From b92c9cf1eadb918cfc4d90864dceac11f5d0b014 Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Thu, 22 Aug 2024 12:20:42 -0400
Subject: [PATCH] Implement tool upgrade assistant script.

Inspect a tool's XML file and provide advice on upgrading to new tool versions. It is implemented as a library in tool_util for integration with Planemo in the future but I've added a script here to run it on the command-line directly. It can also output in JSON for integration with external tools such as the galaxy language server.
---
 lib/galaxy/tool_util/parser/xml.py            |  6 +++++-
 lib/galaxy/tool_util/xsd/galaxy.xsd           |  6 +++++-
 packages/tool_util/setup.cfg                  |  1 +
 test/functional/tools/legacy_interpreter.xml  | 19 +++++++++++++++++++
 .../tools/legacy_interpreter_write_output.py  |  2 ++
 test/functional/tools/output_format_input.xml |  2 +-
 test/functional/tools/sample_tool_conf.xml    |  1 +
 7 files changed, 34 insertions(+), 3 deletions(-)
 create mode 100644 test/functional/tools/legacy_interpreter.xml
 create mode 100644 test/functional/tools/legacy_interpreter_write_output.py

diff --git a/lib/galaxy/tool_util/parser/xml.py b/lib/galaxy/tool_util/parser/xml.py
index 9ab4a30f65b6..8e098236a110 100644
--- a/lib/galaxy/tool_util/parser/xml.py
+++ b/lib/galaxy/tool_util/parser/xml.py
@@ -376,6 +376,10 @@ def _get_option_value(self, key, default):
     def _command_el(self):
         return self.root.find("command")
 
+    @property
+    def _outputs_el(self):
+        return self.root.find("outputs")
+
     def _get_attribute_as_bool(self, attribute, default, elem=None):
         if elem is None:
             elem = self.root
@@ -411,7 +415,7 @@ def parse_input_pages(self) -> "XmlPagesSource":
 
     def parse_provided_metadata_style(self):
         style = None
-        out_elem = self.root.find("outputs")
+        out_elem = self._outputs_el
         if out_elem is not None and "provided_metadata_style" in out_elem.attrib:
             style = out_elem.attrib["provided_metadata_style"]
 
diff --git a/lib/galaxy/tool_util/xsd/galaxy.xsd b/lib/galaxy/tool_util/xsd/galaxy.xsd
index 7c17312c4f0b..de34e758331b 100644
--- a/lib/galaxy/tool_util/xsd/galaxy.xsd
+++ b/lib/galaxy/tool_util/xsd/galaxy.xsd
@@ -29,10 +29,14 @@ List of behavior changes associated with profile versions:
 - Disable default tool version of 1.0.0.
 - Use non zero exit code as default stdio error condition (before non-empty stderr).
 
+#### 17.09
+
+- Introduce `provided_metadata_style` with default `"default"`. Restore legacy behavior by setting
+  this to `"legacy"`.
+
 #### 18.01
 
 - Use a separate home directory for each job.
-- Introduce `provided_metadata_style` with default `"default"` before `"legacy"`.
 
 #### 18.09
 
diff --git a/packages/tool_util/setup.cfg b/packages/tool_util/setup.cfg
index 7c8fd75feec1..a83feee3e048 100644
--- a/packages/tool_util/setup.cfg
+++ b/packages/tool_util/setup.cfg
@@ -49,6 +49,7 @@ python_requires = >=3.7
 [options.entry_points]
 console_scripts =
         galaxy-tool-test = galaxy.tool_util.verify.script:main
+        galaxy-tool-upgrade-advisor = galaxy.tool_util.upgrade.script:main
         mulled-build = galaxy.tool_util.deps.mulled.mulled_build:main
         mulled-build-channel = galaxy.tool_util.deps.mulled.mulled_build_channel:main
         mulled-build-files = galaxy.tool_util.deps.mulled.mulled_build_files:main
diff --git a/test/functional/tools/legacy_interpreter.xml b/test/functional/tools/legacy_interpreter.xml
new file mode 100644
index 000000000000..7ca65584d388
--- /dev/null
+++ b/test/functional/tools/legacy_interpreter.xml
@@ -0,0 +1,19 @@
+<tool id="legacy_interpreter" name="legacy_interpreter" version="1.0.0">
+    <command interpreter="python"><![CDATA[
+legacy_interpreter_write_output.py
+    ]]></command>
+    <inputs>
+    </inputs>
+    <outputs>
+        <data name="output1" format="xml" from_work_dir="output1" />
+    </outputs>
+    <tests>
+        <test>
+            <output name="output1">
+                <assert_contents>
+                    <has_text text="hello world" />
+                </assert_contents>
+            </output>
+        </test>
+    </tests>
+</tool>
diff --git a/test/functional/tools/legacy_interpreter_write_output.py b/test/functional/tools/legacy_interpreter_write_output.py
new file mode 100644
index 000000000000..25791f7b3d86
--- /dev/null
+++ b/test/functional/tools/legacy_interpreter_write_output.py
@@ -0,0 +1,2 @@
+with open("output1", "w") as f:
+    f.write("hello world")
diff --git a/test/functional/tools/output_format_input.xml b/test/functional/tools/output_format_input.xml
index c346b10dedf3..6080f0c21ca2 100644
--- a/test/functional/tools/output_format_input.xml
+++ b/test/functional/tools/output_format_input.xml
@@ -1,6 +1,6 @@
 <tool id="output_format_input" name="output_format_input" version="1.0" profile="21.01">
   <!-- test format="input" for the profile version where the format is set to "input"
-       (for legacy tools, i.e. profile <16.04, the format of a ramdom input is used) -->
+       (for legacy tools, i.e. profile <16.04, the format of a random input is used) -->
   <description></description>
   <command>
     cat '$input' > '$output'
diff --git a/test/functional/tools/sample_tool_conf.xml b/test/functional/tools/sample_tool_conf.xml
index 80c032c93601..4afe5cf253f8 100644
--- a/test/functional/tools/sample_tool_conf.xml
+++ b/test/functional/tools/sample_tool_conf.xml
@@ -176,6 +176,7 @@
   <tool file="identifier_in_actions.xml" />
   <tool file="fail_identifier.xml" />
   <tool file="fail_writing_work_dir_file.xml" />
+  <tool file="legacy_interpreter.xml" />
   <tool file="tool_directory.xml" />
   <tool file="tool_directory_docker.xml" />
   <tool file="output_action_change_format.xml" />