Add URI-based programmatic launch for Protein Viewer from CLI/Python

README.md

@@ -27,6 +27,35 @@ Open the command palette (`⌘ + ⇧ + p`) and simply call the `Start Protein Vi
 
 Right-click on the file or selection of files in the file editor and select `Launch Protein Viewer from File(s)`
 
+You can also launch programmatically (for example from bash or Python) via a VS Code URI:
+
+`vscode://ArianJamasb.protein-viewer/open?file=/absolute/path/to/first.pdb&file=/absolute/path/to/second.cif`
+
+The `file` query parameter can be repeated for multiple files.
+
+Example from bash (using Python for URL encoding):
+
+```bash
+python - <<'PY'
+import urllib.parse
+import webbrowser
+files = ["/abs/a.pdb", "/abs/b.cif"]
+query = "&".join(f"file={urllib.parse.quote(f)}" for f in files)
+webbrowser.open(f"vscode://ArianJamasb.protein-viewer/open?{query}")
+PY
+```
+
+Example from Python:
+
+```python
+import urllib.parse
+import webbrowser
+
+files = ["/abs/a.pdb", "/abs/b.cif"]
+query = "&".join(f"file={urllib.parse.quote(f)}" for f in files)
+webbrowser.open(f"vscode://ArianJamasb.protein-viewer/open?{query}")
+```
+
 **✅ Supported Formats**
 
 * `.pdb`

package.json

@@ -48,7 +48,8 @@
     "onCommand:protein-viewer.start",
     "onCommand:protein-viewer.activateFromFiles",
     "onCommand:protein-viewer.activateFromFolder",
-    "onCommand:protein-viewer.ESMFold"
+    "onCommand:protein-viewer.ESMFold",
+    "onUri"
   ],
   "main": "./out/extension.js",
   "contributes": {

src/extension.ts

@@ -4,6 +4,7 @@ import fetch from 'node-fetch';
 import * as vscode from 'vscode';
 import { ProteinViewerPanel } from "./panels/ProteinViewerPanel";
 const path = require('node:path');
+const URI_SCHEME_PATTERN = /^[a-zA-Z][a-zA-Z0-9+.-]*:/;
 
 export async function activate(context: vscode.ExtensionContext) {
 
@@ -17,7 +18,10 @@ export async function activate(context: vscode.ExtensionContext) {
 	const activateFromFiles = vscode.commands.registerCommand("protein-viewer.activateFromFiles", (file_uri: vscode.Uri, selectedFiles: vscode.Uri[]) => {
 		console.log(file_uri);
 		console.log(selectedFiles);
-		ProteinViewerPanel.renderFromFiles(context.extensionUri, selectedFiles);
+		const filesToOpen = selectedFiles?.length ? selectedFiles : (file_uri ? [file_uri] : []);
+		if (filesToOpen.length > 0) {
+			ProteinViewerPanel.renderFromFiles(context.extensionUri, filesToOpen);
+		}
 	});
 
 	const activateFromFolder = vscode.commands.registerCommand("protein-viewer.activateFromFolder", (folder_uri: vscode.Uri) => {
@@ -39,11 +43,22 @@ export async function activate(context: vscode.ExtensionContext) {
 
 		});
 	});
+	const uriHandler = vscode.window.registerUriHandler({
+		handleUri(uri: vscode.Uri) {
+			const filesToOpen = getFilesFromLaunchUri(uri);
+			if (filesToOpen.length === 0) {
+				vscode.window.showErrorMessage("Protein Viewer: no files were provided in URI. Use ?file=/abs/path/to/file.pdb (repeat file for multiple files).");
+				return;
+			}
+			ProteinViewerPanel.renderFromFiles(context.extensionUri, filesToOpen);
+		}
+	});
 	//context.subscriptions.push(...[helloCommand, activateFromFile]);
 	context.subscriptions.push(helloCommand);
 	context.subscriptions.push(activateFromFiles);
 	context.subscriptions.push(activateFromFolder);
 	context.subscriptions.push(ESMFold);
+	context.subscriptions.push(uriHandler);
 }
 
 // this method is called when your extension is deactivated
@@ -97,3 +112,15 @@ async function getfold(sequence: string | undefined) {
 	const body = await response.text();
 	return body
 }
+
+export function getFilesFromLaunchUri(uri: vscode.Uri): vscode.Uri[] {
+	if (uri.path !== "/open") {
+		return [];
+	}
+	const params = new URLSearchParams(uri.query);
+	const files = params.getAll("file")
+		.map(file => file.trim())
+		.filter(file => file.length > 0)
+		.map(file => file.match(URI_SCHEME_PATTERN) ? vscode.Uri.parse(file, true) : vscode.Uri.file(file));
+	return files;
+}

src/test/suite/uri-handler.test.ts

@@ -0,0 +1,19 @@
+import * as assert from 'assert';
+import * as vscode from 'vscode';
+import { getFilesFromLaunchUri } from '../../extension';
+
+suite('URI Handler Test Suite', () => {
+	test('parses repeated file params from launch uri', () => {
+		const launchUri = vscode.Uri.parse('vscode://ArianJamasb.protein-viewer/open?file=%2Ftmp%2Fa.pdb&file=%2Ftmp%2Fb.cif');
+		const files = getFilesFromLaunchUri(launchUri);
+		assert.strictEqual(files.length, 2);
+		assert.strictEqual(files[0].fsPath, '/tmp/a.pdb');
+		assert.strictEqual(files[1].fsPath, '/tmp/b.cif');
+	});
+
+	test('ignores non-open uri path', () => {
+		const launchUri = vscode.Uri.parse('vscode://ArianJamasb.protein-viewer/other?file=%2Ftmp%2Fa.pdb');
+		const files = getFilesFromLaunchUri(launchUri);
+		assert.strictEqual(files.length, 0);
+	});
+});