Unverified Commit 044442bd authored by Marius van den Beek's avatar Marius van den Beek Committed by GitHub
Browse files

Merge pull request #20511 from mvdbeek/fix_too_strict_validation 

[24.2] Relax validation of XML test assertion parsing
parents dcd4cdca 9523afb1

lib/galaxy/tool_util/linters/tests.py

+10 −4
Original line number Diff line number Diff line
@@ -12,7 +12,11 @@ from packaging.version import Version 


from galaxy.tool_util.lint import Linter

from galaxy.tool_util.parameters import validate_test_cases_for_tool_source

from galaxy.tool_util.verify.assertion_models import assertion_list

from galaxy.tool_util.verify.assertion_models import (

    assertion_list,

    relaxed_assertion_list,

)

from galaxy.tool_util.verify.parse import tag_structure_to_that_structure

from galaxy.util import asbool

from ._util import is_datasource
@@ -148,15 +152,17 @@ class TestsAssertionValidation(Linter): 
            lint_ctx.warn("Failed to parse test dictionaries from tool - cannot lint assertions")

            return

        assert "tests" in raw_tests_dict

        # This really only allows coercion from strings, the values themselves will still be validated

        assert_list_model = relaxed_assertion_list if tool_source.language == "xml" else assertion_list

        for test_idx, test in enumerate(raw_tests_dict["tests"], start=1):

            # TODO: validate command, command_version, element tests. What about children?

            for output in test["outputs"]:

                asserts_raw = output.get("attributes", {}).get("assert_list") or []

                to_yaml_assertions = []

                processed_assertions = []

                for raw_assert in asserts_raw:

                    to_yaml_assertions.append({"that": raw_assert["tag"], **raw_assert.get("attributes", {})})

                    processed_assertions.append(tag_structure_to_that_structure(raw_assert))

                try:

                    assertion_list.model_validate(to_yaml_assertions)

                    assert_list_model.model_validate(processed_assertions)

                except Exception as e:

                    error_str = _cleanup_pydantic_error(e)

                    lint_ctx.warn(

test/unit/tool_util/test_tool_linters.py

+23 −0
Original line number Diff line number Diff line
@@ -850,6 +850,23 @@ VALID_CENTER_OF_MASS = """ 
    </tests>

</tool>

"""

ASSERTS_STRING_COERCION = """

<tool id="id" name="name">

    <outputs>

        <data name="data_name" format="ome.tiff"/>

    </outputs>

    <tests>

        <test>

            <output name="data_name">

               <assert_contents>

                    <!-- channels is defined as an integer, so coercion from string must be applied on validation -->

                    <has_image_channels channels="3" />

                </assert_contents>

            </output>

        </test>

    </tests>

</tool>

"""

TESTS_VALID = """

<tool id="id" name="name">

    <outputs>
@@ -1945,6 +1962,12 @@ def test_tests_asserts(lint_ctx): 
    assert len(lint_ctx.error_messages) == 9





def test_tests_asserts_string_coercion(lint_ctx):

    tool_source = get_xml_tool_source(ASSERTS_STRING_COERCION)

    run_lint_module(lint_ctx, tests, tool_source)

    assert len(lint_ctx.warn_messages) == 0, lint_ctx.warn_messages





def test_tests_assertion_models_valid(lint_ctx):

    tool_source = get_xml_tool_source(VALID_CENTER_OF_MASS)

    run_lint_module(lint_ctx, tests, tool_source)