Merge pull request #18787 from jmchilton/assertion_overhaul

Modelling for Test Assertions
galaxyproject · Sep 17, 2024 · 5acc518 · 5acc518
2 parents 236f1b3 + 90d682f
commit 5acc518
Show file tree

Hide file tree

Showing 18 changed files with 4,393 additions and 1,388 deletions.
diff --git a/Makefile b/Makefile
@@ -186,6 +186,9 @@ else
 	$(IN_VENV) cd client && yarn install $(YARN_INSTALL_OPTS)
 endif
 
+format-xsd:
+	xmllint --format --output galaxy-tmp.xsd lib/galaxy/tool_util/xsd/galaxy.xsd
+	mv galaxy-tmp.xsd lib/galaxy/tool_util/xsd/galaxy.xsd
 
 build-api-schema:
 	$(IN_VENV) python scripts/dump_openapi_schema.py _schema.yaml

diff --git a/doc/parse_gx_xsd.py b/doc/parse_gx_xsd.py
@@ -83,28 +83,20 @@ def _build_tag(tag, hide_attributes):
             assertions_buffer.write(_doc_or_none(assertions_tag))
             assertions_buffer.write("\n\n")
 
-            assertion_groups = assertions_tag.xpath(
-                "xs:choice/xs:group", namespaces={"xs": "http://www.w3.org/2001/XMLSchema"}
+            assertion_tag = xmlschema_doc.find("//{http://www.w3.org/2001/XMLSchema}group[@name='TestAssertion']")
+            elements = assertion_tag.findall(
+                "{http://www.w3.org/2001/XMLSchema}choice/{http://www.w3.org/2001/XMLSchema}element"
             )
-            for group in assertion_groups:
-                ref = group.attrib["ref"]
-                assertion_tag = xmlschema_doc.find("//{http://www.w3.org/2001/XMLSchema}group[@name='" + ref + "']")
-                doc = _doc_or_none(assertion_tag)
-                assertions_buffer.write(f"### {doc}\n\n")
-                elements = assertion_tag.findall(
-                    "{http://www.w3.org/2001/XMLSchema}choice/{http://www.w3.org/2001/XMLSchema}element"
-                )
-                for element in elements:
+            for element in elements:
+                doc = _doc_or_none(element)
+                if doc is None:
                     doc = _doc_or_none(element)
-                    if doc is None:
-                        doc = _doc_or_none(_type_el(element))
-                    assert doc is not None, f"Documentation for {element.attrib['name']} is empty"
-                    doc = doc.strip()
-
-                    element_el = _find_tag_el(element)
-                    element_attributes = _find_attributes(element_el)
-                    doc = _replace_attribute_list(element_el, doc, element_attributes)
-                    assertions_buffer.write(f"#### ``{element.attrib['name']}``:\n\n{doc}\n\n")
+                assert doc is not None, f"Documentation for {element.attrib['name']} is empty"
+                doc = doc.strip()
+
+                element_attributes = _find_attributes(element)
+                doc = _replace_attribute_list(element, doc, element_attributes)
+                assertions_buffer.write(f"#### ``{element.attrib['name']}``:\n\n{doc}\n\n")
             text = text.replace(line, assertions_buffer.getvalue())
     tag_help.write(text)
     if best_practices := _get_bp_link(annotation_el):