diff --git a/lib/galaxy/tool_util/parser/yaml.py b/lib/galaxy/tool_util/parser/yaml.py index 7ebc574c9ad..c3959984974 100644 --- a/lib/galaxy/tool_util/parser/yaml.py +++ b/lib/galaxy/tool_util/parser/yaml.py @@ -267,7 +267,7 @@ def _parse_test(i, test_dict) -> ToolSourceTest: return test_dict -def __to_test_assert_list(assertions) -> AssertionList: +def to_test_assert_list(assertions) -> AssertionList: def expand_dict_form(item): key, value = item new_value = value.copy() @@ -281,6 +281,12 @@ def __to_test_assert_list(assertions) -> AssertionList: for assertion in assertions: # TODO: not handling nested assertions correctly, # not sure these are used though. + if "that" not in assertion: + new_assertion = {} + for assertion_key, assertion_value in assertion.items(): + new_assertion["that"] = assertion_key + new_assertion.update(assertion_value) + assertion = new_assertion children = [] if "children" in assertion: children = assertion["children"] @@ -295,6 +301,9 @@ def __to_test_assert_list(assertions) -> AssertionList: return assert_list or None # XML variant is None if no assertions made +__to_test_assert_list = to_test_assert_list + + class YamlPageSource(PageSource): def __init__(self, inputs_list): self.inputs_list = inputs_list diff --git a/lib/galaxy/tool_util/xsd/galaxy.xsd b/lib/galaxy/tool_util/xsd/galaxy.xsd index 4994e5e7b7e..02d67e1c35b 100644 --- a/lib/galaxy/tool_util/xsd/galaxy.xsd +++ b/lib/galaxy/tool_util/xsd/galaxy.xsd @@ -7322,24 +7322,39 @@ and ``contains``. In addition there is ``sim_size`` which is discouraged in favo Documentation for PermissiveBoolean - - - - - - - - - - + + + + + + + + + + + + + + + + + Number of bytes allowing for suffix (k|K|M|G|P|E)i? - - - + + + + + + + + + + + diff --git a/test/unit/tool_util/test_test_parsing.py b/test/unit/tool_util/test_test_parsing.py new file mode 100644 index 00000000000..c489d9658ca --- /dev/null +++ b/test/unit/tool_util/test_test_parsing.py @@ -0,0 +1,40 @@ +import yaml + +from galaxy.tool_util.parser.yaml import to_test_assert_list + +# Legacy style +ASSERT_THAT_LIST = yaml.safe_load( + """ +- that: "has_text" + text: "Number of input reads |\t1051466" +- that: "has_text" + text: "Uniquely mapped reads number |\t871202" +""" +) +# New list of assertion style +ASSERT_LIST = yaml.safe_load( + """ +- has_text: + text: "Number of input reads |\t1051466" +- has_text: + text: "Uniquely mapped reads number |\t871202" +""" +) +# Singleton assertion +SIMPLE_ASSERT = {"has_text": {"text": "Number of input reads |\t1051466"}} + + +def test_assert_that_list_to_test_assert_list(): + to_test_assert_list(ASSERT_THAT_LIST) + + +def test_assert_list_to_test_assert_list(): + to_test_assert_list(ASSERT_LIST) + + +def test_simple_assert_to_test_assert_list(): + to_test_assert_list(SIMPLE_ASSERT) + + +def test_assert_legacy_same_as_new_list_style(): + assert to_test_assert_list(ASSERT_THAT_LIST) == to_test_assert_list(ASSERT_THAT_LIST)