@galaxy-tool-util/schema 1.1.0 → 1.5.0

package/dist/workflow/cytoscape-layout.js

@@ -0,0 +1,115 @@
+/**
+ * Cross-language topological layout for Cytoscape elements.
+ *
+ * Spec: docs/architecture/cytoscape-layout.md. Any change here is a breaking
+ * visual diff and must land in lockstep with the gxformat2 port.
+ */
+export const COL_STRIDE = 220;
+export const ROW_STRIDE = 100;
+export const LAYOUT_NAMES = [
+    "preset",
+    "topological",
+    "dagre",
+    "breadthfirst",
+    "grid",
+    "cose",
+    "random",
+];
+export function isLayoutName(value) {
+    return LAYOUT_NAMES.includes(value);
+}
+/**
+ * Layouts that bake coordinates into `data.position`. All other layouts are
+ * hint-only and rely on the runtime renderer.
+ */
+export function bakesCoordinates(layout) {
+    return layout === "preset" || layout === "topological";
+}
+/**
+ * Compute positions per the topological layering spec. Returns a map keyed by
+ * node `data.id` so callers can overwrite `node.position` in declaration order.
+ */
+export function topologicalPositions(elements) {
+    const nodeIds = elements.nodes.map((n) => n.data.id);
+    const indexById = new Map();
+    nodeIds.forEach((id, i) => indexById.set(id, i));
+    const incoming = new Map();
+    for (const id of nodeIds)
+        incoming.set(id, []);
+    for (const edge of elements.edges) {
+        const { source, target } = edge.data;
+        if (!indexById.has(source) || !indexById.has(target))
+            continue;
+        incoming.get(target).push(source);
+    }
+    const inDegree = new Map();
+    for (const [id, srcs] of incoming)
+        inDegree.set(id, srcs.length);
+    // Kahn topo sort with declaration-index tie break. We avoid a heap to keep
+    // the algorithm trivially portable; node counts are tiny (workflows
+    // typically <100 steps).
+    const column = new Map();
+    const ready = nodeIds.filter((id) => inDegree.get(id) === 0);
+    const queue = [...ready];
+    // sort once by declaration index — entries already in declaration order, but
+    // keep the sort explicit so the contract stays obvious.
+    queue.sort((a, b) => indexById.get(a) - indexById.get(b));
+    const visited = new Set();
+    const dependents = new Map();
+    for (const id of nodeIds)
+        dependents.set(id, []);
+    for (const [target, sources] of incoming) {
+        for (const s of sources)
+            dependents.get(s).push(target);
+    }
+    while (queue.length > 0) {
+        // pop lowest declaration index
+        let bestIdx = 0;
+        for (let i = 1; i < queue.length; i++) {
+            if (indexById.get(queue[i]) < indexById.get(queue[bestIdx]))
+                bestIdx = i;
+        }
+        const id = queue.splice(bestIdx, 1)[0];
+        visited.add(id);
+        const sources = incoming.get(id);
+        if (sources.length === 0) {
+            column.set(id, 0);
+        }
+        else {
+            let max = 0;
+            for (const s of sources) {
+                const c = column.get(s);
+                if (c !== undefined && c + 1 > max)
+                    max = c + 1;
+            }
+            column.set(id, max);
+        }
+        for (const dep of dependents.get(id)) {
+            const remaining = inDegree.get(dep) - 1;
+            inDegree.set(dep, remaining);
+            if (remaining === 0)
+                queue.push(dep);
+        }
+    }
+    // Cycle fallback: any node not visited gets column = declaration index.
+    for (const id of nodeIds) {
+        if (!visited.has(id))
+            column.set(id, indexById.get(id));
+    }
+    // Row assignment: per column, declaration order.
+    const rowsByColumn = new Map();
+    for (const id of nodeIds) {
+        const c = column.get(id);
+        if (!rowsByColumn.has(c))
+            rowsByColumn.set(c, []);
+        rowsByColumn.get(c).push(id);
+    }
+    const positions = new Map();
+    for (const [c, ids] of rowsByColumn) {
+        ids.forEach((id, row) => {
+            positions.set(id, { x: c * COL_STRIDE, y: row * ROW_STRIDE });
+        });
+    }
+    return positions;
+}
+//# sourceMappingURL=cytoscape-layout.js.map

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

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

@@ -0,0 +1,67 @@
+/**
+ * Output-only TS interfaces for Cytoscape.js workflow visualization elements.
+ *
+ * Port of gxformat2/cytoscape/models.py. Field names stay snake_case so the
+ * emitted JSON is byte-identical to the Python builder.
+ */
+export interface CytoscapePosition {
+    x: number;
+    y: number;
+}
+export interface CytoscapeNodeData {
+    id: string;
+    label: string;
+    doc: string | null;
+    tool_id: string | null;
+    step_type: string;
+    repo_link: string | null;
+}
+export interface CytoscapeEdgeData {
+    id: string;
+    source: string;
+    target: string;
+    input: string;
+    output: string | null;
+    /**
+     * Map-over depth applied at this connection, when annotated. Optional so the
+     * default emit shape stays byte-identical with the Python builder.
+     */
+    map_depth?: number;
+    /** True when the connection reduces a list-like source into a multi-data scalar input. */
+    reduction?: boolean;
+    /** Textual mapping (e.g. "list", "list:paired"); mirrors `ConnectionResult.mapping`. */
+    mapping?: string | null;
+}
+export interface CytoscapeNode {
+    group: "nodes";
+    data: CytoscapeNodeData;
+    classes: string[];
+    /**
+     * Present for `preset` and `topological` layouts; omitted for hint-only
+     * layouts (`dagre`, `breadthfirst`, `grid`, `cose`, `random`) so the runtime
+     * renderer is responsible for placement.
+     */
+    position?: CytoscapePosition;
+}
+export interface CytoscapeEdge {
+    group: "edges";
+    data: CytoscapeEdgeData;
+    /** Optional class hints (e.g. "mapover_2", "reduction") used by the HTML viewer's stylesheet. */
+    classes?: string[];
+}
+export interface CytoscapeLayoutHint {
+    name: string;
+}
+export interface CytoscapeElements {
+    nodes: CytoscapeNode[];
+    edges: CytoscapeEdge[];
+    /**
+     * Present only when the builder was invoked with a non-`preset` layout.
+     * Carried out-of-band so `elementsToList` keeps Python parity for the flat
+     * list shape.
+     */
+    layout?: CytoscapeLayoutHint;
+}
+export type CytoscapeListItem = CytoscapeNode | CytoscapeEdge;
+export declare function elementsToList(els: CytoscapeElements): CytoscapeListItem[];
+//# sourceMappingURL=cytoscape-models.d.ts.map

package/dist/workflow/cytoscape-models.d.ts.map

@@ -0,0 +1 @@
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package/dist/workflow/cytoscape-models.js

@@ -0,0 +1,10 @@
+/**
+ * Output-only TS interfaces for Cytoscape.js workflow visualization elements.
+ *
+ * Port of gxformat2/cytoscape/models.py. Field names stay snake_case so the
+ * emitted JSON is byte-identical to the Python builder.
+ */
+export function elementsToList(els) {
+    return [...els.nodes, ...els.edges];
+}
+//# sourceMappingURL=cytoscape-models.js.map

package/dist/workflow/cytoscape-models.js.map

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

@@ -0,0 +1,29 @@
+/**
+ * Build Cytoscape.js elements from a Galaxy workflow.
+ *
+ * Port of gxformat2/cytoscape/_builder.py. Snake_case field names + edge id
+ * format are preserved byte-for-byte to interop with the Python emitter and
+ * the standalone HTML template.
+ */
+import type { CytoscapeElements } from "./cytoscape-models.js";
+import type { LayoutName } from "./cytoscape-layout.js";
+import type { EdgeAnnotation } from "./edge-annotation.js";
+import type { NormalizedFormat2Workflow } from "./normalized/format2.js";
+export interface CytoscapeOptions {
+    /**
+     * Optional `EdgeAnnotation` map keyed by `edgeAnnotationKey(...)`. When
+     * present, edges gain `data.map_depth`, `data.reduction`, `data.mapping`
+     * and class hints (`mapover_<n>`, `reduction`).
+     */
+    edgeAnnotations?: Map<string, EdgeAnnotation>;
+    /**
+     * Layout strategy. `preset` (default) keeps today's coordinate-from-NF2
+     * behavior with a `(10*i, 10*i)` fallback. `topological` overwrites
+     * coordinates per `cytoscape-layout.ts`. Hint-only layouts (`dagre`,
+     * `breadthfirst`, `grid`, `cose`, `random`) drop coordinates and emit a
+     * top-level `elements.layout = { name }` hint for the runtime renderer.
+     */
+    layout?: LayoutName;
+}
+export declare function cytoscapeElements(workflow: unknown | NormalizedFormat2Workflow, opts?: CytoscapeOptions): CytoscapeElements;
+//# sourceMappingURL=cytoscape.d.ts.map

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

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package/dist/workflow/cytoscape.js

@@ -0,0 +1,172 @@
+/**
+ * Build Cytoscape.js elements from a Galaxy workflow.
+ *
+ * Port of gxformat2/cytoscape/_builder.py. Snake_case field names + edge id
+ * format are preserved byte-for-byte to interop with the Python emitter and
+ * the standalone HTML template.
+ */
+import { bakesCoordinates, topologicalPositions } from "./cytoscape-layout.js";
+import { edgeAnnotationKey } from "./edge-annotation.js";
+import { ensureFormat2 } from "./normalized/ensure.js";
+import { isUnlabeledStep, resolveSourceReference } from "./normalized/labels.js";
+const MAIN_TS_PREFIX = "toolshed.g2.bx.psu.edu/repos/";
+export function cytoscapeElements(workflow, opts = {}) {
+    const wf = typeof workflow === "object" &&
+        workflow !== null &&
+        workflow.class === "GalaxyWorkflow" &&
+        Array.isArray(workflow.inputs) &&
+        "unique_tools" in workflow
+        ? workflow
+        : ensureFormat2(workflow);
+    const layout = opts.layout ?? "preset";
+    const nodes = [];
+    const edges = [];
+    wf.inputs.forEach((inp, i) => {
+        nodes.push(_inputNode(inp, i));
+    });
+    const inputsOffset = wf.inputs.length;
+    const knownLabels = new Set();
+    for (const inp of wf.inputs)
+        knownLabels.add(inp.id);
+    for (const step of wf.steps)
+        knownLabels.add(step.label || step.id);
+    wf.steps.forEach((step, i) => {
+        nodes.push(_stepNode(step, i + inputsOffset));
+        edges.push(..._stepEdges(step, knownLabels, opts.edgeAnnotations));
+    });
+    const elements = { nodes, edges };
+    if (layout === "preset") {
+        return elements;
+    }
+    if (bakesCoordinates(layout)) {
+        // Currently only `topological` reaches here; computed off the
+        // already-built elements per docs/architecture/cytoscape-layout.md.
+        const positions = topologicalPositions(elements);
+        for (const node of nodes) {
+            const p = positions.get(node.data.id);
+            if (p)
+                node.position = p;
+        }
+    }
+    else {
+        // Hint-only layout: positions are the renderer's job.
+        for (const node of nodes)
+            delete node.position;
+    }
+    elements.layout = { name: layout };
+    return elements;
+}
+function _fallbackPosition(orderIndex) {
+    return { x: 10 * orderIndex, y: 10 * orderIndex };
+}
+function _toPosition(raw, orderIndex) {
+    if (raw == null)
+        return _fallbackPosition(orderIndex);
+    const left = raw.left;
+    const top = raw.top;
+    const x = typeof left === "number" ? Math.trunc(left) : Number.parseInt(String(left ?? 0), 10);
+    const y = typeof top === "number" ? Math.trunc(top) : Number.parseInt(String(top ?? 0), 10);
+    return {
+        x: Number.isFinite(x) ? x : 0,
+        y: Number.isFinite(y) ? y : 0,
+    };
+}
+function _inputTypeStr(type) {
+    if (type == null)
+        return "input";
+    if (typeof type === "string")
+        return type;
+    return type.length > 0 ? `${type[0]}[]` : "input";
+}
+function _inputNode(inp, orderIndex) {
+    const inputId = inp.id || String(orderIndex);
+    const typeStr = _inputTypeStr(inp.type);
+    return {
+        group: "nodes",
+        data: {
+            id: inputId,
+            label: inputId,
+            doc: typeof inp.doc === "string" ? inp.doc : null,
+            tool_id: null,
+            step_type: typeStr,
+            repo_link: null,
+        },
+        classes: [`type_${typeStr}`, "input"],
+        position: _toPosition(inp.position, orderIndex),
+    };
+}
+function _stepNode(step, orderIndex) {
+    const stepId = step.label || step.id;
+    // The TS normalizer doesn't infer step.type the way gxformat2 does, so fall
+    // back to a `run`-derived hint for subworkflows (matches mermaid emitter).
+    const stepType = step.type || (step.run != null ? "subworkflow" : "tool");
+    let strippedToolId = step.tool_id ?? null;
+    if (strippedToolId && strippedToolId.startsWith(MAIN_TS_PREFIX)) {
+        strippedToolId = strippedToolId.slice(MAIN_TS_PREFIX.length);
+    }
+    const displayId = step.id && !isUnlabeledStep(step.id) ? step.id : null;
+    const label = step.label || displayId || (strippedToolId ? `tool:${strippedToolId}` : String(orderIndex));
+    let repoLink = null;
+    const repo = step.tool_shed_repository;
+    if (repo) {
+        const toolShed = repo.tool_shed;
+        const owner = repo.owner;
+        const name = repo.name;
+        const changesetRevision = repo.changeset_revision;
+        repoLink = `https://${toolShed}/view/${owner}/${name}/${changesetRevision}`;
+    }
+    return {
+        group: "nodes",
+        data: {
+            id: stepId,
+            label,
+            doc: typeof step.doc === "string" ? step.doc : null,
+            tool_id: step.tool_id ?? null,
+            step_type: stepType,
+            repo_link: repoLink,
+        },
+        classes: [`type_${stepType}`, "runnable"],
+        position: _toPosition(step.position, orderIndex),
+    };
+}
+function _stepEdges(step, knownLabels, edgeAnnotations) {
+    const stepId = step.label || step.id;
+    const edges = [];
+    for (const stepInput of step.in) {
+        if (stepInput.source == null)
+            continue;
+        const inputId = stepInput.id || "unknown";
+        const sources = Array.isArray(stepInput.source) ? stepInput.source : [stepInput.source];
+        for (const source of sources) {
+            const [sourceLabel, outputName] = resolveSourceReference(source, knownLabels);
+            const output = outputName === "output" ? null : outputName;
+            const edgeId = `${stepId}__${inputId}__from__${sourceLabel}`;
+            const edge = {
+                group: "edges",
+                data: {
+                    id: edgeId,
+                    source: sourceLabel,
+                    target: stepId,
+                    input: inputId,
+                    output,
+                },
+            };
+            const annotation = edgeAnnotations?.get(edgeAnnotationKey(sourceLabel, outputName, stepId, inputId));
+            if (annotation) {
+                edge.data.map_depth = annotation.mapDepth;
+                edge.data.reduction = annotation.reduction;
+                edge.data.mapping = annotation.mapping ?? null;
+                const classes = [];
+                if (annotation.mapDepth > 0)
+                    classes.push(`mapover_${annotation.mapDepth}`);
+                if (annotation.reduction)
+                    classes.push("reduction");
+                if (classes.length > 0)
+                    edge.classes = classes;
+            }
+            edges.push(edge);
+        }
+    }
+    return edges;
+}
+//# sourceMappingURL=cytoscape.js.map

package/dist/workflow/cytoscape.js.map

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package/dist/workflow/draft-checks.d.ts

@@ -0,0 +1,205 @@
+/**
+ * Pure logic for Galaxy draft workflows (`class: GalaxyWorkflowDraft`).
+ *
+ * Substrate for the `gxwf draft-validate`, `gxwf draft-next-step`, and
+ * `gxwf _draft-extract` CLI commands. No I/O.
+ *
+ * The sentinel constants mirror `gxformat2/draft.py`. Drift is enforced by
+ * `make check-sync-draft-sentinel` against the JSON snapshot in
+ * `schema-sources/v19_09/draft_constants.json`.
+ */
+export declare const TODO_SENTINEL_PATTERN: RegExp;
+export declare const PLAN_FIELDS: readonly ["_plan_state", "_plan_context", "_plan_in", "_plan_out"];
+export type PlanField = (typeof PLAN_FIELDS)[number];
+export declare const DRAFT_CLASS = "GalaxyWorkflowDraft";
+export declare function isTodoSentinel(value: unknown): value is string;
+export declare function isDraftWorkflow(doc: unknown): boolean;
+export type StepPath = string[];
+export type TodoLocation = {
+    kind: "tool_id";
+} | {
+    kind: "tool_version";
+} | {
+    kind: "in_key";
+    key: string;
+} | {
+    kind: "out_id";
+    id: string;
+} | {
+    kind: "output_source";
+    output_label: string;
+    port: string;
+};
+export interface TodoHit {
+    path: StepPath;
+    location: TodoLocation;
+    sentinel: string;
+}
+export interface PlanHit {
+    path: StepPath;
+    field: PlanField;
+    value: string;
+}
+export interface DraftSurvey {
+    /** True iff `doc.class === "GalaxyWorkflowDraft"`. */
+    isDraft: boolean;
+    /** TODO sentinel hits in declaration order across the (sub)workflow tree. */
+    todos: TodoHit[];
+    /** `_plan_*` field hits on draft steps across the (sub)workflow tree. */
+    planFields: PlanHit[];
+}
+/**
+ * Walk a draft workflow once, returning every TODO sentinel and `_plan_*`
+ * field with its step path. Non-draft documents return `{ isDraft: false }`
+ * with empty arrays.
+ *
+ * Step paths are `[outerLabel, ..., innerStepLabel]`. Subworkflows recurse
+ * only when the inner `run:` block also carries `class: GalaxyWorkflowDraft`.
+ *
+ * Note: this survey is step-focused — it intentionally does NOT report
+ * top-level `_plan_*` fields on a draft workflow root. Those are flagged
+ * by `validateDraft` (a rules-focused walker); `detectDraft` exists to
+ * drive `nextDraftStep` / `extractConcreteSubset`, which only act on
+ * per-step state.
+ */
+export declare function detectDraft(workflow: unknown): DraftSurvey;
+export interface DraftValidationDiagnostic {
+    /** Step path; empty array for workflow-level diagnostics. */
+    path: StepPath;
+    message: string;
+}
+export interface DraftValidationResult {
+    ok: boolean;
+    structureErrors: DraftValidationDiagnostic[];
+    topologyErrors: DraftValidationDiagnostic[];
+    semanticErrors: DraftValidationDiagnostic[];
+    warnings: DraftValidationDiagnostic[];
+    survey: DraftSurvey;
+}
+/**
+ * Validate a draft Galaxy workflow. Collects all diagnostics — does not throw.
+ *
+ *   structureErrors  Effect Schema decode failures.
+ *   topologyErrors   Concrete-topology must hold even in drafts: workflow
+ *                    input labels, output labels, step labels, and step types
+ *                    cannot be TODO sentinels. Step/port edge refs must
+ *                    resolve to a declared step + declared port (TODO_*
+ *                    ports count if declared in the step's `out:`).
+ *   semanticErrors   TODO-shaped strings (start with `TODO`) that don't
+ *                    match the canonical sentinel form (e.g. `TODO-foo`,
+ *                    `TODOfoo`, `TODO_` trailing).
+ *   warnings         Bare `TODO` in port position; top-level `_plan_*`.
+ *
+ * The returned `survey` is the same shape detectDraft() returns and is
+ * usable by downstream nextDraftStep / extractConcreteSubset callers.
+ */
+export declare function validateDraft(workflow: unknown): DraftValidationResult;
+export type NextStepResult = {
+    draft: false;
+} | {
+    draft: true;
+    step: StepPath;
+    work: string[];
+};
+/**
+ * Pick the next step a downstream agent should work on. Pure function;
+ * idempotent — same input → same output, byte-for-byte.
+ *
+ * Walks steps in topological order (steps with no draft-step source deps
+ * first), tie-breaking by alphabetical step label. The first step that
+ * carries any TODO sentinel or `_plan_*` field is returned with a
+ * prompt-shaped `work[]` array. Subworkflows (draft inner `run:`) are
+ * descended only after their outer step is itself fully concrete.
+ *
+ * Returns `{ draft: false }` when the workflow has no remaining work
+ * (this includes non-draft documents — there is nothing to do).
+ */
+export declare function nextDraftStep(workflow: unknown): NextStepResult;
+export type DropReason = {
+    kind: "step_has_todo";
+    locations: TodoLocation[];
+} | {
+    kind: "step_has_plan_field";
+    fields: PlanField[];
+} | {
+    kind: "cascade";
+    depends_on: StepPath[];
+};
+export interface DroppedStep {
+    path: StepPath;
+    reason: DropReason;
+}
+export interface DroppedOutput {
+    /**
+     * Step path of the workflow the output lives in. `[]` for the top-level
+     * document; `[outerStep, ...]` for inner subworkflow outputs.
+     */
+    path: StepPath;
+    label: string;
+    reason: DropReason;
+}
+export interface RewrittenStepInput {
+    path: StepPath;
+    in_key: string;
+    /** Dropped step/port refs removed from this input's `source:`. */
+    removed_refs: string[];
+    /** Surviving step/port refs after the rewrite. Empty when only a `default:` keeps the entry alive. */
+    surviving_refs: string[];
+}
+export interface ExtractResult {
+    /**
+     * Trimmed workflow dict. Still carries `class: GalaxyWorkflowDraft` —
+     * promoting to `GalaxyWorkflow` is the CLI command's call, not B's.
+     * `_plan_*` fields are preserved verbatim (including top-level fields and
+     * any survivor steps — though by construction survivor steps never have
+     * `_plan_*`, since carrying one is itself a drop trigger). Stripping lives
+     * in the `clean` module (E).
+     */
+    workflow: unknown;
+    /**
+     * Dropped steps across the (sub)workflow tree. Ordering within a single
+     * workflow level: by cascade round (round 0 = direct TODO/_plan_* drops;
+     * rounds 1+ = cascade drops), then by alphabetical step-path within a
+     * round. Across levels: a level's drops come first, then for each
+     * surviving subworkflow step (in source iteration order) its drops
+     * follow, recursively. Cascade rounds are local to a workflow level — not
+     * compared across nesting.
+     *
+     * `cascade.depends_on` paths point at the steps cited in the dead `in:`.
+     * In the common case these appear in `dropped_steps` themselves; in the
+     * subworkflow-port-loss case the cited path may be a *surviving* outer
+     * subworkflow step whose inner workflow lost the referenced port — look
+     * under that step's recursed inner drops for the underlying cause.
+     */
+    dropped_steps: DroppedStep[];
+    /**
+     * Workflow outputs dropped because their source step / port went away.
+     * Carries `path` to distinguish top-level outputs (`path: []`) from inner
+     * subworkflow outputs (`path: [outerStep, ...]`). Ordered alphabetically
+     * by label within a level; across levels, top-level first, then per
+     * surviving subworkflow step in iteration order.
+     */
+    dropped_outputs: DroppedOutput[];
+    /**
+     * Per-input rewrites where the source survived in part. Two cases:
+     *   - Multi-source input lost some refs but kept others (rewritten to the
+     *     surviving subset; string form if 1 left, list form if >1).
+     *   - Single-source input lost its only ref but the input has a `default:`
+     *     so the entry stays alive — `surviving_refs` is empty, the rewritten
+     *     value retains the default and drops the `source:` key.
+     */
+    rewritten_step_inputs: RewrittenStepInput[];
+}
+/**
+ * Trim a draft workflow down to its concrete subset: drop any step that
+ * carries a TODO sentinel or `_plan_*` field, then cascade-drop steps whose
+ * `in:` becomes dead, then drop workflow outputs whose source went away.
+ * Multi-source inputs are rewritten in place to the surviving ref subset.
+ *
+ * Pure + idempotent. The result always carries `class: GalaxyWorkflowDraft`
+ * — promotion to concrete is a CLI-layer decision (E).
+ *
+ * Non-draft inputs pass through unchanged with empty drop / rewrite arrays.
+ */
+export declare function extractConcreteSubset(workflow: unknown): ExtractResult;
+//# sourceMappingURL=draft-checks.d.ts.map

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

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