Set local task exit status when time limit is exceeded

Signed-off-by: Ben Sherman <[email protected]>

Author: bentsherman

modules/nextflow/src/main/groovy/nextflow/executor/local/LocalTaskHandler.groovy

@@ -218,6 +218,7 @@ class LocalTaskHandler extends TaskHandler implements FusionAwareTask {
              */
             if( elapsedTimeMillis() > wallTimeMillis ) {
                 destroy()
+                task.exitStatus = process.exitValue()
                 task.stdout = outputFile
                 task.stderr = errorFile
                 task.error = new ProcessException("Process exceeded running time limit (${task.config.getTime()})")

modules/nextflow/src/test/groovy/nextflow/executor/local/LocalTaskHandlerTest.groovy

@@ -21,10 +21,13 @@ import java.nio.file.Path
 
 import nextflow.Global
 import nextflow.container.DockerConfig
+import nextflow.exception.ProcessException
 import nextflow.file.http.XPath
 import nextflow.processor.TaskBean
 import nextflow.processor.TaskConfig
 import nextflow.processor.TaskRun
+import nextflow.processor.TaskStatus
+import nextflow.util.Duration
 import spock.lang.Specification
 /**
  *
@@ -83,4 +86,33 @@ class LocalTaskHandlerTest extends Specification {
         cleanup:
         builder?.redirectOutput()?.file()?.delete()
     }
+
+    def 'should kill task when task exceeds time limit' () {
+        given:
+        def workDir = Path.of('/tmp/test-work-dir')
+        def task = Mock(TaskRun) {
+            getWorkDir() >> workDir
+            getConfig() >> Mock(TaskConfig) {
+                getTime() >> Duration.of(100)
+            }
+        }
+        and:
+        def handler = Spy(new LocalTaskHandler(task, Mock(LocalExecutor))) {
+            buildTaskWrapper() >> {}
+            elapsedTimeMillis() >> 200
+        }
+        handler.@process = Mock(Process) {
+            exitValue() >> 143  // Typical exit code for SIGTERM
+        }
+        handler.status = TaskStatus.RUNNING
+
+        when:
+        def completed = handler.checkIfCompleted()
+
+        then:
+        completed == true
+        1 * task.setExitStatus(143)
+        1 * task.setError(_ as ProcessException)
+        handler.status == TaskStatus.COMPLETED
+    }
 }