From 55c35e4baec1c759a63149a7e4ca2c712009aca6 Mon Sep 17 00:00:00 2001 From: "Arian R. Jamasb" Date: Sat, 31 Oct 2026 13:40:26 +0100 Subject: [PATCH] Add CI and test coverage - GitHub Actions workflow: npm ci, compile, lint, tests under xvfb with coverage, 85% line threshold, coverage artifact upload - Switch to @vscode/test-cli (coverage from the extension host) - Unit tests for format mapping / load commands; integration tests for all file/folder/start command paths - Extract format mapping into src/formats.ts, fixing .ent/.brk/.mcif/ .bcif/.sd format handling and escaping injected IDs/URLs - Fix panel dispose losing `this`; ignore cancelled accession input - Add missing eslint config - Includes pending molstar 4.8.0 / TypeScript 5 upgrade and file handling improvements from the molstar_4.8.0 branch Co-Authored-By: Claude Opus 5.5 --- .eslintrc.json | 12 + .github/workflows/ci.yml | 26 + .gitignore | 2 + .vscode-test.mjs | 14 + .vscodeignore | 2 + out/extension.js | 129 +- out/extension.js.map | 2 +- out/formats.js | 31 + out/formats.js.map | 1 + out/panels/ProteinViewerPanel.js | 48 +- out/panels/ProteinViewerPanel.js.map | 2 +- out/test/runTest.js | 22 - out/test/runTest.js.map | 1 - out/test/suite/extension.test.js | 83 +- out/test/suite/extension.test.js.map | 2 +- out/test/suite/index.js | 40 - out/test/suite/index.js.map | 1 - out/test/unit/formats.test.js | 55 + out/test/unit/formats.test.js.map | 1 + package-lock.json | 9419 ++++++++++++++++++++------ package.json | 17 +- src/extension.ts | 79 +- src/formats.ts | 29 + src/panels/ProteinViewerPanel.ts | 51 +- src/test/runTest.ts | 23 - src/test/suite/extension.test.ts | 96 +- src/test/suite/index.ts | 38 - src/test/unit/formats.test.ts | 62 + tsconfig.json | 1 + 29 files changed, 7847 insertions(+), 2442 deletions(-) create mode 100644 .eslintrc.json create mode 100644 .github/workflows/ci.yml create mode 100644 .vscode-test.mjs create mode 100644 .vscodeignore create mode 100644 out/formats.js create mode 100644 out/formats.js.map delete mode 100644 out/test/runTest.js delete mode 100644 out/test/runTest.js.map delete mode 100644 out/test/suite/index.js delete mode 100644 out/test/suite/index.js.map create mode 100644 out/test/unit/formats.test.js create mode 100644 out/test/unit/formats.test.js.map create mode 100644 src/formats.ts delete mode 100644 src/test/runTest.ts delete mode 100644 src/test/suite/index.ts create mode 100644 src/test/unit/formats.test.ts diff --git a/.eslintrc.json b/.eslintrc.json new file mode 100644 index 000000000..abec772c2 --- /dev/null +++ b/.eslintrc.json @@ -0,0 +1,12 @@ +{ + "root": true, + "parser": "@typescript-eslint/parser", + "parserOptions": { "ecmaVersion": 2020, "sourceType": "module" }, + "plugins": ["@typescript-eslint"], + "rules": { + "curly": "warn", + "eqeqeq": "warn", + "no-throw-literal": "warn" + }, + "ignorePatterns": ["out", "**/*.d.ts"] +} diff --git a/.github/workflows/ci.yml b/.github/workflows/ci.yml new file mode 100644 index 000000000..cabd78672 --- /dev/null +++ b/.github/workflows/ci.yml @@ -0,0 +1,26 @@ +name: CI + +on: + push: + branches: [main] + pull_request: + +jobs: + test: + runs-on: ubuntu-latest + steps: + - uses: actions/checkout@v4 + - uses: actions/setup-node@v4 + with: + node-version: lts/* + cache: npm + - run: npm ci + # pretest compiles and lints; VS Code needs a display on Linux + - run: xvfb-run -a npm run test:coverage + - name: Enforce coverage threshold + run: node -e "const p=require('./coverage/coverage-summary.json').total.lines.pct; console.log('lines:', p + '%'); if (p < 85) process.exit(1)" + - uses: actions/upload-artifact@v4 + if: always() + with: + name: coverage + path: coverage/ diff --git a/.gitignore b/.gitignore index 6db40e9c6..b3d7c4e59 100644 --- a/.gitignore +++ b/.gitignore @@ -1,3 +1,5 @@ *.vsix .DS_Store node_modules/ +.vscode-test/ +coverage/ diff --git a/.vscode-test.mjs b/.vscode-test.mjs new file mode 100644 index 000000000..0a49ff08f --- /dev/null +++ b/.vscode-test.mjs @@ -0,0 +1,14 @@ +import { defineConfig } from '@vscode/test-cli'; + +export default defineConfig({ + tests: [{ + files: 'out/test/**/*.test.js', + workspaceFolder: '.', + launchArgs: ['--disable-extensions'], + mocha: { ui: 'tdd', timeout: 20000 }, + }], + coverage: { + exclude: ['**/test/**'], + reporter: ['text', 'lcov', 'json-summary'], + }, +}); diff --git a/.vscodeignore b/.vscodeignore new file mode 100644 index 000000000..cf38226a0 --- /dev/null +++ b/.vscodeignore @@ -0,0 +1,2 @@ +.vscode-test/** +coverage/** diff --git a/out/extension.js b/out/extension.js index 693fb8d58..78ec98ccf 100644 --- a/out/extension.js +++ b/out/extension.js @@ -1,42 +1,96 @@ "use strict"; Object.defineProperty(exports, "__esModule", { value: true }); -exports.activate = void 0; +exports.activate = activate; // The module 'vscode' contains the VS Code extensibility API // Import the module and reference it with the alias vscode in your code below const node_fetch_1 = require("node-fetch"); const vscode = require("vscode"); const ProteinViewerPanel_1 = require("./panels/ProteinViewerPanel"); -function activate(context) { +const path = require('node:path'); +const supportedFileTypes = [ + 'pdb', + "PDB", + 'cif', + 'bcif', + 'mmcif', + 'mcif', + 'ent', + 'brk', + 'pqr', + 'xyz', + 'sdf', + 'sd', + 'gro', + 'prmtop', + 'parm', + 'psf', + 'top', + 'mol2', + 'MOL2' +]; +async function activate(context) { const helloCommand = vscode.commands.registerCommand("protein-viewer.start", () => { showInputBox().then((accession) => { - console.log(accession); + if (!accession) { + return; + } ProteinViewerPanel_1.ProteinViewerPanel.render(context.extensionUri, accession); }); }); - const activateFromFiles = vscode.commands.registerCommand("protein-viewer.activateFromFiles", (file_uri, selectedFiles) => { - console.log(file_uri); - console.log(selectedFiles); - ProteinViewerPanel_1.ProteinViewerPanel.renderFromFiles(context.extensionUri, selectedFiles); + const activateFromFiles = vscode.commands.registerCommand("protein-viewer.activateFromFiles", (fileUri, selectedFiles) => { + try { + const candidateUris = []; + if (Array.isArray(selectedFiles) && selectedFiles.length > 0) { + candidateUris.push(...selectedFiles); + } + else if (fileUri) { + candidateUris.push(fileUri); + } + else { + const activeUri = vscode.window.activeTextEditor?.document.uri; + if (activeUri) { + candidateUris.push(activeUri); + } + } + if (candidateUris.length === 0) { + vscode.window.showErrorMessage("Protein Viewer: No structure file available for this command."); + return; + } + console.log(candidateUris); + ProteinViewerPanel_1.ProteinViewerPanel.renderFromFiles(context.extensionUri, candidateUris); + } + catch (error) { + console.error("Error in activateFromFiles:", error); + vscode.window.showErrorMessage("Protein Viewer: Failed to open selected structure file(s)."); + } }); - const activateFromFolder = vscode.commands.registerCommand("protein-viewer.activateFromFolder", (folder_uri) => { - vscode.workspace.findFiles(`${vscode.workspace.asRelativePath(folder_uri)}/*.pdb`).then((files_uri) => { - ProteinViewerPanel_1.ProteinViewerPanel.renderFromFiles(context.extensionUri, files_uri); - }); + const activateFromFolder = vscode.commands.registerCommand("protein-viewer.activateFromFolder", async (folderUri) => { + try { + const relativePath = vscode.workspace.asRelativePath(folderUri); + const files = await vscode.workspace.findFiles(`${relativePath}/*.{${supportedFileTypes.join(',')}}`); + if (!files.length) { + vscode.window.showErrorMessage("Protein Viewer: No supported structure files found in the selected folder."); + return; + } + ProteinViewerPanel_1.ProteinViewerPanel.renderFromFiles(context.extensionUri, files); + } + catch (error) { + console.error("Error in activateFromFolder:", error); + vscode.window.showErrorMessage("Protein Viewer: Failed to open folder structure file(s)."); + } }); const ESMFold = vscode.commands.registerCommand("protein-viewer.ESMFold", () => { showSequenceInputBox().then((sequence) => { - console.log(sequence); - const file = getfold(sequence); - console.log(file); + const uri = getfold(sequence).then((pdb) => { + writeFoldToFile(pdb).then(async (file_uri) => { + console.log(file_uri); + ProteinViewerPanel_1.ProteinViewerPanel.renderFromFiles(context.extensionUri, [vscode.Uri.file(file_uri)]); + }); + }); }); }); - //context.subscriptions.push(...[helloCommand, activateFromFile]); - context.subscriptions.push(helloCommand); - context.subscriptions.push(activateFromFiles); - context.subscriptions.push(activateFromFolder); - context.subscriptions.push(ESMFold); + context.subscriptions.push(helloCommand, activateFromFiles, activateFromFolder, ESMFold); } -exports.activate = activate; // this method is called when your extension is deactivated // export function deactivate() {} async function showInputBox() { @@ -53,27 +107,30 @@ async function showSequenceInputBox() { }); return sequence; } +async function writeFoldToFile(file_contents) { + const time = new Date().getTime(); + const fname = "/esmfold_" + time.toString() + ".pdb"; + const setting = vscode.Uri.parse("untitled:" + vscode.workspace.rootPath + fname); + await vscode.workspace.openTextDocument(setting).then((a) => { + vscode.window.showTextDocument(a, 1, false).then(e => { + e.edit(edit => { + edit.insert(new vscode.Position(0, 0), file_contents); + a.save(); + }); + }); + }); + console.log("wrote to test file."); + console.log(setting); + return setting.fsPath; +} async function getfold(sequence) { const url = "https://api.esmatlas.com/foldSequence/v1/pdb/"; + console.log(sequence); const response = await (0, node_fetch_1.default)(url, { method: 'POST', body: sequence, - // headers: { 'Content-Type': 'application/x-www-form-urlencoded; charset=UTF-8' } }); - console.log("Output:"); - console.log(response.text()); - console.log(response.body); - if (!response.ok) { /* Handle */ } - // If you care about a response: - if (response.body !== null) { - // body is ReadableStream - // parse as needed, e.g. reading directly, or - // console.log(response.body); - const response_string = response.body.toString(); // new TextDecoder("utf-8").decode(response.body); - // and further: - // const asJSON = JSON.parse(asString); // implicitly 'any', make sure to verify type on runtime. - //console.log(response_string); - return response_string; - } + const body = await response.text(); + return body; } //# sourceMappingURL=extension.js.map \ No newline at end of file diff --git a/out/extension.js.map b/out/extension.js.map index 9a818ee53..6d327e81f 100644 --- a/out/extension.js.map +++ b/out/extension.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/out/formats.js b/out/formats.js new file mode 100644 index 000000000..1db12f17e --- /dev/null +++ b/out/formats.js @@ -0,0 +1,31 @@ +"use strict"; +// Pure helpers (no `vscode` import) so they can be unit tested in plain Node. +Object.defineProperty(exports, "__esModule", { value: true }); +exports.molstarFormat = molstarFormat; +exports.fileLoadCommand = fileLoadCommand; +exports.accessionLoadCommand = accessionLoadCommand; +// File extension -> Mol* trajectory format. Anything else is passed through as-is. +const FORMAT_ALIASES = { + cif: 'mmcif', + mcif: 'mmcif', + bcif: 'mmcif', + ent: 'pdb', + brk: 'pdb', + sd: 'sdf', +}; +function molstarFormat(filePath) { + const ext = (filePath.split('/').pop()?.split('.').pop() ?? '').toLowerCase(); + return { format: FORMAT_ALIASES[ext] ?? ext, isBinary: ext === 'bcif' }; +} +function fileLoadCommand(url, filePath) { + const { format, isBinary } = molstarFormat(filePath); + return `viewer.loadStructureFromUrl(${JSON.stringify(url)}, ${JSON.stringify(format)}, ${isBinary});`; +} +// 4-character IDs are PDB entries; anything else is treated as a UniProt accession for AlphaFold DB. +function accessionLoadCommand(accession) { + const id = accession.trim(); + return id.length === 4 + ? `viewer.loadPdb(${JSON.stringify(id)});` + : `viewer.loadAlphaFoldDb(${JSON.stringify(id)});`; +} +//# sourceMappingURL=formats.js.map \ No newline at end of file diff --git a/out/formats.js.map b/out/formats.js.map new file mode 100644 index 000000000..4e3b189a9 --- /dev/null +++ b/out/formats.js.map @@ -0,0 +1 @@ +{"version":3,"file":"formats.js","sourceRoot":"","sources":["../src/formats.ts"],"names":[],"mappings":";AAAA,8EAA8E;;AAY9E,sCAGC;AAED,0CAGC;AAGD,oDAKC;AA1BD,mFAAmF;AACnF,MAAM,cAAc,GAA2B;IAC7C,GAAG,EAAE,OAAO;IACZ,IAAI,EAAE,OAAO;IACb,IAAI,EAAE,OAAO;IACb,GAAG,EAAE,KAAK;IACV,GAAG,EAAE,KAAK;IACV,EAAE,EAAE,KAAK;CACV,CAAC;AAEF,SAAgB,aAAa,CAAC,QAAgB;IAC5C,MAAM,GAAG,GAAG,CAAC,QAAQ,CAAC,KAAK,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,EAAE,KAAK,CAAC,GAAG,CAAC,CAAC,GAAG,EAAE,IAAI,EAAE,CAAC,CAAC,WAAW,EAAE,CAAC;IAC9E,OAAO,EAAE,MAAM,EAAE,cAAc,CAAC,GAAG,CAAC,IAAI,GAAG,EAAE,QAAQ,EAAE,GAAG,KAAK,MAAM,EAAE,CAAC;AAC1E,CAAC;AAED,SAAgB,eAAe,CAAC,GAAW,EAAE,QAAgB;IAC3D,MAAM,EAAE,MAAM,EAAE,QAAQ,EAAE,GAAG,aAAa,CAAC,QAAQ,CAAC,CAAC;IACrD,OAAO,+BAA+B,IAAI,CAAC,SAAS,CAAC,GAAG,CAAC,KAAK,IAAI,CAAC,SAAS,CAAC,MAAM,CAAC,KAAK,QAAQ,IAAI,CAAC;AACxG,CAAC;AAED,qGAAqG;AACrG,SAAgB,oBAAoB,CAAC,SAAiB;IACpD,MAAM,EAAE,GAAG,SAAS,CAAC,IAAI,EAAE,CAAC;IAC5B,OAAO,EAAE,CAAC,MAAM,KAAK,CAAC;QACpB,CAAC,CAAC,kBAAkB,IAAI,CAAC,SAAS,CAAC,EAAE,CAAC,IAAI;QAC1C,CAAC,CAAC,0BAA0B,IAAI,CAAC,SAAS,CAAC,EAAE,CAAC,IAAI,CAAC;AACvD,CAAC"} \ No newline at end of file diff --git a/out/panels/ProteinViewerPanel.js b/out/panels/ProteinViewerPanel.js index 83f6135fe..9e8ef0c65 100644 --- a/out/panels/ProteinViewerPanel.js +++ b/out/panels/ProteinViewerPanel.js @@ -2,16 +2,17 @@ Object.defineProperty(exports, "__esModule", { value: true }); exports.ProteinViewerPanel = void 0; const vscode = require("vscode"); +const formats_1 = require("../formats"); class ProteinViewerPanel { constructor(panel, extensionUri, accession, clickedFiles) { this._disposables = []; this._panel = panel; - this._panel.onDidDispose(this.dispose, null, this._disposables); - if (accession != undefined) { + this._panel.onDidDispose(() => this.dispose(), null, this._disposables); + if (accession !== undefined) { this._panel.webview.html = this._getWebviewContent(panel.webview, extensionUri, accession); } ; - if (clickedFiles != undefined) { + if (clickedFiles !== undefined) { this._panel.webview.html = this._getWebviewContentForFiles(panel.webview, extensionUri, clickedFiles); } ; @@ -22,12 +23,7 @@ class ProteinViewerPanel { enableScripts: true, retainContextWhenHidden: true }); - if (accession?.length === 4) { - var loadCommand = `viewer.loadPdb('${accession}');`; - } - else { - var loadCommand = `viewer.loadAlphaFoldDb('${accession}');`; - } + const loadCommand = (0, formats_1.accessionLoadCommand)(accession ?? ''); ProteinViewerPanel.currentPanel = new ProteinViewerPanel(panel, extensionUri, loadCommand, undefined); } static renderFromFiles(extensionUri, clickedFiles) { @@ -131,30 +127,30 @@ class ProteinViewerPanel { }).then(viewer => { var snapshotId = getParam('snapshot-id', '[^&]+').trim(); if (snapshotId) viewer.setRemoteSnapshot(snapshotId); - + var snapshotUrl = getParam('snapshot-url', '[^&]+').trim(); var snapshotUrlType = getParam('snapshot-url-type', '[^&]+').toLowerCase().trim() || 'molj'; if (snapshotUrl && snapshotUrlType) viewer.loadSnapshotFromUrl(snapshotUrl, snapshotUrlType); - + var structureUrl = getParam('structure-url', '[^&]+').trim(); var structureUrlFormat = getParam('structure-url-format', '[a-z]+').toLowerCase().trim(); var structureUrlIsBinary = getParam('structure-url-is-binary', '[^&]+').trim() === '1'; if (structureUrl) viewer.loadStructureFromUrl(structureUrl, structureUrlFormat, structureUrlIsBinary); - + var pdb = getParam('pdb', '[^&]+').trim(); if (pdb) viewer.loadPdb(pdb); - + var pdbDev = getParam('pdb-dev', '[^&]+').trim(); if (pdbDev) viewer.loadPdbDev(pdbDev); - + var emdb = getParam('emdb', '[^&]+').trim(); if (emdb) viewer.loadEmdb(emdb); - + // var afdb = getParam('afdb', '[^&]+').trim(); - // if (afdb) + // if (afdb) // viewer.loadAlphaFoldDb('${accession}'); ${accession}; - + var modelArchive = getParam('model-archive', '[^&]+').trim(); if (modelArchive) viewer.loadModelArchive(modelArchive); }); @@ -167,19 +163,7 @@ class ProteinViewerPanel { _getWebviewContentForFiles(webview, extensionUri, clickedFiles) { const cssUri = webview.asWebviewUri(vscode.Uri.joinPath(extensionUri, 'node_modules', 'molstar', 'build/viewer', 'molstar.css')); const jsUri = webview.asWebviewUri(vscode.Uri.joinPath(extensionUri, 'node_modules', 'molstar', 'build/viewer', 'molstar.js')); - const pdbContents = clickedFiles.map((clickedFile) => webview.asWebviewUri(clickedFile)); - const extensions = clickedFiles.map((clickedFile) => clickedFile.path.split('.').pop()); - let loadCommands = []; - for (let i = 0; i < pdbContents.length; i++) { - const pdbContent = pdbContents[i]; - var extension = extensions[i]; - console.log(extension); - if (extension === 'cif' || extension === 'mmCIF' || extension === 'CIF' || extension === 'MMCIF' || extension == '.mCIF' || extension == '.mcif') { - extension = 'mmcif'; - } - console.log(extension); - loadCommands.push(`viewer.loadStructureFromUrl('${pdbContent}', format='${extension}');`); - } + const loadCommands = clickedFiles.map((file) => (0, formats_1.fileLoadCommand)(webview.asWebviewUri(file).toString(), file.path)); // Tip: Install the es6-string-html VS Code extension to enable code highlighting below return /*html*/ ` @@ -259,11 +243,11 @@ class ProteinViewerPanel { }).then(viewer => { var snapshotId = getParam('snapshot-id', '[^&]+').trim(); if (snapshotId) viewer.setRemoteSnapshot(snapshotId); - + var snapshotUrl = getParam('snapshot-url', '[^&]+').trim(); var snapshotUrlType = getParam('snapshot-url-type', '[^&]+').toLowerCase().trim() || 'molj'; if (snapshotUrl && snapshotUrlType) viewer.loadSnapshotFromUrl(snapshotUrl, snapshotUrlType); - + var structureUrl = getParam('structure-url', '[^&]+').trim(); var structureUrlFormat = getParam('structure-url-format', '[a-z]+').toLowerCase().trim(); var structureUrlIsBinary = getParam('structure-url-is-binary', '[^&]+').trim() === '1'; diff --git a/out/panels/ProteinViewerPanel.js.map b/out/panels/ProteinViewerPanel.js.map index d51aa3c63..c173ef3df 100644 --- a/out/panels/ProteinViewerPanel.js.map +++ b/out/panels/ProteinViewerPanel.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/out/test/runTest.js b/out/test/runTest.js deleted file mode 100644 index 07340e1e0..000000000 --- a/out/test/runTest.js +++ /dev/null @@ -1,22 +0,0 @@ -"use strict"; -Object.defineProperty(exports, "__esModule", { value: true }); -const path = require("path"); -const test_electron_1 = require("@vscode/test-electron"); -async function main() { - try { - // The folder containing the Extension Manifest package.json - // Passed to `--extensionDevelopmentPath` - const extensionDevelopmentPath = path.resolve(__dirname, '../../'); - // The path to test runner - // Passed to --extensionTestsPath - const extensionTestsPath = path.resolve(__dirname, './suite/index'); - // Download VS Code, unzip it and run the integration test - await (0, test_electron_1.runTests)({ extensionDevelopmentPath, extensionTestsPath }); - } - catch (err) { - console.error('Failed to run tests'); - process.exit(1); - } -} -main(); -//# sourceMappingURL=runTest.js.map \ No newline at end of file diff --git a/out/test/runTest.js.map b/out/test/runTest.js.map deleted file mode 100644 index 37b882f21..000000000 --- a/out/test/runTest.js.map +++ /dev/null @@ -1 +0,0 @@ -{"version":3,"file":"runTest.js","sourceRoot":"","sources":["../../src/test/runTest.ts"],"names":[],"mappings":";;AAAA,6BAA6B;AAE7B,yDAAiD;AAEjD,KAAK,UAAU,IAAI;IAClB,IAAI;QACH,4DAA4D;QAC5D,yCAAyC;QACzC,MAAM,wBAAwB,GAAG,IAAI,CAAC,OAAO,CAAC,SAAS,EAAE,QAAQ,CAAC,CAAC;QAEnE,0BAA0B;QAC1B,iCAAiC;QACjC,MAAM,kBAAkB,GAAG,IAAI,CAAC,OAAO,CAAC,SAAS,EAAE,eAAe,CAAC,CAAC;QAEpE,0DAA0D;QAC1D,MAAM,IAAA,wBAAQ,EAAC,EAAE,wBAAwB,EAAE,kBAAkB,EAAE,CAAC,CAAC;KACjE;IAAC,OAAO,GAAG,EAAE;QACb,OAAO,CAAC,KAAK,CAAC,qBAAqB,CAAC,CAAC;QACrC,OAAO,CAAC,IAAI,CAAC,CAAC,CAAC,CAAC;KAChB;AACF,CAAC;AAED,IAAI,EAAE,CAAC"} \ No newline at end of file diff --git a/out/test/suite/extension.test.js b/out/test/suite/extension.test.js index d88089ebf..d7db3c9a4 100644 --- a/out/test/suite/extension.test.js +++ b/out/test/suite/extension.test.js @@ -1,15 +1,82 @@ "use strict"; Object.defineProperty(exports, "__esModule", { value: true }); const assert = require("assert"); -// You can import and use all API from the 'vscode' module -// as well as import your extension to test it +const path = require("path"); const vscode = require("vscode"); -// import * as myExtension from '../../extension'; -suite('Extension Test Suite', () => { - vscode.window.showInformationMessage('Start all tests.'); - test('Sample test', () => { - assert.strictEqual(-1, [1, 2, 3].indexOf(5)); - assert.strictEqual(-1, [1, 2, 3].indexOf(0)); +const ProteinViewerPanel_1 = require("../../panels/ProteinViewerPanel"); +const EXTENSION_ID = 'ArianJamasb.protein-viewer'; +const testFiles = path.resolve(__dirname, '../../../test_files'); +function panelHtml() { + assert.ok(ProteinViewerPanel_1.ProteinViewerPanel.currentPanel, 'expected a viewer panel to be open'); + // eslint-disable-next-line @typescript-eslint/no-explicit-any + return ProteinViewerPanel_1.ProteinViewerPanel.currentPanel._panel.webview.html; +} +suite('Extension', () => { + suiteSetup(async () => { + await vscode.extensions.getExtension(EXTENSION_ID).activate(); + }); + teardown(async () => { + ProteinViewerPanel_1.ProteinViewerPanel.currentPanel?.dispose(); + await vscode.commands.executeCommand('workbench.action.closeAllEditors'); + }); + test('registers all contributed commands', async () => { + const commands = await vscode.commands.getCommands(true); + for (const id of ['start', 'activateFromFiles', 'activateFromFolder', 'ESMFold']) { + assert.ok(commands.includes(`protein-viewer.${id}`), `missing protein-viewer.${id}`); + } + }); + test('activateFromFiles opens a viewer for a single file', async () => { + const file = vscode.Uri.file(path.join(testFiles, '3eiy.PDB')); + await vscode.commands.executeCommand('protein-viewer.activateFromFiles', file); + const html = panelHtml(); + assert.match(html, /molstar\.js/); + assert.match(html, /viewer\.loadStructureFromUrl\("[^"]*3eiy\.PDB", "pdb", false\);/); + }); + test('activateFromFiles prefers the multi-selection over the clicked file', async () => { + const pdb = vscode.Uri.file(path.join(testFiles, '3eiy.PDB')); + const cif = vscode.Uri.file(path.join(testFiles, '3eiy.MMCIF')); + await vscode.commands.executeCommand('protein-viewer.activateFromFiles', pdb, [pdb, cif]); + const html = panelHtml(); + assert.match(html, /3eiy\.PDB", "pdb"/); + assert.match(html, /3eiy\.MMCIF", "mmcif"/); + }); + test('activateFromFiles with nothing selected opens no panel', async () => { + await vscode.commands.executeCommand('protein-viewer.activateFromFiles'); + assert.strictEqual(ProteinViewerPanel_1.ProteinViewerPanel.currentPanel, undefined); + }); + test('activateFromFolder loads supported files from the folder', async () => { + await vscode.commands.executeCommand('protein-viewer.activateFromFolder', vscode.Uri.file(testFiles)); + const html = panelHtml(); + assert.match(html, /3eiy\.PDB", "pdb"/); + assert.match(html, /esmfold\.pdb", "pdb"/); + }); + suite('start', () => { + const realShowInputBox = vscode.window.showInputBox; + const stubInput = (value) => { + // eslint-disable-next-line @typescript-eslint/no-explicit-any + vscode.window.showInputBox = async () => value; + }; + // eslint-disable-next-line @typescript-eslint/no-explicit-any + teardown(() => { vscode.window.showInputBox = realShowInputBox; }); + const startAndWait = async () => { + await vscode.commands.executeCommand('protein-viewer.start'); + await new Promise((r) => setTimeout(r, 50)); // command doesn't await its input box + }; + test('loads a PDB entry for a 4-character ID', async () => { + stubInput('3eiy'); + await startAndWait(); + assert.match(panelHtml(), /viewer\.loadPdb\("3eiy"\);/); + }); + test('loads AlphaFold DB for a UniProt accession', async () => { + stubInput('P69905'); + await startAndWait(); + assert.match(panelHtml(), /viewer\.loadAlphaFoldDb\("P69905"\);/); + }); + test('does nothing when the input box is cancelled', async () => { + stubInput(undefined); + await startAndWait(); + assert.strictEqual(ProteinViewerPanel_1.ProteinViewerPanel.currentPanel, undefined); + }); }); }); //# sourceMappingURL=extension.test.js.map \ No newline at end of file diff --git a/out/test/suite/extension.test.js.map b/out/test/suite/extension.test.js.map index 26e2c09ba..727225227 100644 --- a/out/test/suite/extension.test.js.map +++ b/out/test/suite/extension.test.js.map @@ -1 +1 @@ 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\ No newline at end of file diff --git a/out/test/suite/index.js b/out/test/suite/index.js deleted file mode 100644 index f0da16d94..000000000 --- a/out/test/suite/index.js +++ /dev/null @@ -1,40 +0,0 @@ -"use strict"; -Object.defineProperty(exports, "__esModule", { value: true }); -exports.run = void 0; -const path = require("path"); -const Mocha = require("mocha"); -const glob = require("glob"); -function run() { - // Create the mocha test - const mocha = new Mocha({ - ui: 'tdd', - color: true - }); - const testsRoot = path.resolve(__dirname, '..'); - return new Promise((c, e) => { - glob('**/**.test.js', { cwd: testsRoot }, (err, files) => { - if (err) { - return e(err); - } - // Add files to the test suite - files.forEach(f => mocha.addFile(path.resolve(testsRoot, f))); - try { - // Run the mocha test - mocha.run(failures => { - if (failures > 0) { - e(new Error(`${failures} tests failed.`)); - } - else { - c(); - } - }); - } - catch (err) { - console.error(err); - e(err); - } - }); - }); -} -exports.run = run; -//# sourceMappingURL=index.js.map \ No newline at end of file diff --git a/out/test/suite/index.js.map b/out/test/suite/index.js.map deleted file mode 100644 index dfd0c62e4..000000000 --- a/out/test/suite/index.js.map +++ /dev/null @@ -1 +0,0 @@ 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\ No newline at end of file diff --git a/out/test/unit/formats.test.js b/out/test/unit/formats.test.js new file mode 100644 index 000000000..a9d897600 --- /dev/null +++ b/out/test/unit/formats.test.js @@ -0,0 +1,55 @@ +"use strict"; +Object.defineProperty(exports, "__esModule", { value: true }); +const assert = require("assert"); +const formats_1 = require("../../formats"); +suite('molstarFormat', () => { + const cases = [ + ['/a/3eiy.pdb', 'pdb', false], + ['/a/3eiy.PDB', 'pdb', false], + ['/a/x.ent', 'pdb', false], + ['/a/x.brk', 'pdb', false], + ['/a/x.pdbqt', 'pdbqt', false], + ['/a/x.cif', 'mmcif', false], + ['/a/x.CIF', 'mmcif', false], + ['/a/x.mmcif', 'mmcif', false], + ['/a/3eiy.MMCIF', 'mmcif', false], + ['/a/x.mcif', 'mmcif', false], + ['/a/x.bcif', 'mmcif', true], + ['/a/x.sd', 'sdf', false], + ['/a/x.SDF', 'sdf', false], + ['/a/x.mol2', 'mol2', false], + ['/a/x.MOL2', 'mol2', false], + ['/a/x.gro', 'gro', false], + ['/a/x.xyz', 'xyz', false], + ['/dir.v2/x.mol', 'mol', false], + ]; + for (const [path, format, isBinary] of cases) { + test(`${path} -> ${format}`, () => { + assert.deepStrictEqual((0, formats_1.molstarFormat)(path), { format, isBinary }); + }); + } +}); +suite('fileLoadCommand', () => { + test('emits a quoted loadStructureFromUrl call', () => { + assert.strictEqual((0, formats_1.fileLoadCommand)('https://file+.vscode-resource/a/x.bcif', '/a/x.bcif'), 'viewer.loadStructureFromUrl("https://file+.vscode-resource/a/x.bcif", "mmcif", true);'); + }); + test('escapes quotes in URLs', () => { + const cmd = (0, formats_1.fileLoadCommand)(`https://h/it's".pdb`, `/it's".pdb`); + assert.strictEqual(cmd, `viewer.loadStructureFromUrl("https://h/it's\\".pdb", "pdb", false);`); + }); +}); +suite('accessionLoadCommand', () => { + test('4-character IDs load from the PDB', () => { + assert.strictEqual((0, formats_1.accessionLoadCommand)('3eiy'), 'viewer.loadPdb("3eiy");'); + }); + test('trims whitespace before classifying', () => { + assert.strictEqual((0, formats_1.accessionLoadCommand)(' 1CRN \n'), 'viewer.loadPdb("1CRN");'); + }); + test('other IDs load from AlphaFold DB', () => { + assert.strictEqual((0, formats_1.accessionLoadCommand)('P69905'), 'viewer.loadAlphaFoldDb("P69905");'); + }); + test('cannot break out of the string literal', () => { + assert.strictEqual((0, formats_1.accessionLoadCommand)(`x');alert(1);//`), `viewer.loadAlphaFoldDb("x');alert(1);//");`); + }); +}); +//# sourceMappingURL=formats.test.js.map \ No newline at end of file diff --git a/out/test/unit/formats.test.js.map b/out/test/unit/formats.test.js.map new file mode 100644 index 000000000..3301ce8e2 --- /dev/null +++ b/out/test/unit/formats.test.js.map @@ -0,0 +1 @@ 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\ No newline at end of file diff --git a/package-lock.json b/package-lock.json index 7732dc794..610419e2c 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,34 +1,42 @@ { "name": "protein-viewer", - "version": "0.0.9", + "version": "0.1.0", "lockfileVersion": 2, "requires": true, "packages": { "": { "name": "protein-viewer", - "version": "0.0.9", + "version": "0.1.0", "license": "MIT", "dependencies": { - "molstar": "^3.23.0", + "molstar": "^4.8.0", "node-fetch": "^2.6.1" }, "devDependencies": { - "@types/glob": "^7.1.4", "@types/mocha": "^9.0.0", "@types/node": "14.x", "@types/vscode": "^1.62.0", "@typescript-eslint/eslint-plugin": "^5.1.0", "@typescript-eslint/parser": "^5.1.0", - "@vscode/test-electron": "^1.6.2", + "@vscode/test-cli": "^0.0.15", + "@vscode/test-electron": "^3.1.0", "eslint": "^8.1.0", - "glob": "^7.1.7", - "mocha": "^9.1.3", - "typescript": "^4.4.4" + "typescript": "^5.4.5" }, "engines": { "vscode": "^1.62.0" } }, + "node_modules/@bcoe/v8-coverage": { + 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-p ./", "watch": "tsc -watch -p ./", - "pretest": "npm run compile && npm run lint", "lint": "eslint src --ext ts", - "test": "node ./out/test/runTest.js" + "pretest": "npm run compile && npm run lint", + "test": "vscode-test", + "test:coverage": "npm run pretest && vscode-test --coverage" }, "devDependencies": { - "@types/glob": "^7.1.4", "@types/mocha": "^9.0.0", "@types/node": "14.x", "@types/vscode": "^1.62.0", "@typescript-eslint/eslint-plugin": "^5.1.0", "@typescript-eslint/parser": "^5.1.0", - "@vscode/test-electron": "^1.6.2", + "@vscode/test-cli": "^0.0.15", + "@vscode/test-electron": "^3.1.0", "eslint": "^8.1.0", - "glob": "^7.1.7", - "mocha": "^9.1.3", - "typescript": "^4.4.4" + "typescript": "^5.4.5" }, "dependencies": { - "molstar": "^3.23.0", + "molstar": "^4.8.0", "node-fetch": "^2.6.1" } -} \ No newline at end of file +} diff --git a/src/extension.ts b/src/extension.ts index bea71387d..5925e9815 100644 --- a/src/extension.ts +++ b/src/extension.ts @@ -5,25 +5,80 @@ import * as vscode from 'vscode'; import { ProteinViewerPanel } from "./panels/ProteinViewerPanel"; const path = require('node:path'); + +const supportedFileTypes = [ + 'pdb', + "PDB", + 'cif', + 'bcif', + 'mmcif', + 'mcif', + 'ent', + 'brk', + 'pqr', + 'xyz', + 'sdf', + 'sd', + 'gro', + 'prmtop', + 'parm', + 'psf', + 'top', + 'mol2', + 'MOL2' +] + export async function activate(context: vscode.ExtensionContext) { const helloCommand = vscode.commands.registerCommand("protein-viewer.start", () => { showInputBox().then((accession) => { - console.log(accession); + if (!accession) { + return; + } ProteinViewerPanel.render(context.extensionUri, accession); }); }); - 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 activateFromFiles = vscode.commands.registerCommand("protein-viewer.activateFromFiles", (fileUri?: vscode.Uri, selectedFiles?: vscode.Uri[]) => { + try { + const candidateUris: vscode.Uri[] = []; + if (Array.isArray(selectedFiles) && selectedFiles.length > 0) { + candidateUris.push(...selectedFiles); + } else if (fileUri) { + candidateUris.push(fileUri); + } else { + const activeUri = vscode.window.activeTextEditor?.document.uri; + if (activeUri) { + candidateUris.push(activeUri); + } + } + + if (candidateUris.length === 0) { + vscode.window.showErrorMessage("Protein Viewer: No structure file available for this command."); + return; + } + + console.log(candidateUris); + ProteinViewerPanel.renderFromFiles(context.extensionUri, candidateUris); + } catch (error) { + console.error("Error in activateFromFiles:", error); + vscode.window.showErrorMessage("Protein Viewer: Failed to open selected structure file(s)."); + } }); - const activateFromFolder = vscode.commands.registerCommand("protein-viewer.activateFromFolder", (folder_uri: vscode.Uri) => { - vscode.workspace.findFiles(`${vscode.workspace.asRelativePath(folder_uri)}/*.pdb`).then((files_uri) => { - ProteinViewerPanel.renderFromFiles(context.extensionUri, files_uri) - }); + const activateFromFolder = vscode.commands.registerCommand("protein-viewer.activateFromFolder", async (folderUri: vscode.Uri) => { + try { + const relativePath = vscode.workspace.asRelativePath(folderUri); + const files = await vscode.workspace.findFiles(`${relativePath}/*.{${supportedFileTypes.join(',')}}`); + if (!files.length) { + vscode.window.showErrorMessage("Protein Viewer: No supported structure files found in the selected folder."); + return; + } + ProteinViewerPanel.renderFromFiles(context.extensionUri, files); + } catch (error) { + console.error("Error in activateFromFolder:", error); + vscode.window.showErrorMessage("Protein Viewer: Failed to open folder structure file(s)."); + } }); const ESMFold = vscode.commands.registerCommand("protein-viewer.ESMFold", () => { @@ -39,11 +94,7 @@ export async function activate(context: vscode.ExtensionContext) { }); }); - //context.subscriptions.push(...[helloCommand, activateFromFile]); - context.subscriptions.push(helloCommand); - context.subscriptions.push(activateFromFiles); - context.subscriptions.push(activateFromFolder); - context.subscriptions.push(ESMFold); + context.subscriptions.push(helloCommand, activateFromFiles, activateFromFolder, ESMFold); } // this method is called when your extension is deactivated diff --git a/src/formats.ts b/src/formats.ts new file mode 100644 index 000000000..203aaa92f --- /dev/null +++ b/src/formats.ts @@ -0,0 +1,29 @@ +// Pure helpers (no `vscode` import) so they can be unit tested in plain Node. + +// File extension -> Mol* trajectory format. Anything else is passed through as-is. +const FORMAT_ALIASES: Record = { + cif: 'mmcif', + mcif: 'mmcif', + bcif: 'mmcif', + ent: 'pdb', + brk: 'pdb', + sd: 'sdf', +}; + +export function molstarFormat(filePath: string): { format: string; isBinary: boolean } { + const ext = (filePath.split('/').pop()?.split('.').pop() ?? '').toLowerCase(); + return { format: FORMAT_ALIASES[ext] ?? ext, isBinary: ext === 'bcif' }; +} + +export function fileLoadCommand(url: string, filePath: string): string { + const { format, isBinary } = molstarFormat(filePath); + return `viewer.loadStructureFromUrl(${JSON.stringify(url)}, ${JSON.stringify(format)}, ${isBinary});`; +} + +// 4-character IDs are PDB entries; anything else is treated as a UniProt accession for AlphaFold DB. +export function accessionLoadCommand(accession: string): string { + const id = accession.trim(); + return id.length === 4 + ? `viewer.loadPdb(${JSON.stringify(id)});` + : `viewer.loadAlphaFoldDb(${JSON.stringify(id)});`; +} diff --git a/src/panels/ProteinViewerPanel.ts b/src/panels/ProteinViewerPanel.ts index 012a445a3..b12681a5b 100644 --- a/src/panels/ProteinViewerPanel.ts +++ b/src/panels/ProteinViewerPanel.ts @@ -1,4 +1,5 @@ import * as vscode from "vscode"; +import { accessionLoadCommand, fileLoadCommand } from "../formats"; export class ProteinViewerPanel { public static currentPanel: ProteinViewerPanel | undefined; @@ -7,12 +8,12 @@ export class ProteinViewerPanel { private constructor(panel: vscode.WebviewPanel, extensionUri: vscode.Uri, accession: string | undefined, clickedFiles: vscode.Uri[] | undefined) { this._panel = panel; - this._panel.onDidDispose(this.dispose, null, this._disposables); - if (accession != undefined) { + this._panel.onDidDispose(() => this.dispose(), null, this._disposables); + if (accession !== undefined) { this._panel.webview.html = this._getWebviewContent(panel.webview, extensionUri, accession); }; - if (clickedFiles != undefined) { + if (clickedFiles !== undefined) { this._panel.webview.html = this._getWebviewContentForFiles(panel.webview, extensionUri, clickedFiles); }; @@ -24,11 +25,9 @@ export class ProteinViewerPanel { enableScripts: true, retainContextWhenHidden: true }); - if (accession?.length === 4) { - var loadCommand = `viewer.loadPdb('${accession}');` - } else { - var loadCommand = `viewer.loadAlphaFoldDb('${accession}');` - } + + const loadCommand = accessionLoadCommand(accession ?? ''); + ProteinViewerPanel.currentPanel = new ProteinViewerPanel(panel, extensionUri, loadCommand, undefined); } @@ -139,30 +138,30 @@ export class ProteinViewerPanel { }).then(viewer => { var snapshotId = getParam('snapshot-id', '[^&]+').trim(); if (snapshotId) viewer.setRemoteSnapshot(snapshotId); - + var snapshotUrl = getParam('snapshot-url', '[^&]+').trim(); var snapshotUrlType = getParam('snapshot-url-type', '[^&]+').toLowerCase().trim() || 'molj'; if (snapshotUrl && snapshotUrlType) viewer.loadSnapshotFromUrl(snapshotUrl, snapshotUrlType); - + var structureUrl = getParam('structure-url', '[^&]+').trim(); var structureUrlFormat = getParam('structure-url-format', '[a-z]+').toLowerCase().trim(); var structureUrlIsBinary = getParam('structure-url-is-binary', '[^&]+').trim() === '1'; if (structureUrl) viewer.loadStructureFromUrl(structureUrl, structureUrlFormat, structureUrlIsBinary); - + var pdb = getParam('pdb', '[^&]+').trim(); if (pdb) viewer.loadPdb(pdb); - + var pdbDev = getParam('pdb-dev', '[^&]+').trim(); if (pdbDev) viewer.loadPdbDev(pdbDev); - + var emdb = getParam('emdb', '[^&]+').trim(); if (emdb) viewer.loadEmdb(emdb); - + // var afdb = getParam('afdb', '[^&]+').trim(); - // if (afdb) + // if (afdb) // viewer.loadAlphaFoldDb('${accession}'); ${accession}; - + var modelArchive = getParam('model-archive', '[^&]+').trim(); if (modelArchive) viewer.loadModelArchive(modelArchive); }); @@ -176,21 +175,7 @@ export class ProteinViewerPanel { private _getWebviewContentForFiles(webview: vscode.Webview, extensionUri: vscode.Uri, clickedFiles: vscode.Uri[]) { const cssUri = webview.asWebviewUri(vscode.Uri.joinPath(extensionUri, 'node_modules', 'molstar', 'build/viewer', 'molstar.css')); const jsUri = webview.asWebviewUri(vscode.Uri.joinPath(extensionUri, 'node_modules', 'molstar', 'build/viewer', 'molstar.js')); - const pdbContents = clickedFiles.map((clickedFile) => webview.asWebviewUri(clickedFile)); - const extensions = clickedFiles.map((clickedFile) => clickedFile.path.split('.').pop()?.toLocaleLowerCase()); - let loadCommands: String[] = []; - for (let i = 0; i < pdbContents.length; i++) { - const pdbContent = pdbContents[i]; - var extension = extensions[i]; - console.log(extension); - if (extension === 'cif' || extension === 'mmCIF' || extension === 'CIF' || extension === 'MMCIF' || extension == '.mCIF' || extension == '.mcif') { - extension = 'mmcif'; - } - console.log(extension); - loadCommands.push( - `viewer.loadStructureFromUrl('${pdbContent}', format='${extension}');` - ); - } + const loadCommands = clickedFiles.map((file) => fileLoadCommand(webview.asWebviewUri(file).toString(), file.path)); // Tip: Install the es6-string-html VS Code extension to enable code highlighting below return /*html*/ ` @@ -270,11 +255,11 @@ export class ProteinViewerPanel { }).then(viewer => { var snapshotId = getParam('snapshot-id', '[^&]+').trim(); if (snapshotId) viewer.setRemoteSnapshot(snapshotId); - + var snapshotUrl = getParam('snapshot-url', '[^&]+').trim(); var snapshotUrlType = getParam('snapshot-url-type', '[^&]+').toLowerCase().trim() || 'molj'; if (snapshotUrl && snapshotUrlType) viewer.loadSnapshotFromUrl(snapshotUrl, snapshotUrlType); - + var structureUrl = getParam('structure-url', '[^&]+').trim(); var structureUrlFormat = getParam('structure-url-format', '[a-z]+').toLowerCase().trim(); var structureUrlIsBinary = getParam('structure-url-is-binary', '[^&]+').trim() === '1'; diff --git a/src/test/runTest.ts b/src/test/runTest.ts deleted file mode 100644 index 27b3ceb22..000000000 --- a/src/test/runTest.ts +++ /dev/null @@ -1,23 +0,0 @@ -import * as path from 'path'; - -import { runTests } from '@vscode/test-electron'; - -async function main() { - try { - // The folder containing the Extension Manifest package.json - // Passed to `--extensionDevelopmentPath` - const extensionDevelopmentPath = path.resolve(__dirname, '../../'); - - // The path to test runner - // Passed to --extensionTestsPath - const extensionTestsPath = path.resolve(__dirname, './suite/index'); - - // Download VS Code, unzip it and run the integration test - await runTests({ extensionDevelopmentPath, extensionTestsPath }); - } catch (err) { - console.error('Failed to run tests'); - process.exit(1); - } -} - -main(); diff --git a/src/test/suite/extension.test.ts b/src/test/suite/extension.test.ts index 4ca0ab419..1002fa597 100644 --- a/src/test/suite/extension.test.ts +++ b/src/test/suite/extension.test.ts @@ -1,15 +1,93 @@ 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 path from 'path'; import * as vscode from 'vscode'; -// import * as myExtension from '../../extension'; +import { ProteinViewerPanel } from '../../panels/ProteinViewerPanel'; + +const EXTENSION_ID = 'ArianJamasb.protein-viewer'; +const testFiles = path.resolve(__dirname, '../../../test_files'); + +function panelHtml(): string { + assert.ok(ProteinViewerPanel.currentPanel, 'expected a viewer panel to be open'); + // eslint-disable-next-line @typescript-eslint/no-explicit-any + return (ProteinViewerPanel.currentPanel as any)._panel.webview.html; +} + +suite('Extension', () => { + suiteSetup(async () => { + await vscode.extensions.getExtension(EXTENSION_ID)!.activate(); + }); + + teardown(async () => { + ProteinViewerPanel.currentPanel?.dispose(); + await vscode.commands.executeCommand('workbench.action.closeAllEditors'); + }); + + test('registers all contributed commands', async () => { + const commands = await vscode.commands.getCommands(true); + for (const id of ['start', 'activateFromFiles', 'activateFromFolder', 'ESMFold']) { + assert.ok(commands.includes(`protein-viewer.${id}`), `missing protein-viewer.${id}`); + } + }); + + test('activateFromFiles opens a viewer for a single file', async () => { + const file = vscode.Uri.file(path.join(testFiles, '3eiy.PDB')); + await vscode.commands.executeCommand('protein-viewer.activateFromFiles', file); + const html = panelHtml(); + assert.match(html, /molstar\.js/); + assert.match(html, /viewer\.loadStructureFromUrl\("[^"]*3eiy\.PDB", "pdb", false\);/); + }); + + test('activateFromFiles prefers the multi-selection over the clicked file', async () => { + const pdb = vscode.Uri.file(path.join(testFiles, '3eiy.PDB')); + const cif = vscode.Uri.file(path.join(testFiles, '3eiy.MMCIF')); + await vscode.commands.executeCommand('protein-viewer.activateFromFiles', pdb, [pdb, cif]); + const html = panelHtml(); + assert.match(html, /3eiy\.PDB", "pdb"/); + assert.match(html, /3eiy\.MMCIF", "mmcif"/); + }); + + test('activateFromFiles with nothing selected opens no panel', async () => { + await vscode.commands.executeCommand('protein-viewer.activateFromFiles'); + assert.strictEqual(ProteinViewerPanel.currentPanel, undefined); + }); + + test('activateFromFolder loads supported files from the folder', async () => { + await vscode.commands.executeCommand('protein-viewer.activateFromFolder', vscode.Uri.file(testFiles)); + const html = panelHtml(); + assert.match(html, /3eiy\.PDB", "pdb"/); + assert.match(html, /esmfold\.pdb", "pdb"/); + }); + + suite('start', () => { + const realShowInputBox = vscode.window.showInputBox; + const stubInput = (value: string | undefined) => { + // eslint-disable-next-line @typescript-eslint/no-explicit-any + (vscode.window as any).showInputBox = async () => value; + }; + // eslint-disable-next-line @typescript-eslint/no-explicit-any + teardown(() => { (vscode.window as any).showInputBox = realShowInputBox; }); + + const startAndWait = async () => { + await vscode.commands.executeCommand('protein-viewer.start'); + await new Promise((r) => setTimeout(r, 50)); // command doesn't await its input box + }; + + test('loads a PDB entry for a 4-character ID', async () => { + stubInput('3eiy'); + await startAndWait(); + assert.match(panelHtml(), /viewer\.loadPdb\("3eiy"\);/); + }); -suite('Extension Test Suite', () => { - vscode.window.showInformationMessage('Start all tests.'); + test('loads AlphaFold DB for a UniProt accession', async () => { + stubInput('P69905'); + await startAndWait(); + assert.match(panelHtml(), /viewer\.loadAlphaFoldDb\("P69905"\);/); + }); - test('Sample test', () => { - assert.strictEqual(-1, [1, 2, 3].indexOf(5)); - assert.strictEqual(-1, [1, 2, 3].indexOf(0)); + test('does nothing when the input box is cancelled', async () => { + stubInput(undefined); + await startAndWait(); + assert.strictEqual(ProteinViewerPanel.currentPanel, undefined); + }); }); }); diff --git a/src/test/suite/index.ts b/src/test/suite/index.ts deleted file mode 100644 index 7029e38ed..000000000 --- a/src/test/suite/index.ts +++ /dev/null @@ -1,38 +0,0 @@ -import * as path from 'path'; -import * as Mocha from 'mocha'; -import * as glob from 'glob'; - -export function run(): Promise { - // Create the mocha test - const mocha = new Mocha({ - ui: 'tdd', - color: true - }); - - const testsRoot = path.resolve(__dirname, '..'); - - return new Promise((c, e) => { - glob('**/**.test.js', { cwd: testsRoot }, (err, files) => { - if (err) { - return e(err); - } - - // Add files to the test suite - files.forEach(f => mocha.addFile(path.resolve(testsRoot, f))); - - try { - // Run the mocha test - mocha.run(failures => { - if (failures > 0) { - e(new Error(`${failures} tests failed.`)); - } else { - c(); - } - }); - } catch (err) { - console.error(err); - e(err); - } - }); - }); -} diff --git a/src/test/unit/formats.test.ts b/src/test/unit/formats.test.ts new file mode 100644 index 000000000..44a245ff3 --- /dev/null +++ b/src/test/unit/formats.test.ts @@ -0,0 +1,62 @@ +import * as assert from 'assert'; +import { accessionLoadCommand, fileLoadCommand, molstarFormat } from '../../formats'; + +suite('molstarFormat', () => { + const cases: [string, string, boolean][] = [ + ['/a/3eiy.pdb', 'pdb', false], + ['/a/3eiy.PDB', 'pdb', false], + ['/a/x.ent', 'pdb', false], + ['/a/x.brk', 'pdb', false], + ['/a/x.pdbqt', 'pdbqt', false], + ['/a/x.cif', 'mmcif', false], + ['/a/x.CIF', 'mmcif', false], + ['/a/x.mmcif', 'mmcif', false], + ['/a/3eiy.MMCIF', 'mmcif', false], + ['/a/x.mcif', 'mmcif', false], + ['/a/x.bcif', 'mmcif', true], + ['/a/x.sd', 'sdf', false], + ['/a/x.SDF', 'sdf', false], + ['/a/x.mol2', 'mol2', false], + ['/a/x.MOL2', 'mol2', false], + ['/a/x.gro', 'gro', false], + ['/a/x.xyz', 'xyz', false], + ['/dir.v2/x.mol', 'mol', false], + ]; + for (const [path, format, isBinary] of cases) { + test(`${path} -> ${format}`, () => { + assert.deepStrictEqual(molstarFormat(path), { format, isBinary }); + }); + } +}); + +suite('fileLoadCommand', () => { + test('emits a quoted loadStructureFromUrl call', () => { + assert.strictEqual( + fileLoadCommand('https://file+.vscode-resource/a/x.bcif', '/a/x.bcif'), + 'viewer.loadStructureFromUrl("https://file+.vscode-resource/a/x.bcif", "mmcif", true);' + ); + }); + + test('escapes quotes in URLs', () => { + const cmd = fileLoadCommand(`https://h/it's".pdb`, `/it's".pdb`); + assert.strictEqual(cmd, `viewer.loadStructureFromUrl("https://h/it's\\".pdb", "pdb", false);`); + }); +}); + +suite('accessionLoadCommand', () => { + test('4-character IDs load from the PDB', () => { + assert.strictEqual(accessionLoadCommand('3eiy'), 'viewer.loadPdb("3eiy");'); + }); + + test('trims whitespace before classifying', () => { + assert.strictEqual(accessionLoadCommand(' 1CRN \n'), 'viewer.loadPdb("1CRN");'); + }); + + test('other IDs load from AlphaFold DB', () => { + assert.strictEqual(accessionLoadCommand('P69905'), 'viewer.loadAlphaFoldDb("P69905");'); + }); + + test('cannot break out of the string literal', () => { + assert.strictEqual(accessionLoadCommand(`x');alert(1);//`), `viewer.loadAlphaFoldDb("x');alert(1);//");`); + }); +}); diff --git a/tsconfig.json b/tsconfig.json index 65490914f..7ec71793a 100644 --- a/tsconfig.json +++ b/tsconfig.json @@ -7,6 +7,7 @@ "ES2020", "dom" ], + "skipLibCheck": true, "sourceMap": true, "rootDir": "src", "strict": true /* enable all strict type-checking options */