From 68a8608e161858612fe4c45a8192f67bcbb2d40c Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Wed, 6 Dec 2023 12:54:29 +0100
Subject: [PATCH 1/2] Allow parsing lists of simple test assertions

---
 lib/galaxy/tool_util/parser/yaml.py      | 11 ++++++-
 test/unit/tool_util/test_test_parsing.py | 40 ++++++++++++++++++++++++
 2 files changed, 50 insertions(+), 1 deletion(-)
 create mode 100644 test/unit/tool_util/test_test_parsing.py

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/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)

From 0f76e6ada76ca04e1b178bc32d7184875f2e0506 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Mon, 4 Dec 2023 13:30:15 +0100
Subject: [PATCH 2/2] Add int to Bytes, bool to PermissiveBoolean schema

---
 lib/galaxy/tool_util/xsd/galaxy.xsd | 41 ++++++++++++++++++++---------
 1 file changed, 28 insertions(+), 13 deletions(-)

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
     <xs:annotation>
       <xs:documentation xml:lang="en">Documentation for PermissiveBoolean</xs:documentation>
     </xs:annotation>
-    <xs:restriction base="xs:string">
-      <xs:enumeration value="0"/>
-      <xs:enumeration value="1"/>
-      <xs:enumeration value="true"/>
-      <xs:enumeration value="false"/>
-      <xs:enumeration value="True"/>
-      <xs:enumeration value="False"/>
-      <xs:enumeration value="yes"/>
-      <xs:enumeration value="no"/>
-    </xs:restriction>
+    <xs:union>
+      <xs:simpleType>
+        <xs:restriction base="xs:boolean"/>
+      </xs:simpleType>
+      <xs:simpleType>
+        <xs:restriction base="xs:string">
+          <xs:enumeration value="0"/>
+          <xs:enumeration value="1"/>
+          <xs:enumeration value="true"/>
+          <xs:enumeration value="false"/>
+          <xs:enumeration value="True"/>
+          <xs:enumeration value="False"/>
+          <xs:enumeration value="yes"/>
+          <xs:enumeration value="no"/>
+        </xs:restriction>
+      </xs:simpleType>
+    </xs:union>
   </xs:simpleType>
   <xs:simpleType name="Bytes">
     <xs:annotation>
       <xs:documentation xml:lang="en">Number of bytes allowing for suffix (k|K|M|G|P|E)i? </xs:documentation>
     </xs:annotation>
-    <xs:restriction base="xs:string">
-      <xs:pattern value="(0|[1-9][0-9]*)([kKMGTPE]i?)?"></xs:pattern>
-    </xs:restriction>
+    <xs:union>
+       <xs:simpleType>
+         <xs:restriction base="xs:integer">
+         </xs:restriction>
+       </xs:simpleType>
+       <xs:simpleType>
+         <xs:restriction base="xs:string">
+          <xs:pattern value="(0|[1-9][0-9]*)([kKMGTPE]i?)?"></xs:pattern>
+         </xs:restriction>
+       </xs:simpleType>
+    </xs:union>
   </xs:simpleType>
   <xs:complexType name="EdamTopics">
     <xs:annotation>