Merge branch 'release_25.1' into release_26.0

lib/galaxy/tools/__init__.py

@@ -1959,7 +1959,7 @@ class Tool(UsesDictVisibleKeys, ToolParameterBundle):
         try:
             return rst_to_html(help_content.content)
         except Exception:
-            log.info("Exception while parsing help for tool with id '%s'", self.id)
+            log.warning("Exception while parsing help for tool with id '%s'", self.id, exc_info=True)
             return ""
 
     def render_help(self, static_path: str, host_url: str) -> str:

lib/galaxy/util/rst_to_html.py

@@ -1,5 +1,6 @@
 import functools
 import os
+import threading
 
 try:
     import docutils.core
@@ -57,12 +58,17 @@ def get_publisher(error=False):
     return pub
 
 
+# Cached docutils publishers are stateful and not thread-safe.
+_publish_lock = threading.Lock()
+
+
 @functools.lru_cache(maxsize=None)
 def rst_to_html(s, error=False):
     if docutils is None:
         raise Exception("Attempted to use rst_to_html but docutils unavailable.")
 
-    publisher = get_publisher(error=error)
-    publisher.set_source(s, None)
-    publisher.set_destination(None, None)
-    return publisher.publish(enable_exit_status=False)
+    with _publish_lock:
+        publisher = get_publisher(error=error)
+        publisher.set_source(s, None)
+        publisher.set_destination(None, None)
+        return publisher.publish(enable_exit_status=False)

test/integration_selenium/test_trs_import.py

@@ -49,6 +49,11 @@ class TestTrsImport(SeleniumIntegrationTestCase):
     def trs_config_dir(cls):
         return cls.temp_config_dir("trs")
 
+    def _wait_for_import_redirect(self):
+        # The client redirects to the workflow list only once the import request returns,
+        # which includes the server fetching the workflow from the remote TRS server.
+        self.components.workflows.workflows_list.wait_for_visible(wait_type=self.wait_types.SHED_SEARCH)
+
     def assert_workflow_imported(self, name):
         # surround name with quotes to consider case where name contains colons
         self.workflow_index_search_for(f'"{name}"')
@@ -76,7 +81,7 @@ class TestTrsImport(SeleniumIntegrationTestCase):
             workflow_name="galaxy-workflow-dockstore-example-1"
         ).wait_for_and_click()
         self.components.trs_search.import_button.wait_for_and_click()
-        self.sleep_for(self.wait_types.UX_RENDER)
+        self._wait_for_import_redirect()
         self.workflow_index_open()
         self.assert_workflow_imported("Test Workflow")
 
@@ -85,7 +90,7 @@ class TestTrsImport(SeleniumIntegrationTestCase):
         self.components.trs_search.search.wait_for_and_send_keys("organization: iwc-workflows")
         self.components.trs_search.search_result(workflow_name=TRS_NAME).wait_for_and_click()
         self.components.trs_search.import_version(version="v0.4").wait_for_and_click()
-        self.sleep_for(self.wait_types.UX_RENDER)
+        self._wait_for_import_redirect()
         self.workflow_index_open()
         self.assert_workflow_imported(WORKFLOW_NAME)
         self.components.workflows.trs_icon.wait_for_visible()
@@ -99,7 +104,7 @@ class TestTrsImport(SeleniumIntegrationTestCase):
         self.components.trs_search.search.wait_for_and_send_keys(WORKFLOW_NAME)
         self.components.trs_search.search_result(workflow_name=WORKFLOW_NAME).wait_for_and_click()
         self.components.trs_search.import_button.wait_for_and_click()
-        self.sleep_for(self.wait_types.UX_RENDER)
+        self._wait_for_import_redirect()
         self.workflow_index_open()
         self.assert_workflow_imported(WORKFLOW_NAME)
 
@@ -132,7 +137,7 @@ class TestTrsImport(SeleniumIntegrationTestCase):
         self.components.trs_import.select_server(server=server).wait_for_and_click()
         self.components.trs_import.input.wait_for_and_send_keys(trs_id)
         self.components.trs_import.import_version(version="v0.4").wait_for_and_click()
-        self.sleep_for(self.wait_types.UX_RENDER)
+        self._wait_for_import_redirect()
         self.workflow_index_open()
         self.assert_workflow_imported(WORKFLOW_NAME)
 
@@ -140,6 +145,6 @@ class TestTrsImport(SeleniumIntegrationTestCase):
         self.go_to_trs_by_id()
         self.components.trs_import.url_input.wait_for_and_send_keys(trs_url)
         self.components.trs_import.url_import_button.wait_for_and_click()
-        self.sleep_for(self.wait_types.UX_RENDER)
+        self._wait_for_import_redirect()
         self.workflow_index_open()
         self.assert_workflow_imported(WORKFLOW_NAME)

test/unit/app/tools/test_expression_basics.py

@@ -318,7 +318,8 @@ def test_timeout_kills_worker_under_waiting_wrapper(tmp_path, short_timeout_grac
     pid = int(pid_file.read_text())
     try:
         child = psutil.Process(pid)
-        assert child.status() == psutil.STATUS_ZOMBIE
+        # The orphaned worker is reaped asynchronously by init or a subreaper.
+        assert child.status() in (psutil.STATUS_ZOMBIE, psutil.STATUS_DEAD)
     except psutil.NoSuchProcess:
         pass
 

test/unit/util/test_rst_to_html.py

@@ -0,0 +1,17 @@
+from concurrent.futures import ThreadPoolExecutor
+
+from galaxy.util.rst_to_html import rst_to_html
+
+
+def test_rst_to_html_basic():
+    html = rst_to_html("**bold**")
+    assert "<strong>bold</strong>" in html
+
+
+def test_rst_to_html_concurrent_conversions():
+    documents = [f"Section {i}\n=========={'=' * len(str(i))}\n\nParagraph *{i}* with ``code``.\n" for i in range(50)]
+    with ThreadPoolExecutor(max_workers=8) as executor:
+        results = list(executor.map(rst_to_html, documents))
+    for i, html in enumerate(results):
+        assert f"Section {i}" in html
+        assert f"<em>{i}</em>" in html