Unverified Commit 516f99ff authored by mvdbeek's avatar mvdbeek
Browse files

Allow tool state changes in refactor actions 

This has always been the intention given the correct tool_state_upgrade
messages. Fixes
https://github.com/galaxyproject/planemo/actions/runs/13438714063/job/37547389150
which happened with a tool update that results in an altered tool state.
parent 79681d8f

client/src/components/Workflow/Run/WorkflowRun.vue

+33 −4
Original line number Diff line number Diff line
@@ -5,7 +5,8 @@ import { RouterLink } from "vue-router"; 
import { useRouter } from "vue-router/composables";



import { canMutateHistory } from "@/api";

import { copyWorkflow } from "@/components/Workflow/workflows.services";

import { copyWorkflow, getWorkflowInfo } from "@/components/Workflow/workflows.services";

import { useWorkflowInstance } from "@/composables/useWorkflowInstance";

import { useHistoryItemsStore } from "@/stores/historyItemsStore";

import { useHistoryStore } from "@/stores/historyStore";

import { useUserStore } from "@/stores/userStore";
@@ -52,13 +53,14 @@ const submissionError = ref(""); 
const workflowError = ref("");

const workflowName = ref("");

const workflowModel: any = ref(null);

const owner = ref<string>();



const currentHistoryId = computed(() => historyStore.currentHistoryId);

const editorLink = computed(

    () => `/workflows/edit?id=${props.workflowId}${props.version ? `&version=${props.version}` : ""}`

);

const historyStatusKey = computed(() => `${currentHistoryId.value}_${lastUpdateTime.value}`);

const isOwner = computed(() => userStore.matchesCurrentUsername(workflowModel.value.runData.owner));

const isOwner = computed(() => userStore.matchesCurrentUsername(owner.value));

const lastUpdateTime = computed(() => historyItemsStore.lastUpdateTime);

const canRunOnHistory = computed(() => {

    if (!currentHistoryId.value) {
@@ -68,6 +70,16 @@ const canRunOnHistory = computed(() => { 
    return (history && canMutateHistory(history)) ?? false;

});



if (props.instance) {

    const { workflow } = useWorkflowInstance(props.workflowId);

    watch(workflow, () => {

        if (workflow.value) {

            workflowName.value = workflow.value?.name;

            owner.value = workflow.value?.owner;

        }

    });

}



function handleInvocations(incomingInvocations: any) {

    invocations.value = incomingInvocations;

    // make sure any new histories are added to historyStore
@@ -116,14 +128,31 @@ async function loadRun() { 
        hasStepVersionChanges.value = incomingModel.hasStepVersionChanges;

        workflowName.value = incomingModel.name;

        workflowModel.value = incomingModel;

        owner.value = incomingModel.runData.owner;

        loading.value = false;

    } catch (e) {

        workflowError.value = errorMessageAsString(e);

        const errMessage = errorMessageAsString(e);

        if (errMessage === "Workflow step has upgrade messages") {

            hasUpgradeMessages.value = true;

            if (!props.instance) {

                try {

                    const storedWorkflow = await getWorkflowInfo(props.workflowId);

                    owner.value = storedWorkflow.owner;

                    workflowName.value = storedWorkflow.name;

                } catch {

                    // just show original error

                    workflowError.value = errMessage;

                }

            }

        } else {

            workflowError.value = errMessage;

        }

        loading.value = false;

    }

}



async function onImport() {

    const response = await copyWorkflow(props.workflowId, workflowModel.value.runData.owner, props.version);

    const response = await copyWorkflow(props.workflowId, owner.value, props.version);

    router.push(`/workflows/edit?id=${response.id}`);

}

client/src/components/Workflow/workflows.services.ts

+1 −1
Original line number Diff line number Diff line
@@ -56,7 +56,7 @@ export async function updateWorkflow(id: string, changes: object): Promise<Workf 
    return data;

}



export async function copyWorkflow(id: string, currentOwner: string, version?: string): Promise<Workflow> {

export async function copyWorkflow(id: string, currentOwner?: string, version?: string): Promise<Workflow> {

    let path = `/api/workflows/${id}/download`;

    if (version) {

        path += `?version=${version}`;

lib/galaxy/managers/workflows.py

+1 −1
Original line number Diff line number Diff line
@@ -1983,7 +1983,7 @@ class WorkflowContentsManager(UsesAnnotations): 
            dry_run=refactor_request.dry_run,

        )



        module_injector = WorkflowModuleInjector(trans)

        module_injector = WorkflowModuleInjector(trans, allow_tool_state_corrections=True)

        refactor_executor = WorkflowRefactorExecutor(raw_workflow_description, workflow, module_injector)

        action_executions = refactor_executor.refactor(refactor_request)

        refactored_workflow, errors = self.update_workflow_from_raw_description(

lib/galaxy/workflow/modules.py

+15 −5
Original line number Diff line number Diff line
@@ -322,8 +322,13 @@ class WorkflowModule: 
        the step.

        """

        if inputs := self.get_inputs():

            try:

                return self.state.encode(Bunch(inputs=inputs), self.trans.app, nested=nested)

        else:

            except ValueError:

                log.warning("Tool state invalid for workflow module", exc_info=True)

                # Always preferable to save unmodified and continue, I think ... we're explicit about alterations when retrieving any workflow,

                # and it is what we do if we don't have the tool installed (assuming this is a tool).

                pass

        return self.state.inputs



    def get_export_state(self):
@@ -2613,7 +2618,7 @@ class WorkflowModuleInjector: 
        self.trans = trans

        self.allow_tool_state_corrections = allow_tool_state_corrections



    def inject(self, step: WorkflowStep, step_args=None, steps=None, **kwargs):

    def inject(self, step: WorkflowStep, step_args=None, steps=None, allow_tool_state_corrections=False, **kwargs):

        """Pre-condition: `step` is an ORM object coming from the database, if

        supplied `step_args` is the representation of the inputs for that step

        supplied via web form.
@@ -2646,7 +2651,12 @@ class WorkflowModuleInjector: 


            subworkflow = step.subworkflow

            assert subworkflow

            populate_module_and_state(self.trans, subworkflow, param_map=unjsonified_subworkflow_param_map)

            populate_module_and_state(

                self.trans,

                subworkflow,

                param_map=unjsonified_subworkflow_param_map,

                allow_tool_state_corrections=allow_tool_state_corrections,

            )



    def inject_all(self, workflow: Workflow, param_map=None, ignore_tool_missing_exception=False, **kwargs):

        param_map = param_map or {}

lib/galaxy/workflow/refactor/execute.py

+31 −12
Original line number Diff line number Diff line
@@ -42,19 +42,26 @@ from .schema import ( 
    UpgradeSubworkflowAction,

    UpgradeToolAction,

)

from ..modules import InputParameterModule

from ..modules import (

    InputParameterModule,

    WorkflowModuleInjector,

)



log = logging.getLogger(__name__)





class WorkflowRefactorExecutor:

    def __init__(self, raw_workflow_description, workflow, module_injector):

    def __init__(self, raw_workflow_description, workflow, module_injector: WorkflowModuleInjector):

        # we mostly use the ga representation, but there may be cases where the

        # models/modules of existing workflow are more usable.

        self.raw_workflow_description = raw_workflow_description

        self.workflow = workflow

        self.module_injector = module_injector

        self.module_injector.inject_all(workflow, ignore_tool_missing_exception=True)

        self.module_injector.inject_all(

            workflow,

            ignore_tool_missing_exception=True,

            allow_tool_state_corrections=module_injector.allow_tool_state_corrections,

        )



    def refactor(self, refactor_request: RefactorActions):

        action_executions = []
@@ -460,10 +467,22 @@ class WorkflowRefactorExecutor: 
    def _inject(self, step, execution):

        # compute runtime state, capture upgrade messages that result

        if not hasattr(step, "module"):

            self.module_injector.inject(step)

            self.module_injector.inject(step, allow_tool_state_corrections=True)

        self.module_injector.compute_runtime_state(step)

        if getattr(step, "upgrade_messages", None):

            for key, value in step.upgrade_messages.items():

                if isinstance(value, dict):

                    for input_name, message in value.items():

                        execution.messages.append(

                            RefactorActionExecutionMessage(

                                message=message,

                                message_type=RefactorActionExecutionMessageTypeEnum.tool_state_adjustment,

                                input_name=input_name,

                                step_label=step.label,

                                order_index=step.order_index,

                            )

                        )

                else:

                    message = RefactorActionExecutionMessage(

                        message=value,

                        message_type=RefactorActionExecutionMessageTypeEnum.tool_state_adjustment,