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update index file
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‎.github/workflows/check.yml‎

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@@ -9,19 +9,38 @@ jobs:
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runs-on: ubuntu-latest
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steps:
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- name: Check out the repo
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uses: actions/checkout@v2
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- name: Checkout repo
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uses: actions/checkout@v3
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- name: Setup project
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run: ./setup.sh
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- name: Build the Docker Compose stack
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run: ./setup-testing-mode.sh
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- name: Build Docker Compose stack
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run: docker compose up -d
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- name: Sleep
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uses: jakejarvis/wait-action@master
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with:
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time: '60s'
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run: sleep 10s
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shell: bash
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- name: Check running containers
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run: docker ps
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- name: Run Cypress unit tests
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uses: cypress-io/github-action@v5
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with:
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install: false
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build: npm i -D cypress
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browser: firefox
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env:
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CYPRESS_VIDEO: false
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ELECTRON_EXTRA_LAUNCH_ARGS: '--disable-gpu'
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- name: Store Cypress screenshots
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if: always()
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uses: actions/upload-artifact@v3
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with:
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name: screenshots
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path: cypress/screenshots
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- name: Docker Compose logs
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run: docker compose logs

‎README.md‎

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@@ -46,14 +46,17 @@ in your computer by going to the project folder and running:
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```bash
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./setup-testing-mode.sh # setup files for testing and download Docker images
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docker compose --profile dev up -d # start services and RStudio in detached mode
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docker compose --profile dev up -d # start server in the `dev` profile and detached mode
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```
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You can now visit http://localhost in your web browser. The services should be
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fully operational in about ~30 seconds. Specific services may only be accessible
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via their port, e.g. http://localhost:8000 for plausible and
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http://localhost:8787 for RStudio.
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> [!NOTE]
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> Some services are only available in the `dev` profile (RStudio).
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### Production environment
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Some services are given a default email, user and/or password. The default ones
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You can now visit http://localhost in your web browser.
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> Some services are only available in the `dev` profile (RStudio). To
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> run this profile, type:
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> ```bash
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> docker compose --profile dev up -d
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> [!TIP]
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> If you are using a remote machine, [port forwarding][tunneling] allows to access
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> specific services in your browser. For instance, to access http://localhost:8000
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> (plausible) in your browser, you first need to connect to the machine like so:
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> ```
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> ssh -L 8000:localhost:8000 [server]
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> ```
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[tunneling]: https://en.wikipedia.org/wiki/Port_forwarding
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## Next steps
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- [Add and update apps in ShinyProxy](shinyproxy)

‎cypress.config.js‎

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const { defineConfig } = require('cypress')
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module.exports = defineConfig({
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// These settings apply everywhere unless overridden
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defaultCommandTimeout: 5000,
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viewportWidth: 1000,
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viewportHeight: 600,
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// Viewport settings overridden for component tests
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component: {
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viewportWidth: 500,
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viewportHeight: 500,
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},
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// Command timeout overridden for E2E tests
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e2e: {
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defaultCommandTimeout: 10000,
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baseUrl: 'http://localhost',
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},
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})

‎cypress/e2e/tests.cy.js‎

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describe('ShinyProxy', () => {
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it('main', () => {
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cy.visit('/')
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cy.screenshot()
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cy.contains('psichomics')
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cy.contains('cTRAP')
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})
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it('psichomics', () => {
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cy.visit('/psichomics')
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cy.wait(30000)
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cy.url().should('include', '/app/psichomics')
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cy.screenshot()
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})
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it('cTRAP', () => {
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cy.visit('/cTRAP')
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cy.wait(30000)
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cy.url().should('include', '/app/cTRAP')
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cy.screenshot()
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})
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})
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describe('Flower dashboard', () => {
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it('open', () => {
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cy.visit('http://localhost:5555/flower/dashboard')
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cy.screenshot()
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cy.contains('celery@ctrap').click()
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cy.screenshot()
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})
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})
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describe('Grafana', () => {
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it('open', () => {
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cy.visit('http://localhost:3000')
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cy.screenshot()
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})
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})
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describe('Prometheus', () => {
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it('open', () => {
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cy.visit('http://localhost:9090')
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cy.screenshot()
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})
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})
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// Issues with setting up Plausible because of password issues :(
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// describe('Plausible', () => {
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// it('open', () => {
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// cy.visit('http://localhost:8000/login')
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// cy.screenshot()
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// })
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// })
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describe('404', () => {
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it('open', () => {
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cy.request({url: '/404', failOnStatusCode: false}).its('status').should('equal', 404)
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cy.visit('/404', {failOnStatusCode: false})
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cy.screenshot()
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})
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})

‎cypress/support/e2e.js‎

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// DO NOT DELETE THIS FILE: required for Cypress to run unit tests

‎shinyproxy/templates/index.html‎

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Tutorial
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<a style="margin-right: 0em;" href="https://compbio.imm.medicina.ulisboa.pt/betas/tutorial">[1]</a>
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<a href="https://diseasetranscriptomicslab.github.io/betAS/inst/betAS_tutorial.html">[2]</a>
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</p>
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<!-- App Description -->
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<div class="w3-xlarge w3-section">
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<!-- LOGOS -->
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<a href="https://imm.medicina.ulisboa.pt/pt-pt/" style="text-decoration: none;">
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<img src="assets/img/logos/imm.png" alt="" height="50px">
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<img target="_blank" src="assets/img/logos/imm.png" alt="" height="50px">
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</a>
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<a href="https://www.embo.org/funding/fellowships-grants-and-career-support/young-investigator-programme/" style="text-decoration: none;">
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<img src="assets/img/logos/embo2.png" alt="" height="50px">
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<img target="_blank" src="assets/img/logos/embo2.png" alt="" height="50px">
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</a>
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<a href="https://www.fct.pt/index.phtml.en" style="text-decoration: none;">
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<img src="assets/img/logos/fct.png" alt="" height="50px">
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<img target="_blank" src="assets/img/logos/fct.png" alt="" height="50px">
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</a>
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<a href="https://ribomed.imm.medicina.ulisboa.pt/pt-pt/#homepage" style="text-decoration: none;">
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<img src="assets/img/logos/ribomed.png" alt="" height="50px">
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<img target="_blank" src="assets/img/logos/ribomed.png" alt="" height="50px">
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</a>
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<a href="https://www.genomept.pt/" style="text-decoration: none;">
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<img src="assets/img/logos/genomept.png" alt="" height="50px">
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<img target="_blank" src="assets/img/logos/genomept.png" alt="" height="50px">
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</a>
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<a href="https://imm.medicina.ulisboa.pt/bioinformaticsmatters/doku.php?id=start" style="text-decoration: none;">
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<img src="assets/img/logos/bm.png" alt="" height="50px">
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<img target="_blank" src="assets/img/logos/bm.png" alt="" height="50px">
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</a>
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