@galaxy-tool-util/schema 1.10.1 → 1.13.1

package/dist/workflow/normalized/toNativeStateful.js

@@ -15,6 +15,7 @@
  */
 import { toNative } from "./toNative.js";
 import { encodeStateToNative } from "../stateful-convert.js";
+import { nativeConnectionsFromFormat2In } from "../state-merge.js";
 import { validateFormat2StepState, validateNativeStepState } from "../stateful-validate.js";
 import { makeStepConversionRunner, } from "./stateful-runner.js";
 /**
@@ -35,17 +36,9 @@ export function toNativeStateful(raw, toolInputsResolver) {
             toolId: step.tool_id ?? undefined,
             toolVersion: step.tool_version ?? null,
         }),
-        preValidate: ({ state }, inputs) => {
-            validateFormat2StepState(inputs, state);
-        },
+        preValidate: ({ step, state }, inputs) => validateFormat2StepState(inputs, state, nativeConnectionsFromFormat2In(step.in)),
         convert: ({ state }, inputs) => encodeStateToNative(inputs, state),
-        postValidate: (result, inputs) => {
-            // Reimported native state has no input_connections context here —
-            // the structural toNative pass will re-attach them. We validate the
-            // raw state dict without injected connections; ConnectedValue markers
-            // stripped in the format2 input won't reappear in the walker output.
-            validateNativeStepState(inputs, result);
-        },
+        postValidate: (result, inputs, { step }) => validateNativeStepState(inputs, result, nativeConnectionsFromFormat2In(step.in)),
     });
     const stateEncodeToNative = (step, state) => runner({ step, state });
     const options = { stateEncodeToNative };

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

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

@@ -10,7 +10,7 @@
  */
 import type { DraftValidationResult, DropReason, ExtractResult } from "./draft-checks.js";
 import type { PromoteFullyConcreteDraftsResult } from "./promote-draft.js";
-export type StepStatus = "ok" | "fail" | "skip_tool_not_found" | "skip_replacement_params";
+export type StepStatus = "ok" | "fail" | "skip_tool_not_found" | "skip_replacement_params" | "skip_no_tool_state";
 export declare const SKIP_STATUSES: ReadonlySet<StepStatus>;
 export interface ValidationStepResult {
     step: string;

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

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

@@ -11,6 +11,7 @@
 export const SKIP_STATUSES = new Set([
     "skip_tool_not_found",
     "skip_replacement_params",
+    "skip_no_tool_state",
 ]);
 // ── Builder helpers ──────────────────────────────────────────────────
 /** Compute summary counts for a list of step results. */

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

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

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

@@ -154,6 +154,12 @@ export function convertStateToFormat2(nativeStep, toolInputs) {
  */
 export function encodeStateToNative(toolInputs, state) {
     const leafCallback = (toolInput, value) => {
+        // A leaf absent from format2 state stays absent in native state. The walker
+        // visits every parameter in the selected branch, so without this the
+        // callback would write back `undefined` for keys the source never had —
+        // symmetric with the forward direction, which skips undefined.
+        if (value === undefined)
+            return SKIP_VALUE;
         return reverseScalarValue(toolInput, value);
     };
     return walkFormat2State(toolInputs, state, leafCallback);

package/dist/workflow/stateful-convert.js.map

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

@@ -36,14 +36,21 @@ export declare class ConversionValidationFailure extends Error {
  */
 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).
+ * Validate format2 tool_state after stateful conversion.
+ *
+ * Validation follows the upstream Python two-model pipeline:
+ *
+ * 1. Strip any serialized ConnectedValue markers and validate the stored state
+ *    against `workflow_step`. Every field is optional in this unlinked editor
+ *    representation, but values that are present must still have the right type.
+ * 2. Inject the step's actual `in` connections and validate the effective state
+ *    against `workflow_step_linked`. This restores requiredness while allowing a
+ *    connection marker to satisfy a required leaf.
  *
  * 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;
+export declare function validateFormat2StepState(inputs: ToolParameterModel[], format2State: Record<string, unknown>, inputConnections?: Record<string, unknown>): void;
 /**
  * A single diagnostic produced by tool-state validation.
  *
@@ -70,5 +77,5 @@ export declare function stringContainerDiagnostic(error: StringContainerError):
  * 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[];
+export declare function validateFormat2StepStateStrict(inputs: ToolParameterModel[], format2State: Record<string, unknown>, inputConnections?: Record<string, unknown>): ToolStateDiagnostic[];
 //# sourceMappingURL=stateful-validate.d.ts.map

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

@@ -1 +1 @@
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+{"version":3,"file":"stateful-validate.d.ts","sourceRoot":"","sources":["../../src/workflow/stateful-validate.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AAOH,OAAO,+BAA+B,CAAC;AAEvC,OAAO,KAAK,EAA4B,kBAAkB,EAAE,MAAM,2BAA2B,CAAC;AAE9F,OAAO,EAAE,oBAAoB,EAAE,MAAM,aAAa,CAAC;AAEnD,MAAM,MAAM,eAAe,GAAG,KAAK,GAAG,MAAM,CAAC;AAE7C;;;;GAIG;AACH,qBAAa,2BAA4B,SAAQ,KAAK;aAGlC,KAAK,EAAE,eAAe;aACtB,MAAM,EAAE,MAAM,EAAE;IAHlC,QAAQ,CAAC,IAAI,EAAG,6BAA6B,CAAU;gBAErC,KAAK,EAAE,eAAe,EACtB,MAAM,EAAE,MAAM,EAAE;CAKnC;AA6BD;;;;;;;;GAQG;AACH,wBAAgB,uBAAuB,CACrC,MAAM,EAAE,kBAAkB,EAAE,EAC5B,SAAS,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EAClC,gBAAgB,GAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAM,GAC7C,IAAI,CAaN;AAED;;;;;;;;;;;;;;GAcG;AACH,wBAAgB,wBAAwB,CACtC,MAAM,EAAE,kBAAkB,EAAE,EAC5B,YAAY,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EACrC,gBAAgB,GAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAM,GAC7C,IAAI,CAsBN;AAED;;;;;GAKG;AACH,MAAM,WAAW,mBAAmB;IAClC,4EAA4E;IAC5E,IAAI,EAAE,MAAM,CAAC;IACb,OAAO,EAAE,MAAM,CAAC;IAChB,QAAQ,EAAE,OAAO,GAAG,SAAS,CAAC;CAC/B;AAED;;;;GAIG;AACH,wBAAgB,yBAAyB,CAAC,KAAK,EAAE,oBAAoB,GAAG,mBAAmB,CAO1F;AAED;;;;;;;GAOG;AACH,wBAAgB,8BAA8B,CAC5C,MAAM,EAAE,kBAAkB,EAAE,EAC5B,YAAY,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EACrC,gBAAgB,GAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAM,GAC7C,mBAAmB,EAAE,CAsDvB"}

package/dist/workflow/stateful-validate.js

@@ -39,6 +39,13 @@ function formatIssues(error) {
     const issues = ParseResult.ArrayFormatter.formatErrorSync(error);
     return issues.map((i) => (i.path.length ? `${i.path.join(".")}: ${i.message}` : i.message));
 }
+/** Decode `state` against `model`, throwing a phase-tagged failure on mismatch. */
+function decodeOrThrow(model, state, phase) {
+    const result = S.decodeUnknownEither(model, { onExcessProperty: "ignore" })(state);
+    if (result._tag === "Left") {
+        throw new ConversionValidationFailure(phase, formatIssues(result.left));
+    }
+}
 function buildBundle(inputs) {
     return { parameters: inputs };
 }
@@ -67,32 +74,41 @@ export function validateNativeStepState(inputs, toolState, inputConnections = {}
     if (Object.keys(inputConnections).length > 0) {
         injectConnectionsIntoState(inputs, state, inputConnections);
     }
-    const decode = S.decodeUnknownEither(model, { onExcessProperty: "ignore" });
-    const result = decode(state);
-    if (result._tag === "Left") {
-        throw new ConversionValidationFailure("pre", formatIssues(result.left));
-    }
+    decodeOrThrow(model, state, "pre");
 }
 /**
- * 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).
+ * Validate format2 tool_state after stateful conversion.
+ *
+ * Validation follows the upstream Python two-model pipeline:
+ *
+ * 1. Strip any serialized ConnectedValue markers and validate the stored state
+ *    against `workflow_step`. Every field is optional in this unlinked editor
+ *    representation, but values that are present must still have the right type.
+ * 2. Inject the step's actual `in` connections and validate the effective state
+ *    against `workflow_step_linked`. This restores requiredness while allowing a
+ *    connection marker to satisfy a required leaf.
  *
  * Returns silently on success or if the schema cannot be built. Throws
  * `ConversionValidationFailure` with phase="post" on validation failure.
  */
-export function validateFormat2StepState(inputs, format2State) {
+export function validateFormat2StepState(inputs, format2State, inputConnections = {}) {
     const bundle = buildBundle(inputs);
-    const model = createFieldModel(bundle, "workflow_step");
-    if (!model)
+    const unlinkedModel = createFieldModel(bundle, "workflow_step");
+    const linkedModel = createFieldModel(bundle, "workflow_step_linked");
+    if (!unlinkedModel || !linkedModel)
         return;
     const state = deepClone(format2State);
     stripConnectedValues(inputs, state);
-    const decode = S.decodeUnknownEither(model, { onExcessProperty: "ignore" });
-    const result = decode(state);
-    if (result._tag === "Left") {
-        throw new ConversionValidationFailure("post", formatIssues(result.left));
+    decodeOrThrow(unlinkedModel, state, "post");
+    const linkedState = deepClone(state);
+    const remaining = injectConnectionsIntoState(inputs, linkedState, inputConnections, {
+        linked: true,
+    });
+    const unmatched = Object.keys(remaining);
+    if (unmatched.length > 0) {
+        throw new ConversionValidationFailure("post", unmatched.map((path) => `${path}: input connection does not match a tool parameter`));
     }
+    decodeOrThrow(linkedModel, linkedState, "post");
 }
 /**
  * Map a {@link StringContainerError} thrown by the walker into a located
@@ -115,10 +131,11 @@ export function stringContainerDiagnostic(error) {
  * corresponding parameter definition. Returns an empty array if the schema
  * cannot be built or validation passes.
  */
-export function validateFormat2StepStateStrict(inputs, format2State) {
+export function validateFormat2StepStateStrict(inputs, format2State, inputConnections = {}) {
     const bundle = buildBundle(inputs);
-    const model = createFieldModel(bundle, "workflow_step");
-    if (!model)
+    const unlinkedModel = createFieldModel(bundle, "workflow_step");
+    const linkedModel = createFieldModel(bundle, "workflow_step_linked");
+    if (!unlinkedModel || !linkedModel)
         return [];
     const state = deepClone(format2State);
     // The walker rejects a scalar where a container is expected by throwing; the
@@ -133,16 +150,37 @@ export function validateFormat2StepStateStrict(inputs, format2State) {
         }
         throw error;
     }
-    const decode = S.decodeUnknownEither(model, { onExcessProperty: "error" });
-    const result = decode(state);
-    if (result._tag === "Left") {
-        const issues = ParseResult.ArrayFormatter.formatErrorSync(result.left);
-        return issues.map((i) => ({
+    const decodeStrict = (model, value) => {
+        const result = S.decodeUnknownEither(model, { onExcessProperty: "error" })(value);
+        if (result._tag === "Right")
+            return [];
+        return ParseResult.ArrayFormatter.formatErrorSync(result.left).map((i) => ({
             path: i.path.map(String).join("."),
             message: i.message,
             severity: "error",
         }));
+    };
+    const unlinkedDiagnostics = decodeStrict(unlinkedModel, state);
+    if (unlinkedDiagnostics.length > 0)
+        return unlinkedDiagnostics;
+    const linkedState = deepClone(state);
+    let remaining;
+    try {
+        remaining = injectConnectionsIntoState(inputs, linkedState, inputConnections, { linked: true });
+    }
+    catch (error) {
+        if (error instanceof StringContainerError) {
+            return [stringContainerDiagnostic(error)];
+        }
+        throw error;
     }
-    return [];
+    const unmatchedDiagnostics = Object.keys(remaining).map((path) => ({
+        path: path.split("|").join("."),
+        message: "Input connection does not match a tool parameter.",
+        severity: "error",
+    }));
+    if (unmatchedDiagnostics.length > 0)
+        return unmatchedDiagnostics;
+    return decodeStrict(linkedModel, linkedState);
 }
 //# sourceMappingURL=stateful-validate.js.map

package/dist/workflow/stateful-validate.js.map

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package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@galaxy-tool-util/schema",
-  "version": "1.10.1",
+  "version": "1.13.1",
   "description": "Effect Schema parameter types and validators for Galaxy tools",
   "type": "module",
   "exports": {