@galaxy-tool-util/schema 0.1.0

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

@@ -0,0 +1,97 @@
+/**
+ * Normalized native Galaxy workflow Effect schemas.
+ *
+ * Narrows raw native workflow dicts: optional containers become empty
+ * defaults, tool_state JSON strings are parsed, subworkflows are
+ * recursively normalized. Computed properties (unique_tools,
+ * connected_paths) are derived during normalization.
+ */
+import { Schema } from "effect";
+export declare const ToolReferenceSchema: Schema.Struct<{
+    tool_id: typeof Schema.String;
+    tool_version: Schema.NullOr<typeof Schema.String>;
+}>;
+export type ToolReference = typeof ToolReferenceSchema.Type;
+export declare const NormalizedNativeWorkflowSchema: Schema.Struct<{
+    name: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+    a_galaxy_workflow: typeof Schema.String;
+    "format-version": typeof Schema.String;
+    annotation: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+    tags: Schema.Array$<typeof Schema.String>;
+    version: Schema.optional<Schema.NullOr<typeof Schema.Number>>;
+    license: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+    release: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+    uuid: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+    steps: Schema.Record$<typeof Schema.String, Schema.suspend<any, any, never>>;
+    unique_tools: Schema.Set$<Schema.Struct<{
+        tool_id: typeof Schema.String;
+        tool_version: Schema.NullOr<typeof Schema.String>;
+    }>>;
+}>;
+export type NormalizedNativeWorkflow = typeof NormalizedNativeWorkflowSchema.Type;
+export declare const NormalizedNativeStepSchema: Schema.Struct<{
+    id: typeof Schema.Number;
+    name: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+    type: Schema.optional<Schema.NullOr<Schema.Literal<["data_input", "data_collection_input", "parameter_input", "tool", "subworkflow", "pause", "pick_value"]>>>;
+    label: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+    annotation: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+    when: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+    content_id: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+    tool_state: Schema.Record$<typeof Schema.String, typeof Schema.Unknown>;
+    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.Struct<{
+        name: typeof Schema.String;
+        changeset_revision: typeof Schema.String;
+        owner: typeof Schema.String;
+        tool_shed: typeof Schema.String;
+    }>>>;
+    uuid: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+    errors: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+    position: Schema.optional<Schema.NullOr<Schema.Struct<{
+        top: typeof Schema.Number;
+        left: typeof Schema.Number;
+    }>>>;
+    input_connections: Schema.Record$<typeof Schema.String, Schema.Array$<typeof Schema.Unknown>>;
+    inputs: Schema.Array$<Schema.Struct<{
+        name: typeof Schema.String;
+        description: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
+    }>>;
+    outputs: Schema.Array$<Schema.Struct<{
+        name: typeof Schema.String;
+        type: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
+    }>>;
+    workflow_outputs: Schema.Array$<Schema.Struct<{
+        label: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
+        output_name: typeof Schema.String;
+        uuid: Schema.optional<Schema.Union<[typeof Schema.Null, typeof Schema.String]>>;
+    }>>;
+    post_job_actions: Schema.Record$<typeof Schema.String, Schema.Struct<{
+        action_type: typeof Schema.String;
+        output_name: typeof Schema.String;
+        action_arguments: Schema.optional<Schema.Union<[Schema.Record$<typeof Schema.String, typeof Schema.Unknown>, typeof Schema.Null]>>;
+    }>>;
+    subworkflow: Schema.optional<Schema.NullOr<Schema.Struct<{
+        name: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+        a_galaxy_workflow: typeof Schema.String;
+        "format-version": typeof Schema.String;
+        annotation: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+        tags: Schema.Array$<typeof Schema.String>;
+        version: Schema.optional<Schema.NullOr<typeof Schema.Number>>;
+        license: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+        release: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+        uuid: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+        steps: Schema.Record$<typeof Schema.String, Schema.suspend<any, any, never>>;
+        unique_tools: Schema.Set$<Schema.Struct<{
+            tool_id: typeof Schema.String;
+            tool_version: Schema.NullOr<typeof Schema.String>;
+        }>>;
+    }>>>;
+    tool_uuid: Schema.optional<Schema.NullOr<typeof Schema.String>>;
+    tool_representation: Schema.optional<Schema.NullOr<Schema.Record$<typeof Schema.String, typeof Schema.Unknown>>>;
+    in: Schema.optional<Schema.NullOr<Schema.Record$<typeof Schema.String, typeof Schema.Unknown>>>;
+    connected_paths: Schema.Set$<typeof Schema.String>;
+}>;
+export type NormalizedNativeStep = typeof NormalizedNativeStepSchema.Type;
+export declare function normalizedNative(raw: unknown): NormalizedNativeWorkflow;
+//# sourceMappingURL=native.d.ts.map

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

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

@@ -0,0 +1,189 @@
+/**
+ * Normalized native Galaxy workflow Effect schemas.
+ *
+ * Narrows raw native workflow dicts: optional containers become empty
+ * defaults, tool_state JSON strings are parsed, subworkflows are
+ * recursively normalized. Computed properties (unique_tools,
+ * connected_paths) are derived during normalization.
+ */
+import { Schema } from "effect";
+import { NativeStepTypeSchema, StepPositionSchema, ToolShedRepositorySchema, NativeStepInputSchema, NativeStepOutputSchema, NativeWorkflowOutputSchema, NativePostJobActionSchema, } from "../raw/native.effect.js";
+// --- ToolReference ---
+export const ToolReferenceSchema = Schema.Struct({
+    tool_id: Schema.String,
+    tool_version: Schema.NullOr(Schema.String),
+});
+// --- Normalized workflow schema (defined first; uses suspend for step forward-ref) ---
+export const NormalizedNativeWorkflowSchema = Schema.Struct({
+    name: Schema.optional(Schema.NullOr(Schema.String)),
+    a_galaxy_workflow: Schema.String,
+    "format-version": Schema.String,
+    annotation: Schema.optional(Schema.NullOr(Schema.String)),
+    tags: Schema.Array(Schema.String),
+    version: Schema.optional(Schema.NullOr(Schema.Number)),
+    license: Schema.optional(Schema.NullOr(Schema.String)),
+    release: Schema.optional(Schema.NullOr(Schema.String)),
+    uuid: Schema.optional(Schema.NullOr(Schema.String)),
+    steps: Schema.Record({
+        key: Schema.String,
+        value: Schema.suspend(() => NormalizedNativeStepSchema),
+    }),
+    unique_tools: Schema.Set(ToolReferenceSchema),
+});
+// --- Normalized step schema (references workflow directly) ---
+export const NormalizedNativeStepSchema = Schema.Struct({
+    id: Schema.Number,
+    name: Schema.optional(Schema.NullOr(Schema.String)),
+    type: Schema.optional(Schema.NullOr(NativeStepTypeSchema)),
+    label: Schema.optional(Schema.NullOr(Schema.String)),
+    annotation: Schema.optional(Schema.NullOr(Schema.String)),
+    when: Schema.optional(Schema.NullOr(Schema.String)),
+    content_id: Schema.optional(Schema.NullOr(Schema.String)),
+    tool_state: Schema.Record({ key: Schema.String, value: Schema.Unknown }),
+    tool_id: Schema.optional(Schema.NullOr(Schema.String)),
+    tool_version: Schema.optional(Schema.NullOr(Schema.String)),
+    tool_shed_repository: Schema.optional(Schema.NullOr(ToolShedRepositorySchema)),
+    uuid: Schema.optional(Schema.NullOr(Schema.String)),
+    errors: Schema.optional(Schema.NullOr(Schema.String)),
+    position: Schema.optional(Schema.NullOr(StepPositionSchema)),
+    input_connections: Schema.Record({
+        key: Schema.String,
+        value: Schema.Array(Schema.Unknown),
+    }),
+    inputs: Schema.Array(NativeStepInputSchema),
+    outputs: Schema.Array(NativeStepOutputSchema),
+    workflow_outputs: Schema.Array(NativeWorkflowOutputSchema),
+    post_job_actions: Schema.Record({ key: Schema.String, value: NativePostJobActionSchema }),
+    subworkflow: Schema.optional(Schema.NullOr(NormalizedNativeWorkflowSchema)),
+    tool_uuid: Schema.optional(Schema.NullOr(Schema.String)),
+    tool_representation: Schema.optional(Schema.NullOr(Schema.Record({ key: Schema.String, value: Schema.Unknown }))),
+    in: Schema.optional(Schema.NullOr(Schema.Record({ key: Schema.String, value: Schema.Unknown }))),
+    connected_paths: Schema.Set(Schema.String),
+});
+// --- Normalization function ---
+export function normalizedNative(raw) {
+    const wf = raw;
+    const steps = _normalizeSteps(wf.steps);
+    const tags = _normalizeTags(wf.tags);
+    const uniqueTools = _collectUniqueTools(steps);
+    const result = {
+        name: wf.name,
+        a_galaxy_workflow: wf.a_galaxy_workflow ?? "true",
+        "format-version": wf["format-version"] ?? "0.1",
+        annotation: wf.annotation,
+        tags,
+        version: wf.version,
+        license: wf.license,
+        release: wf.release,
+        uuid: wf.uuid,
+        steps,
+        unique_tools: uniqueTools,
+    };
+    // Pass through comments if present (used by toFormat2 conversion)
+    if (wf.comments != null) {
+        result.comments = wf.comments;
+    }
+    return result;
+}
+// --- Internal helpers ---
+function _normalizeSteps(rawSteps) {
+    const result = {};
+    if (!rawSteps)
+        return result;
+    for (const [key, rawStep] of Object.entries(rawSteps)) {
+        result[key] = _normalizeStep(rawStep);
+    }
+    return result;
+}
+function _normalizeStep(step) {
+    const toolState = _parseToolState(step.tool_state);
+    const inputConnections = _normalizeInputConnections(step.input_connections);
+    const connectedPaths = new Set(Object.keys(inputConnections));
+    let subworkflow = null;
+    if (step.subworkflow != null) {
+        subworkflow = normalizedNative(step.subworkflow);
+    }
+    return {
+        id: step.id ?? 0,
+        name: step.name,
+        type: step.type,
+        label: step.label,
+        annotation: step.annotation,
+        when: step.when,
+        content_id: step.content_id,
+        tool_state: toolState,
+        tool_id: step.tool_id,
+        tool_version: step.tool_version,
+        tool_shed_repository: step.tool_shed_repository,
+        uuid: step.uuid,
+        errors: step.errors,
+        position: _normalizePosition(step.position),
+        input_connections: inputConnections,
+        inputs: step.inputs ?? [],
+        outputs: step.outputs ?? [],
+        workflow_outputs: step.workflow_outputs ?? [],
+        post_job_actions: step.post_job_actions ?? {},
+        subworkflow,
+        tool_uuid: step.tool_uuid,
+        tool_representation: step.tool_representation,
+        in: step.in,
+        connected_paths: connectedPaths,
+    };
+}
+function _normalizePosition(position) {
+    if (position == null)
+        return position;
+    return { top: position.top, left: position.left };
+}
+function _parseToolState(raw) {
+    if (typeof raw === "string") {
+        try {
+            return JSON.parse(raw);
+        }
+        catch {
+            return {};
+        }
+    }
+    if (raw != null && typeof raw === "object") {
+        return raw;
+    }
+    return {};
+}
+function _normalizeInputConnections(raw) {
+    if (!raw)
+        return {};
+    const result = {};
+    for (const [key, val] of Object.entries(raw)) {
+        result[key] = Array.isArray(val) ? val : [val];
+    }
+    return result;
+}
+function _normalizeTags(raw) {
+    if (Array.isArray(raw))
+        return raw;
+    if (typeof raw === "string") {
+        if (!raw)
+            return [];
+        return raw
+            .split(",")
+            .map((t) => t.trim())
+            .filter(Boolean);
+    }
+    return [];
+}
+function _collectUniqueTools(steps) {
+    const tools = new Set();
+    _collectToolsRecursive(steps, tools);
+    return tools;
+}
+function _collectToolsRecursive(steps, into) {
+    for (const step of Object.values(steps)) {
+        if (step.tool_id != null) {
+            into.add({ tool_id: step.tool_id, tool_version: step.tool_version ?? null });
+        }
+        if (step.subworkflow) {
+            _collectToolsRecursive(step.subworkflow.steps, into);
+        }
+    }
+}
+//# sourceMappingURL=native.js.map

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

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package/dist/workflow/normalized/toFormat2.d.ts

@@ -0,0 +1,11 @@
+/**
+ * Native → Format2 conversion.
+ *
+ * Port of gxformat2/normalized/_conversion.py to_format2 + helpers.
+ */
+import type { NormalizedFormat2Workflow } from "./format2.js";
+/**
+ * Convert a native Galaxy workflow to normalized Format2.
+ */
+export declare function toFormat2(raw: unknown): NormalizedFormat2Workflow;
+//# sourceMappingURL=toFormat2.d.ts.map

package/dist/workflow/normalized/toFormat2.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"toFormat2.d.ts","sourceRoot":"","sources":["../../../src/workflow/normalized/toFormat2.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAIH,OAAO,KAAK,EACV,yBAAyB,EAM1B,MAAM,cAAc,CAAC;AAUtB;;GAEG;AACH,wBAAgB,SAAS,CAAC,GAAG,EAAE,OAAO,GAAG,yBAAyB,CAGjE"}