Merge pull request #17890 from mvdbeek/fix_empty_nested_collection_el…

…ement_count

[24.0] Always serialize element_count and populated when listing contents

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

@@ -4996,6 +4996,8 @@ 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,
@@ -7153,7 +7155,9 @@ 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"])