Merge branch 'release_24.2' into dev

galaxyproject · Feb 24, 2025 · ea1f245 · ea1f245
2 parents e4c3590 + 49c0dd0
commit ea1f245
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Showing 11 changed files with 191 additions and 96 deletions.
diff --git a/lib/galaxy/datatypes/text.py b/lib/galaxy/datatypes/text.py
@@ -137,6 +137,7 @@ 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)

diff --git a/lib/galaxy/managers/workflows.py b/lib/galaxy/managers/workflows.py
@@ -31,16 +31,13 @@
 )
 from sqlalchemy import (
     and_,
-    Cast,
-    ColumnElement,
     desc,
     false,
     func,
     or_,
     select,
     true,
 )
-from sqlalchemy.dialects.postgresql import JSONB
 from sqlalchemy.orm import (
     aliased,
     joinedload,
@@ -75,6 +72,7 @@
     StoredWorkflow,
     StoredWorkflowTagAssociation,
     StoredWorkflowUserShareAssociation,
+    to_json,
     User,
     Workflow,
     WorkflowInvocation,
@@ -2070,26 +2068,14 @@ def get_workflow_by_trs_id_and_version(
     ) -> 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,
                 )
             )
         )

diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
@@ -68,8 +68,10 @@
     bindparam,
     Boolean,
     case,
+    Cast,
     Column,
     column,
+    ColumnElement,
     DateTime,
     delete,
     desc,
@@ -100,6 +102,7 @@
     update,
     VARCHAR,
 )
+from sqlalchemy.dialects.postgresql import JSONB
 from sqlalchemy.exc import (
     CompileError,
     OperationalError,
@@ -315,6 +318,19 @@ 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)
@@ -898,8 +914,8 @@ def get_user_data_tables(self, data_table: str):
                 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)
         )

diff --git a/lib/galaxy/tool_util/xsd/galaxy.xsd b/lib/galaxy/tool_util/xsd/galaxy.xsd
@@ -8093,7 +8093,7 @@ favour of a ``has_size`` assertion.</xs:documentation>
 
   <xs:simpleType name="Format">
     <xs:restriction base="xs:string">
-      <xs:pattern value="[0-9a-z.-_]+"/>
+      <xs:pattern value="[0-9a-z._-]+"/>
     </xs:restriction>
   </xs:simpleType>
   <xs:simpleType name="FormatList">

diff --git a/lib/galaxy/tools/__init__.py b/lib/galaxy/tools/__init__.py
@@ -3255,6 +3255,7 @@ def exec_after_process(self, app, inp_data, out_data, param_dict, job, final_job
                     create=True,
                     preserve_symlinks=True,
                 )
+                hda.metadata.is_bundle = True
 
         else:
             raise Exception("Unknown data manager mode encountered type...")