Unverified Commit 81a17055 authored by John Chilton's avatar John Chilton Committed by GitHub
Browse files

Merge pull request #16584 from mvdbeek/when_expression_repeat 

[23.0] Fix conditional step evaluation with datasets in repeats
parents b44d8e2b c001ce0d

lib/galaxy/workflow/modules.py

+69 −63
Original line number Diff line number Diff line
@@ -122,22 +122,7 @@ class ConditionalStepWhen(BooleanToolParameter): 
    pass





def evaluate_value_from_expressions(progress, step, execution_state, extra_step_state):

    when_expression = step.when_expression

    value_from_expressions = {}



    if execution_state:

        for key in execution_state.inputs.keys():

            step_input = step.inputs_by_name.get(key)

            if step_input and step_input.value_from is not None:

                value_from_expressions[key] = step_input.value_from



    if not value_from_expressions and when_expression is None:

        return {}



    hda_references = []



    def to_cwl(value):

def to_cwl(value, hda_references, step):

    element_identifier = None

    if isinstance(value, model.DatasetCollectionElement) and value.hda:

        element_identifier = value.element_identifier
@@ -171,17 +156,22 @@ def evaluate_value_from_expressions(progress, step, execution_state, extra_step_ 
    elif hasattr(value, "collection"):

        collection = value.collection

        if collection.collection_type == "list":

                return [to_cwl(dce) for dce in collection.dataset_elements]

            return [to_cwl(dce, hda_references=hda_references, step=step) for dce in collection.dataset_elements]

        else:

            # Could be record or nested lists

            rval = {}

            for element in collection.elements:

                    rval[element.element_identifier] = to_cwl(element.element_object)

                rval[element.element_identifier] = to_cwl(

                    element.element_object, hda_references=hda_references, step=step

                )

            return rval

    elif isinstance(value, list):

        return [to_cwl(v, hda_references=hda_references, step=step) for v in value]

    else:

        return value



    def from_cwl(value):



def from_cwl(value, hda_references, progress):

    # TODO: turn actual files into HDAs here ... somehow I suppose. Things with

    # file:// locations for instance.

    if isinstance(value, dict) and "class" in value and "location" in value:
@@ -196,12 +186,28 @@ def evaluate_value_from_expressions(progress, step, execution_state, extra_step_ 
    else:

        return value





def evaluate_value_from_expressions(progress, step, execution_state, extra_step_state):

    when_expression = step.when_expression

    value_from_expressions = {}



    if execution_state:

        for key in execution_state.inputs.keys():

            step_input = step.inputs_by_name.get(key)

            if step_input and step_input.value_from is not None:

                value_from_expressions[key] = step_input.value_from



    if not value_from_expressions and when_expression is None:

        return {}



    hda_references: List[model.HistoryDatasetAssociation] = []



    step_state = {}

    for key, value in extra_step_state.items():

        step_state[key] = to_cwl(value)

        step_state[key] = to_cwl(value, hda_references=hda_references, step=step)

    if execution_state:

        for key, value in execution_state.inputs.items():

            step_state[key] = to_cwl(value)

            step_state[key] = to_cwl(value, hda_references=hda_references, step=step)



    if when_expression is not None:

        if when_expression == "${inputs.when}":
@@ -229,7 +235,7 @@ def evaluate_value_from_expressions(progress, step, execution_state, extra_step_ 
                    reason=FailureReason.expression_evaluation_failed, workflow_step_id=step.id

                )

            )

        when_value = from_cwl(as_cwl_value)

        when_value = from_cwl(as_cwl_value, hda_references=hda_references, progress=progress)

        if not isinstance(when_value, bool):

            raise FailWorkflowEvaluation(

                InvocationFailureWhenNotBoolean(

test/unit/workflows/test_modules.py

+12 −0
Original line number Diff line number Diff line
@@ -249,6 +249,18 @@ def test_subworkflow_new_outputs(): 
    assert output2["name"] == "4:out_file1", output2["name"]





def test_to_cwl():

    hda = model.HistoryDatasetAssociation(create_dataset=True, flush=False)

    hda.dataset.state = model.Dataset.states.OK

    hdas = [hda]

    hda_references = []

    result = modules.to_cwl(hdas, hda_references, model.WorkflowStep())

    assert isinstance(result, list)

    assert len(result) == 1

    assert result[0]["class"] == "File"

    assert hda_references == hdas





class MapOverTestCase(NamedTuple):

    data_input: str

    step_input_def: Union[str, List[str]]