@galaxy-tool-util/schema 1.12.0 → 1.14.0

package/dist/workflow/index.d.ts

@@ -1,7 +1,7 @@
 export { serializeWorkflow, resolveFormat, type SerializeWorkflowOptions } from "./serialize.js";
 export { type GalaxyWorkflow, GalaxyWorkflowSchema, type GalaxyWorkflowDraft, GalaxyWorkflowDraftSchema, type DraftWorkflowStep, DraftWorkflowStepSchema, type NativeGalaxyWorkflow, NativeGalaxyWorkflowSchema, } from "./raw/index.js";
 export { galaxyWorkflowDraftJsonSchema } from "./json-schemas.js";
-export { normalizedFormat2, normalizeStepIn, normalizeStepOut, NormalizedFormat2WorkflowSchema, NormalizedFormat2StepSchema, NormalizedFormat2InputSchema, NormalizedFormat2OutputSchema, NormalizedFormat2StepInputSchema, NormalizedFormat2StepOutputSchema, type NormalizedFormat2Workflow, type NormalizedFormat2Step, type NormalizedFormat2Input, type NormalizedFormat2Output, type NormalizedFormat2StepInput, type NormalizedFormat2StepOutput, normalizedNative, NormalizedNativeWorkflowSchema, NormalizedNativeStepSchema, ToolReferenceSchema, type NormalizedNativeWorkflow, type NormalizedNativeStep, type ToolReference, toFormat2, type ToFormat2Options, type Format2StateOverride, toNative, type ToNativeOptions, toFormat2Stateful, toNativeStateful, type StepConversionStatus, type StepConversionFailureClass, type StatefulExportResult, type StatefulNativeResult, type ToolInputsResolver, ensureFormat2, ensureNative, expandedFormat2, expandedNative, isTrsUrl, MAX_EXPANSION_DEPTH, type ExpandedFormat2Workflow, type ExpandedFormat2Step, type ExpandedNativeWorkflow, type ExpandedNativeStep, type RefResolver, type ExpansionOptions, flattenCommentData, unflattenCommentData, resolveSourceReference, stepRenderIdentity, rawStepRenderIdentity, UNLABELED_INPUT_PREFIX, UNLABELED_STEP_PREFIX, } from "./normalized/index.js";
+export { normalizedFormat2, normalizeStepIn, normalizeStepOut, NormalizedFormat2WorkflowSchema, NormalizedFormat2StepSchema, NormalizedFormat2InputSchema, NormalizedFormat2OutputSchema, NormalizedFormat2StepInputSchema, NormalizedFormat2StepOutputSchema, GalaxyUserToolStubSchema, isGalaxyUserToolRun, type GalaxyUserToolStub, type NormalizedFormat2Workflow, type NormalizedFormat2Step, type NormalizedFormat2Input, type NormalizedFormat2Output, type NormalizedFormat2StepInput, type NormalizedFormat2StepOutput, normalizedNative, NormalizedNativeWorkflowSchema, NormalizedNativeStepSchema, ToolReferenceSchema, type NormalizedNativeWorkflow, type NormalizedNativeStep, type ToolReference, toFormat2, type ToFormat2Options, type Format2StateOverride, toNative, type ToNativeOptions, toFormat2Stateful, toNativeStateful, type StepConversionStatus, type StepConversionFailureClass, type StatefulExportResult, type StatefulNativeResult, type ToolInputsResolver, ensureFormat2, ensureNative, expandedFormat2, expandedNative, isTrsUrl, trsDescriptorUrl, MAX_EXPANSION_DEPTH, type ExpandedFormat2Workflow, type ExpandedFormat2Step, type ExpandedNativeWorkflow, type ExpandedNativeStep, type RefResolver, type ExpansionOptions, flattenCommentData, unflattenCommentData, resolveSourceReference, stepRenderIdentity, rawStepRenderIdentity, unlabeledNodeId, UNLABELED_INPUT_PREFIX, UNLABELED_STEP_PREFIX, } from "./normalized/index.js";
 export { flatStatePath, keysStartingWith, repeatInputsToArray, selectWhichWhen, } from "./walk-helpers.js";
 export { injectConnectionsIntoState, stripConnectedValues, nativeConnectionsFromFormat2In, } from "./state-merge.js";
 export { expandToolStateDefaults } from "./fill-defaults.js";
@@ -19,6 +19,8 @@ export { cleanWorkflow, type CleanWorkflowOptions, type CleanWorkflowResult } fr
 export { workflowToMermaid, type MermaidOptions } from "./mermaid.js";
 export { edgeAnnotationKey, type EdgeAnnotation } from "./edge-annotation.js";
 export { cytoscapeElements, type CytoscapeOptions } from "./cytoscape.js";
+export { applyLayout, layeredPositions, layoutPositions, AUTO as LAYOUT_AUTO, LayoutCycleError, type ApplyLayoutOptions, type LayoutPosition, type LayoutStrategy, } from "./layout.js";
+export { GRAPH_PROPERTY_CHECKERS, type GraphPropertyChecker } from "./layout-properties.js";
 export { elementsToList, type CytoscapeEdge, type CytoscapeEdgeData, type CytoscapeElements, type CytoscapeLayoutHint, type CytoscapeListItem, type CytoscapeNode, type CytoscapeNodeData, type CytoscapePlanReason, type CytoscapePosition, } from "./cytoscape-models.js";
 export { COL_STRIDE, ROW_STRIDE, LAYOUT_NAMES, bakesCoordinates, isLayoutName, topologicalPositions, type LayoutName, } from "./cytoscape-layout.js";
 export { detectFormat, type WorkflowFormat } from "./detect-format.js";
@@ -27,7 +29,7 @@ export { stripPlanFields, promoteFullyConcreteDrafts, type StrippedPlanField, ty
 export { withClass, validateFormat2, validateFormat2Strict, validateNative, validateNativeStrict, validatorForFixture, } from "./validators.js";
 export { validateEncodingNative, validateEncodingFormat2, checkStrictEncoding, checkStrictStructure, } from "./strict-checks.js";
 export { LintContext, LintMessage, Linter, LEVEL_ERROR, LEVEL_WARN, lintNative, lintFormat2, lintWorkflow, lintBestPracticesFormat2, lintBestPracticesNative, type LintLevel, type LintResult, type LinterRef, type EmitOptions, } from "./lint.js";
-export { NativeStepKeyNotInteger } from "./lint-rules.js";
+export { NativeStepKeyNotInteger, StepLabelNotUnique } from "./lint-rules.js";
 export { parseLintProfiles, lintProfilesById, rulesForProfile, iwcRuleIds, LINT_PROFILES_FILENAME, IWC_PROFILE_NAMES, type LintProfile, } from "./lint-profiles.js";
 export { type StepStatus, SKIP_STATUSES, type ValidationStepResult, type CleanStepResult, type ResolvedOutputType, type ConnectionResult, type ConnectionStepResult, type ConnectionValidationReport, type WorkflowEntry, type WorkflowIndex, type SingleValidationReport, type SingleLintReport, type SingleCleanReport, type DraftValidationDiagnosticReport, type DraftSurveyReport, type SingleDraftValidationReport, type ConcreteValidationReport, type DraftExtractDropReport, type DraftExtractRewriteReport, type SingleDraftExtractReport, type DiffType, type DiffSeverity, type BenignArtifact, type StepDiff, type SkipWorkflowReason, type FailureClass, type StepResult, type RoundTripResult, type StepIdMappingResult, type RoundTripValidationResult, type SingleRoundTripReport, type SingleExportReport, type StepEncodeStatus, type ToNativeResult, type WorkflowSourceFormat, type ExportResult, type ConvertResult, type WorkflowValidationResult, type LintWorkflowResult, type WorkflowCleanResult, type CategoryGroup, type TreeValidationReport, type LintTreeReport, type TreeCleanReport, type WorkflowExportResult, type ExportTreeReport, type WorkflowToNativeResult, type ToNativeTreeReport, type ToolFailureMode, type RoundTripTreeReport, validationSummary, validationFailures, cleanDisplayLabel, categoryOf, groupByCategory, buildSingleValidationReport, buildSingleLintReport, buildSingleCleanReport, buildSingleDraftValidationReport, buildSingleDraftExtractReport, buildWorkflowValidationResult, buildLintWorkflowResult, buildWorkflowCleanResult, buildTreeValidationReport, buildLintTreeReport, buildTreeCleanReport, buildWorkflowExportResult, buildExportTreeReport, buildWorkflowToNativeResult, buildToNativeTreeReport, buildRoundTripTreeReport, } from "./report-models.js";
 //# sourceMappingURL=index.d.ts.map

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

@@ -1 +1 @@
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package/dist/workflow/index.js

@@ -5,7 +5,7 @@ export { GalaxyWorkflowSchema, GalaxyWorkflowDraftSchema, DraftWorkflowStepSchem
 // Plain JSON Schema siblings for downstream packagers (issue #108)
 export { galaxyWorkflowDraftJsonSchema } from "./json-schemas.js";
 // Normalized workflow types + normalizers
-export { normalizedFormat2, normalizeStepIn, normalizeStepOut, NormalizedFormat2WorkflowSchema, NormalizedFormat2StepSchema, NormalizedFormat2InputSchema, NormalizedFormat2OutputSchema, NormalizedFormat2StepInputSchema, NormalizedFormat2StepOutputSchema, normalizedNative, NormalizedNativeWorkflowSchema, NormalizedNativeStepSchema, ToolReferenceSchema, toFormat2, toNative, toFormat2Stateful, toNativeStateful, ensureFormat2, ensureNative, expandedFormat2, expandedNative, isTrsUrl, MAX_EXPANSION_DEPTH, flattenCommentData, unflattenCommentData, resolveSourceReference, stepRenderIdentity, rawStepRenderIdentity, UNLABELED_INPUT_PREFIX, UNLABELED_STEP_PREFIX, } from "./normalized/index.js";
+export { normalizedFormat2, normalizeStepIn, normalizeStepOut, NormalizedFormat2WorkflowSchema, NormalizedFormat2StepSchema, NormalizedFormat2InputSchema, NormalizedFormat2OutputSchema, NormalizedFormat2StepInputSchema, NormalizedFormat2StepOutputSchema, GalaxyUserToolStubSchema, isGalaxyUserToolRun, normalizedNative, NormalizedNativeWorkflowSchema, NormalizedNativeStepSchema, ToolReferenceSchema, toFormat2, toNative, toFormat2Stateful, toNativeStateful, ensureFormat2, ensureNative, expandedFormat2, expandedNative, isTrsUrl, trsDescriptorUrl, MAX_EXPANSION_DEPTH, flattenCommentData, unflattenCommentData, resolveSourceReference, stepRenderIdentity, rawStepRenderIdentity, unlabeledNodeId, UNLABELED_INPUT_PREFIX, UNLABELED_STEP_PREFIX, } from "./normalized/index.js";
 export { flatStatePath, keysStartingWith, repeatInputsToArray, selectWhichWhen, } from "./walk-helpers.js";
 export { injectConnectionsIntoState, stripConnectedValues, nativeConnectionsFromFormat2In, } from "./state-merge.js";
 export { expandToolStateDefaults } from "./fill-defaults.js";
@@ -23,6 +23,8 @@ export { cleanWorkflow } from "./clean.js";
 export { workflowToMermaid } from "./mermaid.js";
 export { edgeAnnotationKey } from "./edge-annotation.js";
 export { cytoscapeElements } from "./cytoscape.js";
+export { applyLayout, layeredPositions, layoutPositions, AUTO as LAYOUT_AUTO, LayoutCycleError, } from "./layout.js";
+export { GRAPH_PROPERTY_CHECKERS } from "./layout-properties.js";
 export { elementsToList, } from "./cytoscape-models.js";
 export { COL_STRIDE, ROW_STRIDE, LAYOUT_NAMES, bakesCoordinates, isLayoutName, topologicalPositions, } from "./cytoscape-layout.js";
 export { detectFormat } from "./detect-format.js";
@@ -31,7 +33,7 @@ export { stripPlanFields, promoteFullyConcreteDrafts, } from "./promote-draft.js
 export { withClass, validateFormat2, validateFormat2Strict, validateNative, validateNativeStrict, validatorForFixture, } from "./validators.js";
 export { validateEncodingNative, validateEncodingFormat2, checkStrictEncoding, checkStrictStructure, } from "./strict-checks.js";
 export { LintContext, LintMessage, Linter, LEVEL_ERROR, LEVEL_WARN, lintNative, lintFormat2, lintWorkflow, lintBestPracticesFormat2, lintBestPracticesNative, } from "./lint.js";
-export { NativeStepKeyNotInteger } from "./lint-rules.js";
+export { NativeStepKeyNotInteger, StepLabelNotUnique } from "./lint-rules.js";
 export { parseLintProfiles, lintProfilesById, rulesForProfile, iwcRuleIds, LINT_PROFILES_FILENAME, IWC_PROFILE_NAMES, } from "./lint-profiles.js";
 // Structured report models (mirrors Python _report_models.py)
 export { SKIP_STATUSES, validationSummary, validationFailures, cleanDisplayLabel, categoryOf, groupByCategory, buildSingleValidationReport, buildSingleLintReport, buildSingleCleanReport, buildSingleDraftValidationReport, buildSingleDraftExtractReport, buildWorkflowValidationResult, buildLintWorkflowResult, buildWorkflowCleanResult, buildTreeValidationReport, buildLintTreeReport, buildTreeCleanReport, buildWorkflowExportResult, buildExportTreeReport, buildWorkflowToNativeResult, buildToNativeTreeReport, buildRoundTripTreeReport, } from "./report-models.js";

package/dist/workflow/index.js.map

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package/dist/workflow/layout-properties.d.ts

@@ -0,0 +1,10 @@
+/**
+ * Structural graph properties any conforming workflow layout must satisfy.
+ *
+ * Port of gxformat2/layout/_properties.py. The property names are the
+ * cross-language contract for `graph_properties` in layout.yml expectations;
+ * each checker takes a laid-out document and throws on violation.
+ */
+export type GraphPropertyChecker = (workflow: unknown) => void;
+export declare const GRAPH_PROPERTY_CHECKERS: Record<string, GraphPropertyChecker>;
+//# sourceMappingURL=layout-properties.d.ts.map

package/dist/workflow/layout-properties.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"layout-properties.d.ts","sourceRoot":"","sources":["../../src/workflow/layout-properties.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AAeH,MAAM,MAAM,oBAAoB,GAAG,CAAC,QAAQ,EAAE,OAAO,KAAK,IAAI,CAAC;AAkH/D,eAAO,MAAM,uBAAuB,EAAE,MAAM,CAAC,MAAM,EAAE,oBAAoB,CAKxE,CAAC"}

package/dist/workflow/layout-properties.js

@@ -0,0 +1,112 @@
+/**
+ * Structural graph properties any conforming workflow layout must satisfy.
+ *
+ * Port of gxformat2/layout/_properties.py. The property names are the
+ * cross-language contract for `graph_properties` in layout.yml expectations;
+ * each checker takes a laid-out document and throws on violation.
+ */
+import { extractGraph, format2NodeId, isGraphDocument, isNativeDocument, iterSubworkflows, layoutElements, nativeNodeId, } from "./layout.js";
+function isDict(value) {
+    return typeof value === "object" && value !== null && !Array.isArray(value);
+}
+/** Read `{nodeId: position}` straight from the document (not from cytoscape). */
+function readNodePositions(workflow) {
+    const positions = new Map();
+    if (isNativeDocument(workflow)) {
+        if (isDict(workflow.steps)) {
+            for (const [key, step] of Object.entries(workflow.steps)) {
+                if (isDict(step) && step.position != null) {
+                    positions.set(nativeNodeId(key, step), step.position);
+                }
+            }
+        }
+        return positions;
+    }
+    for (const containerKey of ["inputs", "steps"]) {
+        const container = workflow[containerKey];
+        const isInput = containerKey === "inputs";
+        const entries = isDict(container)
+            ? Object.entries(container)
+            : Array.isArray(container)
+                ? container.map((item) => [null, item])
+                : [];
+        for (const [key, item] of entries) {
+            const nodeId = format2NodeId(item, key, isInput);
+            if (isDict(item) && item.position != null && nodeId !== null) {
+                positions.set(nodeId, item.position);
+            }
+        }
+    }
+    return positions;
+}
+function graph(workflow, graphEntries) {
+    const [nodeIds, edges] = extractGraph(layoutElements(workflow, graphEntries));
+    return [nodeIds, edges, readNodePositions(workflow)];
+}
+function check(condition, message) {
+    if (!condition)
+        throw new Error(message);
+}
+/** Every edge points strictly rightward: `target.left > source.left`. */
+function downstreamRightOfUpstream([, edges, positions]) {
+    for (const [source, target] of edges) {
+        const s = positions.get(source);
+        const t = positions.get(target);
+        check(s !== undefined, `edge ${source}->${target}: source ${source} has no position`);
+        check(t !== undefined, `edge ${source}->${target}: target ${target} has no position`);
+        check(t.left > s.left, `edge ${source}->${target}: target.left ${t.left} not strictly right of source.left ${s.left}`);
+    }
+}
+/** Every graph node has a position in the document. */
+function allNodesPositioned([nodeIds, , positions]) {
+    const missing = nodeIds.filter((id) => !positions.has(id)).sort();
+    check(missing.length === 0, `nodes missing a position: ${JSON.stringify(missing)}`);
+}
+/** No two nodes occupy the same `{left, top}` coordinate. */
+function noPositionCollisions([, , positions]) {
+    const seen = new Map();
+    for (const [id, pos] of positions) {
+        const key = `${pos.left},${pos.top}`;
+        check(!seen.has(key), `nodes ${seen.get(key)} and ${id} share position (${key})`);
+        seen.set(key, id);
+    }
+}
+/** Nodes with no incoming edge sit at the minimum `left`. */
+function rootsLeftmost([nodeIds, edges, positions]) {
+    const targets = new Set(edges.map(([, target]) => target));
+    const roots = nodeIds.filter((id) => !targets.has(id));
+    if (roots.length === 0 || positions.size === 0)
+        return;
+    const minLeft = Math.min(...[...positions.values()].map((p) => p.left));
+    for (const id of roots) {
+        const pos = positions.get(id);
+        check(pos !== undefined, `root ${id} has no position`);
+        check(pos.left === minLeft, `root ${id} at left ${pos.left} is not at the minimum left ${minLeft}`);
+    }
+}
+/** The document plus every in-file subworkflow / `$graph` entry it lays out. */
+function* iterLayoutUnits(workflow, graphEntries = []) {
+    if (isGraphDocument(workflow)) {
+        const raw = workflow.$graph;
+        const entries = (Array.isArray(raw) ? raw : isDict(raw) ? Object.values(raw) : []).filter(isDict);
+        for (const entry of entries)
+            yield* iterLayoutUnits(entry, entries);
+        return;
+    }
+    yield graph(workflow, graphEntries);
+    for (const sub of iterSubworkflows(workflow))
+        yield* iterLayoutUnits(sub);
+}
+function recursive(checker) {
+    return (workflow) => {
+        for (const unit of iterLayoutUnits(workflow))
+            checker(unit);
+    };
+}
+export const GRAPH_PROPERTY_CHECKERS = {
+    downstream_right_of_upstream: recursive(downstreamRightOfUpstream),
+    all_nodes_positioned: recursive(allNodesPositioned),
+    no_position_collisions: recursive(noPositionCollisions),
+    roots_leftmost: recursive(rootsLeftmost),
+};
+//# sourceMappingURL=layout-properties.js.map

package/dist/workflow/layout-properties.js.map

@@ -0,0 +1 @@
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package/dist/workflow/layout.d.ts

@@ -0,0 +1,84 @@
+/**
+ * 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 type { CytoscapeElements, CytoscapePosition } from "./cytoscape-models.js";
+/** Sentinel value for `position:` that requests automatic layout. */
+export declare const AUTO = "auto";
+export type LayoutStrategy = "topological" | "layered";
+export interface LayoutPosition {
+    left: number;
+    top: number;
+}
+export interface ApplyLayoutOptions {
+    strategy?: LayoutStrategy;
+    /** Replace explicit positions too (an `auto` sentinel is always replaced). */
+    overwrite?: boolean;
+    /** Also lay out embedded in-file subworkflows. Defaults to true. */
+    recursive?: boolean;
+}
+/**
+ * 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 declare class LayoutCycleError extends Error {
+    constructor(message: string);
+}
+type Dict = Record<string, unknown>;
+export type Edge = [string, string];
+/** Pull `[nodeIds, edges]` out of cytoscape elements, dropping dangling edges. */
+export declare function extractGraph(elements: CytoscapeElements): [string[], Edge[]];
+/**
+ * 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 declare function layerAssignment(nodeIds: string[], edges: Edge[]): Map<string, number>;
+/** Throw {@link LayoutCycleError} if `elements` describes a cyclic graph. */
+export declare function checkAcyclic(elements: CytoscapeElements): void;
+/**
+ * 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 declare function layeredPositions(elements: CytoscapeElements): Map<string, CytoscapePosition>;
+export declare function isNativeDocument(workflow: Dict): boolean;
+/** A `$graph` multi-workflow document (many workflows, one file). */
+export declare function isGraphDocument(workflow: unknown): workflow is Dict;
+/**
+ * Yield in-file subworkflows embedded in `workflow`'s steps (native inline
+ * `subworkflow`, Format2 embedded `run`). String references are not followed.
+ */
+export declare function iterSubworkflows(workflow: Dict): Generator<Dict>;
+/**
+ * Id cytoscape assigns to a Format2 node: inputs by id, steps by render
+ * identity. `key` is the dict-container key, or null for list form.
+ */
+export declare function format2NodeId(item: unknown, key: string | null, isInput: boolean): string | null;
+/** Id normalization assigns to a native step (label, else unlabeled sentinel). */
+export declare function nativeNodeId(key: string, step: Dict): string;
+/**
+ * Compute node positions keyed by node id (Format2 input ids / step render
+ * identities — the ids the cytoscape builder emits).
+ */
+/**
+ * Preset cytoscape elements for one layout unit. `graphEntries` are the
+ * sibling entries when `workflow` is part of a `$graph` document.
+ */
+export declare function layoutElements(workflow: unknown, graphEntries?: Dict[]): CytoscapeElements;
+export declare function layoutPositions(workflow: unknown, strategy?: LayoutStrategy, graphEntries?: Dict[]): Map<string, LayoutPosition>;
+/**
+ * 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 declare function applyLayout(workflow: Dict, opts?: ApplyLayoutOptions): Dict;
+export {};
+//# sourceMappingURL=layout.d.ts.map

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