Implement default format on collection level

lib/galaxy/tool_util/parser/output_collection_def.py

@@ -34,7 +34,13 @@ def dataset_collector_descriptions_from_elem(elem, legacy=True):
     if num_discover_dataset_blocks == 0 and legacy:
         collectors = [DEFAULT_DATASET_COLLECTOR_DESCRIPTION]
     else:
-        collectors = [dataset_collection_description(**e.attrib) for e in primary_dataset_elems]
+        default_format = elem.attrib.get("format")
+        collectors = []
+        for e in primary_dataset_elems:
+            description_attributes = e.attrib
+            if default_format and "format" not in description_attributes and "ext" not in description_attributes:
+                description_attributes["format"] = default_format
+            collectors.append(dataset_collection_description(**description_attributes))
 
     return _validate_collectors(collectors)
 

lib/galaxy/tool_util/xsd/galaxy.xsd

@@ -5360,11 +5360,13 @@ The default is ``galaxy.json``.
   <xs:attributeGroup name="OutputCommon">
     <xs:attribute name="format" type="xs:string">
       <xs:annotation>
-        <xs:documentation xml:lang="en">The short name for the output datatype.
-The valid values for format can be found in
+        <xs:documentation xml:lang="en"><![CDATA[
+The short name for the output datatype. The valid values for format can be found in
 [/config/datatypes_conf.xml.sample](https://github.com/galaxyproject/galaxy/blob/dev/config/datatypes_conf.xml.sample)
-(e.g. ``format="pdf"`` or ``format="fastqsanger"``). For collections this is the default format for all included
-elements. Note that the format specified here is ignored for discovered data sets.</xs:documentation>
+(e.g. ``format="pdf"`` or ``format="fastqsanger"``). For collections this is the default
+format for all included elements. Note that the format specified here is ignored for
+discovered data sets on Galaxy versions prior to 24.0 and should be specified using the ``<discovered_data>`` tag set.
+        ]]></xs:documentation>
       </xs:annotation>
     </xs:attribute>
     <xs:attribute name="format_source" type="xs:string">

test/unit/app/tools/test_collect_primary_datasets.py

@@ -128,6 +128,20 @@ def test_collect_multiple_recurse_dict(self):
         created_hda_3 = datasets[DEFAULT_TOOL_OUTPUT]["test3"]
         assert_created_with_path(self.app.object_store, created_hda_3.dataset, path3)
 
+    def test_collect_collection_default_format(self):
+        self._replace_output_collectors(
+            """<dataset_collection name="parent" format="abcdef">
+            <discover_datasets pattern="__name__" directory="subdir_for_name_discovery" sort_by="reverse_filename" />
+        </dataset_collection>"""
+        )
+        self._setup_extra_file(subdir="subdir_for_name_discovery", filename="test1")
+        self._setup_extra_file(subdir="subdir_for_name_discovery", filename="test2")
+
+        datasets = self._collect()
+        assert DEFAULT_TOOL_OUTPUT in datasets
+        for dataset in datasets[DEFAULT_TOOL_OUTPUT].values():
+            assert dataset.ext == "abcdef"
+
     def test_collect_sorted_reverse(self):
         self._replace_output_collectors(
             """<output>