Wave does not support 'null' container engine

Signed-off-by: Paolo Di Tommaso <paolo.ditommaso@gmail.com>
nextflow-io · Sep 27, 2023 · f3eba3d · f3eba3d
1 parent e4a878b
commit f3eba3d
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Showing 3 changed files with 30 additions and 8 deletions.
diff --git a/modules/nextflow/src/main/groovy/nextflow/Session.groovy b/modules/nextflow/src/main/groovy/nextflow/Session.groovy
@@ -1201,23 +1201,30 @@ class Session implements ISession {
             return new ContainerConfig(result)
         }
 
-        final enabled = allEngines.findAll { it.enabled?.toString() == 'true' }
+        final enabled = allEngines.findAll(it -> it.enabled?.toString() == 'true')
         if( enabled.size() > 1 ) {
-            def names = enabled.collect { it.engine }
+            final names = enabled.collect(it -> it.engine)
             throw new IllegalConfigException("Cannot enable more than one container engine -- Choose either one of: ${names.join(', ')}")
         }
-
-        (enabled ? enabled.get(0) : ( allEngines ? allEngines.get(0) : [engine:'docker'] )) as ContainerConfig
+        if( enabled ) {
+            return new ContainerConfig(enabled.get(0))
+        }
+        if( allEngines ) {
+            return new ContainerConfig(allEngines.get(0))
+        }
+        return new ContainerConfig(engine:'docker')
     }
 
     ContainerConfig getContainerConfig() {
         return getContainerConfig(null)
     }
 
     private void getContainerConfig0(String engine, List<Map> drivers) {
+        assert engine
         final entry = this.config?.get(engine)
         if( entry instanceof Map ) {
-            final config0 = new LinkedHashMap((Map)entry)
+            final config0 = new LinkedHashMap()
+            config0.putAll((Map)entry)
             config0.put('engine', engine)
             drivers.add(config0)
         }

diff --git a/modules/nextflow/src/main/groovy/nextflow/script/WorkflowMetadata.groovy b/modules/nextflow/src/main/groovy/nextflow/script/WorkflowMetadata.groovy
@@ -234,12 +234,12 @@ class WorkflowMetadata {
         this.nextflow = NextflowMeta.instance
         this.workDir = session.workDir
         this.launchDir = Paths.get('.').complete()
-        this.profile = session.profile ?:  ConfigBuilder.DEFAULT_PROFILE
+        this.profile = session.profile ?: ConfigBuilder.DEFAULT_PROFILE
         this.sessionId = session.uniqueId
         this.resume = session.resumeMode
         this.stubRun = session.stubRun
         this.runName = session.runName
-        this.containerEngine = session.containerConfig.with { isEnabled() ? getEngine() : null }
+        this.containerEngine = containerEngine0(session)
         this.configFiles = session.configFiles?.collect { it.toAbsolutePath() }
         this.stats = new WorkflowStats()
         this.userName = System.getProperty('user.name')
@@ -252,6 +252,11 @@ class WorkflowMetadata {
         session.onError( this.&invokeOnError )
     }
 
+    private String containerEngine0(Session session) {
+       final config = session.getContainerConfig()
+       return config.isEnabled() ? config.getEngine() : null
+    }
+
     /**
      * Only for testing purpose -- do not use
      */

diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/resolver/WaveContainerResolver.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/resolver/WaveContainerResolver.groovy
@@ -52,13 +52,23 @@ class WaveContainerResolver implements ContainerResolver {
         return client0 = new WaveClient( Global.session as Session )
     }
 
+    private String getContainerEngine0(TaskRun task) {
+        final config = task.getContainerConfig()
+        final result = config.getEngine()
+        if( result )
+            return result
+        // fallback to docker by default
+        log.warn "Missing engine in container config - offending value: $config"
+        return 'docker'
+    }
+
     @Override
     ContainerInfo resolveImage(TaskRun task, String imageName) {
         if( !client().enabled() )
             return defaultResolver.resolveImage(task, imageName)
 
         final freeze = client().config().freezeMode()
-        final engine= task.getContainerConfig().getEngine()
+        final engine = getContainerEngine0(task)
         final nativeSingularityBuild = freeze && engine in SINGULARITY_LIKE
         if( !imageName ) {
             // when no image name is provided the module bundle should include a