From 9cae33ffa8bd7cdb700ede687d0ec178a6937926 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Tue, 26 Nov 2024 17:14:35 +0100
Subject: [PATCH 1/2] only match filters that are descendants or
 data/collection

otherwise action filters are also checked which results in an error
since there is not text content.
---
 lib/galaxy/tool_util/linters/output.py | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/lib/galaxy/tool_util/linters/output.py b/lib/galaxy/tool_util/linters/output.py
index e9ab7c4aaf4e..e42c797dca0b 100644
--- a/lib/galaxy/tool_util/linters/output.py
+++ b/lib/galaxy/tool_util/linters/output.py
@@ -83,7 +83,7 @@ def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
         tool_xml = getattr(tool_source, "xml_tree", None)
         if not tool_xml:
             return
-        for filter in tool_xml.findall("./outputs//filter"):
+        for filter in tool_xml.findall("./outputs/*/filter"):
             try:
                 ast.parse(filter.text, mode="eval")
             except Exception as e:

From a587336eddf9c4fc19a349adf393a4747537c4b2 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Tue, 26 Nov 2024 17:18:44 +0100
Subject: [PATCH 2/2] strip text

otherwise the parser gives an indentation error

also: we strip the text alo in the application
---
 lib/galaxy/tool_util/linters/output.py   | 2 +-
 test/unit/tool_util/test_tool_linters.py | 2 +-
 2 files changed, 2 insertions(+), 2 deletions(-)

diff --git a/lib/galaxy/tool_util/linters/output.py b/lib/galaxy/tool_util/linters/output.py
index e42c797dca0b..b1d48fd2a60d 100644
--- a/lib/galaxy/tool_util/linters/output.py
+++ b/lib/galaxy/tool_util/linters/output.py
@@ -85,7 +85,7 @@ def lint(cls, tool_source: "ToolSource", lint_ctx: "LintContext"):
             return
         for filter in tool_xml.findall("./outputs/*/filter"):
             try:
-                ast.parse(filter.text, mode="eval")
+                ast.parse(filter.text.strip(), mode="eval")
             except Exception as e:
                 lint_ctx.warn(
                     f"Filter '{filter.text}' is no valid expression: {str(e)}",
diff --git a/test/unit/tool_util/test_tool_linters.py b/test/unit/tool_util/test_tool_linters.py
index ea7f4cd8d5d5..867e85dc2ba3 100644
--- a/test/unit/tool_util/test_tool_linters.py
+++ b/test/unit/tool_util/test_tool_linters.py
@@ -656,7 +656,7 @@
     <outputs>
         <data name="another_valid_name" format="fasta" label="a label">
             <filter>an invalid condition</filter>
-            <filter>an and condition</filter>
+            <filter> an and condition </filter>
         </data>
         <collection name="yet_another_valid_name" type="list" format="fasta" label="another label">
             <filter>another invalid condition</filter>