Merge pull request #21095 from mvdbeek/fix_run_form_input_restrictions

[25.0] Fix workflow run form input restrictions

Author: mvdbeek

lib/galaxy/tool_util/parser/yaml.py

@@ -395,7 +395,10 @@ def parse_input_type(self):
             return "param"
 
     def parse_extensions(self):
-        return [ext.strip().lower() for ext in self.input_dict.get("extensions", ["data"])]
+        extensions = self.input_dict.get("extensions")
+        if not extensions:
+            extensions = self.get("format", "data").split(",")
+        return [ext.strip().lower() for ext in extensions]
 
     def parse_nested_inputs_source(self):
         assert self.parse_input_type() == "repeat"

lib/galaxy_test/api/test_workflows.py

@@ -832,6 +832,33 @@ def test_workflow_download_instance(self):
             assert initial_instance_download["workflow_id"] == first_instance_id
             assert initial_instance_download["name"] == original_name
 
+    def test_workflow_run_input_extension_restriction_applied(self):
+        workflow_id = self.workflow_populator.upload_yaml_workflow(
+            """
+class: GalaxyWorkflow
+inputs:
+  tabular_input:
+    type: data
+    format:
+     - tabular
+steps:
+  first_cat:
+    tool_id: cat1
+    in:
+      input1: tabular_input
+"""
+        )
+        with self.dataset_populator.test_history() as history_id:
+            # Upload a txt file that should NOT be available for the tabular input
+            self.dataset_populator.new_dataset(history_id, content="hello world", file_type="txt", wait=True)
+
+            # Download workflow in run style to get the form with available datasets
+            run_workflow = self._download_workflow(workflow_id, style="run", history_id=history_id)
+            tabular_input_step = run_workflow["steps"][0]
+            input_options = tabular_input_step["inputs"][0]
+            assert input_options["extensions"] == ["tabular"]
+            assert not input_options["options"]["hda"]
+
     def test_update(self):
         original_workflow = self.workflow_populator.load_workflow(name="test_import")
         uuids = {}