Unverified Commit ca1d2f57 authored by Marius van den Beek's avatar Marius van den Beek Committed by GitHub
Browse files

Merge pull request #14572 from bernt-matthias/topic/lint-data-options 

[22.05] linter: allow options elements in data params
parents 7c8d732e 327e4221

lib/galaxy/tool_util/linters/inputs.py

+32 −1
Original line number Diff line number Diff line
@@ -109,7 +109,7 @@ PARAMETER_VALIDATOR_TYPE_COMPATIBILITY = { 
}



PARAM_TYPE_CHILD_COMBINATIONS = [

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

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

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

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

]
@@ -168,6 +168,37 @@ 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")

            has_options_filter_attribute = False

            if len(options) == 1:

                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")}"',

                            node=f,

                        )



        elif param_type == "select":

            # get dynamic/statically defined options

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

lib/galaxy/tool_util/xsd/galaxy.xsd

+8 −5
Original line number Diff line number Diff line
@@ -3968,14 +3968,17 @@ dataset for the contained input of the type specified using the ``type`` tag. 
  <xs:complexType name="ParamOptions">

    <xs:annotation>

      <xs:documentation xml:lang="en"><![CDATA[



See [/tools/extract/liftOver_wrapper.xml](https://github.com/galaxyproject/galaxy/blob/master/tools/extract/liftOver_wrapper.xml)

for an example of how to use this tag set. This tag set is optionally contained

within the ``<param>`` tag when the ``type`` attribute value is ``select`` or

``data`` and used to dynamically generated lists of options. This tag set

dynamically creates a list of options whose values can be

obtained from a predefined file stored locally or a dataset selected from the

current history.

``data`` and used to dynamically generated lists of options.



For data parameters this tag can be used to restrict possible input datasets to datasets that match the ``dbkey`` of another data input by including a ``data_meta`` filter. See for

instance here: [/tools/maf/interval2maf.xml](https://github.com/galaxyproject/galaxy/blob/master/tools/maf/interval2maf.xml)



For select parameters this tag set dynamically creates a list of options whose

values can be obtained from a predefined file stored locally or a dataset

selected from the current history.



There are at least five basic ways to use this tag - four of these correspond to

a ``from_XXX`` attribute on the ``options`` directive and the other is to

test/unit/tool_util/test_tool_linters.py

+74 −1
Original line number Diff line number Diff line
@@ -192,6 +192,43 @@ 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" 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>

</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>
@@ -1034,6 +1071,42 @@ 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_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_invalid_options(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] 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) == 3





def test_inputs_conditional(lint_ctx):

    tool_source = get_xml_tool_source(INPUTS_CONDITIONAL)

    run_lint(lint_ctx, inputs.lint_inputs, tool_source)
@@ -1219,7 +1292,7 @@ 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 (