Allow setting default value for required parameter

galaxyproject · Nov 28, 2024 · 40a8bb1 · 40a8bb1
1 parent a648915
commit 40a8bb1
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Showing 4 changed files with 14 additions and 8 deletions.
diff --git a/lib/galaxy/workflow/modules.py b/lib/galaxy/workflow/modules.py
@@ -1260,12 +1260,15 @@ def get_inputs(self):
 
             when_true = ConditionalWhen()
             when_true.value = "true"
-            when_true.inputs = {}
-            when_true.inputs["default"] = specify_default_cond
+            when_true.inputs = {"default": specify_default_cond}
 
             when_false = ConditionalWhen()
             when_false.value = "false"
-            when_false.inputs = {}
+            # This is only present for backwards compatibility,
+            # We don't need this conditional since you can set
+            # a default value for optional and required parameters.
+            # TODO: version the state and upgrade it to a simpler version
+            when_false.inputs = {"default": specify_default_cond}
 
             optional_cases = [when_true, when_false]
             optional_cond.cases = optional_cases
@@ -1504,6 +1507,7 @@ def get_runtime_inputs(self, step, connections: Optional[Iterable[WorkflowStepCo
         parameter_def = self._parse_state_into_dict()
         parameter_type = parameter_def["parameter_type"]
         optional = parameter_def["optional"]
+        default_value_set = "default" in parameter_def
         default_value = parameter_def.get("default", self.default_default_value)
         if parameter_type not in ["text", "boolean", "integer", "float", "color", "directory_uri"]:
             raise ValueError("Invalid parameter type for workflow parameters encountered.")
@@ -1557,7 +1561,7 @@ def _parameter_def_list_to_options(parameter_value):
 
         parameter_class = parameter_types[client_parameter_type]
 
-        if optional:
+        if default_value_set:
             if client_parameter_type == "select":
                 parameter_kwds["selected"] = default_value
             else:
@@ -1633,7 +1637,6 @@ def step_state_to_tool_state(self, state):
         if "default" in state:
             default_set = True
             default_value = state["default"]
-            state["optional"] = True
         multiple = state.get("multiple")
         source_validators = state.get("validators")
         restrictions = state.get("restrictions")

diff --git a/lib/galaxy/workflow/run.py b/lib/galaxy/workflow/run.py
@@ -574,8 +574,8 @@ def set_outputs_for_input(
         if self.inputs_by_step_id:
             step_id = step.id
             if step_id not in self.inputs_by_step_id and "output" not in outputs:
-                default_value = step.input_default_value
-                if default_value or step.input_optional:
+                default_value = step.get_input_default_value(modules.NO_REPLACEMENT)
+                if default_value is not modules.NO_REPLACEMENT:
                     outputs["output"] = default_value
                 else:
                     log.error(f"{step.log_str()} not found in inputs_step_id {self.inputs_by_step_id}")

diff --git a/lib/galaxy_test/api/test_workflows.py b/lib/galaxy_test/api/test_workflows.py
@@ -3212,7 +3212,7 @@ def test_export_invocation_ro_crate_adv(self):
 """,
                 test_data="""
 num_lines_param:
-  type: int
+  type: raw
   value: 2
 input collection 1:
   collection_type: list
@@ -7034,12 +7034,14 @@ def test_subworkflow_import_order_maintained(self, history_id):
   outer_input_1:
     type: int
     default: 1
+    optional: true
     position:
       left: 0
       top: 0
   outer_input_2:
     type: int
     default: 2
+    optional: true
     position:
       left: 100
       top: 0

diff --git a/lib/galaxy_test/base/workflow_fixtures.py b/lib/galaxy_test/base/workflow_fixtures.py
@@ -617,6 +617,7 @@
   int_input:
     type: integer
     default: 3
+    optional: true
 steps:
   random:
     tool_id: random_lines1