Merge branch 'develop' into dev-plfm-swc-6663

.git-blame-ignore-revs

@@ -1,4 +1,6 @@
 # Exclude the following commits from the git blame -- see https://stackoverflow.com/a/69118451
 # You may need to run git config blame.ignoreRevsFile .git-blame-ignore-revs
 ## 2022-11-09 - Ran prettier code-formatter on entire repo after adding lint-staged to enforce code formatting
-53b439d81b4126848ce42514c6b5cc62fe5f5fa8
+53b439d81b4126848ce42514c6b5cc62fe5f5fa8
+## 2024-03-22 - Reverted prettier-plugin-java to v2.5.0 to avoid regression https://github.com/jhipster/prettier-java/issues/650
+09d3d9ef4c2a24d8079ab8dc7947c680f9c42efa

.github/workflows/build-test-e2e.yml

@@ -39,7 +39,7 @@ jobs:
           retention-days: 1
   playwright-tests:
     needs: [build]
-    runs-on: 'macos-latest'
+    runs-on: 'macos-12'
     timeout-minutes: 60
     # Ensure that at most one playwright-tests job will run at a time in Sage-Bionetworks repo,
     # but allow multiple playwright-test jobs to run concurrently in forked repos
@@ -70,29 +70,6 @@ jobs:
       - name: Check colima and lima version
         if: runner.os == 'macos'
         run: |
-          echo "- runner colima version: $(colima version)" >> $GITHUB_STEP_SUMMARY
-          LIMA_VERSION=$(limactl --version)
-          echo "- runner lima version: ${LIMA_VERSION}" >> $GITHUB_STEP_SUMMARY
-          if [[ !("${LIMA_VERSION}" == "limactl version 0.19.0" || "${LIMA_VERSION}" == "limactl version 0.19.1") ]]; then 
-            echo "::warning::runner lima version has changed. Consider removing lima/colima downgrade, see SWC-6655."
-          fi
-      - name: Downgrade colima/lima versions
-        if: runner.os == 'macos'
-        run: |
-          brew uninstall colima
-          brew uninstall lima
-
-          # install lima
-          LIMA_VERSION="v0.18.0"
-          LIMA_VERSION_URL="https://github.com/lima-vm/lima/releases/download/${LIMA_VERSION}/lima-${LIMA_VERSION:1}-$(uname -s)-$(uname -m).tar.gz"
-          curl -fsSL "${LIMA_VERSION_URL}" | tar Cxzvm /usr/local
-
-          # install colima
-          COLIMA_VERSION="v0.6.6"
-          COLIMA_VERSION_URL="https://github.com/abiosoft/colima/releases/download/${COLIMA_VERSION}/colima-$(uname -s)-$(uname -m)"
-          sudo mkdir -p /usr/local/bin
-          sudo curl -L -o /usr/local/bin/colima "${COLIMA_VERSION_URL}" && sudo chmod +x /usr/local/bin/colima
-
           # Get colima and lima versions
           limactl --version
           colima version
@@ -119,7 +96,7 @@ jobs:
         with:
           node-version: ${{ env.NODE_VERSION }}
       - name: Install dependencies
-        run: yarn install --frozen-lockfile
+        run: yarn install --frozen-lockfile --network-timeout 1000000
       - name: Install Playwright Browsers
         run: yarn playwright install --with-deps
       - name: Check for common errors

.github/workflows/build/action.yml

@@ -3,11 +3,11 @@ description: 'Build SWC'
 runs:
   using: 'composite'
   steps:
-    - name: Set up JDK 8
-      uses: actions/setup-java@v3
+    - name: Set up JDK 11
+      uses: actions/setup-java@v4
       with:
-        java-version: '8'
-        distribution: 'temurin'
+        java-version: '11'
+        distribution: 'corretto'
         cache: maven
     - name: Build with Maven
       shell: bash

.gitignore

@@ -12,6 +12,9 @@ extras/
 /.sass-cache/
 .idea/*
 
+src/main/main.iml
+src/test/test.iml
+
 # We use a maven plugin to download node and required modules.
 # Since these are retrieved at build-time, no need to commit.
 node/*

.prettierignore

@@ -10,7 +10,6 @@
 # These artifacts were generated and/or pre-minified and then checked in
 src/main/webapp/css/**/*
 src/main/webapp/js/**/*
-src/main/webapp/offline/**/*
 src/main/webapp/pdf.js/**/*
 src/main/webapp/research/**/*
 

README.md

@@ -1,9 +1,11 @@
-# Synapse Web Client (SWC) [![Synapse website](https://img.shields.io/website-up-down-brightgreen-red/https/www.synapse.org.svg?label=synapse.org&style=flat-square)](https://www.synapse.org) [![Uptime Robot ratio (7 days)](https://img.shields.io/uptimerobot/ratio/7/m779300534-4f408b1654d840b82b911550.svg?style=flat-square)](https://stats.uptimerobot.com/mqmm6ILGx) [![jfrog](https://img.shields.io/website-available-unavailable-brightgreen-red/https/sagebionetworks.jfrog.io/sagebionetworks/webapp.svg?label=artifact&style=flat-square)](https://sagebionetworks.jfrog.io/sagebionetworks/webapp/#/artifacts/browse/tree/General/libs-releases/org/sagebionetworks/portal) [![license](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
+# Synapse Web Client (SWC) [![Synapse website](https://img.shields.io/website-up-down-brightgreen-red/https/www.synapse.org.svg?label=synapse.org&style=flat-square)](https://www.synapse.org) [![Uptime Robot ratio (7 days)](https://img.shields.io/uptimerobot/ratio/7/m779300534-4f408b1654d840b82b911550.svg?style=flat-square)](https://stats.uptimerobot.com/mqmm6ILGx) [![license](https://img.shields.io/badge/License-Apache%202.0-blue.svg)](https://opensource.org/licenses/Apache-2.0)
 
-The Synapse Web Client is a [Google Web Toolkit](http://www.gwtproject.org/)-based [single-page application](https://en.wikipedia.org/wiki/Single-page_application), the web client of the Synapse REST service core. It provides access to the the cloud-hosted [Synapse backend services](https://github.com/Sage-Bionetworks/Synapse-Repository-Services).
+The Synapse Web Client is a [Google Web Toolkit](http://www.gwtproject.org/)-based [single-page application](https://en.wikipedia.org/wiki/Single-page_application), the web client of the Synapse REST service core. It provides access to the the cloud-hosted [Synapse backend services](https://github.com/Sage-Bionetworks/Synapse-Repository-Services) ([API docs](https://rest-docs.synapse.org/rest/)).
 
 The current SWC release build can be accessed by visiting https://www.synapse.org/
 
 For more information about Synapse, please see the [Synapse Docs](http://docs.synapse.org/).
 
 Interested in spinning up a local web client? Go to the [SWC Developer Bootstrap](https://sagebionetworks.jira.com/wiki/display/SWC/Developer+Bootstrap) to find out how.
+
+A subset of the site is implemented by React components. [Storybook](https://sage-bionetworks.github.io/synapse-web-monorepo/) | [Github](https://github.com/Sage-Bionetworks/synapse-web-monorepo/tree/main/packages/synapse-react-client)

devdocs/ReactIntegration.md

@@ -17,7 +17,7 @@ Using JsInterop to call your React component can be summarized in these basic st
 
 1. Create a class to represent your components' props
 1. Add your component to the SRC JsInterop type
-1. Add a ReactComponentDiv to your View
+1. Add a ReactComponent to your View
 1. In the View, use React and ReactDOM to render the element.
 
 ### Create a Prop Class
@@ -34,9 +34,9 @@ The [SRC class](../src/main/java/org/sagebionetworks/web/client/jsinterop/SRC.ja
 
 Make sure you specify your prop type in the type parameter, and also make sure that your object name exactly matches the named export in `SynapseComponents`.
 
-### Add a ReactComponentDiv or ReactComponentSpan to your View
+### Add a ReactComponent to your View
 
-While you can append your React component to any element, we have [ReactComponentDiv](../src/main/java/org/sagebionetworks/web/client/widget/ReactComponentDiv.java) and [ReactComponentSpan](../src/main/java/org/sagebionetworks/web/client/widget/ReactComponentDiv.java) that contain logic that simplifies managing the lifecycle of a React component. Add this to your View in code or `*.ui.xml` file, and make sure you can reference it for the next step.
+While you can append your React component to any element, we have [ReactComponent](../src/main/java/org/sagebionetworks/web/client/widget/ReactComponent.java) that contains logic that simplifies managing the lifecycle of a React component. Add this to your View in code or `*.ui.xml` file, and make sure you can reference it for the next step.
 
 ### Passing Synapse context
 
@@ -49,6 +49,7 @@ How you manage updating your widget's view will vary based on the scenario, but
 ```java
 import org.sagebionetworks.web.client.context.SynapseReactClientFullContextPropsProvider;
 import org.sagebionetworks.web.client.jsinterop.React;
+import org.sagebionetworks.web.client.jsinterop.ReactElement;
 
 class MyView {
 
@@ -57,12 +58,12 @@ class MyView {
 
   void renderComponent() {
     MyProps props = props.create(/**/);
-    ReactNode reactNode = React.createElementWithSynapseContext(
+    ReactElement reactElement = React.createElementWithSynapseContext(
       SRC.SynapseComponents.MyComponent,
       props,
       propsProvider.getJsInteropContextProps()
     );
-    reactComponentDiv.render(reactNode);
+    reactComponent.render(reactElement);
   }
 }
 

e2e/discussions.spec.ts

@@ -1,4 +1,4 @@
-import { Page, expect, test } from '@playwright/test'
+import { Page, expect } from '@playwright/test'
 import { defaultExpectTimeout } from '../playwright.config'
 import { testAuth } from './fixtures/authenticatedUserPages'
 import {
@@ -109,7 +109,7 @@ const getDiscussionReplyActionButtons = (page: Page, threadReply: string) => {
 let userProject: Project
 const fileHandleIds: string[] = []
 
-test.describe('Discussions', () => {
+testAuth.describe('Discussions', () => {
   testAuth.beforeAll(async ({ browser, storageStatePaths }) => {
     userProject = await setupProjectWithPermissions(
       browser,
@@ -120,7 +120,7 @@ test.describe('Discussions', () => {
   })
 
   testAuth.afterAll(async ({ browser }) => {
-    test.slow()
+    testAuth.slow()
     if (userProject.id) {
       await teardownProjectsAndFileHandles(
         browser,
@@ -133,7 +133,7 @@ test.describe('Discussions', () => {
   testAuth(
     'should allow discussion and reply CRUD',
     async ({ userPage, validatedUserPage }) => {
-      test.slow()
+      testAuth.slow()
 
       const threadTitle = 'The Title of the Thread'
       const threadBody = 'The body of the Thread'

e2e/favorites.spec.ts

@@ -1,4 +1,4 @@
-import { Page, expect, test } from '@playwright/test'
+import { Page, expect } from '@playwright/test'
 import { testAuth } from './fixtures/authenticatedUserPages'
 import { entityUrlPathname } from './helpers/entities'
 import {
@@ -41,7 +41,7 @@ function getFavoriteStarSpiner(page: Page) {
   return page.locator('.pageHeader').locator('.spinner:visible')
 }
 
-test.describe('Favorites', () => {
+testAuth.describe('Favorites', () => {
   testAuth('should be visible', async ({ userPage }) => {
     await goToDashboard(userPage)
     await goToFavorites(userPage)

e2e/files.spec.ts

@@ -1,4 +1,4 @@
-import { Page, expect, test } from '@playwright/test'
+import { Page, expect } from '@playwright/test'
 import path from 'path'
 import { defaultExpectTimeout } from '../playwright.config'
 import { testAuth } from './fixtures/authenticatedUserPages'
@@ -52,12 +52,12 @@ const expectNoAccessPage = async (
   expectTimeout: number = defaultExpectTimeout,
 ) => {
   await expect(
-    page.getByRole('heading', {
-      name: 'Sorry, no access to this page.',
-    }),
+    page.getByText('You don’t have permission to view this.'),
   ).toBeVisible({ timeout: expectTimeout })
   await expect(
-    page.getByText('You are not authorized to access the page requested.'),
+    page.getByText(
+      'This account has not been granted access to view this resource.',
+    ),
   ).toBeVisible({ timeout: expectTimeout })
 }
 
@@ -178,13 +178,13 @@ const getFileMD5 = async (page: Page) => {
 let userProject: Project
 const fileHandleIds: string[] = []
 
-test.describe('Files', () => {
+testAuth.describe('Files', () => {
   testAuth.beforeAll(async ({ browser, storageStatePaths }) => {
     userProject = await setupProject(browser, 'swc-e2e-user', storageStatePaths)
   })
 
   testAuth.afterAll(async ({ browser }) => {
-    test.slow()
+    testAuth.slow()
     if (userProject.id) {
       await teardownProjectsAndFileHandles(
         browser,
@@ -201,7 +201,7 @@ test.describe('Files', () => {
       // when there is a test timeout. Since test timeouts are expensive,
       // Playwright recommends skipping the test entirely with test.fixme.
       // See: https://github.com/microsoft/playwright/issues/16317
-      test.fixme(
+      testAuth.fixme(
         browserName === 'webkit' && !!process.env.CI,
         `Very slow in webkit in CI only (passes after 6min in macos-latest runner, 
           times out after 10min in Sage ubuntu-22.04-4core-16GBRAM-150GBSSD runner). 
@@ -345,7 +345,7 @@ test.describe('Files', () => {
   )
 
   testAuth('should create and delete a file', async ({ userPage }) => {
-    test.slow()
+    testAuth.slow()
 
     const fileName = 'test_file.csv'
     const filePath = `data/${fileName}`
@@ -356,7 +356,10 @@ test.describe('Files', () => {
       await expect(
         userPage.getByRole('heading', { name: userProject.name }),
       ).toBeVisible()
-      await userPage.getByRole('link', { name: 'Files', exact: true }).click()
+      await userPage
+        .getByRole('link', { name: 'Files', exact: true })
+        .first()
+        .click()
     })
 
     await testAuth.step('upload file', async () => {
@@ -474,7 +477,7 @@ test.describe('Files', () => {
         ).toBeVisible()
         await expect(
           userPage.getByText(
-            `Are you sure you want to delete File "${fileName}"?`,
+            `Are you sure you want to delete File ${fileName}?`,
           ),
         ).toBeVisible()
         await expect(
@@ -519,9 +522,10 @@ test.describe('Files', () => {
       })
 
       await testAuth.step('remove file from trash can', async () => {
-        const fileCheckbox = userPage.getByRole('checkbox', {
-          name: `Select ${fileEntityId}`,
-        })
+        const fileCheckbox = userPage
+          .getByRole('row')
+          .filter({ hasText: fileEntityId })
+          .getByRole('checkbox')
         await expect(fileCheckbox).not.toBeChecked()
 
         // Currently programmatically dispatching the click event
@@ -540,6 +544,7 @@ test.describe('Files', () => {
           userPage.getByText('Delete selected items from your Trash?'),
         ).toBeVisible()
         await userPage.getByRole('button', { name: 'Delete' }).click()
+        await expect(userPage.locator('.spinner:visible')).toHaveCount(0)
       })
 
       await testAuth.step(

e2e/helpers/entities.ts

@@ -16,19 +16,19 @@ export function generateEntityName(
   return `swc-e2e-${entityType}-entity-${uuidv4()}`
 }
 
-const entityHashBang = '#!Synapse'
+const entityPlace = 'Synapse'
 
 export function entityUrlPathname(entityId: string) {
-  return `/${entityHashBang}:${entityId}`
+  return `/${entityPlace}:${entityId}`
 }
 
 export function getEntityIdFromPathname(pathname: string) {
-  if (!pathname.includes(entityHashBang)) {
+  if (!pathname.includes(entityPlace)) {
     return ''
   }
 
   return pathname
-    .replace(new RegExp(`.*${entityHashBang}:`), '')
+    .replace(new RegExp(`.*${entityPlace}:`), '')
     .replace(/\/.*/, '')
 }