From 272e9ff159a2d387262977901f861f0206808bca Mon Sep 17 00:00:00 2001
From: John Chilton <jmchilton@gmail.com>
Date: Wed, 13 Nov 2024 09:46:04 -0500
Subject: [PATCH] A test case for running tool on linnked dataset.

---
 lib/galaxy/config/__init__.py               |  8 ++++++++
 test/integration/test_remote_files_posix.py | 12 ++++++++++++
 2 files changed, 20 insertions(+)

diff --git a/lib/galaxy/config/__init__.py b/lib/galaxy/config/__init__.py
index d4b1170673a1..8ccc68ffb631 100644
--- a/lib/galaxy/config/__init__.py
+++ b/lib/galaxy/config/__init__.py
@@ -115,6 +115,14 @@
             "level": "INFO",
             "qualname": "watchdog.observers.inotify_buffer",
         },
+        "py.warnings": {
+            "level": "ERROR",
+            "qualname": "py.warnings",
+        },
+        "celery.utils.functional": {
+            "level": "INFO",
+            "qualname": "celery.utils.functional",
+        },
     },
     "filters": {
         "stack": {
diff --git a/test/integration/test_remote_files_posix.py b/test/integration/test_remote_files_posix.py
index 0fbc4b7f8d93..75a449ff2e45 100644
--- a/test/integration/test_remote_files_posix.py
+++ b/test/integration/test_remote_files_posix.py
@@ -112,6 +112,7 @@ def _assert_access_forbidden_response(self, response):
 
 class TestPreferLinksPosixFileSourceIntegration(PosixFileSourceSetup, integration_util.IntegrationTestCase):
     dataset_populator: DatasetPopulator
+    framework_tool_and_types = True
 
     @classmethod
     def handle_galaxy_config_kwds(cls, config):
@@ -146,3 +147,14 @@ def test_links_by_default(self):
             assert dataset.external_filename.endswith("/root/a")
             assert os.path.exists(dataset.external_filename)
             assert open(dataset.external_filename).read() == "a\n"
+            payload = self.dataset_populator.run_tool(
+                tool_id="cat",
+                inputs={
+                    "input1": {"src": "hda", "id": new_dataset["id"]},
+                },
+                history_id=history_id,
+            )
+            derived_dataset = payload["outputs"][0]
+            self.dataset_populator.wait_for_history(history_id, assert_ok=True)
+            derived_content = self.dataset_populator.get_history_dataset_content(history_id, dataset=derived_dataset)
+            assert derived_content.strip() == "a"