From 8b0c597bccf01d0000612f9cc55ab005f79f1c01 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Mon, 24 Oct 2022 14:59:33 +0200
Subject: [PATCH 1/2] Add test for ignored comments

---
 test/unit/tool_util/test_tool_linters.py | 29 ++++++++++++++++++++++++
 1 file changed, 29 insertions(+)

diff --git a/test/unit/tool_util/test_tool_linters.py b/test/unit/tool_util/test_tool_linters.py
index a02d5351566..7923fc76215 100644
--- a/test/unit/tool_util/test_tool_linters.py
+++ b/test/unit/tool_util/test_tool_linters.py
@@ -5,6 +5,7 @@ import pytest
 
 from galaxy.tool_util.lint import (
     lint_tool_source_with,
+    lint_xml_with,
     LintContext,
     XMLLintMessageLine,
     XMLLintMessageXPath,
@@ -22,6 +23,7 @@ from galaxy.tool_util.linters import (
 )
 from galaxy.tool_util.loader_directory import load_tool_sources_from_path
 from galaxy.tool_util.parser.xml import XmlToolSource
+from galaxy.util import parse_xml
 from galaxy.util.xml_macros import load_with_references
 
 # TODO tests tool xml for general linter
@@ -755,6 +757,17 @@ XML_ORDER = """
 </tool>
 """
 
+TOOL_WITH_COMMENTS = """
+<tool>
+    <stdio>
+    <!-- This is a comment -->
+    </stdio>
+    <outputs>
+    <!-- This is a comment -->
+    </outputs>
+</tool>
+"""
+
 
 @pytest.fixture()
 def lint_ctx():
@@ -774,6 +787,15 @@ def get_xml_tool_source(xml_string):
         return load_with_references(tool_path)[0]
 
 
+def get_tool_xml_exact(xml_string):
+    """Returns the tool XML as it is, without stripping comments or anything else."""
+    with tempfile.NamedTemporaryFile(mode="w", suffix="tool.xml") as tmp:
+        tmp.write(xml_string)
+        tmp.flush()
+        tool_path = tmp.name
+        return parse_xml(tool_path, strip_whitespace=False, remove_comments=False)
+
+
 def failed_assert_print(lint_ctx):
     return (
         f"Valid: {lint_ctx.valid_messages}\n"
@@ -1716,3 +1738,10 @@ def test_linting_cwl_tool(lint_ctx):
     assert len(lint_ctx.valid_messages) == 4
     assert len(lint_ctx.warn_messages) == 2
     assert not lint_ctx.error_messages
+
+
+def test_xml_comments_are_ignored(lint_ctx: LintContext):
+    tool_xml = get_tool_xml_exact(TOOL_WITH_COMMENTS)
+    lint_xml_with(lint_ctx, tool_xml)
+    for lint_message in lint_ctx.message_list:
+        assert "Comment" not in lint_message.message

From defb32047f3da6236146c0793411750cbc72a5a1 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Mon, 24 Oct 2022 15:01:43 +0200
Subject: [PATCH 2/2] Fix skip XML comments when linting

---
 lib/galaxy/tool_util/linters/outputs.py | 7 ++++++-
 lib/galaxy/tool_util/linters/stdio.py   | 3 +++
 2 files changed, 9 insertions(+), 1 deletion(-)

diff --git a/lib/galaxy/tool_util/linters/outputs.py b/lib/galaxy/tool_util/linters/outputs.py
index 87bacb3c77a..7d244d7a690 100644
--- a/lib/galaxy/tool_util/linters/outputs.py
+++ b/lib/galaxy/tool_util/linters/outputs.py
@@ -1,5 +1,8 @@
 """This module contains a linting functions for tool outputs."""
-from galaxy.util import string_as_bool
+from galaxy.util import (
+    etree,
+    string_as_bool,
+)
 from ._util import is_valid_cheetah_placeholder
 from ..parser.output_collection_def import NAMED_PATTERNS
 
@@ -20,6 +23,8 @@ def lint_output(tool_xml, lint_ctx):
     labels = set()
     names = set()
     for output in list(outputs[0]):
+        if output.tag is etree.Comment:
+            continue
         if output.tag not in ["data", "collection"]:
             lint_ctx.warn(f"Unknown element found in outputs [{output.tag}]", node=output)
             continue
diff --git a/lib/galaxy/tool_util/linters/stdio.py b/lib/galaxy/tool_util/linters/stdio.py
index de769e824ed..981882bbde3 100644
--- a/lib/galaxy/tool_util/linters/stdio.py
+++ b/lib/galaxy/tool_util/linters/stdio.py
@@ -1,6 +1,7 @@
 """This module contains a linting functions for tool error detection."""
 import re
 
+from galaxy.util import etree
 from .command import get_command
 
 
@@ -37,6 +38,8 @@ def lint_stdio(tool_source, lint_ctx):
 
     stdio = stdios[0]
     for child in list(stdio):
+        if child.tag is etree.Comment:
+            continue
         if child.tag == "regex":
             _lint_regex(tool_xml, child, lint_ctx)
         elif child.tag == "exit_code":