redirect .command.run output to .command.log when fusion is not enabled

Signed-off-by: jorgee <[email protected]>

Author: jorgee

plugins/nf-k8s/src/main/nextflow/k8s/K8sTaskHandler.groovy

@@ -148,8 +148,11 @@ class K8sTaskHandler extends TaskHandler implements FusionAwareTask {
     }
 
     protected List<String> classicSubmitCli(TaskRun task) {
+        final workDir = Escape.path(task.workDir)
+
         final result = new ArrayList(BashWrapperBuilder.BASH)
-        result.add("${Escape.path(task.workDir)}/${TaskRun.CMD_RUN}".toString())
+        result.add('-c')
+        result.add("bash ${workDir}/${TaskRun.CMD_RUN} 2>&1 | tee ${workDir}/${TaskRun.CMD_LOG}")
         return result
     }
 
@@ -438,7 +441,6 @@ class K8sTaskHandler extends TaskHandler implements FusionAwareTask {
                 task.stderr = errorFile
             }
             status = TaskStatus.COMPLETED
-            savePodLogOnError(task)
             deletePodIfSuccessful(task)
             updateTimestamps(state.terminated as Map)
             determineNode()
@@ -448,31 +450,6 @@ class K8sTaskHandler extends TaskHandler implements FusionAwareTask {
         return false
     }
 
-    protected void savePodLogOnError(TaskRun task) {
-        if( task.isSuccess() )
-            return
-
-        if( errorFile && !errorFile.empty() )
-            return
-
-        final session = executor.getSession()
-        if( session.isAborted() || session.isCancelled() || session.isTerminated() )
-            return
-
-        try {
-            final stream = useJobResource()
-                    ? client.jobLog(podName)
-                    : client.podLog(podName)
-            Files.copy(stream, task.workDir.resolve(TaskRun.CMD_LOG))
-        }
-        catch( FileAlreadyExistsException e ) {
-            log.debug "Log file already exists for ${resourceType.lower()} $podName", e
-        }
-        catch( Exception e ) {
-            log.warn "Failed to copy log for ${resourceType.lower()} $podName", e
-        }
-    }
-
     protected int readExitFile() {
         try {
             exitFile.text as Integer

plugins/nf-k8s/src/test/nextflow/k8s/K8sTaskHandlerTest.groovy

@@ -96,7 +96,7 @@ class K8sTaskHandlerTest extends Specification {
                 containers: [[
                     name:'nf-123',
                     image:'debian:latest',
-                    args:['/bin/bash', '-ue','/some/work/dir/.command.run']
+                    args:['/bin/bash', '-ue','-c','bash /some/work/dir/.command.run 2>&1 | tee /some/work/dir/.command.log']
                 ]]
             ]
         ]
@@ -123,7 +123,7 @@ class K8sTaskHandlerTest extends Specification {
         and:
         result.metadata.labels == [sessionId: 'xxx']
         result.metadata.annotations == [evict: 'false']
-        result.spec.containers[0].command == ['/bin/bash', '-ue', '/some/work/dir/.command.run']
+        result.spec.containers[0].command == ['/bin/bash', '-ue', '-c','bash /some/work/dir/.command.run 2>&1 | tee /some/work/dir/.command.log']
         result.spec.containers[0].resources == [ requests: [cpu:1] ]
         result.spec.containers[0].env == [ [name:'NXF_OWNER', value:'501:502'] ]
 
@@ -148,7 +148,7 @@ class K8sTaskHandlerTest extends Specification {
         and:
         result.metadata.namespace == 'namespace-x'
         result.spec.containers[0].image == 'user/alpine:1.0'
-        result.spec.containers[0].command == ['/bin/bash', '-ue', '/some/work/dir/.command.run']
+        result.spec.containers[0].command == ['/bin/bash', '-ue', '-c','bash /some/work/dir/.command.run 2>&1 | tee /some/work/dir/.command.log']
         result.spec.containers[0].resources == [ requests: [cpu:4, memory:'16384Mi'], limits: [memory:'16384Mi'] ]
 
     }
@@ -428,7 +428,7 @@ class K8sTaskHandlerTest extends Specification {
                         containers: [[
                             name: 'nf-123',
                             image: 'debian:latest',
-                            command: ['/bin/bash', '-ue','/some/work/dir/.command.run']
+                            command: ['/bin/bash', '-ue','-c','bash /some/work/dir/.command.run 2>&1 | tee /some/work/dir/.command.log']
                         ]]
                     ]
                 ]
@@ -498,7 +498,6 @@ class K8sTaskHandlerTest extends Specification {
         1 * handler.updateTimestamps(termState)
         1 * handler.readExitFile() >> EXIT_STATUS
         1 * handler.deletePodIfSuccessful(task) >> null
-        1 * handler.savePodLogOnError(task) >> null
         handler.task.exitStatus == EXIT_STATUS
         handler.task.@stdout == OUT_FILE
         handler.task.@stderr == ERR_FILE
@@ -529,7 +528,6 @@ class K8sTaskHandlerTest extends Specification {
         1 * handler.updateTimestamps(termState)
         0 * handler.readExitFile()
         1 * handler.deletePodIfSuccessful(task) >> null
-        1 * handler.savePodLogOnError(task) >> null
         handler.task.exitStatus == 137
         handler.status == TaskStatus.COMPLETED
         result == true
@@ -788,43 +786,6 @@ class K8sTaskHandlerTest extends Specification {
 
     }
 
-    def 'should save pod log' () {
-
-        given:
-        def folder = Files.createTempDirectory('test')
-        def POD_NAME = 'the-pod-name'
-        def POD_MESSAGE = 'Hello world!'
-        def POD_LOG = new ByteArrayInputStream(new String(POD_MESSAGE).bytes)
-        def session = Mock(Session)
-        def task = Mock(TaskRun)
-        def executor = Mock(K8sExecutor)
-        def client = Mock(K8sClient)
-        and:
-        def handler = Spy(new K8sTaskHandler(executor: executor, client: client, podName: POD_NAME))
-
-        when:
-        handler.savePodLogOnError(task)
-        then:
-        task.isSuccess() >> true
-        0 * client.podLog(_)
-
-        when:
-        handler.savePodLogOnError(task)
-        then:
-        task.isSuccess() >> false
-        task.getWorkDir() >> folder
-        executor.getSession() >> session
-        session.isTerminated() >> false
-        session.isCancelled() >> false
-        session.isAborted() >> false
-        1 * client.podLog(POD_NAME) >> POD_LOG
-
-        folder.resolve( TaskRun.CMD_LOG ).text == POD_MESSAGE
-        cleanup:
-        folder?.deleteDir()
-
-    }
-
     def 'should merge pod options' () {
         given:
         PodOptions opts