Merge pull request #17858 from mvdbeek/fix_tool_version_switch_in_editor

[24.0] Fix tool version switch in editor

client/src/components/Workflow/Editor/Forms/FormTool.vue

@@ -116,7 +116,10 @@ export default {
     },
     computed: {
         id() {
-            return `${this.stepId}:${this.configForm.id}`;
+            // Make sure we compute a unique id. Local tools don't include the version in the id,
+            // but updating tool form when switching tool versions requires that the id changes.
+            // (see https://github.com/galaxyproject/galaxy/blob/f5e07b11f0996e75b2b6f27896b2301d8fa8717d/client/src/components/Form/FormDisplay.vue#L108)
+            return `${this.stepId}:${this.configForm.id}/${this.configForm.version}`;
         },
         toolCardId() {
             return `${this.stepId}`;

lib/galaxy/managers/workflows.py

@@ -1461,8 +1461,14 @@ 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
-            # Export differences for backward compatibility
-            tool_state = module.get_export_state()
+            errors = {}
+            try:
+                tool_state = module.get_export_state()
+            except ValueError:
+                # Fix state if necessary
+                errors = module.check_and_update_state()
+                tool_state = module.get_export_state()
+
             # Step info
             step_dict = {
                 "id": step.order_index,
@@ -1472,7 +1478,7 @@ 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 or module.get_errors(),
                 "uuid": str(step.uuid),
                 "label": step.label or None,
                 "annotation": annotation_str,

lib/galaxy/webapps/galaxy/api/workflows.py

@@ -541,15 +541,18 @@ 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] = {}
-            populate_state(trans, module.get_inputs(), inputs, module_state, check=False)
+            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.get_state(),
+            "tool_state": module_state,
             "content_id": module.get_content_id(),
             "inputs": module.get_all_inputs(connectable_only=True),
             "outputs": module.get_all_outputs(),
             "config_form": module.get_config_form(),
+            "errors": errors or None,
         }
         if payload["type"] == "tool":
             step_dict["tool_version"] = module.get_version()

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)

test/functional/tools/multiple_versions_changes_v01.xml

@@ -4,6 +4,11 @@
     </command>
     <inputs>
         <param name="inttest" value="1" type="integer" />
+        <conditional name="cond">
+            <param name="bool_to_select" type="boolean" truevalue="a" falsevalue="b"></param>
+            <when value="a" />
+            <when value="b" />
+        </conditional>
     </inputs>
     <outputs>
         <data name="out_file1" format="txt" />

test/functional/tools/multiple_versions_changes_v02.xml

@@ -5,6 +5,15 @@
     <inputs>
         <param name="inttest" value="1" type="integer" />
         <param name="floattest" value="1.0" type="float" />
+        <conditional name="cond">
+            <param name="bool_to_select" type="select">
+                <option value="a">a</option>
+                <option value="b" selected="true">b</option>
+            </param>
+            <when value="a" />
+            <when value="b" />
+        </conditional>
+
     </inputs>
     <outputs>
         <data name="out_file1" format="txt" />

test/integration/test_workflow_refactoring.py

@@ -559,7 +559,7 @@ def test_tool_version_upgrade_state_added(self):
 
         assert len(action_executions) == 1
         messages = action_executions[0].messages
-        assert len(messages) == 1
+        assert len(messages) == 2
         message = messages[0]
         assert message.message_type == RefactorActionExecutionMessageTypeEnum.tool_state_adjustment
         assert message.order_index == 0