@galaxy-tool-util/schema 1.12.0 → 1.14.0

package/dist/workflow/layout.js

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+/**
+ * Compute and apply node positions for Galaxy workflows.
+ *
+ * Port of gxformat2/layout. Two strategies: `topological` (the cross-language
+ * layering from `cytoscape-layout.ts`) and `layered` (barycenter Sugiyama
+ * crossing reduction). Layered coordinates are not a cross-language contract;
+ * both strategies are validated by the structural checkers in
+ * `layout-properties.ts`. Cyclic workflows raise {@link LayoutCycleError}.
+ */
+import { COL_STRIDE, ROW_STRIDE, topologicalPositions } from "./cytoscape-layout.js";
+import { cytoscapeElements } from "./cytoscape.js";
+import { rawStepRenderIdentity, unlabeledNodeId } from "./normalized/labels.js";
+import { INPUT_STEP_TYPES } from "./normalized/toFormat2.js";
+/** Sentinel value for `position:` that requests automatic layout. */
+export const AUTO = "auto";
+/**
+ * Raised when a workflow graph contains a cycle. The bake path refuses to lay
+ * out a cyclic graph; the cytoscape viz path keeps its diagonal fallback.
+ */
+export class LayoutCycleError extends Error {
+    constructor(message) {
+        super(message);
+        this.name = "LayoutCycleError";
+    }
+}
+function isDict(value) {
+    return typeof value === "object" && value !== null && !Array.isArray(value);
+}
+function containerItems(container) {
+    if (Array.isArray(container))
+        return container;
+    if (isDict(container))
+        return Object.values(container);
+    return [];
+}
+// --- Graph + layering -------------------------------------------------------
+/** Pull `[nodeIds, edges]` out of cytoscape elements, dropping dangling edges. */
+export function extractGraph(elements) {
+    const nodeIds = elements.nodes.map((n) => n.data.id);
+    const idSet = new Set(nodeIds);
+    const edges = [];
+    for (const edge of elements.edges) {
+        const { source, target } = edge.data;
+        if (idSet.has(source) && idSet.has(target))
+            edges.push([source, target]);
+    }
+    return [nodeIds, edges];
+}
+/**
+ * Longest-path layering via Kahn topological sort with declaration-index tie
+ * break (same as `topologicalPositions`). Throws {@link LayoutCycleError} when
+ * the graph is not a DAG.
+ */
+export function layerAssignment(nodeIds, edges) {
+    const indexById = new Map(nodeIds.map((id, i) => [id, i]));
+    const incoming = new Map(nodeIds.map((id) => [id, []]));
+    const dependents = new Map(nodeIds.map((id) => [id, []]));
+    for (const [source, target] of edges) {
+        incoming.get(target).push(source);
+        dependents.get(source).push(target);
+    }
+    const inDegree = new Map(nodeIds.map((id) => [id, incoming.get(id).length]));
+    const column = new Map();
+    const queue = nodeIds.filter((id) => inDegree.get(id) === 0);
+    while (queue.length > 0) {
+        let best = 0;
+        for (let i = 1; i < queue.length; i++) {
+            if (indexById.get(queue[i]) < indexById.get(queue[best]))
+                best = i;
+        }
+        const id = queue.splice(best, 1)[0];
+        const sources = incoming.get(id);
+        column.set(id, sources.length === 0 ? 0 : Math.max(...sources.map((s) => column.get(s) + 1)));
+        for (const dep of dependents.get(id)) {
+            const remaining = inDegree.get(dep) - 1;
+            inDegree.set(dep, remaining);
+            if (remaining === 0)
+                queue.push(dep);
+        }
+    }
+    if (column.size !== nodeIds.length) {
+        const unplaced = nodeIds.filter((id) => !column.has(id)).sort();
+        throw new LayoutCycleError("Workflow graph contains a cycle; cannot compute a layout. " +
+            `Nodes on or downstream of the cycle: ${JSON.stringify(unplaced)}`);
+    }
+    return column;
+}
+/** Throw {@link LayoutCycleError} if `elements` describes a cyclic graph. */
+export function checkAcyclic(elements) {
+    const [nodeIds, edges] = extractGraph(elements);
+    layerAssignment(nodeIds, edges);
+}
+/** Barycenter sweeps to attempt; the best ordering seen is kept. */
+const MAX_SWEEPS = 8;
+function countCrossingsBetween(upper, lower, successors) {
+    const posLower = new Map(lower.map((id, i) => [id, i]));
+    const edges = [];
+    upper.forEach((u, uIdx) => {
+        for (const v of successors.get(u)) {
+            const vIdx = posLower.get(v);
+            if (vIdx !== undefined)
+                edges.push([uIdx, vIdx]);
+        }
+    });
+    let crossings = 0;
+    for (let i = 0; i < edges.length; i++) {
+        const [ui, vi] = edges[i];
+        for (let j = i + 1; j < edges.length; j++) {
+            const [uj, vj] = edges[j];
+            if ((ui < uj && vi > vj) || (ui > uj && vi < vj))
+                crossings += 1;
+        }
+    }
+    return crossings;
+}
+function countAllCrossings(layers, successors) {
+    let total = 0;
+    for (let col = 0; col < layers.length - 1; col++) {
+        total += countCrossingsBetween(layers[col], layers[col + 1], successors);
+    }
+    return total;
+}
+/** Stable reorder of `layer` by mean position of each node's fixed neighbors. */
+function orderByBarycenter(layer, neighbors, posInFixed) {
+    const keyed = layer.map((id, idx) => {
+        const fixed = neighbors
+            .get(id)
+            .map((m) => posInFixed.get(m))
+            .filter((p) => p !== undefined);
+        const key = fixed.length > 0 ? fixed.reduce((a, b) => a + b, 0) / fixed.length : idx;
+        return { id, key };
+    });
+    // Array.prototype.sort is stable, so ties preserve input order.
+    return keyed.sort((a, b) => a.key - b.key).map((k) => k.id);
+}
+function sweep(layers, neighbors, down) {
+    const columns = [];
+    if (down)
+        for (let col = 1; col < layers.length; col++)
+            columns.push(col);
+    else
+        for (let col = layers.length - 2; col >= 0; col--)
+            columns.push(col);
+    for (const col of columns) {
+        const fixed = layers[down ? col - 1 : col + 1];
+        const posInFixed = new Map(fixed.map((id, i) => [id, i]));
+        layers[col] = orderByBarycenter(layers[col], neighbors, posInFixed);
+    }
+}
+/**
+ * Sugiyama-style layered layout: longest-path layering, barycenter crossing
+ * reduction, then order-index rows per layer. Skip-level edges are not split
+ * into dummy nodes, so results can be suboptimal but every edge still points
+ * rightward.
+ */
+export function layeredPositions(elements) {
+    const [nodeIds, edges] = extractGraph(elements);
+    const column = layerAssignment(nodeIds, edges);
+    const maxCol = Math.max(-1, ...column.values());
+    const layers = Array.from({ length: maxCol + 1 }, () => []);
+    for (const id of nodeIds)
+        layers[column.get(id)].push(id);
+    const predecessors = new Map(nodeIds.map((id) => [id, []]));
+    const successors = new Map(nodeIds.map((id) => [id, []]));
+    for (const [source, target] of edges) {
+        successors.get(source).push(target);
+        predecessors.get(target).push(source);
+    }
+    let bestLayers = layers.map((l) => [...l]);
+    let bestCrossings = countAllCrossings(bestLayers, successors);
+    for (let i = 0; i < MAX_SWEEPS && bestCrossings > 0; i++) {
+        const goingDown = i % 2 === 0;
+        sweep(layers, goingDown ? predecessors : successors, goingDown);
+        const crossings = countAllCrossings(layers, successors);
+        if (crossings < bestCrossings) {
+            bestCrossings = crossings;
+            bestLayers = layers.map((l) => [...l]);
+        }
+    }
+    const positions = new Map();
+    bestLayers.forEach((layer, col) => {
+        layer.forEach((id, row) => positions.set(id, { x: col * COL_STRIDE, y: row * ROW_STRIDE }));
+    });
+    return positions;
+}
+// --- Document helpers (shared with layout-properties.ts) ---------------------
+export function isNativeDocument(workflow) {
+    return workflow.a_galaxy_workflow === "true";
+}
+/** A `$graph` multi-workflow document (many workflows, one file). */
+export function isGraphDocument(workflow) {
+    return isDict(workflow) && "$graph" in workflow && !("class" in workflow);
+}
+function isEmbeddedWorkflow(value) {
+    return isDict(value) && (value.class === "GalaxyWorkflow" || value.a_galaxy_workflow === "true");
+}
+/**
+ * Yield in-file subworkflows embedded in `workflow`'s steps (native inline
+ * `subworkflow`, Format2 embedded `run`). String references are not followed.
+ */
+export function* iterSubworkflows(workflow) {
+    const native = isNativeDocument(workflow);
+    for (const step of containerItems(workflow.steps)) {
+        if (!isDict(step))
+            continue;
+        const candidate = native ? step.subworkflow : step.run;
+        if (isEmbeddedWorkflow(candidate))
+            yield candidate;
+    }
+}
+/**
+ * Id cytoscape assigns to a Format2 node: inputs by id, steps by render
+ * identity. `key` is the dict-container key, or null for list form.
+ */
+export function format2NodeId(item, key, isInput) {
+    if (isInput) {
+        if (key !== null)
+            return key;
+        return isDict(item) && typeof item.id === "string" ? item.id : null;
+    }
+    if (key !== null)
+        return rawStepRenderIdentity(item, key);
+    if (!isDict(item))
+        return null;
+    const id = item.label || item.id;
+    return id ?? null;
+}
+/** Id normalization assigns to a native step (label, else unlabeled sentinel). */
+export function nativeNodeId(key, step) {
+    return unlabeledNodeId(step.label, step.id ?? key, INPUT_STEP_TYPES.has(step.type));
+}
+function stripPositions(workflow) {
+    const cleaned = JSON.parse(JSON.stringify(workflow));
+    const containerKeys = isNativeDocument(cleaned) ? ["steps"] : ["inputs", "steps"];
+    for (const containerKey of containerKeys) {
+        for (const item of containerItems(cleaned[containerKey])) {
+            if (isDict(item))
+                delete item.position;
+        }
+    }
+    return cleaned;
+}
+function shouldWrite(existing, overwrite) {
+    if (existing == null || existing === AUTO)
+        return true;
+    return overwrite;
+}
+// --- Public API ---------------------------------------------------------------
+/**
+ * Compute node positions keyed by node id (Format2 input ids / step render
+ * identities — the ids the cytoscape builder emits).
+ */
+/**
+ * Preset cytoscape elements for one layout unit. `graphEntries` are the
+ * sibling entries when `workflow` is part of a `$graph` document.
+ */
+export function layoutElements(workflow, graphEntries = []) {
+    // Strip positions first: strategies ignore them and `auto` isn't a valid position.
+    let source = isDict(workflow) ? stripPositions(workflow) : workflow;
+    if (graphEntries.length > 0 && isDict(source)) {
+        // Normalize the entry as `main` alongside its siblings so `#id` run
+        // references resolve.
+        const siblings = graphEntries.filter((e) => e !== workflow && e.id !== "main");
+        source = { $graph: [{ ...source, id: "main" }, ...siblings] };
+    }
+    return cytoscapeElements(source, { layout: "preset", draftOverlay: null });
+}
+export function layoutPositions(workflow, strategy = "topological", graphEntries = []) {
+    if (strategy !== "topological" && strategy !== "layered") {
+        throw new Error(`Unknown layout strategy "${strategy}". Valid values: topological, layered.`);
+    }
+    const elements = layoutElements(workflow, graphEntries);
+    let positions;
+    if (strategy === "topological") {
+        // topologicalPositions silently falls back on cycles; refuse up front.
+        checkAcyclic(elements);
+        positions = topologicalPositions(elements);
+    }
+    else {
+        positions = layeredPositions(elements);
+    }
+    const result = new Map();
+    for (const [id, p] of positions)
+        result.set(id, { left: p.x, top: p.y });
+    return result;
+}
+function applyToContainer(container, positions, overwrite, isInput) {
+    if (isDict(container)) {
+        for (const key of Object.keys(container)) {
+            const pos = positions.get(format2NodeId(container[key], key, isInput) ?? "");
+            if (pos === undefined)
+                continue;
+            // Promote Format2 shorthand (e.g. `x: data`) to mapping form.
+            const value = isDict(container[key]) ? container[key] : { type: container[key] };
+            if (shouldWrite(value.position, overwrite))
+                value.position = { ...pos };
+            container[key] = value;
+        }
+    }
+    else if (Array.isArray(container)) {
+        for (const item of container) {
+            if (!isDict(item))
+                continue;
+            const pos = positions.get(format2NodeId(item, null, isInput) ?? "");
+            if (pos !== undefined && shouldWrite(item.position, overwrite))
+                item.position = { ...pos };
+        }
+    }
+    return container;
+}
+function applyNative(workflow, positions, overwrite) {
+    if (!isDict(workflow.steps))
+        return;
+    for (const [key, step] of Object.entries(workflow.steps)) {
+        if (!isDict(step))
+            continue;
+        const pos = positions.get(nativeNodeId(key, step));
+        if (pos !== undefined && shouldWrite(step.position, overwrite))
+            step.position = { ...pos };
+    }
+}
+/**
+ * Merge computed positions into a Format2 or native workflow dict, mutating it
+ * in place and returning it. Explicit positions are kept unless `overwrite`;
+ * `position: auto` is always replaced. With `recursive` (default), embedded
+ * subworkflows and every `$graph` entry get their own coordinate space.
+ */
+export function applyLayout(workflow, opts = {}) {
+    if (isGraphDocument(workflow)) {
+        const entries = containerItems(workflow.$graph).filter(isDict);
+        for (const entry of entries)
+            applyLayoutUnit(entry, opts, entries);
+        return workflow;
+    }
+    return applyLayoutUnit(workflow, opts, []);
+}
+function applyLayoutUnit(workflow, opts, graphEntries) {
+    const { strategy = "topological", overwrite = false, recursive = true } = opts;
+    const positions = layoutPositions(workflow, strategy, graphEntries);
+    if (isNativeDocument(workflow)) {
+        applyNative(workflow, positions, overwrite);
+    }
+    else {
+        for (const containerKey of ["inputs", "steps"]) {
+            if (workflow[containerKey] == null)
+                continue;
+            workflow[containerKey] = applyToContainer(workflow[containerKey], positions, overwrite, containerKey === "inputs");
+        }
+    }
+    if (recursive) {
+        for (const sub of iterSubworkflows(workflow))
+            applyLayout(sub, opts);
+    }
+    return workflow;
+}
+//# sourceMappingURL=layout.js.map

package/dist/workflow/layout.js.map

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package/dist/workflow/lint-rules.d.ts

@@ -12,4 +12,10 @@ export declare class NativeStepKeyNotInteger extends Linter {
     static applies_to: readonly ["native"];
     static profile: string;
 }
+/** Step labels (including inputs) must be unique within a workflow; Galaxy refuses duplicates at import. */
+export declare class StepLabelNotUnique extends Linter {
+    static severity: "error";
+    static applies_to: readonly ["format2", "native"];
+    static profile: string;
+}
 //# sourceMappingURL=lint-rules.d.ts.map

package/dist/workflow/lint-rules.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"lint-rules.d.ts","sourceRoot":"","sources":["../../src/workflow/lint-rules.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,MAAM,EAAE,MAAM,cAAc,CAAC;AAEtC,4EAA4E;AAC5E,qBAAa,uBAAwB,SAAQ,MAAM;IACjD,MAAM,CAAC,QAAQ,EAAG,OAAO,CAAU;IACnC,MAAM,CAAC,UAAU,sBAAuB;IACxC,MAAM,CAAC,OAAO,SAAgB;CAC/B"}
+{"version":3,"file":"lint-rules.d.ts","sourceRoot":"","sources":["../../src/workflow/lint-rules.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,MAAM,EAAE,MAAM,cAAc,CAAC;AAEtC,4EAA4E;AAC5E,qBAAa,uBAAwB,SAAQ,MAAM;IACjD,MAAM,CAAC,QAAQ,EAAG,OAAO,CAAU;IACnC,MAAM,CAAC,UAAU,sBAAuB;IACxC,MAAM,CAAC,OAAO,SAAgB;CAC/B;AAED,4GAA4G;AAC5G,qBAAa,kBAAmB,SAAQ,MAAM;IAC5C,MAAM,CAAC,QAAQ,EAAG,OAAO,CAAU;IACnC,MAAM,CAAC,UAAU,iCAAkC;IACnD,MAAM,CAAC,OAAO,SAAgB;CAC/B"}

package/dist/workflow/lint-rules.js

@@ -12,4 +12,10 @@ export class NativeStepKeyNotInteger extends Linter {
     static applies_to = ["native"];
     static profile = "structural";
 }
+/** Step labels (including inputs) must be unique within a workflow; Galaxy refuses duplicates at import. */
+export class StepLabelNotUnique extends Linter {
+    static severity = "error";
+    static applies_to = ["format2", "native"];
+    static profile = "structural";
+}
 //# sourceMappingURL=lint-rules.js.map

package/dist/workflow/lint-rules.js.map

@@ -1 +1 @@
-{"version":3,"file":"lint-rules.js","sourceRoot":"","sources":["../../src/workflow/lint-rules.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,MAAM,EAAE,MAAM,cAAc,CAAC;AAEtC,4EAA4E;AAC5E,MAAM,OAAO,uBAAwB,SAAQ,MAAM;IACjD,MAAM,CAAC,QAAQ,GAAG,OAAgB,CAAC;IACnC,MAAM,CAAC,UAAU,GAAG,CAAC,QAAQ,CAAU,CAAC;IACxC,MAAM,CAAC,OAAO,GAAG,YAAY,CAAC"}
+{"version":3,"file":"lint-rules.js","sourceRoot":"","sources":["../../src/workflow/lint-rules.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAEH,OAAO,EAAE,MAAM,EAAE,MAAM,cAAc,CAAC;AAEtC,4EAA4E;AAC5E,MAAM,OAAO,uBAAwB,SAAQ,MAAM;IACjD,MAAM,CAAC,QAAQ,GAAG,OAAgB,CAAC;IACnC,MAAM,CAAC,UAAU,GAAG,CAAC,QAAQ,CAAU,CAAC;IACxC,MAAM,CAAC,OAAO,GAAG,YAAY,CAAC;;AAGhC,4GAA4G;AAC5G,MAAM,OAAO,kBAAmB,SAAQ,MAAM;IAC5C,MAAM,CAAC,QAAQ,GAAG,OAAgB,CAAC;IACnC,MAAM,CAAC,UAAU,GAAG,CAAC,SAAS,EAAE,QAAQ,CAAU,CAAC;IACnD,MAAM,CAAC,OAAO,GAAG,YAAY,CAAC"}

package/dist/workflow/lint.d.ts

@@ -29,7 +29,7 @@ export declare function lintWorkflow(workflowDict: Record<string, unknown>): Lin
 export declare function lintBestPracticesFormat2(workflowDict: Record<string, unknown>): LintResult;
 /**
  * Lint best practices for a native Galaxy workflow.
- * Runs shared format2 best practices plus native-specific checks.
+ * Runs top-level checks on the format2 view and step checks on native steps.
  */
 export declare function lintBestPracticesNative(workflowDict: Record<string, unknown>): LintResult;
 //# sourceMappingURL=lint.d.ts.map

package/dist/workflow/lint.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"lint.d.ts","sourceRoot":"","sources":["../../src/workflow/lint.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AAQH,OAAO,EAAe,KAAK,UAAU,EAAE,MAAM,cAAc,CAAC;AAI5D,OAAO,EACL,WAAW,EACX,WAAW,EACX,MAAM,EACN,WAAW,EACX,UAAU,EACV,KAAK,SAAS,EACd,KAAK,UAAU,EACf,KAAK,SAAS,EACd,KAAK,WAAW,GACjB,MAAM,cAAc,CAAC;AA4QtB;;;GAGG;AACH,wBAAgB,UAAU,CAAC,YAAY,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,UAAU,CAU5E;AAED;;;GAGG;AACH,wBAAgB,WAAW,CAAC,YAAY,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,UAAU,CAU7E;AAED;;;GAGG;AACH,wBAAgB,YAAY,CAAC,YAAY,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,UAAU,CAG9E;AA+ID;;;;GAIG;AACH,wBAAgB,wBAAwB,CAAC,YAAY,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,UAAU,CAe1F;AAED;;;GAGG;AACH,wBAAgB,uBAAuB,CAAC,YAAY,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,UAAU,CAuBzF"}

package/dist/workflow/lint.js

@@ -9,7 +9,8 @@ import { normalizedNative } from "./normalized/native.js";
 import { ensureFormat2 } from "./normalized/ensure.js";
 import { detectFormat } from "./detect-format.js";
 import { LintContext } from "./linting.js";
-import { NativeStepKeyNotInteger } from "./lint-rules.js";
+import { nativeInputLabel, nativeStepLabel } from "./normalized/toNative.js";
+import { NativeStepKeyNotInteger, StepLabelNotUnique } from "./lint-rules.js";
 export { LintContext, LintMessage, Linter, LEVEL_ERROR, LEVEL_WARN, } from "./linting.js";
 function toLintResult(ctx) {
     return {
@@ -41,6 +42,34 @@ function validateReport(ctx, report) {
     }
     // Note: Galaxy markdown validation (```galaxy directives) not yet ported
 }
+function nativeStepContext(ctx, stepKey) {
+    return ctx.child("steps").child(stepKey);
+}
+/**
+ * Error on step labels shared by more than one step, as Galaxy rejects these at import.
+ *
+ * `labeledSteps` holds `[label, description, labelContext]` for each step of one
+ * workflow level (subworkflows have their own label namespace); `labelContext`
+ * locates the label, or `undefined` to report at `ctx`. Empty labels are
+ * ignored, matching Galaxy.
+ */
+function lintDuplicateStepLabels(ctx, labeledSteps) {
+    const stepsByLabel = new Map();
+    for (const [label, description, labelContext] of labeledSteps) {
+        if (!label)
+            continue;
+        const steps = stepsByLabel.get(label);
+        if (steps)
+            steps.push([description, labelContext]);
+        else
+            stepsByLabel.set(label, [[description, labelContext]]);
+    }
+    for (const [label, steps] of stepsByLabel) {
+        if (steps.length < 2)
+            continue;
+        (steps[1][1] ?? ctx).error(`Duplicated step label '${label}' (${steps.map(([d]) => d).join(", ")})`, { linter: StepLabelNotUnique });
+    }
+}
 // ---------------------------------------------------------------------------
 // Native workflow linting
 // ---------------------------------------------------------------------------
@@ -66,11 +95,16 @@ function lintNativeWorkflow(ctx, nnw, rawDict) {
     }
     let foundOutputs = false;
     let foundOutputWithoutLabel = false;
+    lintDuplicateStepLabels(ctx, Object.entries(nnw.steps).map(([key, step]) => [
+        step.label,
+        `step ${key}`,
+        nativeStepContext(ctx, key).child("label"),
+    ]));
     for (const [orderIndex, step] of Object.entries(nnw.steps)) {
+        const stepContext = nativeStepContext(ctx, orderIndex);
         if (!/^\d+$/.test(orderIndex)) {
-            ctx.error(`expected step_key to be integer not [${orderIndex}]`, {
+            stepContext.error(`expected step_key to be integer not [${orderIndex}]`, {
                 linter: NativeStepKeyNotInteger,
-                json_pointer: `/steps/${orderIndex}`,
             });
         }
         for (const wo of step.workflow_outputs) {
@@ -85,7 +119,7 @@ function lintNativeWorkflow(ctx, nnw, rawDict) {
                 ctx.error("subworkflow is missing steps or steps are empty");
             }
             else {
-                lintNativeWorkflow(ctx, step.subworkflow);
+                lintNativeWorkflow(stepContext.child("subworkflow"), step.subworkflow);
             }
         }
         lintStepErrors(ctx, step.errors);
@@ -166,6 +200,19 @@ function lintFormat2Workflow(ctx, nf2, rawDict) {
             ctx.error("expected to find key [class] but absent");
         }
     }
+    // Check the labels conversion will assign to the native steps.
+    lintDuplicateStepLabels(ctx, [
+        ...nf2.inputs.map((inp, i) => [
+            nativeInputLabel(inp, i),
+            `input ${inp.id || i}`,
+            undefined,
+        ]),
+        ...nf2.steps.map((step) => [
+            nativeStepLabel(step),
+            `step ${step.id}`,
+            undefined,
+        ]),
+    ]);
     for (const step of nf2.steps) {
         lintStepErrors(ctx, step.errors);
         lintToolIfPresent(ctx, step.tool_id);
@@ -276,6 +323,10 @@ function lintStepBestPractices(ctx, step) {
         ctx.warn(`Workflow step ${stepId} specifies an untyped parameter in the post-job actions.`);
     }
 }
+/**
+ * Native step best-practice checks on native fields, so messages reference
+ * native ids / labels rather than format2 sentinels like `_unlabeled_step_1`.
+ */
 function lintNativeStepBestPractices(ctx, step) {
     const stepId = step.label || step.annotation || String(step.id);
     // disconnected inputs
@@ -286,14 +337,34 @@ function lintNativeStepBestPractices(ctx, step) {
             }
         }
     }
+    // missing metadata
+    if (!step.annotation) {
+        ctx.warn(`Workflow step ${stepId} has no annotation.`);
+    }
+    if (!step.label) {
+        ctx.warn(`Workflow step ${stepId} has no label.`);
+    }
+    // untyped params in tool_state
+    let toolState = step.tool_state;
+    if (typeof toolState === "string") {
+        try {
+            toolState = JSON.parse(toolState);
+        }
+        catch {
+            toolState = {};
+        }
+    }
+    if (toolState && typeof toolState === "object" && checkJsonForUntypedParams(toolState)) {
+        ctx.warn(`Workflow step ${stepId} specifies an untyped parameter as an input.`);
+    }
     // untyped params in post_job_actions
     if (step.post_job_actions && Object.keys(step.post_job_actions).length > 0) {
         if (checkJsonForUntypedParams(step.post_job_actions)) {
-            ctx.warn(`Workflow step with ID ${step.id} specifies an untyped parameter in the post-job actions.`);
+            ctx.warn(`Workflow step ${stepId} specifies an untyped parameter in the post-job actions.`);
         }
     }
 }
-function lintBestPractices(ctx, nf2, rawDict) {
+function lintWorkflowTopLevel(ctx, nf2, rawDict) {
     // annotation/doc
     if (!nf2.doc || !nf2.doc.trim()) {
         ctx.warn("Workflow is not annotated.");
@@ -322,10 +393,6 @@ function lintBestPractices(ctx, nf2, rawDict) {
     if (!nf2.license) {
         ctx.warn("Workflow does not specify a license.");
     }
-    // step-level
-    for (const step of nf2.steps) {
-        lintStepBestPractices(ctx, step);
-    }
 }
 /**
  * Lint best practices for a Format2 Galaxy workflow.
@@ -342,17 +409,19 @@ export function lintBestPracticesFormat2(workflowDict) {
         nf2 = null;
     }
     if (nf2) {
-        lintBestPractices(ctx, nf2, workflowDict);
+        lintWorkflowTopLevel(ctx, nf2, workflowDict);
+        for (const step of nf2.steps) {
+            lintStepBestPractices(ctx, step);
+        }
     }
     return toLintResult(ctx);
 }
 /**
  * Lint best practices for a native Galaxy workflow.
- * Runs shared format2 best practices plus native-specific checks.
+ * Runs top-level checks on the format2 view and step checks on native steps.
  */
 export function lintBestPracticesNative(workflowDict) {
     const ctx = new LintContext();
-    // Shared best practices on format2 view
     let nf2;
     try {
         nf2 = ensureFormat2(workflowDict);
@@ -361,9 +430,8 @@ export function lintBestPracticesNative(workflowDict) {
         nf2 = null;
     }
     if (nf2) {
-        lintBestPractices(ctx, nf2, workflowDict);
+        lintWorkflowTopLevel(ctx, nf2, workflowDict);
     }
-    // Native-specific checks
     let nnw;
     try {
         nnw = normalizedNative(workflowDict);