Merge pull request #20511 from mvdbeek/fix_too_strict_validation

[24.2] Relax validation of XML test assertion parsing

Author: mvdbeek

lib/galaxy/tool_util/linters/tests.py

@@ -12,7 +12,11 @@
 
 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 @@ def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
             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

@@ -850,6 +850,23 @@
     </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)