@galaxy-tool-util/schema 0.2.0 → 0.4.0

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

@@ -20,6 +20,8 @@ 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;
 }
 /**
  * Walk native workflow tool_state using the parameter tree.

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

@@ -1 +1 @@
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+{"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"}

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 +32,7 @@ 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 result = {};
     const visitedKeys = new Set();
     for (const toolInput of toolInputs) {
@@ -47,7 +48,7 @@ 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 });
             if (Object.keys(innerResult).length > 0) {
                 result[name] = innerResult;
             }
@@ -66,10 +67,11 @@ export function walkNativeState(inputConnections, toolInputs, state, leafCallbac
             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 });
                 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;
             }
         }
@@ -78,7 +80,7 @@ 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 });
             if (Object.keys(innerResult).length > 0) {
                 result[name] = innerResult;
             }
@@ -99,6 +101,13 @@ 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 +150,8 @@ 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;
             }
         }

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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@galaxy-tool-util/schema",
-  "version": "0.2.0",
+  "version": "0.4.0",
   "description": "Effect Schema parameter types and validators for Galaxy tools",
   "type": "module",
   "exports": {
@@ -30,15 +30,16 @@
   ],
   "license": "MIT",
   "dependencies": {
-    "effect": "^3.21.0"
+    "ajv": "^8.18.0",
+    "ajv-formats": "^3.0.1",
+    "effect": "^3.21.0",
+    "yaml": "^2.8.3"
   },
   "devDependencies": {
-    "ajv": "^8.18.0",
-    "yaml": "^2.8.3",
-    "@galaxy-tool-util/core": "0.2.0"
+    "@galaxy-tool-util/core": "0.3.0"
   },
   "scripts": {
-    "build": "tsc",
+    "build": "tsc && node ../../scripts/copy-schema-assets.mjs",
     "typecheck": "tsc --noEmit",
     "test": "tsc --noEmit && vitest run",
     "test:watch": "vitest",