@galaxy-tool-util/schema 1.10.1 → 1.12.0

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

@@ -1 +1 @@
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+{"version":3,"file":"stateful-convert.js","sourceRoot":"","sources":["../../src/workflow/stateful-convert.ts"],"names":[],"mappings":"AAAA;;;;;;;GAOG;AAQH,OAAO,EAAE,eAAe,EAAE,gBAAgB,EAAE,UAAU,EAAE,MAAM,aAAa,CAAC;AAE5E,OAAO,EAAE,gBAAgB,EAAE,cAAc,EAAE,MAAM,sBAAsB,CAAC;AACxE,OAAO,EAAE,SAAS,EAAE,WAAW,EAAE,gBAAgB,EAAE,gBAAgB,EAAE,MAAM,gBAAgB,CAAC;AAE5F,2BAA2B;AAE3B;;;;;GAKG;AACH,MAAM,UAAU,kBAAkB,CAAC,SAA6B,EAAE,KAAc;IAC9E,MAAM,SAAS,GAAG,SAAS,CAAC,cAAc,CAAC;IAE3C,IAAI,SAAS,KAAK,YAAY,IAAI,SAAS,KAAK,UAAU,EAAE,CAAC;QAC3D,OAAO,WAAW,CAAC,KAAK,CAAC,IAAI,KAAK,CAAC;IACrC,CAAC;IAED,IAAI,SAAS,KAAK,YAAY,EAAE,CAAC;QAC/B,OAAO,SAAS,CAAC,KAAK,CAAC,IAAI,KAAK,CAAC;IACnC,CAAC;IAED,IAAI,SAAS,KAAK,WAAW,EAAE,CAAC;QAC9B,MAAM,MAAM,GAAG,SAAiC,CAAC;QACjD,IAAI,MAAM,CAAC,QAAQ,EAAE,CAAC;YACpB,OAAO,gBAAgB,CAAC,KAAK,CAAC,IAAI,KAAK,CAAC;QAC1C,CAAC;QACD,OAAO,KAAK,CAAC;IACf,CAAC;IAED,IAAI,SAAS,KAAK,gBAAgB,EAAE,CAAC;QACnC,MAAM,GAAG,GAAG,SAAqC,CAAC;QAClD,IAAI,GAAG,CAAC,QAAQ,EAAE,CAAC;YACjB,OAAO,gBAAgB,CAAC,KAAK,CAAC,IAAI,KAAK,CAAC;QAC1C,CAAC;QACD,OAAO,WAAW,CAAC,KAAK,CAAC,IAAI,KAAK,CAAC;IACrC,CAAC;IAED,mEAAmE;IACnE,gDAAgD;IAChD,OAAO,KAAK,CAAC;AACf,CAAC;AAED;;;;;GAKG;AACH,MAAM,UAAU,kBAAkB,CAAC,SAA6B,EAAE,KAAc;IAC9E,MAAM,SAAS,GAAG,SAAS,CAAC,cAAc,CAAC;IAE3C,IAAI,SAAS,KAAK,WAAW,EAAE,CAAC;QAC9B,MAAM,MAAM,GAAG,SAAiC,CAAC;QACjD,IAAI,MAAM,CAAC,QAAQ,IAAI,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE,CAAC;YAC5C,OAAO,KAAK,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC;QAC3B,CAAC;QACD,OAAO,KAAK,CAAC;IACf,CAAC;IAED,IAAI,SAAS,KAAK,gBAAgB,EAAE,CAAC;QACnC,MAAM,GAAG,GAAG,SAAqC,CAAC;QAClD,IAAI,GAAG,CAAC,QAAQ,IAAI,KAAK,CAAC,OAAO,CAAC,KAAK,CAAC,EAAE,CAAC;YACzC,OAAO,KAAK,CAAC,GAAG,CAAC,MAAM,CAAC,CAAC;QAC3B,CAAC;QACD,OAAO,OAAO,KAAK,KAAK,QAAQ,CAAC,CAAC,CAAC,MAAM,CAAC,KAAK,CAAC,CAAC,CAAC,CAAC,KAAK,CAAC;IAC3D,CAAC;IAED,oCAAoC;IACpC,OAAO,KAAK,CAAC;AACf,CAAC;AASD,sEAAsE;AACtE,MAAM,gBAAgB,GAAG,IAAI,GAAG,CAAC,CAAC,SAAS,EAAE,oBAAoB,CAAC,CAAC,CAAC;AAEpE,yEAAyE;AACzE,SAAS,eAAe,CAAC,SAA6B;IACpD,OAAQ,SAAoC,CAAC,QAAQ,KAAK,IAAI,CAAC;AACjE,CAAC;AAED;;;;;;;;;GASG;AACH,MAAM,UAAU,qBAAqB,CACnC,UAAgC,EAChC,UAAgC;IAEhC,MAAM,SAAS,GAAG,UAAU,CAAC,UAAU,CAAC;IACxC,uEAAuE;IACvE,MAAM,gBAAgB,GAAG,UAAU,CAAC,iBAA4C,CAAC;IACjF,MAAM,cAAc,GAAG,UAAU,CAAC,eAAe,CAAC;IAClD,MAAM,OAAO,GAA2B,EAAE,CAAC;IAE3C,MAAM,YAAY,GAAiB,CAAC,SAAS,EAAE,KAAK,EAAE,SAAS,EAAE,EAAE;QACjE,MAAM,SAAS,GAAG,SAAS,CAAC,cAAc,CAAC;QAE3C,oEAAoE;QACpE,IAAI,gBAAgB,CAAC,GAAG,CAAC,SAAS,CAAC,EAAE,CAAC;YACpC,IAAI,cAAc,CAAC,GAAG,CAAC,SAAS,CAAC,IAAI,gBAAgB,CAAC,KAAK,CAAC,EAAE,CAAC;gBAC7D,0FAA0F;gBAC1F,OAAO,UAAU,CAAC;YACpB,CAAC;YACD,IAAI,cAAc,CAAC,KAAK,CAAC,EAAE,CAAC;gBAC1B,iFAAiF;gBACjF,IAAI,CAAC,eAAe,CAAC,SAAS,CAAC,EAAE,CAAC;oBAChC,OAAO,CAAC,SAAS,CAAC,GAAG,eAAe,CAAC;gBACvC,CAAC;gBACD,OAAO,UAAU,CAAC;YACpB,CAAC;YACD,OAAO,UAAU,CAAC;QACpB,CAAC;QAED,qCAAqC;QACrC,IAAI,SAAS,KAAK,UAAU,EAAE,CAAC;YAC7B,IAAI,KAAK,IAAI,IAAI,IAAI,gBAAgB,CAAC,KAAK,CAAC,EAAE,CAAC;gBAC7C,IAAI,gBAAgB,CAAC,KAAK,CAAC,IAAI,cAAc,CAAC,GAAG,CAAC,SAAS,CAAC,EAAE,CAAC;oBAC7D,kDAAkD;gBACpD,CAAC;gBACD,OAAO,UAAU,CAAC;YACpB,CAAC;YACD,IAAI,OAAO,KAAK,KAAK,QAAQ,EAAE,CAAC;gBAC9B,IAAI,CAAC;oBACH,OAAO,IAAI,CAAC,KAAK,CAAC,KAAK,CAAC,CAAC;gBAC3B,CAAC;gBAAC,MAAM,CAAC;oBACP,OAAO,KAAK,CAAC;gBACf,CAAC;YACH,CAAC;YACD,OAAO,KAAK,CAAC;QACf,CAAC;QAED,6EAA6E;QAC7E,IAAI,cAAc,CAAC,GAAG,CAAC,SAAS,CAAC,IAAI,gBAAgB,CAAC,KAAK,CAAC,EAAE,CAAC;YAC7D,OAAO,UAAU,CAAC;QACpB,CAAC;QAED,iFAAiF;QACjF,IAAI,cAAc,CAAC,KAAK,CAAC,EAAE,CAAC;YAC1B,IAAI,CAAC,eAAe,CAAC,SAAS,CAAC,EAAE,CAAC;gBAChC,OAAO,CAAC,SAAS,CAAC,GAAG,eAAe,CAAC;YACvC,CAAC;YACD,OAAO,UAAU,CAAC;QACpB,CAAC;QAED,8BAA8B;QAC9B,IAAI,KAAK,KAAK,IAAI,IAAI,KAAK,KAAK,SAAS,IAAI,KAAK,KAAK,MAAM,EAAE,CAAC;YAC9D,OAAO,UAAU,CAAC;QACpB,CAAC;QAED,kBAAkB;QAClB,OAAO,kBAAkB,CAAC,SAAS,EAAE,KAAK,CAAC,CAAC;IAC9C,CAAC,CAAC;IAEF,MAAM,KAAK,GAAG,eAAe,CAAC,gBAAgB,EAAE,UAAU,EAAE,SAAS,EAAE,YAAY,CAAC,CAAC;IAErF,OAAO,EAAE,KAAK,EAAE,EAAE,EAAE,OAAO,EAAE,CAAC;AAChC,CAAC;AAED,sCAAsC;AAEtC;;;;;GAKG;AACH,MAAM,UAAU,mBAAmB,CACjC,UAAgC,EAChC,KAA8B;IAE9B,MAAM,YAAY,GAAiB,CAAC,SAAS,EAAE,KAAK,EAAE,EAAE;QACtD,4EAA4E;QAC5E,qEAAqE;QACrE,wEAAwE;QACxE,+DAA+D;QAC/D,IAAI,KAAK,KAAK,SAAS;YAAE,OAAO,UAAU,CAAC;QAC3C,OAAO,kBAAkB,CAAC,SAAS,EAAE,KAAK,CAAC,CAAC;IAC9C,CAAC,CAAC;IAEF,OAAO,gBAAgB,CAAC,UAAU,EAAE,KAAK,EAAE,YAAY,CAAC,CAAC;AAC3D,CAAC"}

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": "1.12.0",
   "description": "Effect Schema parameter types and validators for Galaxy tools",
   "type": "module",
   "exports": {