@galaxy-tool-util/schema 1.13.1 → 1.15.0

package/dist/workflow/semantic-validators.js

@@ -10,8 +10,15 @@
  * (runtime tool-state validation): these are structural-but-cross-field
  * Format2 rules.
  */
+import { inputTypesDeclaring } from "./input-parameter.js";
 const COLUMN_NAME_RE = /^[\w\-_ ?]*$/;
-const TEXT_TYPE_VALUES = new Set(["text", "string"]);
+// Galaxy offers `multiple` on neither.
+const SCALAR_ONLY_TYPE_VALUES = new Set(["color", "directory_uri"]);
+// Parameter fields valid only on the input types whose schema declares them.
+const PARAMETER_FIELD_TYPE_VALUES = new Map(["restrictions", "suggestions", "restrictOnConnections", "validators"].map((field) => [
+    field,
+    inputTypesDeclaring(field),
+]));
 const COLLECTION_TYPE_VALUES = new Set(["collection", "data_collection", "data_collection_input"]);
 function _columnDefaultMatchesType(columnType, value) {
     if (value == null)
@@ -27,8 +34,9 @@ function _columnDefaultMatchesType(columnType, value) {
     return true;
 }
 function validateColumnDefinition(column) {
-    if (!column || typeof column !== "object")
-        return;
+    if (!column || typeof column !== "object" || Array.isArray(column)) {
+        throw new Error("Expected a mapping for semantic validation");
+    }
     const col = column;
     const name = col.name;
     if (typeof name === "string" && !COLUMN_NAME_RE.test(name)) {
@@ -41,8 +49,11 @@ function validateColumnDefinition(column) {
     }
     for (const field of ["restrictions", "suggestions"]) {
         const values = col[field];
-        if (!Array.isArray(values))
+        if (values == null || (Array.isArray(values) && values.length === 0))
             continue;
+        if (!Array.isArray(values)) {
+            throw new Error(`Sample sheet column '${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 ${JSON.stringify(columnType)}`);
@@ -57,14 +68,22 @@ function _typeList(typeValue) {
         return [];
     return [String(typeValue)];
 }
-function validateInputParameter(inputParam) {
+export function validateInputParameter(inputParam) {
     if (!inputParam || typeof inputParam !== "object")
         return;
     const data = inputParam;
     const typeValues = _typeList(data.type);
-    const isTextOnly = typeValues.length > 0 && typeValues.every((t) => TEXT_TYPE_VALUES.has(t));
     const isCollectionOnly = typeValues.length > 0 && typeValues.every((t) => COLLECTION_TYPE_VALUES.has(t));
+    if (Array.isArray(data.type) && typeValues.some((t) => SCALAR_ONLY_TYPE_VALUES.has(t))) {
+        throw new Error(`multiple values are not supported for type=${JSON.stringify(data.type)}`);
+    }
+    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=${JSON.stringify(data.type)}`);
@@ -77,26 +96,29 @@ function validateInputParameter(inputParam) {
             validateColumnDefinition(column);
         }
     }
-    for (const field of ["restrictions", "suggestions", "restrictOnConnections"]) {
-        const value = data[field];
-        if (value == null)
-            continue;
-        if (Array.isArray(value) && value.length === 0)
-            continue;
-        if (value === false)
-            continue;
-        if (typeValues.length > 0 && !isTextOnly) {
-            throw new Error(`${field} is only valid on text/string inputs, got type=${JSON.stringify(data.type)}`);
-        }
-    }
     // Record-input fields validation (mirrors gxformat2 #216).
     const fields = data.fields;
     if (Array.isArray(fields) && fields.length > 0) {
+        if (!isCollectionOnly && typeValues.length > 0) {
+            throw new Error(`fields is only valid on collection inputs, got type=${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=${JSON.stringify(data.collection_type)}`);
         }
     }
+    for (const [field, allowedTypes] of PARAMETER_FIELD_TYPE_VALUES) {
+        const value = data[field];
+        // restrictOnConnections=false is the schema default and harmless.
+        if (value == null || value === false)
+            continue;
+        if (Array.isArray(value) && value.length === 0)
+            continue;
+        if (typeValues.length > 0 && !typeValues.every((t) => allowedTypes.has(t))) {
+            const allowed = [...allowedTypes].sort().join("/");
+            throw new Error(`${field} is only valid on ${allowed} inputs, got type=${JSON.stringify(data.type)}`);
+        }
+    }
 }
 /**
  * True when a step's `state`/`tool_state` field actually carries content.
@@ -124,7 +146,7 @@ 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 +183,7 @@ 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

@@ -1 +1 @@
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package/dist/workflow/strict-checks.d.ts.map

@@ -1 +1 @@
-{"version":3,"file":"strict-checks.d.ts","sourceRoot":"","sources":["../../src/workflow/strict-checks.ts"],"names":[],"mappings":"AAOA,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,oBAAoB,CAAC;AAQzD;;;GAGG;AACH,wBAAgB,sBAAsB,CAAC,YAAY,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,MAAM,EAAE,CAqBtF;AAED;;;;;;GAMG;AACH,wBAAgB,uBAAuB,CAAC,YAAY,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,MAAM,EAAE,CAiBvF;AAED,8DAA8D;AAC9D,wBAAgB,mBAAmB,CACjC,YAAY,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EACrC,MAAM,CAAC,EAAE,cAAc,GACtB,MAAM,EAAE,CAKV;AASD;;;GAGG;AACH,wBAAgB,oBAAoB,CAClC,YAAY,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EACrC,MAAM,CAAC,EAAE,cAAc,GACtB,MAAM,EAAE,CAcV"}
+{"version":3,"file":"strict-checks.d.ts","sourceRoot":"","sources":["../../src/workflow/strict-checks.ts"],"names":[],"mappings":"AAOA,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,oBAAoB,CAAC;AAQzD;;;GAGG;AACH,wBAAgB,sBAAsB,CAAC,YAAY,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,MAAM,EAAE,CAqBtF;AAED;;;;;;GAMG;AACH,wBAAgB,uBAAuB,CAAC,YAAY,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,GAAG,MAAM,EAAE,CAiBvF;AAED,8DAA8D;AAC9D,wBAAgB,mBAAmB,CACjC,YAAY,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EACrC,MAAM,CAAC,EAAE,cAAc,GACtB,MAAM,EAAE,CAKV;AASD;;;GAGG;AACH,wBAAgB,oBAAoB,CAClC,YAAY,EAAE,MAAM,CAAC,MAAM,EAAE,OAAO,CAAC,EACrC,MAAM,CAAC,EAAE,cAAc,GACtB,MAAM,EAAE,CAaV"}

package/dist/workflow/strict-checks.js

@@ -6,7 +6,7 @@
  */
 import { NativeGalaxyWorkflowSchema, GalaxyWorkflowSchema } from "./raw/index.js";
 import { detectFormat } from "./detect-format.js";
-import { withClass } from "./validators.js";
+import { withDecodeClass } from "./validators.js";
 import * as ParseResult from "effect/ParseResult";
 import * as S from "effect/Schema";
 // ── Encoding checks ──────────────────────────────────────────────────
@@ -82,8 +82,7 @@ function formatIssues(error) {
  */
 export function checkStrictStructure(workflowDict, format) {
     const fmt = format ?? detectFormat(workflowDict);
-    const cls = fmt === "native" ? "NativeGalaxyWorkflow" : "GalaxyWorkflow";
-    const data = withClass(workflowDict, cls);
+    const data = withDecodeClass(workflowDict, fmt);
     const schema = fmt === "native" ? NativeGalaxyWorkflowSchema : GalaxyWorkflowSchema;
     const decode = S.decodeUnknownEither(schema, { onExcessProperty: "error" });
     const result = decode(data);

package/dist/workflow/strict-checks.js.map

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

@@ -5,11 +5,12 @@
  * back the decoded value or throw on validation failure. Used by the schema-rule
  * catalog runner and declarative-operation tests.
  *
- * The generated Effect schemas make `class` a required literal; Python's
- * pydantic models default it. `withClass` injects the discriminator when
- * missing so pass/fail semantics match Python byte-for-byte — see the plan
- * note about `Format2MissingClass` being unenforceable today.
+ * The generated Effect schemas make `class` a required literal. Native `.ga`
+ * files never carry it and Format2 inline `run:` subworkflows may omit it, so
+ * `withDecodeClass` injects it there; a Format2 root must declare it
+ * (`Format2MissingClass`, gxformat2 #278).
  */
+import type { WorkflowFormat } from "./detect-format.js";
 /**
  * Return `raw` with `class: cls` injected if missing, and the same injection
  * applied recursively to step subworkflows. Native steps embed subworkflows
@@ -20,6 +21,8 @@
  * subworkflows inherit `"GalaxyWorkflow"`, native inherit `"NativeGalaxyWorkflow"`.
  */
 export declare function withClass(raw: unknown, cls: string): unknown;
+/** Inject `class` where decoding needs it: everywhere for native, inline runs only for Format2. */
+export declare function withDecodeClass(raw: unknown, format: WorkflowFormat): unknown;
 export declare function validateFormat2(wf: unknown): unknown;
 export declare function validateFormat2Strict(wf: unknown): unknown;
 export declare function validateNative(wf: unknown): unknown;

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

@@ -1 +1 @@
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+{"version":3,"file":"validators.d.ts","sourceRoot":"","sources":["../../src/workflow/validators.ts"],"names":[],"mappings":"AAAA;;;;;;;;;;;GAWG;AAIH,OAAO,KAAK,EAAE,cAAc,EAAE,MAAM,oBAAoB,CAAC;AAKzD;;;;;;;;GAQG;AACH,wBAAgB,SAAS,CAAC,GAAG,EAAE,OAAO,EAAE,GAAG,EAAE,MAAM,GAAG,OAAO,CAI5D;AAED,mGAAmG;AACnG,wBAAgB,eAAe,CAAC,GAAG,EAAE,OAAO,EAAE,MAAM,EAAE,cAAc,GAAG,OAAO,CAI7E;AAoCD,wBAAgB,eAAe,CAAC,EAAE,EAAE,OAAO,GAAG,OAAO,CAMpD;AAED,wBAAgB,qBAAqB,CAAC,EAAE,EAAE,OAAO,GAAG,OAAO,CAM1D;AAED,wBAAgB,cAAc,CAAC,EAAE,EAAE,OAAO,GAAG,OAAO,CAInD;AAED,wBAAgB,oBAAoB,CAAC,EAAE,EAAE,OAAO,GAAG,OAAO,CAIzD;AAED;;;;;GAKG;AACH,wBAAgB,mBAAmB,CACjC,WAAW,EAAE,MAAM,EACnB,MAAM,EAAE,OAAO,GACd,CAAC,EAAE,EAAE,OAAO,KAAK,OAAO,CAK1B"}

package/dist/workflow/validators.js

@@ -5,10 +5,10 @@
  * back the decoded value or throw on validation failure. Used by the schema-rule
  * catalog runner and declarative-operation tests.
  *
- * The generated Effect schemas make `class` a required literal; Python's
- * pydantic models default it. `withClass` injects the discriminator when
- * missing so pass/fail semantics match Python byte-for-byte — see the plan
- * note about `Format2MissingClass` being unenforceable today.
+ * The generated Effect schemas make `class` a required literal. Native `.ga`
+ * files never carry it and Format2 inline `run:` subworkflows may omit it, so
+ * `withDecodeClass` injects it there; a Format2 root must declare it
+ * (`Format2MissingClass`, gxformat2 #278).
  */
 import { Schema } from "effect";
 import { GalaxyWorkflowSchema } from "./raw/gxformat2.effect.js";
@@ -27,7 +27,18 @@ export function withClass(raw, cls) {
     if (!raw || typeof raw !== "object" || Array.isArray(raw))
         return raw;
     const obj = raw;
-    const result = "class" in obj ? { ...obj } : { ...obj, class: cls };
+    return withStepSubworkflowClass("class" in obj ? obj : { ...obj, class: cls }, cls);
+}
+/** Inject `class` where decoding needs it: everywhere for native, inline runs only for Format2. */
+export function withDecodeClass(raw, format) {
+    if (format === "native")
+        return withClass(raw, "NativeGalaxyWorkflow");
+    if (!raw || typeof raw !== "object" || Array.isArray(raw))
+        return raw;
+    return withStepSubworkflowClass(raw, "GalaxyWorkflow");
+}
+function withStepSubworkflowClass(obj, cls) {
+    const result = { ...obj };
     const steps = result.steps;
     if (!steps || typeof steps !== "object")
         return result;
@@ -58,20 +69,20 @@ function injectStepSubworkflow(step, cls) {
     return s;
 }
 export function validateFormat2(wf) {
-    const decoded = Schema.decodeUnknownSync(GalaxyWorkflowSchema, { onExcessProperty: "ignore" })(withClass(wf, "GalaxyWorkflow"));
+    const decoded = Schema.decodeUnknownSync(GalaxyWorkflowSchema, { onExcessProperty: "ignore" })(withDecodeClass(wf, "format2"));
     validateWorkflowSemantics(wf);
     return decoded;
 }
 export function validateFormat2Strict(wf) {
-    const decoded = Schema.decodeUnknownSync(GalaxyWorkflowSchema, { onExcessProperty: "error" })(withClass(wf, "GalaxyWorkflow"));
+    const decoded = Schema.decodeUnknownSync(GalaxyWorkflowSchema, { onExcessProperty: "error" })(withDecodeClass(wf, "format2"));
     validateWorkflowSemantics(wf);
     return decoded;
 }
 export function validateNative(wf) {
-    return Schema.decodeUnknownSync(NativeGalaxyWorkflowSchema, { onExcessProperty: "ignore" })(withClass(wf, "NativeGalaxyWorkflow"));
+    return Schema.decodeUnknownSync(NativeGalaxyWorkflowSchema, { onExcessProperty: "ignore" })(withDecodeClass(wf, "native"));
 }
 export function validateNativeStrict(wf) {
-    return Schema.decodeUnknownSync(NativeGalaxyWorkflowSchema, { onExcessProperty: "error" })(withClass(wf, "NativeGalaxyWorkflow"));
+    return Schema.decodeUnknownSync(NativeGalaxyWorkflowSchema, { onExcessProperty: "error" })(withDecodeClass(wf, "native"));
 }
 /**
  * Pick the validator matching a fixture filename's format.

package/dist/workflow/validators.js.map

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

@@ -1,6 +1,6 @@
 {
   "name": "@galaxy-tool-util/schema",
-  "version": "1.13.1",
+  "version": "1.15.0",
   "description": "Effect Schema parameter types and validators for Galaxy tools",
   "type": "module",
   "exports": {