@galaxy-tool-util/schema 1.5.0 → 1.7.0

package/dist/workflow/json-schemas.d.ts

@@ -0,0 +1,10 @@
+/**
+ * Plain JSON Schema siblings of the Effect workflow schemas.
+ *
+ * Effect `Schema.Schema<A>` values are functions and do not survive
+ * `JSON.stringify`; downstream packagers that copy a schema verbatim into a
+ * runtime bundle need a plain-object JSON Schema instead. Mirrors the
+ * `parsedToolSchema` pattern in `schema/parsed-tool.ts`.
+ */
+export declare const galaxyWorkflowDraftJsonSchema: object;
+//# sourceMappingURL=json-schemas.d.ts.map

package/dist/workflow/json-schemas.d.ts.map

@@ -0,0 +1 @@
+{"version":3,"file":"json-schemas.d.ts","sourceRoot":"","sources":["../../src/workflow/json-schemas.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AA+BH,eAAO,MAAM,6BAA6B,QAAkB,CAAC"}

package/dist/workflow/json-schemas.js

@@ -0,0 +1,39 @@
+/**
+ * Plain JSON Schema siblings of the Effect workflow schemas.
+ *
+ * Effect `Schema.Schema<A>` values are functions and do not survive
+ * `JSON.stringify`; downstream packagers that copy a schema verbatim into a
+ * runtime bundle need a plain-object JSON Schema instead. Mirrors the
+ * `parsedToolSchema` pattern in `schema/parsed-tool.ts`.
+ */
+import { JSONSchema } from "effect";
+import { GalaxyWorkflowDraftSchema } from "./raw/gxformat2-draft.effect.js";
+/**
+ * Effect's `JSONSchema.make` emits inline `{$id: "/schemas/unknown", ...}`
+ * nodes wherever it encounters `Schema.Unknown` / `Schema.Any`. The draft
+ * schema hits this dozens of times (free-form `state`, `tool_state`,
+ * `default`, post-job actions, etc.), and Ajv refuses to compile a document
+ * with the same `$id` resolving to multiple distinct nodes. Stripping the
+ * `$id` leaves the node semantically equivalent (still accepts anything)
+ * and lets standard JSON Schema validators load the result.
+ */
+function stripDuplicateUnknownIds(node) {
+    if (node === null || typeof node !== "object")
+        return;
+    if (Array.isArray(node)) {
+        for (const item of node)
+            stripDuplicateUnknownIds(item);
+        return;
+    }
+    const obj = node;
+    if (obj.$id === "/schemas/unknown")
+        delete obj.$id;
+    for (const k of Object.keys(obj))
+        stripDuplicateUnknownIds(obj[k]);
+}
+const draftJsonSchema = JSONSchema.make(GalaxyWorkflowDraftSchema, {
+    target: "jsonSchema2020-12",
+});
+stripDuplicateUnknownIds(draftJsonSchema);
+export const galaxyWorkflowDraftJsonSchema = draftJsonSchema;
+//# sourceMappingURL=json-schemas.js.map

package/dist/workflow/json-schemas.js.map

@@ -0,0 +1 @@
+{"version":3,"file":"json-schemas.js","sourceRoot":"","sources":["../../src/workflow/json-schemas.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,EAAE,UAAU,EAAE,MAAM,QAAQ,CAAC;AAEpC,OAAO,EAAE,yBAAyB,EAAE,MAAM,iCAAiC,CAAC;AAE5E;;;;;;;;GAQG;AACH,SAAS,wBAAwB,CAAC,IAAa;IAC7C,IAAI,IAAI,KAAK,IAAI,IAAI,OAAO,IAAI,KAAK,QAAQ;QAAE,OAAO;IACtD,IAAI,KAAK,CAAC,OAAO,CAAC,IAAI,CAAC,EAAE,CAAC;QACxB,KAAK,MAAM,IAAI,IAAI,IAAI;YAAE,wBAAwB,CAAC,IAAI,CAAC,CAAC;QACxD,OAAO;IACT,CAAC;IACD,MAAM,GAAG,GAAG,IAA+B,CAAC;IAC5C,IAAI,GAAG,CAAC,GAAG,KAAK,kBAAkB;QAAE,OAAO,GAAG,CAAC,GAAG,CAAC;IACnD,KAAK,MAAM,CAAC,IAAI,MAAM,CAAC,IAAI,CAAC,GAAG,CAAC;QAAE,wBAAwB,CAAC,GAAG,CAAC,CAAC,CAAC,CAAC,CAAC;AACrE,CAAC;AAED,MAAM,eAAe,GAAG,UAAU,CAAC,IAAI,CAAC,yBAAyB,EAAE;IACjE,MAAM,EAAE,mBAAmB;CAC5B,CAAW,CAAC;AACb,wBAAwB,CAAC,eAAe,CAAC,CAAC;AAE1C,MAAM,CAAC,MAAM,6BAA6B,GAAG,eAAe,CAAC"}

package/dist/workflow/normalized/toFormat2.js

@@ -159,13 +159,18 @@ function _buildToolFormat2Step(step, labelMap, options) {
     }
     const inList = _buildFormat2StepInputs(step, labelMap);
     const outList = _buildFormat2StepOutputs(step);
-    // Stateful override: if the caller provides a per-step state encoder
-    // and it returns a non-null result, use its state (and optional `in`
-    // block entries) instead of the default schema-free passthrough.
+    // Tool state routing mirrors gxformat2's state_encode_to_format2 contract:
+    // when the per-step encoder succeeds, its schema-aware result is the clean
+    // `state` block (connections/runtime lifted into `in:`); when it returns null
+    // (no encoder, precheck/validation/conversion failure), we fall back to the
+    // raw native `tool_state` passthrough. Only one of the two fields is ever set,
+    // so a step carrying `tool_state` and no `state` unambiguously signals
+    // unconverted/state-unaware output (validators skip it).
     const override = options?.stateEncodeToFormat2?.(step);
+    let state;
     let toolState = null;
     if (override != null) {
-        toolState = Object.keys(override.state).length > 0 ? override.state : null;
+        state = override.state;
         if (override.in) {
             _mergeInOverrides(inList, override.in);
         }
@@ -189,6 +194,7 @@ function _buildToolFormat2Step(step, labelMap, options) {
         tool_shed_repository: step.tool_shed_repository,
         in: inList,
         out: outList,
+        state,
         tool_state: toolState,
         position: step.position,
         when: step.when ?? undefined,

package/dist/workflow/normalized/toFormat2.js.map

@@ -1 +1 @@
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package/dist/workflow/report-models.d.ts

@@ -127,6 +127,48 @@ export interface DraftSurveyReport {
     /** Distinct step paths carrying at least one `_plan_*` field, in walk order. */
     plan_step_paths: string[][];
 }
+/**
+ * Result of `--concrete` validation pass: extract the concrete subset, then
+ * run the regular `gxwf validate` checks on it. The set of populated buckets
+ * depends on which flags were forwarded (cache-dir / no-tool-state /
+ * connections / strict-*). Empty arrays mean the check ran cleanly; absence
+ * of the buckets below means the check was skipped.
+ */
+export interface ConcreteValidationReport {
+    /** Class on the outermost workflow after extract + strip + promote. */
+    class_after: "GalaxyWorkflow" | "GalaxyWorkflowDraft";
+    /**
+     * Reason concrete decode was skipped (e.g., "subset is still a draft —
+     * not fully promoted"). null when decode actually ran.
+     */
+    skipped_reason: string | null;
+    /** Effect Schema decode errors against `GalaxyWorkflowSchema`. */
+    structure_errors: string[];
+    /** Strict-structure check errors. Present only when --strict-structure (or --strict) was set. */
+    strict_structure_errors?: string[];
+    /** Strict-encoding check errors. Present only when --strict-encoding (or --strict) was set. */
+    strict_encoding_errors?: string[];
+    /** Strict-state errors — skipped steps treated as failures. Present only when --strict-state (or --strict) was set. */
+    strict_state_errors?: string[];
+    /** Per-step tool-state validation. Present only when tool-state validation ran. */
+    tool_state?: {
+        results: ValidationStepResult[];
+        summary: {
+            ok: number;
+            fail: number;
+            skip: number;
+        };
+    };
+    /** Connection-type compatibility report. Present only when --connections was set. */
+    connection_report?: ConnectionValidationReport;
+    /**
+     * Tri-state: `true` if every check that ran came back clean, `false` if any
+     * failed, `null` if the concrete pass was skipped (`skipped_reason !== null`).
+     * Consumers must distinguish `null` from `true` — a skipped pass is **not**
+     * an endorsement that the subset would have validated.
+     */
+    ok: boolean | null;
+}
 export interface SingleDraftValidationReport {
     workflow: string;
     ok: boolean;
@@ -135,6 +177,8 @@ export interface SingleDraftValidationReport {
     semantic_errors: DraftValidationDiagnosticReport[];
     warnings: DraftValidationDiagnosticReport[];
     survey: DraftSurveyReport;
+    /** Present only when --concrete was requested. */
+    concrete?: ConcreteValidationReport;
     summary: string;
 }
 export interface DraftExtractDropReport {
@@ -386,7 +430,7 @@ export declare function buildSingleLintReport(workflow: string, lint_errors: num
     lint_warning_messages?: string[];
 }): SingleLintReport;
 export declare function buildSingleCleanReport(workflow: string, results: CleanStepResult[]): SingleCleanReport;
-export declare function buildSingleDraftValidationReport(workflow: string, result: DraftValidationResult): SingleDraftValidationReport;
+export declare function buildSingleDraftValidationReport(workflow: string, result: DraftValidationResult, concrete?: ConcreteValidationReport): SingleDraftValidationReport;
 export declare function buildSingleDraftExtractReport(workflow: string, output: string | null, extract: ExtractResult, promote: PromoteFullyConcreteDraftsResult, classAfter: "GalaxyWorkflowDraft" | "GalaxyWorkflow"): SingleDraftExtractReport;
 export declare function buildWorkflowValidationResult(relativePath: string, stepResults: ValidationStepResult[], opts?: {
     error?: string | null;

package/dist/workflow/report-models.d.ts.map

@@ -1 +1 @@
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package/dist/workflow/report-models.js

@@ -116,15 +116,21 @@ export function buildSingleCleanReport(workflow, results) {
         steps_with_removals: results.filter((r) => r.removed_keys.length > 0).length,
     };
 }
-export function buildSingleDraftValidationReport(workflow, result) {
-    const errorCount = result.structureErrors.length + result.topologyErrors.length + result.semanticErrors.length;
+export function buildSingleDraftValidationReport(workflow, result, concrete) {
+    const errorCount = result.structureErrors.length +
+        result.topologyErrors.length +
+        result.semanticErrors.length +
+        (concrete ? concreteErrorCount(concrete) : 0);
     const warnCount = result.warnings.length;
     const summary = errorCount === 0
         ? `draft valid${warnCount > 0 ? ` (${warnCount} warning${warnCount === 1 ? "" : "s"})` : ""}`
         : `${errorCount} error${errorCount === 1 ? "" : "s"}${warnCount > 0 ? `, ${warnCount} warning${warnCount === 1 ? "" : "s"}` : ""}`;
-    return {
+    // Skipped concrete (ok === null) does NOT drag the aggregate down — it's
+    // informational. Only explicit `false` counts as a failure.
+    const ok = result.ok && concrete?.ok !== false;
+    const report = {
         workflow,
-        ok: result.ok,
+        ok,
         structure_errors: result.structureErrors.map(diagnosticToReport),
         topology_errors: result.topologyErrors.map(diagnosticToReport),
         semantic_errors: result.semanticErrors.map(diagnosticToReport),
@@ -132,10 +138,21 @@ export function buildSingleDraftValidationReport(workflow, result) {
         survey: buildDraftSurveyReport(result.survey),
         summary,
     };
+    if (concrete)
+        report.concrete = concrete;
+    return report;
 }
 function diagnosticToReport(d) {
     return { path: [...d.path], message: d.message };
 }
+function concreteErrorCount(c) {
+    return (c.structure_errors.length +
+        (c.strict_structure_errors?.length ?? 0) +
+        (c.strict_encoding_errors?.length ?? 0) +
+        (c.strict_state_errors?.length ?? 0) +
+        (c.tool_state?.summary.fail ?? 0) +
+        (c.connection_report && !c.connection_report.valid ? 1 : 0));
+}
 export function buildSingleDraftExtractReport(workflow, output, extract, promote, classAfter) {
     const dropped_steps = extract.dropped_steps.map((d) => ({
         path: [...d.path],

package/dist/workflow/report-models.js.map

@@ -1 +1 @@
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package/dist/workflow/semantic-validators.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"semantic-validators.d.ts","sourceRoot":"","sources":["../../src/workflow/semantic-validators.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AAuGH;;;GAGG;AACH,wBAAgB,yBAAyB,CAAC,QAAQ,EAAE,OAAO,GAAG,IAAI,CA4BjE"}
+{"version":3,"file":"semantic-validators.d.ts","sourceRoot":"","sources":["../../src/workflow/semantic-validators.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AAsIH;;;GAGG;AACH,wBAAgB,yBAAyB,CAAC,QAAQ,EAAE,OAAO,GAAG,IAAI,CA6BjE"}

package/dist/workflow/semantic-validators.js

@@ -98,6 +98,37 @@ function validateInputParameter(inputParam) {
         }
     }
 }
+/**
+ * True when a step's `state`/`tool_state` field actually carries content.
+ *
+ * Non-empty semantics: null/undefined, an empty object, and a blank or `{}`
+ * JSON string all count as unspecified — so an empty `state: {}` left by
+ * conversion does not falsely conflict with a populated `tool_state`. Mirrors
+ * gxformat2 `_semantic_validators._state_is_specified`.
+ */
+function _stateIsSpecified(value) {
+    if (value == null)
+        return false;
+    if (typeof value === "string") {
+        const s = value.trim();
+        return s !== "" && s !== "{}";
+    }
+    if (typeof value === "object")
+        return Object.keys(value).length > 0;
+    return Boolean(value);
+}
+/**
+ * Validate cross-field rules on a single workflow step.
+ *
+ * Enforces that `state` and `tool_state` are mutually exclusive (the schema doc
+ * says "Only one or the other should be specified") — they are two encodings of
+ * the same tool state, so carrying both is ambiguous.
+ */
+function validateStep(step) {
+    if (_stateIsSpecified(step.state) && _stateIsSpecified(step.tool_state)) {
+        throw new Error("Workflow step specifies both 'state' and 'tool_state'; only one may be set");
+    }
+}
 /**
  * Walk a (lax or strict) GalaxyWorkflow dict and validate cross-field rules.
  * Recurses into inline subworkflows under step.run.
@@ -126,6 +157,7 @@ export function validateWorkflowSemantics(workflow) {
     for (const step of iterSteps) {
         if (!step || typeof step !== "object")
             continue;
+        validateStep(step);
         const run = step.run;
         if (run &&
             typeof run === "object" &&

package/dist/workflow/semantic-validators.js.map

@@ -1 +1 @@
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package/dist/workflow/state-merge.d.ts

@@ -9,8 +9,29 @@
  * for backward compatibility.
  */
 import type { ToolParameterModel } from "../schema/bundle-types.js";
+import type { NormalizedFormat2StepInput } from "./normalized/format2.js";
 import { flatStatePath, keysStartingWith, repeatInputsToArray, selectWhichWhen } from "./walk-helpers.js";
 export { flatStatePath, keysStartingWith, repeatInputsToArray, selectWhichWhen };
+/**
+ * Build the connections map for a format2 step's `in` block so a verbatim
+ * native `tool_state` block can be validated through the native path.
+ *
+ * injectConnectionsIntoState consumes only the *keys* of this map — it matches
+ * them against state paths and substitutes ConnectedValue markers — so the value
+ * is a bare presence marker. The connection's source is intentionally irrelevant
+ * here; encoding it would be dead computation.
+ */
+export declare function nativeConnectionsFromFormat2In(inputs: readonly NormalizedFormat2StepInput[]): Record<string, true>;
+export interface InjectConnectionsOptions {
+    /**
+     * Target the `workflow_step_linked` representation. A connected `multiple`
+     * select is encoded there as a single-element list `[{ConnectedValue}]` (the
+     * select-multiple linked schema accepts ConnectedValue only as an array item,
+     * per Galaxy's parameter_specification.yml), whereas every other parameter —
+     * and the native representation — uses a bare `{ConnectedValue}`.
+     */
+    linked?: boolean;
+}
 /**
  * Inject ConnectedValue markers into a state dict for all connections.
  *
@@ -20,7 +41,7 @@ export { flatStatePath, keysStartingWith, repeatInputsToArray, selectWhichWhen }
  *
  * @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>;
+export declare function injectConnectionsIntoState(toolInputs: ToolParameterModel[], state: Record<string, unknown>, connections: Record<string, unknown>, options?: InjectConnectionsOptions): Record<string, unknown>;
 /**
  * Strip ConnectedValue markers from a state dict using the parameter tree.
  *

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

@@ -1 +1 @@
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+{"version":3,"file":"state-merge.d.ts","sourceRoot":"","sources":["../../src/workflow/state-merge.ts"],"names":[],"mappings":"AAAA;;;;;;;;;GASG;AAEH,OAAO,KAAK,EAAE,kBAAkB,EAAE,MAAM,2BAA2B,CAAC;AACpE,OAAO,KAAK,EAAE,0BAA0B,EAAE,MAAM,yBAAyB,CAAC;AAG1E,OAAO,EACL,aAAa,EACb,gBAAgB,EAChB,mBAAmB,EACnB,eAAe,EAChB,MAAM,mBAAmB,CAAC;AAG3B,OAAO,EAAE,aAAa,EAAE,gBAAgB,EAAE,mBAAmB,EAAE,eAAe,EAAE,CAAC;AAIjF;;;;;;;;GAQG;AACH,wBAAgB,8BAA8B,CAC5C,MAAM,EAAE,SAAS,0BAA0B,EAAE,GAC5C,MAAM,CAAC,MAAM,EAAE,IAAI,CAAC,CAQtB;AAID,MAAM,WAAW,wBAAwB;IACvC;;;;;;OAMG;IACH,MAAM,CAAC,EAAE,OAAO,CAAC;CAClB;AAOD;;;;;;;;GAQG;AACH,wBAAgB,0BAA0B,CACxC,UAAU,EAAE,kBAAkB,EAAE,EAChC,KAAK,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAC9B,WAAW,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EACpC,OAAO,CAAC,EAAE,wBAAwB,GACjC,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAoBzB;AAID;;;;;;GAMG;AACH,wBAAgB,oBAAoB,CAClC,UAAU,EAAE,kBAAkB,EAAE,EAChC,KAAK,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAC7B,IAAI,CAWN"}

package/dist/workflow/state-merge.js

@@ -13,7 +13,29 @@ 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 ---
+// --- Connection-key construction ---
+/**
+ * Build the connections map for a format2 step's `in` block so a verbatim
+ * native `tool_state` block can be validated through the native path.
+ *
+ * injectConnectionsIntoState consumes only the *keys* of this map — it matches
+ * them against state paths and substitutes ConnectedValue markers — so the value
+ * is a bare presence marker. The connection's source is intentionally irrelevant
+ * here; encoding it would be dead computation.
+ */
+export function nativeConnectionsFromFormat2In(inputs) {
+    const connections = {};
+    for (const input of inputs) {
+        if (input.id && input.source) {
+            connections[input.id] = true;
+        }
+    }
+    return connections;
+}
+function isMultipleSelect(input) {
+    const p = input;
+    return p.parameter_type === "gx_select" && p.multiple === true;
+}
 /**
  * Inject ConnectedValue markers into a state dict for all connections.
  *
@@ -23,12 +45,14 @@ export { flatStatePath, keysStartingWith, repeatInputsToArray, selectWhichWhen }
  *
  * @returns remaining unmatched connection paths (empty if all consumed)
  */
-export function injectConnectionsIntoState(toolInputs, state, connections) {
+export function injectConnectionsIntoState(toolInputs, state, connections, options) {
     const remaining = { ...connections };
-    const result = walkNativeState(connections, toolInputs, state, (_input, value, statePath) => {
+    const result = walkNativeState(connections, toolInputs, state, (input, value, statePath) => {
         if (statePath in remaining) {
             delete remaining[statePath];
-            return { ...CONNECTED_VALUE };
+            return options?.linked && isMultipleSelect(input)
+                ? [{ ...CONNECTED_VALUE }]
+                : { ...CONNECTED_VALUE };
         }
         return value === undefined ? SKIP_VALUE : value;
     }, { preserveUnknownKeys: true });

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

@@ -1 +1 @@
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package/dist/workflow/stateful-convert.d.ts.map

@@ -1 +1 @@
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+{"version":3,"file":"stateful-convert.d.ts","sourceRoot":"","sources":["../../src/workflow/stateful-convert.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAEH,OAAO,KAAK,EACV,kBAAkB,EAGnB,MAAM,2BAA2B,CAAC;AACnC,OAAO,KAAK,EAAE,oBAAoB,EAAE,MAAM,wBAAwB,CAAC;AAQnE;;;;;GAKG;AACH,wBAAgB,kBAAkB,CAAC,SAAS,EAAE,kBAAkB,EAAE,KAAK,EAAE,OAAO,GAAG,OAAO,CA8BzF;AAED;;;;;GAKG;AACH,wBAAgB,kBAAkB,CAAC,SAAS,EAAE,kBAAkB,EAAE,KAAK,EAAE,OAAO,GAAG,OAAO,CAqBzF;AAID,MAAM,WAAW,qBAAqB;IACpC,KAAK,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAAC;IAC/B,EAAE,EAAE,MAAM,CAAC,MAAM,EAAE,MAAM,CAAC,CAAC;CAC5B;AAUD;;;;;;;;;GASG;AACH,wBAAgB,qBAAqB,CACnC,UAAU,EAAE,oBAAoB,EAChC,UAAU,EAAE,kBAAkB,EAAE,GAC/B,qBAAqB,CAqEvB;AAID;;;;;GAKG;AACH,wBAAgB,mBAAmB,CACjC,UAAU,EAAE,kBAAkB,EAAE,EAChC,KAAK,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAC7B,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,CAMzB"}