From 47cad17860039a92da1ab4ddf1b58bc9393135f1 Mon Sep 17 00:00:00 2001 From: jorgee Date: Tue, 5 Nov 2024 13:26:13 +0100 Subject: [PATCH 1/2] Fixing bug when execution with stub and no stub defined Signed-off-by: jorgee --- .../groovy/nextflow/processor/TaskRun.groovy | 2 +- .../nextflow/processor/TaskRunTest.groovy | 17 +++++++++++++++++ 2 files changed, 18 insertions(+), 1 deletion(-) diff --git a/modules/nextflow/src/main/groovy/nextflow/processor/TaskRun.groovy b/modules/nextflow/src/main/groovy/nextflow/processor/TaskRun.groovy index f3926c0b60..940678b6d6 100644 --- a/modules/nextflow/src/main/groovy/nextflow/processor/TaskRun.groovy +++ b/modules/nextflow/src/main/groovy/nextflow/processor/TaskRun.groovy @@ -790,7 +790,7 @@ class TaskRun implements Cloneable { * @param body A {@code BodyDef} object instance */ void resolve(BodyDef body) { - processor.session.stubRun + (processor.session.stubRun && config.getStubBlock()) ? resolveStub(config.getStubBlock()) : resolveBody(body) } diff --git a/modules/nextflow/src/test/groovy/nextflow/processor/TaskRunTest.groovy b/modules/nextflow/src/test/groovy/nextflow/processor/TaskRunTest.groovy index 9ea25d7db8..6f1e988899 100644 --- a/modules/nextflow/src/test/groovy/nextflow/processor/TaskRunTest.groovy +++ b/modules/nextflow/src/test/groovy/nextflow/processor/TaskRunTest.groovy @@ -907,6 +907,23 @@ class TaskRunTest extends Specification { 0 * task.resolveStub(_) >> null } + def 'should resolve task body when no stub' () { + given: + def task = Spy(TaskRun) + task.processor = Mock(TaskProcessor) { + getSession()>>Mock(Session) { getStubRun() >> true} + } + task.config = Mock(TaskConfig) { getStubBlock()>> null } + 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) From 7a7e0962e03ff56eb88a35d0fc8a0a5e195a3021 Mon Sep 17 00:00:00 2001 From: Paolo Di Tommaso Date: Tue, 5 Nov 2024 14:17:09 +0100 Subject: [PATCH 2/2] Update modules/nextflow/src/main/groovy/nextflow/processor/TaskRun.groovy [ci fast] Signed-off-by: Paolo Di Tommaso --- .../nextflow/src/main/groovy/nextflow/processor/TaskRun.groovy | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) diff --git a/modules/nextflow/src/main/groovy/nextflow/processor/TaskRun.groovy b/modules/nextflow/src/main/groovy/nextflow/processor/TaskRun.groovy index 940678b6d6..38b4ba4782 100644 --- a/modules/nextflow/src/main/groovy/nextflow/processor/TaskRun.groovy +++ b/modules/nextflow/src/main/groovy/nextflow/processor/TaskRun.groovy @@ -790,7 +790,7 @@ class TaskRun implements Cloneable { * @param body A {@code BodyDef} object instance */ void resolve(BodyDef body) { - (processor.session.stubRun && config.getStubBlock()) + processor.session.stubRun && config.getStubBlock() ? resolveStub(config.getStubBlock()) : resolveBody(body) }