Simplify determine_output_format

mvdbeek · Jan 10, 2025 · 20dc7b7 · 20dc7b7
1 parent f65b754
commit 20dc7b7
Show file tree

Hide file tree

Showing 2 changed files with 5 additions and 4 deletions.
diff --git a/lib/galaxy/model/__init__.py b/lib/galaxy/model/__init__.py
@@ -7019,7 +7019,7 @@ class HistoryDatasetCollectionAssociation(
     create_time: Mapped[datetime] = mapped_column(default=now, nullable=True)
     update_time: Mapped[datetime] = mapped_column(default=now, onupdate=now, index=True, nullable=True)
 
-    collection = relationship("DatasetCollection")
+    collection: Mapped["DatasetCollection"] = relationship("DatasetCollection")
     history: Mapped[Optional["History"]] = relationship(back_populates="dataset_collections")
 
     copied_from_history_dataset_collection_association = relationship(

diff --git a/lib/galaxy/tools/actions/__init__.py b/lib/galaxy/tools/actions/__init__.py
@@ -3,6 +3,7 @@
 import os
 import re
 from abc import abstractmethod
+from collections import UserDict
 from json import dumps
 from typing import (
     Any,
@@ -533,7 +534,7 @@ def handle_output(name, output, hidden=None):
                     output,
                     wrapped_params.params,
                     inp_data,
-                    inp_dataset_collections,
+                    input_collections,
                     input_ext,
                     python_template_version=tool.python_template_version,
                     execution_cache=execution_cache,
@@ -1156,7 +1157,7 @@ def determine_output_format(
     output: "ToolOutput",
     parameter_context,
     input_datasets,
-    input_dataset_collections,
+    input_dataset_collections: UserDict[str, model.HistoryDatasetCollectionAssociation],
     random_input_ext,
     python_template_version="3",
     execution_cache=None,
@@ -1198,7 +1199,7 @@ def determine_output_format(
 
         if collection_name in input_dataset_collections:
             try:
-                input_collection = input_dataset_collections[collection_name][0][0]
+                input_collection = input_dataset_collections[collection_name]
                 input_collection_collection = input_collection.collection
                 if element_index is None:
                     # just pick the first HDA