Fix issue when retrying with stub (#5359)

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

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

@@ -103,7 +103,7 @@ class TaskConfig extends LazyMap implements Cloneable {
         return eval0(this, path.tokenize('.'), path)
     }
 
-    private Object eval0(Object object, List<String> path, String key ) {
+    private Object eval0(Object object, List<String> path, String key) {
         assert path, "Missing task attribute name"
         def result = null
         if( object instanceof LazyMap ) {

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

@@ -85,7 +85,6 @@ import nextflow.script.BodyDef
 import nextflow.script.ProcessConfig
 import nextflow.script.ScriptMeta
 import nextflow.script.ScriptType
-import nextflow.script.TaskClosure
 import nextflow.script.bundle.ResourcesBundle
 import nextflow.script.params.BaseOutParam
 import nextflow.script.params.CmdEvalParam
@@ -642,14 +641,8 @@ class TaskProcessor {
         if( !checkWhenGuard(task) )
             return
 
-        TaskClosure block
-        if( session.stubRun && (block=task.config.getStubBlock()) ) {
-            task.resolve(block)
-        }
-        else {
-            // -- resolve the task command script
-            task.resolve(taskBody)
-        }
+        // -- resolve the task command script
+        task.resolve(taskBody)
 
         // -- verify if exists a stored result for this case,
         //    if true skip the execution and return the stored data

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

@@ -24,7 +24,6 @@ import java.util.function.Function
 
 import com.google.common.hash.HashCode
 import groovy.transform.Memoized
-import groovy.transform.PackageScope
 import groovy.util.logging.Slf4j
 import nextflow.Session
 import nextflow.conda.CondaCache
@@ -787,7 +786,13 @@ class TaskRun implements Cloneable {
      *
      * @param body A {@code BodyDef} object instance
      */
-    @PackageScope void resolve(BodyDef body) {
+    void resolve(BodyDef body)  {
+        processor.session.stubRun
+            ? resolveStub(config.getStubBlock())
+            : resolveBody(body)
+    }
+
+    protected void resolveBody(BodyDef body) {
 
         // -- initialize the task code to be executed
         this.code = body.closure.clone() as Closure
@@ -829,7 +834,7 @@ class TaskRun implements Cloneable {
             throw new ProcessUnrecoverableException("Process `${getName()}` script is empty")
     }
 
-    @PackageScope void resolve(TaskClosure block) {
+    protected void resolveStub(TaskClosure block) {
         this.code = block.clone() as Closure
         this.code.delegate = this.context
         this.code.setResolveStrategy(Closure.DELEGATE_ONLY)

modules/nextflow/src/test/groovy/nextflow/processor/TaskRunTest.groovy

@@ -402,7 +402,6 @@ class TaskRunTest extends Specification {
     }
 
     def 'should resolve the task body script' () {
-
         given:
         def task = new TaskRun()
         task.processor = [:] as TaskProcessor
@@ -412,7 +411,7 @@ class TaskRunTest extends Specification {
          * plain task script
          */
         when:
-        task.resolve(new BodyDef({-> 'Hello'}, 'Hello', 'script'))
+        task.resolveBody(new BodyDef({-> 'Hello'}, 'Hello', 'script'))
         then:
         task.script == 'Hello'
         task.source == 'Hello'
@@ -422,7 +421,7 @@ class TaskRunTest extends Specification {
          */
         when:
         task.context = new TaskContext(Mock(Script),[x: 'world'],'foo')
-        task.resolve(new BodyDef({-> "Hello ${x}"}, 'Hello ${x}', 'script'))
+        task.resolveBody(new BodyDef({-> "Hello ${x}"}, 'Hello ${x}', 'script'))
         then:
         task.script == 'Hello world'
         task.source == 'Hello ${x}'
@@ -448,7 +447,7 @@ class TaskRunTest extends Specification {
          */
         when:
         task.context = new TaskContext(Mock(Script),VARS,'foo')
-        task.resolve(new BodyDef(body, 'cat ${one}\nhead ${many}', 'script'))
+        task.resolveBody(new BodyDef(body, 'cat ${one}\nhead ${many}', 'script'))
         then:
         task.script == '''
                     cat a\\ b.txt
@@ -481,7 +480,7 @@ class TaskRunTest extends Specification {
         when:
         task.context = new TaskContext(script,local,'foo')
         task.config = new TaskConfig().setContext(task.context)
-        task.resolve(new BodyDef({-> '$BASH_VAR !{nxf_var} - !{params.var_no}'}, '<the source script>', 'shell'))  // <-- note: 'shell' type
+        task.resolveBody(new BodyDef({-> '$BASH_VAR !{nxf_var} - !{params.var_no}'}, '<the source script>', 'shell'))  // <-- note: 'shell' type
         then:
         task.script == '$BASH_VAR YES - NO'
         task.source == '<the source script>'
@@ -493,7 +492,7 @@ class TaskRunTest extends Specification {
         task.context = new TaskContext(Mock(Script),[nxf_var: '>interpolated value<'],'foo')
         task.config = new TaskConfig().setContext(task.context)
         task.config.placeholder = '#' as char
-        task.resolve(new BodyDef({-> '$BASH_VAR #{nxf_var}'}, '$BASH_VAR #{nxf_var}', 'shell'))  // <-- note: 'shell' type
+        task.resolveBody(new BodyDef({-> '$BASH_VAR #{nxf_var}'}, '$BASH_VAR #{nxf_var}', 'shell'))  // <-- note: 'shell' type
         then:
         task.script == '$BASH_VAR >interpolated value<'
         task.source == '$BASH_VAR #{nxf_var}'
@@ -517,7 +516,7 @@ class TaskRunTest extends Specification {
         task.config = new TaskConfig().setContext(task.context)
 
         when:
-        task.resolve( new BodyDef({-> template(my_file)}, 'template($file)', 'script'))
+        task.resolveBody( new BodyDef({-> template(my_file)}, 'template($file)', 'script'))
         then:
         task.script == 'echo Ciao mondo'
         task.source == 'echo ${say_hello}'
@@ -542,7 +541,7 @@ class TaskRunTest extends Specification {
         task.config = new TaskConfig().setContext(task.context)
 
         when:
-        task.resolve( new BodyDef({-> template(my_file)}, 'template($file)', 'shell'))
+        task.resolveBody( new BodyDef({-> template(my_file)}, 'template($file)', 'shell'))
         then:
         task.script == 'echo $HOME ~ Foo bar'
         task.source == 'echo $HOME ~ !{user_name}'
@@ -568,7 +567,7 @@ class TaskRunTest extends Specification {
         task.config.placeholder = '#' as char
 
         when:
-        task.resolve( new BodyDef({-> template(my_file)}, 'template($file)', 'shell'))
+        task.resolveBody( new BodyDef({-> template(my_file)}, 'template($file)', 'shell'))
         then:
         task.script == 'echo $HOME ~ Foo bar'
         task.source == 'echo $HOME ~ #{user_name}'
@@ -750,7 +749,7 @@ class TaskRunTest extends Specification {
         task.context = GroovyMock(TaskContext)
 
         when:
-        task.resolve(new BodyDef({-> "Hello ${x}"}, 'Hello ${x}', 'script'))
+        task.resolveBody(new BodyDef({-> "Hello ${x}"}, 'Hello ${x}', 'script'))
         and:
         def vars = task.getVariableNames()
         then:
@@ -769,7 +768,7 @@ class TaskRunTest extends Specification {
         task.config = new TaskConfig()
 
         when:
-        task.resolve(new BodyDef({-> 'Hello !{foo} !{bar} !{input_x}'}, 'Hello..', 'shell'))
+        task.resolveBody(new BodyDef({-> 'Hello !{foo} !{bar} !{input_x}'}, 'Hello..', 'shell'))
         and:
         def vars = task.getVariableNames()
         then:
@@ -793,7 +792,7 @@ class TaskRunTest extends Specification {
         task.config = new TaskConfig()
 
         when:
-        task.resolve(new BodyDef({-> template }, 'Hello..', 'script'))
+        task.resolveBody(new BodyDef({-> template }, 'Hello..', 'script'))
         and:
         def vars = task.getVariableNames()
         then:
@@ -822,7 +821,7 @@ class TaskRunTest extends Specification {
          * plain task script
          */
         when:
-        task.resolve(dryRun)
+        task.resolveStub(dryRun)
         then:
         task.script == 'echo Hello world'
         task.source == 'command source'
@@ -891,4 +890,38 @@ class TaskRunTest extends Specification {
         expect:
         !task.isArray()
     }
+
+    def 'should resolve task body' () {
+        given:
+        def task = Spy(TaskRun)
+        task.processor = Mock(TaskProcessor) {
+            getSession()>>Mock(Session) { getStubRun() >> false}
+        }
+        and:
+        def body = Mock(BodyDef)
+
+        when:
+        task.resolve(body)
+        then:
+        1 * task.resolveBody(body) >> null
+        0 * task.resolveStub(_) >> null
+    }
+
+    def 'should resolve task stub' () {
+        given:
+        def body = Mock(BodyDef)
+        def stub = Mock(TaskClosure)
+        and:
+        def task = Spy(TaskRun)
+        task.config = Mock(TaskConfig) { getStubBlock()>>stub }
+        task.processor = Mock(TaskProcessor) {
+            getSession()>>Mock(Session) { getStubRun() >> true}
+        }
+
+        when:
+        task.resolve(body)
+        then:
+        1 * task.resolveStub(stub) >> null
+        0 * task.resolveBody(_) >> null
+    }
 }

tests/checks/stub-retry.nf/.checks

@@ -0,0 +1,11 @@
+set -e
+
+echo ''
+$NXF_RUN -stub | tee stdout
+
+[[ `grep 'INFO' .nextflow.log | grep -c 'Submitted process > stubtest'` == 1 ]] || false
+[[ `grep 'INFO' .nextflow.log | grep -c 'Re-submitted process > stubtest'` == 1 ]] || false
+
+[[ `grep -c 'Stubbing. Creating file' stdout` == 1 ]] || false
+
+

tests/stub-retry.nf

@@ -0,0 +1,30 @@
+process stubtest {
+    debug true
+    errorStrategy 'retry'
+
+    output:
+    path("*.txt")
+
+    script:
+    """
+    echo "Not stubbing"
+    touch script.txt
+    """
+
+    stub:
+    if( task.attempt < 2 ) {
+    """
+    echo "Stubbing. Not creating file"
+    """
+    } else {
+    """
+    echo "Stubbing. Creating file"
+    touch script.txt
+    """
+    }
+}
+
+workflow {
+    main:
+    stubtest()
+}