From 1cb1ac3dfd4649a45071c10882fd7f2fcb6e8597 Mon Sep 17 00:00:00 2001
From: Matthias Bernt <m.bernt@ufz.de>
Date: Mon, 19 Sep 2022 10:24:49 +0200
Subject: [PATCH] adapt linter to check also for options_filter_attribute

---
 lib/galaxy/tool_util/linters/inputs.py   | 26 +++++++++++++++++------
 test/unit/tool_util/test_tool_linters.py | 27 ++++++++++++++++++++++--
 2 files changed, 45 insertions(+), 8 deletions(-)

diff --git a/lib/galaxy/tool_util/linters/inputs.py b/lib/galaxy/tool_util/linters/inputs.py
index 3fcf9b5068f..16455b51a32 100644
--- a/lib/galaxy/tool_util/linters/inputs.py
+++ b/lib/galaxy/tool_util/linters/inputs.py
@@ -168,21 +168,35 @@ def lint_inputs(tool_xml, lint_ctx):
                     f"Param input [{param_name}] with no format specified - 'data' format will be assumed.", node=param
                 )
             options = param.findall("./options")
+            has_options_filter_attribute = False
             if len(options) == 1:
-                if len(options[0].attrib) > 0:
-                    lint_ctx.error(
-                        f"Data parameter [{param_name}] uses invalid attributes: {options[0].attrib}", node=param
-                    )
+                for oa in options[0].attrib:
+                    if oa == "options_filter_attribute":
+                        has_options_filter_attribute = True
+                    else:
+                        lint_ctx.error(f"Data parameter [{param_name}] uses invalid attribute: {oa}", node=param)
             elif len(options) > 1:
                 lint_ctx.error(f"Data parameter [{param_name}] contains multiple options elements.", node=options[1])
             # for data params only filters with key='build' of type='data_meta' are allowed
             filters = param.findall("./options/filter")
             for f in filters:
-                if f.get("key") != "dbkey" or f.get("type") != "data_meta":
+                if not f.get("ref"):
                     lint_ctx.error(
-                        f'Data parameter [{param_name}] for filters only type="data_meta" and key="dbkey" are allowed, found type="{f.get("type")}" and key="{f.get("key")}"',
+                        f"Data parameter [{param_name}] filter needs to define a ref attribute",
                         node=f,
                     )
+                if has_options_filter_attribute:
+                    if f.get("type") != "data_meta":
+                        lint_ctx.error(
+                            f'Data parameter [{param_name}] for filters only type="data_meta" is allowed, found type="{f.get("type")}"',
+                            node=f,
+                        )
+                else:
+                    if f.get("key") != "dbkey" or f.get("type") != "data_meta":
+                        lint_ctx.error(
+                            f'Data parameter [{param_name}] for filters only type="data_meta" and key="dbkey" are allowed, found type="{f.get("type")}" and key="{f.get("key")}"',
+                            node=f,
+                        )
 
         elif param_type == "select":
             # get dynamic/statically defined options
diff --git a/test/unit/tool_util/test_tool_linters.py b/test/unit/tool_util/test_tool_linters.py
index 2d28f3b8531..533dcd31e36 100644
--- a/test/unit/tool_util/test_tool_linters.py
+++ b/test/unit/tool_util/test_tool_linters.py
@@ -195,7 +195,19 @@ INPUTS_DATA_PARAM_OPTIONS = """
     <inputs>
         <param name="valid_name" type="data" format="txt">
             <options>
-                <filter type="data_meta" key="dbkey"/>
+                <filter type="data_meta" key="dbkey" ref="input"/>
+            </options>
+        </param>
+    </inputs>
+</tool>
+"""
+
+INPUTS_DATA_PARAM_OPTIONS_FILTER_ATTRIBUTE = """
+<tool>
+    <inputs>
+        <param name="valid_name" type="data" format="txt">
+            <options options_filter_attribute="metadata.foo">
+                <filter type="data_meta" key="foo" ref="input"/>
             </options>
         </param>
     </inputs>
@@ -1047,6 +1059,16 @@ def test_inputs_data_param_options(lint_ctx):
     assert not lint_ctx.error_messages
 
 
+def test_inputs_data_param_options_filter_attribute(lint_ctx):
+    tool_source = get_xml_tool_source(INPUTS_DATA_PARAM_OPTIONS_FILTER_ATTRIBUTE)
+    run_lint(lint_ctx, inputs.lint_inputs, tool_source)
+    assert not lint_ctx.valid_messages
+    assert "Found 1 input parameters." in lint_ctx.info_messages
+    assert len(lint_ctx.info_messages) == 1
+    assert not lint_ctx.warn_messages
+    assert not lint_ctx.error_messages
+
+
 def test_inputs_data_param_invalidoptions(lint_ctx):
     tool_source = get_xml_tool_source(INPUTS_DATA_PARAM_INVALIDOPTIONS)
     run_lint(lint_ctx, inputs.lint_inputs, tool_source)
@@ -1055,11 +1077,12 @@ def test_inputs_data_param_invalidoptions(lint_ctx):
     assert len(lint_ctx.info_messages) == 1
     assert not lint_ctx.warn_messages
     assert "Data parameter [valid_name] contains multiple options elements." in lint_ctx.error_messages
+    assert "Data parameter [valid_name] filter needs to define a ref attribute" in lint_ctx.error_messages
     assert (
         'Data parameter [valid_name] for filters only type="data_meta" and key="dbkey" are allowed, found type="expression" and key="None"'
         in lint_ctx.error_messages
     )
-    assert len(lint_ctx.error_messages) == 2
+    assert len(lint_ctx.error_messages) == 3
 
 
 def test_inputs_conditional(lint_ctx):