Add validation rule to IWC profile to check all steps are documented

client/tests/e2e/suite/extension.ga.e2e.ts

@@ -59,12 +59,12 @@ suite("Native (JSON) Workflows", () => {
         {
           message: "The workflow does not specify a creator.",
           range: new vscode.Range(new vscode.Position(0, 0), new vscode.Position(0, 1)),
-          severity: vscode.DiagnosticSeverity.Error,
+          severity: vscode.DiagnosticSeverity.Warning,
         },
         {
           message: "The workflow does not specify a license.",
           range: new vscode.Range(new vscode.Position(0, 0), new vscode.Position(0, 1)),
-          severity: vscode.DiagnosticSeverity.Error,
+          severity: vscode.DiagnosticSeverity.Warning,
         },
         {
           message: "Missing label in workflow output.",

server/gx-workflow-ls-format2/src/profiles.ts

@@ -3,7 +3,10 @@ import {
   BasicCommonValidationProfile,
   IWCCommonValidationProfile,
 } from "@gxwf/server-common/src/providers/validation/profiles";
-import { RequiredPropertyValidationRule } from "@gxwf/server-common/src/providers/validation/rules";
+import {
+  ChildrenRequiredPropertyValidationRule,
+  RequiredPropertyValidationRule,
+} from "@gxwf/server-common/src/providers/validation/rules";
 import { InputTypeValidationRule } from "./validation/rules/InputTypeValidationRule";
 
 /**
@@ -33,10 +36,18 @@ export class GxFormat2IWCValidationProfile extends IWCCommonValidationProfile {
     new RequiredPropertyValidationRule(
       "doc",
       true,
-      DiagnosticSeverity.Error,
+      DiagnosticSeverity.Warning,
       "The workflow is not documented. Documenting workflows helps users understand the purpose of the workflow."
     ),
     new InputTypeValidationRule(DiagnosticSeverity.Error),
+    new ChildrenRequiredPropertyValidationRule(
+      "steps",
+      "doc",
+      true,
+      DiagnosticSeverity.Warning,
+      "The step is not documented. Documenting steps helps users understand the purpose of the step."
+    ),
+
     // Add more custom rules specific to gxformat2 workflows here...
   ]);
 

server/gx-workflow-ls-format2/tests/integration/validation.test.ts

@@ -1,5 +1,8 @@
 import { Diagnostic, ValidationRule } from "@gxwf/server-common/src/languageTypes";
-import { StepExportErrorValidationRule } from "@gxwf/server-common/src/providers/validation/rules";
+import {
+  ChildrenRequiredPropertyValidationRule,
+  StepExportErrorValidationRule,
+} from "@gxwf/server-common/src/providers/validation/rules";
 import { GalaxyWorkflowFormat2SchemaLoader } from "../../src/schema";
 import { GxFormat2SchemaValidationService } from "../../src/services/schemaValidationService";
 import { InputTypeValidationRule } from "../../src/validation/rules/InputTypeValidationRule";
@@ -274,5 +277,68 @@ steps:
         expect(diagnostics).toHaveLength(0);
       });
     });
+
+    describe("ChildrenRequiredPropertyValidationRule", () => {
+      beforeAll(() => {
+        rule = new ChildrenRequiredPropertyValidationRule("steps", "doc");
+      });
+
+      it("should report error when step is missing required property", async () => {
+        const content = `
+class: GalaxyWorkflow
+steps:
+    step:
+        tool_id: tool_id
+    `;
+        const diagnostics = await validateRule(content);
+        expect(diagnostics).toHaveLength(1);
+        expect(diagnostics[0].message).toBe('Missing required property "doc".');
+      });
+
+      it("should not report error when all steps have required property", async () => {
+        const content = `
+class: GalaxyWorkflow
+steps:
+    step:
+        tool_id: tool_id
+        doc: step doc
+    step2:
+        tool_id: tool_id
+        doc: step2 doc
+    `;
+        const diagnostics = await validateRule(content);
+        expect(diagnostics).toHaveLength(0);
+      });
+
+      it("should report error when step has empty required property", async () => {
+        const content = `
+class: GalaxyWorkflow
+steps:
+    step:
+        tool_id: tool_id
+        doc:
+    `;
+        const diagnostics = await validateRule(content);
+        expect(diagnostics).toHaveLength(1);
+        expect(diagnostics[0].message).toBe('Missing required value in property "doc".');
+      });
+
+      it("should not report error when there are no steps", async () => {
+        const content = `
+class: GalaxyWorkflow
+steps:
+    `;
+        const diagnostics = await validateRule(content);
+        expect(diagnostics).toHaveLength(0);
+      });
+
+      it("should not report error when the steps property does not exist", async () => {
+        const content = `
+class: GalaxyWorkflow
+    `;
+        const diagnostics = await validateRule(content);
+        expect(diagnostics).toHaveLength(0);
+      });
+    });
   });
 });

server/gx-workflow-ls-native/src/profiles.ts

@@ -33,7 +33,7 @@ export class NativeIWCValidationProfile extends IWCCommonValidationProfile {
     new RequiredPropertyValidationRule(
       "annotation",
       true,
-      DiagnosticSeverity.Error,
+      DiagnosticSeverity.Warning,
       "The workflow is not annotated. Annotating workflows helps users understand the purpose of the workflow."
     ),
     new WorkflowOutputLabelValidationRule(DiagnosticSeverity.Error),

server/packages/server-common/src/providers/validation/profiles.ts

@@ -47,13 +47,13 @@ export class IWCCommonValidationProfile implements ValidationProfile {
     new RequiredPropertyValidationRule(
       "creator",
       true,
-      DiagnosticSeverity.Error,
+      DiagnosticSeverity.Warning,
       "The workflow does not specify a creator."
     ),
     new RequiredPropertyValidationRule(
       "license",
       true,
-      DiagnosticSeverity.Error,
+      DiagnosticSeverity.Warning,
       "The workflow does not specify a license."
     ),
     // Add more common rules here...

server/packages/server-common/src/providers/validation/rules/ChildrenRequiredPropertyValidationRule.ts

@@ -0,0 +1,53 @@
+import { DocumentContext, ValidationRule } from "@gxwf/server-common/src/languageTypes";
+import { Diagnostic, DiagnosticSeverity } from "vscode-languageserver-types";
+
+/**
+ * Validation rule to check that all children of a node have a required property.
+ */
+export class ChildrenRequiredPropertyValidationRule implements ValidationRule {
+  constructor(
+    private nodePath: string,
+    private propertyName: string,
+    private valueRequired: boolean = true,
+    private severity: DiagnosticSeverity = DiagnosticSeverity.Error,
+    private message?: string
+  ) {}
+
+  public async validate(documentContext: DocumentContext): Promise<Diagnostic[]> {
+    const result: Diagnostic[] = [];
+    const targetNode = documentContext.nodeManager.getNodeFromPath(this.nodePath);
+    if (!targetNode) {
+      // The target node does not exist, so we can't check for children.
+      return Promise.resolve(result);
+    }
+
+    const children = documentContext.nodeManager.getChildren(targetNode);
+    for (const child of children) {
+      if (child.type !== "object") {
+        continue;
+      }
+      for (const childProperty of child.properties) {
+        const targetChildNode = documentContext.nodeManager.getPropertyNodeByName(childProperty, this.propertyName);
+        if (!targetChildNode) {
+          result.push({
+            message: this.message ?? `Missing required property "${this.propertyName}".`,
+            range: documentContext.nodeManager.getNodeRange(childProperty.keyNode),
+            severity: this.severity,
+          });
+        }
+
+        if (this.valueRequired && targetChildNode) {
+          const missingValue = documentContext.nodeManager.isNodeEmpty(targetChildNode);
+          if (missingValue) {
+            result.push({
+              message: `Missing required value in property "${this.propertyName}".`,
+              range: documentContext.nodeManager.getNodeRange(targetChildNode),
+              severity: this.severity,
+            });
+          }
+        }
+      }
+    }
+    return Promise.resolve(result);
+  }
+}

server/packages/server-common/src/providers/validation/rules/index.ts

@@ -1,9 +1,11 @@
+import { ChildrenRequiredPropertyValidationRule } from "./ChildrenRequiredPropertyValidationRule";
 import { RequiredArrayPropertyValidationRule } from "./RequiredArrayPropertyValidationRule";
 import { RequiredPropertyValidationRule } from "./RequiredPropertyValidationRule";
 import { StepExportErrorValidationRule } from "./StepErrorValidationRule";
 import { TestToolshedValidationRule } from "./TestToolShedValidationRule";
 
 export {
+  ChildrenRequiredPropertyValidationRule,
   RequiredArrayPropertyValidationRule,
   RequiredPropertyValidationRule,
   StepExportErrorValidationRule,