From f226f95da39a0d5d5f0ca48b198813e57137c2c1 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Sun, 9 Jun 2024 10:24:37 +0200
Subject: [PATCH 1/7] Improve document detection

Detect not only .yml but also .yaml document extensions.
---
 client/package-lock.json           | 13 +++-
 client/package.json                |  3 +-
 client/src/common/utils.ts         | 98 ++++++++++++++++++++----------
 client/src/requests/gxworkflows.ts | 25 ++++++--
 package-lock.json                  |  4 +-
 5 files changed, 101 insertions(+), 42 deletions(-)

diff --git a/client/package-lock.json b/client/package-lock.json
index ad46de4..ac0b888 100644
--- a/client/package-lock.json
+++ b/client/package-lock.json
@@ -9,7 +9,8 @@
       "version": "0.1.0",
       "license": "MIT",
       "dependencies": {
-        "vscode-languageclient": "^8.1.0"
+        "vscode-languageclient": "^8.1.0",
+        "vscode-uri": "^3.0.8"
       },
       "engines": {
         "vscode": "^1.63.0"
@@ -99,6 +100,11 @@
       "resolved": "https://registry.npmjs.org/vscode-languageserver-types/-/vscode-languageserver-types-3.17.3.tgz",
       "integrity": "sha512-SYU4z1dL0PyIMd4Vj8YOqFvHu7Hz/enbWtpfnVbJHU4Nd1YNYx8u0ennumc6h48GQNeOLxmwySmnADouT/AuZA=="
     },
+    "node_modules/vscode-uri": {
+      "version": "3.0.8",
+      "resolved": "https://registry.npmjs.org/vscode-uri/-/vscode-uri-3.0.8.tgz",
+      "integrity": "sha512-AyFQ0EVmsOZOlAnxoFOGOq1SQDWAB7C6aqMGS23svWAllfOaxbuFvcT8D1i8z3Gyn8fraVeZNNmN6e9bxxXkKw=="
+    },
     "node_modules/yallist": {
       "version": "4.0.0",
       "resolved": "https://registry.npmjs.org/yallist/-/yallist-4.0.0.tgz",
@@ -172,6 +178,11 @@
       "resolved": "https://registry.npmjs.org/vscode-languageserver-types/-/vscode-languageserver-types-3.17.3.tgz",
       "integrity": "sha512-SYU4z1dL0PyIMd4Vj8YOqFvHu7Hz/enbWtpfnVbJHU4Nd1YNYx8u0ennumc6h48GQNeOLxmwySmnADouT/AuZA=="
     },
+    "vscode-uri": {
+      "version": "3.0.8",
+      "resolved": "https://registry.npmjs.org/vscode-uri/-/vscode-uri-3.0.8.tgz",
+      "integrity": "sha512-AyFQ0EVmsOZOlAnxoFOGOq1SQDWAB7C6aqMGS23svWAllfOaxbuFvcT8D1i8z3Gyn8fraVeZNNmN6e9bxxXkKw=="
+    },
     "yallist": {
       "version": "4.0.0",
       "resolved": "https://registry.npmjs.org/yallist/-/yallist-4.0.0.tgz",
diff --git a/client/package.json b/client/package.json
index fef8b52..b8b8e13 100644
--- a/client/package.json
+++ b/client/package.json
@@ -16,7 +16,8 @@
     "vscode": "^1.63.0"
   },
   "dependencies": {
-    "vscode-languageclient": "^8.1.0"
+    "vscode-languageclient": "^8.1.0",
+    "vscode-uri": "^3.0.8"
   },
   "scripts": {
     "webpack": "webpack",
diff --git a/client/src/common/utils.ts b/client/src/common/utils.ts
index 1d69a51..c143596 100644
--- a/client/src/common/utils.ts
+++ b/client/src/common/utils.ts
@@ -1,4 +1,5 @@
-import { OutputChannel, Uri, workspace } from "vscode";
+import { workspace } from "vscode";
+import { URI } from "vscode-uri";
 
 /**
  * Determines if the current workspace contains
@@ -22,8 +23,8 @@ export function getWorkspaceScheme(): "file" | "vscode-vfs" {
  * @param targetScheme The new scheme.
  * @returns A new copy of the URI with the new scheme.
  */
-export function replaceUriScheme(uri: Uri, targetScheme: string): Uri {
-  return Uri.parse(uri.toString().replace(uri.scheme, targetScheme));
+export function replaceUriScheme(uri: URI, targetScheme: string): URI {
+  return URI.parse(uri.toString().replace(uri.scheme, targetScheme));
 }
 
 /**
@@ -32,44 +33,77 @@ export function replaceUriScheme(uri: Uri, targetScheme: string): Uri {
  * @param ref The git ref to add to the URI query
  * @returns The URI with a ref query value set
  */
-export function addRefToUri(uri: Uri, ref: string): Uri {
-  return Uri.parse(uri.toString() + `?ref=${ref}`);
+export function addRefToUri(uri: URI, ref: string): URI {
+  return URI.parse(uri.toString() + `?ref=${ref}`);
 }
 
-/** Just for debugging */
-export function debugPrintCommandArgs(command: string, args: unknown[], outputChannel: OutputChannel): void {
-  outputChannel.appendLine(`Command ${command} args:`);
-  for (let index = 0; index < args.length; index++) {
-    const element = args[index];
-    outputChannel.appendLine(` [${index}] ${JSON.stringify(element)}`);
-  }
-  outputChannel.appendLine(`---\n`);
+// Workflow tests document can end with -test.yml, -tests.yml, -test.yaml, -tests.yaml
+const workflowTestsDocumentPattern = /(.*)-(test|tests)\.(yml|yaml)$/;
+
+// Workflow format1 documents can end with .ga
+// Workflow format2 documents can end with .gxwf.yml or .gxwf.yaml
+const format1WorkflowDocumentPattern = /\.ga$/;
+const format2WorkflowDocumentPattern = /\.gxwf\.(yml|yaml)$/;
+
+export function isWorkflowTestsDocument(uri: URI): boolean {
+  return workflowTestsDocumentPattern.test(uri.path);
+}
+
+export function isNativeWorkflowDocument(uri: URI): boolean {
+  return format1WorkflowDocumentPattern.test(uri.path);
 }
 
-export function isWorkflowTestsDocument(uri: Uri): boolean {
-  return uri.path.endsWith("-test.yml") || uri.path.endsWith("-tests.yml");
+export function isFormat2WorkflowDocument(uri: URI): boolean {
+  return format2WorkflowDocumentPattern.test(uri.path);
+}
+
+export async function getAssociatedWorkflowUriFromTestsUri(workflowTestsDocumentUri: URI): Promise<URI | undefined> {
+  if (!isWorkflowTestsDocument(workflowTestsDocumentUri)) {
+    return undefined;
+  }
+
+  //Try to find a format1 workflow document first
+  let workflowDocumentUri = replaceUriPattern(workflowTestsDocumentUri, workflowTestsDocumentPattern, ".ga");
+  if (await fileUriExistsInWorkspace(workflowDocumentUri)) {
+    return workflowDocumentUri;
+  }
+  //Try to find a format2 workflow document
+  workflowDocumentUri = replaceUriPattern(workflowTestsDocumentUri, workflowTestsDocumentPattern, ".gxwf.yaml");
+  if (await fileUriExistsInWorkspace(workflowDocumentUri)) {
+    return workflowDocumentUri;
+  }
+
+  workflowDocumentUri = replaceUriPattern(workflowTestsDocumentUri, workflowTestsDocumentPattern, ".gxwf.yml");
+  if (await fileUriExistsInWorkspace(workflowDocumentUri)) {
+    return workflowDocumentUri;
+  }
+  return undefined;
 }
 
-export function isNativeWorkflowDocument(uri: Uri): boolean {
-  return uri.path.endsWith(".ga");
+/**
+ * Replaces the matched pattern in the URI path with the replacement.
+ * @param uri The URI to be modified.
+ * @param pattern The pattern to match in the URI path.
+ * @param replacement The replacement string.
+ * @returns A new copy of the URI with the pattern replaced.
+ */
+export function replaceUriPattern(uri: URI, pattern: RegExp, replacement: string): URI {
+  const uriString = uri.toString();
+  const newUriString = uriString.replace(pattern, `$1${replacement}`);
+  const result = URI.parse(newUriString);
+  return result;
 }
 
-export async function getAssociatedWorkflowUriFromTestsUri(workflowTestsDocumentUri: Uri): Promise<Uri | undefined> {
-  const format2WorkflowUri = Uri.parse(
-    workflowTestsDocumentUri.toString().replace("-test.yml", ".gxwf.yml").replace("-tests.yml", ".gxwf.yml")
-  );
+/**
+ * Determines if a file exists at the given URI in the workspace.
+ * @param uri The URI to check for existence.
+ * @returns true if the (virtual) file exists, false otherwise.
+ */
+export async function fileUriExistsInWorkspace(uri: URI): Promise<boolean> {
   try {
-    await workspace.fs.stat(format2WorkflowUri);
-    return format2WorkflowUri;
+    await workspace.fs.stat(uri);
+    return true;
   } catch {
-    const nativeWorkflowUri = Uri.parse(
-      workflowTestsDocumentUri.toString().replace("-test.yml", ".ga").replace("-tests.yml", ".ga")
-    );
-    try {
-      await workspace.fs.stat(nativeWorkflowUri);
-      return nativeWorkflowUri;
-    } catch {
-      return undefined;
-    }
+    return false;
   }
 }
diff --git a/client/src/requests/gxworkflows.ts b/client/src/requests/gxworkflows.ts
index baad2f4..42ec2a7 100644
--- a/client/src/requests/gxworkflows.ts
+++ b/client/src/requests/gxworkflows.ts
@@ -12,6 +12,8 @@ import {
   TargetWorkflowDocumentParams,
 } from "../languageTypes";
 
+const TEST_DOCUMENT_TO_WORKFLOW_DOCUMENT_URI_MAP = new Map<string, Uri>();
+
 export function setupRequests(
   context: ExtensionContext,
   nativeWorkflowClient: BaseLanguageClient,
@@ -19,23 +21,34 @@ export function setupRequests(
 ): void {
   function createRequestHandler<TResult>(requestIdentifier: string) {
     return async (params: TargetWorkflowDocumentParams) => {
-      let targetUri: Uri | undefined = Uri.parse(params.uri);
+      const targetUri: Uri | undefined = Uri.parse(params.uri);
+      let resultUri: Uri | undefined = undefined;
       if (isWorkflowTestsDocument(targetUri)) {
         // If the target is a test file, we need to find the associated workflow file
-        targetUri = await getAssociatedWorkflowUriFromTestsUri(targetUri);
+        //Try cache first
+        const cacheKey = targetUri.toString();
+        if (TEST_DOCUMENT_TO_WORKFLOW_DOCUMENT_URI_MAP.has(cacheKey)) {
+          resultUri = TEST_DOCUMENT_TO_WORKFLOW_DOCUMENT_URI_MAP.get(cacheKey)!;
+        }
+        if (!resultUri) {
+          resultUri = await getAssociatedWorkflowUriFromTestsUri(targetUri);
+          if (resultUri) {
+            TEST_DOCUMENT_TO_WORKFLOW_DOCUMENT_URI_MAP.set(cacheKey, resultUri);
+          }
+        }
       }
-      if (!targetUri) {
+      if (!resultUri) {
         console.debug("No associated workflow file found for:", params.uri);
         return undefined;
       }
       // Open the file to include it in the document cache
-      await workspace.openTextDocument(targetUri);
+      await workspace.openTextDocument(resultUri);
 
       let languageClient = gxFormat2Client;
-      if (isNativeWorkflowDocument(targetUri)) {
+      if (isNativeWorkflowDocument(resultUri)) {
         languageClient = nativeWorkflowClient;
       }
-      const requestParams: TargetWorkflowDocumentParams = { uri: targetUri.toString() };
+      const requestParams: TargetWorkflowDocumentParams = { uri: resultUri.toString() };
       const result = await languageClient.sendRequest<TResult>(requestIdentifier, requestParams);
       return result;
     };
diff --git a/package-lock.json b/package-lock.json
index fe78658..bc3ca55 100644
--- a/package-lock.json
+++ b/package-lock.json
@@ -1,12 +1,12 @@
 {
   "name": "galaxy-workflows",
-  "version": "0.3.1",
+  "version": "0.4.0",
   "lockfileVersion": 2,
   "requires": true,
   "packages": {
     "": {
       "name": "galaxy-workflows",
-      "version": "0.3.1",
+      "version": "0.4.0",
       "hasInstallScript": true,
       "license": "MIT",
       "devDependencies": {

From 42d6114ba812619a49e4385a3e6f7993e18d1fab Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Sun, 9 Jun 2024 10:25:00 +0200
Subject: [PATCH 2/7] Add unit tests for isWorkflowTestsDocument,
 isNativeWorkflowDocument, and isFormat2WorkflowDocument

---
 client/tests/unit/utils.test.ts | 62 +++++++++++++++++++++++++++++++++
 1 file changed, 62 insertions(+)
 create mode 100644 client/tests/unit/utils.test.ts

diff --git a/client/tests/unit/utils.test.ts b/client/tests/unit/utils.test.ts
new file mode 100644
index 0000000..f3e3428
--- /dev/null
+++ b/client/tests/unit/utils.test.ts
@@ -0,0 +1,62 @@
+import { it } from "@jest/globals"; // This is a workaround for type clashes between jest and mocha
+import { URI } from "vscode-uri";
+import { isFormat2WorkflowDocument, isNativeWorkflowDocument, isWorkflowTestsDocument } from "../../src/common/utils";
+
+jest.mock(
+  "vscode",
+  () => ({
+    workspace: {
+      // Mock properties and methods of `workspace` as needed for your tests
+    },
+    // Add other vscode namespaces and members you need to mock
+  }),
+  { virtual: true }
+);
+
+describe("Common Utils", () => {
+  describe("isWorkflowTestsDocument", () => {
+    it.each([
+      ["-test.yml", true],
+      ["-tests.yml", true],
+      ["-test.yaml", true],
+      ["-tests.yaml", true],
+      ["test.txt", false],
+      ["tests.txt", false],
+      ["test.yml", false],
+      ["tests.yml", false],
+      ["whatever.test.yml", false],
+      ["whatever.gxwf.test.yml", false],
+      ["whatevertest.yml", false],
+      ["whatever.gxwftest.yml", false],
+    ])("given '%s' should return %s", (input: string, expected: boolean) => {
+      expect(isWorkflowTestsDocument(URI.parse(input))).toBe(expected);
+    });
+  });
+
+  describe("isNativeWorkflowDocument", () => {
+    it.each([
+      ["test.ga", true],
+      ["whatever.ga", true],
+      ["asd.txt", false],
+      ["test.yaml", false],
+    ])("given '%s' should return %s", (input: string, expected: boolean) => {
+      expect(isNativeWorkflowDocument(URI.parse(input))).toBe(expected);
+    });
+  });
+
+  describe("isFormat2WorkflowDocument", () => {
+    it.each([
+      ["test.gxwf.yaml", true],
+      ["whatever.gxwf.yaml", true],
+      ["test.gxwf.yml", true],
+      ["whatever.gxwf.yml", true],
+      ["asd.txt", false],
+      ["-test.yaml", false],
+      ["whatever-test.yaml", false],
+      ["whatever.gxwf-test.yaml", false],
+      ["whatever.gxwf.test.yaml", false],
+    ])("given '%s' should return %s", (input: string, expected: boolean) => {
+      expect(isFormat2WorkflowDocument(URI.parse(input))).toBe(expected);
+    });
+  });
+});

From 842af7afaf6e19b64e54da01d4d2df10ec1e8101 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Sun, 9 Jun 2024 17:11:37 +0200
Subject: [PATCH 3/7] Add test coverage for
 getAssociatedWorkflowUriFromTestsUri

---
 client/tests/unit/utils.test.ts | 57 +++++++++++++++++++++++++++++++--
 1 file changed, 54 insertions(+), 3 deletions(-)

diff --git a/client/tests/unit/utils.test.ts b/client/tests/unit/utils.test.ts
index f3e3428..9728616 100644
--- a/client/tests/unit/utils.test.ts
+++ b/client/tests/unit/utils.test.ts
@@ -1,14 +1,33 @@
 import { it } from "@jest/globals"; // This is a workaround for type clashes between jest and mocha
 import { URI } from "vscode-uri";
-import { isFormat2WorkflowDocument, isNativeWorkflowDocument, isWorkflowTestsDocument } from "../../src/common/utils";
+import {
+  getAssociatedWorkflowUriFromTestsUri,
+  isFormat2WorkflowDocument,
+  isNativeWorkflowDocument,
+  isWorkflowTestsDocument,
+} from "../../src/common/utils";
+
+// Partially mimics vscode FileStat interface
+interface FileStat {
+  size: number;
+}
+
+const FILES_IN_WORKSPACE = ["workflow1.ga", "workflow2.gxwf.yaml", "workflow3.gxwf.yml"];
 
 jest.mock(
   "vscode",
   () => ({
     workspace: {
-      // Mock properties and methods of `workspace` as needed for your tests
+      fs: {
+        stat: (uri: URI) => {
+          const file = FILES_IN_WORKSPACE.find((f) => URI.parse(f).path === uri.path);
+          if (file) {
+            return Promise.resolve<FileStat>({ size: file.length });
+          }
+          throw new Error(`File not found: ${uri.path}`);
+        },
+      },
     },
-    // Add other vscode namespaces and members you need to mock
   }),
   { virtual: true }
 );
@@ -59,4 +78,36 @@ describe("Common Utils", () => {
       expect(isFormat2WorkflowDocument(URI.parse(input))).toBe(expected);
     });
   });
+
+  describe("getAssociatedWorkflowUriFromTestsUri", () => {
+    it("should return undefined if the input URI is not a workflow tests document", async () => {
+      const uri = URI.parse("test.txt");
+      const result = await getAssociatedWorkflowUriFromTestsUri(uri);
+      expect(result).toBeUndefined();
+    });
+
+    it("should return the associated (.ga) workflow document URI if it exists in workspace", async () => {
+      const uri = URI.parse("workflow1-test.yaml");
+      const result = await getAssociatedWorkflowUriFromTestsUri(uri);
+      expect(result?.path.endsWith("workflow1.ga")).toBe(true);
+    });
+
+    it("should return the associated (yaml) workflow document URI if it exists in workspace", async () => {
+      const uri = URI.parse("workflow2-test.yaml");
+      const result = await getAssociatedWorkflowUriFromTestsUri(uri);
+      expect(result?.path.endsWith("workflow2.gxwf.yaml")).toBe(true);
+    });
+
+    it("should return the associated (yml) workflow document URI if it exists in workspace", async () => {
+      const uri = URI.parse("workflow3-tests.yaml");
+      const result = await getAssociatedWorkflowUriFromTestsUri(uri);
+      expect(result?.path.endsWith("workflow3.gxwf.yml")).toBe(true);
+    });
+
+    it("should return undefined if the associated workflow document does not exist in workspace", async () => {
+      const uri = URI.parse("nonexistent-test.yaml");
+      const result = await getAssociatedWorkflowUriFromTestsUri(uri);
+      expect(result).toBeUndefined();
+    });
+  });
 });

From 7521fae99ae4b7070c7427d942cb220a0dcd18cc Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Sun, 9 Jun 2024 17:21:11 +0200
Subject: [PATCH 4/7] Add support for additional workflow file extensions

This improves the document detection for Galaxy workflow and tests files.
---
 package.json | 8 ++++++--
 1 file changed, 6 insertions(+), 2 deletions(-)

diff --git a/package.json b/package.json
index eb9c3cc..0155651 100644
--- a/package.json
+++ b/package.json
@@ -57,7 +57,8 @@
           "Galaxy Workflow (YAML)"
         ],
         "extensions": [
-          ".gxwf.yml"
+          ".gxwf.yml",
+          ".gxwf.yaml"
         ],
         "configuration": "./workflow-languages/configurations/yml.language-configuration.json"
       },
@@ -67,7 +68,10 @@
           "Galaxy Workflow Tests (YAML)"
         ],
         "extensions": [
-          "-tests.yml"
+          "-test.yml",
+          "-tests.yml",
+          "-test.yaml",
+          "-tests.yaml"
         ],
         "configuration": "./workflow-languages/configurations/yml.language-configuration.json"
       }

From 4d6f322e14d52b7adf8e061a93d3399a8016b598 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Sun, 9 Jun 2024 17:25:52 +0200
Subject: [PATCH 5/7] Remove placeholder test file

---
 client/tests/unit/client.test.ts | 5 -----
 1 file changed, 5 deletions(-)
 delete mode 100644 client/tests/unit/client.test.ts

diff --git a/client/tests/unit/client.test.ts b/client/tests/unit/client.test.ts
deleted file mode 100644
index 7d80b5d..0000000
--- a/client/tests/unit/client.test.ts
+++ /dev/null
@@ -1,5 +0,0 @@
-describe("Client", () => {
-  it("should test", () => {
-    expect(true).toBe(true);
-  });
-});

From 52f3f807bb8d4543c6f95560f3adee6718b6585a Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Sun, 9 Jun 2024 17:55:59 +0200
Subject: [PATCH 6/7] Update vscode launch configuration and e2e test file
 paths

---
 .vscode/launch.json               | 4 ++--
 client/tests/e2e/suite/helpers.ts | 6 +++---
 package.json                      | 6 +++---
 server/package.json               | 1 +
 4 files changed, 9 insertions(+), 8 deletions(-)

diff --git a/.vscode/launch.json b/.vscode/launch.json
index 848517e..c4af8a1 100644
--- a/.vscode/launch.json
+++ b/.vscode/launch.json
@@ -82,9 +82,9 @@
       "args": [
         "--disable-extensions",
         "--extensionDevelopmentPath=${workspaceFolder}",
-        "--extensionTestsPath=${workspaceFolder}/client/out/e2e/suite/index"
+        "--extensionTestsPath=${workspaceFolder}/client/out/tests/e2e/suite/index"
       ],
-      "outFiles": ["${workspaceFolder}client/out/e2e/**/*.js"],
+      "outFiles": ["${workspaceFolder}client/out/tests/e2e/**/*.js"],
       "preLaunchTask": {
         "type": "npm",
         "script": "test-compile"
diff --git a/client/tests/e2e/suite/helpers.ts b/client/tests/e2e/suite/helpers.ts
index 39d742a..29edd10 100644
--- a/client/tests/e2e/suite/helpers.ts
+++ b/client/tests/e2e/suite/helpers.ts
@@ -1,6 +1,6 @@
-import * as vscode from "vscode";
-import * as path from "path";
 import * as assert from "assert";
+import * as path from "path";
+import * as vscode from "vscode";
 
 /**
  * Contains the document and its corresponding editor
@@ -60,7 +60,7 @@ export async function waitForDiagnostics(docUri: vscode.Uri, timeoutInMillisecon
 }
 
 export const getDocPath = (filePath: string): string => {
-  return path.resolve(__dirname, path.join("..", "..", "..", "..", "test-data", filePath));
+  return path.resolve(__dirname, path.join("..", "..", "..", "..", "..", "test-data", filePath));
 };
 
 export const getDocUri = (filePath: string): vscode.Uri => {
diff --git a/package.json b/package.json
index 0155651..17b3e5e 100644
--- a/package.json
+++ b/package.json
@@ -219,7 +219,7 @@
     "postinstall": "cd client && npm install && cd ../server && npm install && cd ..",
     "lint": "eslint ./client/src ./server --ext .ts,.tsx",
     "format": "prettier --write .",
-    "clean": "rimraf client/dist && rimraf server/dist",
+    "clean": "rimraf client/dist && rimraf client/out && cd server && npm run clean && cd ..",
     "compile-servers": "cd server && npm run compile",
     "compile": "npm run clean && webpack --config ./client/webpack.config.js && npm run compile-servers",
     "vscode:prepublish": "npm run compile",
@@ -230,8 +230,8 @@
     "test-client": "cd client && npm test",
     "test-server": "cd server && npm test",
     "test-compile": "tsc --project ./client --outDir client/out",
-    "pretest:e2e": "npm run compile && npm run test-compile",
-    "test:e2e": "node ./client/out/e2e/runTests.js",
+    "pretest:e2e": "npm run clean && npm run compile && npm run test-compile",
+    "test:e2e": "node ./client/out/tests/e2e/runTests.js",
     "test-browser": "vscode-test-web --extensionDevelopmentPath=. ./test-data"
   },
   "devDependencies": {
diff --git a/server/package.json b/server/package.json
index a75b4d1..7461cd8 100644
--- a/server/package.json
+++ b/server/package.json
@@ -6,6 +6,7 @@
   "author": "davelopez",
   "license": "MIT",
   "scripts": {
+    "clean": "rimraf ./gx-workflow-ls-native/dist && rimraf ./gx-workflow-ls-format2/dist",
     "compile-native-server": "webpack --config ./gx-workflow-ls-native/webpack.config.js",
     "compile-format2-server": "webpack --config ./gx-workflow-ls-format2/webpack.config.js",
     "compile": "npm run compile-native-server && npm run compile-format2-server",

From 866a8a649df9fbfc5d6ef7c5e74cb6f342011b30 Mon Sep 17 00:00:00 2001
From: davelopez <46503462+davelopez@users.noreply.github.com>
Date: Mon, 10 Jun 2024 09:32:47 +0200
Subject: [PATCH 7/7] Refactor e2e tests configuration + strict types in client

---
 client/package-lock.json                   | 65 ++++++++++++++++++++++
 client/package.json                        |  3 +
 client/src/commands/index.ts               |  5 ++
 client/tests/e2e/runTests.ts               |  2 +-
 client/tests/e2e/suite/extension.ga.e2e.ts | 15 +++--
 client/tests/e2e/suite/helpers.ts          | 10 ++--
 client/tests/e2e/tsconfig.json             | 11 ++++
 client/tsconfig.json                       |  5 +-
 package.json                               |  2 +-
 9 files changed, 104 insertions(+), 14 deletions(-)
 create mode 100644 client/tests/e2e/tsconfig.json

diff --git a/client/package-lock.json b/client/package-lock.json
index ac0b888..7489b81 100644
--- a/client/package-lock.json
+++ b/client/package-lock.json
@@ -12,10 +12,38 @@
         "vscode-languageclient": "^8.1.0",
         "vscode-uri": "^3.0.8"
       },
+      "devDependencies": {
+        "@types/glob": "^8.1.0"
+      },
       "engines": {
         "vscode": "^1.63.0"
       }
     },
+    "node_modules/@types/glob": {
+      "version": "8.1.0",
+      "resolved": "https://registry.npmjs.org/@types/glob/-/glob-8.1.0.tgz",
+      "integrity": "sha512-IO+MJPVhoqz+28h1qLAcBEH2+xHMK6MTyHJc7MTnnYb6wsoLR29POVGJ7LycmVXIqyy/4/2ShP5sUwTXuOwb/w==",
+      "dev": true,
+      "dependencies": {
+        "@types/minimatch": "^5.1.2",
+        "@types/node": "*"
+      }
+    },
+    "node_modules/@types/minimatch": {
+      "version": "5.1.2",
+      "resolved": "https://registry.npmjs.org/@types/minimatch/-/minimatch-5.1.2.tgz",
+      "integrity": "sha512-K0VQKziLUWkVKiRVrx4a40iPaxTUefQmjtkQofBkYRcoaaL/8rhwDWww9qWbrgicNOgnpIsMxyNIUM4+n6dUIA==",
+      "dev": true
+    },
+    "node_modules/@types/node": {
+      "version": "20.14.2",
+      "resolved": "https://registry.npmjs.org/@types/node/-/node-20.14.2.tgz",
+      "integrity": "sha512-xyu6WAMVwv6AKFLB+e/7ySZVr/0zLCzOa7rSpq6jNwpqOrUbcACDWC+53d4n2QHOnDou0fbIsg8wZu/sxrnI4Q==",
+      "dev": true,
+      "dependencies": {
+        "undici-types": "~5.26.4"
+      }
+    },
     "node_modules/balanced-match": {
       "version": "1.0.2",
       "resolved": "https://registry.npmjs.org/balanced-match/-/balanced-match-1.0.2.tgz",
@@ -65,6 +93,12 @@
         "node": ">=10"
       }
     },
+    "node_modules/undici-types": {
+      "version": "5.26.5",
+      "resolved": "https://registry.npmjs.org/undici-types/-/undici-types-5.26.5.tgz",
+      "integrity": "sha512-JlCMO+ehdEIKqlFxk6IfVoAUVmgz7cU7zD/h9XZ0qzeosSHmUJVOzSQvvYSYWXkFXC+IfLKSIffhv0sVZup6pA==",
+      "dev": true
+    },
     "node_modules/vscode-jsonrpc": {
       "version": "8.1.0",
       "resolved": "https://registry.npmjs.org/vscode-jsonrpc/-/vscode-jsonrpc-8.1.0.tgz",
@@ -112,6 +146,31 @@
     }
   },
   "dependencies": {
+    "@types/glob": {
+      "version": "8.1.0",
+      "resolved": "https://registry.npmjs.org/@types/glob/-/glob-8.1.0.tgz",
+      "integrity": "sha512-IO+MJPVhoqz+28h1qLAcBEH2+xHMK6MTyHJc7MTnnYb6wsoLR29POVGJ7LycmVXIqyy/4/2ShP5sUwTXuOwb/w==",
+      "dev": true,
+      "requires": {
+        "@types/minimatch": "^5.1.2",
+        "@types/node": "*"
+      }
+    },
+    "@types/minimatch": {
+      "version": "5.1.2",
+      "resolved": "https://registry.npmjs.org/@types/minimatch/-/minimatch-5.1.2.tgz",
+      "integrity": "sha512-K0VQKziLUWkVKiRVrx4a40iPaxTUefQmjtkQofBkYRcoaaL/8rhwDWww9qWbrgicNOgnpIsMxyNIUM4+n6dUIA==",
+      "dev": true
+    },
+    "@types/node": {
+      "version": "20.14.2",
+      "resolved": "https://registry.npmjs.org/@types/node/-/node-20.14.2.tgz",
+      "integrity": "sha512-xyu6WAMVwv6AKFLB+e/7ySZVr/0zLCzOa7rSpq6jNwpqOrUbcACDWC+53d4n2QHOnDou0fbIsg8wZu/sxrnI4Q==",
+      "dev": true,
+      "requires": {
+        "undici-types": "~5.26.4"
+      }
+    },
     "balanced-match": {
       "version": "1.0.2",
       "resolved": "https://registry.npmjs.org/balanced-match/-/balanced-match-1.0.2.tgz",
@@ -149,6 +208,12 @@
         "lru-cache": "^6.0.0"
       }
     },
+    "undici-types": {
+      "version": "5.26.5",
+      "resolved": "https://registry.npmjs.org/undici-types/-/undici-types-5.26.5.tgz",
+      "integrity": "sha512-JlCMO+ehdEIKqlFxk6IfVoAUVmgz7cU7zD/h9XZ0qzeosSHmUJVOzSQvvYSYWXkFXC+IfLKSIffhv0sVZup6pA==",
+      "dev": true
+    },
     "vscode-jsonrpc": {
       "version": "8.1.0",
       "resolved": "https://registry.npmjs.org/vscode-jsonrpc/-/vscode-jsonrpc-8.1.0.tgz",
diff --git a/client/package.json b/client/package.json
index b8b8e13..9b90320 100644
--- a/client/package.json
+++ b/client/package.json
@@ -23,5 +23,8 @@
     "webpack": "webpack",
     "watch": "webpack --watch --progress",
     "test": "jest"
+  },
+  "devDependencies": {
+    "@types/glob": "^8.1.0"
   }
 }
diff --git a/client/src/commands/index.ts b/client/src/commands/index.ts
index e903df1..3de261b 100644
--- a/client/src/commands/index.ts
+++ b/client/src/commands/index.ts
@@ -57,6 +57,11 @@ export class ComparableWorkflow {
   uri: Uri;
   ref?: string;
 
+  constructor(uri: Uri, ref?: string) {
+    this.uri = uri;
+    this.ref = ref;
+  }
+
   // TODO: This is no longer working until a new API is available
   // ref: https://github.com/microsoft/vscode/issues/177319
   // ref: https://github.com/microsoft/vscode/issues/84297
diff --git a/client/tests/e2e/runTests.ts b/client/tests/e2e/runTests.ts
index c871f34..3d87e91 100644
--- a/client/tests/e2e/runTests.ts
+++ b/client/tests/e2e/runTests.ts
@@ -6,7 +6,7 @@ async function main(): Promise<void> {
   try {
     // The folder containing the Extension Manifest package.json
     // Passed to `--extensionDevelopmentPath`
-    const extensionDevelopmentPath = path.resolve(__dirname, "../../../");
+    const extensionDevelopmentPath = path.resolve(__dirname, "../../../../");
 
     // The path to test runner
     // Passed to --extensionTestsPath
diff --git a/client/tests/e2e/suite/extension.ga.e2e.ts b/client/tests/e2e/suite/extension.ga.e2e.ts
index 8cab3cd..1f387db 100644
--- a/client/tests/e2e/suite/extension.ga.e2e.ts
+++ b/client/tests/e2e/suite/extension.ga.e2e.ts
@@ -1,18 +1,18 @@
 // You can import and use all API from the 'vscode' module
 // as well as import your extension to test it
-import * as vscode from "vscode";
-import * as path from "path";
 import * as assert from "assert";
 import { beforeEach } from "mocha";
+import * as path from "path";
+import * as vscode from "vscode";
 import {
   activateAndOpenInEditor,
-  getDocUri,
+  assertDiagnostics,
   closeAllEditors,
+  getDocUri,
   openDocument,
+  resetSettings,
   sleep,
-  assertDiagnostics,
   updateSettings,
-  resetSettings,
   waitForDiagnostics,
 } from "./helpers";
 
@@ -22,7 +22,9 @@ suite("Native (JSON) Workflows", () => {
     test("Clean workflow command removes non-essential properties", async () => {
       const dirtyDocUri = getDocUri(path.join("json", "clean", "wf_01_dirty.ga"));
       const cleanDocUri = getDocUri(path.join("json", "clean", "wf_01_clean.ga"));
-      const { document } = await activateAndOpenInEditor(dirtyDocUri);
+      const editor = await activateAndOpenInEditor(dirtyDocUri);
+      const document = editor?.document;
+      assert.ok(document);
       await sleep(500); // Wait for extension to fully activate... yes Windows CI I'm looking at you...
       const dirtyDoc = document.getText();
       await vscode.commands.executeCommand("galaxy-workflows.cleanWorkflow");
@@ -30,6 +32,7 @@ suite("Native (JSON) Workflows", () => {
       const actualCleanJson = document.getText();
       assert.notEqual(dirtyDoc, actualCleanJson);
       const expectedCleanDocument = await openDocument(cleanDocUri);
+      assert.ok(expectedCleanDocument);
       const expectedCleanJson = expectedCleanDocument.getText();
       assert.strictEqual(actualCleanJson, expectedCleanJson);
     });
diff --git a/client/tests/e2e/suite/helpers.ts b/client/tests/e2e/suite/helpers.ts
index 29edd10..939ac28 100644
--- a/client/tests/e2e/suite/helpers.ts
+++ b/client/tests/e2e/suite/helpers.ts
@@ -12,11 +12,11 @@ export interface DocumentEditor {
 
 export async function activate(): Promise<unknown> {
   const ext = vscode.extensions.getExtension("davelopez.galaxy-workflows");
-  const api = ext.isActive ? ext.exports : await ext.activate();
+  const api = ext?.isActive ? ext.exports : await ext?.activate();
   return api;
 }
 
-export async function openDocumentInEditor(docUri: vscode.Uri): Promise<DocumentEditor> {
+export async function openDocumentInEditor(docUri: vscode.Uri): Promise<DocumentEditor | undefined> {
   try {
     const document = await vscode.workspace.openTextDocument(docUri);
     const editor = await vscode.window.showTextDocument(document);
@@ -29,16 +29,18 @@ export async function openDocumentInEditor(docUri: vscode.Uri): Promise<Document
   }
 }
 
-export async function openDocument(docUri: vscode.Uri): Promise<vscode.TextDocument> {
+export async function openDocument(docUri: vscode.Uri): Promise<vscode.TextDocument | undefined> {
   try {
     const document = await vscode.workspace.openTextDocument(docUri);
     return document;
   } catch (e) {
     console.error(e);
   }
+
+  return undefined;
 }
 
-export async function activateAndOpenInEditor(docUri: vscode.Uri): Promise<DocumentEditor> {
+export async function activateAndOpenInEditor(docUri: vscode.Uri): Promise<DocumentEditor | undefined> {
   await activate();
   const documentEditor = await openDocumentInEditor(docUri);
   return documentEditor;
diff --git a/client/tests/e2e/tsconfig.json b/client/tests/e2e/tsconfig.json
new file mode 100644
index 0000000..e5954c9
--- /dev/null
+++ b/client/tests/e2e/tsconfig.json
@@ -0,0 +1,11 @@
+{
+  "compilerOptions": {
+    "target": "es2019",
+    "lib": ["ES2019", "WebWorker"],
+    "module": "commonjs",
+    "sourceMap": true,
+    "strict": true,
+    "baseUrl": ".",
+    "skipLibCheck": true
+  }
+}
diff --git a/client/tsconfig.json b/client/tsconfig.json
index c7417ce..4c4d44d 100644
--- a/client/tsconfig.json
+++ b/client/tsconfig.json
@@ -1,10 +1,11 @@
 {
   "compilerOptions": {
-    "module": "commonjs",
     "target": "es2019",
     "lib": ["ES2019", "WebWorker"],
-    "rootDirs": ["src", "tests"],
+    "module": "commonjs",
     "sourceMap": true,
+    "strict": true,
+    "baseUrl": ".",
     "skipLibCheck": true
   },
   "include": ["tests"],
diff --git a/package.json b/package.json
index 17b3e5e..b76536f 100644
--- a/package.json
+++ b/package.json
@@ -229,7 +229,7 @@
     "test": "npm run test-client && npm run test-server",
     "test-client": "cd client && npm test",
     "test-server": "cd server && npm test",
-    "test-compile": "tsc --project ./client --outDir client/out",
+    "test-compile": "tsc --project ./client/tests/e2e --outDir client/out/tests/e2e",
     "pretest:e2e": "npm run clean && npm run compile && npm run test-compile",
     "test:e2e": "node ./client/out/tests/e2e/runTests.js",
     "test-browser": "vscode-test-web --extensionDevelopmentPath=. ./test-data"