Unverified Commit 53dec0c5 authored by Marius van den Beek's avatar Marius van den Beek Committed by GitHub
Browse files

Merge pull request #19790 from mvdbeek/fix_converter_linting 

[24.2] Fix parameter model constructions with leading underscores, fixes converter linting
parents bd75278e 773301a6

.github/workflows/converter_tests.yaml

+1 −1
Original line number Diff line number Diff line
@@ -60,7 +60,7 @@ jobs: 
      - name: Lint converters

        run: |

          mapfile -t TOOL_ARRAY < tool_list.txt

          planemo lint --skip citations,stdio,help --report_level warn "${TOOL_ARRAY[@]}"

          planemo lint --skip CitationsMissing,HelpEmpty,HelpMissing --report_level warn "${TOOL_ARRAY[@]}"

      - name: Run tests

        run: |

          mapfile -t TOOL_ARRAY < tool_list.txt

lib/galaxy/datatypes/converters/interval_to_tabix_converter.xml

+9 −3
Original line number Diff line number Diff line
@@ -41,6 +41,7 @@ 
    <tests>

        <test>

            <param name="input1" ftype="bed" value="droPer1.bed"/>

            <param name="bgzip" ftype="bgzip" value="droPer1.bed.gz"/>

            <output name="output1" ftype="tabix">

                <assert_contents>

                    <has_size value="133"/>
@@ -55,6 +56,7 @@ 
        </test>

        <test>

            <param name="input1" ftype="encodepeak" value="encode.broad.peak"/>

            <param name="bgzip" ftype="bgzip" value="encode.broad.peak.gz"/>

            <output name="output1" ftype="tabix">

                <assert_contents>

                    <has_size value="110" delta="10"/>
@@ -69,6 +71,7 @@ 
        </test>

        <test>

            <param name="input1" ftype="gff" value="gff_filter_by_feature_count_out2.gff"/>

            <param name="bgzip" ftype="bgzip" value="gff_filter_by_feature_count_out2.gff.gz"/>

            <output name="output1" ftype="tabix">

                <assert_contents>

                    <has_size value="120"/>
@@ -83,6 +86,7 @@ 
        </test>

        <test>

            <param name="input1" ftype="interval" value="2.interval"/>

            <param name="bgzip" ftype="bgzip" value="2.interval.gz"/>

            <output name="output1" ftype="tabix">

                <assert_contents>

                    <has_size value="247"/>
@@ -97,6 +101,7 @@ 
        </test>

        <test>

            <param name="input1" ftype="vcf" value="vcf_to_maf_in.vcf"/>

            <param name="bgzip" ftype="bgzip" value="vcf_to_maf_in.vcf.gz"/>

            <output name="output1" ftype="tabix">

                <assert_contents>

                    <has_size value="143"/>
@@ -111,6 +116,7 @@ 
        </test>

        <test>

            <param name="input1" ftype="gtf" value="cufflinks_out1.gtf"/>

            <param name="bgzip" ftype="bgzip" value="cufflinks_out1.gtf.gz"/>

            <output name="output1" ftype="tabix">

                <assert_contents>

                    <has_size value="125"/>

lib/galaxy/tool_util/parameters/models.py

+9 −3
Original line number Diff line number Diff line
@@ -145,10 +145,16 @@ class ParamModel(Protocol): 
        ...





def safe_field_name(name: str) -> str:

    if name.startswith("_"):

        return f"X{name}"

    return name





def dynamic_model_information_from_py_type(

    param_model: ParamModel, py_type: Type, requires_value: Optional[bool] = None, validators=None

):

    name = param_model.name

    name = safe_field_name(param_model.name)

    if requires_value is None:

        requires_value = param_model.request_requires_value

    initialize = ... if requires_value else None
@@ -159,7 +165,7 @@ def dynamic_model_information_from_py_type( 


    return DynamicModelInformation(

        name,

        (py_type, initialize),

        (py_type, Field(initialize, alias=param_model.name if param_model.name != name else None)),

        validators,

    )
@@ -1520,8 +1526,8 @@ def create_field_model( 


    for input_model in tool_parameter_models:

        input_model = to_simple_model(input_model)

        input_name = input_model.name

        pydantic_request_template = input_model.pydantic_template(state_representation)

        input_name = pydantic_request_template.name

        kwd[input_name] = pydantic_request_template.definition

        input_validators = pydantic_request_template.validators

        for validator_name, validator_callable in input_validators.items():