@galaxy-tool-util/schema 1.1.0 → 1.5.0

package/dist/workflow/normalized/toNative.js

@@ -302,7 +302,7 @@ function _buildToolStep(step, orderIndex, ctx) {
         Object.assign(toolState, finalState);
     }
     const inputConnections = _buildInputConnections(connect, ctx);
-    const postJobActions = _buildPostJobActions(step.out);
+    const postJobActions = _buildPostJobActions(step.out, step.post_job_actions);
     const connectedPaths = new Set(Object.keys(inputConnections));
     const isUserDefinedTool = toolRepresentation != null;
     const toolId = isUserDefinedTool ? null : (step.tool_id ?? undefined);
@@ -317,6 +317,7 @@ function _buildToolStep(step, orderIndex, ctx) {
         tool_shed_repository: step.tool_shed_repository,
         tool_state: toolState,
         tool_representation: toolRepresentation,
+        in: _extractStepInDefaults(step),
         tool_uuid: isUserDefinedTool ? null : (step.uuid ?? undefined),
         input_connections: inputConnections,
         post_job_actions: postJobActions,
@@ -347,7 +348,7 @@ function _buildSubworkflowStep(step, orderIndex, ctx) {
     const connect = _extractConnections(step);
     const isSubworkflow = subworkflow != null;
     const inputConnections = _buildInputConnections(connect, ctx, isSubworkflow, childCtx);
-    const postJobActions = _buildPostJobActions(step.out);
+    const postJobActions = _buildPostJobActions(step.out, step.post_job_actions);
     const connectedPaths = new Set(Object.keys(inputConnections));
     return {
         id: orderIndex,
@@ -357,6 +358,7 @@ function _buildSubworkflowStep(step, orderIndex, ctx) {
         tool_state: {},
         subworkflow,
         content_id: contentId,
+        in: _extractStepInDefaults(step),
         input_connections: inputConnections,
         post_job_actions: postJobActions,
         position: _defaultPosition(step.position, orderIndex),
@@ -401,7 +403,7 @@ function _buildPickValueStep(step, orderIndex, ctx) {
     if (numInputs > 0) {
         toolState.num_inputs = Math.max(2, numInputs);
     }
-    const postJobActions = _buildPostJobActions([...step.out]);
+    const postJobActions = _buildPostJobActions([...step.out], step.post_job_actions);
     return {
         id: orderIndex,
         type: "pick_value",
@@ -438,6 +440,21 @@ function _extractConnections(step) {
     }
     return connect;
 }
+function _extractStepInDefaults(step) {
+    // Galaxy reads step_dict["in"][name]["default"] to seed
+    // WorkflowStepInput.default_value; preserve Format2 step input defaults
+    // (tool-state scalars, File-class defaults) through to_native.
+    const result = {};
+    for (const stepInput of step.in) {
+        const inputId = stepInput.id;
+        if (!inputId)
+            continue;
+        if (stepInput.default == null)
+            continue;
+        result[inputId] = { default: stepInput.default };
+    }
+    return Object.keys(result).length > 0 ? result : undefined;
+}
 function _buildInputConnections(connect, ctx, isSubworkflow = false, subworkflowCtx) {
     const inputConnections = {};
     for (const [key, values] of Object.entries(connect)) {
@@ -462,7 +479,7 @@ function _buildInputConnections(connect, ctx, isSubworkflow = false, subworkflow
     return inputConnections;
 }
 // --- Post job actions ---
-function _buildPostJobActions(outputs) {
+function _buildPostJobActions(outputs, explicit) {
     const postJobActions = {};
     for (const output of outputs) {
         const outputName = output.id;
@@ -484,6 +501,14 @@ function _buildPostJobActions(outputs) {
             }
         }
     }
+    // Explicit step.post_job_actions wins over out:-shorthand-derived entries on
+    // key collision; entries without a matching shorthand (e.g. ValidateOutputsAction)
+    // are merged in alongside.
+    if (explicit) {
+        for (const [key, value] of Object.entries(explicit)) {
+            postJobActions[key] = value;
+        }
+    }
     return postJobActions;
 }
 function _isTruthy(val) {

package/dist/workflow/normalized/toNative.js.map

@@ -1 +1 @@
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package/dist/workflow/promote-draft.d.ts

@@ -0,0 +1,53 @@
+/**
+ * Post-extract cleanup for draft workflows.
+ *
+ * `stripPlanFields` removes the four `_plan_*` planning fields from every
+ * step (recursively into inline draft subworkflows) and from the workflow
+ * root. `promoteFullyConcreteDrafts` flips `class: GalaxyWorkflowDraft` →
+ * `class: GalaxyWorkflow` on any (sub)workflow that is now fully concrete
+ * — zero TODO sentinels, zero `_plan_*` fields anywhere — recursively.
+ *
+ * Both functions mutate the workflow dict in place (matching the
+ * `cleanWorkflow` style) and return arrays of paths describing what
+ * changed, for sidecar reporting.
+ */
+import { PLAN_FIELDS, type StepPath } from "./draft-checks.js";
+/**
+ * Path of a stripped `_plan_*` field. `path: []` means the workflow root
+ * (or, when recursing, the inner subworkflow's root reached via `prefix`).
+ */
+export interface StrippedPlanField {
+    /** Step path to the carrier; `[]` for the workflow root. */
+    path: StepPath;
+    /** Which `_plan_*` field was removed. */
+    field: (typeof PLAN_FIELDS)[number];
+}
+export interface StripPlanFieldsResult {
+    workflow: unknown;
+    removedPaths: StrippedPlanField[];
+}
+/**
+ * Strip `_plan_state` / `_plan_context` / `_plan_in` / `_plan_out` from
+ * every step and from the workflow root. Recurses into inline draft
+ * subworkflow `run:` blocks; leaves string-form `run:` and concrete
+ * `class: GalaxyWorkflow` `run:` untouched.
+ *
+ * Mutates the workflow dict in place. Pure on non-records (passes
+ * through unchanged with empty `removedPaths`).
+ */
+export declare function stripPlanFields(workflow: unknown): StripPlanFieldsResult;
+export interface PromoteFullyConcreteDraftsResult {
+    workflow: unknown;
+    /** Step paths whose inner workflow was flipped to `GalaxyWorkflow`. `[]` = the outermost workflow itself. */
+    promotedPaths: StepPath[];
+}
+/**
+ * Flip `class: GalaxyWorkflowDraft` → `class: GalaxyWorkflow` on any
+ * (sub)workflow that is now fully concrete: zero TODO sentinels, zero
+ * `_plan_*` fields anywhere in steps / root. Recurses into inline draft
+ * subworkflows; still-drafty inner workflows are left alone.
+ *
+ * Mutates in place. Pure on non-records.
+ */
+export declare function promoteFullyConcreteDrafts(workflow: unknown): PromoteFullyConcreteDraftsResult;
+//# sourceMappingURL=promote-draft.d.ts.map

package/dist/workflow/promote-draft.d.ts.map

@@ -0,0 +1 @@
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package/dist/workflow/promote-draft.js

@@ -0,0 +1,133 @@
+/**
+ * Post-extract cleanup for draft workflows.
+ *
+ * `stripPlanFields` removes the four `_plan_*` planning fields from every
+ * step (recursively into inline draft subworkflows) and from the workflow
+ * root. `promoteFullyConcreteDrafts` flips `class: GalaxyWorkflowDraft` →
+ * `class: GalaxyWorkflow` on any (sub)workflow that is now fully concrete
+ * — zero TODO sentinels, zero `_plan_*` fields anywhere — recursively.
+ *
+ * Both functions mutate the workflow dict in place (matching the
+ * `cleanWorkflow` style) and return arrays of paths describing what
+ * changed, for sidecar reporting.
+ */
+import { DRAFT_CLASS, PLAN_FIELDS, detectDraft, isDraftWorkflow, } from "./draft-checks.js";
+function isRecord(value) {
+    return typeof value === "object" && value !== null && !Array.isArray(value);
+}
+/**
+ * Strip `_plan_state` / `_plan_context` / `_plan_in` / `_plan_out` from
+ * every step and from the workflow root. Recurses into inline draft
+ * subworkflow `run:` blocks; leaves string-form `run:` and concrete
+ * `class: GalaxyWorkflow` `run:` untouched.
+ *
+ * Mutates the workflow dict in place. Pure on non-records (passes
+ * through unchanged with empty `removedPaths`).
+ */
+export function stripPlanFields(workflow) {
+    const removed = [];
+    if (!isRecord(workflow)) {
+        return { workflow, removedPaths: removed };
+    }
+    stripPlanFieldsIn(workflow, [], removed);
+    return { workflow, removedPaths: removed };
+}
+function stripPlanFieldsIn(workflow, prefix, removed) {
+    // Root-level _plan_* (only meaningful on draft workflows, but we strip
+    // unconditionally — root _plan_* on a non-draft is dead weight too).
+    for (const field of PLAN_FIELDS) {
+        if (field in workflow) {
+            delete workflow[field];
+            removed.push({ path: [...prefix], field });
+        }
+    }
+    // Step-level _plan_* + recurse into draft subworkflows.
+    for (const [label, step] of iterateStepEntries(workflow.steps)) {
+        if (!isRecord(step))
+            continue;
+        const path = [...prefix, label];
+        for (const field of PLAN_FIELDS) {
+            if (field in step) {
+                delete step[field];
+                removed.push({ path: [...path], field });
+            }
+        }
+        if (isDraftWorkflow(step.run)) {
+            stripPlanFieldsIn(step.run, path, removed);
+        }
+    }
+}
+/**
+ * Flip `class: GalaxyWorkflowDraft` → `class: GalaxyWorkflow` on any
+ * (sub)workflow that is now fully concrete: zero TODO sentinels, zero
+ * `_plan_*` fields anywhere in steps / root. Recurses into inline draft
+ * subworkflows; still-drafty inner workflows are left alone.
+ *
+ * Mutates in place. Pure on non-records.
+ */
+export function promoteFullyConcreteDrafts(workflow) {
+    const promoted = [];
+    if (!isRecord(workflow)) {
+        return { workflow, promotedPaths: promoted };
+    }
+    promoteFullyConcreteDraftsIn(workflow, [], promoted);
+    return { workflow, promotedPaths: promoted };
+}
+function promoteFullyConcreteDraftsIn(workflow, prefix, promoted) {
+    // Recurse first — flipping an outer draft before its inner drafts get
+    // a chance would mask still-drafty inner workflows under a now-concrete
+    // outer.
+    for (const [label, step] of iterateStepEntries(workflow.steps)) {
+        if (!isRecord(step))
+            continue;
+        if (isDraftWorkflow(step.run)) {
+            promoteFullyConcreteDraftsIn(step.run, [...prefix, label], promoted);
+        }
+    }
+    if (workflow.class !== DRAFT_CLASS)
+        return;
+    if (!isFullyConcrete(workflow))
+        return;
+    workflow.class = "GalaxyWorkflow";
+    promoted.push([...prefix]);
+}
+function isFullyConcrete(workflow) {
+    // detectDraft's step-walk covers TODOs + step-level _plan_*. We also
+    // check workflow root + step roots for any lingering _plan_* (detectDraft
+    // intentionally skips workflow-root _plan_*).
+    const survey = detectDraft(workflow);
+    if (survey.todos.length > 0)
+        return false;
+    if (survey.planFields.length > 0)
+        return false;
+    for (const field of PLAN_FIELDS) {
+        if (field in workflow)
+            return false;
+    }
+    // An inner draft `run:` still carrying its own work blocks promotion of
+    // the outer (we don't flip while one of our subworkflow steps is still
+    // a GalaxyWorkflowDraft).
+    for (const [, step] of iterateStepEntries(workflow.steps)) {
+        if (!isRecord(step))
+            continue;
+        if (isRecord(step.run) && step.run.class === DRAFT_CLASS)
+            return false;
+    }
+    return true;
+}
+function* iterateStepEntries(steps) {
+    if (Array.isArray(steps)) {
+        for (const step of steps) {
+            if (isRecord(step)) {
+                const label = typeof step.label === "string" ? step.label : typeof step.id === "string" ? step.id : "";
+                yield [label, step];
+            }
+        }
+    }
+    else if (isRecord(steps)) {
+        for (const [key, value] of Object.entries(steps)) {
+            yield [key, value];
+        }
+    }
+}
+//# sourceMappingURL=promote-draft.js.map

package/dist/workflow/promote-draft.js.map

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