@galaxy-tool-util/schema 0.1.0 → 0.4.0

package/dist/workflow/stateful-validate.js

@@ -0,0 +1,123 @@
+/**
+ * Schema validation wrappers for stateful conversion.
+ *
+ * Runs the generated Effect Schema (`createFieldModel`) against native
+ * tool_state (pre-conversion) and format2 state (post-conversion), throwing
+ * a tagged `ConversionValidationFailure` on mismatch. The stateful wrappers
+ * catch this and push a structured fallback entry so callers can
+ * distinguish validation failures from walker errors.
+ *
+ * Deferred from Step 2 of TS_STATEFUL_CONVERSION_PLAN — integration point
+ * is the stateful runner, which calls these pre/post `convert`.
+ */
+import * as S from "effect/Schema";
+import * as ParseResult from "effect/ParseResult";
+// Side-effect import: registers all parameter generators so createFieldModel
+// can look them up. Without this, a direct import of model-factory returns
+// undefined for every call (the parameters/index.js side-effects never run).
+import "../schema/parameters/index.js";
+import { createFieldModel } from "../schema/model-factory.js";
+import { injectConnectionsIntoState, stripConnectedValues } from "./state-merge.js";
+/**
+ * Thrown when tool_state fails Effect Schema validation before or after
+ * stateful conversion. Carries the phase and formatted issue list so the
+ * runner can emit a structured fallback status.
+ */
+export class ConversionValidationFailure extends Error {
+    phase;
+    issues;
+    _tag = "ConversionValidationFailure";
+    constructor(phase, issues) {
+        super(`state failed ${phase}-conversion validation: ${issues.join("; ")}`);
+        this.phase = phase;
+        this.issues = issues;
+        this.name = "ConversionValidationFailure";
+    }
+}
+function formatIssues(error) {
+    const issues = ParseResult.ArrayFormatter.formatErrorSync(error);
+    return issues.map((i) => (i.path.length ? `${i.path.join(".")}: ${i.message}` : i.message));
+}
+function buildBundle(inputs) {
+    return { parameters: inputs };
+}
+/** JSON-safe deep clone — tool_state is plain data. Avoids `structuredClone`
+ * which isn't in the schema package's TS lib (no `@types/node`). */
+function deepClone(value) {
+    return JSON.parse(JSON.stringify(value));
+}
+/**
+ * Validate native tool_state against `workflow_step_native`. Connection
+ * paths are merged as `ConnectedValue` markers before validation so linked
+ * fields don't trip the schema.
+ *
+ * Returns silently if the schema cannot be built (unsupported parameter
+ * types) or if validation passes. Throws `ConversionValidationFailure`
+ * with phase="pre" on validation failure.
+ */
+export function validateNativeStepState(inputs, toolState, inputConnections = {}) {
+    const bundle = buildBundle(inputs);
+    const model = createFieldModel(bundle, "workflow_step_native");
+    if (!model)
+        return; // unsupported parameter types — skip validation, conversion may still work
+    // Deep copy + inject connections so ConnectedValue markers appear where the
+    // schema expects them (matches validate-workflow's native path).
+    const state = deepClone(toolState);
+    if (Object.keys(inputConnections).length > 0) {
+        injectConnectionsIntoState(inputs, state, inputConnections);
+    }
+    const decode = S.decodeUnknownEither(model, { onExcessProperty: "ignore" });
+    const result = decode(state);
+    if (result._tag === "Left") {
+        throw new ConversionValidationFailure("pre", formatIssues(result.left));
+    }
+}
+/**
+ * Validate format2 tool_state against `workflow_step`. Any stray
+ * `ConnectedValue` markers left over from normalization are stripped
+ * before validation (they belong in the `in` block, not the state).
+ *
+ * Returns silently on success or if the schema cannot be built. Throws
+ * `ConversionValidationFailure` with phase="post" on validation failure.
+ */
+export function validateFormat2StepState(inputs, format2State) {
+    const bundle = buildBundle(inputs);
+    const model = createFieldModel(bundle, "workflow_step");
+    if (!model)
+        return;
+    const state = deepClone(format2State);
+    stripConnectedValues(inputs, state);
+    const decode = S.decodeUnknownEither(model, { onExcessProperty: "ignore" });
+    const result = decode(state);
+    if (result._tag === "Left") {
+        throw new ConversionValidationFailure("post", formatIssues(result.left));
+    }
+}
+/**
+ * Strict variant of {@link validateFormat2StepState}: reports unknown keys as
+ * diagnostics rather than silently ignoring them.
+ *
+ * Uses `onExcessProperty: "error"` so Effect Schema flags any key that has no
+ * corresponding parameter definition. Returns an empty array if the schema
+ * cannot be built or validation passes.
+ */
+export function validateFormat2StepStateStrict(inputs, format2State) {
+    const bundle = buildBundle(inputs);
+    const model = createFieldModel(bundle, "workflow_step");
+    if (!model)
+        return [];
+    const state = deepClone(format2State);
+    stripConnectedValues(inputs, state);
+    const decode = S.decodeUnknownEither(model, { onExcessProperty: "error" });
+    const result = decode(state);
+    if (result._tag === "Left") {
+        const issues = ParseResult.ArrayFormatter.formatErrorSync(result.left);
+        return issues.map((i) => ({
+            path: i.path.map(String).join("."),
+            message: i.message,
+            severity: "error",
+        }));
+    }
+    return [];
+}
+//# sourceMappingURL=stateful-validate.js.map

package/dist/workflow/stateful-validate.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"stateful-validate.js","sourceRoot":"","sources":["../../src/workflow/stateful-validate.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AAEH,OAAO,KAAK,CAAC,MAAM,eAAe,CAAC;AACnC,OAAO,KAAK,WAAW,MAAM,oBAAoB,CAAC;AAClD,6EAA6E;AAC7E,2EAA2E;AAC3E,6EAA6E;AAC7E,OAAO,+BAA+B,CAAC;AACvC,OAAO,EAAE,gBAAgB,EAAE,MAAM,4BAA4B,CAAC;AAE9D,OAAO,EAAE,0BAA0B,EAAE,oBAAoB,EAAE,MAAM,kBAAkB,CAAC;AAIpF;;;;GAIG;AACH,MAAM,OAAO,2BAA4B,SAAQ,KAAK;IAGlC;IACA;IAHT,IAAI,GAAG,6BAAsC,CAAC;IACvD,YACkB,KAAsB,EACtB,MAAgB;QAEhC,KAAK,CAAC,gBAAgB,KAAK,2BAA2B,MAAM,CAAC,IAAI,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;QAH3D,UAAK,GAAL,KAAK,CAAiB;QACtB,WAAM,GAAN,MAAM,CAAU;QAGhC,IAAI,CAAC,IAAI,GAAG,6BAA6B,CAAC;IAC5C,CAAC;CACF;AAED,SAAS,YAAY,CAAC,KAA6B;IACjD,MAAM,MAAM,GAAG,WAAW,CAAC,cAAc,CAAC,eAAe,CAAC,KAAK,CAAC,CAAC;IACjE,OAAO,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,CAAC,CAAC,CAAC,IAAI,CAAC,MAAM,CAAC,CAAC,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,OAAO,EAAE,CAAC,CAAC,CAAC,CAAC,CAAC,OAAO,CAAC,CAAC,CAAC;AAC9F,CAAC;AAED,SAAS,WAAW,CAAC,MAA4B;IAC/C,OAAO,EAAE,UAAU,EAAE,MAAM,EAAE,CAAC;AAChC,CAAC;AAED;oEACoE;AACpE,SAAS,SAAS,CAAI,KAAQ;IAC5B,OAAO,IAAI,CAAC,KAAK,CAAC,IAAI,CAAC,SAAS,CAAC,KAAK,CAAC,CAAM,CAAC;AAChD,CAAC;AAED;;;;;;;;GAQG;AACH,MAAM,UAAU,uBAAuB,CACrC,MAA4B,EAC5B,SAAkC,EAClC,mBAA4C,EAAE;IAE9C,MAAM,MAAM,GAAG,WAAW,CAAC,MAAM,CAAC,CAAC;IACnC,MAAM,KAAK,GAAG,gBAAgB,CAAC,MAAM,EAAE,sBAAsB,CAAC,CAAC;IAC/D,IAAI,CAAC,KAAK;QAAE,OAAO,CAAC,2EAA2E;IAE/F,4EAA4E;IAC5E,iEAAiE;IACjE,MAAM,KAAK,GAAG,SAAS,CAAC,SAAS,CAAC,CAAC;IACnC,IAAI,MAAM,CAAC,IAAI,CAAC,gBAAgB,CAAC,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;QAC7C,0BAA0B,CAAC,MAAM,EAAE,KAAK,EAAE,gBAAgB,CAAC,CAAC;IAC9D,CAAC;IAED,MAAM,MAAM,GAAG,CAAC,CAAC,mBAAmB,CAAC,KAA0B,EAAE,EAAE,gBAAgB,EAAE,QAAQ,EAAE,CAAC,CAAC;IACjG,MAAM,MAAM,GAAG,MAAM,CAAC,KAAK,CAAC,CAAC;IAC7B,IAAI,MAAM,CAAC,IAAI,KAAK,MAAM,EAAE,CAAC;QAC3B,MAAM,IAAI,2BAA2B,CAAC,KAAK,EAAE,YAAY,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC;IAC1E,CAAC;AACH,CAAC;AAED;;;;;;;GAOG;AACH,MAAM,UAAU,wBAAwB,CACtC,MAA4B,EAC5B,YAAqC;IAErC,MAAM,MAAM,GAAG,WAAW,CAAC,MAAM,CAAC,CAAC;IACnC,MAAM,KAAK,GAAG,gBAAgB,CAAC,MAAM,EAAE,eAAe,CAAC,CAAC;IACxD,IAAI,CAAC,KAAK;QAAE,OAAO;IAEnB,MAAM,KAAK,GAAG,SAAS,CAAC,YAAY,CAAC,CAAC;IACtC,oBAAoB,CAAC,MAAM,EAAE,KAAK,CAAC,CAAC;IAEpC,MAAM,MAAM,GAAG,CAAC,CAAC,mBAAmB,CAAC,KAA0B,EAAE,EAAE,gBAAgB,EAAE,QAAQ,EAAE,CAAC,CAAC;IACjG,MAAM,MAAM,GAAG,MAAM,CAAC,KAAK,CAAC,CAAC;IAC7B,IAAI,MAAM,CAAC,IAAI,KAAK,MAAM,EAAE,CAAC;QAC3B,MAAM,IAAI,2BAA2B,CAAC,MAAM,EAAE,YAAY,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC,CAAC;IAC3E,CAAC;AACH,CAAC;AAeD;;;;;;;GAOG;AACH,MAAM,UAAU,8BAA8B,CAC5C,MAA4B,EAC5B,YAAqC;IAErC,MAAM,MAAM,GAAG,WAAW,CAAC,MAAM,CAAC,CAAC;IACnC,MAAM,KAAK,GAAG,gBAAgB,CAAC,MAAM,EAAE,eAAe,CAAC,CAAC;IACxD,IAAI,CAAC,KAAK;QAAE,OAAO,EAAE,CAAC;IAEtB,MAAM,KAAK,GAAG,SAAS,CAAC,YAAY,CAAC,CAAC;IACtC,oBAAoB,CAAC,MAAM,EAAE,KAAK,CAAC,CAAC;IAEpC,MAAM,MAAM,GAAG,CAAC,CAAC,mBAAmB,CAAC,KAA0B,EAAE,EAAE,gBAAgB,EAAE,OAAO,EAAE,CAAC,CAAC;IAChG,MAAM,MAAM,GAAG,MAAM,CAAC,KAAK,CAAC,CAAC;IAC7B,IAAI,MAAM,CAAC,IAAI,KAAK,MAAM,EAAE,CAAC;QAC3B,MAAM,MAAM,GAAG,WAAW,CAAC,cAAc,CAAC,eAAe,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC;QACvE,OAAO,MAAM,CAAC,GAAG,CACf,CAAC,CAAC,EAAuB,EAAE,CAAC,CAAC;YAC3B,IAAI,EAAE,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC,IAAI,CAAC,GAAG,CAAC;YAClC,OAAO,EAAE,CAAC,CAAC,OAAO;YAClB,QAAQ,EAAE,OAAO;SAClB,CAAC,CACH,CAAC;IACJ,CAAC;IACD,OAAO,EAAE,CAAC;AACZ,CAAC"}

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

@@ -0,0 +1,22 @@
+import type { WorkflowFormat } from "./detect-format.js";
+/**
+ * Native: reject tool_state that is a JSON string instead of a parsed dict.
+ * Walks top-level steps only (matching Python `validate_encoding_native`).
+ */
+export declare function validateEncodingNative(workflowDict: Record<string, unknown>): string[];
+/**
+ * Format2: reject steps using `tool_state` field instead of `state`.
+ *
+ * No string-state check — format2 state comes from YAML parsing so
+ * it's always a dict. The Python side checks this defensively but
+ * it's not a real-world scenario.
+ */
+export declare function validateEncodingFormat2(workflowDict: Record<string, unknown>): string[];
+/** Dispatch encoding check based on format auto-detection. */
+export declare function checkStrictEncoding(workflowDict: Record<string, unknown>, format?: WorkflowFormat): string[];
+/**
+ * Strict structure check — decode with onExcessProperty: "error" to
+ * catch unknown keys at envelope and step level.
+ */
+export declare function checkStrictStructure(workflowDict: Record<string, unknown>, format?: WorkflowFormat): string[];
+//# sourceMappingURL=strict-checks.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"strict-checks.d.ts","sourceRoot":"","sources":["../../src/workflow/strict-checks.ts"],"names":[],"mappings":"AAOA,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,oBAAoB,CAAC;AAQzD;;;GAGG;AACH,wBAAgB,sBAAsB,CAAC,YAAY,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,MAAM,EAAE,CAqBtF;AAED;;;;;;GAMG;AACH,wBAAgB,uBAAuB,CAAC,YAAY,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,MAAM,EAAE,CAiBvF;AAED,8DAA8D;AAC9D,wBAAgB,mBAAmB,CACjC,YAAY,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EACrC,MAAM,CAAC,EAAE,cAAc,GACtB,MAAM,EAAE,CAKV;AASD;;;GAGG;AACH,wBAAgB,oBAAoB,CAClC,YAAY,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EACrC,MAAM,CAAC,EAAE,cAAc,GACtB,MAAM,EAAE,CAcV"}

package/dist/workflow/strict-checks.js

@@ -0,0 +1,95 @@
+/**
+ * Pre-normalization strict validation checks for workflows.
+ *
+ * These run on raw workflow dicts before any schema normalization,
+ * matching the Python pattern of failing fast before decoding.
+ */
+import { NativeGalaxyWorkflowSchema, GalaxyWorkflowSchema } from "./raw/index.js";
+import { detectFormat } from "./detect-format.js";
+import { withClass } from "./validators.js";
+import * as ParseResult from "effect/ParseResult";
+import * as S from "effect/Schema";
+// ── Encoding checks ──────────────────────────────────────────────────
+/**
+ * Native: reject tool_state that is a JSON string instead of a parsed dict.
+ * Walks top-level steps only (matching Python `validate_encoding_native`).
+ */
+export function validateEncodingNative(workflowDict) {
+    const errors = [];
+    const steps = workflowDict.steps;
+    if (!steps || typeof steps !== "object")
+        return errors;
+    const entries = Array.isArray(steps)
+        ? steps.map((s, i) => [String(i), s])
+        : Object.entries(steps);
+    for (const [key, step] of entries) {
+        if (!step || typeof step !== "object")
+            continue;
+        const s = step;
+        if (s.type === "subworkflow")
+            continue;
+        if (!s.tool_id)
+            continue;
+        const toolState = s.tool_state;
+        if (typeof toolState === "string") {
+            errors.push(`step ${key}: tool_state is a JSON string (legacy encoding), expected a dict`);
+        }
+    }
+    return errors;
+}
+/**
+ * Format2: reject steps using `tool_state` field instead of `state`.
+ *
+ * No string-state check — format2 state comes from YAML parsing so
+ * it's always a dict. The Python side checks this defensively but
+ * it's not a real-world scenario.
+ */
+export function validateEncodingFormat2(workflowDict) {
+    const errors = [];
+    const steps = workflowDict.steps;
+    if (!steps || !Array.isArray(steps))
+        return errors;
+    for (let i = 0; i < steps.length; i++) {
+        const step = steps[i];
+        if (!step || typeof step !== "object")
+            continue;
+        const s = step;
+        if (s.run && typeof s.run === "object")
+            continue; // subworkflow
+        if (!s.tool_id)
+            continue;
+        if ("tool_state" in s && !("state" in s)) {
+            errors.push(`step ${i}: uses "tool_state" instead of "state" (format2 should use "state")`);
+        }
+    }
+    return errors;
+}
+/** Dispatch encoding check based on format auto-detection. */
+export function checkStrictEncoding(workflowDict, format) {
+    const fmt = format ?? detectFormat(workflowDict);
+    return fmt === "native"
+        ? validateEncodingNative(workflowDict)
+        : validateEncodingFormat2(workflowDict);
+}
+// ── Structure checks ─────────────────────────────────────────────────
+function formatIssues(error) {
+    const issues = ParseResult.ArrayFormatter.formatErrorSync(error);
+    return issues.map((i) => `${i.path.join(".")}: ${i.message}`);
+}
+/**
+ * Strict structure check — decode with onExcessProperty: "error" to
+ * catch unknown keys at envelope and step level.
+ */
+export function checkStrictStructure(workflowDict, format) {
+    const fmt = format ?? detectFormat(workflowDict);
+    const cls = fmt === "native" ? "NativeGalaxyWorkflow" : "GalaxyWorkflow";
+    const data = withClass(workflowDict, cls);
+    const schema = fmt === "native" ? NativeGalaxyWorkflowSchema : GalaxyWorkflowSchema;
+    const decode = S.decodeUnknownEither(schema, { onExcessProperty: "error" });
+    const result = decode(data);
+    if (result._tag === "Left") {
+        return formatIssues(result.left);
+    }
+    return [];
+}
+//# sourceMappingURL=strict-checks.js.map

package/dist/workflow/strict-checks.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"strict-checks.js","sourceRoot":"","sources":["../../src/workflow/strict-checks.ts"],"names":[],"mappings":"AAAA;;;;;GAKG;AACH,OAAO,EAAE,0BAA0B,EAAE,oBAAoB,EAAE,MAAM,gBAAgB,CAAC;AAElF,OAAO,EAAE,YAAY,EAAE,MAAM,oBAAoB,CAAC;AAClD,OAAO,EAAE,SAAS,EAAE,MAAM,iBAAiB,CAAC;AAC5C,OAAO,KAAK,WAAW,MAAM,oBAAoB,CAAC;AAClD,OAAO,KAAK,CAAC,MAAM,eAAe,CAAC;AAEnC,wEAAwE;AAExE;;;GAGG;AACH,MAAM,UAAU,sBAAsB,CAAC,YAAqC;IAC1E,MAAM,MAAM,GAAa,EAAE,CAAC;IAC5B,MAAM,KAAK,GAAG,YAAY,CAAC,KAAK,CAAC;IACjC,IAAI,CAAC,KAAK,IAAI,OAAO,KAAK,KAAK,QAAQ;QAAE,OAAO,MAAM,CAAC;IAEvD,MAAM,OAAO,GAAwB,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC;QACvD,CAAC,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,CAAC,EAAE,EAAE,CAAC,CAAC,MAAM,CAAC,CAAC,CAAC,EAAE,CAAC,CAAC,CAAC;QACrC,CAAC,CAAC,MAAM,CAAC,OAAO,CAAC,KAAgC,CAAC,CAAC;IAErD,KAAK,MAAM,CAAC,GAAG,EAAE,IAAI,CAAC,IAAI,OAAO,EAAE,CAAC;QAClC,IAAI,CAAC,IAAI,IAAI,OAAO,IAAI,KAAK,QAAQ;YAAE,SAAS;QAChD,MAAM,CAAC,GAAG,IAA+B,CAAC;QAC1C,IAAI,CAAC,CAAC,IAAI,KAAK,aAAa;YAAE,SAAS;QACvC,IAAI,CAAC,CAAC,CAAC,OAAO;YAAE,SAAS;QAEzB,MAAM,SAAS,GAAG,CAAC,CAAC,UAAU,CAAC;QAC/B,IAAI,OAAO,SAAS,KAAK,QAAQ,EAAE,CAAC;YAClC,MAAM,CAAC,IAAI,CAAC,QAAQ,GAAG,kEAAkE,CAAC,CAAC;QAC7F,CAAC;IACH,CAAC;IACD,OAAO,MAAM,CAAC;AAChB,CAAC;AAED;;;;;;GAMG;AACH,MAAM,UAAU,uBAAuB,CAAC,YAAqC;IAC3E,MAAM,MAAM,GAAa,EAAE,CAAC;IAC5B,MAAM,KAAK,GAAG,YAAY,CAAC,KAAK,CAAC;IACjC,IAAI,CAAC,KAAK,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC;QAAE,OAAO,MAAM,CAAC;IAEnD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,KAAK,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;QACtC,MAAM,IAAI,GAAG,KAAK,CAAC,CAAC,CAAC,CAAC;QACtB,IAAI,CAAC,IAAI,IAAI,OAAO,IAAI,KAAK,QAAQ;YAAE,SAAS;QAChD,MAAM,CAAC,GAAG,IAA+B,CAAC;QAC1C,IAAI,CAAC,CAAC,GAAG,IAAI,OAAO,CAAC,CAAC,GAAG,KAAK,QAAQ;YAAE,SAAS,CAAC,cAAc;QAChE,IAAI,CAAC,CAAC,CAAC,OAAO;YAAE,SAAS;QAEzB,IAAI,YAAY,IAAI,CAAC,IAAI,CAAC,CAAC,OAAO,IAAI,CAAC,CAAC,EAAE,CAAC;YACzC,MAAM,CAAC,IAAI,CAAC,QAAQ,CAAC,qEAAqE,CAAC,CAAC;QAC9F,CAAC;IACH,CAAC;IACD,OAAO,MAAM,CAAC;AAChB,CAAC;AAED,8DAA8D;AAC9D,MAAM,UAAU,mBAAmB,CACjC,YAAqC,EACrC,MAAuB;IAEvB,MAAM,GAAG,GAAG,MAAM,IAAI,YAAY,CAAC,YAAY,CAAC,CAAC;IACjD,OAAO,GAAG,KAAK,QAAQ;QACrB,CAAC,CAAC,sBAAsB,CAAC,YAAY,CAAC;QACtC,CAAC,CAAC,uBAAuB,CAAC,YAAY,CAAC,CAAC;AAC5C,CAAC;AAED,wEAAwE;AAExE,SAAS,YAAY,CAAC,KAA6B;IACjD,MAAM,MAAM,GAAG,WAAW,CAAC,cAAc,CAAC,eAAe,CAAC,KAAK,CAAC,CAAC;IACjE,OAAO,MAAM,CAAC,GAAG,CAAC,CAAC,CAAC,EAAE,EAAE,CAAC,GAAG,CAAC,CAAC,IAAI,CAAC,IAAI,CAAC,GAAG,CAAC,KAAK,CAAC,CAAC,OAAO,EAAE,CAAC,CAAC;AAChE,CAAC;AAED;;;GAGG;AACH,MAAM,UAAU,oBAAoB,CAClC,YAAqC,EACrC,MAAuB;IAEvB,MAAM,GAAG,GAAG,MAAM,IAAI,YAAY,CAAC,YAAY,CAAC,CAAC;IACjD,MAAM,GAAG,GAAG,GAAG,KAAK,QAAQ,CAAC,CAAC,CAAC,sBAAsB,CAAC,CAAC,CAAC,gBAAgB,CAAC;IACzE,MAAM,IAAI,GAAG,SAAS,CAAC,YAAY,EAAE,GAAG,CAAC,CAAC;IAE1C,MAAM,MAAM,GACV,GAAG,KAAK,QAAQ,CAAC,CAAC,CAAC,0BAA0B,CAAC,CAAC,CAAC,oBAAoB,CAAC;IACvE,MAAM,MAAM,GAAG,CAAC,CAAC,mBAAmB,CAAC,MAAM,EAAE,EAAE,gBAAgB,EAAE,OAAO,EAAE,CAAC,CAAC;IAC5E,MAAM,MAAM,GAAG,MAAM,CAAC,IAAI,CAAC,CAAC;IAE5B,IAAI,MAAM,CAAC,IAAI,KAAK,MAAM,EAAE,CAAC;QAC3B,OAAO,YAAY,CAAC,MAAM,CAAC,IAAI,CAAC,CAAC;IACnC,CAAC;IACD,OAAO,EAAE,CAAC;AACZ,CAAC"}

package/dist/workflow/tool-state-io.d.ts

@@ -0,0 +1,14 @@
+/**
+ * Shared helper for reading a native step's `tool_state`.
+ *
+ * Native workflows store parameter state as either:
+ *   - a JSON-encoded string (`.ga` on disk), or
+ *   - a parsed dict (after normalization / in-memory manipulation).
+ *
+ * Consumers elsewhere in the package duplicated this logic (cross-check
+ * extractor, normalized native builder, clean). Kept here as the shared
+ * root. `clean.ts` wraps this with legacy-dict decoding; it's a superset, not
+ * a replacement.
+ */
+export declare function parseToolState(raw: unknown): Record<string, unknown>;
+//# sourceMappingURL=tool-state-io.d.ts.map

package/dist/workflow/tool-state-io.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"tool-state-io.d.ts","sourceRoot":"","sources":["../../src/workflow/tool-state-io.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AACH,wBAAgB,cAAc,CAAC,GAAG,EAAE,OAAO,GAAG,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAiBpE"}

package/dist/workflow/tool-state-io.js

@@ -0,0 +1,33 @@
+/**
+ * Shared helper for reading a native step's `tool_state`.
+ *
+ * Native workflows store parameter state as either:
+ *   - a JSON-encoded string (`.ga` on disk), or
+ *   - a parsed dict (after normalization / in-memory manipulation).
+ *
+ * Consumers elsewhere in the package duplicated this logic (cross-check
+ * extractor, normalized native builder, clean). Kept here as the shared
+ * root. `clean.ts` wraps this with legacy-dict decoding; it's a superset, not
+ * a replacement.
+ */
+export function parseToolState(raw) {
+    if (typeof raw === "string") {
+        if (raw === "")
+            return {};
+        try {
+            const parsed = JSON.parse(raw);
+            if (parsed && typeof parsed === "object" && !Array.isArray(parsed)) {
+                return parsed;
+            }
+        }
+        catch {
+            /* fall through to empty */
+        }
+        return {};
+    }
+    if (raw && typeof raw === "object" && !Array.isArray(raw)) {
+        return raw;
+    }
+    return {};
+}
+//# sourceMappingURL=tool-state-io.js.map

package/dist/workflow/tool-state-io.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"tool-state-io.js","sourceRoot":"","sources":["../../src/workflow/tool-state-io.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AACH,MAAM,UAAU,cAAc,CAAC,GAAY;IACzC,IAAI,OAAO,GAAG,KAAK,QAAQ,EAAE,CAAC;QAC5B,IAAI,GAAG,KAAK,EAAE;YAAE,OAAO,EAAE,CAAC;QAC1B,IAAI,CAAC;YACH,MAAM,MAAM,GAAG,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC;YAC/B,IAAI,MAAM,IAAI,OAAO,MAAM,KAAK,QAAQ,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,MAAM,CAAC,EAAE,CAAC;gBACnE,OAAO,MAAiC,CAAC;YAC3C,CAAC;QACH,CAAC;QAAC,MAAM,CAAC;YACP,2BAA2B;QAC7B,CAAC;QACD,OAAO,EAAE,CAAC;IACZ,CAAC;IACD,IAAI,GAAG,IAAI,OAAO,GAAG,KAAK,QAAQ,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,GAAG,CAAC,EAAE,CAAC;QAC1D,OAAO,GAA8B,CAAC;IACxC,CAAC;IACD,OAAO,EAAE,CAAC;AACZ,CAAC"}

package/dist/workflow/validators.d.ts

@@ -0,0 +1,34 @@
+/**
+ * Shared Effect-schema validator dispatch for workflow dict inputs.
+ *
+ * Mirrors gxformat2/validators.py. Callers pass a parsed workflow dict and get
+ * back the decoded value or throw on validation failure. Used by the schema-rule
+ * catalog runner and declarative-operation tests.
+ *
+ * The generated Effect schemas make `class` a required literal; Python's
+ * pydantic models default it. `withClass` injects the discriminator when
+ * missing so pass/fail semantics match Python byte-for-byte — see the plan
+ * note about `Format2MissingClass` being unenforceable today.
+ */
+/**
+ * Return `raw` with `class: cls` injected if missing, and the same injection
+ * applied recursively to step subworkflows. Native steps embed subworkflows
+ * under `.subworkflow`; format2 steps embed them under `.run` (when `run` is
+ * an inline dict, not a URL).
+ *
+ * The cls string must match the parent document's class: nested format2
+ * subworkflows inherit `"GalaxyWorkflow"`, native inherit `"NativeGalaxyWorkflow"`.
+ */
+export declare function withClass(raw: unknown, cls: string): unknown;
+export declare function validateFormat2(wf: unknown): unknown;
+export declare function validateFormat2Strict(wf: unknown): unknown;
+export declare function validateNative(wf: unknown): unknown;
+export declare function validateNativeStrict(wf: unknown): unknown;
+/**
+ * Pick the validator matching a fixture filename's format.
+ *
+ * `.ga` → native; anything else → format2. `strict` picks the closed-schema
+ * flavor that rejects unknown fields.
+ */
+export declare function validatorForFixture(fixtureName: string, strict: boolean): (wf: unknown) => unknown;
+//# sourceMappingURL=validators.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"validators.d.ts","sourceRoot":"","sources":["../../src/workflow/validators.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AAOH;;;;;;;;GAQG;AACH,wBAAgB,SAAS,CAAC,GAAG,EAAE,OAAO,EAAE,GAAG,EAAE,MAAM,GAAG,OAAO,CAkB5D;AAgBD,wBAAgB,eAAe,CAAC,EAAE,EAAE,OAAO,GAAG,OAAO,CAIpD;AAED,wBAAgB,qBAAqB,CAAC,EAAE,EAAE,OAAO,GAAG,OAAO,CAI1D;AAED,wBAAgB,cAAc,CAAC,EAAE,EAAE,OAAO,GAAG,OAAO,CAInD;AAED,wBAAgB,oBAAoB,CAAC,EAAE,EAAE,OAAO,GAAG,OAAO,CAIzD;AAED;;;;;GAKG;AACH,wBAAgB,mBAAmB,CACjC,WAAW,EAAE,MAAM,EACnB,MAAM,EAAE,OAAO,GACd,CAAC,EAAE,EAAE,OAAO,KAAK,OAAO,CAK1B"}

package/dist/workflow/validators.js

@@ -0,0 +1,83 @@
+/**
+ * Shared Effect-schema validator dispatch for workflow dict inputs.
+ *
+ * Mirrors gxformat2/validators.py. Callers pass a parsed workflow dict and get
+ * back the decoded value or throw on validation failure. Used by the schema-rule
+ * catalog runner and declarative-operation tests.
+ *
+ * The generated Effect schemas make `class` a required literal; Python's
+ * pydantic models default it. `withClass` injects the discriminator when
+ * missing so pass/fail semantics match Python byte-for-byte — see the plan
+ * note about `Format2MissingClass` being unenforceable today.
+ */
+import { Schema } from "effect";
+import { GalaxyWorkflowSchema } from "./raw/gxformat2.effect.js";
+import { NativeGalaxyWorkflowSchema } from "./raw/native.effect.js";
+/**
+ * Return `raw` with `class: cls` injected if missing, and the same injection
+ * applied recursively to step subworkflows. Native steps embed subworkflows
+ * under `.subworkflow`; format2 steps embed them under `.run` (when `run` is
+ * an inline dict, not a URL).
+ *
+ * The cls string must match the parent document's class: nested format2
+ * subworkflows inherit `"GalaxyWorkflow"`, native inherit `"NativeGalaxyWorkflow"`.
+ */
+export function withClass(raw, cls) {
+    if (!raw || typeof raw !== "object" || Array.isArray(raw))
+        return raw;
+    const obj = raw;
+    const result = "class" in obj ? { ...obj } : { ...obj, class: cls };
+    const steps = result.steps;
+    if (!steps || typeof steps !== "object")
+        return result;
+    if (Array.isArray(steps)) {
+        result.steps = steps.map((step) => injectStepSubworkflow(step, cls));
+    }
+    else {
+        const next = {};
+        for (const [key, step] of Object.entries(steps)) {
+            next[key] = injectStepSubworkflow(step, cls);
+        }
+        result.steps = next;
+    }
+    return result;
+}
+function injectStepSubworkflow(step, cls) {
+    if (!step || typeof step !== "object")
+        return step;
+    const s = step;
+    if (s.subworkflow && typeof s.subworkflow === "object") {
+        return { ...s, subworkflow: withClass(s.subworkflow, cls) };
+    }
+    // format2 steps embed subworkflows under `run` when it's an inline dict.
+    // Skip string runs (URLs) and missing runs.
+    if (s.run && typeof s.run === "object" && !Array.isArray(s.run)) {
+        return { ...s, run: withClass(s.run, cls) };
+    }
+    return s;
+}
+export function validateFormat2(wf) {
+    return Schema.decodeUnknownSync(GalaxyWorkflowSchema, { onExcessProperty: "ignore" })(withClass(wf, "GalaxyWorkflow"));
+}
+export function validateFormat2Strict(wf) {
+    return Schema.decodeUnknownSync(GalaxyWorkflowSchema, { onExcessProperty: "error" })(withClass(wf, "GalaxyWorkflow"));
+}
+export function validateNative(wf) {
+    return Schema.decodeUnknownSync(NativeGalaxyWorkflowSchema, { onExcessProperty: "ignore" })(withClass(wf, "NativeGalaxyWorkflow"));
+}
+export function validateNativeStrict(wf) {
+    return Schema.decodeUnknownSync(NativeGalaxyWorkflowSchema, { onExcessProperty: "error" })(withClass(wf, "NativeGalaxyWorkflow"));
+}
+/**
+ * Pick the validator matching a fixture filename's format.
+ *
+ * `.ga` → native; anything else → format2. `strict` picks the closed-schema
+ * flavor that rejects unknown fields.
+ */
+export function validatorForFixture(fixtureName, strict) {
+    if (fixtureName.endsWith(".ga")) {
+        return strict ? validateNativeStrict : validateNative;
+    }
+    return strict ? validateFormat2Strict : validateFormat2;
+}
+//# sourceMappingURL=validators.js.map

package/dist/workflow/validators.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"validators.js","sourceRoot":"","sources":["../../src/workflow/validators.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AAEH,OAAO,EAAE,MAAM,EAAE,MAAM,QAAQ,CAAC;AAEhC,OAAO,EAAE,oBAAoB,EAAE,MAAM,2BAA2B,CAAC;AACjE,OAAO,EAAE,0BAA0B,EAAE,MAAM,wBAAwB,CAAC;AAEpE;;;;;;;;GAQG;AACH,MAAM,UAAU,SAAS,CAAC,GAAY,EAAE,GAAW;IACjD,IAAI,CAAC,GAAG,IAAI,OAAO,GAAG,KAAK,QAAQ,IAAI,KAAK,CAAC,OAAO,CAAC,GAAG,CAAC;QAAE,OAAO,GAAG,CAAC;IACtE,MAAM,GAAG,GAAG,GAA8B,CAAC;IAC3C,MAAM,MAAM,GAA4B,OAAO,IAAI,GAAG,CAAC,CAAC,CAAC,EAAE,GAAG,GAAG,EAAE,CAAC,CAAC,CAAC,EAAE,GAAG,GAAG,EAAE,KAAK,EAAE,GAAG,EAAE,CAAC;IAE7F,MAAM,KAAK,GAAG,MAAM,CAAC,KAAK,CAAC;IAC3B,IAAI,CAAC,KAAK,IAAI,OAAO,KAAK,KAAK,QAAQ;QAAE,OAAO,MAAM,CAAC;IAEvD,IAAI,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE,CAAC;QACzB,MAAM,CAAC,KAAK,GAAG,KAAK,CAAC,GAAG,CAAC,CAAC,IAAI,EAAE,EAAE,CAAC,qBAAqB,CAAC,IAAI,EAAE,GAAG,CAAC,CAAC,CAAC;IACvE,CAAC;SAAM,CAAC;QACN,MAAM,IAAI,GAA4B,EAAE,CAAC;QACzC,KAAK,MAAM,CAAC,GAAG,EAAE,IAAI,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,KAAgC,CAAC,EAAE,CAAC;YAC3E,IAAI,CAAC,GAAG,CAAC,GAAG,qBAAqB,CAAC,IAAI,EAAE,GAAG,CAAC,CAAC;QAC/C,CAAC;QACD,MAAM,CAAC,KAAK,GAAG,IAAI,CAAC;IACtB,CAAC;IACD,OAAO,MAAM,CAAC;AAChB,CAAC;AAED,SAAS,qBAAqB,CAAC,IAAa,EAAE,GAAW;IACvD,IAAI,CAAC,IAAI,IAAI,OAAO,IAAI,KAAK,QAAQ;QAAE,OAAO,IAAI,CAAC;IACnD,MAAM,CAAC,GAAG,IAA+B,CAAC;IAC1C,IAAI,CAAC,CAAC,WAAW,IAAI,OAAO,CAAC,CAAC,WAAW,KAAK,QAAQ,EAAE,CAAC;QACvD,OAAO,EAAE,GAAG,CAAC,EAAE,WAAW,EAAE,SAAS,CAAC,CAAC,CAAC,WAAW,EAAE,GAAG,CAAC,EAAE,CAAC;IAC9D,CAAC;IACD,yEAAyE;IACzE,4CAA4C;IAC5C,IAAI,CAAC,CAAC,GAAG,IAAI,OAAO,CAAC,CAAC,GAAG,KAAK,QAAQ,IAAI,CAAC,KAAK,CAAC,OAAO,CAAC,CAAC,CAAC,GAAG,CAAC,EAAE,CAAC;QAChE,OAAO,EAAE,GAAG,CAAC,EAAE,GAAG,EAAE,SAAS,CAAC,CAAC,CAAC,GAAG,EAAE,GAAG,CAAC,EAAE,CAAC;IAC9C,CAAC;IACD,OAAO,CAAC,CAAC;AACX,CAAC;AAED,MAAM,UAAU,eAAe,CAAC,EAAW;IACzC,OAAO,MAAM,CAAC,iBAAiB,CAAC,oBAAoB,EAAE,EAAE,gBAAgB,EAAE,QAAQ,EAAE,CAAC,CACnF,SAAS,CAAC,EAAE,EAAE,gBAAgB,CAAC,CAChC,CAAC;AACJ,CAAC;AAED,MAAM,UAAU,qBAAqB,CAAC,EAAW;IAC/C,OAAO,MAAM,CAAC,iBAAiB,CAAC,oBAAoB,EAAE,EAAE,gBAAgB,EAAE,OAAO,EAAE,CAAC,CAClF,SAAS,CAAC,EAAE,EAAE,gBAAgB,CAAC,CAChC,CAAC;AACJ,CAAC;AAED,MAAM,UAAU,cAAc,CAAC,EAAW;IACxC,OAAO,MAAM,CAAC,iBAAiB,CAAC,0BAA0B,EAAE,EAAE,gBAAgB,EAAE,QAAQ,EAAE,CAAC,CACzF,SAAS,CAAC,EAAE,EAAE,sBAAsB,CAAC,CACtC,CAAC;AACJ,CAAC;AAED,MAAM,UAAU,oBAAoB,CAAC,EAAW;IAC9C,OAAO,MAAM,CAAC,iBAAiB,CAAC,0BAA0B,EAAE,EAAE,gBAAgB,EAAE,OAAO,EAAE,CAAC,CACxF,SAAS,CAAC,EAAE,EAAE,sBAAsB,CAAC,CACtC,CAAC;AACJ,CAAC;AAED;;;;;GAKG;AACH,MAAM,UAAU,mBAAmB,CACjC,WAAmB,EACnB,MAAe;IAEf,IAAI,WAAW,CAAC,QAAQ,CAAC,KAAK,CAAC,EAAE,CAAC;QAChC,OAAO,MAAM,CAAC,CAAC,CAAC,oBAAoB,CAAC,CAAC,CAAC,cAAc,CAAC;IACxD,CAAC;IACD,OAAO,MAAM,CAAC,CAAC,CAAC,qBAAqB,CAAC,CAAC,CAAC,eAAe,CAAC;AAC1D,CAAC"}

package/dist/workflow/walk-helpers.d.ts

@@ -0,0 +1,29 @@
+/**
+ * Pure helper functions for walking Galaxy parameter trees.
+ *
+ * Extracted from state-merge.ts to break a circular dependency:
+ * walker.ts needs these helpers, and state-merge.ts needs walkNativeState.
+ *
+ * Ported from Python galaxy.tool_util.parameters.visitor.
+ */
+import type { ConditionalParameterModel, ConditionalWhen } from "../schema/bundle-types.js";
+/** Build flat pipe-separated state path: `name` or `prefix|name`. */
+export declare function flatStatePath(name: string, prefix?: string): string;
+/** Filter a flat key-value map to keys starting with a given prefix. */
+export declare function keysStartingWith<T>(map: Record<string, T>, prefix: string): Record<string, T>;
+/**
+ * Split flat connection keys for a repeat into per-instance arrays.
+ *
+ * Connection keys use the pattern `repeatName_N|paramName`.
+ * Returns an array of per-instance connection dicts.
+ */
+export declare function repeatInputsToArray<T>(statePath: string, inputs: Record<string, T>): Record<string, T>[];
+/**
+ * Select the matching ConditionalWhen for a conditional state dict.
+ *
+ * Matches the test parameter's value in state against each when's
+ * discriminator. Falls back to the default when if no match found.
+ * Returns null if no match at all (graceful degradation).
+ */
+export declare function selectWhichWhen(conditional: ConditionalParameterModel, state: Record<string, unknown>): ConditionalWhen | null;
+//# sourceMappingURL=walk-helpers.d.ts.map

package/dist/workflow/walk-helpers.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"walk-helpers.d.ts","sourceRoot":"","sources":["../../src/workflow/walk-helpers.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,KAAK,EACV,yBAAyB,EACzB,eAAe,EAGhB,MAAM,2BAA2B,CAAC;AAKnC,qEAAqE;AACrE,wBAAgB,aAAa,CAAC,IAAI,EAAE,MAAM,EAAE,MAAM,CAAC,EAAE,MAAM,GAAG,MAAM,CAEnE;AAED,wEAAwE;AACxE,wBAAgB,gBAAgB,CAAC,CAAC,EAAE,GAAG,EAAE,MAAM,CAAC,MAAM,EAAE,CAAC,CAAC,EAAE,MAAM,EAAE,MAAM,GAAG,MAAM,CAAC,MAAM,EAAE,CAAC,CAAC,CAQ7F;AAED;;;;;GAKG;AACH,wBAAgB,mBAAmB,CAAC,CAAC,EACnC,SAAS,EAAE,MAAM,EACjB,MAAM,EAAE,MAAM,CAAC,MAAM,EAAE,CAAC,CAAC,GACxB,MAAM,CAAC,MAAM,EAAE,CAAC,CAAC,EAAE,CAuBrB;AAID;;;;;;GAMG;AACH,wBAAgB,eAAe,CAC7B,WAAW,EAAE,yBAAyB,EACtC,KAAK,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAC7B,eAAe,GAAG,IAAI,CAmBxB"}

package/dist/workflow/walk-helpers.js

@@ -0,0 +1,89 @@
+/**
+ * Pure helper functions for walking Galaxy parameter trees.
+ *
+ * Extracted from state-merge.ts to break a circular dependency:
+ * walker.ts needs these helpers, and state-merge.ts needs walkNativeState.
+ *
+ * Ported from Python galaxy.tool_util.parameters.visitor.
+ */
+import { parseBool } from "./coercions.js";
+// --- Path helpers ---
+/** Build flat pipe-separated state path: `name` or `prefix|name`. */
+export function flatStatePath(name, prefix) {
+    return prefix != null ? `${prefix}|${name}` : name;
+}
+/** Filter a flat key-value map to keys starting with a given prefix. */
+export function keysStartingWith(map, prefix) {
+    const result = {};
+    for (const [key, value] of Object.entries(map)) {
+        if (key.startsWith(prefix)) {
+            result[key] = value;
+        }
+    }
+    return result;
+}
+/**
+ * Split flat connection keys for a repeat into per-instance arrays.
+ *
+ * Connection keys use the pattern `repeatName_N|paramName`.
+ * Returns an array of per-instance connection dicts.
+ */
+export function repeatInputsToArray(statePath, inputs) {
+    const repeatInputs = keysStartingWith(inputs, statePath + "_");
+    let highestCount = -1;
+    for (const key of Object.keys(repeatInputs)) {
+        const numStr = key.slice(statePath.length + 1).split("|")[0];
+        const num = parseInt(numStr, 10);
+        if (!isNaN(num) && num > highestCount) {
+            highestCount = num;
+        }
+    }
+    const params = [];
+    for (let i = 0; i <= highestCount; i++) {
+        params.push({});
+    }
+    for (const [key, value] of Object.entries(repeatInputs)) {
+        const numStr = key.slice(statePath.length + 1).split("|")[0];
+        const num = parseInt(numStr, 10);
+        if (!isNaN(num)) {
+            params[num][key] = value;
+        }
+    }
+    return params;
+}
+// --- Conditional branch selection ---
+/**
+ * Select the matching ConditionalWhen for a conditional state dict.
+ *
+ * Matches the test parameter's value in state against each when's
+ * discriminator. Falls back to the default when if no match found.
+ * Returns null if no match at all (graceful degradation).
+ */
+export function selectWhichWhen(conditional, state) {
+    const testParam = conditional.test_parameter;
+    const testValue = state[testParam.name];
+    // Try exact match first
+    for (const when of conditional.whens) {
+        if (_testValueMatchesDiscriminator(testParam, testValue, when.discriminator)) {
+            return when;
+        }
+    }
+    // Fall back to default when
+    for (const when of conditional.whens) {
+        if (when.is_default_when) {
+            return when;
+        }
+    }
+    return null;
+}
+function _testValueMatchesDiscriminator(testParam, testValue, discriminator) {
+    if (testParam.parameter_type === "gx_boolean") {
+        // Boolean coercion: handle string "true"/"false"/"True"/"False" and actual booleans
+        const boolValue = parseBool(testValue);
+        const discBool = typeof discriminator === "boolean" ? discriminator : parseBool(discriminator);
+        return boolValue === discBool;
+    }
+    // Select: string comparison
+    return String(testValue) === String(discriminator);
+}
+//# sourceMappingURL=walk-helpers.js.map

package/dist/workflow/walk-helpers.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"walk-helpers.js","sourceRoot":"","sources":["../../src/workflow/walk-helpers.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAQH,OAAO,EAAE,SAAS,EAAE,MAAM,gBAAgB,CAAC;AAE3C,uBAAuB;AAEvB,qEAAqE;AACrE,MAAM,UAAU,aAAa,CAAC,IAAY,EAAE,MAAe;IACzD,OAAO,MAAM,IAAI,IAAI,CAAC,CAAC,CAAC,GAAG,MAAM,IAAI,IAAI,EAAE,CAAC,CAAC,CAAC,IAAI,CAAC;AACrD,CAAC;AAED,wEAAwE;AACxE,MAAM,UAAU,gBAAgB,CAAI,GAAsB,EAAE,MAAc;IACxE,MAAM,MAAM,GAAsB,EAAE,CAAC;IACrC,KAAK,MAAM,CAAC,GAAG,EAAE,KAAK,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,GAAG,CAAC,EAAE,CAAC;QAC/C,IAAI,GAAG,CAAC,UAAU,CAAC,MAAM,CAAC,EAAE,CAAC;YAC3B,MAAM,CAAC,GAAG,CAAC,GAAG,KAAK,CAAC;QACtB,CAAC;IACH,CAAC;IACD,OAAO,MAAM,CAAC;AAChB,CAAC;AAED;;;;;GAKG;AACH,MAAM,UAAU,mBAAmB,CACjC,SAAiB,EACjB,MAAyB;IAEzB,MAAM,YAAY,GAAG,gBAAgB,CAAC,MAAM,EAAE,SAAS,GAAG,GAAG,CAAC,CAAC;IAC/D,IAAI,YAAY,GAAG,CAAC,CAAC,CAAC;IACtB,KAAK,MAAM,GAAG,IAAI,MAAM,CAAC,IAAI,CAAC,YAAY,CAAC,EAAE,CAAC;QAC5C,MAAM,MAAM,GAAG,GAAG,CAAC,KAAK,CAAC,SAAS,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC;QAC7D,MAAM,GAAG,GAAG,QAAQ,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC;QACjC,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,IAAI,GAAG,GAAG,YAAY,EAAE,CAAC;YACtC,YAAY,GAAG,GAAG,CAAC;QACrB,CAAC;IACH,CAAC;IAED,MAAM,MAAM,GAAwB,EAAE,CAAC;IACvC,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,IAAI,YAAY,EAAE,CAAC,EAAE,EAAE,CAAC;QACvC,MAAM,CAAC,IAAI,CAAC,EAAE,CAAC,CAAC;IAClB,CAAC;IACD,KAAK,MAAM,CAAC,GAAG,EAAE,KAAK,CAAC,IAAI,MAAM,CAAC,OAAO,CAAC,YAAY,CAAC,EAAE,CAAC;QACxD,MAAM,MAAM,GAAG,GAAG,CAAC,KAAK,CAAC,SAAS,CAAC,MAAM,GAAG,CAAC,CAAC,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC;QAC7D,MAAM,GAAG,GAAG,QAAQ,CAAC,MAAM,EAAE,EAAE,CAAC,CAAC;QACjC,IAAI,CAAC,KAAK,CAAC,GAAG,CAAC,EAAE,CAAC;YAChB,MAAM,CAAC,GAAG,CAAC,CAAC,GAAG,CAAC,GAAG,KAAK,CAAC;QAC3B,CAAC;IACH,CAAC;IACD,OAAO,MAAM,CAAC;AAChB,CAAC;AAED,uCAAuC;AAEvC;;;;;;GAMG;AACH,MAAM,UAAU,eAAe,CAC7B,WAAsC,EACtC,KAA8B;IAE9B,MAAM,SAAS,GAAG,WAAW,CAAC,cAAc,CAAC;IAC7C,MAAM,SAAS,GAAG,KAAK,CAAC,SAAS,CAAC,IAAI,CAAC,CAAC;IAExC,wBAAwB;IACxB,KAAK,MAAM,IAAI,IAAI,WAAW,CAAC,KAAK,EAAE,CAAC;QACrC,IAAI,8BAA8B,CAAC,SAAS,EAAE,SAAS,EAAE,IAAI,CAAC,aAAa,CAAC,EAAE,CAAC;YAC7E,OAAO,IAAI,CAAC;QACd,CAAC;IACH,CAAC;IAED,4BAA4B;IAC5B,KAAK,MAAM,IAAI,IAAI,WAAW,CAAC,KAAK,EAAE,CAAC;QACrC,IAAI,IAAI,CAAC,eAAe,EAAE,CAAC;YACzB,OAAO,IAAI,CAAC;QACd,CAAC;IACH,CAAC;IAED,OAAO,IAAI,CAAC;AACd,CAAC;AAED,SAAS,8BAA8B,CACrC,SAAuD,EACvD,SAAkB,EAClB,aAA+B;IAE/B,IAAI,SAAS,CAAC,cAAc,KAAK,YAAY,EAAE,CAAC;QAC9C,oFAAoF;QACpF,MAAM,SAAS,GAAG,SAAS,CAAC,SAAS,CAAC,CAAC;QACvC,MAAM,QAAQ,GAAG,OAAO,aAAa,KAAK,SAAS,CAAC,CAAC,CAAC,aAAa,CAAC,CAAC,CAAC,SAAS,CAAC,aAAa,CAAC,CAAC;QAC/F,OAAO,SAAS,KAAK,QAAQ,CAAC;IAChC,CAAC;IACD,4BAA4B;IAC5B,OAAO,MAAM,CAAC,SAAS,CAAC,KAAK,MAAM,CAAC,aAAa,CAAC,CAAC;AACrD,CAAC"}

package/dist/workflow/walker.d.ts

@@ -0,0 +1,55 @@
+/**
+ * Schema-aware state walkers for native and format2 workflow tool state.
+ *
+ * Port of Python galaxy.tool_util.workflow_state._walker.
+ *
+ * Walks the parameter tree using tool definitions, calling a leaf callback
+ * for each scalar parameter. Handles conditionals (branch selection),
+ * repeats (instance expansion), and sections (recursion). Builds a new
+ * state dict from callback return values.
+ *
+ * Design principles:
+ * - No double encoding: containers must be proper dicts/lists, never JSON strings
+ * - No legacy decode: string containers are errors, not silently accommodated
+ * - SKIP_VALUE sentinel omits a value from the output
+ */
+import type { ToolParameterModel } from "../schema/bundle-types.js";
+/** Sentinel: return from leaf callback to omit a value from output. */
+export declare const SKIP_VALUE: unique symbol;
+export type LeafCallback = (toolInput: ToolParameterModel, value: unknown, statePath: string) => unknown | typeof SKIP_VALUE;
+export interface WalkNativeOptions {
+    prefix?: string;
+    checkUnknownKeys?: boolean;
+    /** Copy undeclared keys from input state to output (default: false). */
+    preserveUnknownKeys?: boolean;
+}
+/**
+ * Walk native workflow tool_state using the parameter tree.
+ *
+ * For each leaf parameter, calls `leafCallback(toolInput, value, statePath)`.
+ * Return values build the output dict; return SKIP_VALUE to omit.
+ *
+ * Containers (conditionals, repeats, sections) are recursed into.
+ * Bookkeeping keys (__current_case__, etc.) are stripped.
+ * Input connections are used to determine repeat instance counts.
+ *
+ * @throws Error if a container parameter value is a string (legacy encoding)
+ */
+export declare function walkNativeState(inputConnections: Record<string, unknown>, toolInputs: ToolParameterModel[], state: Record<string, unknown>, leafCallback: LeafCallback, options?: WalkNativeOptions): Record<string, unknown>;
+/**
+ * Walk format2 workflow tool state using the parameter tree.
+ *
+ * Simpler than native walking — no bookkeeping keys, no input connections,
+ * no double-encoding concerns. Clean dict walking with conditional branch
+ * selection, repeat iteration, section recursion.
+ *
+ * @throws Error if a container parameter value is a string
+ */
+export declare function walkFormat2State(toolInputs: ToolParameterModel[], state: Record<string, unknown>, leafCallback: LeafCallback, prefix?: string): Record<string, unknown>;
+/** Error thrown when unknown keys are detected in native state. */
+export declare class UnknownKeyError extends Error {
+    readonly key: string;
+    readonly prefix?: string | undefined;
+    constructor(key: string, prefix?: string | undefined);
+}
+//# sourceMappingURL=walker.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"walker.d.ts","sourceRoot":"","sources":["../../src/workflow/walker.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;GAcG;AAEH,OAAO,KAAK,EACV,kBAAkB,EAInB,MAAM,2BAA2B,CAAC;AAKnC,uEAAuE;AACvE,eAAO,MAAM,UAAU,EAAE,OAAO,MAA6B,CAAC;AAE9D,MAAM,MAAM,YAAY,GAAG,CACzB,SAAS,EAAE,kBAAkB,EAC7B,KAAK,EAAE,OAAO,EACd,SAAS,EAAE,MAAM,KACd,OAAO,GAAG,OAAO,UAAU,CAAC;AAEjC,MAAM,WAAW,iBAAiB;IAChC,MAAM,CAAC,EAAE,MAAM,CAAC;IAChB,gBAAgB,CAAC,EAAE,OAAO,CAAC;IAC3B,wEAAwE;IACxE,mBAAmB,CAAC,EAAE,OAAO,CAAC;CAC/B;AAED;;;;;;;;;;;GAWG;AACH,wBAAgB,eAAe,CAC7B,gBAAgB,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EACzC,UAAU,EAAE,kBAAkB,EAAE,EAChC,KAAK,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC9B,YAAY,EAAE,YAAY,EAC1B,OAAO,CAAC,EAAE,iBAAiB,GAC1B,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CA6GzB;AAED;;;;;;;;GAQG;AACH,wBAAgB,gBAAgB,CAC9B,UAAU,EAAE,kBAAkB,EAAE,EAChC,KAAK,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC9B,YAAY,EAAE,YAAY,EAC1B,MAAM,CAAC,EAAE,MAAM,GACd,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CA4EzB;AAED,mEAAmE;AACnE,qBAAa,eAAgB,SAAQ,KAAK;aAEtB,GAAG,EAAE,MAAM;aACX,MAAM,CAAC,EAAE,MAAM;gBADf,GAAG,EAAE,MAAM,EACX,MAAM,CAAC,EAAE,MAAM,YAAA;CAMlC"}