Skip data_manager_json files that aren't bundles

The file_size hack turns out to not work, since people report related
bugs that they shouldn't have been able to run into without generating
bundles.
It's probably still true that bundles should produce a distinct
datatype.

lib/galaxy/datatypes/text.py

@@ -138,6 +138,7 @@ class DataManagerJson(Json):
     MetadataElement(
         name="data_tables", default=None, desc="Data tables represented by this dataset", readonly=True, visible=True
     )
+    MetadataElement(name="is_bundle", default=False, desc="Dataset represents bundle", readonly=True, visible=True)
 
     def set_meta(self, dataset: DatasetProtocol, overwrite: bool = True, **kwd):
         super().set_meta(dataset=dataset, overwrite=overwrite, **kwd)

lib/galaxy/managers/workflows.py

@@ -31,8 +31,6 @@ from pydantic import (
 )
 from sqlalchemy import (
     and_,
-    Cast,
-    ColumnElement,
     desc,
     false,
     func,
@@ -40,7 +38,6 @@ from sqlalchemy import (
     select,
     true,
 )
-from sqlalchemy.dialects.postgresql import JSONB
 from sqlalchemy.orm import (
     aliased,
     joinedload,
@@ -72,6 +69,7 @@ from galaxy.model import (
     StoredWorkflow,
     StoredWorkflowTagAssociation,
     StoredWorkflowUserShareAssociation,
+    to_json,
     User,
     Workflow,
     WorkflowInvocation,
@@ -2067,26 +2065,14 @@ class WorkflowContentsManager(UsesAnnotations):
     ) -> Optional[model.StoredWorkflow]:
         sa_session = self.app.model.session
 
-        def to_json(column, keys: List[str]):
-            assert sa_session.bind
-            if sa_session.bind.dialect.name == "postgresql":
-                cast: Union[ColumnElement[Any], Cast[Any]] = func.cast(func.convert_from(column, "UTF8"), JSONB)
-                for key in keys:
-                    cast = cast.__getitem__(key)
-                return cast.astext
-            else:
-                for key in keys:
-                    column = func.json_extract(column, f"$.{key}")
-                return column
-
         stmnt = (
             select(model.StoredWorkflow)
             .join(model.Workflow, model.Workflow.id == model.StoredWorkflow.latest_workflow_id)
             .filter(
                 and_(
                     model.StoredWorkflow.deleted == false(),
-                    to_json(model.Workflow.source_metadata, ["trs_tool_id"]) == trs_id,
-                    to_json(model.Workflow.source_metadata, ["trs_version_id"]) == trs_version,
+                    to_json(sa_session, model.Workflow.source_metadata, ["trs_tool_id"]) == trs_id,
+                    to_json(sa_session, model.Workflow.source_metadata, ["trs_version_id"]) == trs_version,
                 )
             )
         )

lib/galaxy/model/__init__.py

@@ -68,8 +68,10 @@ from sqlalchemy import (
     bindparam,
     Boolean,
     case,
+    Cast,
     Column,
     column,
+    ColumnElement,
     DateTime,
     delete,
     desc,
@@ -100,6 +102,7 @@ from sqlalchemy import (
     update,
     VARCHAR,
 )
+from sqlalchemy.dialects.postgresql import JSONB
 from sqlalchemy.exc import (
     CompileError,
     OperationalError,
@@ -318,6 +321,19 @@ def get_uuid(uuid: Optional[Union[UUID, str]] = None) -> UUID:
     return UUID(str(uuid))
 
 
+def to_json(sa_session, column, keys: List[str]):
+    assert sa_session.bind
+    if sa_session.bind.dialect.name == "postgresql":
+        cast: Union[ColumnElement[Any], Cast[Any]] = func.cast(func.convert_from(column, "UTF8"), JSONB)
+        for key in keys:
+            cast = cast.__getitem__(key)
+        return cast.astext
+    else:
+        for key in keys:
+            column = func.json_extract(column, f"$.{key}")
+        return column
+
+
 class Base(DeclarativeBase, _HasTable):
     __abstract__ = True
     metadata = MetaData(naming_convention=NAMING_CONVENTION)
@@ -904,8 +920,8 @@ class User(Base, Dictifiable, RepresentById):
                 Dataset.state == "ok",
                 # excludes data manager runs that actually populated tables.
                 # maybe track this formally by creating a different datatype for bundles ?
-                Dataset.total_size != Dataset.file_size,
                 HistoryDatasetAssociation._metadata.contains(data_table),
+                to_json(session, HistoryDatasetAssociation._metadata, ["is_bundle"]) == "true",
             )
             .order_by(HistoryDatasetAssociation.id)
         )

lib/galaxy/tools/__init__.py

@@ -3261,6 +3261,7 @@ class DataManagerTool(OutputParameterJSONTool):
                     create=True,
                     preserve_symlinks=True,
                 )
+                hda.metadata.is_bundle = True
 
         else:
             raise Exception("Unknown data manager mode encountered type...")