Switch from yarn to pnpm for frontend dependency management.

.github/workflows/ci-test.yml

@@ -42,16 +42,17 @@ jobs:
 
     steps:
       - uses: actions/checkout@v3 #Checkout the project from git
-      - name: Cache PNP #Pull the Yarn cache for PNP (package management strategy - see https://classic.yarnpkg.com/en/docs/pnp).  This caches all dependencies assuming the yarn.lock file stays the same
+      - name: Get pnpm store directory
+        id: pnpm-cache
+        run: |
+          echo "::set-output name=pnpm_cache_dir::$(./gradlew pnpmCacheDir -q)"
+      - name: Setup pnpm cache
         uses: actions/cache@v3
         with:
-          path: "**/.pnp.js"
-          key: ${{ runner.os }}-pnp-${{ hashFiles('**/yarn.lock') }}
-      - name: Cache yarn #Pull the cache for yarn.  This caches all dependencies assuming the yarn.lock file stays the same
-        uses: actions/cache@v2
-        with:
-          path: "**/.yarn"
-          key: ${{ runner.os }}-yarn-${{ hashFiles('**/yarn.lock') }}
+          path: ${{ steps.pnpm-cache.outputs.pnpm_cache_dir }}
+          key: ${{ runner.os }}-pnpm-store-${{ hashFiles('**/pnpm-lock.yaml') }}
+          restore-keys: |
+            ${{ runner.os }}-pnpm-store-
       - name: Setup MySQL
         uses: mirromutth/[email protected]
         with:
@@ -97,16 +98,17 @@ jobs:
 
     steps:
       - uses: actions/checkout@v3 #Checkout the project from git
-      - name: Cache PNP #Pull the Yarn cache for PNP (package management strategy - see https://classic.yarnpkg.com/en/docs/pnp).  This caches all dependencies assuming the yarn.lock file stays the same
+      - name: Get pnpm store directory
+        id: pnpm-cache
+        run: |
+          echo "::set-output name=pnpm_cache_dir::$(./gradlew pnpmCacheDir -q)"
+      - name: Setup pnpm cache
         uses: actions/cache@v3
         with:
-          path: "**/.pnp.js"
-          key: ${{ runner.os }}-pnp-${{ hashFiles('**/yarn.lock') }}
-      - name: Cache yarn #Pull the cache for yarn.  This caches all dependencies assuming the yarn.lock file stays the same
-        uses: actions/cache@v2
-        with:
-          path: "**/.yarn"
-          key: ${{ runner.os }}-yarn-${{ hashFiles('**/yarn.lock') }}
+          path: ${{ steps.pnpm-cache.outputs.pnpm_cache_dir }}
+          key: ${{ runner.os }}-pnpm-store-${{ hashFiles('**/pnpm-lock.yaml') }}
+          restore-keys: |
+            ${{ runner.os }}-pnpm-store-
       - name: Setup MySQL
         uses: mirromutth/[email protected]
         with:

.gitignore

@@ -48,15 +48,8 @@ src/main/webapp/node_modules
 /src/main/webapp/dist
 /src/main/webapp/pages/templates/i18n/*.html
 
-### YARN ###
-/src/main/webapp/.pnp.*
-/src/main/webapp/.yarn/*
-!/src/main/webapp/.yarn/patches
-!/src/main/webapp/.yarn/plugins
-!/src/main/webapp/.yarn/releases
-!/src/main/webapp/.yarn/sdks
-!/src/main/webapp/.yarn/versions
-/yarn.lock
+### PNPM ###
+/src/main/webapp/.pnpm-debug.log*
 
 ### MISC ###
 /.theia/launch.json

CHANGELOG.md

@@ -9,6 +9,7 @@
 * [UI]: Fixed user routes for admin panel. See [PR 1323](https://github.com/phac-nml/irida/pull/1323)
 * [Developer/UI]: Added `eslint-prettier-pluggin`. See [PR 1328](https://github.com/phac-nml/irida/pull/1328)
 * [Developer]: Replaced Maven with Gradle for build. See [PR 1300](https://github.com/phac-nml/irida/pull/1300)
+* [Developer/UI]: Switched to pnpm from yarn for frontend dependency management. See [PR 1332](https://github.com/phac-nml/irida/pull/1334)
 
 ## [22.05.5] - 2022/06/28
 * [UI]: Fixed bug preventing export of project samples table due to invalid url. [PR 1331](https://github.com/phac-nml/irida/pull/1331)

build.gradle.kts

@@ -1,4 +1,4 @@
-import com.github.gradle.node.yarn.task.YarnTask
+import com.github.gradle.node.pnpm.task.PnpmTask
 import org.springframework.boot.gradle.tasks.run.BootRun
 
 plugins {
@@ -255,13 +255,12 @@ tasks.bootWar { enabled = false }
 tasks.war {
     archiveClassifier.set("")
     destinationDirectory.set(layout.buildDirectory.dir("dist"))
-    exclude("node")
     exclude("node_modules/")
-    exclude(".yarn/")
     exclude("resources/css/")
     exclude("resources/js/")
     exclude("webpack*")
-    exclude(".yarn*")
+    exclude(".npmrc")
+    exclude("pnpm-lock.yaml")
     exclude("package.json")
     exclude("styles.js")
     exclude("entries.js")
@@ -272,20 +271,42 @@ tasks.war {
 node {
     download.set(true)
     version.set("16.15.1")
-    yarnVersion.set("1.22.17") // we actualy use yarn 3 but we cannot specify that here
+    pnpmVersion.set("7.4.0")
     workDir.set(file("${project.projectDir}/.gradle/nodejs"))
-    yarnWorkDir.set(file("${project.projectDir}/.gradle/yarn"))
-    nodeProjectDir.set(file("${projectDir}/src/main/webapp"))
+    nodeProjectDir.set(file("${project.projectDir}/src/main/webapp"))
 }
 
-tasks.register<YarnTask>("cleanWebapp") {
-    dependsOn("yarn_install")
-    yarnCommand.set(listOf("clean"))
+tasks.register<PnpmTask>("pnpmCachePrune") {
+    group = "pnpm"
+    description = "Prune pnpm cache directory."
+    pnpmCommand.set(listOf("store", "prune"))
 }
 
-tasks.register<YarnTask>("buildWebapp") {
+tasks.register<PnpmTask>("pnpmCacheDir") {
+    group = "pnpm"
+    description = "Report pnpm cache directory."
+    pnpmCommand.set(listOf("store", "path"))
+}
+
+tasks.named<PnpmTask>("pnpmInstall") {
+    finalizedBy(":pnpmCachePrune")
+}
+
+tasks.register<PnpmTask>("cleanWebapp") {
+    dependsOn(":pnpmInstall")
+    pnpmCommand.set(listOf("clean"))
+}
+
+tasks.register<PnpmTask>("buildWebapp") {
+    dependsOn(":cleanWebapp")
+    pnpmCommand.set(listOf("build"))
+    inputs.dir("${project.projectDir}/src/main/webapp/resources")
+    outputs.dir("${project.projectDir}/src/main/webapp/dist")
+}
+
+tasks.register<PnpmTask>("startWebapp") {
     dependsOn(":cleanWebapp")
-    yarnCommand.set(listOf("build"))
+    pnpmCommand.set(listOf("start"))
     inputs.dir("${project.projectDir}/src/main/webapp/resources")
     outputs.dir("${project.projectDir}/src/main/webapp/dist")
 }
@@ -320,6 +341,8 @@ val permittedTestSystemProperties = listOf(
 
 fun createIntegrationTestTask(name: String, tags: String?, excludeListeners: String?): TaskProvider<Test> {
     return tasks.register<Test>("${name}ITest") {
+        group = "verification"
+        description = "Runs the ${name} integration test suite."
         val defaultSystemProperties = mapOf(
             "junit.platform.execution.listeners.deactivate" to excludeListeners,
             "spring.datasource.url" to "jdbc:mysql://localhost:3306/irida_integration_test",

doc/administrator/web/building/index.md

@@ -20,7 +20,7 @@ The following software is required to build IRIDA from source:
 * Java 11 JDK (http://www.oracle.com/technetwork/java/javase/downloads/index.html)
 * Git (http://git-scm.com/)
 * Node (http://nodejs.org/)
-* Yarn (https://yarnpkg.com/lang/en/)
+* Pnpm (https://pnpm.io/)
 
 Installing these dependencies varies greatly, depending on the host operating system that you are using, so no install instructions are provided. The following commands must be available on your `$PATH`:
 
@@ -41,7 +41,7 @@ git clone https://github.com/phac-nml/irida.git
 
 ### Installing dependencies
 
-IRIDA uses Gradle and Yarn for managing external dependencies. Some of the libraries that we're using to build IRIDA are either not available in the Maven central repository, or we've had to seperately modify/update the code to accomplish the task we want, and the changes have not yet been accepted upstream.
+IRIDA uses Gradle and Pnpm for managing external dependencies. Some of the libraries that we're using to build IRIDA are either not available in the Maven central repository, or we've had to seperately modify/update the code to accomplish the task we want, and the changes have not yet been accepted upstream.
 
 These libraries are located in `/lib` folder and are automatically installed via gradle.
 

doc/developer/interface/index.md

@@ -29,13 +29,13 @@ IRIDA uses the design system [Ant Design](https://ant.design/), a [React JS](htt
 
 ### Build Process:
 
-#### Production Mode: `yarn build`
+#### Production Mode: `./gradlew buildWebapp`
 - Minimal source map
 - File minification
 - Bundle Chunking: Splits code into various bundles which can then me loaded on demand or in parallel. This makes for smaller bundle sizes and controls resource load prioritization. Bundle chunking also for code that is loaded on different pages be bundled together and cached by the browser.
 - Hash code added to file name to allow for browser cache breaking.
 
-#### Development Mode: `yarn start`
+#### Development Mode: `./gradlew startWebapp`
 - **watch** mode set; any changes to JavaScript of CSS files will be automatically compiled
 - Extensive source map
 - No file minification
@@ -49,6 +49,17 @@ Current babel plugins for UI development:
 - [Export default from](https://babeljs.io/docs/en/babel-plugin-proposal-export-default-from) 
 - [Optional Chaining](https://babeljs.io/docs/en/babel-plugin-proposal-optional-chaining)
 
+#### Adding dependencies
+
+IRIDA uses [pnpm](https://pnpm.io/) to manage node dependencies.
+
+To add a new dependency you can run the following command:
+```bash
+./gradlew pnpm_add DEPENDENCY
+```
+
+This follows the same argument structure as https://pnpm.io/cli/add.
+
 ### CSS
 
 IRIDA uses [PostCSS](https://postcss.org/) to transform CSS:
@@ -86,7 +97,7 @@ For entries:
 
 ##### Webpack
 
-- `yarn build`: runs webpack in production mode
+- `./gradlew buildWebapp`: runs webpack in production mode
     * Compilation, minification, and chunking of CSS and JavaScript assets.
     * Extraction for internationalization strings.
     * Creation of webpack manifest file

doc/developer/setup/index.md

@@ -132,7 +132,7 @@ will cause Tomcat to start up much faster.
 
 Other arguments can be be passed to the script:
 
-* `--no-yarn`: Skip running the `yarn build` script along with the build, useful during development.
+* `--no-webapp-build`: Skip running the `buildWebapp` task along with the build, useful during development.
 * `--prod`: Run spring using the production profile.
 
 #### Integration Testing
@@ -151,18 +151,13 @@ Please refer to the [Galaxy Install Guide][galaxy-install] for information on se
 Front End Development Setup
 ---------------------------
 
-IRIDA uses [Yarn 2](https://yarnpkg.com) for front-end dependency management.  [Install yarn](https://yarnpkg.com/getting-started/install) by following the directions for your machine.  For production, it is automatically installed during the build process.
-
-From within `src/main/webapp/`:
-
-You will need to run `yarn install` to install all dependencies required to run the following from the command line.
+IRIDA uses [Pnpm](hhttps://pnpm.io/) for front-end dependency management. It is automatically installed when running gradle tasks that require the webapp to be built.
 
 Tasks
 =====
 
-* `yarn sass` - compile all `.scss` files into `.css` files, with sourcemaps.
-* `yarn build` - compile all es6 files to es2015.
-* `yarn start` - use when developing front end code.  Webpack will monitor for changes to the entry files, compile them, and then updates the browser with the changes.
+* `./gradlew buildWebapp` - compile all es6 files to es2015.
+* `./gradlew startWebapp` - use when developing front end code.  Webpack will monitor for changes to the entry files, compile them, and then updates the browser with the changes.
 
 JavaScript and SCSS Code Formatting and Linting
 ===============================================

run.sh

@@ -13,7 +13,7 @@ while [ $# -ne 0 ];
        SPRING_BOOT_ARGS+=("--hbm.dev.auto=create")
        ADD_DB=true
        echo "Dropping then Creating/Recreating database schema"
-    elif [ "$1" = "--no-yarn" ];
+    elif [ "$1" = "--no-webapp-build" ];
     then
       GRADLE_ARGS+=("-xbuildWebapp")
     elif [ "$1" = "--prod" ];

settings.gradle.kts

@@ -4,7 +4,7 @@ pluginManagement {
         gradlePluginPortal()
     }
     plugins {
-        id("com.github.node-gradle.node") version "3.3.0"
+        id("com.github.node-gradle.node") version "3.4.0"
         id("io.spring.dependency-management") version "1.0.11.RELEASE"
         id("org.gradle.test-retry") version "1.4.0"
         id("org.springframework.boot") version "2.6.6"

src/main/webapp/.npmrc

@@ -0,0 +1 @@
+shamefully-hoist=true