Commit 3ed87bff authored by Matthias Bernt's avatar Matthias Bernt
Browse files

linter: allow options elements in data params 

linting of valid childs for params has been added here:
https://github.com/galaxyproject/galaxy/pull/12232

options for data params has been forgotten

in addition also checks for valid attribs and filter types
has been added to linting
parent 70b2ea42

lib/galaxy/tool_util/linters/inputs.py

+18 −1
Original line number Diff line number Diff line
@@ -108,7 +108,7 @@ PARAMETER_VALIDATOR_TYPE_COMPATIBILITY = { 
}



PARAM_TYPE_CHILD_COMBINATIONS = [

    ("./options", ["select", "drill_down"]),

    ("./options", ["data", "select", "drill_down"]),

    ("./options/option", ["drill_down"]),

    ("./column", ["data_column"]),

]
@@ -167,6 +167,23 @@ def lint_inputs(tool_xml, lint_ctx): 
                lint_ctx.warn(

                    f"Param input [{param_name}] with no format specified - 'data' format will be assumed.", node=param

                )

            options = param.findall("./options")

            if len(options) == 1:

                if len(options[0].attrib) > 0:

                    lint_ctx.error(

                        f"Data parameter [{param_name}] uses invalid attributes: {options[0].attrib}", node=param

                    )

            elif len(options) > 1:

                lint_ctx.error(f"Data parameter [{param_name}] contains multiple options elements.", node=options[1])

            # for data params only filters with key='build' of type='data_meta' are allowed

            filters = param.findall("./options/filter")

            for f in filters:

                if f.get("key") != "dbkey" or f.get("type") != "data_meta":

                    lint_ctx.error(

                        f'Data parameter [{param_name}] for filters only type="data_meta" and key="dbkey" are allowed, found type="{f.get("type")}" and key="{f.get("key")}"',

                        node=f,

                    )



        elif param_type == "select":

            # get dynamic/statically defined options

            dynamic_options = param.get("dynamic_options", None)

test/unit/tool_util/test_tool_linters.py

+51 −1
Original line number Diff line number Diff line
@@ -190,6 +190,31 @@ INPUTS_DATA_PARAM = """ 
</tool>

"""



INPUTS_DATA_PARAM_OPTIONS = """

<tool>

    <inputs>

        <param name="valid_name" type="data" format="txt">

            <options>

                <filter type="data_meta" key="dbkey"/>

            </options>

        </param>

    </inputs>

</tool>

"""



INPUTS_DATA_PARAM_INVALIDOPTIONS = """

<tool>

    <inputs>

        <param name="valid_name" type="data" format="txt">

            <options/>

            <options from_file="blah">

                <filter type="expression"/>

            </options>

        </param>

    </inputs>

</tool>

"""



INPUTS_CONDITIONAL = """

<tool>

    <inputs>
@@ -1012,6 +1037,31 @@ def test_inputs_data_param(lint_ctx): 
    assert not lint_ctx.error_messages





def test_inputs_data_param_options(lint_ctx):

    tool_source = get_xml_tool_source(INPUTS_DATA_PARAM_OPTIONS)

    run_lint(lint_ctx, inputs.lint_inputs, tool_source)

    assert not lint_ctx.valid_messages

    assert "Found 1 input parameters." in lint_ctx.info_messages

    assert len(lint_ctx.info_messages) == 1

    assert not lint_ctx.warn_messages

    assert not lint_ctx.error_messages





def test_inputs_data_param_invalidoptions(lint_ctx):

    tool_source = get_xml_tool_source(INPUTS_DATA_PARAM_INVALIDOPTIONS)

    run_lint(lint_ctx, inputs.lint_inputs, tool_source)

    assert not lint_ctx.valid_messages

    assert "Found 1 input parameters." in lint_ctx.info_messages

    assert len(lint_ctx.info_messages) == 1

    assert not lint_ctx.warn_messages

    assert "Data parameter [valid_name] contains multiple options elements." in lint_ctx.error_messages

    assert (

        'Data parameter [valid_name] for filters only type="data_meta" and key="dbkey" are allowed, found type="expression" and key="None"'

        in lint_ctx.error_messages

    )

    assert len(lint_ctx.error_messages) == 2





def test_inputs_conditional(lint_ctx):

    tool_source = get_xml_tool_source(INPUTS_CONDITIONAL)

    run_lint(lint_ctx, inputs.lint_inputs, tool_source)
@@ -1197,7 +1247,7 @@ def test_inputs_type_child_combinations(lint_ctx): 
    assert not lint_ctx.valid_messages

    assert not lint_ctx.warn_messages

    assert (

        "Parameter [text_param] './options' tags are only allowed for parameters of type ['select', 'drill_down']"

        "Parameter [text_param] './options' tags are only allowed for parameters of type ['data', 'select', 'drill_down']"

        in lint_ctx.error_messages

    )

    assert (