@galaxy-tool-util/schema 0.1.0

package/dist/schema/validators/regex.js

@@ -0,0 +1,100 @@
+import * as S from "effect/Schema";
+import { registerValidatorType } from "./registry.js";
+/**
+ * Convert Python inline flags (?aiLmsux) at the start of a pattern to JS RegExp flags.
+ * Unsupported flags (a, L, u, x) are silently dropped.
+ * Also handles ^(?flags) where the anchor precedes the flag group.
+ */
+export function pythonToJsRegex(expression) {
+    const m = expression.match(/^(\^?)\(\?([aiLmsux]+)\)/);
+    if (!m)
+        return { pattern: expression, flags: "" };
+    const anchor = m[1]; // "" or "^"
+    const flagChars = m[2];
+    let flags = "";
+    if (flagChars.includes("i"))
+        flags += "i";
+    if (flagChars.includes("m"))
+        flags += "m";
+    if (flagChars.includes("s"))
+        flags += "s";
+    return { pattern: anchor + expression.slice(m[0].length), flags };
+}
+/**
+ * Strip Python identity escapes that are invalid under ECMA-262 unicode mode.
+ * Python allows \X for any character X (it's an identity escape), but JS /u mode
+ * only allows escaping syntax characters. We strip backslashes before non-syntax chars.
+ *
+ * ECMA-262 syntax characters (safe to escape): ^ $ \ . * + ? ( ) [ ] { } |
+ */
+export function stripPythonIdentityEscapes(pattern) {
+    // Match \\ (escaped backslash) first to skip it, then \X where X is not
+    // an ECMA-262 syntax char or standard escape letter.
+    // Standard escape letters: d, D, w, W, s, S, b, B, n, r, t, f, v, 0, c, x, u, p, P, k
+    return pattern.replace(/\\\\|\\([^\\^$.*+?()[\]{}|dDwWsSnrtfv0cxupPkbB])/g, (match, captured) => captured !== undefined ? captured : match);
+}
+/**
+ * Convert []] (legacy PCRE/Python idiom for literal ]) to [\]] for ECMA-262 /u compat.
+ */
+export function fixBracketCharClass(pattern) {
+    return pattern.replace(/\[\]\]/g, "[\\]]");
+}
+/**
+ * Make a pattern safe for JSON Schema's `pattern` keyword (ECMA-262, validated in /u mode by AJV).
+ * Returns null if the pattern can't be made safe.
+ */
+export function jsonSchemaSafePattern(pattern) {
+    let safe = stripPythonIdentityEscapes(pattern);
+    safe = fixBracketCharClass(safe);
+    // Pre-flight: verify the result compiles under /u mode (AJV's validation mode)
+    try {
+        new RegExp(safe, "u");
+        return safe;
+    }
+    catch {
+        return null;
+    }
+}
+function safeRegExp(expression) {
+    const { pattern, flags } = pythonToJsRegex(expression);
+    try {
+        return new RegExp(pattern, flags);
+    }
+    catch {
+        return null;
+    }
+}
+function applyRegex(schema, validator) {
+    const v = validator;
+    // Galaxy treats "" as "not set" — regex validators only apply to non-empty values.
+    if (v.negate) {
+        const re = safeRegExp(v.expression);
+        if (!re)
+            return schema;
+        return schema.pipe(S.filter((value) => value === "" || !re.test(value), { jsonSchema: {} }));
+    }
+    const { pattern, flags } = pythonToJsRegex(v.expression);
+    let anchored = pattern;
+    if (!anchored.startsWith("^"))
+        anchored = "^" + anchored;
+    try {
+        const re = new RegExp(anchored, flags);
+        // JSON Schema `pattern` doesn't support regex flags (s, i, m).
+        // When flags are present, skip the pattern annotation.
+        // Otherwise, make the pattern /u-safe for AJV and wrap with empty-string exemption.
+        let jsonAnnotation;
+        if (flags) {
+            jsonAnnotation = { jsonSchema: {} };
+        }
+        else {
+            const safe = jsonSchemaSafePattern(anchored);
+            jsonAnnotation = safe ? { jsonSchema: { pattern: `(^$|${safe})` } } : { jsonSchema: {} };
+        }
+        return schema.pipe(S.filter((value) => value === "" || re.test(value), jsonAnnotation));
+    }
+    catch {
+        return schema;
+    }
+}
+registerValidatorType("regex", applyRegex);
+//# sourceMappingURL=regex.js.map

package/dist/schema/validators/regex.js.map

@@ -0,0 +1 @@
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package/dist/schema/validators/registry.d.ts

@@ -0,0 +1,19 @@
+import type * as S from "effect/Schema";
+/**
+ * A function that applies a validator's constraint to an existing schema.
+ * Returns a new schema with the filter applied.
+ */
+export type ValidatorApplier = (schema: S.Schema.Any, validator: any) => S.Schema.Any;
+export declare function registerValidatorType(type: string, applier: ValidatorApplier): void;
+export declare function getValidatorApplier(type: string): ValidatorApplier | undefined;
+export declare function isValidatorTypeRegistered(type: string): boolean;
+export declare function registeredValidatorTypes(): Set<string>;
+/**
+ * Apply a list of validators to a schema, folding left.
+ * Unknown validator types are silently skipped (skip logic should have
+ * already filtered tools with unregistered validators).
+ */
+export declare function applyValidators(schema: S.Schema.Any, validators: {
+    type: string;
+}[]): S.Schema.Any;
+//# sourceMappingURL=registry.d.ts.map

package/dist/schema/validators/registry.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"registry.d.ts","sourceRoot":"","sources":["../../../src/schema/validators/registry.ts"],"names":[],"mappings":"AAAA,OAAO,KAAK,KAAK,CAAC,MAAM,eAAe,CAAC;AAExC;;;GAGG;AACH,MAAM,MAAM,gBAAgB,GAAG,CAAC,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC,GAAG,EAAE,SAAS,EAAE,GAAG,KAAK,CAAC,CAAC,MAAM,CAAC,GAAG,CAAC;AAItF,wBAAgB,qBAAqB,CAAC,IAAI,EAAE,MAAM,EAAE,OAAO,EAAE,gBAAgB,GAAG,IAAI,CAEnF;AAED,wBAAgB,mBAAmB,CAAC,IAAI,EAAE,MAAM,GAAG,gBAAgB,GAAG,SAAS,CAE9E;AAED,wBAAgB,yBAAyB,CAAC,IAAI,EAAE,MAAM,GAAG,OAAO,CAE/D;AAED,wBAAgB,wBAAwB,IAAI,GAAG,CAAC,MAAM,CAAC,CAEtD;AAED;;;;GAIG;AACH,wBAAgB,eAAe,CAC7B,MAAM,EAAE,CAAC,CAAC,MAAM,CAAC,GAAG,EACpB,UAAU,EAAE;IAAE,IAAI,EAAE,MAAM,CAAA;CAAE,EAAE,GAC7B,CAAC,CAAC,MAAM,CAAC,GAAG,CASd"}

package/dist/schema/validators/registry.js

@@ -0,0 +1,29 @@
+const registry = new Map();
+export function registerValidatorType(type, applier) {
+    registry.set(type, applier);
+}
+export function getValidatorApplier(type) {
+    return registry.get(type);
+}
+export function isValidatorTypeRegistered(type) {
+    return registry.has(type);
+}
+export function registeredValidatorTypes() {
+    return new Set(registry.keys());
+}
+/**
+ * Apply a list of validators to a schema, folding left.
+ * Unknown validator types are silently skipped (skip logic should have
+ * already filtered tools with unregistered validators).
+ */
+export function applyValidators(schema, validators) {
+    let result = schema;
+    for (const v of validators) {
+        const applier = registry.get(v.type);
+        if (applier) {
+            result = applier(result, v);
+        }
+    }
+    return result;
+}
+//# sourceMappingURL=registry.js.map

package/dist/schema/validators/registry.js.map

@@ -0,0 +1 @@
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package/dist/workflow/clean.d.ts

@@ -0,0 +1,13 @@
+/**
+ * Workflow tool_state cleaning — strip stale keys and decode legacy encoding.
+ *
+ * Port of Galaxy's workflow_state clean operation. Removes bookkeeping keys
+ * (__page__, __rerun_remap_job_id__), runtime leak keys (chromInfo, __input_ext),
+ * and decodes JSON-encoded tool_state strings into proper dicts.
+ */
+/**
+ * Clean a workflow — strip stale keys and decode legacy tool_state encoding.
+ * Mutates and returns the workflow dict. Format2 workflows pass through unchanged.
+ */
+export declare function cleanWorkflow(workflowDict: Record<string, unknown>): Record<string, unknown>;
+//# sourceMappingURL=clean.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"clean.d.ts","sourceRoot":"","sources":["../../src/workflow/clean.ts"],"names":[],"mappings":"AAAA;;;;;;GAMG;AA0HH;;;GAGG;AACH,wBAAgB,aAAa,CAAC,YAAY,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAM5F"}

package/dist/workflow/clean.js

@@ -0,0 +1,131 @@
+/**
+ * Workflow tool_state cleaning — strip stale keys and decode legacy encoding.
+ *
+ * Port of Galaxy's workflow_state clean operation. Removes bookkeeping keys
+ * (__page__, __rerun_remap_job_id__), runtime leak keys (chromInfo, __input_ext),
+ * and decodes JSON-encoded tool_state strings into proper dicts.
+ */
+/** Keys injected by Galaxy's tool form machinery — never meaningful in saved workflows. */
+const BOOKKEEPING_KEYS = new Set(["__page__", "__rerun_remap_job_id__"]);
+/** Keys leaked from runtime context into saved state. */
+const RUNTIME_LEAK_KEYS = new Set(["chromInfo", "__input_ext"]);
+/** Internal indexing keys within conditionals and repeats. */
+const INTERNAL_KEYS = new Set(["__current_case__", "__index__"]);
+const STALE_KEYS = new Set([...BOOKKEEPING_KEYS, ...RUNTIME_LEAK_KEYS, ...INTERNAL_KEYS]);
+/**
+ * Decode a legacy JSON-encoded tool_state value. If the value is a string
+ * that parses to a compound type (object/array), return the parsed value and
+ * recurse. Primitive JSON strings (numbers, booleans, "null", quoted strings)
+ * are left as their original string form.
+ */
+function decodeLegacyValue(value) {
+    if (typeof value !== "string")
+        return value;
+    try {
+        const parsed = JSON.parse(value);
+        if (parsed !== null && typeof parsed === "object") {
+            // Compound type — recurse into it
+            if (Array.isArray(parsed)) {
+                return parsed.map(decodeLegacyValue);
+            }
+            return decodeLegacyDict(parsed);
+        }
+        // Primitive — keep original string
+        return value;
+    }
+    catch {
+        return value;
+    }
+}
+/** Recursively decode all values in a dict that are legacy JSON strings. */
+function decodeLegacyDict(dict) {
+    const result = {};
+    for (const [key, value] of Object.entries(dict)) {
+        result[key] = decodeLegacyValue(value);
+    }
+    return result;
+}
+/**
+ * Parse and decode a tool_state. Handles both:
+ * - String tool_state (JSON-encoded, possibly with nested legacy encoding)
+ * - Dict tool_state (already parsed, values are proper types)
+ */
+function parseToolState(toolState) {
+    if (typeof toolState === "string") {
+        try {
+            const parsed = JSON.parse(toolState);
+            if (parsed !== null && typeof parsed === "object" && !Array.isArray(parsed)) {
+                return decodeLegacyDict(parsed);
+            }
+        }
+        catch {
+            /* not valid JSON */
+        }
+        return null;
+    }
+    if (toolState !== null && typeof toolState === "object" && !Array.isArray(toolState)) {
+        return toolState;
+    }
+    return null;
+}
+/** Recursively remove stale keys from a tool_state dict. */
+function stripStaleKeys(state) {
+    const result = {};
+    for (const [key, value] of Object.entries(state)) {
+        if (STALE_KEYS.has(key))
+            continue;
+        result[key] = stripStaleValue(value);
+    }
+    return result;
+}
+/** Recurse into nested values (conditional dicts, repeat arrays). */
+function stripStaleValue(value) {
+    if (Array.isArray(value)) {
+        return value.map(stripStaleValue);
+    }
+    if (value !== null && typeof value === "object") {
+        return stripStaleKeys(value);
+    }
+    return value;
+}
+/** Clean a single native step's tool_state in place. */
+function cleanNativeStep(stepDef) {
+    const toolId = stepDef.tool_id;
+    if (!toolId)
+        return;
+    const rawState = stepDef.tool_state;
+    if (rawState === undefined || rawState === null)
+        return;
+    const parsed = parseToolState(rawState);
+    if (!parsed)
+        return;
+    stepDef.tool_state = stripStaleKeys(parsed);
+}
+/** Recursively clean all steps in a native workflow dict. */
+function cleanNativeSteps(workflowDict) {
+    const steps = workflowDict.steps;
+    if (!steps)
+        return;
+    for (const stepDef of Object.values(steps)) {
+        // Subworkflow steps don't have meaningful tool_state — recurse into the
+        // embedded subworkflow's steps instead.
+        if (stepDef.type === "subworkflow" && stepDef.subworkflow) {
+            cleanNativeSteps(stepDef.subworkflow);
+            continue;
+        }
+        cleanNativeStep(stepDef);
+    }
+}
+import { detectFormat } from "./detect-format.js";
+/**
+ * Clean a workflow — strip stale keys and decode legacy tool_state encoding.
+ * Mutates and returns the workflow dict. Format2 workflows pass through unchanged.
+ */
+export function cleanWorkflow(workflowDict) {
+    if (detectFormat(workflowDict) === "format2") {
+        return workflowDict;
+    }
+    cleanNativeSteps(workflowDict);
+    return workflowDict;
+}
+//# sourceMappingURL=clean.js.map

package/dist/workflow/clean.js.map

@@ -0,0 +1 @@
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package/dist/workflow/detect-format.d.ts

@@ -0,0 +1,5 @@
+/** Workflow format — native (.ga) or format2 (.gxwf.yml). */
+export type WorkflowFormat = "native" | "format2";
+/** Detect whether a workflow dict is native or format2. */
+export declare function detectFormat(data: Record<string, unknown>): WorkflowFormat;
+//# sourceMappingURL=detect-format.d.ts.map

package/dist/workflow/detect-format.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"detect-format.d.ts","sourceRoot":"","sources":["../../src/workflow/detect-format.ts"],"names":[],"mappings":"AAAA,6DAA6D;AAC7D,MAAM,MAAM,cAAc,GAAG,QAAQ,GAAG,SAAS,CAAC;AAElD,2DAA2D;AAC3D,wBAAgB,YAAY,CAAC,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,cAAc,CAK1E"}

package/dist/workflow/detect-format.js

@@ -0,0 +1,11 @@
+/** Detect whether a workflow dict is native or format2. */
+export function detectFormat(data) {
+    if ("a_galaxy_workflow" in data)
+        return "native";
+    if (data.class === "GalaxyWorkflow")
+        return "format2";
+    if ("format-version" in data)
+        return "native";
+    return "format2";
+}
+//# sourceMappingURL=detect-format.js.map

package/dist/workflow/detect-format.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"detect-format.js","sourceRoot":"","sources":["../../src/workflow/detect-format.ts"],"names":[],"mappings":"AAGA,2DAA2D;AAC3D,MAAM,UAAU,YAAY,CAAC,IAA6B;IACxD,IAAI,mBAAmB,IAAI,IAAI;QAAE,OAAO,QAAQ,CAAC;IACjD,IAAI,IAAI,CAAC,KAAK,KAAK,gBAAgB;QAAE,OAAO,SAAS,CAAC;IACtD,IAAI,gBAAgB,IAAI,IAAI;QAAE,OAAO,QAAQ,CAAC;IAC9C,OAAO,SAAS,CAAC;AACnB,CAAC"}

package/dist/workflow/index.d.ts

@@ -0,0 +1,9 @@
+export { type GalaxyWorkflow, GalaxyWorkflowSchema, type NativeGalaxyWorkflow, NativeGalaxyWorkflowSchema, } from "./raw/index.js";
+export { normalizedFormat2, NormalizedFormat2WorkflowSchema, NormalizedFormat2StepSchema, NormalizedFormat2InputSchema, NormalizedFormat2OutputSchema, NormalizedFormat2StepInputSchema, NormalizedFormat2StepOutputSchema, type NormalizedFormat2Workflow, type NormalizedFormat2Step, type NormalizedFormat2Input, type NormalizedFormat2Output, type NormalizedFormat2StepInput, type NormalizedFormat2StepOutput, normalizedNative, NormalizedNativeWorkflowSchema, NormalizedNativeStepSchema, ToolReferenceSchema, type NormalizedNativeWorkflow, type NormalizedNativeStep, type ToolReference, toFormat2, toNative, ensureFormat2, ensureNative, expandedFormat2, expandedNative, isTrsUrl, MAX_EXPANSION_DEPTH, type ExpandedFormat2Workflow, type ExpandedFormat2Step, type ExpandedNativeWorkflow, type ExpandedNativeStep, type RefResolver, type ExpansionOptions, flattenCommentData, unflattenCommentData, resolveSourceReference, UNLABELED_INPUT_PREFIX, UNLABELED_STEP_PREFIX, } from "./normalized/index.js";
+export { injectConnectionsIntoState, stripConnectedValues, flatStatePath, keysStartingWith, repeatInputsToArray, selectWhichWhen, } from "./state-merge.js";
+export { scanForReplacements, type ReplacementClassification } from "./replacement-scan.js";
+export { scanToolState, type LegacyEncodingClassification, type LegacyEncodingHit, type LegacyEncodingScanResult, } from "./legacy-encoding.js";
+export { cleanWorkflow } from "./clean.js";
+export { detectFormat, type WorkflowFormat } from "./detect-format.js";
+export { LintContext, lintNative, lintFormat2, lintWorkflow, lintBestPracticesFormat2, lintBestPracticesNative, type LintResult, } from "./lint.js";
+//# sourceMappingURL=index.d.ts.map

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

@@ -0,0 +1 @@
+{"version":3,"file":"index.d.ts","sourceRoot":"","sources":["../../src/workflow/index.ts"],"names":[],"mappings":"AACA,OAAO,EACL,KAAK,cAAc,EACnB,oBAAoB,EACpB,KAAK,oBAAoB,EACzB,0BAA0B,GAC3B,MAAM,gBAAgB,CAAC;AAGxB,OAAO,EACL,iBAAiB,EACjB,+BAA+B,EAC/B,2BAA2B,EAC3B,4BAA4B,EAC5B,6BAA6B,EAC7B,gCAAgC,EAChC,iCAAiC,EACjC,KAAK,yBAAyB,EAC9B,KAAK,qBAAqB,EAC1B,KAAK,sBAAsB,EAC3B,KAAK,uBAAuB,EAC5B,KAAK,0BAA0B,EAC/B,KAAK,2BAA2B,EAChC,gBAAgB,EAChB,8BAA8B,EAC9B,0BAA0B,EAC1B,mBAAmB,EACnB,KAAK,wBAAwB,EAC7B,KAAK,oBAAoB,EACzB,KAAK,aAAa,EAClB,SAAS,EACT,QAAQ,EACR,aAAa,EACb,YAAY,EACZ,eAAe,EACf,cAAc,EACd,QAAQ,EACR,mBAAmB,EACnB,KAAK,uBAAuB,EAC5B,KAAK,mBAAmB,EACxB,KAAK,sBAAsB,EAC3B,KAAK,kBAAkB,EACvB,KAAK,WAAW,EAChB,KAAK,gBAAgB,EACrB,kBAAkB,EAClB,oBAAoB,EACpB,sBAAsB,EACtB,sBAAsB,EACtB,qBAAqB,GACtB,MAAM,uBAAuB,CAAC;AAE/B,OAAO,EACL,0BAA0B,EAC1B,oBAAoB,EACpB,aAAa,EACb,gBAAgB,EAChB,mBAAmB,EACnB,eAAe,GAChB,MAAM,kBAAkB,CAAC;AAE1B,OAAO,EAAE,mBAAmB,EAAE,KAAK,yBAAyB,EAAE,MAAM,uBAAuB,CAAC;AAE5F,OAAO,EACL,aAAa,EACb,KAAK,4BAA4B,EACjC,KAAK,iBAAiB,EACtB,KAAK,wBAAwB,GAC9B,MAAM,sBAAsB,CAAC;AAE9B,OAAO,EAAE,aAAa,EAAE,MAAM,YAAY,CAAC;AAE3C,OAAO,EAAE,YAAY,EAAE,KAAK,cAAc,EAAE,MAAM,oBAAoB,CAAC;AAEvE,OAAO,EACL,WAAW,EACX,UAAU,EACV,WAAW,EACX,YAAY,EACZ,wBAAwB,EACxB,uBAAuB,EACvB,KAAK,UAAU,GAChB,MAAM,WAAW,CAAC"}

package/dist/workflow/index.js

@@ -0,0 +1,11 @@
+// Raw (generated) workflow schema types
+export { GalaxyWorkflowSchema, NativeGalaxyWorkflowSchema, } from "./raw/index.js";
+// Normalized workflow types + normalizers
+export { normalizedFormat2, NormalizedFormat2WorkflowSchema, NormalizedFormat2StepSchema, NormalizedFormat2InputSchema, NormalizedFormat2OutputSchema, NormalizedFormat2StepInputSchema, NormalizedFormat2StepOutputSchema, normalizedNative, NormalizedNativeWorkflowSchema, NormalizedNativeStepSchema, ToolReferenceSchema, toFormat2, toNative, ensureFormat2, ensureNative, expandedFormat2, expandedNative, isTrsUrl, MAX_EXPANSION_DEPTH, flattenCommentData, unflattenCommentData, resolveSourceReference, UNLABELED_INPUT_PREFIX, UNLABELED_STEP_PREFIX, } from "./normalized/index.js";
+export { injectConnectionsIntoState, stripConnectedValues, flatStatePath, keysStartingWith, repeatInputsToArray, selectWhichWhen, } from "./state-merge.js";
+export { scanForReplacements } from "./replacement-scan.js";
+export { scanToolState, } from "./legacy-encoding.js";
+export { cleanWorkflow } from "./clean.js";
+export { detectFormat } from "./detect-format.js";
+export { LintContext, lintNative, lintFormat2, lintWorkflow, lintBestPracticesFormat2, lintBestPracticesNative, } from "./lint.js";
+//# sourceMappingURL=index.js.map

package/dist/workflow/index.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"index.js","sourceRoot":"","sources":["../../src/workflow/index.ts"],"names":[],"mappings":"AAAA,wCAAwC;AACxC,OAAO,EAEL,oBAAoB,EAEpB,0BAA0B,GAC3B,MAAM,gBAAgB,CAAC;AAExB,0CAA0C;AAC1C,OAAO,EACL,iBAAiB,EACjB,+BAA+B,EAC/B,2BAA2B,EAC3B,4BAA4B,EAC5B,6BAA6B,EAC7B,gCAAgC,EAChC,iCAAiC,EAOjC,gBAAgB,EAChB,8BAA8B,EAC9B,0BAA0B,EAC1B,mBAAmB,EAInB,SAAS,EACT,QAAQ,EACR,aAAa,EACb,YAAY,EACZ,eAAe,EACf,cAAc,EACd,QAAQ,EACR,mBAAmB,EAOnB,kBAAkB,EAClB,oBAAoB,EACpB,sBAAsB,EACtB,sBAAsB,EACtB,qBAAqB,GACtB,MAAM,uBAAuB,CAAC;AAE/B,OAAO,EACL,0BAA0B,EAC1B,oBAAoB,EACpB,aAAa,EACb,gBAAgB,EAChB,mBAAmB,EACnB,eAAe,GAChB,MAAM,kBAAkB,CAAC;AAE1B,OAAO,EAAE,mBAAmB,EAAkC,MAAM,uBAAuB,CAAC;AAE5F,OAAO,EACL,aAAa,GAId,MAAM,sBAAsB,CAAC;AAE9B,OAAO,EAAE,aAAa,EAAE,MAAM,YAAY,CAAC;AAE3C,OAAO,EAAE,YAAY,EAAuB,MAAM,oBAAoB,CAAC;AAEvE,OAAO,EACL,WAAW,EACX,UAAU,EACV,WAAW,EACX,YAAY,EACZ,wBAAwB,EACxB,uBAAuB,GAExB,MAAM,WAAW,CAAC"}

package/dist/workflow/legacy-encoding.d.ts

@@ -0,0 +1,40 @@
+/**
+ * Classified detection of legacy parameter encoding in native workflow tool state.
+ *
+ * Port of Galaxy's `galaxy.tool_util.workflow_state.legacy_encoding`.
+ *
+ * Galaxy has two native tool_state serialization formats:
+ *
+ * - **Modern encoding** (nested=True): used in .ga files / IWC.
+ *   After json.loads, all values at all depths are already correct types.
+ *
+ * - **Legacy parameter encoding** (nested=False): used in the workflow
+ *   editor API and some old framework test workflows.  Root values are
+ *   individually JSON-stringified, so containers are still JSON strings
+ *   and typed scalars are stringified (int 2 → "2").
+ *
+ * Detection signals:
+ *   1. Container params (conditional, section, repeat): a string value
+ *      is definitive legacy encoding; a dict/list is definitive modern.
+ *   2. Select params with static options: a quoted value that doesn't
+ *      match any option but unquoted does → definitive legacy encoding.
+ */
+import type { ToolParameterModel } from "../schema/bundle-types.js";
+export type LegacyEncodingClassification = "yes" | "maybe_assumed_no" | "no";
+export interface LegacyEncodingHit {
+    parameterName: string;
+    parameterType: string;
+    detail: string;
+}
+export interface LegacyEncodingScanResult {
+    classification: LegacyEncodingClassification;
+    hits: LegacyEncodingHit[];
+    signalsChecked: number;
+}
+/**
+ * Scan decoded native tool_state for legacy parameter encoding.
+ *
+ * Checks root-level container params and select params with static options.
+ */
+export declare function scanToolState(toolInputs: ToolParameterModel[], toolState: Record<string, unknown>): LegacyEncodingScanResult;
+//# sourceMappingURL=legacy-encoding.d.ts.map

package/dist/workflow/legacy-encoding.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"legacy-encoding.d.ts","sourceRoot":"","sources":["../../src/workflow/legacy-encoding.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;;;;;;;;;;GAoBG;AAEH,OAAO,KAAK,EAAE,kBAAkB,EAAwB,MAAM,2BAA2B,CAAC;AAE1F,MAAM,MAAM,4BAA4B,GAAG,KAAK,GAAG,kBAAkB,GAAG,IAAI,CAAC;AAE7E,MAAM,WAAW,iBAAiB;IAChC,aAAa,EAAE,MAAM,CAAC;IACtB,aAAa,EAAE,MAAM,CAAC;IACtB,MAAM,EAAE,MAAM,CAAC;CAChB;AAED,MAAM,WAAW,wBAAwB;IACvC,cAAc,EAAE,4BAA4B,CAAC;IAC7C,IAAI,EAAE,iBAAiB,EAAE,CAAC;IAC1B,cAAc,EAAE,MAAM,CAAC;CACxB;AAWD;;;;GAIG;AACH,wBAAgB,aAAa,CAC3B,UAAU,EAAE,kBAAkB,EAAE,EAChC,SAAS,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GACjC,wBAAwB,CA+C1B"}

package/dist/workflow/legacy-encoding.js

@@ -0,0 +1,81 @@
+/**
+ * Classified detection of legacy parameter encoding in native workflow tool state.
+ *
+ * Port of Galaxy's `galaxy.tool_util.workflow_state.legacy_encoding`.
+ *
+ * Galaxy has two native tool_state serialization formats:
+ *
+ * - **Modern encoding** (nested=True): used in .ga files / IWC.
+ *   After json.loads, all values at all depths are already correct types.
+ *
+ * - **Legacy parameter encoding** (nested=False): used in the workflow
+ *   editor API and some old framework test workflows.  Root values are
+ *   individually JSON-stringified, so containers are still JSON strings
+ *   and typed scalars are stringified (int 2 → "2").
+ *
+ * Detection signals:
+ *   1. Container params (conditional, section, repeat): a string value
+ *      is definitive legacy encoding; a dict/list is definitive modern.
+ *   2. Select params with static options: a quoted value that doesn't
+ *      match any option but unquoted does → definitive legacy encoding.
+ */
+const CONTAINER_TYPES = new Set(["gx_conditional", "gx_section", "gx_repeat"]);
+function stripQuotes(value) {
+    if (value.length >= 2 && value.startsWith('"') && value.endsWith('"')) {
+        return value.slice(1, -1);
+    }
+    return value;
+}
+/**
+ * Scan decoded native tool_state for legacy parameter encoding.
+ *
+ * Checks root-level container params and select params with static options.
+ */
+export function scanToolState(toolInputs, toolState) {
+    const hits = [];
+    let signalsChecked = 0;
+    for (const toolInput of toolInputs) {
+        const parameterType = toolInput.parameter_type;
+        const name = toolInput.name;
+        const value = toolState[name];
+        if (value === undefined || value === null) {
+            continue;
+        }
+        if (CONTAINER_TYPES.has(parameterType)) {
+            signalsChecked++;
+            if (typeof value === "string") {
+                hits.push({
+                    parameterName: name,
+                    parameterType,
+                    detail: "container value is a string",
+                });
+            }
+        }
+        else if (parameterType === "gx_select" && typeof value === "string") {
+            const select = toolInput;
+            if (select.options) {
+                const optionValues = new Set(select.options.map((o) => o.value));
+                signalsChecked++;
+                if (!optionValues.has(value) && optionValues.has(stripQuotes(value))) {
+                    hits.push({
+                        parameterName: name,
+                        parameterType,
+                        detail: `quoted value ${JSON.stringify(value)} doesn't match options, unquoted does`,
+                    });
+                }
+            }
+        }
+    }
+    let classification;
+    if (hits.length > 0) {
+        classification = "yes";
+    }
+    else if (signalsChecked === 0) {
+        classification = "maybe_assumed_no";
+    }
+    else {
+        classification = "no";
+    }
+    return { classification, hits, signalsChecked };
+}
+//# sourceMappingURL=legacy-encoding.js.map

package/dist/workflow/legacy-encoding.js.map

@@ -0,0 +1 @@
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package/dist/workflow/lint.d.ts

@@ -0,0 +1,49 @@
+/**
+ * Workflow linting — structural checks and best-practice warnings.
+ *
+ * Port of gxformat2's lint.py + linting.py. Checks workflow structure,
+ * output labels, step errors, tool references, output source resolution,
+ * input default types, and report markdown.
+ */
+export declare class LintContext {
+    errors: string[];
+    warnings: string[];
+    private _prefix;
+    constructor(prefix?: string);
+    error(message: string): void;
+    warn(message: string): void;
+    child(prefix: string): LintContext;
+}
+export interface LintResult {
+    errors: string[];
+    warnings: string[];
+    error_count: number;
+    warn_count: number;
+}
+/**
+ * Lint a native Galaxy workflow (.ga format).
+ * Returns structured lint results with errors and warnings.
+ */
+export declare function lintNative(workflowDict: Record<string, unknown>): LintResult;
+/**
+ * Lint a Format2 Galaxy workflow (.gxwf.yml format).
+ * Returns structured lint results with errors and warnings.
+ */
+export declare function lintFormat2(workflowDict: Record<string, unknown>): LintResult;
+/**
+ * Lint a workflow, auto-detecting format.
+ * Returns structured lint results with errors and warnings.
+ */
+export declare function lintWorkflow(workflowDict: Record<string, unknown>): LintResult;
+/**
+ * Lint best practices for a Format2 Galaxy workflow.
+ * Returns structured lint results with warnings about missing annotations,
+ * creators, licenses, step labels, and disconnected inputs.
+ */
+export declare function lintBestPracticesFormat2(workflowDict: Record<string, unknown>): LintResult;
+/**
+ * Lint best practices for a native Galaxy workflow.
+ * Runs shared format2 best practices plus native-specific checks.
+ */
+export declare function lintBestPracticesNative(workflowDict: Record<string, unknown>): LintResult;
+//# sourceMappingURL=lint.d.ts.map

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

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