Fix correctness of assertion validation in new linter.

galaxyproject · Nov 25, 2024 · 2c66985 · 2c66985
1 parent 78aa6f9
commit 2c66985
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Showing 6 changed files with 1,545 additions and 14 deletions.
diff --git a/lib/galaxy/tool_util/linters/tests.py b/lib/galaxy/tool_util/linters/tests.py
@@ -11,6 +11,7 @@
 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.asserts import parse_xml_assertions
 from galaxy.util import asbool
 from ._util import is_datasource
 
@@ -150,11 +151,9 @@ def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
             # 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 = []
-                for raw_assert in asserts_raw:
-                    to_yaml_assertions.append({"that": raw_assert["tag"], **raw_assert.get("attributes", {})})
+                as_python_dicts = parse_xml_assertions(asserts_raw)
                 try:
-                    assertion_list.model_validate(to_yaml_assertions)
+                    assertion_list.model_validate(as_python_dicts)
                 except Exception as e:
                     error_str = _cleanup_pydantic_error(e)
                     lint_ctx.warn(

diff --git a/lib/galaxy/tool_util/parser/xml.py b/lib/galaxy/tool_util/parser/xml.py
@@ -746,10 +746,10 @@ def _test_elem_to_dict(test_elem, i, profile=None) -> ToolSourceTest:
         output_collections=__parse_output_collection_elems(test_elem, profile=profile),
         inputs=__parse_input_elems(test_elem, i),
         expect_num_outputs=test_elem.get("expect_num_outputs"),
-        command=__parse_assert_list_from_elem(test_elem.find("assert_command")),
-        command_version=__parse_assert_list_from_elem(test_elem.find("assert_command_version")),
-        stdout=__parse_assert_list_from_elem(test_elem.find("assert_stdout")),
-        stderr=__parse_assert_list_from_elem(test_elem.find("assert_stderr")),
+        command=parse_assert_list_from_elem(test_elem.find("assert_command")),
+        command_version=parse_assert_list_from_elem(test_elem.find("assert_command_version")),
+        stdout=parse_assert_list_from_elem(test_elem.find("assert_stdout")),
+        stderr=parse_assert_list_from_elem(test_elem.find("assert_stderr")),
         expect_exit_code=test_elem.get("expect_exit_code"),
         expect_failure=string_as_bool(test_elem.get("expect_failure", False)),
         expect_test_failure=string_as_bool(test_elem.get("expect_test_failure", False)),
@@ -783,7 +783,7 @@ def __parse_output_elem(output_elem):
 
 def __parse_command_elem(test_elem):
     assert_elem = test_elem.find("command")
-    return __parse_assert_list_from_elem(assert_elem)
+    return parse_assert_list_from_elem(assert_elem)
 
 
 def __parse_output_collection_elems(test_elem, profile=None):
@@ -918,10 +918,10 @@ def __parse_test_attributes(
 
 def __parse_assert_list(output_elem) -> AssertionList:
     assert_elem = output_elem.find("assert_contents")
-    return __parse_assert_list_from_elem(assert_elem)
+    return parse_assert_list_from_elem(assert_elem)
 
 
-def __parse_assert_list_from_elem(assert_elem) -> AssertionList:
+def parse_assert_list_from_elem(assert_elem) -> AssertionList:
     assert_list = None
 
     def convert_elem(elem):