Commit 1cb1ac3d authored by Matthias Bernt's avatar Matthias Bernt
Browse files

adapt linter to check also for options_filter_attribute

parent 6ebfa1ca

lib/galaxy/tool_util/linters/inputs.py

+20 −6
Original line number Diff line number Diff line
@@ -168,16 +168,30 @@ def lint_inputs(tool_xml, lint_ctx): 
                    f"Param input [{param_name}] with no format specified - 'data' format will be assumed.", node=param

                )

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

            has_options_filter_attribute = False

            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

                    )

                for oa in options[0].attrib:

                    if oa == "options_filter_attribute":

                        has_options_filter_attribute = True

                    else:

                        lint_ctx.error(f"Data parameter [{param_name}] uses invalid attribute: {oa}", 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 not f.get("ref"):

                    lint_ctx.error(

                        f"Data parameter [{param_name}] filter needs to define a ref attribute",

                        node=f,

                    )

                if has_options_filter_attribute:

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

                        lint_ctx.error(

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

                            node=f,

                        )

                else:

                    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")}"',

test/unit/tool_util/test_tool_linters.py

+25 −2
Original line number Diff line number Diff line
@@ -195,7 +195,19 @@ INPUTS_DATA_PARAM_OPTIONS = """ 
    <inputs>

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

            <options>

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

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

            </options>

        </param>

    </inputs>

</tool>

"""



INPUTS_DATA_PARAM_OPTIONS_FILTER_ATTRIBUTE = """

<tool>

    <inputs>

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

            <options options_filter_attribute="metadata.foo">

                <filter type="data_meta" key="foo" ref="input"/>

            </options>

        </param>

    </inputs>
@@ -1047,6 +1059,16 @@ def test_inputs_data_param_options(lint_ctx): 
    assert not lint_ctx.error_messages





def test_inputs_data_param_options_filter_attribute(lint_ctx):

    tool_source = get_xml_tool_source(INPUTS_DATA_PARAM_OPTIONS_FILTER_ATTRIBUTE)

    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)
@@ -1055,11 +1077,12 @@ def test_inputs_data_param_invalidoptions(lint_ctx): 
    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] filter needs to define a ref attribute" 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

    assert len(lint_ctx.error_messages) == 3





def test_inputs_conditional(lint_ctx):