@galaxy-tool-util/schema 0.1.0 → 0.4.0

package/dist/workflow/state-merge.js

@@ -1,248 +1,54 @@
 /**
- * Inject ConnectedValue markers into workflow state dicts.
+ * ConnectedValue injection and stripping for workflow state dicts.
  *
- * Port of Python galaxy.tool_util.workflow_state._state_merge +
- * helper functions from galaxy.tool_util.parameters.visitor.
+ * Thin wrappers around walkNativeState that inject or strip
+ * ConnectedValue markers. Mutate state in-place for caller compat.
  *
- * 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.
+ * Port of Python galaxy.tool_util.workflow_state._state_merge.
+ * Tree-walking helpers live in walk-helpers.ts; re-exported here
+ * for backward compatibility.
  */
-// --- 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;
-}
+import { CONNECTED_VALUE, isConnectedValue } from "./runtime-markers.js";
+import { walkNativeState, SKIP_VALUE } from "./walker.js";
+import { flatStatePath, keysStartingWith, repeatInputsToArray, selectWhichWhen, } from "./walk-helpers.js";
+// Re-export helpers so existing importers don't break
+export { flatStatePath, keysStartingWith, repeatInputsToArray, selectWhichWhen };
 // --- 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.
+ * Uses walkNativeState with a leaf callback that replaces connected
+ * leaves with ConnectedValue markers, then reassigns the input state
+ * in-place to preserve the mutation contract callers expect.
  *
  * @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);
-    }
+    const result = walkNativeState(connections, toolInputs, state, (_input, value, statePath) => {
+        if (statePath in remaining) {
+            delete remaining[statePath];
+            return { ...CONNECTED_VALUE };
+        }
+        return value === undefined ? SKIP_VALUE : value;
+    }, { preserveUnknownKeys: true });
+    for (const key of Object.keys(state))
+        delete state[key];
+    Object.assign(state, result);
     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.
+ * Uses walkNativeState with a leaf callback that omits ConnectedValue
+ * entries via SKIP_VALUE, then reassigns the input state in-place to
+ * preserve the mutation contract callers expect.
  */
 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];
-        }
-    }
+    const cleaned = walkNativeState({}, toolInputs, state, (_input, value) => isConnectedValue(value) ? SKIP_VALUE : value === undefined ? SKIP_VALUE : value, { preserveUnknownKeys: true });
+    for (const key of Object.keys(state))
+        delete state[key];
+    Object.assign(state, cleaned);
 }
 //# sourceMappingURL=state-merge.js.map

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

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package/dist/workflow/stateful-convert.d.ts

@@ -0,0 +1,47 @@
+/**
+ * Schema-aware (stateful) state conversion between native and format2 formats.
+ *
+ * Uses the walker to traverse tool_state with parameter definitions,
+ * coercing scalar types and separating connections/runtime values.
+ *
+ * Design: no double encoding, no legacy decode, clean dicts throughout.
+ */
+import type { ToolParameterModel } from "../schema/bundle-types.js";
+import type { NormalizedNativeStep } from "./normalized/native.js";
+/**
+ * Coerce a native scalar value to its format2 representation.
+ *
+ * Native tool_state may have string-typed numbers, booleans, or
+ * comma-delimited multi-selects. Format2 uses proper JS types.
+ */
+export declare function convertScalarValue(toolInput: ToolParameterModel, value: unknown): unknown;
+/**
+ * Reverse-coerce a format2 scalar value back to native representation.
+ *
+ * Format2 uses proper JS types; native may need string coercions for
+ * multi-select and data_column values.
+ */
+export declare function reverseScalarValue(toolInput: ToolParameterModel, value: unknown): unknown;
+export interface Format2ConvertedState {
+    state: Record<string, unknown>;
+    in: Record<string, string>;
+}
+/**
+ * Convert a native step's tool_state to format2 state + in block.
+ *
+ * Walks the parameter tree:
+ * - Data params → `in` block (connected/runtime) or SKIP
+ * - ConnectedValue/RuntimeValue markers → `in` block
+ * - gx_rules → parse JSON string, SKIP if null/connected
+ * - Null/"null" values → SKIP
+ * - Scalars → coerce via convertScalarValue()
+ */
+export declare function convertStateToFormat2(nativeStep: NormalizedNativeStep, toolInputs: ToolParameterModel[]): Format2ConvertedState;
+/**
+ * Encode format2 state back to native tool_state.
+ *
+ * Walks format2 state reversing coercions (e.g. number arrays → string arrays
+ * for multi-select/data_column). Returns a clean dict — no JSON.stringify per key.
+ */
+export declare function encodeStateToNative(toolInputs: ToolParameterModel[], state: Record<string, unknown>): Record<string, unknown>;
+//# sourceMappingURL=stateful-convert.d.ts.map

package/dist/workflow/stateful-convert.d.ts.map

@@ -0,0 +1 @@
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package/dist/workflow/stateful-convert.js

@@ -0,0 +1,151 @@
+/**
+ * Schema-aware (stateful) state conversion between native and format2 formats.
+ *
+ * Uses the walker to traverse tool_state with parameter definitions,
+ * coercing scalar types and separating connections/runtime values.
+ *
+ * Design: no double encoding, no legacy decode, clean dicts throughout.
+ */
+import { walkNativeState, walkFormat2State, SKIP_VALUE } from "./walker.js";
+import { isConnectedValue, isRuntimeValue } from "./runtime-markers.js";
+import { parseBool, parseNumber, parseStringArray, parseNumberArray } from "./coercions.js";
+// --- Scalar coercions ---
+/**
+ * Coerce a native scalar value to its format2 representation.
+ *
+ * Native tool_state may have string-typed numbers, booleans, or
+ * comma-delimited multi-selects. Format2 uses proper JS types.
+ */
+export function convertScalarValue(toolInput, value) {
+    const paramType = toolInput.parameter_type;
+    if (paramType === "gx_integer" || paramType === "gx_float") {
+        return parseNumber(value) ?? value;
+    }
+    if (paramType === "gx_boolean") {
+        return parseBool(value) ?? value;
+    }
+    if (paramType === "gx_select") {
+        const select = toolInput;
+        if (select.multiple) {
+            return parseStringArray(value) ?? value;
+        }
+        return value;
+    }
+    if (paramType === "gx_data_column") {
+        const col = toolInput;
+        if (col.multiple) {
+            return parseNumberArray(value) ?? value;
+        }
+        return parseNumber(value) ?? value;
+    }
+    // Passthrough for text, color, hidden, directory_uri, genomebuild,
+    // baseurl, drill_down, group_tag, and CWL types
+    return value;
+}
+/**
+ * Reverse-coerce a format2 scalar value back to native representation.
+ *
+ * Format2 uses proper JS types; native may need string coercions for
+ * multi-select and data_column values.
+ */
+export function reverseScalarValue(toolInput, value) {
+    const paramType = toolInput.parameter_type;
+    if (paramType === "gx_select") {
+        const select = toolInput;
+        if (select.multiple && Array.isArray(value)) {
+            return value.map(String);
+        }
+        return value;
+    }
+    if (paramType === "gx_data_column") {
+        const col = toolInput;
+        if (col.multiple && Array.isArray(value)) {
+            return value.map(String);
+        }
+        return typeof value === "number" ? String(value) : value;
+    }
+    // Most types pass through unchanged
+    return value;
+}
+/** Data parameter types — always go to `in` block, never to state. */
+const DATA_PARAM_TYPES = new Set(["gx_data", "gx_data_collection"]);
+/**
+ * Convert a native step's tool_state to format2 state + in block.
+ *
+ * Walks the parameter tree:
+ * - Data params → `in` block (connected/runtime) or SKIP
+ * - ConnectedValue/RuntimeValue markers → `in` block
+ * - gx_rules → parse JSON string, SKIP if null/connected
+ * - Null/"null" values → SKIP
+ * - Scalars → coerce via convertScalarValue()
+ */
+export function convertStateToFormat2(nativeStep, toolInputs) {
+    const toolState = nativeStep.tool_state;
+    // Widen readonly tuples to unknown for the walker's connection lookup.
+    const inputConnections = nativeStep.input_connections;
+    const connectedPaths = nativeStep.connected_paths;
+    const inBlock = {};
+    const leafCallback = (toolInput, value, statePath) => {
+        const paramType = toolInput.parameter_type;
+        // Data parameters: always to `in` block
+        if (DATA_PARAM_TYPES.has(paramType)) {
+            if (isConnectedValue(value) || connectedPaths.has(statePath)) {
+                // Connected data param — recorded via input_connections, handled by structural conversion
+            }
+            if (isRuntimeValue(value)) {
+                inBlock[statePath] = "runtime_value";
+            }
+            return SKIP_VALUE;
+        }
+        // Rules parameter: parse JSON string
+        if (paramType === "gx_rules") {
+            if (value == null || isConnectedValue(value)) {
+                if (isConnectedValue(value) || connectedPaths.has(statePath)) {
+                    // Will be in `in` block via structural conversion
+                }
+                return SKIP_VALUE;
+            }
+            if (typeof value === "string") {
+                try {
+                    return JSON.parse(value);
+                }
+                catch {
+                    return value;
+                }
+            }
+            return value;
+        }
+        // ConnectedValue → record in `in` block, skip from state
+        if (isConnectedValue(value)) {
+            // Connection source handled by structural conversion's input_connections
+            return SKIP_VALUE;
+        }
+        // RuntimeValue → record in `in` block, skip from state
+        if (isRuntimeValue(value)) {
+            inBlock[statePath] = "runtime_value";
+            return SKIP_VALUE;
+        }
+        // Null / "null" values → skip
+        if (value === null || value === undefined || value === "null") {
+            return SKIP_VALUE;
+        }
+        // Scalar coercion
+        return convertScalarValue(toolInput, value);
+    };
+    const state = walkNativeState(inputConnections, toolInputs, toolState, leafCallback);
+    return { state, in: inBlock };
+}
+// --- Format2 → Native conversion ---
+/**
+ * Encode format2 state back to native tool_state.
+ *
+ * Walks format2 state reversing coercions (e.g. number arrays → string arrays
+ * for multi-select/data_column). Returns a clean dict — no JSON.stringify per key.
+ */
+export function encodeStateToNative(toolInputs, state) {
+    const leafCallback = (toolInput, value) => {
+        return reverseScalarValue(toolInput, value);
+    };
+    return walkFormat2State(toolInputs, state, leafCallback);
+}
+//# sourceMappingURL=stateful-convert.js.map

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package/dist/workflow/stateful-validate.d.ts

@@ -0,0 +1,67 @@
+/**
+ * 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 "../schema/parameters/index.js";
+import type { ToolParameterModel } from "../schema/bundle-types.js";
+export type ValidationPhase = "pre" | "post";
+/**
+ * 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 declare class ConversionValidationFailure extends Error {
+    readonly phase: ValidationPhase;
+    readonly issues: string[];
+    readonly _tag: "ConversionValidationFailure";
+    constructor(phase: ValidationPhase, issues: string[]);
+}
+/**
+ * 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 declare function validateNativeStepState(inputs: ToolParameterModel[], toolState: Record<string, unknown>, inputConnections?: Record<string, unknown>): void;
+/**
+ * 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 declare function validateFormat2StepState(inputs: ToolParameterModel[], format2State: Record<string, unknown>): void;
+/**
+ * A single diagnostic produced by tool-state validation.
+ *
+ * Defined here (lower-level module) so both {@link validateFormat2StepStateStrict}
+ * and the higher-level {@link ToolStateValidator} share one canonical type.
+ */
+export interface ToolStateDiagnostic {
+    /** Dot-separated parameter path, or "" for top-level / unlocated issues. */
+    path: string;
+    message: string;
+    severity: "error" | "warning";
+}
+/**
+ * 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 declare function validateFormat2StepStateStrict(inputs: ToolParameterModel[], format2State: Record<string, unknown>): ToolStateDiagnostic[];
+//# sourceMappingURL=stateful-validate.d.ts.map

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