diff --git a/.github/workflows/main.yml b/.github/workflows/main.yml index 38561f970e..76016cd62a 100644 --- a/.github/workflows/main.yml +++ b/.github/workflows/main.yml @@ -28,13 +28,13 @@ jobs: test_type: ['UNIT', 'INDEX', 'DOCKER'] # We are really not set up for these next two to be multiplicative, so be careful adding more. python_version: ['3.11'] - node_version: ['18'] + node_version: ['20'] # Steps represent a sequence of tasks that will be executed as part of the job steps: # Checks-out your repository under $GITHUB_WORKSPACE, so your job can access it - - uses: actions/checkout@v2 - - uses: actions/setup-python@v2 + - uses: actions/checkout@v4 + - uses: actions/setup-python@v5 with: python-version: ${{ matrix.python_version }} diff --git a/CHANGELOG.rst b/CHANGELOG.rst index 11dfc3acdb..73132c19ee 100644 --- a/CHANGELOG.rst +++ b/CHANGELOG.rst @@ -6,6 +6,23 @@ cgap-portal Change Log ---------- +16.0.0 +======= + +`PR 775: Bootstrap v5, React bootstrap v2, React 18, Redux and Misc. Npm Packages Upgrade `_ + +* Upgrade: React v17 to v18 +* Upgrade: Redux v4 to v5 (there are breaking changes in store and dispatchers. SPC is updated to support both new and legacy usage) +* Upgrade: HiGlass (React 18-compatible) +* Upgrade: auth0-Lock v11 to v12 +* Upgrade: gulp.js v4 to v5 +* Upgrade: react-workflow-viz (animation updates to eliminate findDOMNode errors) +* Fix: User Content updates to fix markdown, jsx, and HTML static section rendering +* Upgrade: Bootstrap v5 +* Upgrade: React-Bootstrap v2 +* Upgrade: FontAwesome v6 + + 15.6.0 ======= * 2024-10-11/dmichaels diff --git a/Dockerfile b/Dockerfile index a3ea5f066f..55fc40f75b 100644 --- a/Dockerfile +++ b/Dockerfile @@ -23,7 +23,7 @@ ENV NGINX_USER=nginx \ PIP_DISABLE_PIP_VERSION_CHECK=on \ PIP_DEFAULT_TIMEOUT=100 \ NVM_VERSION=v0.39.1 \ - NODE_VERSION=18.17.0 + NODE_VERSION=20.17.0 # Configure Python3.7 venv ENV VIRTUAL_ENV=/opt/venv diff --git a/deploy/post_deploy_testing/cypress/e2e/05b_case_view_fsui.cy.js b/deploy/post_deploy_testing/cypress/e2e/05b_case_view_fsui.cy.js index a99278098f..2c763cf2b7 100644 --- a/deploy/post_deploy_testing/cypress/e2e/05b_case_view_fsui.cy.js +++ b/deploy/post_deploy_testing/cypress/e2e/05b_case_view_fsui.cy.js @@ -51,11 +51,11 @@ describe('Case View - FSUI', function () { it("Save buttons disabled initially", function(){ - cy.get("div#case-info\\.filtering #snv-filtering .above-variantsample-table-ui .filter-set-ui-header div.pl-16 button:first-child").should(function($btn){ + cy.get("div#case-info\\.filtering #snv-filtering .above-variantsample-table-ui .filter-set-ui-header div.ps-16 button:first-child").should(function($btn){ expect($btn.children("span")).to.have.text('Save Case FilterSet'); expect($btn).to.have.attr('disabled'); }).end() - .get("div#case-info\\.filtering #snv-filtering .above-variantsample-table-ui .filter-set-ui-header div.pl-16 button:last-child").should(function($btn){ + .get("div#case-info\\.filtering #snv-filtering .above-variantsample-table-ui .filter-set-ui-header div.ps-16 button:last-child").should(function($btn){ expect($btn).to.have.text('Create Preset'); expect($btn).to.have.attr('disabled'); }); diff --git a/deploy/post_deploy_testing/cypress/support/e2e.js b/deploy/post_deploy_testing/cypress/support/e2e.js index 0e7290a13d..8faef5a814 100644 --- a/deploy/post_deploy_testing/cypress/support/e2e.js +++ b/deploy/post_deploy_testing/cypress/support/e2e.js @@ -17,4 +17,18 @@ import './commands' // Alternatively you can use CommonJS syntax: -// require('./commands') \ No newline at end of file +// require('./commands') + +Cypress.on("uncaught:exception", (err) => { + // TODO: Investigate hydration errors occurring during SSR in Cypress tests. + // It appears that Cypress injects a prop into the div on the client side, which doesn't exist on the server side, leading to hydration issues. + // This suppression is temporary and should be removed once the issue is resolved. + // https://github.com/cypress-io/cypress/issues/27204 + if ( + /hydrat/i.test(err.message) || + /Minified React error #418/.test(err.message) || + /Minified React error #423/.test(err.message) + ) { + return false; + } +}); \ No newline at end of file diff --git a/package-lock.json b/package-lock.json index b781e2e8dc..fce0f8d47d 100644 --- a/package-lock.json +++ b/package-lock.json @@ -9,12 +9,13 @@ "version": "0.0.0", "license": "MIT", "dependencies": { - "@fortawesome/fontawesome-free": "^5.15.4", + "@fortawesome/fontawesome-free": "^6.6.0", "@gmod/tabix": "^1.5.11", "@gmod/vcf": "^5.0.6", - "@hms-dbmi-bgm/react-workflow-viz": "0.1.5", - "@hms-dbmi-bgm/shared-portal-components": "github:4dn-dcic/shared-portal-components#0.1.80", - "auth0-lock": "^11.33.0", + "@hms-dbmi-bgm/react-workflow-viz": "0.1.11", + "@hms-dbmi-bgm/shared-portal-components": "github:4dn-dcic/shared-portal-components#0.1.91", + "@reduxjs/toolkit": "^2.2.6", + "auth0-lock": "^12.5.1", "buffer": "^6.0.3", "d3": "^5.16.0", "date-fns": "^2.28.0", @@ -22,7 +23,7 @@ "domready": "^1.0.8", "form-serialize": "^0.7.2", "generic-filehandle": "^3.0.0", - "higlass": "1.12.2", + "higlass": "1.13.4", "higlass-bigwig-datafetcher": "0.2.0", "higlass-clinvar": "0.2.5", "higlass-cohort": "0.3.5", @@ -35,22 +36,22 @@ "higlass-sv": "1.0.5", "higlass-text": "0.1.6", "higlass-transcripts": "0.3.8", - "markdown-to-jsx": "^6.11.4", + "markdown-to-jsx": "^7.1.6", "memoize-one": "^5.1.1", "pagedjs": "^0.2.0", - "pixi.js": "^5.2.4", + "pixi.js": "^6.5.10", "process": "^0.11.10", "prop-types": "^15.8.1", "query-string": "^4.3.4", - "react": "^17.0.2", - "react-bootstrap": "1.6.4", - "react-dom": "^17.0.2", + "react": "^18.3.1", + "react-bootstrap": "^2.10.4", + "react-dom": "^18.3.1", "react-draggable": "^4.4.4", - "react-jsx-parser": "^1.25.1", - "react-redux": "^7.2.6", - "react-tooltip": "4.2.10", + "react-jsx-parser": "^2.0.0", + "react-redux": "^9.1.2", + "react-tooltip": "^4.2.21", "react-transition-group": "^4.4.2", - "redux": "^3.7.0", + "redux": "^5.0.1", "stream-browserify": "^3.0.0", "subprocess-middleware": "0.2.0", "underscore": "^1.10.2", @@ -75,13 +76,13 @@ "babel-jest": "^29.1.2", "babel-loader": "^8.2.3", "babel-plugin-minify-dead-code-elimination": "^0.5.1", - "bootstrap": "^4.6.1", + "bootstrap": "^5.3.0", "bufferutil": "^4.0.7", "eslint": "^8.10.0", "eslint-plugin-cypress": "^2.12.1", "eslint-plugin-react": "^7.29.2", "fancy-log": "^1.3.3", - "gulp": "^4.0.2", + "gulp": "^5.0.0", "plugin-error": "^1.0.1", "sass": "^1.51.0", "sinon": "^1.17.6", @@ -1990,11 +1991,12 @@ "dev": true }, "node_modules/@babel/runtime": { - 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"sha256:55c570405f142630c6b9f72fe09d9b67cf1477fcf543ae5b8dcb1f5b7377da81"}, - {file = "wheel-0.43.0.tar.gz", hash = "sha256:465ef92c69fa5c5da2d1cf8ac40559a8c940886afcef87dcf14b9470862f1d85"}, + {file = "wheel-0.44.0-py3-none-any.whl", hash = "sha256:2376a90c98cc337d18623527a97c31797bd02bad0033d41547043a1cbfbe448f"}, + {file = "wheel-0.44.0.tar.gz", hash = "sha256:a29c3f2817e95ab89aa4660681ad547c0e9547f20e75b0562fe7723c9a2a9d49"}, ] [package.extras] @@ -4564,29 +4743,33 @@ files = [ [[package]] name = "xmltodict" -version = "0.13.0" +version = "0.14.2" description = "Makes working with XML feel like you are working with JSON" optional = false -python-versions = ">=3.4" +python-versions = ">=3.6" files = [ - {file = "xmltodict-0.13.0-py2.py3-none-any.whl", hash = "sha256:aa89e8fd76320154a40d19a0df04a4695fb9dc5ba977cbb68ab3e4eb225e7852"}, - {file = "xmltodict-0.13.0.tar.gz", hash = "sha256:341595a488e3e01a85a9d8911d8912fd922ede5fecc4dce437eb4b6c8d037e56"}, + {file = 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(>=0.2.1)"] +cover = ["pytest-cov"] doc = ["furo", "jaraco.packaging (>=9.3)", "jaraco.tidelift (>=1.4)", "rst.linker (>=1.9)", "sphinx (>=3.5)", "sphinx-lint"] -test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-checkdocs (>=2.4)", "pytest-cov", "pytest-enabler (>=2.2)", "pytest-ignore-flaky", "pytest-mypy", "pytest-ruff (>=0.2.1)"] +enabler = ["pytest-enabler (>=2.2)"] +test = ["big-O", "importlib-resources", "jaraco.functools", "jaraco.itertools", "jaraco.test", "more-itertools", "pytest (>=6,!=8.1.*)", "pytest-ignore-flaky"] +type = ["pytest-mypy"] [[package]] name = "zope-deprecation" @@ -4682,4 +4865,4 @@ test = ["zope.testing"] [metadata] lock-version = "2.0" python-versions = ">=3.9,<3.13" -content-hash = "e160ce903cf53de7ea5ae1ad2e2a7190bc5765c10d2b01e651be7fdff95047f7" +content-hash = "41d7883017891cc631ec9ffbf82de4919498bc9176dc2a4b58e6a30672be3f2a" diff --git a/pyproject.toml b/pyproject.toml index bdd4e263f1..9feb38fae7 100644 --- a/pyproject.toml +++ b/pyproject.toml @@ -1,7 +1,7 @@ [tool.poetry] # Note: Various modules refer to this system as "encoded", not "cgap-portal". name = "encoded" -version = "15.6.0" +version = "16.0.0" description = "Computational Genome Analysis Platform" authors = ["4DN-DCIC Team "] license = "MIT" @@ -53,7 +53,7 @@ codeguru-profiler-agent = "^1.2.4" cryptography = "^43.0.1" colorama = "0.3.3" dcicpyvcf = "^3.1.0" -dcicsnovault = "^11.18.0" +dcicsnovault = "^11.22.0" dcicutils = "^8.16.1" elasticsearch = "7.13.4" execnet = "1.4.1" diff --git a/src/encoded/static/browser.js b/src/encoded/static/browser.js index bedd0b1dd9..51d0bf4a16 100644 --- a/src/encoded/static/browser.js +++ b/src/encoded/static/browser.js @@ -2,11 +2,11 @@ // Entry point for browser, compiled into bundle[.chunkHash].js. import React from 'react'; -import ReactDOM from 'react-dom'; +import ReactDOM from 'react-dom/client'; import App from './components'; var domready = require('domready'); -import { store, mapStateToProps } from './store'; +import { store, mapStateToProps, batchDispatch } from './store'; import { Provider, connect } from 'react-redux'; import { patchedConsoleInstance as console } from '@hms-dbmi-bgm/shared-portal-components/es/components/util/patched-console'; import * as JWT from '@hms-dbmi-bgm/shared-portal-components/es/components/util/json-web-token'; @@ -63,20 +63,25 @@ if (typeof window !== 'undefined' && window.document && !window.TEST_RUNNER) { // into