Merge branch 'release_24.0' into dev

doc/source/conf.py

@@ -14,8 +14,6 @@
 import os
 import sys
 
-import sphinx_rtd_theme
-
 # Set GALAXY_DOCS_SKIP_VIEW_CODE=1 to skip embedding highlighted source
 # code into docs.
 SKIP_VIEW_CODE = os.environ.get("GALAXY_DOCS_SKIP_VIEW_CODE", False) == "1"
@@ -161,11 +159,10 @@ def setup(app):
     "collapse_navigation": False,
     "display_version": True,
     "navigation_depth": 2,
-    "canonical_url": "https://docs.galaxyproject.org/en/master/",
 }
 
 # Add any paths that contain custom themes here, relative to this directory.
-html_theme_path = [sphinx_rtd_theme.get_html_theme_path()]
+# html_theme_path = []
 
 # The name for this set of Sphinx documents.  If None, it defaults to
 # "<project> v<release> documentation".
@@ -174,6 +171,8 @@ def setup(app):
 # A shorter title for the navigation bar.  Default is the same as html_title.
 # html_short_title = None
 
+html_baseurl = "https://docs.galaxyproject.org/en/master/"
+
 # The name of an image file (relative to this directory) to place at the top
 # of the sidebar.
 # html_logo = None

lib/galaxy/managers/collections_util.py

@@ -1,5 +1,9 @@
 import logging
 import math
+from typing import (
+    Any,
+    Dict,
+)
 
 from galaxy import (
     exceptions,
@@ -153,35 +157,38 @@ def dictify_dataset_collection_instance(
     return dict_value
 
 
-def dictify_element_reference(element, rank_fuzzy_counts=None, recursive=True, security=None):
+def dictify_element_reference(
+    element: model.DatasetCollectionElement, rank_fuzzy_counts=None, recursive=True, security=None
+):
     """Load minimal details of elements required to show outline of contents in history panel.
 
     History panel can use this reference to expand to full details if individual dataset elements
     are clicked.
     """
     dictified = element.to_dict(view="element")
     if (element_object := element.element_object) is not None:
-        object_details = dict(
+        object_details: Dict[str, Any] = dict(
             id=element_object.id,
             model_class=element_object.__class__.__name__,
         )
-        if element.child_collection:
+        if isinstance(element_object, model.DatasetCollection):
             object_details["collection_type"] = element_object.collection_type
+            object_details["element_count"] = element_object.element_count
+            object_details["populated"] = element_object.populated_optimized
 
             # Recursively yield elements for each nested collection...
             if recursive:
-                child_collection = element.child_collection
-                elements, rest_fuzzy_counts = get_fuzzy_count_elements(child_collection, rank_fuzzy_counts)
+                elements, rest_fuzzy_counts = get_fuzzy_count_elements(element_object, rank_fuzzy_counts)
                 object_details["elements"] = [
                     dictify_element_reference(_, rank_fuzzy_counts=rest_fuzzy_counts, recursive=recursive)
                     for _ in elements
                 ]
-                object_details["element_count"] = child_collection.element_count
         else:
             object_details["state"] = element_object.state
             object_details["hda_ldda"] = "hda"
-            object_details["history_id"] = element_object.history_id
-            object_details["tags"] = element_object.make_tag_string_list()
+            if isinstance(element_object, model.HistoryDatasetAssociation):
+                object_details["history_id"] = element_object.history_id
+                object_details["tags"] = element_object.make_tag_string_list()
 
         dictified["object"] = object_details
     else:

lib/galaxy/model/__init__.py

@@ -1757,15 +1757,13 @@ def set_state(self, state: JobState) -> bool:
             return False
         session = object_session(self)
         if session and self.id and state not in Job.finished_states:
-            # generate statement that will not revert DELETING or DELETED back to anything non-terminal
+            # Do not update if job is in a terminal state
             rval = session.execute(
-                update(Job)
-                .where(Job.id == self.id, ~Job.state.in_((Job.states.DELETING, Job.states.DELETED)))
-                .values(state=state)
+                update(Job).where(Job.id == self.id, ~Job.state.in_((state, *Job.finished_states))).values(state=state)
             )
+            with transaction(session):
+                session.commit()
             if rval.rowcount == 1:
-                # Need to expire state since we just updated it, but ORM doesn't know about it.
-                session.expire(self, ["state"])
                 self.state_history.append(JobStateHistory(self))
                 return True
             else:
@@ -3065,7 +3063,7 @@ class History(Base, HasTags, Dictifiable, UsesAnnotations, HasName, Serializable
         "HistoryDatasetAssociation",
         primaryjoin=(
             lambda: and_(
-                HistoryDatasetAssociation.history_id == History.id,  # type: ignore[attr-defined]
+                HistoryDatasetAssociation.history_id == History.id,  # type: ignore[arg-type]
                 not_(HistoryDatasetAssociation.deleted),  # type: ignore[has-type]
             )
         ),
@@ -3090,7 +3088,7 @@ class History(Base, HasTags, Dictifiable, UsesAnnotations, HasName, Serializable
         "HistoryDatasetAssociation",
         primaryjoin=(
             lambda: and_(
-                HistoryDatasetAssociation.history_id == History.id,  # type: ignore[attr-defined]
+                HistoryDatasetAssociation.history_id == History.id,  # type: ignore[arg-type]
                 not_(HistoryDatasetAssociation.deleted),  # type: ignore[has-type]
                 HistoryDatasetAssociation.visible,  # type: ignore[has-type]
             )
@@ -5108,6 +5106,8 @@ class HistoryDatasetAssociation(DatasetInstance, HasTags, Dictifiable, UsesAnnot
     Resource class that creates a relation between a dataset and a user history.
     """
 
+    history_id: Optional[int]
+
     def __init__(
         self,
         hid=None,
@@ -7301,7 +7301,9 @@ def is_collection(self):
         return self.element_type == "dataset_collection"
 
     @property
-    def element_object(self):
+    def element_object(
+        self,
+    ) -> Optional[Union[HistoryDatasetAssociation, LibraryDatasetDatasetAssociation, DatasetCollection]]:
         if self.hda:
             return self.hda
         elif self.ldda:

lib/galaxy/tools/__init__.py

@@ -3461,7 +3461,9 @@ def _get_new_elements(self, history, elements_to_copy):
 
     @staticmethod
     def element_is_valid(element: model.DatasetCollectionElement):
-        return element.element_object.is_ok
+        element_object = element.element_object
+        assert isinstance(element_object, model.DatasetInstance)
+        return element_object.is_ok
 
     def produce_outputs(self, trans, out_data, output_collections, incoming, history, **kwds):
         collection = incoming["input"]
@@ -3503,7 +3505,9 @@ class FilterFailedDatasetsTool(FilterDatasetsTool):
 
     @staticmethod
     def element_is_valid(element: model.DatasetCollectionElement):
-        return element.element_object.is_ok
+        element_object = element.element_object
+        assert isinstance(element_object, model.DatasetInstance)
+        return element_object.is_ok
 
 
 class KeepSuccessDatasetsTool(FilterDatasetsTool):
@@ -3514,12 +3518,14 @@ class KeepSuccessDatasetsTool(FilterDatasetsTool):
 
     @staticmethod
     def element_is_valid(element: model.DatasetCollectionElement):
+        element_object = element.element_object
+        assert isinstance(element_object, model.DatasetInstance)
         if (
-            element.element_object.state != model.Dataset.states.PAUSED
-            and element.element_object.state in model.Dataset.non_ready_states
+            element_object.state != model.Dataset.states.PAUSED
+            and element_object.state in model.Dataset.non_ready_states
         ):
             raise ToolInputsNotReadyException("An input dataset is pending.")
-        return element.element_object.is_ok
+        return element_object.is_ok
 
 
 class FilterEmptyDatasetsTool(FilterDatasetsTool):
@@ -3528,10 +3534,11 @@ class FilterEmptyDatasetsTool(FilterDatasetsTool):
 
     @staticmethod
     def element_is_valid(element: model.DatasetCollectionElement):
-        dataset_instance: model.DatasetInstance = element.element_object
-        if dataset_instance.has_data():
+        element_object = element.element_object
+        assert isinstance(element_object, model.DatasetInstance)
+        if element_object.has_data():
             # We have data, but it might just be a compressed archive of nothing
-            file_name = dataset_instance.get_file_name()
+            file_name = element_object.get_file_name()
             _, fh = get_fileobj_raw(file_name, mode="rb")
             if len(fh.read(1)):
                 return True

lib/galaxy_test/api/test_dataset_collections.py

@@ -455,7 +455,7 @@ def test_show_dataset_collection_contents(self, history_id):
         # Get contents_url from history contents, use it to show the first level
         # of collection contents in the created HDCA, then use it again to drill
         # down into the nested collection contents
-        hdca = self.dataset_collection_populator.create_list_of_list_in_history(history_id).json()
+        hdca = self.dataset_collection_populator.create_list_of_list_in_history(history_id, wait=True).json()
         root_contents_url = self._get_contents_url_for_hdca(history_id, hdca)
 
         # check root contents for this collection
@@ -466,6 +466,8 @@ def test_show_dataset_collection_contents(self, history_id):
         # drill down, retrieve nested collection contents
         assert "object" in root_contents[0]
         assert "contents_url" in root_contents[0]["object"]
+        assert root_contents[0]["object"]["element_count"] == 3
+        assert root_contents[0]["object"]["populated"]
         drill_contents_url = root_contents[0]["object"]["contents_url"]
         drill_contents = self._get(drill_contents_url).json()
         assert len(drill_contents) == len(hdca["elements"][0]["object"]["elements"])

lib/galaxy_test/api/test_workflows.py

@@ -5477,7 +5477,7 @@ def test_optional_workflow_output(self):
     tool_id: output_filter
     state:
       produce_out_1: False
-      filter_text_1: '1'
+      filter_text_1: 'foo'
       produce_collection: False
 """,
                 test_data={},

lib/galaxy_test/base/populators.py

@@ -630,7 +630,8 @@ def has_active_jobs():
             raise TimeoutAssertionError(message)
 
         if assert_ok:
-            self.wait_for_history(history_id, assert_ok=True, timeout=timeout)
+            for job in self.history_jobs(history_id=history_id):
+                assert job["state"] in ("ok", "skipped"), f"Job {job} not in expected state"
 
     def wait_for_jobs(
         self,

test/functional/tools/output_filter.xml

@@ -59,15 +59,9 @@ echo 'p2.reverse' > p2.reverse
                 </assert_contents>
             </output>
         </test>
-        <!-- tool runs with no outputs should fail -->
-        <test expect_num_outputs="0" expect_test_failure="true">
+        <test expect_num_outputs="0">
             <param name="produce_out_1" value="false" />
             <param name="filter_text_1" value="not_foo_or_bar" />
-            <output name="out_3">
-                <assert_contents>
-                    <has_line line="test" />
-                </assert_contents>
-            </output>
             <assert_stdout>
                 <has_n_lines n="0"/>
             </assert_stdout>