Unverified Commit f4d52d7d authored by Nicola Soranzo's avatar Nicola Soranzo Committed by GitHub
Browse files

Merge pull request #16641 from mvdbeek/nested_subworkflow_skip 

[23.1] Fix nested conditional workflow steps
parents 47628efd 0df12cb9

lib/galaxy/workflow/modules.py

+11 −8
Original line number Diff line number Diff line
@@ -770,12 +770,15 @@ class SubWorkflowModule(WorkflowModule): 
                assert len(progress.when_values) == 1, "Got more than 1 when value, this shouldn't be possible"

            iteration_elements_iter = [(None, progress.when_values[0] if progress.when_values else None)]



        when_values = []

        if step.when_expression:

        when_values: List[Union[bool, None]] = []

        for iteration_elements, when_value in iteration_elements_iter:

                if when_value is False:

            if when_value is False or not step.when_expression:

                # We're skipping this step (when==False) or we keep

                # the current when_value if there is no explicit when_expression on this step.

                when_values.append(when_value)

                    continue

            else:

                # Got a conditional step and we could potentially run it,

                # so we have to build the step state and evaluate the expression

                extra_step_state = {}

                for step_input in step.inputs:

                    step_input_name = step_input.name

lib/galaxy_test/api/test_workflows.py

+78 −0
Original line number Diff line number Diff line
@@ -2157,6 +2157,84 @@ should_run: 
                if step["workflow_step_label"] == "a_tool_step":

                    assert sum(1 for j in step["jobs"] if j["state"] == "skipped") == 1



    def test_run_nested_conditional_workflow_steps(self):

        with self.dataset_populator.test_history() as history_id:

            summary = self._run_workflow(

                """

class: GalaxyWorkflow

inputs:

  dataset:

    type: data

  when:

    type: boolean

outputs:

  output:

    outputSource: outer_subworkflow/output

steps:

- label: outer_subworkflow

  when: $(inputs.when)

  in:

    dataset:

      source: dataset

    when:

      source: when

  run:

    class: GalaxyWorkflow

    label: subworkflow cat1

    inputs:

      dataset:

        type: data

    outputs:

      output:

        outputSource: cat1_workflow/output

    steps:

    - label: cat1_workflow

      in:

        dataset:

          source: dataset

      run:

        class: GalaxyWorkflow

        label: cat1

        inputs:

          dataset:

            type: data

        outputs:

          output:

            outputSource: cat1/out_file1

        steps:

        - tool_id: cat1

          label: cat1

          in:

            input1:

              source: dataset

""",

                test_data="""

dataset:

  value: 1.bed

  type: File

when:

  value: false

  type: raw

""",

                history_id=history_id,

                wait=True,

                assert_ok=True,

            )

            invocation_details = self.workflow_populator.get_invocation(summary.invocation_id, step_details=True)

            subworkflow_invocation_id = invocation_details["steps"][-1]["subworkflow_invocation_id"]

            self.workflow_populator.wait_for_invocation_and_jobs(

                history_id=history_id, workflow_id="whatever", invocation_id=subworkflow_invocation_id

            )

            invocation_details = self.workflow_populator.get_invocation(subworkflow_invocation_id, step_details=True)

            subworkflow_invocation_id = invocation_details["steps"][-1]["subworkflow_invocation_id"]

            self.workflow_populator.wait_for_invocation_and_jobs(

                history_id=history_id, workflow_id="whatever", invocation_id=subworkflow_invocation_id

            )

            invocation_details = self.workflow_populator.get_invocation(subworkflow_invocation_id, step_details=True)

            for step in invocation_details["steps"]:

                if step["workflow_step_label"] == "cat1":

                    assert sum(1 for j in step["jobs"] if j["state"] == "skipped") == 1



    def test_run_workflow_conditional_step_map_over_expression_tool(self):

        with self.dataset_populator.test_history() as history_id:

            summary = self._run_workflow(