From cbd10c098633458abcd0ba9c46f9df2712992ad3 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Mon, 21 Mar 2022 13:33:08 +0100
Subject: [PATCH] linter: allow setting output format with actions

---
 lib/galaxy/tool_util/linters/outputs.py  |  2 ++
 test/unit/tool_util/test_tool_linters.py | 28 ++++++++++++++++++++++++
 2 files changed, 30 insertions(+)

diff --git a/lib/galaxy/tool_util/linters/outputs.py b/lib/galaxy/tool_util/linters/outputs.py
index 2e8cd878e1a..f537f342043 100644
--- a/lib/galaxy/tool_util/linters/outputs.py
+++ b/lib/galaxy/tool_util/linters/outputs.py
@@ -63,6 +63,8 @@ def __check_format(node, lint_ctx, allow_ext=False):
         lint_ctx.warn(f"Tool {node.tag} output '{node.attrib.get('name', 'with missing name')}' should use either format_source or format/ext", node=node)
     if "format_source" in node.attrib:
         return True
+    if node.find(".//action[@type='format']") is not None:
+        return True
     # if allowed (e.g. for discover_datasets), ext takes precedence over format
     fmt = None
     if allow_ext:
diff --git a/test/unit/tool_util/test_tool_linters.py b/test/unit/tool_util/test_tool_linters.py
index e9ddcd1d4a5..bc6aeea0a42 100644
--- a/test/unit/tool_util/test_tool_linters.py
+++ b/test/unit/tool_util/test_tool_linters.py
@@ -442,6 +442,25 @@ OUTPUTS_COLLECTION_FORMAT_SOURCE = """
 </tool>
 """
 
+# check that setting format with actions is supported
+OUTPUTS_FORMAT_ACTION = """
+<tool>
+    <outputs>
+        <data name="output">
+            <actions>
+                <conditional name="library.type">
+                    <when value="paired">
+                        <action type="format">
+                            <option type="from_param" name="library.input_2" param_attribute="ext" />
+                        </action>
+                    </when>
+                </conditional>
+            </actions>
+        </data>
+    </outputs>
+</tool>
+"""
+
 # check that linter does not complain about missing format if from_tool_provided_metadata is used
 OUTPUTS_DISCOVER_TOOL_PROVIDED_METADATA = """
 <tool>
@@ -1102,6 +1121,15 @@ def test_outputs_collection_format_source(lint_ctx):
     assert not lint_ctx.error_messages
 
 
+def test_outputs_format_action(lint_ctx):
+    tool_source = get_xml_tool_source(OUTPUTS_FORMAT_ACTION)
+    run_lint(lint_ctx, outputs.lint_output, tool_source)
+    assert len(lint_ctx.info_messages) == 1
+    assert not lint_ctx.valid_messages
+    assert not lint_ctx.warn_messages
+    assert not lint_ctx.error_messages
+
+
 def test_outputs_discover_tool_provided_metadata(lint_ctx):
     tool_source = get_xml_tool_source(OUTPUTS_DISCOVER_TOOL_PROVIDED_METADATA)
     run_lint(lint_ctx, outputs.lint_output, tool_source)