From 94c75a083c25612b5f9e4aac6fc53d0ac2c77253 Mon Sep 17 00:00:00 2001
From: mvdbeek <m.vandenbeek@gmail.com>
Date: Thu, 25 Aug 2022 14:27:37 +0200
Subject: [PATCH] Fix setting metadata elements in conditional tool action

Fixes https://github.com/galaxyproject/galaxy/issues/14509
---
 lib/galaxy/tool_util/parser/output_actions.py | 16 ++++++++---
 lib/galaxy/tools/actions/__init__.py          | 27 ++-----------------
 .../tools/identifier_in_actions.xml           | 16 +++++++++++
 3 files changed, 31 insertions(+), 28 deletions(-)

diff --git a/lib/galaxy/tool_util/parser/output_actions.py b/lib/galaxy/tool_util/parser/output_actions.py
index dd04cfdb766..e190d50d43f 100644
--- a/lib/galaxy/tool_util/parser/output_actions.py
+++ b/lib/galaxy/tool_util/parser/output_actions.py
@@ -7,6 +7,7 @@ import os.path
 import re
 
 from galaxy import util
+from galaxy.util.template import fill_template
 
 log = logging.getLogger(__name__)
 
@@ -81,7 +82,7 @@ class ValueToolOutputActionConditionalWhen(ToolOutputActionConditionalWhen):
 
     def is_case(self, output_dataset, other_values):
         ref = self.get_ref(output_dataset, other_values)
-        return bool(str(ref) == self.value)
+        return ref == self.value
 
 
 class DatatypeIsInstanceToolOutputActionConditionalWhen(ToolOutputActionConditionalWhen):
@@ -304,8 +305,17 @@ class MetadataToolOutputAction(ToolOutputAction):
 
     def apply_action(self, output_dataset, other_values):
         value = self.option.get_value(other_values)
-        if value is None and self.default is not None:
-            value = self.default
+        # TODO: figure out correct type based on MetadataElementSpec,
+        # but MetadataElementSpec doesn't actually define a type (but it should).
+        # That would avoid the ad-hoc comma splitting here for defaults.
+        if self.default:
+            # For historical reasons the default value takes preference over value,
+            # and we only treat the default value as potentially containing cheetah.
+            value = fill_template(
+                self.default,
+                context=other_values,
+                python_template_version=other_values.get("__python_template_version__"),
+            ).split(",")
         if value is not None:
             setattr(output_dataset.metadata, self.name, value)
 
diff --git a/lib/galaxy/tools/actions/__init__.py b/lib/galaxy/tools/actions/__init__.py
index aa9f97e500a..8927e06f74d 100644
--- a/lib/galaxy/tools/actions/__init__.py
+++ b/lib/galaxy/tools/actions/__init__.py
@@ -538,12 +538,9 @@ class DefaultToolAction(ToolAction):
             if output.actions:
                 # Apply pre-job tool-output-dataset actions; e.g. setting metadata, changing format
                 output_action_params = dict(out_data)
-                output_action_params.update(incoming)
+                output_action_params.update(wrapped_params.params)
+                output_action_params["__python_template_version__"] = tool.python_template_version
                 output.actions.apply_action(data, output_action_params)
-            # Also set the default values of actions of type metadata
-            self.set_metadata_defaults(
-                output, data, tool, on_text, trans, incoming, history, wrapped_params.params, job_params
-            )
             # Flush all datasets at once.
             return data
 
@@ -913,26 +910,6 @@ class DefaultToolAction(ToolAction):
                 job_params=job_params,
             )
 
-    def set_metadata_defaults(self, output, dataset, tool, on_text, trans, incoming, history, params, job_params):
-        """
-        This allows to map names of input files to metadata default values. Example:
-
-        .. code-block::
-
-            <data format="tabular" name="output" label="Tabular output, aggregates data from individual_inputs" >
-                <actions>
-                    <action name="column_names" type="metadata" default="${','.join(input.name for input in $individual_inputs)}" />
-                </actions>
-            </data>
-        """
-        if output.actions:
-            for action in output.actions.actions:
-                if action.tag == "metadata" and action.default:
-                    metadata_new_value = fill_template(
-                        action.default, context=params, python_template_version=tool.python_template_version
-                    ).split(",")
-                    dataset.metadata.__setattr__(str(action.name), metadata_new_value)
-
     def _get_default_data_name(
         self, dataset, tool, on_text=None, trans=None, incoming=None, history=None, params=None, job_params=None, **kwd
     ):
diff --git a/test/functional/tools/identifier_in_actions.xml b/test/functional/tools/identifier_in_actions.xml
index ecccf112a47..a7aba432006 100644
--- a/test/functional/tools/identifier_in_actions.xml
+++ b/test/functional/tools/identifier_in_actions.xml
@@ -4,6 +4,7 @@
     ]]></command>
     <inputs>
         <param name="input" type="data" multiple="false" />
+        <param name="the_conditional" type="boolean" checked="true" />
     </inputs>
     <outputs>
         <data format="tabular" name="output">
@@ -11,6 +12,18 @@
                 <action name="column_names" type="metadata" default="First,${input.element_identifier}" />
             </actions>
         </data>
+        <data format="tabular" name="output_conditional_metadata">
+            <actions>
+                <conditional name="the_conditional">
+                    <when value="true">
+                        <action name="column_names" type="metadata" default="True,${input.element_identifier}" />
+                    </when>
+                    <when value="false">
+                        <action name="column_names" type="metadata" default="False,${input.element_identifier}" />
+                    </when>
+                </conditional>
+            </actions>
+        </data>
     </outputs>
     <tests>
         <test>
@@ -18,6 +31,9 @@
             <output name="output">
                 <metadata name="column_names" value="First,2.tabular"/>
             </output>
+            <output name="output_conditional_metadata">
+                <metadata name="column_names" value="True,2.tabular" />
+            </output>
         </test>
     </tests>
 </tool>