@galaxy-tool-util/schema 0.1.0 → 0.2.0

package/dist/workflow/walker.js

@@ -0,0 +1,189 @@
+/**
+ * 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 { flatStatePath, repeatInputsToArray, selectWhichWhen } from "./state-merge.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");
+/**
+ * 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 function walkNativeState(inputConnections, toolInputs, state, leafCallback, options) {
+    const prefix = options?.prefix;
+    const checkUnknownKeys = options?.checkUnknownKeys ?? false;
+    const result = {};
+    const visitedKeys = new Set();
+    for (const toolInput of toolInputs) {
+        const name = toolInput.name;
+        visitedKeys.add(name);
+        const parameterType = toolInput.parameter_type;
+        const statePath = flatStatePath(name, prefix);
+        if (parameterType === "gx_conditional") {
+            const conditional = toolInput;
+            const conditionalState = state[name];
+            _assertNotStringContainer(name, parameterType, conditionalState);
+            const stateDict = conditionalState ?? {};
+            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 });
+            if (Object.keys(innerResult).length > 0) {
+                result[name] = innerResult;
+            }
+        }
+        else if (parameterType === "gx_repeat") {
+            const repeat = toolInput;
+            const repeatState = state[name];
+            _assertNotStringContainer(name, parameterType, repeatState);
+            // Determine instance count from state array or input connections
+            const stateArray = Array.isArray(repeatState)
+                ? repeatState
+                : [];
+            const connectionInstances = repeatInputsToArray(statePath, inputConnections);
+            const 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 });
+                instances.push(instanceResult);
+            }
+            if (instances.length > 0) {
+                result[name] = instances;
+            }
+        }
+        else if (parameterType === "gx_section") {
+            const section = toolInput;
+            const sectionState = state[name];
+            _assertNotStringContainer(name, parameterType, sectionState);
+            const stateDict = sectionState ?? {};
+            const innerResult = walkNativeState(inputConnections, section.parameters, stateDict, leafCallback, { prefix: statePath, checkUnknownKeys });
+            if (Object.keys(innerResult).length > 0) {
+                result[name] = innerResult;
+            }
+        }
+        else {
+            // Leaf parameter
+            const value = state[name];
+            const callbackResult = leafCallback(toolInput, value, statePath);
+            if (callbackResult !== SKIP_VALUE) {
+                result[name] = callbackResult;
+            }
+        }
+    }
+    if (checkUnknownKeys) {
+        for (const key of Object.keys(state)) {
+            if (!visitedKeys.has(key) && !STALE_KEYS.has(key)) {
+                throw new UnknownKeyError(key, prefix);
+            }
+        }
+    }
+    return result;
+}
+/**
+ * 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 function walkFormat2State(toolInputs, state, leafCallback, prefix) {
+    const result = {};
+    for (const toolInput of toolInputs) {
+        const name = toolInput.name;
+        const parameterType = toolInput.parameter_type;
+        const statePath = flatStatePath(name, prefix);
+        if (parameterType === "gx_conditional") {
+            const conditional = toolInput;
+            const conditionalState = state[name];
+            _assertNotStringContainer(name, parameterType, conditionalState);
+            const stateDict = conditionalState ?? {};
+            const when = selectWhichWhen(conditional, stateDict);
+            const branchParams = when != null ? when.parameters : [];
+            const innerResult = walkFormat2State([conditional.test_parameter, ...branchParams], stateDict, leafCallback, statePath);
+            if (Object.keys(innerResult).length > 0) {
+                result[name] = innerResult;
+            }
+        }
+        else if (parameterType === "gx_repeat") {
+            const repeat = toolInput;
+            const repeatState = state[name];
+            _assertNotStringContainer(name, parameterType, repeatState);
+            const stateArray = Array.isArray(repeatState)
+                ? repeatState
+                : [];
+            const instances = [];
+            for (let i = 0; i < stateArray.length; i++) {
+                const instancePrefix = `${statePath}_${i}`;
+                const instanceResult = walkFormat2State(repeat.parameters, stateArray[i], leafCallback, instancePrefix);
+                instances.push(instanceResult);
+            }
+            if (instances.length > 0) {
+                result[name] = instances;
+            }
+        }
+        else if (parameterType === "gx_section") {
+            const section = toolInput;
+            const sectionState = state[name];
+            _assertNotStringContainer(name, parameterType, sectionState);
+            const stateDict = sectionState ?? {};
+            const innerResult = walkFormat2State(section.parameters, stateDict, leafCallback, statePath);
+            if (Object.keys(innerResult).length > 0) {
+                result[name] = innerResult;
+            }
+        }
+        else {
+            // Leaf parameter
+            const value = state[name];
+            const callbackResult = leafCallback(toolInput, value, statePath);
+            if (callbackResult !== SKIP_VALUE) {
+                result[name] = callbackResult;
+            }
+        }
+    }
+    return result;
+}
+/** Error thrown when unknown keys are detected in native state. */
+export class UnknownKeyError extends Error {
+    key;
+    prefix;
+    constructor(key, prefix) {
+        const location = prefix ? ` under "${prefix}"` : " at root";
+        super(`Unknown key "${key}"${location} in tool state`);
+        this.key = key;
+        this.prefix = prefix;
+        this.name = "UnknownKeyError";
+    }
+}
+/** Assert that a container parameter value is not a string (legacy encoding). */
+function _assertNotStringContainer(name, parameterType, value) {
+    if (typeof value === "string") {
+        throw new Error(`Container parameter "${name}" (${parameterType}) has string value — ` +
+            `expected dict/list. This indicates legacy parameter encoding which is not supported. ` +
+            `Decode the workflow first.`);
+    }
+}
+//# sourceMappingURL=walker.js.map

package/dist/workflow/walker.js.map

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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@galaxy-tool-util/schema",
-  "version": "0.1.0",
+  "version": "0.2.0",
   "description": "Effect Schema parameter types and validators for Galaxy tools",
   "type": "module",
   "exports": {
@@ -9,7 +9,11 @@
       "import": "./dist/index.js"
     }
   },
-  "files": ["dist", "README.md", "LICENSE"],
+  "files": [
+    "dist",
+    "README.md",
+    "LICENSE"
+  ],
   "repository": {
     "type": "git",
     "url": "https://github.com/jmchilton/galaxy-tool-util-ts",
@@ -19,15 +23,6 @@
     "access": "public",
     "provenance": true
   },
-  "scripts": {
-    "build": "tsc",
-    "typecheck": "tsc --noEmit",
-    "test": "tsc --noEmit && vitest run",
-    "test:watch": "vitest",
-    "lint": "eslint src/ test/",
-    "format": "prettier --check 'src/**/*.ts' 'test/**/*.ts'",
-    "format-fix": "prettier --write 'src/**/*.ts' 'test/**/*.ts'"
-  },
   "keywords": [
     "galaxy",
     "tool-util",
@@ -38,8 +33,17 @@
     "effect": "^3.21.0"
   },
   "devDependencies": {
-    "@galaxy-tool-util/core": "workspace:*",
     "ajv": "^8.18.0",
-    "yaml": "^2.8.3"
+    "yaml": "^2.8.3",
+    "@galaxy-tool-util/core": "0.2.0"
+  },
+  "scripts": {
+    "build": "tsc",
+    "typecheck": "tsc --noEmit",
+    "test": "tsc --noEmit && vitest run",
+    "test:watch": "vitest",
+    "lint": "eslint src/ test/",
+    "format": "prettier --check 'src/**/*.ts' 'test/**/*.ts'",
+    "format-fix": "prettier --write 'src/**/*.ts' 'test/**/*.ts'"
   }
-}
+}