 +671,74 @@ class GoogleBatchTaskHandlerTest extends Specification {
             .build()
 
     }
+
+     def 'should check if completed from task status' () {
+         given:
+         def jobId = '1'
+         def taskId = '1'
+         def client = Mock(BatchClient){
+             getTaskInArrayStatus(jobId, taskId) >> makeTaskStatus(STATE,"", EXIT_CODE)
+             getTaskStatus(jobId, taskId) >> makeTaskStatus(STATE,"", EXIT_CODE)
+             getJobStatus(jobId) >> makeJobStatus(JOB_STATUS,"")
+         }
+         def logging = Mock(BatchLogging)
+         def executor = Mock(GoogleBatchExecutor){
+             getLogging() >> logging
+         }
+         def task = new TaskRun()
+         task.name = 'hello'
+         def handler = Spy(new GoogleBatchTaskHandler(jobId: jobId, taskId: taskId, client: client, task: task, isArrayChild: ARRAY_CHILD, status: nextflow.processor.TaskStatus.RUNNING, executor: executor))
+         when:
+         def result = handler.checkIfCompleted()
+         then:
+         handler.status == TASK_STATUS
+         handler.task.exitStatus == EXIT_STATUS
+         result == RESULT
+
+         where:
+         JOB_STATUS                 | STATE                          | EXIT_CODE | ARRAY_CHILD | TASK_STATUS                               | EXIT_STATUS       | RESULT
+         JobStatus.State.SUCCEEDED  | TaskStatus.State.SUCCEEDED     | 0         | true        | nextflow.processor.TaskStatus.COMPLETED   | 0                 | true
+         JobStatus.State.FAILED     | TaskStatus.State.FAILED        | 1         | true        | nextflow.processor.TaskStatus.COMPLETED   | 1                 | true
+         JobStatus.State.RUNNING    | TaskStatus.State.RUNNING       | null      | true        | nextflow.processor.TaskStatus.RUNNING     | Integer.MAX_VALUE | false
+         JobStatus.State.SUCCEEDED  | TaskStatus.State.SUCCEEDED     | 0         | false       | nextflow.processor.TaskStatus.COMPLETED   | 0                 | true
+         JobStatus.State.FAILED     | TaskStatus.State.FAILED        | 1         | false       | nextflow.processor.TaskStatus.COMPLETED   | 1                 | true
+         JobStatus.State.RUNNING    | TaskStatus.State.RUNNING       | null      | false       | nextflow.processor.TaskStatus.RUNNING     | Integer.MAX_VALUE | false
+
+     }
+
+    def 'should check if completed from read file' () {
+        given:
+        def jobId = '1'
+        def taskId = '1'
+        def client = Mock(BatchClient){
+            getTaskInArrayStatus(jobId, taskId) >> { TASK_STATE ? makeTaskStatus(TASK_STATE, DESC, EXIT_CODE): null }
+            getTaskStatus(jobId, taskId) >> { TASK_STATE ? makeTaskStatus(TASK_STATE, DESC, EXIT_CODE): null }
+            getJobStatus(jobId ) >> makeJobStatus(JobStatus.State.FAILED,DESC)
+        }
+        def logging = Mock(BatchLogging)
+        def executor = Mock(GoogleBatchExecutor){
+            getLogging() >> logging
+        }
+        def task = new TaskRun()
+        task.name = 'hello'
+        def handler = Spy(new GoogleBatchTaskHandler(jobId: jobId, taskId: taskId, client: client, task: task, isArrayChild: ARRAY_CHILD, status: nextflow.processor.TaskStatus.RUNNING, executor: executor))
+        when:
+        def result = handler.checkIfCompleted()
+        then:
+        1 * handler.readExitFile() >> EXIT_STATUS
+        handler.status == TASK_STATUS
+        handler.task.exitStatus == EXIT_STATUS
+        handler.task.error?.message == TASK_ERROR
+        result == RESULT
+
+        where:
+        TASK_STATE              | DESC                                                          | EXIT_CODE | ARRAY_CHILD    | TASK_STATUS                               | EXIT_STATUS       | RESULT    | TASK_ERROR
+        TaskStatus.State.FAILED | "Error"                                                       | null      | true           | nextflow.processor.TaskStatus.COMPLETED   | 0                 | true      | null
+        null                    | "Error"                                                       | null      | true           | nextflow.processor.TaskStatus.COMPLETED   | 1                 | true      | null
+        TaskStatus.State.FAILED | 'Task failed due to Spot VM preemption with exit code 50001.' | 50001     | true           | nextflow.processor.TaskStatus.COMPLETED   | Integer.MAX_VALUE | true      | 'Task failed due to Spot VM preemption with exit code 50001.'
+        TaskStatus.State.FAILED | "Error"                                                       | null      | false          | nextflow.processor.TaskStatus.COMPLETED   | 0                 | true      | null
+        null                    | "Error"                                                       | null      | false          | nextflow.processor.TaskStatus.COMPLETED   | 1                 | true      | null
+        TaskStatus.State.FAILED | 'Task failed due to Spot VM preemption with exit code 50001.' | 50001     | false          | nextflow.processor.TaskStatus.COMPLETED   | Integer.MAX_VALUE | true      | 'Task failed due to Spot VM preemption with exit code 50001.'
+    }
+
 }