Fix tool state in build_module and refactor action

that can result form upgrading tools.
galaxyproject · Apr 8, 2024 · 8e8d7fa · 8e8d7fa
1 parent b321760
commit 8e8d7fa
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Showing 3 changed files with 35 additions and 2 deletions.
diff --git a/lib/galaxy/managers/workflows.py b/lib/galaxy/managers/workflows.py
@@ -1461,6 +1461,8 @@ def _workflow_to_dict_export(self, trans, stored=None, workflow=None, internal=F
             if not annotation_str and annotation_owner:
                 annotation_str = self.get_item_annotation_str(trans.sa_session, annotation_owner, step) or ""
             content_id = module.get_content_id() if allow_upgrade else step.content_id
+            # Fix state if necessary
+            errors = module.check_and_update_state()
             # Export differences for backward compatibility
             tool_state = module.get_export_state()
             # Step info
@@ -1472,7 +1474,7 @@ def _workflow_to_dict_export(self, trans, stored=None, workflow=None, internal=F
                 "tool_version": module.get_version() if allow_upgrade else step.tool_version,
                 "name": module.get_name(),
                 "tool_state": json.dumps(tool_state),
-                "errors": module.get_errors(),
+                "errors": errors,
                 "uuid": str(step.uuid),
                 "label": step.label or None,
                 "annotation": annotation_str,

diff --git a/lib/galaxy/webapps/galaxy/api/workflows.py b/lib/galaxy/webapps/galaxy/api/workflows.py
@@ -541,9 +541,10 @@ def build_module(self, trans: GalaxyWebTransaction, payload=None):
         module = module_factory.from_dict(trans, payload, from_tool_form=True)
         if "tool_state" not in payload:
             module_state: Dict[str, Any] = {}
-            errors = {}
+            errors: Dict[str, str] = {}
             populate_state(trans, module.get_inputs(), inputs, module_state, errors=errors, check=True)
             module.recover_state(module_state, from_tool_form=True)
+            module.check_and_update_state()
         step_dict = {
             "name": module.get_name(),
             "tool_state": module_state,

diff --git a/lib/galaxy_test/api/test_workflows.py b/lib/galaxy_test/api/test_workflows.py
@@ -970,6 +970,36 @@ def test_refactor(self):
         workflow_dict = self.workflow_populator.download_workflow(workflow_id)
         assert workflow_dict["steps"]["0"]["label"] == "new_label"
 
+    def test_refactor_tool_state_upgrade(self):
+        workflow_id = self.workflow_populator.upload_yaml_workflow(
+            """
+class: GalaxyWorkflow
+inputs: {}
+steps:
+  multiple_versions_changes:
+    tool_id: multiple_versions_changes
+    tool_version: "0.1"
+    state:
+      inttest: 1
+      cond:
+        bool_to_select: false
+"""
+        )
+        actions = [{"action_type": "upgrade_all_steps"}]
+        refactor_response = self.workflow_populator.refactor_workflow(workflow_id, actions, dry_run=True)
+        refactor_response.raise_for_status()
+        refactor_result = refactor_response.json()
+        upgrade_result = refactor_result["action_executions"][0]
+        assert upgrade_result["action"]["action_type"] == "upgrade_all_steps"
+        message_one, message_two = upgrade_result["messages"]
+        assert message_one["message"] == "No value found for 'floattest'. Using default: '1.0'."
+        assert message_one["input_name"] == "floattest"
+        assert message_two["message"] == "The selected case is unavailable/invalid. Using default: 'b'."
+        assert message_two["input_name"] == "cond|bool_to_select"
+
+        refactor_response = self.workflow_populator.refactor_workflow(workflow_id, actions, dry_run=False)
+        refactor_response.raise_for_status()
+
     def test_update_no_tool_id(self):
         workflow_object = self.workflow_populator.load_workflow(name="test_import")
         upload_response = self.__test_upload(workflow=workflow_object)