Add post job action support to PickValueModule

Backend: PJA round-trip (from_dict, from_workflow_step, save_to_step,
get_post_job_actions) and execution via ActionBox.execute_on_mapped_over.
Added execute_on_mapped_over to ChangeDatatypeAction and ColumnSetAction
in post.py to enable jobless PJA execution.

Frontend: FormPickValue renders FormSection for PJA UI (rename, change
datatype, tags, columns). Wired through FormDefault and NodeInspector.

Framework tests: 4 workflow tests for change_datatype, rename, add_tag,
and multi-PJA (all three combined).

Co-Authored-By: Claude Opus 4.6 (1M context) <noreply@anthropic.com>

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

@@ -46,7 +46,11 @@
             <FormPickValue
                 v-if="type == 'pick_value'"
                 :step="step"
-                @onChange="onChange" />
+                :datatypes="datatypes"
+                :node-inputs="stepInputs"
+                :post-job-actions="postJobActions"
+                @onChange="onChange"
+                @onChangePostJobActions="onChangePostJobActions" />
             <FormInputCollection
                 v-else-if="type == 'data_collection_input'"
                 :step="step"
@@ -104,9 +108,11 @@ const emit = defineEmits([
     "onEditSubworkflow",
     "onSetData",
     "onUpdateStep",
+    "onChangePostJobActions",
 ]);
 const stepRef = toRef(props, "step");
-const { stepId, contentId, annotation, label, name, type, configForm } = useStepProps(stepRef);
+const { stepId, contentId, annotation, label, name, type, configForm, stepInputs, postJobActions } =
+    useStepProps(stepRef);
 const { stepStore } = useWorkflowStores();
 const uniqueErrorLabel = useUniqueLabelError(stepStore, label.value);
 const stepTitle = computed(() => {
@@ -132,6 +138,9 @@ function onEditSubworkflow() {
 function onUpgradeSubworkflow() {
     emit("onAttemptRefactor", [{ action_type: "upgrade_subworkflow", step: { order_index: stepId.value } }]);
 }
+function onChangePostJobActions(postJobActions: unknown) {
+    emit("onChangePostJobActions", stepId.value, postJobActions);
+}
 
 // keeps the component from emitting the onCreate change event
 const initialChange = ref(true);

client/src/components/Workflow/Editor/Forms/FormPickValue.test.ts

@@ -35,7 +35,7 @@ function makeStep(overrides: Partial<Step> = {}): Step {
 }
 
 function mountPickValue(step?: Step): Wrapper<Vue> {
-    return shallowMount(FormPickValue, {
+    return shallowMount(FormPickValue as any, {
         propsData: {
             step: step ?? makeStep(),
         },

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

@@ -1,20 +1,33 @@
 <script setup lang="ts">
 import { toRef, watch } from "vue";
 
-import type { Step } from "@/stores/workflowStepStore";
+import type { DatatypesMapperModel } from "@/components/Datatypes/model";
+import type { InputTerminalSource, PostJobActions, Step } from "@/stores/workflowStepStore";
 
 import { useToolState } from "../composables/useToolState";
 
 import FormElement from "@/components/Form/FormElement.vue";
+import FormSection from "@/components/Workflow/Editor/Forms/FormSection.vue";
+import Heading from "@/components/Common/Heading.vue";
 
 interface ToolState {
     mode: string;
     num_inputs: number;
 }
 
-const props = defineProps<{
-    step: Step;
-}>();
+const props = withDefaults(
+    defineProps<{
+        step: Step;
+        datatypes?: DatatypesMapperModel["datatypes"];
+        nodeInputs?: InputTerminalSource[];
+        postJobActions?: PostJobActions;
+    }>(),
+    {
+        datatypes: undefined,
+        nodeInputs: () => [],
+        postJobActions: () => ({}),
+    }
+);
 
 const stepRef = toRef(props, "step");
 const { toolState } = useToolState(stepRef);
@@ -34,7 +47,7 @@ function cleanToolState(): ToolState {
     return { mode: "first_non_null", num_inputs: 2 };
 }
 
-const emit = defineEmits(["onChange"]);
+const emit = defineEmits(["onChange", "onChangePostJobActions"]);
 
 const modeOptions = [
     ["First non-null (error if all null)", "first_non_null"],
@@ -49,6 +62,10 @@ function onMode(newMode: string) {
     emit("onChange", state);
 }
 
+function onChangePostJobActions(postJobActions: PostJobActions) {
+    emit("onChangePostJobActions", postJobActions);
+}
+
 // Grow-on-connect: watch step connections, add terminal when last empty one gets connected
 watch(
     () => props.step.input_connections,
@@ -77,5 +94,16 @@ emit("onChange", cleanToolState());
             :options="modeOptions"
             help="How to select among the connected inputs."
             @input="onMode" />
+        <div v-if="datatypes && step.outputs && step.outputs.length > 0" class="mt-2 mb-4">
+            <Heading h2 separator bold size="sm"> Additional Options </Heading>
+            <FormSection
+                :id="step.id"
+                :node-inputs="nodeInputs ?? []"
+                :node-outputs="step.outputs"
+                :step="step"
+                :datatypes="datatypes"
+                :post-job-actions="postJobActions ?? {}"
+                @onChange="onChangePostJobActions" />
+        </div>
     </div>
 </template>

client/src/components/Workflow/Editor/NodeInspector.vue

@@ -129,6 +129,7 @@ function updateStored(v: boolean) {
                     :datatypes="datatypes"
                     @onSetData="(id, d) => emit('dataChanged', id, d)"
                     @onUpdateStep="(id, s) => emit('stepUpdated', id, s)"
+                    @onChangePostJobActions="(id, a) => emit('postJobActionsChanged', id, a)"
                     @onAnnotation="(id, a) => emit('annotationChanged', id, a)"
                     @onLabel="(id, l) => emit('labelChanged', id, l)"
                     @onEditSubworkflow="(id) => emit('editSubworkflow', id)"

lib/galaxy/job_execution/actions/post.py

@@ -107,6 +107,21 @@ class ChangeDatatypeAction(DefaultJobAction):
     name = "ChangeDatatypeAction"
     verbose_name = "Change Datatype"
 
+    @classmethod
+    def execute_on_mapped_over(
+        cls, trans, sa_session, action, step_inputs, step_outputs, replacement_dict, final_job_state=None
+    ):
+        if action.action_arguments and action.action_arguments.get("newtype"):
+            newtype = action.action_arguments["newtype"]
+            for name, step_output in step_outputs.items():
+                if action.output_name == "" or name == action.output_name:
+                    if hasattr(step_output, "dataset_instances"):
+                        for element in step_output.dataset_instances:
+                            if element:
+                                trans.app.datatypes_registry.change_datatype(element, newtype)
+                    else:
+                        trans.app.datatypes_registry.change_datatype(step_output, newtype)
+
     @classmethod
     def execute(cls, app, sa_session, action, job, replacement_dict=None, final_job_state=None):
         if job.state == job.states.SKIPPED:
@@ -329,19 +344,31 @@ class ColumnSetAction(DefaultJobAction):
     name = "ColumnSetAction"
     verbose_name = "Assign Columns"
 
+    @classmethod
+    def _apply_column_set(cls, dataset, action_arguments):
+        for k, v in action_arguments.items():
+            if v:
+                if not isinstance(v, int):
+                    if v[0] == "c":
+                        v = v[1:]
+                    v = int(v)
+                if v != 0:
+                    setattr(dataset.metadata, k, v)
+
+    @classmethod
+    def execute_on_mapped_over(
+        cls, trans, sa_session, action, step_inputs, step_outputs, replacement_dict, final_job_state=None
+    ):
+        if action.action_arguments:
+            for name, step_output in step_outputs.items():
+                if action.output_name == "" or name == action.output_name:
+                    cls._apply_column_set(step_output, action.action_arguments)
+
     @classmethod
     def execute(cls, app, sa_session, action, job, replacement_dict=None, final_job_state=None):
         for dataset_assoc in job.output_datasets:
             if action.output_name == "" or dataset_assoc.name == action.output_name:
-                for k, v in action.action_arguments.items():
-                    if v:
-                        # Try to use both pure integer and 'cX' format.
-                        if not isinstance(v, int):
-                            if v[0] == "c":
-                                v = v[1:]
-                            v = int(v)
-                        if v != 0:
-                            setattr(dataset_assoc.dataset.metadata, k, v)
+                cls._apply_column_set(dataset_assoc.dataset, action.action_arguments)
 
     @classmethod
     def get_short_str(cls, pja):

lib/galaxy/workflow/modules.py

@@ -1961,6 +1961,27 @@ class PickValueModule(WorkflowModule):
 
     MODES = ("first_non_null", "first_or_skip", "the_only_non_null", "all_non_null")
 
+    def __init__(self, trans, content_id=None, **kwds):
+        super().__init__(trans, content_id=content_id, **kwds)
+        self.post_job_actions: dict[str, Any] = {}
+
+    @classmethod
+    def from_dict(Class, trans, d, **kwds):
+        module = super().from_dict(trans, d, **kwds)
+        module.post_job_actions = d.get("post_job_actions", {})
+        return module
+
+    @classmethod
+    def from_workflow_step(Class, trans, step, **kwds):
+        module = super().from_workflow_step(trans, step, **kwds)
+        module.post_job_actions = {}
+        for pja in step.post_job_actions:
+            module.post_job_actions[pja.action_type + pja.output_name] = pja
+        return module
+
+    def get_post_job_actions(self, incoming):
+        return self.post_job_actions
+
     def get_inputs(self):
         # State managed by frontend Vue component, not backend forms
         return {}
@@ -1981,6 +2002,10 @@ class PickValueModule(WorkflowModule):
     def save_to_step(self, step, detached=False):
         step.type = self.type
         step.tool_inputs = self._get_state_dict()
+        if not detached:
+            for k, v in self.post_job_actions.items():
+                pja = self._to_pja(k, v, step)
+                self.trans.sa_session.add(pja)
 
     @property
     def _num_inputs(self):
@@ -2093,6 +2118,7 @@ class PickValueModule(WorkflowModule):
             raise ValueError(f"Unknown pick_value mode: {mode}")
 
         progress.set_step_outputs(invocation_step, {"output": output})
+        self._apply_post_job_actions(trans, step, output, progress.effective_replacement_dict())
         return None
 
     def _create_skipped_output(self, trans, invocation_step):
@@ -2133,6 +2159,28 @@ class PickValueModule(WorkflowModule):
         )
         return hdca
 
+    def _apply_post_job_actions(self, trans, step, output, replacement_dict):
+        """Apply post job actions directly to module output via ActionBox.
+
+        Uses execute_on_mapped_over which operates on step_outputs dict
+        rather than requiring a Job object.
+        """
+        step_outputs = {"output": output}
+        step_inputs = {}
+        for pja in step.post_job_actions:
+            ActionBox.execute_on_mapped_over(
+                trans, trans.sa_session, pja, step_inputs, step_outputs, replacement_dict
+            )
+
+    @staticmethod
+    def _to_pja(key, value, step):
+        if isinstance(value, PostJobAction):
+            return value
+        output_name = value.get("output_name") if isinstance(value, dict) else None
+        action_arguments = value.get("action_arguments") if isinstance(value, dict) else None
+        action_type = value.get("action_type", key) if isinstance(value, dict) else key
+        return PostJobAction(action_type, step, output_name, action_arguments)
+
 
 class ToolModule(WorkflowModule):
     type = "tool"

lib/galaxy_test/workflow/pick_value_add_tag.gxwf-tests.yml

@@ -0,0 +1,15 @@
+- doc: |
+    Test that TagDatasetAction on pick_value adds a tag to the output.
+  job:
+    input_data:
+      type: File
+      value: 1.bed
+      file_type: bed
+    when:
+      type: raw
+      value: true
+  outputs:
+    picked:
+      class: File
+      metadata:
+        tags: "picktag"

lib/galaxy_test/workflow/pick_value_add_tag.gxwf.yml

@@ -0,0 +1,29 @@
+class: GalaxyWorkflow
+inputs:
+  input_data:
+    type: data
+  when:
+    type: boolean
+outputs:
+  picked:
+    outputSource: pick/output
+steps:
+  branch:
+    tool_id: cat
+    in:
+      input1:
+        source: input_data
+      when:
+        source: when
+    when: $(inputs.when)
+  pick:
+    type: pick_value
+    in:
+      input_0:
+        source: branch/out_file1
+    state:
+      mode: first_or_skip
+    out:
+      output:
+        add_tags:
+          - picktag

lib/galaxy_test/workflow/pick_value_change_datatype.gxwf-tests.yml

@@ -0,0 +1,17 @@
+- doc: |
+    Test that ChangeDatatypeAction on pick_value changes output datatype.
+  job:
+    input_data:
+      type: File
+      value: 1.bed
+      file_type: bed
+    when:
+      type: raw
+      value: true
+  outputs:
+    picked:
+      class: File
+      ftype: txt
+      asserts:
+        - that: has_text
+          text: chr1

lib/galaxy_test/workflow/pick_value_change_datatype.gxwf.yml

@@ -0,0 +1,28 @@
+class: GalaxyWorkflow
+inputs:
+  input_data:
+    type: data
+  when:
+    type: boolean
+outputs:
+  picked:
+    outputSource: pick/output
+steps:
+  branch:
+    tool_id: cat
+    in:
+      input1:
+        source: input_data
+      when:
+        source: when
+    when: $(inputs.when)
+  pick:
+    type: pick_value
+    in:
+      input_0:
+        source: branch/out_file1
+    state:
+      mode: first_or_skip
+    out:
+      output:
+        change_datatype: txt

lib/galaxy_test/workflow/pick_value_multi_pja.gxwf-tests.yml

@@ -0,0 +1,17 @@
+- doc: |
+    Test multiple PJAs on pick_value: change datatype, rename, and add tag.
+  job:
+    input_data:
+      type: File
+      value: 1.bed
+      file_type: bed
+    when:
+      type: raw
+      value: true
+  outputs:
+    picked:
+      class: File
+      ftype: txt
+      metadata:
+        name: "picked_and_typed"
+        tags: "pv_tag"

lib/galaxy_test/workflow/pick_value_multi_pja.gxwf.yml

@@ -0,0 +1,31 @@
+class: GalaxyWorkflow
+inputs:
+  input_data:
+    type: data
+  when:
+    type: boolean
+outputs:
+  picked:
+    outputSource: pick/output
+steps:
+  branch:
+    tool_id: cat
+    in:
+      input1:
+        source: input_data
+      when:
+        source: when
+    when: $(inputs.when)
+  pick:
+    type: pick_value
+    in:
+      input_0:
+        source: branch/out_file1
+    state:
+      mode: first_or_skip
+    out:
+      output:
+        change_datatype: txt
+        rename: "picked_and_typed"
+        add_tags:
+          - pv_tag

lib/galaxy_test/workflow/pick_value_rename.gxwf-tests.yml

@@ -0,0 +1,15 @@
+- doc: |
+    Test that RenameDatasetAction on pick_value renames the output.
+  job:
+    input_data:
+      type: File
+      value: 1.bed
+      file_type: bed
+    when:
+      type: raw
+      value: true
+  outputs:
+    picked:
+      class: File
+      metadata:
+        name: "picked_result"

lib/galaxy_test/workflow/pick_value_rename.gxwf.yml

@@ -0,0 +1,28 @@
+class: GalaxyWorkflow
+inputs:
+  input_data:
+    type: data
+  when:
+    type: boolean
+outputs:
+  picked:
+    outputSource: pick/output
+steps:
+  branch:
+    tool_id: cat
+    in:
+      input1:
+        source: input_data
+      when:
+        source: when
+    when: $(inputs.when)
+  pick:
+    type: pick_value
+    in:
+      input_0:
+        source: branch/out_file1
+    state:
+      mode: first_or_skip
+    out:
+      output:
+        rename: "picked_result"