@galaxy-tool-util/schema 0.1.0

package/dist/workflow/normalized/expanded.d.ts.map

@@ -0,0 +1 @@
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package/dist/workflow/normalized/expanded.js

@@ -0,0 +1,173 @@
+/**
+ * Expanded workflow models.
+ *
+ * Expansion resolves all external references (@import, URL, TRS, base64)
+ * in step run/subworkflow fields. Supports async URL fetching via a
+ * configurable resolver callback.
+ *
+ * Port of gxformat2/normalized/_conversion.py expanded_format2/expanded_native
+ * and gxformat2/options.py (UrlResolverFn, default_url_resolver, ConversionOptions).
+ */
+import { normalizedFormat2 } from "./format2.js";
+import { normalizedNative } from "./native.js";
+import { toFormat2 } from "./toFormat2.js";
+import { toNative } from "./toNative.js";
+// --- Constants ---
+export const MAX_EXPANSION_DEPTH = 10;
+const TRS_URL_REGEX = /^https?:\/\/.+\/ga4gh\/trs\/v2\/tools\/.+\/versions\/[^/]+/;
+// --- Helpers ---
+/** Check if a URL matches the GA4GH TRS v2 tools/versions pattern. */
+export function isTrsUrl(url) {
+    return TRS_URL_REGEX.test(url);
+}
+/** Check if a content_id is a URL that can be fetched. */
+function _isResolvableUrl(contentId) {
+    return (contentId.startsWith("http://") ||
+        contentId.startsWith("https://") ||
+        contentId.startsWith("base64://"));
+}
+/** Detect if a raw dict is a native Galaxy workflow (vs Format2). */
+function _isNativeWorkflow(raw) {
+    return raw.a_galaxy_workflow === "true";
+}
+/** Convert a fetched workflow dict to NormalizedFormat2, handling cross-format. */
+function _ensureFormat2(resolved) {
+    if (_isNativeWorkflow(resolved)) {
+        return toFormat2(resolved);
+    }
+    return normalizedFormat2(resolved);
+}
+/** Convert a fetched workflow dict to NormalizedNativeWorkflow, handling cross-format. */
+function _ensureNative(resolved) {
+    if (_isNativeWorkflow(resolved)) {
+        return normalizedNative(resolved);
+    }
+    return toNative(resolved);
+}
+// --- Expansion context (cycle detection + depth limiting) ---
+class ExpansionContext {
+    _resolver;
+    _resolvingRefs;
+    constructor(resolver, resolvingRefs = new Set()) {
+        this._resolver = resolver;
+        this._resolvingRefs = resolvingRefs;
+    }
+    async resolve(ref) {
+        if (this._resolvingRefs.has(ref)) {
+            throw new Error(`Circular subworkflow reference: ${ref}`);
+        }
+        if (this._resolvingRefs.size >= MAX_EXPANSION_DEPTH) {
+            throw new Error(`Max expansion depth (${MAX_EXPANSION_DEPTH}) exceeded`);
+        }
+        return this._resolver(ref);
+    }
+    child(ref) {
+        const childRefs = new Set(this._resolvingRefs);
+        childRefs.add(ref);
+        return new ExpansionContext(this._resolver, childRefs);
+    }
+}
+// --- Public entry points ---
+/**
+ * Normalize and expand a Format2 workflow.
+ *
+ * Resolves @import, URL, TRS URL, and base64 references in step `run`
+ * fields. Uses `options.resolver` (or a no-op that leaves strings as-is)
+ * for fetching external references.
+ */
+export async function expandedFormat2(raw, options) {
+    const wf = normalizedFormat2(raw);
+    if (!options?.resolver) {
+        // No resolver provided — sync expansion only (inline subworkflows)
+        return _expandFormat2Sync(wf);
+    }
+    const ctx = new ExpansionContext(options.resolver);
+    return _expandFormat2(wf, ctx);
+}
+/**
+ * Normalize and expand a native workflow.
+ *
+ * Resolves content_id URL references by fetching and converting them.
+ * Uses `options.resolver` for fetching external references.
+ */
+export async function expandedNative(raw, options) {
+    const wf = normalizedNative(raw);
+    if (!options?.resolver) {
+        // No resolver provided — sync expansion only (inline subworkflows)
+        return _expandNativeSync(wf);
+    }
+    const ctx = new ExpansionContext(options.resolver);
+    return _expandNative(wf, ctx);
+}
+// --- Sync expansion (no resolver — inline subworkflows only) ---
+function _expandFormat2Sync(wf) {
+    const expandedSteps = wf.steps.map((step) => {
+        if (step.run && typeof step.run === "object") {
+            return { ...step, run: _expandFormat2Sync(step.run) };
+        }
+        return { ...step, run: step.run ?? null };
+    });
+    return { ...wf, steps: expandedSteps };
+}
+function _expandNativeSync(wf) {
+    const expandedSteps = {};
+    for (const [key, step] of Object.entries(wf.steps)) {
+        if (step.subworkflow != null) {
+            expandedSteps[key] = { ...step, subworkflow: _expandNativeSync(step.subworkflow) };
+        }
+        else {
+            expandedSteps[key] = step;
+        }
+    }
+    return { ...wf, steps: expandedSteps };
+}
+// --- Async expansion (with resolver) ---
+async function _expandFormat2(wf, ctx) {
+    const expandedSteps = [];
+    for (const step of wf.steps) {
+        let expandedRun = null;
+        if (step.run && typeof step.run === "object") {
+            // Already-inlined subworkflow — recurse
+            expandedRun = await _expandFormat2(step.run, ctx);
+        }
+        else if (typeof step.run === "string") {
+            // External reference (URL, file path, base64)
+            const resolved = await ctx.resolve(step.run);
+            const childCtx = ctx.child(step.run);
+            const normalized = _ensureFormat2(resolved);
+            expandedRun = await _expandFormat2(normalized, childCtx);
+        }
+        expandedSteps.push({
+            ...step,
+            run: expandedRun,
+        });
+    }
+    return { ...wf, steps: expandedSteps };
+}
+async function _expandNative(wf, ctx) {
+    const expandedSteps = {};
+    for (const [key, step] of Object.entries(wf.steps)) {
+        let expandedSub = null;
+        if (step.subworkflow != null) {
+            // Already-inlined subworkflow — recurse
+            expandedSub = await _expandNative(step.subworkflow, ctx);
+        }
+        else if (step.content_id && _isResolvableUrl(step.content_id)) {
+            // External URL content_id — fetch, convert to native, recurse
+            const resolved = await ctx.resolve(step.content_id);
+            const childCtx = ctx.child(step.content_id);
+            const normalized = _ensureNative(resolved);
+            expandedSub = await _expandNative(normalized, childCtx);
+        }
+        if (expandedSub != null) {
+            // Replace content_id with inline subworkflow
+            const { content_id: _dropped, ...rest } = step;
+            expandedSteps[key] = { ...rest, subworkflow: expandedSub };
+        }
+        else {
+            expandedSteps[key] = step;
+        }
+    }
+    return { ...wf, steps: expandedSteps };
+}
+//# sourceMappingURL=expanded.js.map

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

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package/dist/workflow/normalized/format2.d.ts

@@ -0,0 +1,149 @@
+/**
+ * Normalized Format2 Galaxy workflow Effect schemas.
+ *
+ * Normalizes raw gxformat2 workflow dicts: $graph extraction with
+ * #ref subworkflow inlining, dict→list conversion for inputs/outputs/steps,
+ * shorthand expansion for inputs and step in/out, doc array joining.
+ * Computed properties (unique_tools) are derived during normalization.
+ */
+import { Schema } from "effect";
+export declare const NormalizedFormat2StepInputSchema: Schema.Struct<{
+    id: typeof Schema.String;
+    source: Schema.optional<Schema.NullOr<Schema.Union<[typeof Schema.String, Schema.Array$<typeof Schema.String>]>>>;
+    label: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+    default: Schema.optional<Schema.NullOr<typeof Schema.Unknown>>;
+}>;
+export type NormalizedFormat2StepInput = typeof NormalizedFormat2StepInputSchema.Type;
+export declare const NormalizedFormat2StepOutputSchema: Schema.Struct<{
+    id: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+    add_tags: Schema.optional<Schema.NullOr<Schema.Array$<typeof Schema.String>>>;
+    change_datatype: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+    delete_intermediate_datasets: Schema.optional<Schema.NullOr<typeof Schema.Boolean>>;
+    hide: Schema.optional<Schema.NullOr<typeof Schema.Boolean>>;
+    remove_tags: Schema.optional<Schema.NullOr<Schema.Array$<typeof Schema.String>>>;
+    rename: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+    set_columns: Schema.optional<Schema.NullOr<Schema.Record$<typeof Schema.String, typeof Schema.Unknown>>>;
+}>;
+export type NormalizedFormat2StepOutput = typeof NormalizedFormat2StepOutputSchema.Type;
+export declare const NormalizedFormat2InputSchema: Schema.Struct<{
+    id: typeof Schema.String;
+    label: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+    doc: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+    type: Schema.optional<Schema.NullOr<Schema.Union<[typeof Schema.String, Schema.Array$<typeof Schema.String>]>>>;
+    optional: Schema.optional<Schema.NullOr<typeof Schema.Boolean>>;
+    default: Schema.optional<Schema.NullOr<typeof Schema.Unknown>>;
+    format: Schema.optional<Schema.NullOr<Schema.Array$<typeof Schema.String>>>;
+    collection_type: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+    position: Schema.optional<Schema.NullOr<Schema.Record$<typeof Schema.String, typeof Schema.Unknown>>>;
+}>;
+export type NormalizedFormat2Input = typeof NormalizedFormat2InputSchema.Type;
+export declare const NormalizedFormat2OutputSchema: Schema.Struct<{
+    id: typeof Schema.String;
+    label: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+    doc: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+    outputSource: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+    type: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+}>;
+export type NormalizedFormat2Output = typeof NormalizedFormat2OutputSchema.Type;
+export declare const NormalizedFormat2WorkflowSchema: Schema.Struct<{
+    class: Schema.Literal<["GalaxyWorkflow"]>;
+    label: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+    doc: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+    inputs: Schema.Array$<Schema.Struct<{
+        id: typeof Schema.String;
+        label: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+        doc: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+        type: Schema.optional<Schema.NullOr<Schema.Union<[typeof Schema.String, Schema.Array$<typeof Schema.String>]>>>;
+        optional: Schema.optional<Schema.NullOr<typeof Schema.Boolean>>;
+        default: Schema.optional<Schema.NullOr<typeof Schema.Unknown>>;
+        format: Schema.optional<Schema.NullOr<Schema.Array$<typeof Schema.String>>>;
+        collection_type: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+        position: Schema.optional<Schema.NullOr<Schema.Record$<typeof Schema.String, typeof Schema.Unknown>>>;
+    }>>;
+    outputs: Schema.Array$<Schema.Struct<{
+        id: typeof Schema.String;
+        label: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+        doc: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+        outputSource: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+        type: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+    }>>;
+    steps: Schema.Array$<Schema.suspend<any, any, never>>;
+    tags: Schema.optional<Schema.NullOr<Schema.Array$<typeof Schema.String>>>;
+    uuid: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+    report: Schema.optional<Schema.NullOr<Schema.Record$<typeof Schema.String, typeof Schema.Unknown>>>;
+    license: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+    release: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+    unique_tools: Schema.Set$<Schema.Struct<{
+        tool_id: typeof Schema.String;
+        tool_version: Schema.NullOr<typeof Schema.String>;
+    }>>;
+}>;
+export type NormalizedFormat2Workflow = typeof NormalizedFormat2WorkflowSchema.Type;
+export declare const NormalizedFormat2StepSchema: Schema.Struct<{
+    id: typeof Schema.String;
+    label: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+    doc: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+    tool_id: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+    tool_version: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+    tool_shed_repository: Schema.optional<Schema.NullOr<Schema.Record$<typeof Schema.String, typeof Schema.Unknown>>>;
+    type: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+    run: Schema.optional<Schema.NullOr<Schema.Union<[Schema.Struct<{
+        class: Schema.Literal<["GalaxyWorkflow"]>;
+        label: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+        doc: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+        inputs: Schema.Array$<Schema.Struct<{
+            id: typeof Schema.String;
+            label: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+            doc: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+            type: Schema.optional<Schema.NullOr<Schema.Union<[typeof Schema.String, Schema.Array$<typeof Schema.String>]>>>;
+            optional: Schema.optional<Schema.NullOr<typeof Schema.Boolean>>;
+            default: Schema.optional<Schema.NullOr<typeof Schema.Unknown>>;
+            format: Schema.optional<Schema.NullOr<Schema.Array$<typeof Schema.String>>>;
+            collection_type: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+            position: Schema.optional<Schema.NullOr<Schema.Record$<typeof Schema.String, typeof Schema.Unknown>>>;
+        }>>;
+        outputs: Schema.Array$<Schema.Struct<{
+            id: typeof Schema.String;
+            label: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+            doc: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+            outputSource: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+            type: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+        }>>;
+        steps: Schema.Array$<Schema.suspend<any, any, never>>;
+        tags: Schema.optional<Schema.NullOr<Schema.Array$<typeof Schema.String>>>;
+        uuid: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+        report: Schema.optional<Schema.NullOr<Schema.Record$<typeof Schema.String, typeof Schema.Unknown>>>;
+        license: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+        release: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+        unique_tools: Schema.Set$<Schema.Struct<{
+            tool_id: typeof Schema.String;
+            tool_version: Schema.NullOr<typeof Schema.String>;
+        }>>;
+    }>, typeof Schema.String]>>>;
+    in: Schema.Array$<Schema.Struct<{
+        id: typeof Schema.String;
+        source: Schema.optional<Schema.NullOr<Schema.Union<[typeof Schema.String, Schema.Array$<typeof Schema.String>]>>>;
+        label: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+        default: Schema.optional<Schema.NullOr<typeof Schema.Unknown>>;
+    }>>;
+    out: Schema.Array$<Schema.Struct<{
+        id: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+        add_tags: Schema.optional<Schema.NullOr<Schema.Array$<typeof Schema.String>>>;
+        change_datatype: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+        delete_intermediate_datasets: Schema.optional<Schema.NullOr<typeof Schema.Boolean>>;
+        hide: Schema.optional<Schema.NullOr<typeof Schema.Boolean>>;
+        remove_tags: Schema.optional<Schema.NullOr<Schema.Array$<typeof Schema.String>>>;
+        rename: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+        set_columns: Schema.optional<Schema.NullOr<Schema.Record$<typeof Schema.String, typeof Schema.Unknown>>>;
+    }>>;
+    state: Schema.optional<Schema.NullOr<Schema.Record$<typeof Schema.String, typeof Schema.Unknown>>>;
+    tool_state: Schema.optional<Schema.NullOr<Schema.Record$<typeof Schema.String, typeof Schema.Unknown>>>;
+    when: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+    position: Schema.optional<Schema.NullOr<Schema.Record$<typeof Schema.String, typeof Schema.Unknown>>>;
+    errors: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+    uuid: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+    runtime_inputs: Schema.optional<Schema.NullOr<Schema.Array$<typeof Schema.String>>>;
+}>;
+export type NormalizedFormat2Step = typeof NormalizedFormat2StepSchema.Type;
+export declare function normalizedFormat2(raw: unknown): NormalizedFormat2Workflow;
+//# sourceMappingURL=format2.d.ts.map

package/dist/workflow/normalized/format2.d.ts.map

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