[25.0] Rerun workflows for the correct version/instance

In `GET /api/workflows/{encoded_workflow_id}/download`, for the case when `instance = True`, we were correctly obtaining the stored workflow.

However, then in `WorkflowContentsManager.workflow_to_dict` we were not considering the case that when `instance = True`, we need to not return the `latest_workflow.workflow_to_dict`, and instead return the specific workflow instance which has been specified.

We did handle the case when `version` is explicitly provided here, but not instance.

Fixes https://github.com/galaxyproject/galaxy/issues/20223

lib/galaxy/managers/workflows.py

@@ -925,7 +925,7 @@ class WorkflowContentsManager(UsesAnnotations):
 
         return workflow, missing_tool_tups
 
-    def workflow_to_dict(self, trans, stored, style="export", version=None, history=None):
+    def workflow_to_dict(self, trans, stored, style="export", version=None, history=None, instance_id=None):
         """Export the workflow contents to a dictionary ready for JSON-ification and to be
         sent out via API for instance. There are three styles of export allowed 'export', 'instance', and
         'editor'. The Galaxy team will do its best to preserve the backward compatibility of the
@@ -942,6 +942,12 @@ class WorkflowContentsManager(UsesAnnotations):
             version = None
         if version is not None:
             version = int(version)
+        elif instance_id:
+            # If the instance_id is provided, we need to extract the workflow instance via the version.
+            for i, workflow in enumerate(reversed(stored.workflows)):
+                if workflow.id == instance_id:
+                    version = i
+                    break
         workflow = stored.get_internal_version(version)
         if style == "export":
             style = self.app.config.default_workflow_export_format

lib/galaxy/webapps/galaxy/api/workflows.py

@@ -339,13 +339,15 @@ class WorkflowsAPIController(
         style = kwd.get("style", "export")
         download_format = kwd.get("format")
         version = kwd.get("version")
+        instance = util.string_as_bool(kwd.get("instance", "false"))
+        instance_id = self.decode_id(workflow_id) if instance else None
         history = None
         if history_id := kwd.get("history_id"):
             history = self.history_manager.get_accessible(
                 self.decode_id(history_id), trans.user, current_history=trans.history
             )
         ret_dict = self.workflow_contents_manager.workflow_to_dict(
-            trans, stored_workflow, style=style, version=version, history=history
+            trans, stored_workflow, style=style, version=version, history=history, instance_id=instance_id
         )
         if download_format == "json-download":
             sname = stored_workflow.name