diff --git a/.github/workflows/node.js.yml b/.github/workflows/node.js.yml new file mode 100644 index 000000000..d8172629b --- /dev/null +++ b/.github/workflows/node.js.yml @@ -0,0 +1,55 @@ +# This workflow will do a clean installation of node dependencies, cache/restore them, build the source code and run tests across different versions of node +# For more information see: https://docs.github.com/en/actions/automating-builds-and-tests/building-and-testing-nodejs + +name: Node.js CI + +on: + push: + branches: [ develop, main ] + pull_request: + branches: [ develop, main ] + +jobs: + build: + timeout-minutes: 60 + + runs-on: ubuntu-latest + + strategy: + matrix: + node-version: [16.x] + # See supported Node.js release schedule at https://nodejs.org/en/about/releases/ + # Allow OIDC Integration (so we can assume the AWS role to deploy) + # permissions: + # id-token: write + # contents: read + steps: + - uses: actions/checkout@v3 + - name: Use Node.js ${{ matrix.node-version }} + uses: actions/setup-node@v3 + with: + node-version: ${{ matrix.node-version }} + cache: 'npm' + - run: npm ci + - run: APP_ENV=develop npm run ci:build:develop + # Background dev server + # - run: npm run dev & + - run: npm test + + # - name: Configure AWS Credentials + # uses: aws-actions/configure-aws-credentials@v4 + # with: + # aws-region: "us-east-1" + # role-to-assume: "arn:aws:iam::607346494281:role/sagebase-github-oidc-agora-eb-deploy" + # role-session-name: GitHubActions-${{ github.repository_owner }}-${{ github.event.repository.name }}-${{ github.run_id }} + # role-duration-seconds: 1200 + # - name: Install Playwright Browsers + # run: npx playwright install --with-deps + # - name: Run Playwright tests + # run: npx playwright test + # - uses: actions/upload-artifact@v3 + # if: always() + # with: + # name: playwright-report + # path: playwright-report/ + # retention-days: 30 diff --git a/.github/workflows/playwright.yml b/.github/workflows/playwright.yml deleted file mode 100644 index 90b6b700d..000000000 --- a/.github/workflows/playwright.yml +++ /dev/null @@ -1,27 +0,0 @@ -name: Playwright Tests -on: - push: - branches: [ main, master ] - pull_request: - branches: [ main, master ] -jobs: - test: - timeout-minutes: 60 - runs-on: ubuntu-latest - steps: - - uses: actions/checkout@v3 - - uses: actions/setup-node@v3 - with: - node-version: 18 - - name: Install dependencies - run: npm ci - - name: Install Playwright Browsers - run: npx playwright install --with-deps - - name: Run Playwright tests - run: npx playwright test - - uses: actions/upload-artifact@v3 - if: always() - with: - name: playwright-report - path: playwright-report/ - retention-days: 30 diff --git a/.travis.yml b/.travis.yml index fd479b42c..a8abde986 100644 --- a/.travis.yml +++ b/.travis.yml @@ -26,8 +26,6 @@ before_script: - echo -e "[ci-user-prod]\naws_access_key_id=${AwsTravisAccessKey_prod}\naws_secret_access_key=${AwsTravisSecretAccessKey_prod}\n" >> ~/.aws/credentials # setup npm dependencies - npm install - # setup playwright dependencies - - npx playwright install --with-deps stages: - name: test - name: eb-deploy-develop @@ -41,8 +39,6 @@ jobs: script: - npm run test - npm run build - - npm run start & - - npx playwright test - stage: deploy-develop if: (NOT type IN (pull_request)) AND (branch = develop) node_js: 16.15.0 diff --git a/package-lock.json b/package-lock.json index 8e88c671f..977ce37f9 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,12 +1,12 @@ { "name": "agora", - "version": "3.3.0", + "version": "3.4.0", "lockfileVersion": 2, "requires": true, "packages": { "": { "name": "agora", - "version": "3.3.0", + "version": "3.4.0", "dependencies": { "@angular/animations": "^13.3.0", "@angular/cdk": "^13.3.9", @@ -43,7 +43,7 @@ "rimraf": "^3.0.2", "rollbar": "^2.25.0", "rxjs": "^7.5.0", - "sanitize-html": "^2.7.0", + "sanitize-html": "^2.12.1", "screenfull": "^6.0.1", "zone.js": "^0.11.4" }, @@ -105,7 +105,7 @@ "sass": "^1.52.2", "sass-loader": "^13.0.0", "source-map-loader": "^4.0.0", - "start-server-and-test": "^1.14.0", + "start-server-and-test": "^2.0.3", "stream-browserify": "^3.0.0", "stream-http": "^3.2.0", "style-loader": "^3.3.1", @@ -4393,9 +4393,9 @@ "dev": true }, "node_modules/@sideway/address": { - 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"version": "6.0.0", - "resolved": "https://registry.npmjs.org/wait-on/-/wait-on-6.0.0.tgz", - "integrity": "sha512-tnUJr9p5r+bEYXPUdRseolmz5XqJTTj98JgOsfBn7Oz2dxfE2g3zw1jE+Mo8lopM3j3et/Mq1yW7kKX6qw7RVw==", + "version": "7.2.0", + "resolved": "https://registry.npmjs.org/wait-on/-/wait-on-7.2.0.tgz", + "integrity": "sha512-wCQcHkRazgjG5XoAq9jbTMLpNIjoSlZslrJ2+N9MxDsGEv1HnFoVjOCexL0ESva7Y9cu350j+DWADdk54s4AFQ==", "dev": true, "requires": { - "axios": "^0.21.1", - "joi": "^17.4.0", + "axios": "^1.6.1", + "joi": "^17.11.0", "lodash": "^4.17.21", - "minimist": "^1.2.5", - "rxjs": "^7.1.0" + "minimist": "^1.2.8", + "rxjs": "^7.8.1" } }, "watchpack": { diff --git a/package.json b/package.json index 02aa737fc..ff5d75aa9 100644 --- a/package.json +++ b/package.json @@ -1,8 +1,8 @@ { "name": "agora", - "version": "3.3.0", + "version": "3.4.0", "data-file": "syn13363290", - "data-version": "66", + "data-version": "68", "private": true, "scripts": { "dev": "concurrently --kill-others \"npm:dev:server\" \"npm:dev:app\"", @@ -83,7 +83,7 @@ "rimraf": "^3.0.2", "rollbar": "^2.25.0", "rxjs": "^7.5.0", - "sanitize-html": "^2.7.0", + "sanitize-html": "^2.12.1", "screenfull": "^6.0.1", "zone.js": "^0.11.4" }, @@ -145,7 +145,7 @@ "sass": "^1.52.2", "sass-loader": "^13.0.0", "source-map-loader": "^4.0.0", - "start-server-and-test": "^1.14.0", + "start-server-and-test": "^2.0.3", "stream-browserify": "^3.0.0", "stream-http": "^3.2.0", "style-loader": "^3.3.1", diff --git a/playwright.config.ts b/playwright.config.ts index 2eb974524..9c6e531af 100644 --- a/playwright.config.ts +++ b/playwright.config.ts @@ -1,5 +1,7 @@ import { defineConfig, devices } from '@playwright/test'; +export const baseURL = 'http://localhost:8080'; + /** * Read environment variables from file. * https://github.com/motdotla/dotenv @@ -11,6 +13,8 @@ import { defineConfig, devices } from '@playwright/test'; */ export default defineConfig({ testDir: './tests', + // timeout for every test + timeout: 25 * 60 * 1000, /* Run tests in files in parallel */ fullyParallel: true, /* Fail the build on CI if you accidentally left test.only in the source code. */ @@ -24,7 +28,7 @@ export default defineConfig({ /* Shared settings for all the projects below. See https://playwright.dev/docs/api/class-testoptions. */ use: { /* Base URL to use in actions like `await page.goto('/')`. */ - baseURL: 'http://127.0.0.1:8080', + baseURL: baseURL, /* Collect trace when retrying the failed test. See https://playwright.dev/docs/trace-viewer */ trace: 'on-first-retry', @@ -69,9 +73,9 @@ export default defineConfig({ ], /* Run your local dev server before starting the tests */ - // webServer: { - // command: 'npm run start', - // url: 'http://127.0.0.1:3000', - // reuseExistingServer: !process.env.CI, - // }, + webServer: { + command: 'npm run start', + url: baseURL, + reuseExistingServer: !process.env.CI, + }, }); diff --git a/scripts/mongo-create-Indexes.js b/scripts/mongo-create-Indexes.js index 67b3c7ba5..54f4e5772 100644 --- a/scripts/mongo-create-Indexes.js +++ b/scripts/mongo-create-Indexes.js @@ -46,6 +46,12 @@ const collections = [ { ensembl_gene_id: 1 } ] }, + { + name: 'proteomicssrm', + indexes: [ + { ensembl_gene_id: 1 } + ] + }, { name: 'genesbiodomains', indexes: [ diff --git a/scripts/mongo-import.sh b/scripts/mongo-import.sh index c73a829f4..2148594c2 100644 --- a/scripts/mongo-import.sh +++ b/scripts/mongo-import.sh @@ -20,6 +20,7 @@ mongoimport --db agora --collection genesoverallscores --jsonArray --drop --file mongoimport --db agora --collection rnaboxdistribution --jsonArray --drop --file ./rna_distribution_data.json mongoimport --db agora --collection proteomicsboxdistribution --jsonArray --drop --file ./proteomics_distribution_data.json mongoimport --db agora --collection proteomicstmt --jsonArray --drop --file ./proteomics_tmt.json +mongoimport --db agora --collection proteomicssrm --jsonArray --drop --file ./proteomics_srm.json mongoimport --db agora --collection genesbiodomains --jsonArray --drop --file ./genes_biodomains.json mongoimport --db agora --collection biodomaininfo --jsonArray --drop --file ./biodomain_info.json diff --git a/src/app/core/components/footer/footer.component.html b/src/app/core/components/footer/footer.component.html index 65c2e2f5a..b0f80b2f4 100644 --- a/src/app/core/components/footer/footer.component.html +++ b/src/app/core/components/footer/footer.component.html @@ -3,82 +3,23 @@