From 396f4dac64f954211023e9c7ae9445ad7b6e81b2 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Thu, 2 Jun 2022 19:07:55 +0200
Subject: [PATCH 1/9] Refactor rename ValidationContributor

to ValidationRule.
---
 server/src/languageTypes.ts                          | 12 ++++++------
 .../validation/MissingPropertyValidation.ts          |  4 ++--
 2 files changed, 8 insertions(+), 8 deletions(-)

diff --git a/server/src/languageTypes.ts b/server/src/languageTypes.ts
index 32f40dd..e38ae36 100644
--- a/server/src/languageTypes.ts
+++ b/server/src/languageTypes.ts
@@ -130,7 +130,7 @@ export interface HoverContentContributor {
 /**
  * Interface for contributing additional diagnostics to the validation process.
  */
-export interface ValidationContributor {
+export interface ValidationRule {
   /**
    * Validates the given workflow document and provides diagnostics.
    * @param workflowDocument The workflow document
@@ -139,7 +139,7 @@ export interface ValidationContributor {
 }
 
 export abstract class WorkflowLanguageService {
-  protected _validationContributors: ValidationContributor[] = [];
+  protected _customValidationRules: ValidationRule[] = [];
   public abstract format(document: TextDocument, range: Range, options: FormattingOptions): TextEdit[];
   public abstract parseWorkflowDocument(document: TextDocument): WorkflowDocument;
   public abstract doHover(workflowDocument: WorkflowDocument, position: Position): Promise<Hover | null>;
@@ -147,14 +147,14 @@ export abstract class WorkflowLanguageService {
 
   protected abstract doValidation(workflowDocument: WorkflowDocument): Promise<Diagnostic[]>;
 
-  public setValidationContributors(contributors: ValidationContributor[]): void {
-    this._validationContributors = contributors;
+  public setValidationRules(validationRules: ValidationRule[]): void {
+    this._customValidationRules = validationRules;
   }
 
   public async validate(workflowDocument: WorkflowDocument): Promise<Diagnostic[]> {
     const diagnostics = await this.doValidation(workflowDocument);
-    this._validationContributors.forEach(async (contributor) => {
-      const contributedDiagnostics = await contributor.validate(workflowDocument);
+    this._customValidationRules.forEach(async (validationRule) => {
+      const contributedDiagnostics = await validationRule.validate(workflowDocument);
       diagnostics.push(...contributedDiagnostics);
     });
     return diagnostics;
diff --git a/server/src/providers/validation/MissingPropertyValidation.ts b/server/src/providers/validation/MissingPropertyValidation.ts
index 9302385..f7e792b 100644
--- a/server/src/providers/validation/MissingPropertyValidation.ts
+++ b/server/src/providers/validation/MissingPropertyValidation.ts
@@ -1,7 +1,7 @@
 import { Diagnostic, DiagnosticSeverity } from "vscode-languageserver-types";
-import { ValidationContributor, WorkflowDocument } from "../../languageTypes";
+import { ValidationRule, WorkflowDocument } from "../../languageTypes";
 
-export class MissingPropertyValidationRule implements ValidationContributor {
+export class MissingPropertyValidationRule implements ValidationRule {
   constructor(readonly nodePath: string, readonly severity?: DiagnosticSeverity | undefined) {}
 
   validate(workflowDocument: WorkflowDocument): Promise<Diagnostic[]> {

From 7ec98e0d9d6f0720683eb03cc11fb839bb370d5f Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Fri, 3 Jun 2022 19:06:24 +0200
Subject: [PATCH 2/9] Unify missing property message

To display the same kind of message as the schema validator for missing properties.
---
 server/src/providers/validation/MissingPropertyValidation.ts | 2 +-
 1 file changed, 1 insertion(+), 1 deletion(-)

diff --git a/server/src/providers/validation/MissingPropertyValidation.ts b/server/src/providers/validation/MissingPropertyValidation.ts
index f7e792b..d82daf3 100644
--- a/server/src/providers/validation/MissingPropertyValidation.ts
+++ b/server/src/providers/validation/MissingPropertyValidation.ts
@@ -9,7 +9,7 @@ export class MissingPropertyValidationRule implements ValidationRule {
     const targetNode = workflowDocument.getNodeFromPath(this.nodePath);
     if (!targetNode) {
       result.push({
-        message: `Property '${this.nodePath}' is missing`,
+        message: `Missing property "${this.nodePath}".`,
         range: workflowDocument.getDefaultRange(),
         severity: this.severity,
       });

From 3244136953c7b9c42809c11e7e7c3f9e2d841eeb Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Sun, 5 Jun 2022 16:28:50 +0200
Subject: [PATCH 3/9] Add `getStepNodes` to WorkflowDocument

---
 server/src/models/nativeWorkflowDocument.ts | 20 +++++++++++++++++++-
 server/src/models/workflowDocument.ts       |  4 +++-
 2 files changed, 22 insertions(+), 2 deletions(-)

diff --git a/server/src/models/nativeWorkflowDocument.ts b/server/src/models/nativeWorkflowDocument.ts
index b16bc6d..52cf929 100644
--- a/server/src/models/nativeWorkflowDocument.ts
+++ b/server/src/models/nativeWorkflowDocument.ts
@@ -1,4 +1,4 @@
-import { JSONDocument } from "vscode-json-languageservice";
+import { JSONDocument, ObjectASTNode } from "vscode-json-languageservice";
 import { getPropertyNodeFromPath } from "../jsonUtils";
 import { TextDocument, Range, Position, ASTNode, WorkflowDocument } from "../languageTypes";
 
@@ -72,4 +72,22 @@ export class NativeWorkflowDocument extends WorkflowDocument {
     if (!root) return null;
     return getPropertyNodeFromPath(root, path);
   }
+
+  public override getStepNodes(): ObjectASTNode[] {
+    const root = this._jsonDocument.root;
+    if (!root) {
+      return [];
+    }
+    const result: ObjectASTNode[] = [];
+    const stepsNode = this.getNodeFromPath("steps");
+    if (stepsNode && stepsNode.type === "property" && stepsNode.valueNode && stepsNode.valueNode.type === "object") {
+      stepsNode.valueNode.properties.forEach((stepProperty) => {
+        const stepNode = stepProperty.valueNode;
+        if (stepNode && stepNode.type === "object") {
+          result.push(stepNode);
+        }
+      });
+    }
+    return result;
+  }
 }
diff --git a/server/src/models/workflowDocument.ts b/server/src/models/workflowDocument.ts
index bb135a8..fcb010d 100644
--- a/server/src/models/workflowDocument.ts
+++ b/server/src/models/workflowDocument.ts
@@ -1,4 +1,4 @@
-import { TextDocument, Range, Position, ASTNode } from "../languageTypes";
+import { TextDocument, Range, Position, ASTNode, ObjectASTNode } from "../languageTypes";
 import { URI } from "vscode-uri";
 
 /**
@@ -28,6 +28,8 @@ export abstract class WorkflowDocument {
 
   public abstract getNodeFromPath(path: string): ASTNode | null;
 
+  public abstract getStepNodes(): ObjectASTNode[];
+
   /** Returns a small Range at the beginning of the document */
   public getDefaultRange(): Range {
     return Range.create(this.textDocument.positionAt(0), this.textDocument.positionAt(1));

From cd569b75e1ad98271527d975d9ade07fd71764e6 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Sun, 5 Jun 2022 16:29:47 +0200
Subject: [PATCH 4/9] Add `TestWorkflowProvider` for unit testing

This providers just loads the appropriate workflow document in an object with some documentation.
---
 server/tests/testWorkflowProvider.ts    | 31 +++++++++
 test-data/json/validation/test_wf_00.ga |  6 ++
 test-data/json/validation/test_wf_01.ga | 81 ++---------------------
 test-data/json/validation/test_wf_02.ga | 87 +++++++++++++++++++++++++
 4 files changed, 130 insertions(+), 75 deletions(-)
 create mode 100644 server/tests/testWorkflowProvider.ts
 create mode 100644 test-data/json/validation/test_wf_00.ga
 create mode 100644 test-data/json/validation/test_wf_02.ga

diff --git a/server/tests/testWorkflowProvider.ts b/server/tests/testWorkflowProvider.ts
new file mode 100644
index 0000000..fa7e7cf
--- /dev/null
+++ b/server/tests/testWorkflowProvider.ts
@@ -0,0 +1,31 @@
+import * as fs from "fs";
+import * as path from "path";
+
+const TEST_DATA_PATH = path.join(__dirname, "..", "..", "test-data");
+
+interface TestJsonWorkflows {
+  /** Workflows for testing validation issues. */
+  validation: {
+    /** Invalid workflow without steps. */
+    withoutSteps: string;
+    /** Valid workflow with 1 step. */
+    withOneStep: string;
+    /** Invalid workflow with 3 steps. The steps are missing UUID and workflow_outputs. */
+    withThreeSteps: string;
+  };
+}
+
+export class TestWorkflowProvider {
+  private static _jsonWorkflows: TestJsonWorkflows = {
+    validation: {
+      withoutSteps: fs.readFileSync(path.join(TEST_DATA_PATH, "json", "validation", "test_wf_00.ga"), "utf-8"),
+      withOneStep: fs.readFileSync(path.join(TEST_DATA_PATH, "json", "validation", "test_wf_01.ga"), "utf-8"),
+      withThreeSteps: fs.readFileSync(path.join(TEST_DATA_PATH, "json", "validation", "test_wf_02.ga"), "utf-8"),
+    },
+  };
+
+  /** Workflows in native JSON format. */
+  public static get nativeJson(): TestJsonWorkflows {
+    return this._jsonWorkflows;
+  }
+}
diff --git a/test-data/json/validation/test_wf_00.ga b/test-data/json/validation/test_wf_00.ga
new file mode 100644
index 0000000..bcb73ce
--- /dev/null
+++ b/test-data/json/validation/test_wf_00.ga
@@ -0,0 +1,6 @@
+{
+    "a_galaxy_workflow": "true",
+    "format-version": "0.1",
+    "name": "Test Workflow Without Steps",
+    "steps": {}
+}
diff --git a/test-data/json/validation/test_wf_01.ga b/test-data/json/validation/test_wf_01.ga
index b45ce03..a0a51e1 100644
--- a/test-data/json/validation/test_wf_01.ga
+++ b/test-data/json/validation/test_wf_01.ga
@@ -1,87 +1,18 @@
 {
     "a_galaxy_workflow": "true",
-    "annotation": "simple workflow",
     "format-version": "0.1",
-    "name": "TestWorkflow1",
+    "name": "Test Workflow Minimum Valid",
     "steps": {
         "0": {
-            "annotation": "input1 description",
             "id": 0,
-            "input_connections": {},
-            "inputs": [
-                {
-                    "description": "input1 description",
-                    "name": "WorkflowInput1"
-                }
-            ],
-            "name": "Input dataset",
-            "outputs": [],
-            "position": {
-                "left": 199.55555772781372,
-                "top": 200.66666460037231
-            },
-            "tool_errors": null,
-            "tool_id": null,
-            "tool_state": "{\"name\": \"WorkflowInput1\"}",
-            "tool_version": null,
+            "name": "Test Step",
             "type": "data_input",
-            "user_outputs": []
-        },
-        "1": {
-            "annotation": "",
-            "id": 1,
+            "annotation": "Step description",
+            "uuid": "692d2674-5e70-4e01-ad12-4ce5572c39e5",
             "input_connections": {},
-            "inputs": [
-                {
-                    "description": "",
-                    "name": "WorkflowInput2"
-                }
-            ],
-            "name": "Input dataset",
-            "outputs": [],
-            "position": {
-                "left": 206.22221422195435,
-                "top": 327.33335161209106
-            },
-            "tool_errors": null,
-            "tool_id": null,
-            "tool_state": "{\"name\": \"WorkflowInput2\"}",
-            "tool_version": null,
-            "type": "data_input",
-            "user_outputs": []
-        },
-        "2": {
-            "annotation": "",
-            "id": 2,
-            "input_connections": {
-                "input1": {
-                    "id": 0,
-                    "output_name": "output"
-                },
-                "queries_0|input2": {
-                    "id": 1,
-                    "output_name": "output"
-                }
-            },
             "inputs": [],
-            "name": "Concatenate datasets",
-            "outputs": [
-                {
-                    "name": "out_file1",
-                    "type": "input"
-                }
-            ],
-            "position": {
-                "left": 419.33335876464844,
-                "top": 200.44446563720703
-            },
-            "post_job_actions": {},
-            "tool_errors": null,
-            "tool_id": "cat1",
-            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"queries\": \"[{\\\"input2\\\": null, \\\"__index__\\\": 0}]\"}",
-            "tool_version": "1.0.0",
-            "type": "tool",
-            "user_outputs": []
+            "outputs": [],
+            "workflow_outputs": []
         }
     }
 }
diff --git a/test-data/json/validation/test_wf_02.ga b/test-data/json/validation/test_wf_02.ga
new file mode 100644
index 0000000..b45ce03
--- /dev/null
+++ b/test-data/json/validation/test_wf_02.ga
@@ -0,0 +1,87 @@
+{
+    "a_galaxy_workflow": "true",
+    "annotation": "simple workflow",
+    "format-version": "0.1",
+    "name": "TestWorkflow1",
+    "steps": {
+        "0": {
+            "annotation": "input1 description",
+            "id": 0,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "input1 description",
+                    "name": "WorkflowInput1"
+                }
+            ],
+            "name": "Input dataset",
+            "outputs": [],
+            "position": {
+                "left": 199.55555772781372,
+                "top": 200.66666460037231
+            },
+            "tool_errors": null,
+            "tool_id": null,
+            "tool_state": "{\"name\": \"WorkflowInput1\"}",
+            "tool_version": null,
+            "type": "data_input",
+            "user_outputs": []
+        },
+        "1": {
+            "annotation": "",
+            "id": 1,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "",
+                    "name": "WorkflowInput2"
+                }
+            ],
+            "name": "Input dataset",
+            "outputs": [],
+            "position": {
+                "left": 206.22221422195435,
+                "top": 327.33335161209106
+            },
+            "tool_errors": null,
+            "tool_id": null,
+            "tool_state": "{\"name\": \"WorkflowInput2\"}",
+            "tool_version": null,
+            "type": "data_input",
+            "user_outputs": []
+        },
+        "2": {
+            "annotation": "",
+            "id": 2,
+            "input_connections": {
+                "input1": {
+                    "id": 0,
+                    "output_name": "output"
+                },
+                "queries_0|input2": {
+                    "id": 1,
+                    "output_name": "output"
+                }
+            },
+            "inputs": [],
+            "name": "Concatenate datasets",
+            "outputs": [
+                {
+                    "name": "out_file1",
+                    "type": "input"
+                }
+            ],
+            "position": {
+                "left": 419.33335876464844,
+                "top": 200.44446563720703
+            },
+            "post_job_actions": {},
+            "tool_errors": null,
+            "tool_id": "cat1",
+            "tool_state": "{\"__page__\": 0, \"__rerun_remap_job_id__\": null, \"input1\": \"null\", \"queries\": \"[{\\\"input2\\\": null, \\\"__index__\\\": 0}]\"}",
+            "tool_version": "1.0.0",
+            "type": "tool",
+            "user_outputs": []
+        }
+    }
+}

From 3b583ca19e3fa35d1c714c372de903a84b89ef2a Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Sun, 5 Jun 2022 16:32:54 +0200
Subject: [PATCH 5/9] Add unit test for `getStepNodes`

---
 server/tests/testHelpers.ts                     |  6 ++++++
 .../tests/unit/nativeWorkflowDocument.test.ts   | 17 +++++++++++++++++
 2 files changed, 23 insertions(+)
 create mode 100644 server/tests/unit/nativeWorkflowDocument.test.ts

diff --git a/server/tests/testHelpers.ts b/server/tests/testHelpers.ts
index 305cc57..878f286 100644
--- a/server/tests/testHelpers.ts
+++ b/server/tests/testHelpers.ts
@@ -1,6 +1,7 @@
 import { ASTNode, getLanguageService, JSONDocument, JSONPath } from "vscode-json-languageservice";
 import { TextDocument } from "../src/languageTypes";
 import * as Json from "jsonc-parser";
+import { NativeWorkflowDocument } from "../src/models/nativeWorkflowDocument";
 
 export function toJsonDocument(contents: string): { textDoc: TextDocument; jsonDoc: JSONDocument } {
   const textDoc = TextDocument.create("foo://bar/file.json", "json", 0, contents);
@@ -23,3 +24,8 @@ export function getNodeValue(node: ASTNode): unknown {
 export function getNodePath(node: ASTNode): JSONPath {
   return Json.getNodePath(node);
 }
+
+export function createNativeWorkflowDocument(contents: string): NativeWorkflowDocument {
+  const { textDoc, jsonDoc } = toJsonDocument(contents);
+  return new NativeWorkflowDocument(textDoc, jsonDoc);
+}
diff --git a/server/tests/unit/nativeWorkflowDocument.test.ts b/server/tests/unit/nativeWorkflowDocument.test.ts
new file mode 100644
index 0000000..c1bd22d
--- /dev/null
+++ b/server/tests/unit/nativeWorkflowDocument.test.ts
@@ -0,0 +1,17 @@
+import { createNativeWorkflowDocument } from "../testHelpers";
+import { TestWorkflowProvider } from "../testWorkflowProvider";
+
+describe("NativeWorkflowDocument", () => {
+  describe("getStepNodes", () => {
+    it.each([
+      ["", 0],
+      [TestWorkflowProvider.nativeJson.validation.withoutSteps, 0],
+      [TestWorkflowProvider.nativeJson.validation.withOneStep, 1],
+      [TestWorkflowProvider.nativeJson.validation.withThreeSteps, 3],
+    ])("returns the expected number of steps", (wf_content: string, expectedNumSteps: number) => {
+      const wfDocument = createNativeWorkflowDocument(wf_content);
+      const stepNodes = wfDocument.getStepNodes();
+      expect(stepNodes).toHaveLength(expectedNumSteps);
+    });
+  });
+});

From 0ac2aac06c09568a099f175faefb6ed8755a3abb Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Sun, 5 Jun 2022 17:11:51 +0200
Subject: [PATCH 6/9] Udate native schema

- Move UUID to definition.
- Define some properties for `workflow_outputs`
---
 workflow-languages/schemas/native.schema.json | 33 +++++++++++++++----
 1 file changed, 26 insertions(+), 7 deletions(-)

diff --git a/workflow-languages/schemas/native.schema.json b/workflow-languages/schemas/native.schema.json
index 27b72db..9ae077a 100644
--- a/workflow-languages/schemas/native.schema.json
+++ b/workflow-languages/schemas/native.schema.json
@@ -59,9 +59,8 @@
       "$ref": "#/definitions/tags"
     },
     "uuid": {
-      "type": "string",
-      "markdownDescription": "UUID associated with the workflow.",
-      "pattern": "^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$"
+      "$ref": "#/definitions/uuid",
+      "markdownDescription": "UUID associated with the workflow."
     },
     "steps": {
       "$ref": "#/definitions/steps"
@@ -226,9 +225,8 @@
           "enum": ["tool", "subworkflow", "parameter_input", "data_input", "data_collection_input"]
         },
         "uuid": {
-          "type": "string",
-          "markdownDescription": "UUID associated with the workflow step.",
-          "pattern": "^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$"
+          "$ref": "#/definitions/uuid",
+          "markdownDescription": "UUID associated with the workflow step."
         },
         "workflow_outputs": {
           "$ref": "#/definitions/workflowOutputs"
@@ -303,7 +301,24 @@
     },
     "workflowOutputs": {
       "type": "array",
-      "items": {}
+      "items": {
+        "$ref": "#/definitions/workflowOutput"
+      }
+    },
+    "workflowOutput": {
+      "type": "object",
+      "properties": {
+        "label": {
+          "type": "string"
+        },
+        "output_name": {
+          "type": "string"
+        },
+        "uuid": {
+          "$ref": "#/definitions/uuid",
+          "markdownDescription": "UUID associated with the workflow output."
+        }
+      }
     },
     "position": {
       "type": "object",
@@ -319,6 +334,10 @@
     },
     "optionalString": {
       "type": ["string", "null"]
+    },
+    "uuid": {
+      "type": "string",
+      "pattern": "^[0-9a-f]{8}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{4}-[0-9a-f]{12}$"
     }
   }
 }

From c128f12527b4f576b0febec98af47b80128db956 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Sun, 5 Jun 2022 17:13:30 +0200
Subject: [PATCH 7/9] Add `WorkflowOutputLabelValidation` custom rule

---
 .../WorkflowOutputLabelValidation.ts          | 29 +++++++++++++++++++
 1 file changed, 29 insertions(+)
 create mode 100644 server/src/providers/validation/WorkflowOutputLabelValidation.ts

diff --git a/server/src/providers/validation/WorkflowOutputLabelValidation.ts b/server/src/providers/validation/WorkflowOutputLabelValidation.ts
new file mode 100644
index 0000000..7c3a75b
--- /dev/null
+++ b/server/src/providers/validation/WorkflowOutputLabelValidation.ts
@@ -0,0 +1,29 @@
+import { Diagnostic, DiagnosticSeverity } from "vscode-languageserver-types";
+import { ValidationRule, WorkflowDocument } from "../../languageTypes";
+
+export class WorkflowOutputLabelValidation implements ValidationRule {
+  constructor(readonly severity: DiagnosticSeverity = DiagnosticSeverity.Error) {}
+
+  validate(workflowDocument: WorkflowDocument): Promise<Diagnostic[]> {
+    const result: Diagnostic[] = [];
+    const stepNodes = workflowDocument.getStepNodes();
+    stepNodes.forEach((step) => {
+      const workflowOutputs = step.properties.find((property) => property.keyNode.value === "workflow_outputs");
+      if (workflowOutputs && workflowOutputs.valueNode && workflowOutputs.valueNode.type === "array") {
+        workflowOutputs.valueNode.items.forEach((outputNode) => {
+          if (outputNode.type === "object") {
+            const labelNode = outputNode.properties.find((property) => property.keyNode.value === "label");
+            if (!labelNode?.valueNode?.value) {
+              result.push({
+                message: `Missing label in workflow output.`,
+                range: workflowDocument.getNodeRange(outputNode),
+                severity: this.severity,
+              });
+            }
+          }
+        });
+      }
+    });
+    return Promise.resolve(result);
+  }
+}

From a30e776c43ffb5de46a402257aadbc8ce4b6d49d Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Sun, 5 Jun 2022 17:14:04 +0200
Subject: [PATCH 8/9] Add more test workflows

For testing WorkflowOutputLabelValidation
---
 server/tests/testWorkflowProvider.ts    | 12 ++++++++++
 test-data/json/validation/test_wf_02.ga |  4 ++--
 test-data/json/validation/test_wf_03.ga | 28 +++++++++++++++++++++++
 test-data/json/validation/test_wf_04.ga | 30 +++++++++++++++++++++++++
 4 files changed, 72 insertions(+), 2 deletions(-)
 create mode 100644 test-data/json/validation/test_wf_03.ga
 create mode 100644 test-data/json/validation/test_wf_04.ga

diff --git a/server/tests/testWorkflowProvider.ts b/server/tests/testWorkflowProvider.ts
index fa7e7cf..7b94c6f 100644
--- a/server/tests/testWorkflowProvider.ts
+++ b/server/tests/testWorkflowProvider.ts
@@ -12,6 +12,10 @@ interface TestJsonWorkflows {
     withOneStep: string;
     /** Invalid workflow with 3 steps. The steps are missing UUID and workflow_outputs. */
     withThreeSteps: string;
+    /** Workflow with 1 step. The step has 2 workflow_outputs without labels. */
+    withoutWorkflowOutputLabels: string;
+    /** Workflow with 1 step. The step has 2 workflow_outputs with labels. */
+    withWorkflowOutputLabels: string;
   };
 }
 
@@ -21,6 +25,14 @@ export class TestWorkflowProvider {
       withoutSteps: fs.readFileSync(path.join(TEST_DATA_PATH, "json", "validation", "test_wf_00.ga"), "utf-8"),
       withOneStep: fs.readFileSync(path.join(TEST_DATA_PATH, "json", "validation", "test_wf_01.ga"), "utf-8"),
       withThreeSteps: fs.readFileSync(path.join(TEST_DATA_PATH, "json", "validation", "test_wf_02.ga"), "utf-8"),
+      withoutWorkflowOutputLabels: fs.readFileSync(
+        path.join(TEST_DATA_PATH, "json", "validation", "test_wf_03.ga"),
+        "utf-8"
+      ),
+      withWorkflowOutputLabels: fs.readFileSync(
+        path.join(TEST_DATA_PATH, "json", "validation", "test_wf_04.ga"),
+        "utf-8"
+      ),
     },
   };
 
diff --git a/test-data/json/validation/test_wf_02.ga b/test-data/json/validation/test_wf_02.ga
index b45ce03..0b9827b 100644
--- a/test-data/json/validation/test_wf_02.ga
+++ b/test-data/json/validation/test_wf_02.ga
@@ -1,8 +1,8 @@
 {
     "a_galaxy_workflow": "true",
-    "annotation": "simple workflow",
+    "annotation": "The steps are missing UUIDs and workflow_outputs",
     "format-version": "0.1",
-    "name": "TestWorkflow1",
+    "name": "Test Workflow with 3 steps",
     "steps": {
         "0": {
             "annotation": "input1 description",
diff --git a/test-data/json/validation/test_wf_03.ga b/test-data/json/validation/test_wf_03.ga
new file mode 100644
index 0000000..2def6a9
--- /dev/null
+++ b/test-data/json/validation/test_wf_03.ga
@@ -0,0 +1,28 @@
+{
+    "a_galaxy_workflow": "true",
+    "annotation": "Workflow without labels in the workflow_outputs",
+    "format-version": "0.1",
+    "name": "Test Workflow",
+    "steps": {
+        "0": {
+            "id": 0,
+            "name": "Test Step",
+            "type": "data_input",
+            "annotation": "Step description",
+            "uuid": "692d2674-5e70-4e01-ad12-4ce5572c39e5",
+            "input_connections": {},
+            "inputs": [],
+            "outputs": [],
+            "workflow_outputs": [
+                {
+                    "output_name": "output1",
+                    "uuid": "7f08baab-5426-427e-9640-85815d809261"
+                },
+                {
+                    "output_name": "output2",
+                    "uuid": "b58fce9c-e507-4714-abfc-739607e02eed"
+                }
+            ]
+        }
+    }
+}
diff --git a/test-data/json/validation/test_wf_04.ga b/test-data/json/validation/test_wf_04.ga
new file mode 100644
index 0000000..58aec62
--- /dev/null
+++ b/test-data/json/validation/test_wf_04.ga
@@ -0,0 +1,30 @@
+{
+    "a_galaxy_workflow": "true",
+    "annotation": "Valid workflow with labels in the workflow_outputs",
+    "format-version": "0.1",
+    "name": "Test Workflow",
+    "steps": {
+        "0": {
+            "id": 0,
+            "name": "Test Step",
+            "type": "data_input",
+            "annotation": "Step description",
+            "uuid": "692d2674-5e70-4e01-ad12-4ce5572c39e5",
+            "input_connections": {},
+            "inputs": [],
+            "outputs": [],
+            "workflow_outputs": [
+                {
+                    "label": "The first output",
+                    "output_name": "output1",
+                    "uuid": "7f08baab-5426-427e-9640-85815d809261"
+                },
+                {
+                    "label": "The second output",
+                    "output_name": "output2",
+                    "uuid": "b58fce9c-e507-4714-abfc-739607e02eed"
+                }
+            ]
+        }
+    }
+}

From 6fa19487fa77f66955a523f15a738a0eded18811 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Sun, 5 Jun 2022 17:14:28 +0200
Subject: [PATCH 9/9] Add unit tests for WorkflowOutputLabelValidation

---
 .../tests/unit/customValidationRules.test.ts  | 44 +++++++++++++++++++
 1 file changed, 44 insertions(+)
 create mode 100644 server/tests/unit/customValidationRules.test.ts

diff --git a/server/tests/unit/customValidationRules.test.ts b/server/tests/unit/customValidationRules.test.ts
new file mode 100644
index 0000000..9eef510
--- /dev/null
+++ b/server/tests/unit/customValidationRules.test.ts
@@ -0,0 +1,44 @@
+import { createNativeWorkflowDocument } from "../testHelpers";
+import { WorkflowOutputLabelValidation } from "../../src/providers/validation/WorkflowOutputLabelValidation";
+import { TestWorkflowProvider } from "../testWorkflowProvider";
+
+describe("Custom Validation Rules", () => {
+  describe("WorkflowOutputLabelValidation Rule", () => {
+    let rule: WorkflowOutputLabelValidation;
+
+    beforeEach(() => {
+      rule = new WorkflowOutputLabelValidation();
+    });
+
+    it("should not provide diagnostics when there are no steps", async () => {
+      const wfDocument = createNativeWorkflowDocument(TestWorkflowProvider.nativeJson.validation.withoutSteps);
+      const diagnostics = await rule.validate(wfDocument);
+      expect(diagnostics).toHaveLength(0);
+    });
+
+    it("should not provide diagnostics when there are no workflow_outputs in the steps", async () => {
+      const wfDocument = createNativeWorkflowDocument(TestWorkflowProvider.nativeJson.validation.withThreeSteps);
+      const diagnostics = await rule.validate(wfDocument);
+      expect(diagnostics).toHaveLength(0);
+    });
+
+    it("should not provide diagnostics when the steps contains workflow_outputs with label", async () => {
+      const wfDocument = createNativeWorkflowDocument(
+        TestWorkflowProvider.nativeJson.validation.withWorkflowOutputLabels
+      );
+      const diagnostics = await rule.validate(wfDocument);
+      expect(diagnostics).toHaveLength(0);
+    });
+
+    it("should provide diagnostics when the steps contains workflow_outputs without label", async () => {
+      const wfDocument = createNativeWorkflowDocument(
+        TestWorkflowProvider.nativeJson.validation.withoutWorkflowOutputLabels
+      );
+      const diagnostics = await rule.validate(wfDocument);
+      expect(diagnostics).toHaveLength(2);
+      diagnostics.forEach((diagnostic) => {
+        expect(diagnostic.message).toBe("Missing label in workflow output.");
+      });
+    });
+  });
+});