@galaxy-tool-util/schema 0.1.0

package/dist/workflow/replacement-scan.js

@@ -0,0 +1,92 @@
+/**
+ * Detect legacy replacement parameters (${...}) in workflow tool state.
+ *
+ * Port of Python galaxy.tool_util.workflow_state.legacy_parameters.
+ *
+ * Walks the parameter tree type-aware: ${...} in text/hidden fields is
+ * MAYBE (could be literal), in typed fields (integer, float, etc.) is YES
+ * (definitely a replacement). Validation should be skipped when YES.
+ */
+/** Check if a string value contains legacy replacement syntax. */
+function _isReplacementParam(value) {
+    return typeof value === "string" && value.includes("${");
+}
+const _MAYBE_TYPES = new Set(["gx_text", "gx_hidden"]);
+const _SKIP_TYPES = new Set(["gx_data", "gx_data_collection", "gx_rules"]);
+function _classifyHit(parameterType) {
+    if (_MAYBE_TYPES.has(parameterType))
+        return "maybe_assumed_no";
+    return "yes";
+}
+/**
+ * Scan a state dict for replacement parameters, walking the tool input tree
+ * for type-aware classification.
+ *
+ * Returns "yes" if any typed field contains ${...} (skip validation),
+ * "maybe_assumed_no" if only text/hidden fields have it (still validate),
+ * "no" if no replacement params found.
+ */
+export function scanForReplacements(toolInputs, state) {
+    let hasYes = false;
+    let hasMaybe = false;
+    _scanParams(toolInputs, state, (classification) => {
+        if (classification === "yes")
+            hasYes = true;
+        else
+            hasMaybe = true;
+    });
+    if (hasYes)
+        return "yes";
+    if (hasMaybe)
+        return "maybe_assumed_no";
+    return "no";
+}
+function _scanParams(toolInputs, state, onHit) {
+    for (const param of toolInputs) {
+        const paramType = param.parameter_type;
+        if (paramType === "gx_conditional") {
+            const cond = param;
+            const condState = state[param.name];
+            if (condState) {
+                // Check test parameter
+                const testValue = condState[cond.test_parameter.name];
+                if (_isReplacementParam(testValue) &&
+                    !_SKIP_TYPES.has(cond.test_parameter.parameter_type)) {
+                    onHit(_classifyHit(cond.test_parameter.parameter_type));
+                }
+                // Check all when branches (scan all since we can't always determine the active branch)
+                for (const when of cond.whens) {
+                    _scanParams(when.parameters, condState, onHit);
+                }
+            }
+        }
+        else if (paramType === "gx_repeat") {
+            const repeat = param;
+            const repeatState = state[param.name];
+            if (Array.isArray(repeatState)) {
+                for (const instance of repeatState) {
+                    if (instance && typeof instance === "object") {
+                        _scanParams(repeat.parameters, instance, onHit);
+                    }
+                }
+            }
+        }
+        else if (paramType === "gx_section") {
+            const section = param;
+            const sectionState = state[param.name];
+            if (sectionState) {
+                _scanParams(section.parameters, sectionState, onHit);
+            }
+        }
+        else {
+            // Leaf parameter
+            if (_SKIP_TYPES.has(paramType))
+                continue;
+            const value = state[param.name];
+            if (_isReplacementParam(value)) {
+                onHit(_classifyHit(paramType));
+            }
+        }
+    }
+}
+//# sourceMappingURL=replacement-scan.js.map

package/dist/workflow/replacement-scan.js.map

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package/dist/workflow/state-merge.d.ts

@@ -0,0 +1,49 @@
+/**
+ * Inject ConnectedValue markers into workflow state dicts.
+ *
+ * Port of Python galaxy.tool_util.workflow_state._state_merge +
+ * helper functions from galaxy.tool_util.parameters.visitor.
+ *
+ * Walks the parameter tree to match pipe-separated connection paths
+ * (e.g. "queries_0|input2") to tool parameters. Handles conditionals,
+ * repeats, and sections. Used by validate-workflow for both native
+ * and format2 validation paths.
+ */
+import type { ToolParameterModel, 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;
+/**
+ * Inject ConnectedValue markers into a state dict for all connections.
+ *
+ * Walks the parameter tree to match connection paths to tool parameters,
+ * setting matched leaves to `{"__class__": "ConnectedValue"}`.
+ * Mutates `state` in-place.
+ *
+ * @returns remaining unmatched connection paths (empty if all consumed)
+ */
+export declare function injectConnectionsIntoState(toolInputs: ToolParameterModel[], state: Record<string, unknown>, connections: Record<string, unknown>): Record<string, unknown>;
+/**
+ * Strip ConnectedValue markers from a state dict using the parameter tree.
+ *
+ * Walks conditionals, repeats, and sections so nested markers inside
+ * container parameters are removed. Mutates `state` in-place.
+ */
+export declare function stripConnectedValues(toolInputs: ToolParameterModel[], state: Record<string, unknown>): void;
+//# sourceMappingURL=state-merge.d.ts.map

package/dist/workflow/state-merge.d.ts.map

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package/dist/workflow/state-merge.js

@@ -0,0 +1,248 @@
+/**
+ * Inject ConnectedValue markers into workflow state dicts.
+ *
+ * Port of Python galaxy.tool_util.workflow_state._state_merge +
+ * helper functions from galaxy.tool_util.parameters.visitor.
+ *
+ * Walks the parameter tree to match pipe-separated connection paths
+ * (e.g. "queries_0|input2") to tool parameters. Handles conditionals,
+ * repeats, and sections. Used by validate-workflow for both native
+ * and format2 validation paths.
+ */
+// --- Helpers (ported from Python visitor.py) ---
+/** 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;
+}
+/**
+ * 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 = _coerceToBool(testValue);
+        const discBool = typeof discriminator === "boolean" ? discriminator : _coerceToBool(discriminator);
+        return boolValue === discBool;
+    }
+    // Select: string comparison
+    return String(testValue) === String(discriminator);
+}
+function _coerceToBool(value) {
+    if (typeof value === "boolean")
+        return value;
+    if (typeof value === "string") {
+        const lower = value.toLowerCase();
+        if (lower === "true")
+            return true;
+        if (lower === "false")
+            return false;
+    }
+    return null;
+}
+// --- Main injection function ---
+const CONNECTED_VALUE = { __class__: "ConnectedValue" };
+/**
+ * Inject ConnectedValue markers into a state dict for all connections.
+ *
+ * Walks the parameter tree to match connection paths to tool parameters,
+ * setting matched leaves to `{"__class__": "ConnectedValue"}`.
+ * Mutates `state` in-place.
+ *
+ * @returns remaining unmatched connection paths (empty if all consumed)
+ */
+export function injectConnectionsIntoState(toolInputs, state, connections) {
+    const remaining = { ...connections };
+    for (const toolInput of toolInputs) {
+        _mergeParam(remaining, toolInput, state);
+    }
+    return remaining;
+}
+function _mergeParam(connections, toolInput, state, prefix, branchConnections) {
+    if (branchConnections == null) {
+        branchConnections = connections;
+    }
+    const name = toolInput.name;
+    const parameterType = toolInput.parameter_type;
+    const statePath = flatStatePath(name, prefix);
+    if (parameterType === "gx_conditional") {
+        const conditional = toolInput;
+        let conditionalState = state[name];
+        if (conditionalState == null) {
+            conditionalState = {};
+            state[name] = conditionalState;
+        }
+        const when = selectWhichWhen(conditional, conditionalState);
+        const conditionalConnections = keysStartingWith(branchConnections, statePath);
+        _mergeParam(connections, conditional.test_parameter, conditionalState, statePath, conditionalConnections);
+        if (when != null) {
+            for (const whenParameter of when.parameters) {
+                _mergeParam(connections, whenParameter, conditionalState, statePath, conditionalConnections);
+            }
+        }
+    }
+    else if (parameterType === "gx_repeat") {
+        const repeat = toolInput;
+        let repeatStateArray = state[name];
+        if (repeatStateArray == null) {
+            repeatStateArray = [];
+        }
+        const repeatInstanceConnects = repeatInputsToArray(statePath, connections);
+        for (let i = 0; i < repeatInstanceConnects.length; i++) {
+            while (repeatStateArray.length <= i) {
+                repeatStateArray.push({});
+            }
+            const instancePrefix = `${statePath}_${i}`;
+            for (const repeatParameter of repeat.parameters) {
+                _mergeParam(connections, repeatParameter, repeatStateArray[i], instancePrefix, repeatInstanceConnects[i]);
+            }
+        }
+        if (repeatStateArray.length > 0 && !(name in state)) {
+            state[name] = repeatStateArray;
+        }
+    }
+    else if (parameterType === "gx_section") {
+        const section = toolInput;
+        let sectionState = state[name];
+        if (sectionState == null) {
+            sectionState = {};
+            state[name] = sectionState;
+        }
+        const sectionConnections = keysStartingWith(branchConnections, statePath);
+        for (const sectionParameter of section.parameters) {
+            _mergeParam(connections, sectionParameter, sectionState, statePath, sectionConnections);
+        }
+    }
+    else {
+        // Leaf parameter
+        if (statePath in branchConnections) {
+            state[name] = { ...CONNECTED_VALUE };
+            delete connections[statePath];
+        }
+    }
+}
+// --- ConnectedValue stripping ---
+function _isConnectedValue(value) {
+    return (value != null &&
+        typeof value === "object" &&
+        !Array.isArray(value) &&
+        value.__class__ === "ConnectedValue");
+}
+/**
+ * Strip ConnectedValue markers from a state dict using the parameter tree.
+ *
+ * Walks conditionals, repeats, and sections so nested markers inside
+ * container parameters are removed. Mutates `state` in-place.
+ */
+export function stripConnectedValues(toolInputs, state) {
+    for (const toolInput of toolInputs) {
+        _stripParam(toolInput, state);
+    }
+}
+function _stripParam(toolInput, state, prefix) {
+    const name = toolInput.name;
+    const parameterType = toolInput.parameter_type;
+    if (parameterType === "gx_conditional") {
+        const conditional = toolInput;
+        const conditionalState = state[name];
+        if (conditionalState == null)
+            return;
+        const statePath = flatStatePath(name, prefix);
+        _stripParam(conditional.test_parameter, conditionalState, statePath);
+        const when = selectWhichWhen(conditional, conditionalState);
+        if (when != null) {
+            for (const whenParameter of when.parameters) {
+                _stripParam(whenParameter, conditionalState, statePath);
+            }
+        }
+    }
+    else if (parameterType === "gx_repeat") {
+        const repeat = toolInput;
+        const repeatStateArray = state[name];
+        if (!Array.isArray(repeatStateArray))
+            return;
+        const statePath = flatStatePath(name, prefix);
+        for (let i = 0; i < repeatStateArray.length; i++) {
+            const instancePrefix = `${statePath}_${i}`;
+            for (const repeatParameter of repeat.parameters) {
+                _stripParam(repeatParameter, repeatStateArray[i], instancePrefix);
+            }
+        }
+    }
+    else if (parameterType === "gx_section") {
+        const section = toolInput;
+        const sectionState = state[name];
+        if (sectionState == null)
+            return;
+        const statePath = flatStatePath(name, prefix);
+        for (const sectionParameter of section.parameters) {
+            _stripParam(sectionParameter, sectionState, statePath);
+        }
+    }
+    else {
+        // Leaf parameter
+        if (_isConnectedValue(state[name])) {
+            delete state[name];
+        }
+    }
+}
+//# sourceMappingURL=state-merge.js.map

package/dist/workflow/state-merge.js.map

@@ -0,0 +1 @@
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package/package.json

@@ -0,0 +1,45 @@
+{
+  "name": "@galaxy-tool-util/schema",
+  "version": "0.1.0",
+  "description": "Effect Schema parameter types and validators for Galaxy tools",
+  "type": "module",
+  "exports": {
+    ".": {
+      "types": "./dist/index.d.ts",
+      "import": "./dist/index.js"
+    }
+  },
+  "files": ["dist", "README.md", "LICENSE"],
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/jmchilton/galaxy-tool-util-ts",
+    "directory": "packages/schema"
+  },
+  "publishConfig": {
+    "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",
+    "schema"
+  ],
+  "license": "MIT",
+  "dependencies": {
+    "effect": "^3.21.0"
+  },
+  "devDependencies": {
+    "@galaxy-tool-util/core": "workspace:*",
+    "ajv": "^8.18.0",
+    "yaml": "^2.8.3"
+  }
+}