Apply suggestions from review

Signed-off-by: Ben Sherman <bentshermann@gmail.com>
nextflow-io · Dec 11, 2024 · e7aa3a7 · e7aa3a7
1 parent 53d6c61
commit e7aa3a7
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Showing 9 changed files with 22 additions and 14 deletions.
diff --git a/modules/nextflow/src/main/groovy/nextflow/cli/CmdInspect.groovy b/modules/nextflow/src/main/groovy/nextflow/cli/CmdInspect.groovy
@@ -70,7 +70,8 @@ class CmdInspect extends CmdBase {
 
     @Override
     void run() {
-        ContainerInspectMode.activate(!concretize)
+        ContainerInspectMode.activate(true)
+        ContainerInspectMode.concretize(concretize)
         // configure quiet mode
         LoggerHelper.setQuiet(true)
         // setup the target run command

diff --git a/modules/nextflow/src/main/groovy/nextflow/container/ContainerHandler.groovy b/modules/nextflow/src/main/groovy/nextflow/container/ContainerHandler.groovy
@@ -70,7 +70,7 @@ class ContainerHandler {
             if( normalizedImageName.startsWith('docker://') && config.canRunOciImage() )
                 return normalizedImageName
             final requiresCaching = normalizedImageName =~ IMAGE_URL_PREFIX
-            if( ContainerInspectMode.active() && requiresCaching )
+            if( ContainerInspectMode.concretizeEnabled() && requiresCaching )
                 return imageName
             final result = requiresCaching ? createSingularityCache(this.config, normalizedImageName) : normalizedImageName
             return Escape.path(result)
@@ -82,7 +82,7 @@ class ContainerHandler {
             if( normalizedImageName.startsWith('docker://') && config.canRunOciImage() )
                 return normalizedImageName
             final requiresCaching = normalizedImageName =~ IMAGE_URL_PREFIX
-            if( ContainerInspectMode.active() && requiresCaching )
+            if( ContainerInspectMode.concretizeEnabled() && requiresCaching )
                 return imageName
             final result = requiresCaching ? createApptainerCache(this.config, normalizedImageName) : normalizedImageName
             return Escape.path(result)
@@ -94,7 +94,7 @@ class ContainerHandler {
             // if the imagename starts with '/' it's an absolute path
             // otherwise we assume it's in a remote registry and pull it from there
             final requiresCaching = !imageName.startsWith('/')
-            if( ContainerInspectMode.active() && requiresCaching )
+            if( ContainerInspectMode.concretizeEnabled() && requiresCaching )
                 return imageName
             final result = requiresCaching ? createCharliecloudCache(this.config, normalizedImageName) : normalizedImageName
             return Escape.path(result)

diff --git a/modules/nextflow/src/main/groovy/nextflow/container/inspect/ContainerInspectMode.groovy b/modules/nextflow/src/main/groovy/nextflow/container/inspect/ContainerInspectMode.groovy
@@ -28,8 +28,14 @@ class ContainerInspectMode {
 
     private static Boolean active
 
+    private static Boolean concretize = true
+
     static boolean active() { return active==true }
 
     static void activate(boolean value) { active = value }
 
+    static boolean concretizeEnabled() { return concretize==true }
+
+    static void concretize(boolean value) { concretize = value }
+
 }
diff --git a/modules/nextflow/src/main/groovy/nextflow/container/inspect/ContainersInspector.groovy b/modules/nextflow/src/main/groovy/nextflow/container/inspect/ContainersInspector.groovy
@@ -83,7 +83,7 @@ class ContainersInspector {
         for( final process : ScriptMeta.allProcesses() ) {
             try {
                 // get container preview
-                final task = process.getTaskProcessor().createTaskPreview()
+                final task = process.createTaskProcessor().createTaskPreview()
                 final containerName = task.getContainer()
                 containers[process.name] = containerName
                 if( containerName )

diff --git a/modules/nextflow/src/main/groovy/nextflow/script/ProcessDef.groovy b/modules/nextflow/src/main/groovy/nextflow/script/ProcessDef.groovy
@@ -210,14 +210,14 @@ class ProcessDef extends BindableDef implements IterableDef, ChainableDef {
         output = new ChannelOut(declaredOutputs.clone())
 
         // start processor
-        getTaskProcessor().run()
+        createTaskProcessor().run()
 
         // the result channels
         assert declaredOutputs.size()>0, "Process output should contains at least one channel"
         return output
     }
 
-    TaskProcessor getTaskProcessor() {
+    TaskProcessor createTaskProcessor() {
         if( !processConfig )
             initialize()
         final executor = session

diff --git a/modules/nextflow/src/main/groovy/nextflow/script/ScriptRunner.groovy b/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
@@ -226,8 +227,8 @@ class ScriptRunner {
     protected void parseScript( ScriptFile scriptFile, String entryName ) {
         scriptParser = new ScriptParser(session)
         scriptParser.setEntryName(entryName)
-        // don't execute entry workflow if preview action (i.e. inspect command) is specified
-        if( previewAction )
+        // don't execute entry workflow in the inspect command
+        if( ContainerInspectMode.acitve() )
             scriptParser.setModule(true)
         scriptParser.parse(scriptFile.main)
         session.script = scriptParser.script

diff --git a/modules/nextflow/src/test/groovy/nextflow/container/inspect/ContainersInspectorTest.groovy b/modules/nextflow/src/test/groovy/nextflow/container/inspect/ContainersInspectorTest.groovy
@@ -41,7 +41,7 @@ class ContainersInspectorTest extends Specification {
         }
         final processDef = Mock(ProcessDef) {
             getName() >> name
-            getTaskProcessor() >> Mock(TaskProcessor) {
+            createTaskProcessor() >> Mock(TaskProcessor) {
                 createTaskPreview() >> Mock(TaskRun) {
                     getContainer() >> container
                 }

diff --git a/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy b/plugins/nf-wave/src/main/io/seqera/wave/plugin/WaveClient.groovy
@@ -222,7 +222,7 @@ class WaveClient {
                 fingerprint: assets.fingerprint(),
                 freeze: config.freezeMode(),
                 format: assets.singularity ? 'sif' : null,
-                dryRun: ContainerInspectMode.active(),
+                dryRun: ContainerInspectMode.concretizeEnabled(),
                 mirror: config.mirrorMode(),
                 scanMode: config.scanMode(),
                 scanLevels: config.scanAllowedLevels()
@@ -249,7 +249,7 @@ class WaveClient {
                 towerEndpoint: tower.endpoint,
                 workflowId: tower.workflowId,
                 freeze: config.freezeMode(),
-                dryRun: ContainerInspectMode.active(),
+                dryRun: ContainerInspectMode.concretizeEnabled(),
                 mirror: config.mirrorMode(),
                 scanMode: config.scanMode(),
                 scanLevels: config.scanAllowedLevels()

diff --git a/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy b/plugins/nf-wave/src/test/io/seqera/wave/plugin/WaveClientTest.groovy
@@ -285,7 +285,7 @@ class WaveClientTest extends Specification {
 
     def 'should create request object with dry-run mode' () {
         given:
-        ContainerInspectMode.activate(true)
+        ContainerInspectMode.concretize(false)
         def session = Mock(Session) { getConfig() >> [:]}
         def IMAGE =  'foo:latest'
         def wave = new WaveClient(session)
@@ -306,7 +306,7 @@ class WaveClientTest extends Specification {
         req.timestamp instanceof String
 
         cleanup:
-        ContainerInspectMode.activate(false)
+        ContainerInspectMode.concretize(true)
     }
 
     def 'should create request object and platform' () {