Include all processes in inspect command (#5580)

Signed-off-by: Ben Sherman <[email protected]>
Signed-off-by: Paolo Di Tommaso <[email protected]>
Co-authored-by: Paolo Di Tommaso <[email protected]>

Author: bentsherman

modules/nextflow/src/main/groovy/nextflow/cli/CmdInspect.groovy

@@ -92,7 +92,7 @@ class CmdInspect extends CmdBase {
 
     protected void applyInspect(Session session) {
         // run the inspector
-        new ContainersInspector(session.dag, concretize)
+        new ContainersInspector(concretize)
                 .withFormat(format)
                 .withIgnoreErrors(ignoreErrors)
                 .printContainers()

modules/nextflow/src/main/groovy/nextflow/container/ContainerHandler.groovy

@@ -308,4 +308,4 @@ class ContainerHandler {
         // in all other case it's supposed to be the name of an image
         return "${normalizeDockerImageName(img)}"
     }
-}
+}

modules/nextflow/src/main/groovy/nextflow/container/inspect/ContainersInspector.groovy

@@ -24,9 +24,9 @@ import groovy.json.JsonBuilder
 import groovy.json.JsonOutput
 import groovy.transform.CompileStatic
 import groovy.util.logging.Slf4j
-import nextflow.dag.DAG
 import nextflow.exception.AbortOperationException
 import nextflow.processor.TaskRun
+import nextflow.script.ScriptMeta
 import org.codehaus.groovy.util.ListHashMap
 /**
  * Preview the list of containers used by a pipeline.
@@ -37,16 +37,13 @@ import org.codehaus.groovy.util.ListHashMap
 @CompileStatic
 class ContainersInspector {
 
-    private DAG dag
-
     private String format
 
     private boolean ignoreErrors
 
     private boolean concretize
 
-    ContainersInspector(DAG dag, boolean concretize) {
-        this.dag = dag
+    ContainersInspector(boolean concretize) {
         this.concretize = concretize
     }
 
@@ -83,15 +80,10 @@ class ContainersInspector {
         final containers = new ListHashMap<String,String>()
 
         List<TaskRun> tasks = new ArrayList<>()
-        for( def vertex : dag.vertices ) {
-            // skip nodes that are not processes
-            final process = vertex.process
-            if( !process )
-                continue
-
+        for( final process : ScriptMeta.allProcesses() ) {
             try {
                 // get container preview
-                final task = process.createTaskPreview()
+                final task = process.createTaskProcessor().createTaskPreview()
                 final containerName = task.getContainer()
                 containers[process.name] = containerName
                 if( containerName )

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

@@ -23,6 +23,7 @@ import nextflow.Global
 import nextflow.Session
 import nextflow.exception.ScriptRuntimeException
 import nextflow.extension.CH
+import nextflow.processor.TaskProcessor
 import nextflow.script.params.BaseInParam
 import nextflow.script.params.BaseOutParam
 import nextflow.script.params.EachInParam
@@ -208,20 +209,23 @@ class ProcessDef extends BindableDef implements IterableDef, ChainableDef {
         // make a copy of the output list because execution can change it
         output = new ChannelOut(declaredOutputs.clone())
 
-        // create the executor
-        final executor = session
-                .executorFactory
-                .getExecutor(processName, processConfig, taskBody, session)
-
-        // create processor class
-        session
-                .newProcessFactory(owner)
-                .newTaskProcessor(processName, executor, processConfig, taskBody)
-                .run()
+        // start processor
+        createTaskProcessor().run()
 
         // the result channels
         assert declaredOutputs.size()>0, "Process output should contains at least one channel"
         return output
     }
 
+    TaskProcessor createTaskProcessor() {
+        if( !processConfig )
+            initialize()
+        final executor = session
+            .executorFactory
+            .getExecutor(processName, processConfig, taskBody, session)
+        return session
+            .newProcessFactory(owner)
+            .newTaskProcessor(processName, executor, processConfig, taskBody)
+    }
+
 }

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

@@ -70,6 +70,15 @@ class ScriptMeta {
         return result
     }
 
+    static Set<ProcessDef> allProcesses() {
+        final result = new HashSet()
+        for( final entry : REGISTRY.values() ) {
+            final processes = entry.getDefinitions().findAll { d -> d instanceof ProcessDef }
+            result.addAll(processes)
+        }
+        return result
+    }
+
     static void addResolvedName(String name) {
         resolvedProcessNames.add(name)
     }

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

@@ -25,6 +25,7 @@ import groovy.transform.PackageScope
 import groovy.util.logging.Slf4j
 import nextflow.Global
 import nextflow.Session
+import nextflow.container.inspect.ContainerInspectMode
 import nextflow.exception.AbortOperationException
 import nextflow.exception.AbortRunException
 import nextflow.plugin.Plugins
@@ -226,6 +227,8 @@ class ScriptRunner {
     protected void parseScript( ScriptFile scriptFile, String entryName ) {
         scriptParser = new ScriptParser(session)
                             .setEntryName(entryName)
+                            // setting module true when running in "inspect" mode to prevent the running the entry workflow
+                            .setModule(ContainerInspectMode.active())
                             .parse(scriptFile.main)
         session.script = scriptParser.script
     }

modules/nextflow/src/test/groovy/nextflow/container/inspect/ContainersInspectorTest.groovy

@@ -17,40 +17,46 @@
 
 package nextflow.container.inspect
 
-
-import nextflow.dag.DAG
+import nextflow.NF
 import nextflow.processor.TaskProcessor
 import nextflow.processor.TaskRun
+import nextflow.script.BaseScript
+import nextflow.script.ProcessDef
+import nextflow.script.ScriptMeta
 import spock.lang.Specification
 /**
  *
  * @author Ben Sherman <[email protected]>
  */
 class ContainersInspectorTest extends Specification {
 
-    def makeVertex(DAG dag, String name, String container) {
-        final processor = Mock(TaskProcessor)
-        processor.name >> name
-        processor.createTaskPreview() >> Mock(TaskRun) {
-            getContainer() >> container
-        }
-
-        final vertex = new DAG.Vertex(dag, DAG.Type.PROCESS)
-        vertex.process = processor
+    def setup() {
+        ScriptMeta.reset()
+        NF.init()
+    }
 
-        return vertex
+    def makeProcess(String name, String container) {
+        final script = new BaseScript() {
+            Object runScript() {}
+        }
+        final processDef = Mock(ProcessDef) {
+            getName() >> name
+            createTaskProcessor() >> Mock(TaskProcessor) {
+                createTaskPreview() >> Mock(TaskRun) {
+                    getContainer() >> container
+                }
+            }
+        }
+        ScriptMeta.get(script).addDefinition(processDef)
     }
 
     def 'should get containers' () {
         given:
-        def dag = Mock(DAG)
-        dag.vertices >> [
-            makeVertex(dag, 'proc1', 'container1'),
-            makeVertex(dag, 'proc2', 'container2')
-        ]
+        makeProcess('proc1', 'container1')
+        makeProcess('proc2', 'container2')
 
         when:
-        def observer = new ContainersInspector(dag, false)
+        def observer = new ContainersInspector(false)
         then:
         observer.getContainers() == [
             'proc1': 'container1',
@@ -60,14 +66,11 @@ class ContainersInspectorTest extends Specification {
 
     def 'should render containers as json' () {
         given:
-        def dag = Mock(DAG)
-        dag.vertices >> [
-                makeVertex(dag, 'proc1', 'container1'),
-                makeVertex(dag, 'proc2', 'container2')
-        ]
+        makeProcess('proc1', 'container1')
+        makeProcess('proc2', 'container2')
 
         when:
-        def result = new ContainersInspector(dag, false)
+        def result = new ContainersInspector(false)
                 .withFormat('json')
                 .renderContainers()
         then:
@@ -89,14 +92,11 @@ class ContainersInspectorTest extends Specification {
 
     def 'should render containers as nextflow config' () {
         given:
-        def dag = Mock(DAG)
-        dag.vertices >> [
-                makeVertex(dag, 'proc1', 'container1'),
-                makeVertex(dag, 'proc2', 'container2')
-        ]
+        makeProcess('proc1', 'container1')
+        makeProcess('proc2', 'container2')
 
         when:
-        def result = new ContainersInspector(dag,false)
+        def result = new ContainersInspector(false)
                 .withFormat('config')
                 .renderContainers()
         then: