Update schema, lint

Author: guerler

client/src/api/schema/schema.ts

@@ -7217,7 +7217,7 @@ export interface components {
              */
             outputs: (
                 | components["schemas"]["IncomingToolOutputDataset"]
-                | components["schemas"]["IncomingToolOutputCollection-Input"]
+                | components["schemas"]["IncomingToolOutputCollection"]
                 | components["schemas"]["ToolOutputText"]
                 | components["schemas"]["ToolOutputInteger"]
                 | components["schemas"]["ToolOutputFloat"]
@@ -12308,6 +12308,12 @@ export interface components {
          * @description Data of an export record associated with a history that was archived.
          */
         ExportRecordData: {
+            /**
+             * Ignore Errors
+             * @description Last resort. If True, skip serialization errors caused by missing provenance (e.g. orphan implicit collection job associations, null job param refs from older histories that pre-date collections) instead of failing. Exported data may be incomplete or corrupt.
+             * @default false
+             */
+            ignore_errors: boolean;
             /**
              * Include deleted
              * @description Include file contents for deleted datasets (if include_files is True).
@@ -15751,32 +15757,7 @@ export interface components {
             type: "in_range";
         };
         /** IncomingToolOutputCollection */
-        "IncomingToolOutputCollection-Input": {
-            /**
-             * hidden
-             * @description If true, the output will not be shown in the history.
-             */
-            hidden?: boolean | null;
-            /**
-             * label
-             * @description Output label. Will be used as dataset name in history.
-             */
-            label?: string | null;
-            /**
-             * name
-             * @description Parameter name. Used when referencing parameter in workflows.
-             */
-            name?: string | null;
-            /** structure */
-            structure: components["schemas"]["ToolOutputCollectionStructure"];
-            /**
-             * @description discriminator enum property added by openapi-typescript
-             * @enum {string}
-             */
-            type: "collection";
-        };
-        /** IncomingToolOutputCollection */
-        "IncomingToolOutputCollection-Output": {
+        IncomingToolOutputCollection: {
             /**
              * hidden
              * @description If true, the output will not be shown in the history.
@@ -24786,7 +24767,7 @@ export interface components {
              */
             outputs: (
                 | components["schemas"]["IncomingToolOutputDataset"]
-                | components["schemas"]["IncomingToolOutputCollection-Input"]
+                | components["schemas"]["IncomingToolOutputCollection"]
                 | components["schemas"]["ToolOutputText"]
                 | components["schemas"]["ToolOutputInteger"]
                 | components["schemas"]["ToolOutputFloat"]
@@ -24881,7 +24862,7 @@ export interface components {
              */
             outputs: (
                 | components["schemas"]["IncomingToolOutputDataset"]
-                | components["schemas"]["IncomingToolOutputCollection-Output"]
+                | components["schemas"]["IncomingToolOutputCollection"]
                 | components["schemas"]["ToolOutputText"]
                 | components["schemas"]["ToolOutputInteger"]
                 | components["schemas"]["ToolOutputFloat"]
@@ -25778,6 +25759,12 @@ export interface components {
              * @description Override xref for 'description domain' when generating BioCompute object.
              */
             bco_override_xref?: components["schemas"]["XrefItem"][] | null;
+            /**
+             * Ignore Errors
+             * @description Last resort. If True, skip serialization errors caused by missing provenance (e.g. orphan implicit collection job associations, null job param refs from older histories that pre-date collections) instead of failing. Exported data may be incomplete or corrupt.
+             * @default false
+             */
+            ignore_errors: boolean;
             /**
              * Include deleted
              * @description Include file contents for deleted datasets (if include_files is True).
@@ -25809,6 +25796,12 @@ export interface components {
         };
         /** WriteStoreToPayload */
         WriteStoreToPayload: {
+            /**
+             * Ignore Errors
+             * @description Last resort. If True, skip serialization errors caused by missing provenance (e.g. orphan implicit collection job associations, null job param refs from older histories that pre-date collections) instead of failing. Exported data may be incomplete or corrupt.
+             * @default false
+             */
+            ignore_errors: boolean;
             /**
              * Include deleted
              * @description Include file contents for deleted datasets (if include_files is True).

lib/galaxy/managers/model_stores.py

@@ -268,7 +268,7 @@ def write_history_to(self, request: WriteHistoryTo):
                 model_store_format,
                 export_files=export_files,
                 user_context=user_context,
-                tolerate_missing_data=request.tolerate_missing_data,
+                ignore_errors=request.ignore_errors,
             )(request.target_uri)
             with export_store:
                 history = self._history_manager.by_id(request.history_id)

lib/galaxy/model/__init__.py

@@ -459,7 +459,7 @@ def __init__(
         serialize_dataset_objects: Optional[bool] = None,
         serialize_files_handler: Optional[SerializeFilesHandler] = None,
         strip_metadata_files: Optional[bool] = None,
-        tolerate_missing_data: bool = False,
+        ignore_errors: bool = False,
     ) -> None:
         self.for_edit = for_edit
         if serialize_dataset_objects is None:
@@ -474,7 +474,7 @@ def __init__(
         # When True, serializers emit best-effort output for histories whose imports left
         # unresolved references (orphan ImplicitCollectionJobsJobAssociation rows, null-id
         # job param refs) instead of raising. Intended for background archival exports.
-        self.tolerate_missing_data = tolerate_missing_data
+        self.ignore_errors = ignore_errors
 
     def attach_identifier(self, id_encoder, obj, ret_val):
         if self.for_edit and obj.id:
@@ -498,7 +498,7 @@ def get_identifier(self, id_encoder, obj):
 
     def get_identifier_for_id(self, id_encoder, obj_id):
         if not obj_id:
-            if self.tolerate_missing_data:
+            if self.ignore_errors:
                 return obj_id
             raise NotImplementedError()
         if self.for_edit:
@@ -2961,7 +2961,7 @@ def _serialize(self, id_encoder, serialization_options):
             jobs=[
                 serialization_options.get_identifier(id_encoder, j_a.job)
                 for j_a in self.jobs
-                if j_a.job is not None or not serialization_options.tolerate_missing_data
+                if j_a.job is not None or not serialization_options.ignore_errors
             ],
         )
         serialization_options.attach_identifier(id_encoder, self, rval)

lib/galaxy/model/store/__init__.py

@@ -1965,7 +1965,7 @@ def __init__(
         strip_metadata_files: bool = True,
         serialize_jobs: bool = True,
         user_context=None,
-        tolerate_missing_data: bool = False,
+        ignore_errors: bool = False,
     ) -> None:
         """
         :param export_directory: path to export directory. Will be created if it does not exist.
@@ -2002,7 +2002,7 @@ def __init__(
             serialize_dataset_objects=serialize_dataset_objects,
             strip_metadata_files=strip_metadata_files,
             serialize_files_handler=self,
-            tolerate_missing_data=tolerate_missing_data,
+            ignore_errors=ignore_errors,
         )
         self.export_files = export_files
         self.included_datasets: dict[model.DatasetInstance, tuple[model.DatasetInstance, bool]] = {}
@@ -3042,15 +3042,15 @@ def get_export_store_factory(
     export_files=None,
     bco_export_options: Optional[BcoExportOptions] = None,
     user_context=None,
-    tolerate_missing_data: bool = False,
+    ignore_errors: bool = False,
 ) -> Callable[[StrPath], FileSourceModelExportStore]:
     export_store_class: type[FileSourceModelExportStore]
     export_store_class_kwds = {
         "app": app,
         "export_files": export_files,
         "serialize_dataset_objects": False,
         "user_context": user_context,
-        "tolerate_missing_data": tolerate_missing_data,
+        "ignore_errors": ignore_errors,
     }
     if download_format in ["tar.gz", "tgz"]:
         export_store_class = TarModelExportStore

lib/galaxy/schema/schema.py

@@ -1924,9 +1924,14 @@ class WriteStoreToPayload(StoreExportPayload):
         title="Target URI",
         description="Galaxy Files URI to write mode store content to.",
     )
-    tolerate_missing_data: bool = Field(
+    ignore_errors: bool = Field(
         default=False,
-        description="Best-effort export: skip unresolved references instead of failing.",
+        description=(
+            "Last resort. If True, skip serialization errors caused by missing "
+            "provenance (e.g. orphan implicit collection job associations, null "
+            "job param refs from older histories that pre-date collections) "
+            "instead of failing. Exported data may be incomplete or corrupt."
+        ),
     )
 
 

test/unit/data/model/test_model_store.py

@@ -778,7 +778,7 @@ def test_export_history_with_orphan_icjja(tmp_path):
     """Orphan ImplicitCollectionJobsJobAssociation rows (job_id NULL) are
     persisted by the import path when an ICJ references a job key not in
     object_import_tracker.jobs_by_key. The next export crashes in
-    get_identifier(j_a.job=None); tolerate_missing_data skips the orphan."""
+    get_identifier(j_a.job=None); ignore_errors skips the orphan."""
     app = _mock_app()
     u, h, _d1, _d2, j = _setup_simple_cat_job(app)
 
@@ -794,17 +794,15 @@ def test_export_history_with_orphan_icjja(tmp_path):
     app.add_and_commit(icj, linked, to_orphan)
 
     # Mimic the post-import state: drop the FK so the row becomes an orphan.
-    to_orphan.job = None
+    to_orphan.job = None  # type: ignore[assignment]
     app.commit()
 
     with pytest.raises(AttributeError):
         with store.TarModelExportStore(str(tmp_path / "strict.tgz"), app=app, export_files="copy") as export_store:
             export_store.export_history(h)
 
     tolerant_archive = str(tmp_path / "tolerant.tgz")
-    with store.TarModelExportStore(
-        tolerant_archive, app=app, export_files="copy", tolerate_missing_data=True
-    ) as export_store:
+    with store.TarModelExportStore(tolerant_archive, app=app, export_files="copy", ignore_errors=True) as export_store:
         export_store.export_history(h)
 
     imported_history = import_archive(tolerant_archive, app, u)
@@ -817,7 +815,7 @@ def test_export_history_with_null_param_id(tmp_path):
     """Job params shaped {"src": "hda"|"hdca"|"dce", "id": null} are persisted
     by the import path at model/store/__init__.py:1860-1888 when a referenced
     HDA/HDCA/DCE can't be resolved. Strict export raises in
-    get_identifier_for_id; tolerate_missing_data passes the null through.
+    get_identifier_for_id; ignore_errors passes the null through.
 
     Reproducing the on-disk state directly: the only producer is the import
     path itself, so deleting the referenced HDA wouldn't null the persisted
@@ -832,9 +830,7 @@ def test_export_history_with_null_param_id(tmp_path):
             export_store.export_history(h)
 
     tolerant_archive = str(tmp_path / "tolerant.tgz")
-    with store.TarModelExportStore(
-        tolerant_archive, app=app, export_files="copy", tolerate_missing_data=True
-    ) as export_store:
+    with store.TarModelExportStore(tolerant_archive, app=app, export_files="copy", ignore_errors=True) as export_store:
         export_store.export_history(h)
 
     imported_history = import_archive(tolerant_archive, app, u)