From 6cbb4b913bd1a5386f3ebcfc946285987c005226 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Sun, 26 Nov 2023 14:11:05 +0100
Subject: [PATCH] make xml_order a Linter

---
 lib/galaxy/tool_util/linters/xml_order.py | 41 ++++++++++++++---------
 test/unit/tool_util/test_tool_linters.py  | 10 +++---
 2 files changed, 29 insertions(+), 22 deletions(-)

diff --git a/lib/galaxy/tool_util/linters/xml_order.py b/lib/galaxy/tool_util/linters/xml_order.py
index 7fb2bd261331..82d17f4e5ac7 100644
--- a/lib/galaxy/tool_util/linters/xml_order.py
+++ b/lib/galaxy/tool_util/linters/xml_order.py
@@ -1,8 +1,15 @@
-"""This module contains a linting functions for tool XML block order.
+"""This module contains a linter for tool XML block order.
 
 For more information on the IUC standard for XML block order see -
 https://github.com/galaxy-iuc/standards.
 """
+from typing import TYPE_CHECKING
+
+from galaxy.tool_util.lint import Linter
+
+if TYPE_CHECKING:
+    from galaxy.tool_util.lint import LintContext
+    from galaxy.tool_util.parser.interface import ToolSource
 
 # https://github.com/galaxy-iuc/standards
 # https://github.com/galaxy-iuc/standards/pull/7/files
@@ -43,21 +50,25 @@
 ]
 
 
-# Ensure the XML blocks appear in the correct order prescribed
-# by the tool author best practices.
-def lint_xml_order(tool_xml, lint_ctx):
-    tool_root = tool_xml.getroot()
+class XMLOrder(Linter):
+    @classmethod
+    def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
+        tool_xml = getattr(tool_source, "xml_tree", None)
+        if not tool_xml:
+            return
+        tool_root = tool_xml.getroot()
 
-    if tool_root.attrib.get("tool_type", "") == "data_source":
-        tag_ordering = DATASOURCE_TAG_ORDER
-    else:
-        tag_ordering = TAG_ORDER
+        if tool_root.attrib.get("tool_type", "") == "data_source":
+            tag_ordering = DATASOURCE_TAG_ORDER
+        else:
+            tag_ordering = TAG_ORDER
 
-    last_tag = None
-    last_key = None
-    for elem in tool_root:
-        tag = elem.tag
-        if tag in tag_ordering:
+        last_tag = None
+        last_key = None
+        for elem in tool_root:
+            tag = elem.tag
+            if tag not in tag_ordering:
+                continue
             key = tag_ordering.index(tag)
             if last_key:
                 if last_key > key:
@@ -66,5 +77,3 @@ def lint_xml_order(tool_xml, lint_ctx):
                     )
             last_tag = tag
             last_key = key
-        else:
-            lint_ctx.info(f"Unknown tag [{tag}] encountered, this may result in a warning in the future.", node=elem)
diff --git a/test/unit/tool_util/test_tool_linters.py b/test/unit/tool_util/test_tool_linters.py
index 5026a5a63a39..3df95db07f90 100644
--- a/test/unit/tool_util/test_tool_linters.py
+++ b/test/unit/tool_util/test_tool_linters.py
@@ -1778,13 +1778,11 @@ def test_tests_compare_attrib_incompatibility(lint_ctx):
 
 
 def test_xml_order(lint_ctx):
-    tool_xml_tree = get_xml_tree(XML_ORDER)
-    run_lint_module(lint_ctx, xml_order, tool_xml_tree)
-    assert "Unknown tag [wrong_tag] encountered, this may result in a warning in the future." in lint_ctx.info_messages
-    assert "Best practice violation [stdio] elements should come before [command]" in lint_ctx.warn_messages
-    assert len(lint_ctx.info_messages) == 1
+    tool_source = get_xml_tool_source(XML_ORDER)
+    run_lint_module(lint_ctx, xml_order, tool_source)
+    assert lint_ctx.warn_messages == ["Best practice violation [stdio] elements should come before [command]"]
+    assert not lint_ctx.info_messages
     assert not lint_ctx.valid_messages
-    assert len(lint_ctx.warn_messages) == 1
     assert not lint_ctx.error_messages