Unverified Commit a5960ee2 authored by mvdbeek's avatar mvdbeek
Browse files

Fix map over calculation for runtime inputs 

Fixes https://github.com/galaxyproject/galaxy/issues/18506
parent ce36118d

lib/galaxy/tools/parameters/wrapped.py

+30 −1
Original line number Diff line number Diff line
@@ -3,6 +3,8 @@ from typing import ( 
    Any,

    Dict,

    List,

    Sequence,

    Union,

)



from galaxy.tools.parameters.basic import (
@@ -187,6 +189,26 @@ def process_key(incoming_key: str, incoming_value: Any, d: Dict[str, Any]): 
        process_key("|".join(key_parts[1:]), incoming_value=incoming_value, d=subdict)





def nested_key_to_path(key: str) -> Sequence[Union[str, int]]:

    """

    Convert a tool state key that is separated with '|' and '_n' into path iterable.

    E.g. "cond|repeat_0|paramA" -> ["cond", "repeat", 0, "paramA"].

    Return value can be used with `boltons.iterutils.get_path`.

    """

    path: List[Union[str, int]] = []

    key_parts = key.split("|")

    if len(key_parts) == 1:

        return key_parts

    for key_part in key_parts:

        if "_" in key_part:

            input_name, _index = key_part.rsplit("_", 1)

            if _index.isdigit():

                path.extend((input_name, int(_index)))

                continue

        path.append(key_part)

    return path





def flat_to_nested_state(incoming: Dict[str, Any]):

    nested_state: Dict[str, Any] = {}

    for key, value in incoming.items():
@@ -194,4 +216,11 @@ def flat_to_nested_state(incoming: Dict[str, Any]): 
    return nested_state





__all__ = ("LegacyUnprefixedDict", "WrappedParameters", "make_dict_copy", "process_key", "flat_to_nested_state")
 
__all__ = (

    "LegacyUnprefixedDict",

    "WrappedParameters",

    "make_dict_copy",

    "process_key",

    "flat_to_nested_state",

    "nested_key_to_path",

)

lib/galaxy/workflow/run.py

+6 −0
Original line number Diff line number Diff line
@@ -10,6 +10,7 @@ from typing import ( 
    Union,

)



from boltons.iterutils import get_path

from typing_extensions import Protocol



from galaxy import model
@@ -35,6 +36,7 @@ from galaxy.schema.invocation import ( 
    WarningReason,

)

from galaxy.tools.parameters.basic import raw_to_galaxy

from galaxy.tools.parameters.wrapped import nested_key_to_path

from galaxy.util import ExecutionTimer

from galaxy.workflow import modules

from galaxy.workflow.run_request import (
@@ -444,6 +446,10 @@ class WorkflowProgress: 
                    replacement = temp

            else:

                replacement = self.replacement_for_connection(connection[0], is_data=is_data)

        elif step.state and (state_input := get_path(step.state.inputs, nested_key_to_path(prefixed_name), None)):

            # workflow submitted with step parameters populates state directly

            # via populate_module_and_state

            replacement = state_input

        else:

            for step_input in step.inputs:

                if step_input.name == prefixed_name and step_input.default_value_set:

test/unit/app/tools/test_parameter_parsing.py

+19 −1
Original line number Diff line number Diff line
@@ -3,10 +3,28 @@ from typing import ( 
    Dict,

)



from galaxy.tools.parameters.wrapped import process_key

from galaxy.tools.parameters.wrapped import (

    nested_key_to_path,

    process_key,

)

from .util import BaseParameterTestCase





def test_nested_key_to_path():

    assert nested_key_to_path("param") == ["param"]

    assert nested_key_to_path("param_x") == ["param_x"]

    assert nested_key_to_path("cond|param_x") == ["cond", "param_x"]

    assert nested_key_to_path("param_") == ["param_"]

    assert nested_key_to_path("cond|param_") == ["cond", "param_"]

    assert nested_key_to_path("repeat_1|inner_repeat_1|data_table_column_value") == [

        "repeat",

        1,

        "inner_repeat",

        1,

        "data_table_column_value",

    ]





class TestProcessKey:

    def test_process_key(self):

        nested_dict: Dict[str, Any] = {}