npm - @galaxy-tool-util/schema - Versions diffs - 1.13.1 → 1.14.0 - Mend

@galaxy-tool-util/schema 1.13.1 → 1.14.0

This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.

Files changed (57) hide show

package/dist/index.d.ts +4 -2
package/dist/index.d.ts.map +1 -1
package/dist/index.js +4 -2
package/dist/index.js.map +1 -1
package/dist/test-format/tests.schema.generated.d.ts +47 -0
package/dist/test-format/tests.schema.generated.d.ts.map +1 -1
package/dist/test-format/tests.schema.generated.js +62 -0
package/dist/test-format/tests.schema.generated.js.map +1 -1
package/dist/workflow/draft-checks.d.ts.map +1 -1
package/dist/workflow/draft-checks.js +105 -59
package/dist/workflow/draft-checks.js.map +1 -1
package/dist/workflow/index.d.ts +4 -2
package/dist/workflow/index.d.ts.map +1 -1
package/dist/workflow/index.js +4 -2
package/dist/workflow/index.js.map +1 -1
package/dist/workflow/layout-properties.d.ts +10 -0
package/dist/workflow/layout-properties.d.ts.map +1 -0
package/dist/workflow/layout-properties.js +112 -0
package/dist/workflow/layout-properties.js.map +1 -0
package/dist/workflow/layout.d.ts +84 -0
package/dist/workflow/layout.d.ts.map +1 -0
package/dist/workflow/layout.js +356 -0
package/dist/workflow/layout.js.map +1 -0
package/dist/workflow/lint-rules.d.ts +6 -0
package/dist/workflow/lint-rules.d.ts.map +1 -1
package/dist/workflow/lint-rules.js +6 -0
package/dist/workflow/lint-rules.js.map +1 -1
package/dist/workflow/lint.d.ts +1 -1
package/dist/workflow/lint.d.ts.map +1 -1
package/dist/workflow/lint.js +83 -15
package/dist/workflow/lint.js.map +1 -1
package/dist/workflow/lint_profiles.yml +1 -0
package/dist/workflow/normalized/expanded.d.ts +12 -0
package/dist/workflow/normalized/expanded.d.ts.map +1 -1
package/dist/workflow/normalized/expanded.js +42 -1
package/dist/workflow/normalized/expanded.js.map +1 -1
package/dist/workflow/normalized/index.d.ts +2 -2
package/dist/workflow/normalized/index.d.ts.map +1 -1
package/dist/workflow/normalized/index.js +2 -2
package/dist/workflow/normalized/index.js.map +1 -1
package/dist/workflow/normalized/labels.d.ts +7 -0
package/dist/workflow/normalized/labels.d.ts.map +1 -1
package/dist/workflow/normalized/labels.js +11 -0
package/dist/workflow/normalized/labels.js.map +1 -1
package/dist/workflow/normalized/toFormat2.d.ts +1 -0
package/dist/workflow/normalized/toFormat2.d.ts.map +1 -1
package/dist/workflow/normalized/toFormat2.js +4 -12
package/dist/workflow/normalized/toFormat2.js.map +1 -1
package/dist/workflow/normalized/toNative.d.ts +16 -1
package/dist/workflow/normalized/toNative.d.ts.map +1 -1
package/dist/workflow/normalized/toNative.js +23 -6
package/dist/workflow/normalized/toNative.js.map +1 -1
package/dist/workflow/semantic-validators.d.ts +9 -0
package/dist/workflow/semantic-validators.d.ts.map +1 -1
package/dist/workflow/semantic-validators.js +27 -14
package/dist/workflow/semantic-validators.js.map +1 -1
package/package.json +1 -1

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

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package/dist/workflow/normalized/toNative.d.ts CHANGED Viewed

@@ -4,7 +4,7 @@
  * Port of gxformat2/normalized/_conversion.py to_native + helpers.
  */
 import type { NormalizedNativeWorkflow } from "./native.js";
-import type { NormalizedFormat2Step } from "./format2.js";
+import type { NormalizedFormat2Step, NormalizedFormat2Input } from "./format2.js";
 export interface ToNativeOptions {
     /**
      * Per-step callback: given a format2 step and its merged pre-native
@@ -17,4 +17,19 @@ export interface ToNativeOptions {
  * Convert a Format2 workflow to normalized native Galaxy format.
  */
 export declare function toNative(raw: unknown, options?: ToNativeOptions): NormalizedNativeWorkflow;
+/**
+ * Native step label for a Format2 input at `orderIndex`.
+ *
+ * Inputs are labeled by `id`, falling back to `Input <orderIndex>`.
+ * Sentinel labels (`_unlabeled_*`) are cleared to null.
+ */
+export declare function nativeInputLabel(inp: NormalizedFormat2Input, orderIndex: number): string | null;
+/**
+ * Native step label for a Format2 step.
+ *
+ * An explicit `label` wins; otherwise a non-numeric `id` is a user label and
+ * numeric ids are auto-assigned indices. Sentinel labels (`_unlabeled_*`) are
+ * cleared to null.
+ */
+export declare function nativeStepLabel(step: NormalizedFormat2Step): string | null | undefined;
 //# sourceMappingURL=toNative.d.ts.map

package/dist/workflow/normalized/toNative.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"version":3,"file":"toNative.d.ts","sourceRoot":"","sources":["../../../src/workflow/normalized/toNative.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,KAAK,EAAE,wBAAwB,EAAwB,MAAM,aAAa,CAAC;AAClF,OAAO,KAAK,EAEV,qBAAqB,~~EAGtB~~,MAAM,cAAc,CAAC;AA2FtB,MAAM,WAAW,eAAe;IAC9B;;;;OAIG;IACH,mBAAmB,CAAC,EAAE,CACpB,IAAI,EAAE,qBAAqB,EAC3B,KAAK,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,KAC3B,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,IAAI,CAAC;CACrC;AAED;;GAEG;AACH,wBAAgB,QAAQ,CAAC,GAAG,EAAE,OAAO,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,wBAAwB,CAS1F"}
1	+ {"version":3,"file":"toNative.d.ts","sourceRoot":"","sources":["../../../src/workflow/normalized/toNative.ts"],"names":[],"mappings":"AAAA;;;;GAIG;AAEH,OAAO,KAAK,EAAE,wBAAwB,EAAwB,MAAM,aAAa,CAAC;AAClF,OAAO,KAAK,EAEV,qBAAqB,EACrB,sBAAsB,EAEvB,MAAM,cAAc,CAAC;AA2FtB,MAAM,WAAW,eAAe;IAC9B;;;;OAIG;IACH,mBAAmB,CAAC,EAAE,CACpB,IAAI,EAAE,qBAAqB,EAC3B,KAAK,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,KAC3B,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,IAAI,CAAC;CACrC;AAED;;GAEG;AACH,wBAAgB,QAAQ,CAAC,GAAG,EAAE,OAAO,EAAE,OAAO,CAAC,EAAE,eAAe,GAAG,wBAAwB,CAS1F;AA4kBD;;;;;GAKG;AACH,wBAAgB,gBAAgB,CAAC,GAAG,EAAE,sBAAsB,EAAE,UAAU,EAAE,MAAM,GAAG,MAAM,GAAG,IAAI,CAG/F;AAED;;;;;;GAMG;AACH,wBAAgB,eAAe,CAAC,IAAI,EAAE,qBAAqB,GAAG,MAAM,GAAG,IAAI,GAAG,SAAS,CAUtF"}

package/dist/workflow/normalized/toNative.js CHANGED Viewed

@@ -148,7 +148,7 @@ function _buildNativeWorkflow(wf, ctx) {
 // --- Input step building ---
 function _buildInputStep(inp, orderIndex) {
     const rawLabel = inp.id || `Input ${orderIndex}`;
-    const label = isUnlabeled(rawLabel) ? undefined : rawLabel;
+    const label = nativeInputLabel(inp, orderIndex);
     let inputType = inp.type;
     let multiple = false;
     if (Array.isArray(inputType)) {
@@ -299,7 +299,7 @@ function _buildToolStep(step, orderIndex, ctx) {
     return {
         id: orderIndex,
         type: "tool",
-        label: _stepLabel(step),
+        label: nativeStepLabel(step),
         name: toolId ?? toolRepresentation?.name ?? "User Defined Tool",
         annotation: step.doc ?? "",
         tool_id: toolId,
@@ -345,7 +345,7 @@ function _buildSubworkflowStep(step, orderIndex, ctx) {
     return {
         id: orderIndex,
         type: "subworkflow",
-        label: _stepLabel(step),
+        label: nativeStepLabel(step),
         annotation: step.doc ?? "",
         tool_state: {},
         subworkflow,
@@ -370,7 +370,7 @@ function _buildPauseStep(step, orderIndex, ctx) {
     return {
         id: orderIndex,
         type: "pause",
-        label: _stepLabel(step),
+        label: nativeStepLabel(step),
         name,
         annotation: step.doc ?? "",
         tool_state: { name },
@@ -399,7 +399,7 @@ function _buildPickValueStep(step, orderIndex, ctx) {
     return {
         id: orderIndex,
         type: "pick_value",
-        label: _stepLabel(step),
+        label: nativeStepLabel(step),
         name,
         annotation: step.doc ?? "",
         tool_state: toolState,
@@ -581,7 +581,24 @@ function _buildNativeComments(wf, ctx) {
     return result;
 }
 // --- Helpers ---
-function _stepLabel(step) {
+/**
+ * Native step label for a Format2 input at `orderIndex`.
+ *
+ * Inputs are labeled by `id`, falling back to `Input <orderIndex>`.
+ * Sentinel labels (`_unlabeled_*`) are cleared to null.
+ */
+export function nativeInputLabel(inp, orderIndex) {
+    const rawLabel = inp.id || `Input ${orderIndex}`;
+    return isUnlabeled(rawLabel) ? null : rawLabel;
+}
+/**
+ * Native step label for a Format2 step.
+ *
+ * An explicit `label` wins; otherwise a non-numeric `id` is a user label and
+ * numeric ids are auto-assigned indices. Sentinel labels (`_unlabeled_*`) are
+ * cleared to null.
+ */
+export function nativeStepLabel(step) {
     if (step.label != null) {
         if (isUnlabeled(step.label))
             return null;

package/dist/workflow/normalized/toNative.js.map CHANGED Viewed

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

@@ -10,6 +10,15 @@
  * (runtime tool-state validation): these are structural-but-cross-field
  * Format2 rules.
  */
+export declare function validateInputParameter(inputParam: unknown): void;
+/**
+ * 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.
+ */
+export declare function validateStep(step: Record<string, unknown>): void;
 /**
  * Walk a (lax or strict) GalaxyWorkflow dict and validate cross-field rules.
  * Recurses into inline subworkflows under step.run.

package/dist/workflow/semantic-validators.d.ts.map CHANGED Viewed

	@@ -1 +1 @@
1	- {"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~~"}
1	+ {"version":3,"file":"semantic-validators.d.ts","sourceRoot":"","sources":["../../src/workflow/semantic-validators.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AA0DH,wBAAgB,sBAAsB,CAAC,UAAU,EAAE,OAAO,GAAG,IAAI,CA2DhE;AAoBD;;;;;;GAMG;AACH,wBAAgB,YAAY,CAAC,IAAI,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,IAAI,CAIhE;AAED;;;GAGG;AACH,wBAAgB,yBAAyB,CAAC,QAAQ,EAAE,OAAO,GAAG,IAAI,CA+BjE"}

package/dist/workflow/semantic-validators.js CHANGED Viewed

@@ -27,8 +27,9 @@ function _columnDefaultMatchesType(columnType, value) {
     return true;
 }
 function validateColumnDefinition(column) {
-    if (!column || typeof column !== "object")
-        return;
+    if (!column || typeof column !== "object" || Array.isArray(column)) {
+        throw new Error("Expected a mapping for semantic validation");
+    }
     const col = column;
     const name = col.name;
     if (typeof name === "string" && !COLUMN_NAME_RE.test(name)) {
@@ -41,8 +42,11 @@ function validateColumnDefinition(column) {
     }
     for (const field of ["restrictions", "suggestions"]) {
         const values = col[field];
-        if (!Array.isArray(values))
+        if (values == null || (Array.isArray(values) && values.length === 0))
             continue;
+        if (!Array.isArray(values)) {
+            throw new Error(`Sample sheet column '${String(name)}' ${field} must be a list`);
+        }
         for (const v of values) {
             if (!_columnDefaultMatchesType(columnType, v)) {
                 throw new Error(`Sample sheet column '${String(name)}' ${field} entry ${JSON.stringify(v)} does not match column type ${JSON.stringify(columnType)}`);
@@ -57,14 +61,20 @@ function _typeList(typeValue) {
         return [];
     return [String(typeValue)];
 }
-function validateInputParameter(inputParam) {
+export function validateInputParameter(inputParam) {
     if (!inputParam || typeof inputParam !== "object")
         return;
     const data = inputParam;
     const typeValues = _typeList(data.type);
     const isTextOnly = typeValues.length > 0 && typeValues.every((t) => TEXT_TYPE_VALUES.has(t));
     const isCollectionOnly = typeValues.length > 0 && typeValues.every((t) => COLLECTION_TYPE_VALUES.has(t));
+    if (data.collection_type != null && typeof data.collection_type !== "string") {
+        throw new Error("collection_type must be a string");
+    }
     const columnDefinitions = data.column_definitions;
+    if (columnDefinitions != null && !Array.isArray(columnDefinitions)) {
+        throw new Error("column_definitions must be a list");
+    }
     if (Array.isArray(columnDefinitions) && columnDefinitions.length > 0) {
         if (!isCollectionOnly && typeValues.length > 0) {
             throw new Error(`column_definitions is only valid on collection inputs, got type=${JSON.stringify(data.type)}`);
@@ -77,6 +87,17 @@ function validateInputParameter(inputParam) {
             validateColumnDefinition(column);
         }
     }
+    // Record-input fields validation (mirrors gxformat2 #216).
+    const fields = data.fields;
+    if (Array.isArray(fields) && fields.length > 0) {
+        if (!isCollectionOnly && typeValues.length > 0) {
+            throw new Error(`fields is only valid on collection inputs, got type=${JSON.stringify(data.type)}`);
+        }
+        const collectionType = typeof data.collection_type === "string" ? data.collection_type : "";
+        if (!collectionType.split(":").some((part) => part === "record")) {
+            throw new Error(`fields is only valid on record-typed collection inputs, got collection_type=${JSON.stringify(data.collection_type)}`);
+        }
+    }
     for (const field of ["restrictions", "suggestions", "restrictOnConnections"]) {
         const value = data[field];
         if (value == null)
@@ -89,14 +110,6 @@ function validateInputParameter(inputParam) {
             throw new Error(`${field} is only valid on text/string inputs, got type=${JSON.stringify(data.type)}`);
         }
     }
-    // Record-input fields validation (mirrors gxformat2 #216).
-    const fields = data.fields;
-    if (Array.isArray(fields) && fields.length > 0) {
-        const collectionType = typeof data.collection_type === "string" ? data.collection_type : "";
-        if (!collectionType.split(":").some((part) => part === "record")) {
-            throw new Error(`fields is only valid on record-typed collection inputs, got collection_type=${JSON.stringify(data.collection_type)}`);
-        }
-    }
 }
 /**
  * True when a step's `state`/`tool_state` field actually carries content.
@@ -124,7 +137,7 @@ function _stateIsSpecified(value) {
  * 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) {
+export 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");
     }
@@ -161,7 +174,7 @@ export function validateWorkflowSemantics(workflow) {
         const run = step.run;
         if (run &&
             typeof run === "object" &&
-            run.class === "GalaxyWorkflow") {
+            ["GalaxyWorkflow", "GalaxyWorkflowDraft"].includes(String(run.class))) {
             validateWorkflowSemantics(run);
         }
     }

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

	@@ -1 +1 @@
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1	+ 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package/package.json CHANGED Viewed

@@ -1,6 +1,6 @@
 {
   "name": "@galaxy-tool-util/schema",
-  "version": "1.13.1",
+  "version": "1.14.0",
   "description": "Effect Schema parameter types and validators for Galaxy tools",
   "type": "module",
   "exports": {