feat(install): Add --update-checksums to cli install (yarnpkg#4860)

**Summary**

Fixes yarnpkg#4817.
When the `--update-checksums` flag is set, yarn would know to ignore a checksum mismatch between `yarn.lock` and the repository, and instead update the yarn.lock file with the proper checksum(s).

**Test plan**

Added new tests.

To manually check this:
1. Change one or more of the package checksums in `yarn.lock`
2. Delete node_modules (optionally also run `yarn cache clean`)
3. Run `yarn` => checksum mismatch error will be received.
4. Run `yarn --update-checksums` => will install successfully and fix the damaged checksums in `yarn.lock`

__tests__/commands/_helpers.js

@@ -88,6 +88,7 @@ export function makeConfigFromDirectory(cwd: string, reporter: Reporter, flags:
       linkFolder: flags.linkFolder || path.join(cwd, '.yarn-link'),
       prefix: flags.prefix,
       production: flags.production,
+      updateChecksums: !!flags.updateChecksums,
     },
     reporter,
   );

__tests__/commands/install/integration.js

@@ -732,6 +732,21 @@ test.concurrent('install should add missing deps to yarn and mirror (PR import s
   });
 });
 
+test.concurrent('install should update checksums in yarn.lock (--update-checksums)', (): Promise<void> => {
+  const packageRealHash = '5faad9c2c07f60dd76770f71cf025b62a63cfd4e';
+  const packageCacheName = `npm-abab-1.0.4-${packageRealHash}`;
+  return runInstall({updateChecksums: true}, 'install-update-checksums', async config => {
+    const lockFileContent = await fs.readFile(path.join(config.cwd, 'yarn.lock'));
+    const lockFileLines = explodeLockfile(lockFileContent);
+    const packageHashInLockfile = lockFileLines[2].replace(/(^.*#)|("$)/g, '');
+    const installedPackageJson = path.resolve(config.cwd, 'node_modules', 'abab', 'package.json');
+    const cachePackageJson = path.resolve(config.cwd, '.yarn-cache/v1/', packageCacheName, 'package.json');
+    expect(packageHashInLockfile).toEqual(packageRealHash);
+    expect(await fs.exists(installedPackageJson)).toBe(true);
+    expect(await fs.exists(cachePackageJson)).toBe(true);
+  });
+});
+
 test.concurrent('install should update a dependency to yarn and mirror (PR import scenario 2)', (): Promise<void> => {
   // [email protected] is gets updated to [email protected] via
   // a change in package.json,

__tests__/fetchers.js

@@ -171,6 +171,28 @@ test('TarballFetcher.fetch throws on invalid hash', async () => {
   expect(readdirSync(path.join(offlineMirrorDir))).toEqual([]);
 });
 
+test('TarballFetcher.fetch fixes hash if updateChecksums flag is true', async () => {
+  const wrongHash = 'foo';
+  const dir = await mkdir(`tarball-fetcher-${wrongHash}`);
+  const config = await Config.create({}, new Reporter());
+  config.updateChecksums = true;
+  const url = 'https://github.com/sindresorhus/beeper/archive/master.tar.gz';
+  const fetcher = new TarballFetcher(
+    dir,
+    {
+      type: 'tarball',
+      hash: wrongHash,
+      reference: url,
+      registry: 'npm',
+    },
+    config,
+  );
+  await fetcher.fetch();
+  const dirWithProperHash = dir.replace(wrongHash, fetcher.hash);
+  const name = (await fs.readJson(path.join(dirWithProperHash, 'package.json'))).name;
+  expect(name).toBe('beeper');
+});
+
 test('TarballFetcher.fetch supports local ungzipped tarball', async () => {
   const dir = await mkdir('tarball-fetcher');
   const fetcher = new LocalTarballFetcher(

__tests__/fixtures/install/install-update-checksums/package.json

@@ -0,0 +1,15 @@
+{
+  "name": "install-update-checksums",
+  "version": "1.0.0",
+  "description": "",
+  "main": "index.js",
+  "scripts": {
+    "test": "echo \"Error: no test specified\" && exit 1"
+  },
+  "author": "",
+  "license": "ISC",
+  "dependencies": {
+    "abab": "^1.0.4",
+    "leftpad": "^0.0.1"
+  }
+}

__tests__/fixtures/install/install-update-checksums/yarn.lock

@@ -0,0 +1,11 @@
+# THIS IS AN AUTOGENERATED FILE. DO NOT EDIT THIS FILE DIRECTLY.
+# yarn lockfile v1
+
+
+abab@^1.0.4:
+  version "1.0.4"
+  resolved "https://registry.yarnpkg.com/abab/-/abab-1.0.4.tgz#foo"
+
+leftpad@^0.0.1:
+  version "0.0.1"
+  resolved "https://registry.yarnpkg.com/leftpad/-/leftpad-0.0.1.tgz#86b1a4de4face180ac545a83f1503523d8fed115"

src/cli/commands/install.js

@@ -133,6 +133,7 @@ function normalizeFlags(config: Config, rawFlags: Object): Flags {
     flat: !!rawFlags.flat,
     lockfile: rawFlags.lockfile !== false,
     pureLockfile: !!rawFlags.pureLockfile,
+    updateChecksums: !!rawFlags.updateChecksums,
     skipIntegrityCheck: !!rawFlags.skipIntegrityCheck,
     frozenLockfile: !!rawFlags.frozenLockfile,
     linkDuplicates: !!rawFlags.linkDuplicates,

src/cli/index.js

@@ -84,6 +84,7 @@ export function main({
   commander.option('--no-lockfile', "don't read or generate a lockfile");
   commander.option('--pure-lockfile', "don't generate a lockfile");
   commander.option('--frozen-lockfile', "don't generate a lockfile and fail if an update is needed");
+  commander.option('--update-checksums', 'update package checksums from current repository');
   commander.option('--link-duplicates', 'create hardlinks to the repeated modules in node_modules');
   commander.option('--link-folder <path>', 'specify a custom folder to store global links');
   commander.option('--global-folder <path>', 'specify a custom folder to store global packages');
@@ -488,6 +489,7 @@ export function main({
       networkTimeout: commander.networkTimeout,
       nonInteractive: commander.nonInteractive,
       scriptsPrependNodePath: commander.scriptsPrependNodePath,
+      updateChecksums: commander.updateChecksums,
     })
     .then(() => {
       // lockfile check must happen after config.init sets lockfileFolder

src/config.js

@@ -57,6 +57,8 @@ export type ConfigOptions = {
 
   commandName?: ?string,
   registry?: ?string,
+
+  updateChecksums?: boolean,
 };
 
 type PackageMetadata = {
@@ -102,6 +104,7 @@ export default class Config {
   linkFileDependencies: boolean;
   ignorePlatform: boolean;
   binLinks: boolean;
+  updateChecksums: boolean;
 
   //
   linkedModules: Array<string>;
@@ -364,6 +367,7 @@ export default class Config {
     this.linkFolder = opts.linkFolder || constants.LINK_REGISTRY_DIRECTORY;
     this.offline = !!opts.offline;
     this.binLinks = !!opts.binLinks;
+    this.updateChecksums = !!opts.updateChecksums;
 
     this.ignorePlatform = !!opts.ignorePlatform;
     this.ignoreScripts = !!opts.ignoreScripts;

src/fetchers/base-fetcher.js

@@ -43,28 +43,27 @@ export default class BaseFetcher {
   }
 
   fetch(defaultManifest: ?Object): Promise<FetchedMetadata> {
-    const {dest} = this;
-    return fs.lockQueue.push(dest, async (): Promise<FetchedMetadata> => {
-      await fs.mkdirp(dest);
+    return fs.lockQueue.push(this.dest, async (): Promise<FetchedMetadata> => {
+      await fs.mkdirp(this.dest);
 
       // fetch package and get the hash
       const {hash} = await this._fetch();
 
       const pkg = await (async () => {
         // load the new normalized manifest
         try {
-          return await this.config.readManifest(dest, this.registry);
+          return await this.config.readManifest(this.dest, this.registry);
         } catch (e) {
           if (e.code === 'ENOENT' && defaultManifest) {
-            return normalizeManifest(defaultManifest, dest, this.config, false);
+            return normalizeManifest(defaultManifest, this.dest, this.config, false);
           } else {
             throw e;
           }
         }
       })();
 
       await fs.writeFile(
-        path.join(dest, constants.METADATA_FILENAME),
+        path.join(this.dest, constants.METADATA_FILENAME),
         JSON.stringify(
           {
             manifest: pkg,
@@ -80,7 +79,7 @@ export default class BaseFetcher {
 
       return {
         hash,
-        dest,
+        dest: this.dest,
         package: pkg,
         cached: false,
       };

src/fetchers/tarball-fetcher.js

@@ -78,14 +78,25 @@ export default class TarballFetcher extends BaseFetcher {
         error.message = `${error.message}${tarballPath ? ` (${tarballPath})` : ''}`;
         reject(error);
       })
-      .on('finish', () => {
+      .on('finish', async () => {
         const expectHash = this.hash;
         const actualHash = validateStream.getHash();
 
         if (!expectHash || expectHash === actualHash) {
           resolve({
             hash: actualHash,
           });
+        } else if (this.config.updateChecksums) {
+          // checksums differ and should be updated
+          // update hash, destination and cached package
+          const destUpdatedHash = this.dest.replace(this.hash || '', actualHash);
+          await fsUtil.unlink(destUpdatedHash);
+          await fsUtil.rename(this.dest, destUpdatedHash);
+          this.dest = this.dest.replace(this.hash || '', actualHash);
+          this.hash = actualHash;
+          resolve({
+            hash: actualHash,
+          });
         } else {
           reject(
             new SecurityError(

src/package-fetcher.js

@@ -108,6 +108,18 @@ export function fetch(pkgs: Array<Manifest>, config: Config): Promise<Array<Mani
         // update with new remote
         // but only if there was a hash previously as the tarball fetcher does not provide a hash.
         if (ref.remote.hash) {
+          // if the checksum was updated, also update resolved and cache
+          if (ref.remote.hash !== res.hash && config.updateChecksums) {
+            const oldHash = ref.remote.hash;
+            if (ref.remote.resolved) {
+              ref.remote.resolved = ref.remote.resolved.replace(oldHash, res.hash);
+            }
+            ref.config.cache = Object.keys(ref.config.cache).reduce((cache, entry) => {
+              const entryWithNewHash = entry.replace(oldHash, res.hash);
+              cache[entryWithNewHash] = ref.config.cache[entry];
+              return cache;
+            }, {});
+          }
           ref.remote.hash = res.hash;
         }
       }