Merge branch 'release_25.0' into release_25.1

Author: mvdbeek

lib/galaxy/tool_util/data/__init__.py

@@ -211,7 +211,7 @@ def _add_entry(
         persist: bool = False,
         entry_source: EntrySource = None,
         tool_data_file_path: Optional[str] = None,
-        use_first_file_path: bool = False,
+        bundle_mode: bool = False,
         **kwd,
     ) -> None:
         raise NotImplementedError("Abstract method")
@@ -223,7 +223,7 @@ def add_entry(
         persist: bool = False,
         entry_source: EntrySource = None,
         tool_data_file_path: Optional[str] = None,
-        use_first_file_path: bool = False,
+        bundle_mode: bool = False,
         **kwd,
     ) -> int:
         self._add_entry(
@@ -232,7 +232,7 @@ def add_entry(
             persist=persist,
             entry_source=entry_source,
             tool_data_file_path=tool_data_file_path,
-            use_first_file_path=use_first_file_path,
+            bundle_mode=bundle_mode,
             **kwd,
         )
         return self._update_version()
@@ -670,7 +670,7 @@ def _add_entry(
         persist: bool = False,
         entry_source: EntrySource = None,
         tool_data_file_path: Optional[str] = None,
-        use_first_file_path: bool = False,
+        bundle_mode: bool = False,
         **kwd,
     ) -> None:
         # accepts dict or list of columns
@@ -703,19 +703,9 @@ def _add_entry(
             raise MessageException(
                 f"Attempted to add fields ({fields}) to data table '{self.name}', but there were not enough fields specified ( {len(fields)} < {self.largest_index + 1} )."
             )
-        filename = None
 
         if persist:
-            if tool_data_file_path is not None:
-                filename = tool_data_file_path
-                if os.path.realpath(filename) not in [os.path.realpath(n) for n in self.filenames]:
-                    raise MessageException(f"Path '{tool_data_file_path}' is not a known data table file path.")
-            elif not use_first_file_path:
-                filename = self.get_filename_for_source(entry_source)
-            else:
-                for name in self.filenames:
-                    filename = name
-                    break
+            filename = self._locate_filename(tool_data_file_path, entry_source, bundle_mode)
             if filename is None:
                 # If we reach this point, there is no data table with a corresponding .loc file.
                 raise MessageException(
@@ -742,6 +732,19 @@ def _add_entry(
                 fields_collapsed = f"{self.separator.join(fields)}\n"
                 data_table_fh.write(fields_collapsed.encode("utf-8"))
 
+    def _locate_filename(self, tool_data_file_path, entry_source, bundle_mode):
+        if tool_data_file_path is not None:
+            filename = tool_data_file_path
+            if os.path.realpath(filename) not in [os.path.realpath(n) for n in self.filenames]:
+                raise MessageException(f"Path '{tool_data_file_path}' is not a known data table file path.")
+        elif not bundle_mode:
+            filename = self.get_filename_for_source(entry_source)
+        else:
+            for name in self.filenames:
+                filename = name
+                break
+        return filename
+
     def _remove_entry(self, values):
         # update every file
         for filename in self.filenames:
@@ -1183,7 +1186,7 @@ def import_bundle(
         bundle = DataTableBundle(**index)
         assert bundle.output_name
         out_data = {bundle.output_name: DirectoryAsExtraFiles(target_directory)}
-        return _process_bundle(out_data, bundle, options, self)
+        return _process_bundle(out_data, bundle, options, self, bundle_mode=True)
 
     def write_bundle(
         self,
@@ -1255,6 +1258,7 @@ def _process_bundle(
     bundle: DataTableBundle,
     options: BundleProcessingOptions,
     tool_data_tables: ToolDataTableManager,
+    bundle_mode: bool = False,
 ):
     updated_data_tables = []
     data_tables_dict = bundle.data_tables
@@ -1319,7 +1323,7 @@ def _process_bundle(
                 persist=True,
                 entry_source=bundle.repo_info,
                 tool_data_file_path=options.tool_data_file_path,
-                use_first_file_path=True,
+                bundle_mode=bundle_mode,
             )
         # Removes data table entries
         for data_table_row in data_table_remove_values:
@@ -1344,7 +1348,12 @@ def _process_bundle(
                 for name, value in data_table_row.items():
                     if name in path_column_names:
                         data_table_value[name] = os.path.abspath(os.path.join(options.data_manager_path, value))
-                data_table.add_entry(data_table_value, persist=True, entry_source=bundle.repo_info)
+                data_table.add_entry(
+                    data_table_value,
+                    persist=True,
+                    entry_source=bundle.repo_info,
+                    bundle_mode=bundle_mode,
+                )
             updated_data_tables.append(data_table_name)
     else:
         for data_table_name, data_table_values in data_tables_dict.items():

lib/galaxy/workflow/modules.py

@@ -1507,10 +1507,15 @@ def callback(input, prefixed_name, context, **kwargs):
                     subworkflow_input_name = connection.input_name
                     for step in module.subworkflow.input_steps:
                         if step.input_type == "parameter" and step.label == subworkflow_input_name:
+                            # static_options are raw tuples, convert to ParameterOption namedtuples
+                            # to match ToolModule path and support intersection logic
                             static_options.append(
-                                step.module.get_runtime_inputs(step, connections=step.output_connections)[
-                                    "input"
-                                ].static_options
+                                [
+                                    ParameterOption(*o)
+                                    for o in step.module.get_runtime_inputs(step, connections=step.output_connections)[
+                                        "input"
+                                    ].static_options
+                                ]
                             )
 
             options: Optional[list[OptionDict]] = None

lib/galaxy_test/api/test_workflows.py

@@ -7799,6 +7799,62 @@ def test_value_restriction_with_select_from_subworkflow_input(self):
         assert len(options) == 5
         assert options[0] == ["Ex1", "--ex1", False]
 
+    def test_value_restriction_with_select_from_multiple_subworkflow_inputs(self):
+        # Regression test for https://github.com/galaxyproject/galaxy/issues/21602
+        # When a workflow input with restrictOnConnections connects to multiple subworkflows,
+        # the options should be the intersection of all connected subworkflow options.
+        workflow_id = self.workflow_populator.upload_yaml_workflow(
+            """
+class: GalaxyWorkflow
+inputs:
+  Outer input parameter:
+    optional: false
+    restrictOnConnections: true
+    type: string
+steps:
+- in:
+    inner input parameter:
+      source: Outer input parameter
+  run:
+    class: GalaxyWorkflow
+    label: First subworkflow
+    inputs:
+      inner input parameter:
+        optional: false
+        restrictOnConnections: true
+        type: string
+    steps:
+    - tool_id: multi_select
+      in:
+        select_ex:
+          source: inner input parameter
+- in:
+    inner input parameter:
+      source: Outer input parameter
+  run:
+    class: GalaxyWorkflow
+    label: Second subworkflow
+    inputs:
+      inner input parameter:
+        optional: false
+        restrictOnConnections: true
+        type: string
+    steps:
+    - tool_id: multi_select
+      in:
+        select_ex:
+          source: inner input parameter
+"""
+        )
+        with self.dataset_populator.test_history() as history_id:
+            run_workflow = self._download_workflow(workflow_id, style="run", history_id=history_id)
+        options = run_workflow["steps"][0]["inputs"][0]["options"]
+        # Both subworkflows use multi_select with same options, so intersection should have all 5 options
+        assert len(options) == 5
+        # Options are sorted by label when there are multiple connections
+        option_values = {opt[1] for opt in options}
+        assert option_values == {"--ex1", "ex2", "--ex3", "--ex4", "ex5"}
+
     @skip_without_tool("random_lines1")
     def test_run_replace_params_by_tool(self):
         workflow_request, history_id, workflow_id = self._setup_random_x2_workflow("test_for_replace_tool_params")