Rename pod directive to podOptions

docs/config.rst

@@ -396,7 +396,7 @@ serviceAccount      Defines the Kubernetes `service account name <https://kubern
 launchDir           Defines the path where the workflow is launched and the user data is stored. This must be a path in a shared K8s persistent volume (default: ``<volume-claim-mount-path>/<user-name>``.
 workDir             Defines the path where the workflow temporary data is stored. This must be a path in a shared K8s persistent volume (default:``<user-dir>/work``).
 projectDir          Defines the path where Nextflow projects are downloaded. This must be a path in a shared K8s persistent volume (default: ``<volume-claim-mount-path>/projects``).
-pod                 Allows the definition of one or more pod configuration options such as environment variables, config maps, secrets, etc. It allows the same settings as the :ref:`process-pod` process directive.
+podOptions          Defines one or more pod configuration options such as environment variables, config maps, secrets, etc. It allows the same options as the :ref:`process-podOptions` process directive.
 pullPolicy          Defines the strategy to be used to pull the container image e.g. ``pullPolicy: 'Always'``.
 runAsUser           Defines the user ID to be used to run the containers. Shortcut for the ``securityContext`` option.
 securityContext     Defines the `security context <https://kubernetes.io/docs/tasks/configure-pod-container/security-context/>`_ for all pods.

docs/kubernetes.rst

@@ -118,13 +118,13 @@ with the directory in the volume to be mounted (default: ``/``).
     one specified in your Nextflow configuration file.
     Note also that the ``run`` command does not support the ``-v`` option.
 
-.. tip:: It is also possible to mount multiple volumes using the ``pod`` directive, setting such as ``k8s.pod = [ [volumeClaim: "other-pvc", mountPath: "/other" ]]``
+.. tip:: It is also possible to mount multiple volumes using the ``podOptions`` directive, setting such as ``k8s.podOptions = [ [volumeClaim: "other-pvc", mountPath: "/other" ]]``
 
-Pod settings
-============
+Pod options
+===========
 
-The process :ref:`process-pod` directive allows the definition of pods specific settings, such as environment variables,
-secrets and config maps when using the :ref:`k8s-executor` executor. See the :ref:`process-pod` directive for more details.
+The process :ref:`process-podOptions` directive allows the definition of pod-specific options, such as environment variables,
+secrets and config maps when using the :ref:`k8s-executor` executor. See the :ref:`process-podOptions` directive for more details.
 
 Limitation
 ==========

docs/process.rst

@@ -1352,7 +1352,7 @@ The directives are:
 * `memory`_
 * `module`_
 * `penv`_
-* `pod`_
+* `podOptions`_
 * `publishDir`_
 * `queue`_
 * `scratch`_
@@ -1981,18 +1981,18 @@ cluster documentation or contact your admin to learn more about this.
 See also: `cpus`_, `memory`_, `time`_
 
 
-.. _process-pod:
+.. _process-podOptions:
 
-pod
----
+podOptions
+----------
 
-The ``pod`` directive allows the definition of pods specific settings, such as environment variables, secrets
+The ``podOptions`` directive allows the definition of pod-specific options, such as environment variables, secrets
 and config maps when using the :ref:`k8s-executor` executor.
 
 For example::
 
   process your_task {
-    pod env: 'FOO', value: 'bar'
+    podOptions env: 'FOO', value: 'bar'
 
     '''
     echo $FOO
@@ -2001,7 +2001,7 @@ For example::
 
 The above snippet defines an environment variable named ``FOO`` which value is ``bar``.
 
-The ``pod`` directive allows the definition of the following options:
+The ``podOptions`` directive supports the following options:
 
 ================================================= =================================================
 ``label: <K>, value: <V>``                        Defines a pod label with key ``K`` and value ``V``.
@@ -2023,17 +2023,20 @@ The ``pod`` directive allows the definition of the following options:
 ``priorityClassName: <V>``                        Specifies the `priority class name <https://kubernetes.io/docs/concepts/scheduling-eviction/pod-priority-preemption/>`_ for pods.
 ================================================= =================================================
 
-When defined in the Nextflow configuration file, a pod setting can be defined using the canonical
+When defined in the Nextflow configuration file, a pod option can be defined using the canonical
 associative array syntax. For example::
 
   process {
-    pod = [env: 'FOO', value: 'bar']
+    podOptions = [env: 'FOO', value: 'bar']
   }
 
-When more than one setting needs to be provides they must be enclosed in a list definition as shown below::
+When more than one option needs to be provided they must be enclosed in a list as shown below::
 
   process {
-    pod = [ [env: 'FOO', value: 'bar'], [secret: 'my-secret/key1', mountPath: '/etc/file.txt'] ]
+    podOptions = [
+      [env: 'FOO', value: 'bar'],
+      [secret: 'my-secret/key1', mountPath: '/etc/file.txt']
+    ]
   }
 
 

modules/nextflow/src/main/groovy/nextflow/k8s/K8sConfig.groovy

@@ -47,7 +47,16 @@ class K8sConfig implements Map<String,Object> {
     K8sConfig(Map<String,Object> config) {
         target = config ?: Collections.<String,Object>emptyMap()
 
-        this.podOptions = createPodOptions(target.pod)
+        // -- backward compatibility
+        if( target.pod ) {
+            log.warn "Process directive 'pod' has been renamed to 'podOptions'"
+            target.put('podOptions', target.pod)
+        }
+
+        // -- initialize pod options
+        this.podOptions = createPodOptions(target.podOptions)
+
+        // -- add pod volume claim
         if( getStorageClaimName() ) {
             final name = getStorageClaimName()
             final mount = getStorageMountPath()

modules/nextflow/src/main/groovy/nextflow/k8s/K8sDriverLauncher.groovy

@@ -279,17 +279,22 @@ class K8sDriverLauncher {
         }
 
         def config = loadConfig(pipelineName)
-
-        // normalize pod entries
         def k8s = config.k8s
 
-        if( !k8s.isSet('pod') )
-            k8s.pod = []
-        else if( k8s.pod instanceof Map ) {
-            k8s.pod = [ k8s.pod ]
+        // -- backward compatibility
+        if( k8s.pod ) {
+            log.warn "Config setting k8s.pod has been renamed to k8s.podOptions"
+            k8s.put('podOptions', k8s.pod)
+            k8s.remove('pod')
         }
-        else if( !(k8s.pod instanceof List) )
-            throw new IllegalArgumentException("Illegal k8s.pod configuratun value: ${k8s.pod}")
+
+        // -- normalize pod options
+        if( !k8s.podOptions )
+            k8s.podOptions = []
+        else if( k8s.podOptions instanceof Map )
+            k8s.podOptions = [ k8s.podOptions ]
+        else if( !(k8s.podOptions instanceof List) )
+            throw new IllegalArgumentException("Illegal k8s.podOptions configuratun value: ${k8s.podOptions}")
 
         // -- use the volume claims specified in the command line
         //   to populate the pod config
@@ -303,7 +308,7 @@ class K8sDriverLauncher {
                 k8s.storageMountPath = path
             }
             else {
-                k8s.pod.add( [volumeClaim: name, mountPath: path] )
+                k8s.podOptions.add( [volumeClaim: name, mountPath: path] )
             }
         }
 
@@ -318,7 +323,7 @@ class K8sDriverLauncher {
                     k8s.storageMountPath = path
                 }
                 else if( !cmd.volMounts ) {
-                    k8s.pod.add( [volumeClaim: name, mountPath: path] )
+                    k8s.podOptions.add( [volumeClaim: name, mountPath: path] )
                 }
             }
             // remove it
@@ -339,8 +344,8 @@ class K8sDriverLauncher {
             k8s.workDir = config.workDir
 
         // -- some cleanup
-        if( !k8s.pod )
-            k8s.remove('pod')
+        if( !k8s.podOptions )
+            k8s.remove('podOptions')
 
         if( !k8s.storageClaimName )
             k8s.remove('storageClaimName')

modules/nextflow/src/main/groovy/nextflow/processor/TaskConfig.groovy

@@ -380,7 +380,7 @@ class TaskConfig extends LazyMap implements Cloneable {
     }
 
     PodOptions getPodOptions() {
-        new PodOptions((List)get('pod'))
+        new PodOptions((List)get('podOptions'))
     }
 
     AcceleratorResource getAccelerator() {

modules/nextflow/src/main/groovy/nextflow/script/ProcessConfig.groovy

@@ -60,17 +60,18 @@ class ProcessConfig implements Map<String,Object>, Cloneable {
             'errorStrategy',
             'executor',
             'ext',
-            'machineType',
-            'queue',
             'label',
+            'machineType',
             'maxErrors',
             'maxForks',
             'maxRetries',
             'memory',
             'module',
             'penv',
             'pod',
+            'podOptions',
             'publishDir',
+            'queue',
             'scratch',
             'shell',
             'storeDir',
@@ -93,7 +94,13 @@ class ProcessConfig implements Map<String,Object>, Cloneable {
      * Names of directives that can be used more than once in the process definition
      */
     @PackageScope
-    static final List<String> repeatableDirectives = ['label','module','pod','publishDir']
+    static final List<String> repeatableDirectives = [
+        'label',
+        'module',
+        'pod',
+        'podOptions',
+        'publishDir'
+    ]
 
     /**
      * Default directives values
@@ -825,22 +832,22 @@ class ProcessConfig implements Map<String,Object>, Cloneable {
     }
 
     /**
-     * Allow use to specify K8s `pod` options
+     * Allow the user to specify K8s pod options
      *
      * @param entry
      *      A map object representing pod config options
      * @return
      *      The {@link ProcessConfig} instance itself
      */
-    ProcessConfig pod( Map entry ) {
+    ProcessConfig podOptions( Map entry ) {
 
         if( !entry )
             return this
 
-        def allOptions = (List)configProperties.get('pod')
+        def allOptions = (List)configProperties.get('podOptions')
         if( !allOptions ) {
             allOptions = new ConfigList()
-            configProperties.put('pod', allOptions)
+            configProperties.put('podOptions', allOptions)
         }
 
         allOptions.add(entry)

modules/nextflow/src/test/groovy/nextflow/k8s/K8sConfigTest.groovy

@@ -89,17 +89,20 @@ class K8sConfigTest extends Specification {
 
         when:
         cfg = new K8sConfig([
-                storageClaimName: 'pvc-2',
-                storageMountPath: '/data',
-                pod: [  [volumeClaim:'foo', mountPath: '/here'],
-                        [volumeClaim: 'bar', mountPath: '/there']] ])
+            storageClaimName: 'pvc-2',
+            storageMountPath: '/data',
+            podOptions: [
+                [volumeClaim:'foo', mountPath: '/here'],
+                [volumeClaim: 'bar', mountPath: '/there']
+            ]
+        ])
         then:
         cfg.getStorageClaimName() == 'pvc-2'
         cfg.getStorageMountPath() == '/data'
         cfg.getPodOptions().getVolumeClaims() == [
-                new PodVolumeClaim('pvc-2', '/data'),
-                new PodVolumeClaim('foo', '/here'),
-                new PodVolumeClaim('bar', '/there')
+            new PodVolumeClaim('pvc-2', '/data'),
+            new PodVolumeClaim('foo', '/here'),
+            new PodVolumeClaim('bar', '/there')
         ] as Set
 
 
@@ -185,7 +188,7 @@ class K8sConfigTest extends Specification {
 
 
         when:
-        opts = new K8sConfig(pod: [ [pullPolicy: 'Always'], [env: 'HELLO', value: 'WORLD'] ]).getPodOptions()
+        opts = new K8sConfig(podOptions: [ [pullPolicy: 'Always'], [env: 'HELLO', value: 'WORLD'] ]).getPodOptions()
         then:
         opts.getImagePullPolicy() == 'Always'
         opts.getEnvVars() == [ PodEnv.value('HELLO','WORLD') ] as Set
@@ -285,20 +288,20 @@ class K8sConfigTest extends Specification {
     def 'should create k8s config with one volume claim' () {
 
         when:
-        def cfg = new K8sConfig( pod: [runAsUser: 1000] )
+        def cfg = new K8sConfig( podOptions: [runAsUser: 1000] )
         then:
         cfg.getPodOptions().getSecurityContext() == new PodSecurityContext(1000)
         cfg.getPodOptions().getVolumeClaims().size() == 0
 
         when:
-        cfg = new K8sConfig( pod: [volumeClaim: 'nf-0001', mountPath: '/workspace'] )
+        cfg = new K8sConfig( podOptions: [volumeClaim: 'nf-0001', mountPath: '/workspace'] )
         then:
         cfg.getPodOptions().getSecurityContext() == null
         cfg.getPodOptions().getVolumeClaims() == [new PodVolumeClaim('nf-0001', '/workspace')] as Set
 
 
         when:
-        cfg = new K8sConfig( pod: [
+        cfg = new K8sConfig( podOptions: [
                 [runAsUser: 1000],
                 [volumeClaim: 'nf-0001', mountPath: '/workspace'],
                 [volumeClaim: 'nf-0002', mountPath: '/data', subPath: '/home']