Fix clean workflow

client/tests/e2e/runTests.ts

@@ -2,11 +2,11 @@ import * as path from "path";
 
 import { runTests } from "@vscode/test-electron";
 
-async function main() {
+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

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

@@ -1,14 +1,27 @@
-import * as assert from "assert";
-
 // 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 myExtension from '../../extension';
+import * as path from "path";
+import * as assert from "assert";
+import { activateAndOpenInEditor, getDocUri, closeAllEditors, openDocument, sleep } from "./helpers";
 
 suite("Extension Test Suite", () => {
-  vscode.window.showInformationMessage("Start all tests.");
-
-  test("Sample test", () => {
-    assert.strictEqual([1, 2, 3].indexOf(5), -1);
+  teardown(closeAllEditors);
+  suite("Native (JSON) Workflows", () => {
+    suite("Commands Tests", () => {
+      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 dirtyDoc = document.getText();
+        await vscode.commands.executeCommand("galaxy-workflows.cleanWorkflow");
+        await sleep(1000); // Wait for command to apply changes
+        const actualCleanJson = document.getText();
+        assert.notEqual(dirtyDoc, actualCleanJson);
+        const expectedCleanDocument = await openDocument(cleanDocUri);
+        const expectedCleanJson = expectedCleanDocument.getText();
+        assert.strictEqual(actualCleanJson, expectedCleanJson);
+      });
+    });
   });
 });

client/tests/e2e/suite/helpers.ts

@@ -0,0 +1,84 @@
+import * as vscode from "vscode";
+import * as path from "path";
+import * as assert from "assert";
+
+/**
+ * Contains the document and its corresponding editor
+ */
+export interface DocumentEditor {
+  editor: vscode.TextEditor;
+  document: vscode.TextDocument;
+}
+
+export async function activate(): Promise<unknown> {
+  const ext = vscode.extensions.getExtension("davelopez.galaxy-workflows");
+  const api = ext.isActive ? ext.exports : await ext.activate();
+  return api;
+}
+
+export async function openDocumentInEditor(docUri: vscode.Uri): Promise<DocumentEditor> {
+  try {
+    const document = await vscode.workspace.openTextDocument(docUri);
+    const editor = await vscode.window.showTextDocument(document);
+    return {
+      editor,
+      document,
+    };
+  } catch (e) {
+    console.error(e);
+  }
+}
+
+export async function openDocument(docUri: vscode.Uri): Promise<vscode.TextDocument> {
+  try {
+    const document = await vscode.workspace.openTextDocument(docUri);
+    return document;
+  } catch (e) {
+    console.error(e);
+  }
+}
+
+export async function activateAndOpenInEditor(docUri: vscode.Uri): Promise<DocumentEditor> {
+  await activate();
+  const documentEditor = await openDocumentInEditor(docUri);
+  await sleep(2000); // Wait for server activation
+  return documentEditor;
+}
+
+export async function sleep(ms: number): Promise<void> {
+  return new Promise((resolve) => setTimeout(resolve, ms));
+}
+
+export const getDocPath = (filePath: string): string => {
+  return path.resolve(__dirname, path.join("..", "..", "..", "..", "test-data", filePath));
+};
+
+export const getDocUri = (filePath: string): vscode.Uri => {
+  return vscode.Uri.file(getDocPath(filePath));
+};
+
+export async function assertDiagnostics(docUri: vscode.Uri, expectedDiagnostics: vscode.Diagnostic[]): Promise<void> {
+  const actualDiagnostics = vscode.languages.getDiagnostics(docUri);
+
+  assert.equal(actualDiagnostics.length, expectedDiagnostics.length);
+
+  expectedDiagnostics.forEach((expectedDiagnostic, i) => {
+    const actualDiagnostic = actualDiagnostics[i];
+    assert.equal(actualDiagnostic.message, expectedDiagnostic.message);
+    assert.deepEqual(actualDiagnostic.range, expectedDiagnostic.range);
+    assert.equal(actualDiagnostic.severity, expectedDiagnostic.severity);
+  });
+}
+
+/**
+ * Asserts that the given workflow document has no diagnostics i.e. is valid.
+ * @param docUri Workflow document URI
+ */
+export async function assertValid(docUri: vscode.Uri): Promise<void> {
+  const actualDiagnostics = vscode.languages.getDiagnostics(docUri);
+  assert.equal(actualDiagnostics.length, 0);
+}
+
+export function closeAllEditors(): Thenable<unknown> {
+  return vscode.commands.executeCommand("workbench.action.closeAllEditors");
+}

client/tests/e2e/suite/index.ts

@@ -7,6 +7,8 @@ export function run(): Promise<void> {
   const mocha = new Mocha({
     ui: "tdd",
     color: true,
+    timeout: 60000,
+    inlineDiffs: true,
   });
 
   const testsRoot = path.resolve(__dirname, "..");

package.json

@@ -181,7 +181,7 @@
     "test-unit-client": "cd client && npm run test-unit && cd ..",
     "test-unit-server": "cd server && npm run test-unit && cd ..",
     "test-compile": "tsc --project ./client --outDir client/out",
-    "pretest:e2e": "npm run test-compile",
+    "pretest:e2e": "npm run compile && npm run test-compile",
     "test:e2e": "node ./client/out/e2e/runTests.js"
   },
   "devDependencies": {

server/src/commands/cleanWorkflow.ts

@@ -105,7 +105,10 @@ export class CleanWorkflowCommand extends CustomCommand {
       // Remove trailing comma in previous property node
       const isLastNode = workflowDocument.isLastNodeInParent(node);
       if (isLastNode) {
-        const previousNode = workflowDocument.getPreviousSiblingNode(node);
+        let previousNode = workflowDocument.getPreviousSiblingNode(node);
+        while (previousNode && nodesToRemove.includes(previousNode)) {
+          previousNode = workflowDocument.getPreviousSiblingNode(previousNode);
+        }
         if (previousNode) {
           const range = this.getFullNodeRange(workflowDocument.textDocument, previousNode);
           const nodeText = workflowDocument.textDocument.getText(range);
@@ -132,10 +135,7 @@ export class CleanWorkflowCommand extends CustomCommand {
     return result;
   }
 
-  private getNonEssentialNodes(
-    workflowDocument: WorkflowDocument,
-    cleanablePropertyNames: Set<string>
-  ): PropertyASTNode[] {
+  private getNonEssentialNodes(workflowDocument: WorkflowDocument, cleanablePropertyNames: Set<string>): ASTNode[] {
     const root = workflowDocument.rootNode;
     if (!root) {
       return [];

test-data/json/clean/wf_01_clean.ga

@@ -0,0 +1,71 @@
+{
+    "a_galaxy_workflow": "true",
+    "annotation": "This is a cool workflow",
+    "format-version": "0.1",
+    "license": "MIT",
+    "name": "Cool workflow",
+    "steps": {
+        "0": {
+            "annotation": "Some text",
+            "content_id": null,
+            "id": 0,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "Some text",
+                    "name": "The cool input"
+                }
+            ],
+            "label": "The cool input",
+            "name": "Input dataset",
+            "outputs": [],
+            "tool_id": null,
+            "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+            "tool_version": null,
+            "type": "data_input",
+            "workflow_outputs": [
+                {
+                    "label": null,
+                    "output_name": "output"
+                }
+            ]
+        },
+        "1": {
+            "annotation": "",
+            "content_id": "wc_gnu",
+            "id": 1,
+            "input_connections": {
+                "input1": {
+                    "id": 0,
+                    "output_name": "output"
+                }
+            },
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Line/Word/Character count",
+                    "name": "input1"
+                }
+            ],
+            "label": null,
+            "name": "Line/Word/Character count",
+            "outputs": [
+                {
+                    "name": "out_file1",
+                    "type": "tabular"
+                }
+            ],
+            "post_job_actions": {},
+            "tool_id": "wc_gnu",
+            "tool_state": "{\"include_header\": \"true\", \"input1\": {\"__class__\": \"RuntimeValue\"}, \"options\": [\"lines\", \"words\", \"characters\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "1.0.0",
+            "type": "tool",
+            "workflow_outputs": [
+                {
+                    "label": "Text Count Result",
+                    "output_name": "out_file1"
+                }
+            ]
+        }
+    },
+    "tags": []
+}

test-data/json/clean/wf_01_dirty.ga

@@ -0,0 +1,99 @@
+{
+    "a_galaxy_workflow": "true",
+    "annotation": "This is a cool workflow",
+    "format-version": "0.1",
+    "license": "MIT",
+    "name": "Cool workflow",
+    "steps": {
+        "0": {
+            "annotation": "Some text",
+            "content_id": null,
+            "errors": null,
+            "id": 0,
+            "input_connections": {},
+            "inputs": [
+                {
+                    "description": "Some text",
+                    "name": "The cool input"
+                }
+            ],
+            "label": "The cool input",
+            "name": "Input dataset",
+            "outputs": [],
+            "position": {
+                "bottom": 610.28125,
+                "height": 61.78125,
+                "left": 824,
+                "right": 1024,
+                "top": 548.5,
+                "width": 200,
+                "x": 824,
+                "y": 548.5
+            },
+            "tool_id": null,
+            "tool_state": "{\"optional\": false, \"tag\": \"\"}",
+            "tool_version": null,
+            "type": "data_input",
+            "uuid": "f0019f6a-b5ee-476e-8e5f-11cd3bcfaccf",
+            "workflow_outputs": [
+                {
+                    "label": null,
+                    "output_name": "output",
+                    "uuid": "2216c468-98e3-42f9-9174-1e4b65f07e8e"
+                }
+            ]
+        },
+        "1": {
+            "annotation": "",
+            "content_id": "wc_gnu",
+            "errors": null,
+            "id": 1,
+            "input_connections": {
+                "input1": {
+                    "id": 0,
+                    "output_name": "output"
+                }
+            },
+            "inputs": [
+                {
+                    "description": "runtime parameter for tool Line/Word/Character count",
+                    "name": "input1"
+                }
+            ],
+            "label": null,
+            "name": "Line/Word/Character count",
+            "outputs": [
+                {
+                    "name": "out_file1",
+                    "type": "tabular"
+                }
+            ],
+            "position": {
+                "bottom": 781.453125,
+                "height": 133.953125,
+                "left": 1146,
+                "right": 1346,
+                "top": 647.5,
+                "width": 200,
+                "x": 1146,
+                "y": 647.5
+            },
+            "post_job_actions": {},
+            "tool_id": "wc_gnu",
+            "tool_state": "{\"include_header\": \"true\", \"input1\": {\"__class__\": \"RuntimeValue\"}, \"options\": [\"lines\", \"words\", \"characters\"], \"__page__\": null, \"__rerun_remap_job_id__\": null}",
+            "tool_version": "1.0.0",
+            "type": "tool",
+            "uuid": "1ca6f40f-7b65-46ae-a366-9592279a07cc",
+            "workflow_outputs": [
+                {
+                    "label": "Text Count Result",
+                    "output_name": "out_file1",
+                    "uuid": "d9a1c36f-bb05-4dc8-b6d8-10b94ddffb77"
+                }
+            ]
+        }
+    },
+    "tags": [],
+    "uuid": "1bcc69fb-e8ec-49db-bd60-c7ac7fa87838",
+    "version": 2
+}