@galaxy-tool-util/schema 0.2.0 → 1.0.0

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

@@ -20,6 +20,18 @@ export type LeafCallback = (toolInput: ToolParameterModel, value: unknown, state
 export interface WalkNativeOptions {
     prefix?: string;
     checkUnknownKeys?: boolean;
+    /** Copy undeclared keys from input state to output (default: false). */
+    preserveUnknownKeys?: boolean;
+    /**
+     * Switch repeat handling to `_initialize_repeat_state` semantics (default: false).
+     * When true:
+     *   - inputConnections are ignored for instance count,
+     *   - instance count is padded to `repeat.min` (never shrinks existing state),
+     *   - the repeat key is always written to output, even when empty (`[]`).
+     * Used by expand-defaults, which must surface every declared repeat as a
+     * container the user can populate.
+     */
+    repeatMinPad?: boolean;
 }
 /**
  * Walk native workflow tool_state using the parameter tree.

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

@@ -1 +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;CAC5B;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,CAqGzB;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,CA2EzB;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"}
+{"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;IAC9B;;;;;;;;OAQG;IACH,YAAY,CAAC,EAAE,OAAO,CAAC;CACxB;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,CAqHzB;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"}

package/dist/workflow/walker.js

@@ -13,7 +13,7 @@
  * - No legacy decode: string containers are errors, not silently accommodated
  * - SKIP_VALUE sentinel omits a value from the output
  */
-import { flatStatePath, repeatInputsToArray, selectWhichWhen } from "./state-merge.js";
+import { flatStatePath, repeatInputsToArray, selectWhichWhen } from "./walk-helpers.js";
 import { STALE_KEYS } from "./stale-keys.js";
 /** Sentinel: return from leaf callback to omit a value from output. */
 export const SKIP_VALUE = Symbol("SKIP_VALUE");
@@ -32,6 +32,8 @@ export const SKIP_VALUE = Symbol("SKIP_VALUE");
 export function walkNativeState(inputConnections, toolInputs, state, leafCallback, options) {
     const prefix = options?.prefix;
     const checkUnknownKeys = options?.checkUnknownKeys ?? false;
+    const preserveUnknownKeys = options?.preserveUnknownKeys ?? false;
+    const repeatMinPad = options?.repeatMinPad ?? false;
     const result = {};
     const visitedKeys = new Set();
     for (const toolInput of toolInputs) {
@@ -47,7 +49,7 @@ export function walkNativeState(inputConnections, toolInputs, state, leafCallbac
             const when = selectWhichWhen(conditional, stateDict);
             const branchParams = when != null ? when.parameters : [];
             // Walk the test parameter + branch parameters
-            const innerResult = walkNativeState(inputConnections, [conditional.test_parameter, ...branchParams], stateDict, leafCallback, { prefix: statePath, checkUnknownKeys });
+            const innerResult = walkNativeState(inputConnections, [conditional.test_parameter, ...branchParams], stateDict, leafCallback, { prefix: statePath, checkUnknownKeys, preserveUnknownKeys, repeatMinPad });
             if (Object.keys(innerResult).length > 0) {
                 result[name] = innerResult;
             }
@@ -60,16 +62,25 @@ export function walkNativeState(inputConnections, toolInputs, state, leafCallbac
             const stateArray = Array.isArray(repeatState)
                 ? repeatState
                 : [];
-            const connectionInstances = repeatInputsToArray(statePath, inputConnections);
-            const instanceCount = Math.max(stateArray.length, connectionInstances.length);
+            let instanceCount;
+            if (repeatMinPad) {
+                instanceCount = Math.max(stateArray.length, repeat.min ?? 0);
+            }
+            else {
+                const connectionInstances = repeatInputsToArray(statePath, inputConnections);
+                instanceCount = Math.max(stateArray.length, connectionInstances.length);
+            }
             const instances = [];
             for (let i = 0; i < instanceCount; i++) {
                 const instanceState = stateArray[i] ?? {};
                 const instancePrefix = `${statePath}_${i}`;
-                const instanceResult = walkNativeState(inputConnections, repeat.parameters, instanceState, leafCallback, { prefix: instancePrefix, checkUnknownKeys });
+                const instanceResult = walkNativeState(inputConnections, repeat.parameters, instanceState, leafCallback, { prefix: instancePrefix, checkUnknownKeys, preserveUnknownKeys, repeatMinPad });
                 instances.push(instanceResult);
             }
-            if (instances.length > 0) {
+            // Preserve explicit empty arrays (valid state); omit only when key is absent.
+            // In repeatMinPad mode (expand-defaults), always write the key — mirrors
+            // Python's _initialize_repeat_state which creates tool_state[name] = [].
+            if (repeatMinPad || name in state || instances.length > 0) {
                 result[name] = instances;
             }
         }
@@ -78,7 +89,7 @@ export function walkNativeState(inputConnections, toolInputs, state, leafCallbac
             const sectionState = state[name];
             _assertNotStringContainer(name, parameterType, sectionState);
             const stateDict = sectionState ?? {};
-            const innerResult = walkNativeState(inputConnections, section.parameters, stateDict, leafCallback, { prefix: statePath, checkUnknownKeys });
+            const innerResult = walkNativeState(inputConnections, section.parameters, stateDict, leafCallback, { prefix: statePath, checkUnknownKeys, preserveUnknownKeys, repeatMinPad });
             if (Object.keys(innerResult).length > 0) {
                 result[name] = innerResult;
             }
@@ -99,6 +110,13 @@ export function walkNativeState(inputConnections, toolInputs, state, leafCallbac
             }
         }
     }
+    else if (preserveUnknownKeys) {
+        for (const key of Object.keys(state)) {
+            if (!visitedKeys.has(key)) {
+                result[key] = state[key];
+            }
+        }
+    }
     return result;
 }
 /**
@@ -141,7 +159,8 @@ export function walkFormat2State(toolInputs, state, leafCallback, prefix) {
                 const instanceResult = walkFormat2State(repeat.parameters, stateArray[i], leafCallback, instancePrefix);
                 instances.push(instanceResult);
             }
-            if (instances.length > 0) {
+            // Preserve explicit empty arrays (valid state); omit only when key is absent
+            if (name in state || instances.length > 0) {
                 result[name] = instances;
             }
         }

package/dist/workflow/walker.js.map

@@ -1 +1 @@
-{"version":3,"file":"walker.js","sourceRoot":"","sources":["../../src/workflow/walker.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;GAcG;AASH,OAAO,EAAE,aAAa,EAAE,mBAAmB,EAAE,eAAe,EAAE,MAAM,kBAAkB,CAAC;AACvF,OAAO,EAAE,UAAU,EAAE,MAAM,iBAAiB,CAAC;AAE7C,uEAAuE;AACvE,MAAM,CAAC,MAAM,UAAU,GAAkB,MAAM,CAAC,YAAY,CAAC,CAAC;AAa9D;;;;;;;;;;;GAWG;AACH,MAAM,UAAU,eAAe,CAC7B,gBAAyC,EACzC,UAAgC,EAChC,KAA8B,EAC9B,YAA0B,EAC1B,OAA2B;IAE3B,MAAM,MAAM,GAAG,OAAO,EAAE,MAAM,CAAC;IAC/B,MAAM,gBAAgB,GAAG,OAAO,EAAE,gBAAgB,IAAI,KAAK,CAAC;IAC5D,MAAM,MAAM,GAA4B,EAAE,CAAC;IAC3C,MAAM,WAAW,GAAG,IAAI,GAAG,EAAU,CAAC;IAEtC,KAAK,MAAM,SAAS,IAAI,UAAU,EAAE,CAAC;QACnC,MAAM,IAAI,GAAG,SAAS,CAAC,IAAI,CAAC;QAC5B,WAAW,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC;QACtB,MAAM,aAAa,GAAG,SAAS,CAAC,cAAc,CAAC;QAC/C,MAAM,SAAS,GAAG,aAAa,CAAC,IAAI,EAAE,MAAM,CAAC,CAAC;QAE9C,IAAI,aAAa,KAAK,gBAAgB,EAAE,CAAC;YACvC,MAAM,WAAW,GAAG,SAAsC,CAAC;YAC3D,MAAM,gBAAgB,GAAG,KAAK,CAAC,IAAI,CAAC,CAAC;YAErC,yBAAyB,CAAC,IAAI,EAAE,aAAa,EAAE,gBAAgB,CAAC,CAAC;YACjE,MAAM,SAAS,GAAI,gBAA4C,IAAI,EAAE,CAAC;YAEtE,MAAM,IAAI,GAAG,eAAe,CAAC,WAAW,EAAE,SAAS,CAAC,CAAC;YACrD,MAAM,YAAY,GAAG,IAAI,IAAI,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,EAAE,CAAC;YAEzD,8CAA8C;YAC9C,MAAM,WAAW,GAAG,eAAe,CACjC,gBAAgB,EAChB,CAAC,WAAW,CAAC,cAAc,EAAE,GAAG,YAAY,CAAC,EAC7C,SAAS,EACT,YAAY,EACZ,EAAE,MAAM,EAAE,SAAS,EAAE,gBAAgB,EAAE,CACxC,CAAC;YAEF,IAAI,MAAM,CAAC,IAAI,CAAC,WAAW,CAAC,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;gBACxC,MAAM,CAAC,IAAI,CAAC,GAAG,WAAW,CAAC;YAC7B,CAAC;QACH,CAAC;aAAM,IAAI,aAAa,KAAK,WAAW,EAAE,CAAC;YACzC,MAAM,MAAM,GAAG,SAAiC,CAAC;YACjD,MAAM,WAAW,GAAG,KAAK,CAAC,IAAI,CAAC,CAAC;YAEhC,yBAAyB,CAAC,IAAI,EAAE,aAAa,EAAE,WAAW,CAAC,CAAC;YAE5D,iEAAiE;YACjE,MAAM,UAAU,GAAG,KAAK,CAAC,OAAO,CAAC,WAAW,CAAC;gBAC3C,CAAC,CAAE,WAAyC;gBAC5C,CAAC,CAAC,EAAE,CAAC;YACP,MAAM,mBAAmB,GAAG,mBAAmB,CAAC,SAAS,EAAE,gBAAgB,CAAC,CAAC;YAC7E,MAAM,aAAa,GAAG,IAAI,CAAC,GAAG,CAAC,UAAU,CAAC,MAAM,EAAE,mBAAmB,CAAC,MAAM,CAAC,CAAC;YAE9E,MAAM,SAAS,GAA8B,EAAE,CAAC;YAChD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,aAAa,EAAE,CAAC,EAAE,EAAE,CAAC;gBACvC,MAAM,aAAa,GAAG,UAAU,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;gBAC1C,MAAM,cAAc,GAAG,GAAG,SAAS,IAAI,CAAC,EAAE,CAAC;gBAC3C,MAAM,cAAc,GAAG,eAAe,CACpC,gBAAgB,EAChB,MAAM,CAAC,UAAU,EACjB,aAAa,EACb,YAAY,EACZ,EAAE,MAAM,EAAE,cAAc,EAAE,gBAAgB,EAAE,CAC7C,CAAC;gBACF,SAAS,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC;YACjC,CAAC;YAED,IAAI,SAAS,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;gBACzB,MAAM,CAAC,IAAI,CAAC,GAAG,SAAS,CAAC;YAC3B,CAAC;QACH,CAAC;aAAM,IAAI,aAAa,KAAK,YAAY,EAAE,CAAC;YAC1C,MAAM,OAAO,GAAG,SAAkC,CAAC;YACnD,MAAM,YAAY,GAAG,KAAK,CAAC,IAAI,CAAC,CAAC;YAEjC,yBAAyB,CAAC,IAAI,EAAE,aAAa,EAAE,YAAY,CAAC,CAAC;YAC7D,MAAM,SAAS,GAAI,YAAwC,IAAI,EAAE,CAAC;YAElE,MAAM,WAAW,GAAG,eAAe,CACjC,gBAAgB,EAChB,OAAO,CAAC,UAAU,EAClB,SAAS,EACT,YAAY,EACZ,EAAE,MAAM,EAAE,SAAS,EAAE,gBAAgB,EAAE,CACxC,CAAC;YAEF,IAAI,MAAM,CAAC,IAAI,CAAC,WAAW,CAAC,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;gBACxC,MAAM,CAAC,IAAI,CAAC,GAAG,WAAW,CAAC;YAC7B,CAAC;QACH,CAAC;aAAM,CAAC;YACN,iBAAiB;YACjB,MAAM,KAAK,GAAG,KAAK,CAAC,IAAI,CAAC,CAAC;YAC1B,MAAM,cAAc,GAAG,YAAY,CAAC,SAAS,EAAE,KAAK,EAAE,SAAS,CAAC,CAAC;YACjE,IAAI,cAAc,KAAK,UAAU,EAAE,CAAC;gBAClC,MAAM,CAAC,IAAI,CAAC,GAAG,cAAc,CAAC;YAChC,CAAC;QACH,CAAC;IACH,CAAC;IAED,IAAI,gBAAgB,EAAE,CAAC;QACrB,KAAK,MAAM,GAAG,IAAI,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC;YACrC,IAAI,CAAC,WAAW,CAAC,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC;gBAClD,MAAM,IAAI,eAAe,CAAC,GAAG,EAAE,MAAM,CAAC,CAAC;YACzC,CAAC;QACH,CAAC;IACH,CAAC;IAED,OAAO,MAAM,CAAC;AAChB,CAAC;AAED;;;;;;;;GAQG;AACH,MAAM,UAAU,gBAAgB,CAC9B,UAAgC,EAChC,KAA8B,EAC9B,YAA0B,EAC1B,MAAe;IAEf,MAAM,MAAM,GAA4B,EAAE,CAAC;IAE3C,KAAK,MAAM,SAAS,IAAI,UAAU,EAAE,CAAC;QACnC,MAAM,IAAI,GAAG,SAAS,CAAC,IAAI,CAAC;QAC5B,MAAM,aAAa,GAAG,SAAS,CAAC,cAAc,CAAC;QAC/C,MAAM,SAAS,GAAG,aAAa,CAAC,IAAI,EAAE,MAAM,CAAC,CAAC;QAE9C,IAAI,aAAa,KAAK,gBAAgB,EAAE,CAAC;YACvC,MAAM,WAAW,GAAG,SAAsC,CAAC;YAC3D,MAAM,gBAAgB,GAAG,KAAK,CAAC,IAAI,CAAC,CAAC;YAErC,yBAAyB,CAAC,IAAI,EAAE,aAAa,EAAE,gBAAgB,CAAC,CAAC;YACjE,MAAM,SAAS,GAAI,gBAA4C,IAAI,EAAE,CAAC;YAEtE,MAAM,IAAI,GAAG,eAAe,CAAC,WAAW,EAAE,SAAS,CAAC,CAAC;YACrD,MAAM,YAAY,GAAG,IAAI,IAAI,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,EAAE,CAAC;YAEzD,MAAM,WAAW,GAAG,gBAAgB,CAClC,CAAC,WAAW,CAAC,cAAc,EAAE,GAAG,YAAY,CAAC,EAC7C,SAAS,EACT,YAAY,EACZ,SAAS,CACV,CAAC;YAEF,IAAI,MAAM,CAAC,IAAI,CAAC,WAAW,CAAC,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;gBACxC,MAAM,CAAC,IAAI,CAAC,GAAG,WAAW,CAAC;YAC7B,CAAC;QACH,CAAC;aAAM,IAAI,aAAa,KAAK,WAAW,EAAE,CAAC;YACzC,MAAM,MAAM,GAAG,SAAiC,CAAC;YACjD,MAAM,WAAW,GAAG,KAAK,CAAC,IAAI,CAAC,CAAC;YAEhC,yBAAyB,CAAC,IAAI,EAAE,aAAa,EAAE,WAAW,CAAC,CAAC;YAC5D,MAAM,UAAU,GAAG,KAAK,CAAC,OAAO,CAAC,WAAW,CAAC;gBAC3C,CAAC,CAAE,WAAyC;gBAC5C,CAAC,CAAC,EAAE,CAAC;YAEP,MAAM,SAAS,GAA8B,EAAE,CAAC;YAChD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;gBAC3C,MAAM,cAAc,GAAG,GAAG,SAAS,IAAI,CAAC,EAAE,CAAC;gBAC3C,MAAM,cAAc,GAAG,gBAAgB,CACrC,MAAM,CAAC,UAAU,EACjB,UAAU,CAAC,CAAC,CAAC,EACb,YAAY,EACZ,cAAc,CACf,CAAC;gBACF,SAAS,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC;YACjC,CAAC;YAED,IAAI,SAAS,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;gBACzB,MAAM,CAAC,IAAI,CAAC,GAAG,SAAS,CAAC;YAC3B,CAAC;QACH,CAAC;aAAM,IAAI,aAAa,KAAK,YAAY,EAAE,CAAC;YAC1C,MAAM,OAAO,GAAG,SAAkC,CAAC;YACnD,MAAM,YAAY,GAAG,KAAK,CAAC,IAAI,CAAC,CAAC;YAEjC,yBAAyB,CAAC,IAAI,EAAE,aAAa,EAAE,YAAY,CAAC,CAAC;YAC7D,MAAM,SAAS,GAAI,YAAwC,IAAI,EAAE,CAAC;YAElE,MAAM,WAAW,GAAG,gBAAgB,CAAC,OAAO,CAAC,UAAU,EAAE,SAAS,EAAE,YAAY,EAAE,SAAS,CAAC,CAAC;YAE7F,IAAI,MAAM,CAAC,IAAI,CAAC,WAAW,CAAC,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;gBACxC,MAAM,CAAC,IAAI,CAAC,GAAG,WAAW,CAAC;YAC7B,CAAC;QACH,CAAC;aAAM,CAAC;YACN,iBAAiB;YACjB,MAAM,KAAK,GAAG,KAAK,CAAC,IAAI,CAAC,CAAC;YAC1B,MAAM,cAAc,GAAG,YAAY,CAAC,SAAS,EAAE,KAAK,EAAE,SAAS,CAAC,CAAC;YACjE,IAAI,cAAc,KAAK,UAAU,EAAE,CAAC;gBAClC,MAAM,CAAC,IAAI,CAAC,GAAG,cAAc,CAAC;YAChC,CAAC;QACH,CAAC;IACH,CAAC;IAED,OAAO,MAAM,CAAC;AAChB,CAAC;AAED,mEAAmE;AACnE,MAAM,OAAO,eAAgB,SAAQ,KAAK;IAEtB;IACA;IAFlB,YACkB,GAAW,EACX,MAAe;QAE/B,MAAM,QAAQ,GAAG,MAAM,CAAC,CAAC,CAAC,WAAW,MAAM,GAAG,CAAC,CAAC,CAAC,UAAU,CAAC;QAC5D,KAAK,CAAC,gBAAgB,GAAG,IAAI,QAAQ,gBAAgB,CAAC,CAAC;QAJvC,QAAG,GAAH,GAAG,CAAQ;QACX,WAAM,GAAN,MAAM,CAAS;QAI/B,IAAI,CAAC,IAAI,GAAG,iBAAiB,CAAC;IAChC,CAAC;CACF;AAED,iFAAiF;AACjF,SAAS,yBAAyB,CAAC,IAAY,EAAE,aAAqB,EAAE,KAAc;IACpF,IAAI,OAAO,KAAK,KAAK,QAAQ,EAAE,CAAC;QAC9B,MAAM,IAAI,KAAK,CACb,wBAAwB,IAAI,MAAM,aAAa,uBAAuB;YACpE,uFAAuF;YACvF,4BAA4B,CAC/B,CAAC;IACJ,CAAC;AACH,CAAC"}
+{"version":3,"file":"walker.js","sourceRoot":"","sources":["../../src/workflow/walker.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;GAcG;AASH,OAAO,EAAE,aAAa,EAAE,mBAAmB,EAAE,eAAe,EAAE,MAAM,mBAAmB,CAAC;AACxF,OAAO,EAAE,UAAU,EAAE,MAAM,iBAAiB,CAAC;AAE7C,uEAAuE;AACvE,MAAM,CAAC,MAAM,UAAU,GAAkB,MAAM,CAAC,YAAY,CAAC,CAAC;AAyB9D;;;;;;;;;;;GAWG;AACH,MAAM,UAAU,eAAe,CAC7B,gBAAyC,EACzC,UAAgC,EAChC,KAA8B,EAC9B,YAA0B,EAC1B,OAA2B;IAE3B,MAAM,MAAM,GAAG,OAAO,EAAE,MAAM,CAAC;IAC/B,MAAM,gBAAgB,GAAG,OAAO,EAAE,gBAAgB,IAAI,KAAK,CAAC;IAC5D,MAAM,mBAAmB,GAAG,OAAO,EAAE,mBAAmB,IAAI,KAAK,CAAC;IAClE,MAAM,YAAY,GAAG,OAAO,EAAE,YAAY,IAAI,KAAK,CAAC;IACpD,MAAM,MAAM,GAA4B,EAAE,CAAC;IAC3C,MAAM,WAAW,GAAG,IAAI,GAAG,EAAU,CAAC;IAEtC,KAAK,MAAM,SAAS,IAAI,UAAU,EAAE,CAAC;QACnC,MAAM,IAAI,GAAG,SAAS,CAAC,IAAI,CAAC;QAC5B,WAAW,CAAC,GAAG,CAAC,IAAI,CAAC,CAAC;QACtB,MAAM,aAAa,GAAG,SAAS,CAAC,cAAc,CAAC;QAC/C,MAAM,SAAS,GAAG,aAAa,CAAC,IAAI,EAAE,MAAM,CAAC,CAAC;QAE9C,IAAI,aAAa,KAAK,gBAAgB,EAAE,CAAC;YACvC,MAAM,WAAW,GAAG,SAAsC,CAAC;YAC3D,MAAM,gBAAgB,GAAG,KAAK,CAAC,IAAI,CAAC,CAAC;YAErC,yBAAyB,CAAC,IAAI,EAAE,aAAa,EAAE,gBAAgB,CAAC,CAAC;YACjE,MAAM,SAAS,GAAI,gBAA4C,IAAI,EAAE,CAAC;YAEtE,MAAM,IAAI,GAAG,eAAe,CAAC,WAAW,EAAE,SAAS,CAAC,CAAC;YACrD,MAAM,YAAY,GAAG,IAAI,IAAI,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,EAAE,CAAC;YAEzD,8CAA8C;YAC9C,MAAM,WAAW,GAAG,eAAe,CACjC,gBAAgB,EAChB,CAAC,WAAW,CAAC,cAAc,EAAE,GAAG,YAAY,CAAC,EAC7C,SAAS,EACT,YAAY,EACZ,EAAE,MAAM,EAAE,SAAS,EAAE,gBAAgB,EAAE,mBAAmB,EAAE,YAAY,EAAE,CAC3E,CAAC;YAEF,IAAI,MAAM,CAAC,IAAI,CAAC,WAAW,CAAC,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;gBACxC,MAAM,CAAC,IAAI,CAAC,GAAG,WAAW,CAAC;YAC7B,CAAC;QACH,CAAC;aAAM,IAAI,aAAa,KAAK,WAAW,EAAE,CAAC;YACzC,MAAM,MAAM,GAAG,SAAiC,CAAC;YACjD,MAAM,WAAW,GAAG,KAAK,CAAC,IAAI,CAAC,CAAC;YAEhC,yBAAyB,CAAC,IAAI,EAAE,aAAa,EAAE,WAAW,CAAC,CAAC;YAE5D,iEAAiE;YACjE,MAAM,UAAU,GAAG,KAAK,CAAC,OAAO,CAAC,WAAW,CAAC;gBAC3C,CAAC,CAAE,WAAyC;gBAC5C,CAAC,CAAC,EAAE,CAAC;YACP,IAAI,aAAqB,CAAC;YAC1B,IAAI,YAAY,EAAE,CAAC;gBACjB,aAAa,GAAG,IAAI,CAAC,GAAG,CAAC,UAAU,CAAC,MAAM,EAAE,MAAM,CAAC,GAAG,IAAI,CAAC,CAAC,CAAC;YAC/D,CAAC;iBAAM,CAAC;gBACN,MAAM,mBAAmB,GAAG,mBAAmB,CAAC,SAAS,EAAE,gBAAgB,CAAC,CAAC;gBAC7E,aAAa,GAAG,IAAI,CAAC,GAAG,CAAC,UAAU,CAAC,MAAM,EAAE,mBAAmB,CAAC,MAAM,CAAC,CAAC;YAC1E,CAAC;YAED,MAAM,SAAS,GAA8B,EAAE,CAAC;YAChD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,aAAa,EAAE,CAAC,EAAE,EAAE,CAAC;gBACvC,MAAM,aAAa,GAAG,UAAU,CAAC,CAAC,CAAC,IAAI,EAAE,CAAC;gBAC1C,MAAM,cAAc,GAAG,GAAG,SAAS,IAAI,CAAC,EAAE,CAAC;gBAC3C,MAAM,cAAc,GAAG,eAAe,CACpC,gBAAgB,EAChB,MAAM,CAAC,UAAU,EACjB,aAAa,EACb,YAAY,EACZ,EAAE,MAAM,EAAE,cAAc,EAAE,gBAAgB,EAAE,mBAAmB,EAAE,YAAY,EAAE,CAChF,CAAC;gBACF,SAAS,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC;YACjC,CAAC;YAED,8EAA8E;YAC9E,yEAAyE;YACzE,yEAAyE;YACzE,IAAI,YAAY,IAAI,IAAI,IAAI,KAAK,IAAI,SAAS,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;gBAC1D,MAAM,CAAC,IAAI,CAAC,GAAG,SAAS,CAAC;YAC3B,CAAC;QACH,CAAC;aAAM,IAAI,aAAa,KAAK,YAAY,EAAE,CAAC;YAC1C,MAAM,OAAO,GAAG,SAAkC,CAAC;YACnD,MAAM,YAAY,GAAG,KAAK,CAAC,IAAI,CAAC,CAAC;YAEjC,yBAAyB,CAAC,IAAI,EAAE,aAAa,EAAE,YAAY,CAAC,CAAC;YAC7D,MAAM,SAAS,GAAI,YAAwC,IAAI,EAAE,CAAC;YAElE,MAAM,WAAW,GAAG,eAAe,CACjC,gBAAgB,EAChB,OAAO,CAAC,UAAU,EAClB,SAAS,EACT,YAAY,EACZ,EAAE,MAAM,EAAE,SAAS,EAAE,gBAAgB,EAAE,mBAAmB,EAAE,YAAY,EAAE,CAC3E,CAAC;YAEF,IAAI,MAAM,CAAC,IAAI,CAAC,WAAW,CAAC,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;gBACxC,MAAM,CAAC,IAAI,CAAC,GAAG,WAAW,CAAC;YAC7B,CAAC;QACH,CAAC;aAAM,CAAC;YACN,iBAAiB;YACjB,MAAM,KAAK,GAAG,KAAK,CAAC,IAAI,CAAC,CAAC;YAC1B,MAAM,cAAc,GAAG,YAAY,CAAC,SAAS,EAAE,KAAK,EAAE,SAAS,CAAC,CAAC;YACjE,IAAI,cAAc,KAAK,UAAU,EAAE,CAAC;gBAClC,MAAM,CAAC,IAAI,CAAC,GAAG,cAAc,CAAC;YAChC,CAAC;QACH,CAAC;IACH,CAAC;IAED,IAAI,gBAAgB,EAAE,CAAC;QACrB,KAAK,MAAM,GAAG,IAAI,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC;YACrC,IAAI,CAAC,WAAW,CAAC,GAAG,CAAC,GAAG,CAAC,IAAI,CAAC,UAAU,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC;gBAClD,MAAM,IAAI,eAAe,CAAC,GAAG,EAAE,MAAM,CAAC,CAAC;YACzC,CAAC;QACH,CAAC;IACH,CAAC;SAAM,IAAI,mBAAmB,EAAE,CAAC;QAC/B,KAAK,MAAM,GAAG,IAAI,MAAM,CAAC,IAAI,CAAC,KAAK,CAAC,EAAE,CAAC;YACrC,IAAI,CAAC,WAAW,CAAC,GAAG,CAAC,GAAG,CAAC,EAAE,CAAC;gBAC1B,MAAM,CAAC,GAAG,CAAC,GAAG,KAAK,CAAC,GAAG,CAAC,CAAC;YAC3B,CAAC;QACH,CAAC;IACH,CAAC;IAED,OAAO,MAAM,CAAC;AAChB,CAAC;AAED;;;;;;;;GAQG;AACH,MAAM,UAAU,gBAAgB,CAC9B,UAAgC,EAChC,KAA8B,EAC9B,YAA0B,EAC1B,MAAe;IAEf,MAAM,MAAM,GAA4B,EAAE,CAAC;IAE3C,KAAK,MAAM,SAAS,IAAI,UAAU,EAAE,CAAC;QACnC,MAAM,IAAI,GAAG,SAAS,CAAC,IAAI,CAAC;QAC5B,MAAM,aAAa,GAAG,SAAS,CAAC,cAAc,CAAC;QAC/C,MAAM,SAAS,GAAG,aAAa,CAAC,IAAI,EAAE,MAAM,CAAC,CAAC;QAE9C,IAAI,aAAa,KAAK,gBAAgB,EAAE,CAAC;YACvC,MAAM,WAAW,GAAG,SAAsC,CAAC;YAC3D,MAAM,gBAAgB,GAAG,KAAK,CAAC,IAAI,CAAC,CAAC;YAErC,yBAAyB,CAAC,IAAI,EAAE,aAAa,EAAE,gBAAgB,CAAC,CAAC;YACjE,MAAM,SAAS,GAAI,gBAA4C,IAAI,EAAE,CAAC;YAEtE,MAAM,IAAI,GAAG,eAAe,CAAC,WAAW,EAAE,SAAS,CAAC,CAAC;YACrD,MAAM,YAAY,GAAG,IAAI,IAAI,IAAI,CAAC,CAAC,CAAC,IAAI,CAAC,UAAU,CAAC,CAAC,CAAC,EAAE,CAAC;YAEzD,MAAM,WAAW,GAAG,gBAAgB,CAClC,CAAC,WAAW,CAAC,cAAc,EAAE,GAAG,YAAY,CAAC,EAC7C,SAAS,EACT,YAAY,EACZ,SAAS,CACV,CAAC;YAEF,IAAI,MAAM,CAAC,IAAI,CAAC,WAAW,CAAC,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;gBACxC,MAAM,CAAC,IAAI,CAAC,GAAG,WAAW,CAAC;YAC7B,CAAC;QACH,CAAC;aAAM,IAAI,aAAa,KAAK,WAAW,EAAE,CAAC;YACzC,MAAM,MAAM,GAAG,SAAiC,CAAC;YACjD,MAAM,WAAW,GAAG,KAAK,CAAC,IAAI,CAAC,CAAC;YAEhC,yBAAyB,CAAC,IAAI,EAAE,aAAa,EAAE,WAAW,CAAC,CAAC;YAC5D,MAAM,UAAU,GAAG,KAAK,CAAC,OAAO,CAAC,WAAW,CAAC;gBAC3C,CAAC,CAAE,WAAyC;gBAC5C,CAAC,CAAC,EAAE,CAAC;YAEP,MAAM,SAAS,GAA8B,EAAE,CAAC;YAChD,KAAK,IAAI,CAAC,GAAG,CAAC,EAAE,CAAC,GAAG,UAAU,CAAC,MAAM,EAAE,CAAC,EAAE,EAAE,CAAC;gBAC3C,MAAM,cAAc,GAAG,GAAG,SAAS,IAAI,CAAC,EAAE,CAAC;gBAC3C,MAAM,cAAc,GAAG,gBAAgB,CACrC,MAAM,CAAC,UAAU,EACjB,UAAU,CAAC,CAAC,CAAC,EACb,YAAY,EACZ,cAAc,CACf,CAAC;gBACF,SAAS,CAAC,IAAI,CAAC,cAAc,CAAC,CAAC;YACjC,CAAC;YAED,6EAA6E;YAC7E,IAAI,IAAI,IAAI,KAAK,IAAI,SAAS,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;gBAC1C,MAAM,CAAC,IAAI,CAAC,GAAG,SAAS,CAAC;YAC3B,CAAC;QACH,CAAC;aAAM,IAAI,aAAa,KAAK,YAAY,EAAE,CAAC;YAC1C,MAAM,OAAO,GAAG,SAAkC,CAAC;YACnD,MAAM,YAAY,GAAG,KAAK,CAAC,IAAI,CAAC,CAAC;YAEjC,yBAAyB,CAAC,IAAI,EAAE,aAAa,EAAE,YAAY,CAAC,CAAC;YAC7D,MAAM,SAAS,GAAI,YAAwC,IAAI,EAAE,CAAC;YAElE,MAAM,WAAW,GAAG,gBAAgB,CAAC,OAAO,CAAC,UAAU,EAAE,SAAS,EAAE,YAAY,EAAE,SAAS,CAAC,CAAC;YAE7F,IAAI,MAAM,CAAC,IAAI,CAAC,WAAW,CAAC,CAAC,MAAM,GAAG,CAAC,EAAE,CAAC;gBACxC,MAAM,CAAC,IAAI,CAAC,GAAG,WAAW,CAAC;YAC7B,CAAC;QACH,CAAC;aAAM,CAAC;YACN,iBAAiB;YACjB,MAAM,KAAK,GAAG,KAAK,CAAC,IAAI,CAAC,CAAC;YAC1B,MAAM,cAAc,GAAG,YAAY,CAAC,SAAS,EAAE,KAAK,EAAE,SAAS,CAAC,CAAC;YACjE,IAAI,cAAc,KAAK,UAAU,EAAE,CAAC;gBAClC,MAAM,CAAC,IAAI,CAAC,GAAG,cAAc,CAAC;YAChC,CAAC;QACH,CAAC;IACH,CAAC;IAED,OAAO,MAAM,CAAC;AAChB,CAAC;AAED,mEAAmE;AACnE,MAAM,OAAO,eAAgB,SAAQ,KAAK;IAEtB;IACA;IAFlB,YACkB,GAAW,EACX,MAAe;QAE/B,MAAM,QAAQ,GAAG,MAAM,CAAC,CAAC,CAAC,WAAW,MAAM,GAAG,CAAC,CAAC,CAAC,UAAU,CAAC;QAC5D,KAAK,CAAC,gBAAgB,GAAG,IAAI,QAAQ,gBAAgB,CAAC,CAAC;QAJvC,QAAG,GAAH,GAAG,CAAQ;QACX,WAAM,GAAN,MAAM,CAAS;QAI/B,IAAI,CAAC,IAAI,GAAG,iBAAiB,CAAC;IAChC,CAAC;CACF;AAED,iFAAiF;AACjF,SAAS,yBAAyB,CAAC,IAAY,EAAE,aAAqB,EAAE,KAAc;IACpF,IAAI,OAAO,KAAK,KAAK,QAAQ,EAAE,CAAC;QAC9B,MAAM,IAAI,KAAK,CACb,wBAAwB,IAAI,MAAM,aAAa,uBAAuB;YACpE,uFAAuF;YACvF,4BAA4B,CAC/B,CAAC;IACJ,CAAC;AACH,CAAC"}

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@galaxy-tool-util/schema",
-  "version": "0.2.0",
+  "version": "1.0.0",
   "description": "Effect Schema parameter types and validators for Galaxy tools",
   "type": "module",
   "exports": {
@@ -30,15 +30,14 @@
   ],
   "license": "MIT",
   "dependencies": {
-    "effect": "^3.21.0"
-  },
-  "devDependencies": {
     "ajv": "^8.18.0",
-    "yaml": "^2.8.3",
-    "@galaxy-tool-util/core": "0.2.0"
+    "ajv-formats": "^3.0.1",
+    "effect": "^3.21.0",
+    "yaml": "^2.8.3"
   },
+  "devDependencies": {},
   "scripts": {
-    "build": "tsc",
+    "build": "tsc && node ../../scripts/copy-schema-assets.mjs",
     "typecheck": "tsc --noEmit",
     "test": "tsc --noEmit && vitest run",
     "test:watch": "vitest",