Fix Disable ansi logging when using kuberun command nextflow-io#1161

This commit disables the rich ansi logging feature when using the `kuberun` command since the output is not rendered correctly. Likely this is due to the wrong encoding of ANSI escape code when written/read over the http api.
sivkovic · Jun 6, 2019 · eb2da47 · eb2da47
1 parent ed80517
commit eb2da47
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Showing 5 changed files with 15 additions and 4 deletions.
diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/CliOptions.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/CliOptions.groovy
@@ -109,4 +109,8 @@ class CliOptions {
         return Ansi.isEnabled()
     }
 
+    boolean hasAnsiLogFlag() {
+        ansiLog==true || System.getenv('NXF_ANSI_LOG')=='true'
+    }
+
 }
diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/CmdKubeRun.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/CmdKubeRun.groovy
@@ -59,12 +59,16 @@ class CmdKubeRun extends CmdRun {
 
     protected boolean background() { launcher.options.background }
 
+    protected hasAnsiLogFlag() { launcher.options.hasAnsiLogFlag() }
+
     @Override
     void run() {
         final scriptArgs = (args?.size()>1 ? args[1..-1] : []) as List<String>
         final pipeline = stdin ? '-' : ( args ? args[0] : null )
         if( !pipeline )
             throw new AbortOperationException("No project name was specified")
+        if( hasAnsiLogFlag() )
+            log.warn "Ansi logging not supported by kuberun command"
         checkRunName()
         new K8sDriverLauncher(cmd: this, runName: runName, podImage: podImage, background: background())
                 .run(pipeline, scriptArgs)

diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/CmdRun.groovy
@@ -130,12 +130,12 @@ class CmdRun extends CmdBase implements HubOptions {
     boolean stdin
 
     @Parameter(names = ['-ansi'], hidden = true, arity = 0)
-    boolean setAnsi(boolean value) {
+    void setAnsi(boolean value) {
         launcher.options.ansiLog = value
     }
 
     @Parameter(names = ['-ansi-log'], description = 'Enable/disable ANSI console logging', arity = 1)
-    boolean setAnsiLog(boolean value) {
+    void setAnsiLog(boolean value) {
         launcher.options.ansiLog = value
     }
 

diff --git a/modules/nextflow/src/main/groovy/nextflow/k8s/K8sDriverLauncher.groovy b/modules/nextflow/src/main/groovy/nextflow/k8s/K8sDriverLauncher.groovy
@@ -417,6 +417,7 @@ class K8sDriverLauncher {
             .withEnv( PodEnv.value('NXF_WORK', k8sConfig.getWorkDir()) )
             .withEnv( PodEnv.value('NXF_ASSETS', k8sConfig.getProjectDir()) )
             .withEnv( PodEnv.value('NXF_EXECUTOR', 'k8s'))
+            .withEnv( PodEnv.value('NXF_ANSI_LOG', 'false'))
             .build()
 
         // note: do *not* set the work directory because it may need to be created  by the init script

diff --git a/modules/nextflow/src/test/groovy/nextflow/k8s/K8sDriverLauncherTest.groovy b/modules/nextflow/src/test/groovy/nextflow/k8s/K8sDriverLauncherTest.groovy
@@ -166,7 +166,8 @@ class K8sDriverLauncherTest extends Specification {
                                  env:[
                                          [name:'NXF_WORK', value:'/the/work/dir'],
                                          [name:'NXF_ASSETS', value:'/the/project/dir'],
-                                         [name:'NXF_EXECUTOR', value:'k8s']],
+                                         [name:'NXF_EXECUTOR', value:'k8s'],
+                                         [name:'NXF_ANSI_LOG', value: 'false']],
                                  volumeMounts:[
                                          [name:'vol-1', mountPath:'/mnt/path/data'],
                                          [name:'vol-2', mountPath:'/mnt/path/cfg']]]
@@ -214,7 +215,8 @@ class K8sDriverLauncherTest extends Specification {
                                  env:[
                                          [name:'NXF_WORK', value:'/the/work/dir'],
                                          [name:'NXF_ASSETS', value:'/the/project/dir'],
-                                         [name:'NXF_EXECUTOR', value:'k8s']],
+                                         [name:'NXF_EXECUTOR', value:'k8s'],
+                                         [name:'NXF_ANSI_LOG', value: 'false'] ],
                                  volumeMounts:[
                                          [name:'vol-1', mountPath:'/mnt/path/data'],
                                          [name:'vol-2', mountPath:'/mnt/path/cfg']]]