From 5896437310ec98366bdb5cf5c8bf9f6cc9b1b338 Mon Sep 17 00:00:00 2001 From: craigrbarnes Date: Wed, 13 Mar 2024 17:19:52 -0500 Subject: [PATCH 01/22] remove override name in quay build (#17) Co-authored-by: craigrbarnes --- .github/workflows/image_build_push.yaml | 1 - 1 file changed, 1 deletion(-) diff --git a/.github/workflows/image_build_push.yaml b/.github/workflows/image_build_push.yaml index 556f862..4cdc3f2 100644 --- a/.github/workflows/image_build_push.yaml +++ b/.github/workflows/image_build_push.yaml @@ -13,7 +13,6 @@ jobs: name: Build Image and Push to Quay uses: uc-cdis/.github/.github/workflows/image_build_push.yaml@master with: - OVERRIDE_REPO_NAME: "commons-frontend-app" USE_QUAY_ONLY: true secrets: ECR_AWS_ACCESS_KEY_ID: ${{ secrets.ECR_AWS_ACCESS_KEY_ID }} From 5b592c417178bd1d1dce695d678b1a565b0d2cea Mon Sep 17 00:00:00 2001 From: craigrbarnes Date: Mon, 18 Mar 2024 15:46:04 -0500 Subject: [PATCH 02/22] Update package.json (#19) * Update package.json * update package-lock to v0.10.15 --------- Co-authored-by: craigrbarnes --- package-lock.json | 10661 ++++++++++++++++++++++++++++++++++---------- package.json | 6 +- 2 files changed, 8286 insertions(+), 2381 deletions(-) diff --git a/package-lock.json b/package-lock.json index 2d5dc99..8de4b38 100644 --- a/package-lock.json +++ b/package-lock.json @@ -8,7 +8,7 @@ "name": "@gen3/commons-portal-app-base", "version": "0.1.0", "dependencies": { - "@gen3/frontend": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-frontend-0.10.14.tgz", + "@gen3/frontend": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-frontend-0.10.15.tgz", "@mantine/core": "^6.0.21", "@mdx-js/loader": "^3.0.0", "@mdx-js/react": "^3.0.0", @@ -19,7 +19,7 @@ "react-responsive-carousel": "^3.2.23" }, "devDependencies": { - "@gen3/toolsff": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-toolsff-0.10.14.tgz", + 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"https://registry.npmjs.org/sisteransi/-/sisteransi-1.0.5.tgz", diff --git a/package.json b/package.json index 871d68f..c1b43cc 100644 --- a/package.json +++ b/package.json @@ -18,7 +18,7 @@ "getDRSToHostname": "node ./node_modules/@gen3/toolsff/dist/getDRSToHostname.esm.js --out=config/" }, "dependencies": { - "@gen3/frontend": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-frontend-0.10.14.tgz", + "@gen3/frontend": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-frontend-0.10.15.tgz", "@mantine/core": "^6.0.21", "@mdx-js/loader": "^3.0.0", "@mdx-js/react": "^3.0.0", @@ -29,7 +29,7 @@ "react-responsive-carousel": "^3.2.23" }, "devDependencies": { - "@gen3/toolsff": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-toolsff-0.10.14.tgz", + "@gen3/toolsff": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-toolsff-0.10.15.tgz", "@tailwindcss/aspect-ratio": "^0.4.2", "@tailwindcss/forms": "^0.5.3", "@tailwindcss/line-clamp": "^0.4.2", @@ -49,7 +49,7 @@ "typescript": "5.0.2" }, "peerDependencies": { - "@gen3/core": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-core-0.10.14.tgz", + "@gen3/core": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-core-0.10.15.tgz", "react": "^18.2.0", "react-dom": "^18.2.0" } From 831872b8599c60c67d662bc9063e54a0836f9c9b Mon Sep 17 00:00:00 2001 From: craigrbarnes Date: Thu, 25 Apr 2024 09:56:16 -0500 Subject: [PATCH 03/22] Add Gen3FF updates to sample app (#23) * add updates to sample app * Add modals config --------- Co-authored-by: craigrbarnes --- config/modals.json | 21 ++++++ package-lock.json | 85 +++++++++++++++++++------ package.json | 8 +-- src/pages/404.tsx | 5 ++ src/pages/Workspaces.tsx | 7 ++ src/pages/_app.tsx | 14 +++- src/pages/api/auth/credentialsLogin.ts | 2 + src/pages/api/auth/credentialsLogout.ts | 2 + src/pages/api/auth/sessionLogout.ts | 3 + src/pages/api/auth/sessionToken.ts | 40 +----------- 10 files changed, 121 insertions(+), 66 deletions(-) create mode 100644 config/modals.json create mode 100644 src/pages/404.tsx create mode 100644 src/pages/Workspaces.tsx create mode 100644 src/pages/api/auth/credentialsLogin.ts create mode 100644 src/pages/api/auth/credentialsLogout.ts create mode 100644 src/pages/api/auth/sessionLogout.ts diff --git a/config/modals.json b/config/modals.json new file mode 100644 index 0000000..8eb9663 --- /dev/null +++ b/config/modals.json @@ -0,0 +1,21 @@ +{ + "systemUseModal": { + "title": "Data Use Agreement for Academic and Institutional Users", + "content": { + "text": [ + "Please see the below two Data Use Agreements: the first one is for Academic and Institutional users for non-commercial use; the second agreement is for commercial use.", + "", + "", + "Data Use Agreement - Non-Commercial Research Use Only", + "This Data Use Agreement for Academic and Institutional Users (this “Agreement”) is by and between you and the University and governs your access to and use of the deidentified imaging and associated demographic and clinical data provided to you by the University. By accessing, using, or downloading any data, you are agreeing to be bound by the terms and conditions of this Agreement.", + "1. The University is the legal entity that hosts data.", + "", + "DATA USE AGREEMENT – COMMERCIAL USE PERMITTED", + "This Data Use Agreement (this “Agreement”) is by and between you or the entity you represent (“you”) and the University of Chicago (the “University”) and governs your access to and use of the deidentified imaging and associated demographic and clinical data provided to you by the University. By accessing, using, or downloading any data, you are agreeing to be bound by the terms and conditions of this Agreement. If you are entering into this Agreement for an entity, such as the company you work for, you represent and warrant that you have legal authority to bind that entity", + "1. The University may terminate this Agreement at any time upon notice to you. The University shall have no liability in the event of any such termination. Upon such termination, the University may direct that you immediately return or destroy all copies of any data and, upon the University’s request, you will certify the foregoing to the University in writing." + ] + }, + "expireDays": 365, + "showOnlyOnLogin": true + } +} diff --git a/package-lock.json b/package-lock.json index 8de4b38..a6ce806 100644 --- a/package-lock.json +++ b/package-lock.json @@ -8,18 +8,18 @@ "name": "@gen3/commons-portal-app-base", "version": "0.1.0", "dependencies": { - "@gen3/frontend": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-frontend-0.10.15.tgz", + "@gen3/frontend": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-frontend-0.10.23.tgz", "@mantine/core": "^6.0.21", "@mdx-js/loader": "^3.0.0", "@mdx-js/react": "^3.0.0", "@next/mdx": "^14.1.0", "@types/mdx": "^2.0.11", "cookies-next": "^4.1.1", - "jose": "^4.15.4", + "jose": "4.15.5", "react-responsive-carousel": "^3.2.23" }, "devDependencies": { - 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"version": "0.10.15", - "resolved": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-core-0.10.15.tgz", - "integrity": "sha512-GVGxADUAmRRYoImjk+ehQZ3bpFn+Qix+6GIZBvR4N6fhl/FBBGAaZ2TM2Szq1HlmTtuUtFjAelc7yMybpEuLeQ==", + "version": "0.10.23", + "resolved": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-core-0.10.23.tgz", + "integrity": "sha512-Uinw7D+JdDvl1bvybNKQkq3HzAwuD3+J+8/liz8/ZIT3vlXAqfMV3zxt5HWadaRSsX3hHWC0Dxgcfj4Jsbh7RA==", "license": "Apache-2.0", "peer": true, "dependencies": { @@ -1768,9 +1768,9 @@ } }, "node_modules/@gen3/frontend": { - "version": "0.10.15", - "resolved": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-frontend-0.10.15.tgz", - "integrity": "sha512-hJ5o1VT5PYwCT7ai7EdeX0uhyFy8lRXVjEqjg22MDrPfVxMBG/coszhRGtVkUL3jrRKip1NSJcyF211sKT3s2Q==", + "version": "0.10.23", + "resolved": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-frontend-0.10.23.tgz", + "integrity": "sha512-gWQrxcO5Dv74ukFf9XEJzyFQDIA/OB+j6nE79ZgFWsWCy0y01kcCD/RhJT7hRdqP0c4pGcUjovBe4mAG6Ewmyw==", "license": "Apache-2.0", "dependencies": { "@fontsource/montserrat": "^4.5.12", @@ -1780,6 +1780,7 @@ "@mantine/core": "^6.0.21", "@mantine/form": "^6.0.21", "@mantine/hooks": "^6.0.21", + "@mantine/modals": "^6.0.21", "@mantine/next": "^6.0.21", "@mantine/notifications": "^6.0.21", "@mdx-js/loader": "^2.1.5", @@ -1793,10 +1794,12 @@ "@types/dompurify": "^3.0.3", "chart.js": "^4.0.1", "cookies-next": "^2.1.1", + "default-composer": "^0.6.0", "dompurify": "^3.0.5", "echarts": "^5.4.3", "fetch-retry": "^5.0.6", "file-saver": "^2.0.5", + "filesize": "^10.1.1", "graphiql": "^3.0.5", "graphql": "^16.8.0", "graphql-ws": "^5.14.0", @@ -1804,7 +1807,7 @@ "jose": "^4.13.1", "js-cookie": "^3.0.5", "jsonpath-plus": "^8.0.0", - "mantine-react-table": "^1.3.1", + "mantine-react-table": "^1.3.3", "minisearch": "^6.3.0", "next": "^14.1.0", "next-compose-plugins": "^2.2.1", @@ -1828,6 +1831,7 @@ "sharp": "^0.33.2", "stable-hash": "^0.0.3", "swr": "^2.1.5", + "tailwind-merge": "^2.2.2", "tailwind-styled-components": "^2.2.0", "tinycolor2": "^1.6.0", "use-deep-compare": "^1.1.0", @@ -1840,7 +1844,7 @@ "npm": ">=10.2.3" }, "peerDependencies": { - "@gen3/core": "^0.10.12", + "@gen3/core": "^0.10.21", "react": "^18.2.0", "react-dom": "^18.2.0", "typescript": "5.0.2" @@ -1898,10 +1902,22 @@ "node": ">= 8" } }, + "node_modules/@gen3/frontend/node_modules/tailwind-merge": { + "version": "2.3.0", + "resolved": "https://registry.npmjs.org/tailwind-merge/-/tailwind-merge-2.3.0.tgz", + "integrity": "sha512-vkYrLpIP+lgR0tQCG6AP7zZXCTLc1Lnv/CCRT3BqJ9CZ3ui2++GPaGb1x/ILsINIMSYqqvrpqjUFsMNLlW99EA==", + "dependencies": { + "@babel/runtime": "^7.24.1" + }, + "funding": { + "type": "github", + "url": "https://github.com/sponsors/dcastil" + } + }, "node_modules/@gen3/toolsff": { - "version": "0.10.15", - "resolved": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-toolsff-0.10.15.tgz", - "integrity": "sha512-gYaFTjUDLCA0SmnslhteIz7NvoC2Rvymmg7baTN3nlxAXptgphrvOSWkSiV9ptBOlNCVdLI9xL3EzdoKkMomSg==", + "version": "0.10.23", + "resolved": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-toolsff-0.10.23.tgz", + "integrity": "sha512-8o2nGL7p/Ga1I/ReEglamB8cDUkpH+bO+Ld99rHUnTYOhnKAjsxeOf7ePiI04/IV/AiHg8bTfnonLPKFSY0l0A==", "dev": true, "license": "Apache-2.0", "dependencies": { @@ -3095,6 +3111,20 @@ "react": ">=16.8.0" } }, + "node_modules/@mantine/modals": { + "version": "6.0.21", + "resolved": "https://registry.npmjs.org/@mantine/modals/-/modals-6.0.21.tgz", + "integrity": "sha512-Gx2D/ZHMUuYF197JKMWey4K9FeGP9rxYp4lmAEXUrjXiST2fEhLZOdiD75KuOHXd1/sYAU9NcNRo9wXrlF/gUA==", + "dependencies": { + "@mantine/utils": "6.0.21" + }, + "peerDependencies": { + "@mantine/core": "6.0.21", + "@mantine/hooks": "6.0.21", + "react": ">=16.8.0", + "react-dom": ">=16.8.0" + } + }, "node_modules/@mantine/next": { "version": "6.0.21", "resolved": "https://registry.npmjs.org/@mantine/next/-/next-6.0.21.tgz", @@ -8130,6 +8160,11 @@ "node": ">=0.10.0" } }, + "node_modules/default-composer": { + "version": "0.6.0", + "resolved": "https://registry.npmjs.org/default-composer/-/default-composer-0.6.0.tgz", + "integrity": "sha512-icLwAqlLJUAhLCPN9jBntg3B70VWWisLoayrPQThriuKCUmdj0k/UdUXmjzfHs9YT4j61EroqYsYG9nqeiGc8Q==" + }, "node_modules/defined": { "version": "1.0.1", "resolved": "https://registry.npmjs.org/defined/-/defined-1.0.1.tgz", @@ -9080,6 +9115,14 @@ "resolved": "https://registry.npmjs.org/file-saver/-/file-saver-2.0.5.tgz", "integrity": "sha512-P9bmyZ3h/PRG+Nzga+rbdI4OEpNDzAVyy74uVO9ATgzLK6VtAsYybF/+TOCvrc0MO793d6+42lLyZTw7/ArVzA==" }, + "node_modules/filesize": { + "version": "10.1.1", + "resolved": "https://registry.npmjs.org/filesize/-/filesize-10.1.1.tgz", + "integrity": "sha512-L0cdwZrKlwZQkMSFnCflJ6J2Y+5egO/p3vgRSDQGxQt++QbUZe5gMbRO6kg6gzwQDPvq2Fk9AmoxUNfZ5gdqaQ==", + "engines": { + "node": ">= 10.4.0" + } + }, "node_modules/fill-range": { "version": "7.0.1", "resolved": "https://registry.npmjs.org/fill-range/-/fill-range-7.0.1.tgz", @@ -11934,9 +11977,9 @@ } }, "node_modules/jose": { - "version": "4.15.4", - "resolved": "https://registry.npmjs.org/jose/-/jose-4.15.4.tgz", - "integrity": "sha512-W+oqK4H+r5sITxfxpSU+MMdr/YSWGvgZMQDIsNoBDGGy4i7GBPTtvFKibQzW06n3U3TqHjhvBJsirShsEJ6eeQ==", + "version": "4.15.5", + "resolved": "https://registry.npmjs.org/jose/-/jose-4.15.5.tgz", + "integrity": "sha512-jc7BFxgKPKi94uOvEmzlSWFFe2+vASyXaKUpdQKatWAESU2MWjDfFf0fdfc83CDKcA5QecabZeNLyfhe3yKNkg==", "funding": { "url": "https://github.com/sponsors/panva" } diff --git a/package.json b/package.json index c1b43cc..6ac3d3c 100644 --- a/package.json +++ b/package.json @@ -18,18 +18,18 @@ "getDRSToHostname": "node ./node_modules/@gen3/toolsff/dist/getDRSToHostname.esm.js --out=config/" }, "dependencies": { - "@gen3/frontend": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-frontend-0.10.15.tgz", + "@gen3/frontend": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-frontend-0.10.23.tgz", "@mantine/core": "^6.0.21", "@mdx-js/loader": "^3.0.0", "@mdx-js/react": "^3.0.0", "@next/mdx": "^14.1.0", "@types/mdx": "^2.0.11", "cookies-next": "^4.1.1", - "jose": "^4.15.4", + "jose": "4.15.5", "react-responsive-carousel": "^3.2.23" }, "devDependencies": { - "@gen3/toolsff": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-toolsff-0.10.15.tgz", + "@gen3/toolsff": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-toolsff-0.10.23.tgz", "@tailwindcss/aspect-ratio": "^0.4.2", "@tailwindcss/forms": "^0.5.3", "@tailwindcss/line-clamp": "^0.4.2", @@ -49,7 +49,7 @@ "typescript": "5.0.2" }, "peerDependencies": { - "@gen3/core": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-core-0.10.15.tgz", + "@gen3/core": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-core-0.10.23.tgz", "react": "^18.2.0", "react-dom": "^18.2.0" } diff --git a/src/pages/404.tsx b/src/pages/404.tsx new file mode 100644 index 0000000..9c8f2c6 --- /dev/null +++ b/src/pages/404.tsx @@ -0,0 +1,5 @@ +import { + Custom404Page +} from '@gen3/frontend'; + +export default Custom404Page; diff --git a/src/pages/Workspaces.tsx b/src/pages/Workspaces.tsx new file mode 100644 index 0000000..e4578be --- /dev/null +++ b/src/pages/Workspaces.tsx @@ -0,0 +1,7 @@ +import { + WorkspacesPage, + WorkspacesPageGetServerSideProps as getServerSideProps, +} from '@gen3/frontend'; +export default WorkspacesPage; + +export { getServerSideProps }; diff --git a/src/pages/_app.tsx b/src/pages/_app.tsx index 68e58e8..c3fe391 100644 --- a/src/pages/_app.tsx +++ b/src/pages/_app.tsx @@ -1,6 +1,6 @@ import type { AppProps } from 'next/app'; import { useEffect } from 'react'; -import { Gen3Provider, TenStringArray } from '@gen3/frontend'; +import { Gen3Provider, TenStringArray, type ModalsConfig } from '@gen3/frontend'; import themeColors from '../../config/themeColors.json'; import themeFonts from '../../config/themeFonts.json'; import icons from '../../config/icons/gen3.json'; @@ -11,8 +11,9 @@ import '@graphiql/react/dist/style.css'; import { setDRSHostnames } from '@gen3/core'; -// TODO: THis must be done in a better way using newer NextJS features +// TODO: This can be done in a better way using newer NextJS features import sessionConfig from '../../config/session.json'; +import modalsConfig from '../../config/modals.json'; import drsHostnames from '../../config/drsHostnames.json'; const colors = Object.fromEntries( @@ -26,10 +27,17 @@ export default function App({ Component, pageProps }: AppProps) { useEffect(() => { setDRSHostnames(drsHostnames); + }, []); return ( - + ); diff --git a/src/pages/api/auth/credentialsLogin.ts b/src/pages/api/auth/credentialsLogin.ts new file mode 100644 index 0000000..ffc5cb6 --- /dev/null +++ b/src/pages/api/auth/credentialsLogin.ts @@ -0,0 +1,2 @@ +import { credentialsLogin } from '@gen3/frontend'; +export default credentialsLogin; diff --git a/src/pages/api/auth/credentialsLogout.ts b/src/pages/api/auth/credentialsLogout.ts new file mode 100644 index 0000000..f12c02e --- /dev/null +++ b/src/pages/api/auth/credentialsLogout.ts @@ -0,0 +1,2 @@ +import { credentialsLogout } from '@gen3/frontend'; +export default credentialsLogout; diff --git a/src/pages/api/auth/sessionLogout.ts b/src/pages/api/auth/sessionLogout.ts new file mode 100644 index 0000000..2441be7 --- /dev/null +++ b/src/pages/api/auth/sessionLogout.ts @@ -0,0 +1,3 @@ +import { sessionLogout } from '@gen3/frontend'; + +export default sessionLogout; diff --git a/src/pages/api/auth/sessionToken.ts b/src/pages/api/auth/sessionToken.ts index 6320f53..2cd128b 100644 --- a/src/pages/api/auth/sessionToken.ts +++ b/src/pages/api/auth/sessionToken.ts @@ -1,39 +1,3 @@ -import type { NextApiRequest, NextApiResponse } from 'next'; -import { getCookie } from 'cookies-next'; -import { decodeJwt, JWTPayload } from 'jose'; +import { sessionToken } from '@gen3/frontend'; -export const isExpired = (value: number) => value - Date.now() > 0; - -export interface JWTPayloadAndUser extends JWTPayload { - context: Record; -} - -/** - * returns the access_token expiration, user, and status - * @param req - * @param res - */ -export default async function (req: NextApiRequest, res: NextApiResponse) { - - const access_token = getCookie('access_token', { req, res }); - if (access_token && typeof access_token === 'string') { - // TODO: validate the token - const decodedAccessToken = decodeJwt( - access_token - ) as unknown as JWTPayloadAndUser; - return res.status(200).json({ - issued: decodedAccessToken.iat, - expires: decodedAccessToken.exp, - user: decodedAccessToken.context.user, - status: decodedAccessToken.exp - ? isExpired(decodedAccessToken.exp) - ? 'expired' - : 'issued' - : 'invalid', - }); - } - - return res.status(200).json({ - status: 'not present', - }); -} +export default sessionToken; From 9ee2dc10fb94654cf2d6d055bce70ca4464efe4a Mon Sep 17 00:00:00 2001 From: craigrbarnes Date: Thu, 25 Apr 2024 12:32:09 -0500 Subject: [PATCH 04/22] fix broken links/missing images (#24) Co-authored-by: craigrbarnes --- config/gen3/footer.json | 4 ++-- config/gen3/navigation.json | 2 +- package-lock.json | 36 ++++-------------------------------- package.json | 4 +--- src/pages/_app.tsx | 1 - 5 files changed, 8 insertions(+), 39 deletions(-) diff --git a/config/gen3/footer.json b/config/gen3/footer.json index 9bcdfb8..2429d38 100644 --- a/config/gen3/footer.json +++ b/config/gen3/footer.json @@ -2,13 +2,13 @@ "footerRightLogos": [ [ { - "logo": "gen3.png", + "logo": "/icons/gen3.png", "width": 132, "height": 60, "description": "Gen3 Logo" }, { - "logo": "createdby.png", + "logo": "/icons/createdby.png", "width": 170, "height": 60, "description": "Created by CTDS" diff --git a/config/gen3/navigation.json b/config/gen3/navigation.json index f0b6637..f8959b9 100644 --- a/config/gen3/navigation.json +++ b/config/gen3/navigation.json @@ -39,7 +39,7 @@ }, { "icon": "gen3:workspace", - "href": "/#hostname#workspace/", + "href": "/Workspace", "name": "Workspace", "tooltip": "Gen3 workspaces are secure data analysis environments in the cloud that can access data from one or more data resources." }, diff --git a/package-lock.json b/package-lock.json index a6ce806..067a46d 100644 --- a/package-lock.json +++ b/package-lock.json @@ -14,9 +14,7 @@ "@mdx-js/react": "^3.0.0", "@next/mdx": "^14.1.0", "@types/mdx": "^2.0.11", - "cookies-next": "^4.1.1", - "jose": "4.15.5", - "react-responsive-carousel": "^3.2.23" + "cookies-next": "^4.1.1" }, "devDependencies": { "@gen3/toolsff": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-toolsff-0.10.23.tgz", @@ -7292,11 +7290,6 @@ "integrity": "sha512-kgMuFyE78OC6Dyu3Dy7vcx4uy97EIbVxJB/B0eJ3bUNAkwdNcxYzgKltnyADiYwsR7SEqkkUPsEUT//OVS6XMA==", "peer": true }, - "node_modules/classnames": { - "version": "2.5.1", - "resolved": "https://registry.npmjs.org/classnames/-/classnames-2.5.1.tgz", - "integrity": "sha512-saHYOzhIQs6wy2sVxTM6bUDsQO4F50V9RQ22qBpEdCW+I+/Wmke2HOl6lS6dTpdxVhb88/I6+Hs+438c3lfUow==" - }, "node_modules/client-only": { "version": "0.0.1", "resolved": "https://registry.npmjs.org/client-only/-/client-only-0.0.1.tgz", @@ -7593,9 +7586,9 @@ } }, "node_modules/cookies-next/node_modules/@types/node": { - "version": "16.18.84", - "resolved": "https://registry.npmjs.org/@types/node/-/node-16.18.84.tgz", - "integrity": "sha512-mtn6ixzrUK5IMf6gyyMVUsm0TIeF3IYpUr3i0HHTuPJVbdZ6kc93poZ+wCkFNtxXoP/tyGrdVPOL6/WqGXjfXw==" + "version": "16.18.96", + "resolved": "https://registry.npmjs.org/@types/node/-/node-16.18.96.tgz", + "integrity": "sha512-84iSqGXoO+Ha16j8pRZ/L90vDMKX04QTYMTfYeE1WrjWaZXuchBehGUZEpNgx7JnmlrIHdnABmpjrQjhCnNldQ==" }, "node_modules/copy-to-clipboard": { "version": "3.3.3", @@ -19132,17 +19125,6 @@ "react": "^18.2.0" } }, - "node_modules/react-easy-swipe": { - "version": "0.0.21", - "resolved": "https://registry.npmjs.org/react-easy-swipe/-/react-easy-swipe-0.0.21.tgz", - "integrity": "sha512-OeR2jAxdoqUMHIn/nS9fgreI5hSpgGoL5ezdal4+oO7YSSgJR8ga+PkYGJrSrJ9MKlPcQjMQXnketrD7WNmNsg==", - "dependencies": { - "prop-types": "^15.5.8" - }, - "engines": { - "node": ">= 6" - } - }, "node_modules/react-fast-compare": { "version": "3.2.2", "resolved": "https://registry.npmjs.org/react-fast-compare/-/react-fast-compare-3.2.2.tgz", @@ -19947,16 +19929,6 @@ } } }, - "node_modules/react-responsive-carousel": { - "version": "3.2.23", - "resolved": "https://registry.npmjs.org/react-responsive-carousel/-/react-responsive-carousel-3.2.23.tgz", - "integrity": "sha512-pqJLsBaKHWJhw/ItODgbVoziR2z4lpcJg+YwmRlSk4rKH32VE633mAtZZ9kDXjy4wFO+pgUZmDKPsPe1fPmHCg==", - "dependencies": { - "classnames": "^2.2.5", - "prop-types": "^15.5.8", - "react-easy-swipe": "^0.0.21" - } - }, "node_modules/react-smooth": { "version": "4.0.0", "resolved": "https://registry.npmjs.org/react-smooth/-/react-smooth-4.0.0.tgz", diff --git a/package.json b/package.json index 6ac3d3c..dbef4a5 100644 --- a/package.json +++ b/package.json @@ -24,9 +24,7 @@ "@mdx-js/react": "^3.0.0", "@next/mdx": "^14.1.0", "@types/mdx": "^2.0.11", - "cookies-next": "^4.1.1", - "jose": "4.15.5", - "react-responsive-carousel": "^3.2.23" + "cookies-next": "^4.1.1" }, "devDependencies": { "@gen3/toolsff": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-toolsff-0.10.23.tgz", diff --git a/src/pages/_app.tsx b/src/pages/_app.tsx index c3fe391..85551da 100644 --- a/src/pages/_app.tsx +++ b/src/pages/_app.tsx @@ -5,7 +5,6 @@ import themeColors from '../../config/themeColors.json'; import themeFonts from '../../config/themeFonts.json'; import icons from '../../config/icons/gen3.json'; import '../styles/globals.css'; -import 'react-responsive-carousel/lib/styles/carousel.min.css'; import 'graphiql/graphiql.css'; import '@graphiql/react/dist/style.css'; import { setDRSHostnames } from '@gen3/core'; From d0305e93f7ec2e5753bfbc7a47a9f4bd690caa69 Mon Sep 17 00:00:00 2001 From: Craig Barnes Date: Fri, 7 Jun 2024 13:03:20 -0500 Subject: [PATCH 05/22] Chore/update to Gen3.2 version 0.10.30 (#29) * update config and dependencies * update config/package.json * add eslint/prettier * update typescript esplugin * update github ci * update Dockerfile --- .dockerignore | 1 + .eslintrc.js | 55 + .eslintrc.json | 3 + .github/workflows/ci.yaml | 23 +- .npmignore | 3 + .nvmrc | 1 + .prettierignore | 4 + .prettierrc | 6 + Dockerfile | 9 +- config/gen3/discovery.json | 290 +- config/{ => gen3}/modals.json | 0 config/gen3/navigation.json | 5 + config/{ => gen3}/session.json | 0 config/{ => gen3}/themeColors.json | 218 +- config/{ => gen3}/themeFonts.json | 0 config/siteConfig.json | 3 - package-lock.json | 3471 +++++++++++++++++-- package.json | 27 +- src/lib/Discovery/CustomCellRenderers.tsx | 57 +- src/lib/Discovery/CustomRowRenderers.tsx | 119 +- src/lib/Discovery/Filemap.tsx | 183 + src/lib/plugins/index.js | 51 +- src/pages/AISearch.tsx | 9 + src/pages/Explorer.tsx | 2 +- src/pages/SamplePage.tsx | 2 +- src/pages/Submission.tsx | 7 + src/pages/{Workspaces.tsx => Workspace.tsx} | 0 src/pages/_app.tsx | 118 +- tailwind.config.js | 7 +- 29 files changed, 3972 insertions(+), 702 deletions(-) create mode 100644 .dockerignore create mode 100644 .eslintrc.js create mode 100644 .eslintrc.json create mode 100644 .npmignore create mode 100644 .nvmrc create mode 100644 .prettierignore create mode 100644 .prettierrc rename config/{ => gen3}/modals.json (100%) rename config/{ => gen3}/session.json (100%) rename config/{ => gen3}/themeColors.json (76%) rename config/{ => gen3}/themeFonts.json (100%) delete mode 100644 config/siteConfig.json create mode 100644 src/lib/Discovery/Filemap.tsx create mode 100644 src/pages/AISearch.tsx create mode 100644 src/pages/Submission.tsx rename src/pages/{Workspaces.tsx => Workspace.tsx} (100%) diff --git a/.dockerignore b/.dockerignore new file mode 100644 index 0000000..3c3629e --- /dev/null +++ b/.dockerignore @@ -0,0 +1 @@ +node_modules diff --git a/.eslintrc.js b/.eslintrc.js new file mode 100644 index 0000000..edf6734 --- /dev/null +++ b/.eslintrc.js @@ -0,0 +1,55 @@ +module.exports = { + env: { + browser: true, + es2021: true, + node: true, + }, + extends: [ + 'eslint:recommended', + 'plugin:jsx-a11y/recommended', + 'plugin:react/recommended', + 'plugin:react-hooks/recommended', + 'plugin:@typescript-eslint/recommended', + 'plugin:@next/next/recommended', + 'prettier', + ], + parser: '@typescript-eslint/parser', + parserOptions: { + ecmaFeatures: { + jsx: true, + }, + ecmaVersion: 12, + sourceType: 'module', + }, + plugins: ['jsx-a11y', 'react', 'react-hooks', '@typescript-eslint'], + rules: { + 'no-underscore-dangle': 'off', + 'import/prefer-default-export': 'off', + 'linebreak-style': ['error', 'unix'], + '@typescript-eslint/quotes': ['warn', 'single'], + quotes: ['warn', 'single'], + 'jsx-quotes': ['warn', 'prefer-double'], + semi: ['error', 'always'], + 'prefer-destructuring': ['error', { object: true, array: false }], + 'react/jsx-fragments': ['warn', 'element'], + // disable these because we're using React 17+ with the jsx transform + 'react/jsx-uses-react': 'off', + 'react/react-in-jsx-scope': 'off', + }, + overrides: [ + { + files: ['**/*.tsx'], + rules: { + 'react/prop-types': 'off', + }, + }, + ], + settings: { + react: { + version: 'detect', + }, + next: { + rootDir: './', + }, + }, +}; diff --git a/.eslintrc.json b/.eslintrc.json new file mode 100644 index 0000000..bffb357 --- /dev/null +++ b/.eslintrc.json @@ -0,0 +1,3 @@ +{ + "extends": "next/core-web-vitals" +} diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 77d0dc9..642f40d 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -4,13 +4,16 @@ jobs: build: runs-on: ubuntu-latest steps: - - uses: actions/checkout@v2 - - uses: actions/setup-node@v3 - with: - node-version: 20 - - name: Setup npm - run: npm install -g npm@10.2.4 - - name: Install modules - run: npm ci - - name: Run ESLint - run: npm run lint + - uses: actions/checkout@v2 + - uses: actions/setup-node@v3.4.1 + with: + node-version: 20.11.0 + - name: install npm version + run: npm install -g npm + - name: Get Version + run: npm -v + - name: Install modules + + run: npm ci + - name: Run ESLint + run: npm run lint diff --git a/.npmignore b/.npmignore new file mode 100644 index 0000000..10900e7 --- /dev/null +++ b/.npmignore @@ -0,0 +1,3 @@ +.DS_Store +node_modules +.next/cache/* diff --git a/.nvmrc b/.nvmrc new file mode 100644 index 0000000..209e3ef --- /dev/null +++ b/.nvmrc @@ -0,0 +1 @@ +20 diff --git a/.prettierignore b/.prettierignore new file mode 100644 index 0000000..78960da --- /dev/null +++ b/.prettierignore @@ -0,0 +1,4 @@ +node_modules +.next +public +dist diff --git a/.prettierrc b/.prettierrc new file mode 100644 index 0000000..65a45ac --- /dev/null +++ b/.prettierrc @@ -0,0 +1,6 @@ +{ + "tabWidth": 2, + "useTabs": false, + "trailingComma": "all", + "singleQuote": true +} diff --git a/Dockerfile b/Dockerfile index e5c2456..e04c407 100644 --- a/Dockerfile +++ b/Dockerfile @@ -24,20 +24,13 @@ RUN apt-get update && apt-get install -y --no-install-recommends \ curl \ git \ gnupg \ - nginx \ - python3 \ - time \ - vim \ && mkdir -p /etc/apt/keyrings \ && curl -fsSL https://deb.nodesource.com/gpgkey/nodesource-repo.gpg.key | gpg --dearmor -o /etc/apt/keyrings/nodesource.gpg \ && echo "deb [signed-by=/etc/apt/keyrings/nodesource.gpg] https://deb.nodesource.com/node_$NODE_VERSION.x nodistro main" | tee /etc/apt/sources.list.d/nodesource.list \ && apt-get update \ && apt-get install -y nodejs \ && apt-get clean \ - && rm -rf /var/src/apt/lists/* \ - && ln -sf /dev/stdout /var/log/nginx/access.log \ - && ln -sf /dev/stderr /var/log/nginx/error.log \ - && npm install -g npm@10.2.4 + && npm install -g npm@10.5.2 RUN addgroup --system --gid 1001 nextjs && adduser --system --uid 1001 nextjs COPY ./package.json ./package-lock.json ./ diff --git a/config/gen3/discovery.json b/config/gen3/discovery.json index e49aaf3..45c2750 100644 --- a/config/gen3/discovery.json +++ b/config/gen3/discovery.json @@ -5,7 +5,7 @@ }, "features": { "advSearchFilters": { - "enabled": true, + "enabled": false, "field": "advSearchFilters", "displayName": "Filters", "filters": [ @@ -46,28 +46,17 @@ "verifyExternalLogins": true }, "pageTitle": { - "enabled": false + "enabled": true, + "title": "Discover Datasets" }, "search": { "searchBar": { "enabled": true, - "inputSubtitle": "Examples: pain, buprenorphine, intervention", + "inputSubtitle": "Search studies by keywords", "searchableTextFields": [ - "study_metadata.minimal_info.study_description", - "institutions", - "investigators_name", - "study_metadata.minimal_info.study_name", - "project_number", - "study_metadata.metadata_location.nih_application_id", - "_hdp_uid", - "dataset_1_title", - "dataset_2_title", - "dataset_3_title", - "dataset_4_title", - "administering_ic", - "research_program", - "doi_identifier", - "doi_resolvable_link" + "study_description", + "_unique_id", + "full_name" ] }, "tagSearchDropdown": { @@ -101,7 +90,7 @@ "aggregations": [ { "name": "Studies", - "field": "_hdp_uid", + "field": "_unique_id", "type": "count" } ], @@ -111,181 +100,126 @@ "studies": [], "studyColumns": [ { - "name": "Project Title", - "field": "study_metadata.minimal_info.study_name", + "name": "Study ID", + "field": "_unique_id", + "contentType": "string", + "errorIfNotAvailable": false, + "valueIfNotAvailable": "n/a" + }, + { + "name": "Study Name", + "field": "full_name", + "contentType": "string", + "errorIfNotAvailable": false, + "valueIfNotAvailable": "n/a" + }, + { + "name": "Study Title", + "field": "study_title", + "contentType": "string", "errorIfNotAvailable": false, "valueIfNotAvailable": "n/a" }, { - "name": "HEAL Research Focus Area", - "field": "research_focus_area", + "name": "Source", + "field": "source", + "contentType": "string", "errorIfNotAvailable": false, "valueIfNotAvailable": "n/a" }, { - "name": "HEAL Research Program", - "field": "research_program", + "name": "Data Files", + "field": "__manifest", + "contentType": "manifest", "errorIfNotAvailable": false, "valueIfNotAvailable": "n/a" }, { - "name": "Investigator(s)", - "field": "investigators_name", + "name": "Subjects", + "field": "subjects_count", + "contentType": "string", "errorIfNotAvailable": false, "valueIfNotAvailable": "n/a" } ], "studyPreviewField": { - "name": "Summary", - "field": "study_metadata.minimal_info.study_description", + "name": "Study Description", + "field": "study_description", "contentType": "string", - "includeName": false, - "includeIfNotAvailable": true, + "includeName": true, + "includeIfNotAvailable": false, "valueIfNotAvailable": "No summary has been provided for this study." }, - "detailView": { - "headerField": "study_metadata.minimal_info.study_name", - "tabs": [ + "simpleDetailsView": { + "header": { + "field": "study_title" + }, + "downloadLinks": { + "field": "data_download_links" + }, + "fieldsToShow": [ { - "tabName": "Summary", - "groups": [ + "groupWidth": "half", + "fields": [ { - "header": "Study Description Summary", - "fields": [ - { - "type": "block", - "sourceField": "study_metadata.minimal_info.study_description" - } - ] + "name": "Study Name", + "field": "full_name", + "contentType": "string", + "includeIfNotAvailable": false }, { - "header": "HEAL Research Initiative/Award Administration", - "fields": [ - { - "type": "text", - "label": "Project Number", - "sourceField": "project_number", - "default": "" - }, - { - "type": "text", - "label": "HEAL Research Program", - "sourceField": "research_program", - "default": "Not specified" - }, - { - "type": "text", - "label": "Institution(s)", - "sourceField": "institutions" - }, - { - "type": "text", - "label": "Investigator(s)", - "sourceField": "investigators_name" - }, - { - "type": "text", - "label": "Administering IC(s)", - "sourceField": "administering_ic" - }, - { - "type": "text", - "label": "Year Grant Awarded", - "sourceField": "year_awarded" - }, - { - "type": "link", - "label": "NIH RePORTER Link", - "sourceField": "study_metadata.metadata_location.nih_reporter_link" - }, - { - "type": "text", - "label": "Clinical Trial ID", - "sourceField": "study_metadata.metadata_location.clinical_trials_study_ID" - }, - { - "type": "link", - "label": "Clinical Trial Link", - "sourceField": "study_metadata.metadata_location.clinical_trials_study_link" - }, - { - "type": "text", - "label": "DOI", - "sourceField": "doi_identifier" - }, - { - "type": "link", - "label": "DOI Link", - "sourceField": "doi_resolvable_link" - } - ] + "name": "Study Title", + "field": "study_title", + "contentType": "string", + "includeIfNotAvailable": false }, { - "header": "Study Characteristics", - "fields": [ - { - "type": "tags", - "sourceField": "tags" - } - ] - } - ] - }, - { - "tabName": "Data", - "groups": [ + "name": "Funding", + "field": "funding", + "contentType": "string", + "includeIfNotAvailable": false + }, { - "fields": [ - { - "type": "accessDescriptor" - } - ] + "name": "Source", + "field": "source", + "contentType": "string", + "includeIfNotAvailable": false }, { - "header": "Repository", - "fields": [ - { - "sourceField": "study_metadata.metadata_location.data_repositories[*].repository_study_link", - "type": "linkList", - "label": "" - } - ] - } - ] - }, - { - "tabName": "Cite", - "groups": [ + "name": "Data Files", + "field": "data_files_count", + "contentType": "string", + "includeIfNotAvailable": false + }, + { + "name": "Subjects", + "field": "subjects_count", + "contentType": "string", + "includeIfNotAvailable": false + }, + { + "name": "Project ID", + "field": "project_id", + "contentType": "string", + "includeIfNotAvailable": false + }, { - "header": "Citation Requirements", - "fields": [ - { - "type": "text", - "label": "Cite the study on the HEAL Data Platform", - "sourceField": "study_metadata.citation.heal_platform_citation" - }, - { - "type": "text", - "label": "Cite the study at the local repository", - "sourceField": "study_metadata.metadata_location.data_repositories[*].repository_citation" - } - ] + "name": "Link", + "field": "link", + "contentType": "link", + "includeIfNotAvailable": false } ] }, { - "tabName": "Related Studies", - "groups": [ + "groupWidth": "half", + "fields": [ { - "header": "Related Studies", - "fields": [ - { - "type": "linkList", - "sourceField": "related_studies", - "label": "", - "renderFunction": "linkWithTitle" - } - ] + "name": "Study Description", + "field": "study_description", + "contentType": "paragraph", + "includeIfNotAvailable": false, + "valueIfNotAvailable": "No summary has been provided for this study." } ] } @@ -301,7 +235,7 @@ }, "tagCategories": [ { - "name": "Study Type", + "name": "Condition", "color": "#532565", "display": false }, @@ -309,42 +243,6 @@ "name": "Data Type", "color": "#982568", "display": false - }, - { - "name": "Subject Type", - "color": "#981f32", - "display": false - }, - { - "name": "Gender", - "color": "#bf362e", - "display": false - }, - { - "name": "Age", - "color": "#e07c3e", - "display": false - }, - { - "name": "Research Program", - "color": "#532565", - "display": false - }, - { - "name": "Commons", - "displayName": "Data Resources", - "color": "#981f32", - "display": false - }, - { - "name": "Other", - "color": "#bf362e", - "display": false - }, - { - "name": "Data Repository", - "color": "#bf362e", - "display": true } ] } diff --git a/config/modals.json b/config/gen3/modals.json similarity index 100% rename from config/modals.json rename to config/gen3/modals.json diff --git a/config/gen3/navigation.json b/config/gen3/navigation.json index f8959b9..a6ba423 100644 --- a/config/gen3/navigation.json +++ b/config/gen3/navigation.json @@ -1,6 +1,11 @@ { "type": "horizontal", "navigation": { + "classNames": { + "root": "pl-1 mr-6 bg-base-max text-primary opacity-100 hover:opacity-100", + "item": "py-2 px-4 hover:bg-base-lightest hover:text-base-contrast", + "navigationPanel": "bg-base-max text-primary" + }, "logo": { "src": "/icons/gen3-dark.svg", "height": 128, diff --git a/config/session.json b/config/gen3/session.json similarity index 100% rename from config/session.json rename to config/gen3/session.json diff --git a/config/themeColors.json b/config/gen3/themeColors.json similarity index 76% rename from config/themeColors.json rename to config/gen3/themeColors.json index 8927c01..aaa8efd 100644 --- a/config/themeColors.json +++ b/config/gen3/themeColors.json @@ -1,147 +1,147 @@ { "primary": { + "max": "#ebeeed", + "lightest": "#bdc9c4", + "lighter": "#8fa49a", + "light": "#627e71", "DEFAULT": "#345948", "vivid": "#2d6049", - "min": "#050907", - "darkest": "#111d17", - "darker": "#1d3128", "dark": "#284538", - "light": "#627e71", - "lighter": "#8fa49a", - "lightest": "#bdc9c4", - "max": "#ebeeed" + "darker": "#1d3128", + "darkest": "#111d17", + "min": "#050907" }, "primary-contrast": { + "max": "#111111", + "lightest": "#111111", + "lighter": "#111111", + "light": "#000000", "DEFAULT": "#fefefe", "vivid": "#fefefe", - "min": "#fefefe", - "darkest": "#fefefe", - "darker": "#fefefe", "dark": "#fefefe", - "light": "#000000", - "lighter": "#111111", - "lightest": "#111111", - "max": "#111111" + "darker": "#fefefe", + "darkest": "#fefefe", + "min": "#fefefe" }, "secondary": { + "max": "#f9f2e6", + "lightest": "#ead5ae", + "lighter": "#dcb876", + "light": "#cd9b3e", "DEFAULT": "#BF7E06", "vivid": "#c58000", - "min": "#130d99", - "darkest": "#3e2902", - "darker": "#694503", "dark": "#946205", - "light": "#cd9b3e", - "lighter": "#dcb876", - "lightest": "#ead5ae", - "max": "#f9f2e6" + "darker": "#694503", + "darkest": "#3e2902", + "min": "#130d99" }, "secondary-contrast": { + "max": "#111111", + "lightest": "#111111", + "lighter": "#111111", + "light": "#111111", "DEFAULT": "#111111", "vivid": "#111111", - "min": "#fefefe", - "darkest": "#fefefe", - "darker": "#fefefe", "dark": "#fefefe", - "light": "#111111", - "lighter": "#111111", - "lightest": "#111111", - "max": "#111111" + "darker": "#fefefe", + "darkest": "#fefefe", + "min": "#fefefe" }, "accent": { + "max": "#f4e6e6", + "lightest": "#daadad", + "lighter": "#c07575", + "light": "#a63c3c", "DEFAULT": "#8C0404", "vivid": "#900000", - "min": "#0e6666", - "darkest": "#2d0101", - "darker": "#4d0202", "dark": "#6d0303", - "light": "#a63c3c", - "lighter": "#c07575", - "lightest": "#daadad", - "max": "#f4e6e6" + "darker": "#4d0202", + "darkest": "#2d0101", + "min": "#0e6666" }, "accent-contrast": { + "max": "#111111", + "lightest": "#111111", + "lighter": "#111111", + "light": "#fefefe", "DEFAULT": "#fefefe", "vivid": "#fefefe", - "min": "#fefefe", - "darkest": "#fefefe", - "darker": "#fefefe", "dark": "#fefefe", - "light": "#fefefe", - "lighter": "#111111", - "lightest": "#111111", - "max": "#111111" + "darker": "#fefefe", + "darkest": "#fefefe", + "min": "#fefefe" }, "accent-warm": { + "max": "#eeede6", + "lightest": "#c9c5ad", + "lighter": "#a49c75", + "light": "#7e743c", "DEFAULT": "#594B04", "vivid": "#5d4e00", - "min": "#090766", - "darkest": "#1d1801", - "darker": "#312902", "dark": "#453a03", - "light": "#7e743c", - "lighter": "#a49c75", - "lightest": "#c9c5ad", - "max": "#eeede6" + "darker": "#312902", + "darkest": "#1d1801", + "min": "#090766" }, "accent-warm-contrast": { + "max": "#111111", + "lightest": "#111111", + "lighter": "#111111", + "light": "#fefefe", "DEFAULT": "#fefefe", "vivid": "#fefefe", - "min": "#fefefe", - "darkest": "#fefefe", - "darker": "#fefefe", "dark": "#fefefe", - "light": "#fefefe", - "lighter": "#111111", - "lightest": "#111111", - "max": "#111111" + "darker": "#fefefe", + "darkest": "#fefefe", + "min": "#fefefe" }, "accent-cool": { + "max": "#f4f3e8", + "lightest": "#dbd8b4", + "lighter": "#c2bd81", + "light": "#a9a24d", "DEFAULT": "#908719", "vivid": "#988e11", - "min": "#0e0d02", - "darkest": "#2f2c08", - "darker": "#4f4a0e", "dark": "#706913", - "light": "#a9a24d", - "lighter": "#c2bd81", - "lightest": "#dbd8b4", - "max": "#f4f3e8" + "darker": "#4f4a0e", + "darkest": "#2f2c08", + "min": "#0e0d02" }, "accent-cool-contrast": { + "max": "#111111", + "lightest": "#111111", + "lighter": "#111111", + "light": "#111111", "DEFAULT": "#111111", "vivid": "#111111", - "min": "#fefefe", - "darkest": "#fefefe", - "darker": "#fefefe", "dark": "#fefefe", - "light": "#111111", - "lighter": "#111111", - "lightest": "#111111", - "max": "#111111" + "darker": "#fefefe", + "darkest": "#fefefe", + "min": "#fefefe" }, "base": { + "max": "#fafafa", + "lightest": "#eeeeee", + "lighter": "#e3e3e3", + "light": "#d7d7d7", "DEFAULT": "#CCCCCC", "vivid": "#d1c7c7", - "min": "#141414", - "darkest": "#424242", - "darker": "#707070", "dark": "#9e9e9e", - "light": "#d7d7d7", - "lighter": "#e3e3e3", - "lightest": "#eeeeee", - "max": "#fafafa" + "darker": "#707070", + "darkest": "#424242", + "min": "#141414" }, "base-contrast": { + "max": "#111111", + "lightest": "#111111", + "lighter": "#111111", + "light": "#111111", "DEFAULT": "#111111", "vivid": "#111111", - "min": "#fefefe", - "darkest": "#fefefe", - "darker": "#fefefe", "dark": "#111111", - "light": "#111111", - "lighter": "#111111", - "lightest": "#111111", - "max": "#111111" + "darker": "#fefefe", + "darkest": "#fefefe", + "min": "#fefefe" }, "utility": { "link": "#155276", @@ -168,27 +168,51 @@ "category4": "#1b1b1b" }, "chart": { + "max": "#e7f4f6", + "lightest": "#b0dde0", + "lighter": "#7ac5cb", + "light": "#43adb6", "DEFAULT": "#0d95A1", "vivid": "#049caa", - "min": "#010f10", - "darkest": "#043034", - "darker": "#075259", "dark": "#0a737d", - "light": "#43adb6", - "lighter": "#7ac5cb", - "lightest": "#b0dde0", - "max": "#e7f4f6" + "darker": "#075259", + "darkest": "#043034", + "min": "#010f10" }, "chart-contrast": { + "max": "#111111", + "lightest": "#111111", + "lighter": "#111111", + "light": "#111111", "DEFAULT": "#111111", "vivid": "#111111", - "min": "#fefefe", - "darkest": "#fefefe", - "darker": "#fefefe", "dark": "#fefefe", - "light": "#111111", - "lighter": "#111111", + "darker": "#fefefe", + "darkest": "#fefefe", + "min": "#fefefe" + }, + "table": { + "max": "#ffffff", + "lightest": "#ffffff", + "lighter": "#ffffff", + "light": "#ffffff", + "DEFAULT": "#ffffff", + "vivid": "#ffffff", + "dark": "#c6c6c6", + "darker": "#8c8c8c", + "darkest": "#535353", + "min": "#191919" + }, + "tablePallet-contrast": { + "max": "#111111", "lightest": "#111111", - "max": "#111111" + "lighter": "#111111", + "light": "#111111", + "DEFAULT": "#111111", + "vivid": "#111111", + "dark": "#111111", + "darker": "#111111", + "darkest": "#fefefe", + "min": "#fefefe" } } diff --git a/config/themeFonts.json b/config/gen3/themeFonts.json similarity index 100% rename from config/themeFonts.json rename to config/gen3/themeFonts.json diff --git a/config/siteConfig.json b/config/siteConfig.json deleted file mode 100644 index 44fcd28..0000000 --- a/config/siteConfig.json +++ /dev/null @@ -1,3 +0,0 @@ -{ - "commons": "gen3" -} diff --git a/package-lock.json b/package-lock.json index 067a46d..9dc48d6 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,23 +1,23 @@ { "name": "@gen3/commons-portal-app-base", - "version": "0.1.0", + "version": "0.10.30", "lockfileVersion": 3, "requires": true, "packages": { "": { "name": "@gen3/commons-portal-app-base", - "version": "0.1.0", + "version": "0.10.30", "dependencies": { - "@gen3/frontend": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-frontend-0.10.23.tgz", + "@gen3/frontend": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-frontend-0.10.30.tgz", "@mantine/core": "^6.0.21", "@mdx-js/loader": "^3.0.0", "@mdx-js/react": "^3.0.0", - "@next/mdx": "^14.1.0", + "@next/mdx": "^14.2.3", "@types/mdx": "^2.0.11", "cookies-next": "^4.1.1" }, "devDependencies": { - "@gen3/toolsff": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-toolsff-0.10.23.tgz", + "@gen3/toolsff": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-toolsff-0.10.30.tgz", "@tailwindcss/aspect-ratio": "^0.4.2", "@tailwindcss/forms": "^0.5.3", "@tailwindcss/line-clamp": "^0.4.2", @@ -25,10 +25,19 @@ "@types/lodash": "^4.14.202", "@types/react": "^18.2.21", "@types/react-dom": "^18.2.7", - "next": "^14.1.0", + "@typescript-eslint/eslint-plugin": "^7.12.0", + "eslint": "8.57.0", + "eslint-config-next": "14.2.3", + "eslint-config-prettier": "^8.8.0", + "eslint-plugin-import": "^2.27.5", + "eslint-plugin-jsx-a11y": "^6.6.1", + "eslint-plugin-react": "^7.30.1", + "eslint-plugin-react-hooks": "^4.6.0", + "next": "^14.2.3", "postcss": "^8.4.29", "postcss-loader": "^7.3.2", "postcss-preset-env": "^8.4.2", + "prettier": "^2.7.1", "react": "^18.2.0", "react-dom": "18.2.0", "tailwindcss": "^3.3.7", @@ -41,7 +50,7 @@ "npm": ">=10.2.3" }, "peerDependencies": { - "@gen3/core": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-core-0.10.23.tgz", + "@gen3/core": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-core-0.10.30.tgz", "react": "^18.2.0", "react-dom": "^18.2.0" } @@ -1683,6 +1692,107 @@ "integrity": "sha512-EsBwpc7hBUJWAsNPBmJy4hxWx12v6bshQsldrVmjxJoc3isbxhOrF2IcCpaXxfvq03NwkI7sbsOLXbYuqF/8Ww==", "peer": true }, + "node_modules/@eslint-community/eslint-utils": { + 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"https://registry.npmjs.org/world-calendars/-/world-calendars-1.0.3.tgz", diff --git a/package.json b/package.json index dbef4a5..82e03b5 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "@gen3/commons-portal-app-base", - "version": "0.1.0", + "version": "0.10.30", "private": "true", "engines": { "npm": ">=10.2.3", @@ -12,22 +12,22 @@ "build": "next build", "start": "next start", "setupCommons": "npm run buildColors && npm run getSchema && npm run getDRSToHostname", - "buildColors": "node ./node_modules/@gen3/toolsff/dist/buildColors.esm.js --themeFile=config/gen3/colors.json --out=config/", - "bundleIcons": "node ./node_modules/@gen3/toolsff/dist/bundleIcons.esm.js --inpath=config/icons --outpath=config/icons", + "build:colors": "node ./node_modules/@gen3/toolsff/dist/buildColors.esm.js --themeFile=config/$npm_config_commons/colors.json --out=config/$npm_config_commons", + "build:icons": "node ./node_modules/@gen3/toolsff/dist/bundleIcons.esm.js --inpath=config/icons --outpath=config/icons", "getSchema": "node ./node_modules/@gen3/toolsff/dist/getSchema.esm.js --out=config/", "getDRSToHostname": "node ./node_modules/@gen3/toolsff/dist/getDRSToHostname.esm.js --out=config/" }, "dependencies": { - "@gen3/frontend": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-frontend-0.10.23.tgz", + "@gen3/frontend": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-frontend-0.10.30.tgz", "@mantine/core": "^6.0.21", "@mdx-js/loader": "^3.0.0", "@mdx-js/react": "^3.0.0", - "@next/mdx": "^14.1.0", + "@next/mdx": "^14.2.3", "@types/mdx": "^2.0.11", "cookies-next": "^4.1.1" }, "devDependencies": { - "@gen3/toolsff": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-toolsff-0.10.23.tgz", + "@gen3/toolsff": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-toolsff-0.10.30.tgz", "@tailwindcss/aspect-ratio": "^0.4.2", "@tailwindcss/forms": "^0.5.3", "@tailwindcss/line-clamp": "^0.4.2", @@ -35,19 +35,28 @@ "@types/lodash": "^4.14.202", "@types/react": "^18.2.21", "@types/react-dom": "^18.2.7", - "next": "^14.1.0", + "eslint": "8.57.0", + "eslint-config-prettier": "^8.8.0", + "eslint-plugin-import": "^2.27.5", + "eslint-plugin-jsx-a11y": "^6.6.1", + "eslint-plugin-react": "^7.30.1", + "eslint-plugin-react-hooks": "^4.6.0", + "eslint-config-next": "14.2.3", + "next": "^14.2.3", "postcss": "^8.4.29", "postcss-loader": "^7.3.2", "postcss-preset-env": "^8.4.2", + "prettier": "^2.7.1", "react": "^18.2.0", "react-dom": "18.2.0", "tailwindcss": "^3.3.7", "ts-jest": "^29.0.3", "ts-node": "^10.9.1", - "typescript": "5.0.2" + "typescript": "5.0.2", + "@typescript-eslint/eslint-plugin": "^7.12.0" }, "peerDependencies": { - "@gen3/core": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-core-0.10.23.tgz", + "@gen3/core": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-core-0.10.30.tgz", "react": "^18.2.0", "react-dom": "^18.2.0" } diff --git a/src/lib/Discovery/CustomCellRenderers.tsx b/src/lib/Discovery/CustomCellRenderers.tsx index 312297d..4a30224 100644 --- a/src/lib/Discovery/CustomCellRenderers.tsx +++ b/src/lib/Discovery/CustomCellRenderers.tsx @@ -11,55 +11,56 @@ import { import { isArray } from 'lodash'; import { JSONObject } from '@gen3/core'; import { toString } from 'lodash'; +import { FilemapPopup, FilemapInline } from '@/lib/Discovery/Filemap'; /** - * Custom cell renderer for the linked study column + * Custom cell renderer for the linked study column for HEAL * @param cell */ export const LinkedStudyCell = ({ - value: cellValue, - }: CellRenderFunctionProps) => { + value: cellValue, +}: CellRenderFunctionProps) => { const value = cellValue as boolean; return value ? ( - } - color="green" - > - Linked - + } + color="green" + > + Linked + ) : ( - } color="primary"> - Not Linked - + } color="primary"> + Not Linked + ); }; const WrappedStringCell = ( - { value }: CellRenderFunctionProps, - // eslint-disable-next-line @typescript-eslint/no-unused-vars - params?: JSONObject, + { value }: CellRenderFunctionProps, + // eslint-disable-next-line @typescript-eslint/no-unused-vars + params?: JSONObject, ) => { if (value === undefined || value === null || toString(value) === '') { return ( - - {`${ - params && params?.valueIfNotAvailable - ? params?.valueIfNotAvailable - : '' - }`}{' '} - + + {`${ + params && params?.valueIfNotAvailable + ? params?.valueIfNotAvailable + : '' + }`}{' '} + ); } const content = value as string | string[]; return ( -
+
{isArray(content) ? content.join(', ') : content} -
+
); }; @@ -70,10 +71,14 @@ const WrappedStringCell = ( export const registerDiscoveryCustomCellRenderers = () => { DiscoveryCellRendererFactory.registerCellRendererCatalog({ string: { - sampleString: WrappedStringCell, + default: WrappedStringCell, }, boolean: { LinkedStudyCell, }, + manifest: { + default: FilemapPopup, + inline: FilemapInline, + } }); }; diff --git a/src/lib/Discovery/CustomRowRenderers.tsx b/src/lib/Discovery/CustomRowRenderers.tsx index 6030dd9..3772d93 100644 --- a/src/lib/Discovery/CustomRowRenderers.tsx +++ b/src/lib/Discovery/CustomRowRenderers.tsx @@ -10,74 +10,75 @@ import { getTagColor, } from '@gen3/frontend'; -// TODO: This is a hack to get around the fact that the data is not typed + interface TagData { name: string; category: string; } const DetailsWithTagsRowRenderer = - ( - { row } : RowRenderFunctionParams, - studyPreviewConfig?: StudyDetailsField, - ): ReactElement => { - const { discoveryConfig: config, setStudyDetails } = useDiscoveryContext(); + ( + { row } : RowRenderFunctionParams, + studyPreviewConfig?: StudyDetailsField, + ): ReactElement => { + const { discoveryConfig: config, setStudyDetails } = useDiscoveryContext(); - if (!studyPreviewConfig) { - return ; - } - const value = - JSONPath({ - json: row.original, - path: studyPreviewConfig.field, - }) ?? - config?.studyPreviewField?.valueIfNotAvailable ?? - ''; + if (!studyPreviewConfig) { + return ; + } + const value = + JSONPath({ + json: row.original, + path: studyPreviewConfig.field, + }) ?? + config?.studyPreviewField?.valueIfNotAvailable ?? + ''; - return ( - { - setStudyDetails(() => { - return { ...row.original }; - }); - }} - > -
- - {value} - + return ( + { + setStudyDetails(() => { + return { ...row.original }; + }); + }} + > +
+ + {value} + -
- {row.original?.tags.map(({ name, category }: TagData) => { - const color = getTagColor(category, config.tagCategories); - return ( - - {name} - - ); - })} -
-
- - ); - }; +
+ {row.original?.tags.map(({ name, category }: TagData) => { + const color = getTagColor(category, config.tagCategories); + if (name === '') return null; // no tag + return ( + + {name} + + ); + })} +
+
+ + ); + }; export default DetailsWithTagsRowRenderer; diff --git a/src/lib/Discovery/Filemap.tsx b/src/lib/Discovery/Filemap.tsx new file mode 100644 index 0000000..8c859c2 --- /dev/null +++ b/src/lib/Discovery/Filemap.tsx @@ -0,0 +1,183 @@ +import { + CellRenderFunctionProps, + ReactECharts, + ReactEChartsProps, +} from '@gen3/frontend'; +import { Button, Popover, Text } from '@mantine/core'; +import { isArray } from 'lodash'; +import { useDeepCompareMemo } from 'use-deep-compare'; +import { useDisclosure } from '@mantine/hooks'; + +/** + * Represents a manifest item. + * @interface ManifestItem + */ +interface ManifestItem { + md5sum: string; + file_name: string; + file_size?: number; + object_id: string; + commons_name?: string; +} + +/** + * Interface representing the data structure for Bar Chart. + * + * @interface + * @name BarChartData + * @property {number} value - The numerical value associated with the bar. + * @property {string} name - The name or label associated with the bar. + */ +interface BarChartData { + value: number; + name: string; +} + +/** + * Counts the number of occurrences of file types in the given data array and returns an array of objects + * representing the file type and its percentage value within the total count. + * + * @param {Array} data - The array of data containing ManifestItem objects. + * @returns {Array} - The array of objects representing file types and their percentages. + */ +const countTypes = (data: Array): BarChartData[] => { + const counts: Record = {}; + data.forEach((item: ManifestItem) => { + const filetype = item.file_name.split('.').pop(); + if (!filetype) return; + counts[filetype] = counts[filetype] ? counts[filetype] + 1 : 1; + }); + const total = Object.values(counts).reduce((acc, val) => acc + val, 0); + return Object.entries(counts).map(([name, value]) => ({ + name, + value: Number(((value / total) * 100).toFixed(2)), + })); +}; + +/** + * Converts an array of manifest items into a chart definition for React ECharts. + * + * @param {Array} data - The array of manifest items to convert. + * @returns {ReactEChartsProps['option'] | undefined} - The chart definition or undefined if the data is invalid or empty. + */ +const useProcessManifestToChart = ( + values: Array, + showLabel = true, + showToolip = false, +): ReactEChartsProps['option'] | undefined => { + const chartDefinition = useDeepCompareMemo((): + | ReactEChartsProps['option'] + | undefined => { + if ( + values === undefined || + values === null || + !isArray(values) || + values.length === 0 + ) { + return undefined; + } + + const data = countTypes(values); + + return { + grid: { + left: 2, + top: 2, + right: 2, + bottom: 2, + }, + tooltip: { + trigger: 'item', + show: showToolip, + formatter: '{a} - {c}%', + position: 'right', + z: 100, + }, + xAxis: { + type: 'value', + show: false, + }, + yAxis: { + type: 'category', + data: data.map((d) => d.name), + show: false, + }, + series: data.map((d) => ({ + type: 'bar', + stack: 'total', + barWidth: 40, + name: d.name, + data: [d.value], + label: { + show: showLabel, + position: 'top', + minMargin: 8, + formatter: '{a} - {c}%', + }, + labelLine: { + show: true, + }, + labelLayout: () => { + return { + y: '35%', + moveOverlap: 'shiftX', + }; + }, + })), + }; + }, [values]); + + return chartDefinition; +}; + +/** + * Represents a Filemap popup component. + * + * @component + * @param {Object} value - An object containing the __manifest value to render. + * @returns {JSX.Element} - The rendered JSX element. + */ +export const FilemapPopup = ({ value }: CellRenderFunctionProps) => { + const [opened, { close, open }] = useDisclosure(false); + const chartDefinition = useProcessManifestToChart(value[0]); + + if (!chartDefinition) { + return n/a; + } + return ( + + + + + +
+ +
+ + + ); +}; + +/** + * Render a chart component based on the provided value. + * + * @param {object} value - An object or array containing the value for the chart component. + * @returns {JSX.Element} - The rendered chart component. + */ +export const FilemapInline = ({ value }: CellRenderFunctionProps) => { + const chartDefinition = useProcessManifestToChart(value[0], false, true); + + if (!chartDefinition) { + return n/a; + } + return ( +
+ +
+ ); +}; diff --git a/src/lib/plugins/index.js b/src/lib/plugins/index.js index c9426cb..2d8f48e 100644 --- a/src/lib/plugins/index.js +++ b/src/lib/plugins/index.js @@ -5,32 +5,37 @@ const fs = require('fs'); // eslint-disable-next-line @typescript-eslint/no-var-requires const path = require('path'); -if (!fs.existsSync(path.join(process.cwd(), 'config', 'plugins.json'))) { - console.log('No plugins to generate.'); - return; -} -console.log('Generating plugins...'); +function main() { + if (!fs.existsSync(path.join(process.cwd(), 'config', 'plugins.json'))) { + console.log('No plugins to generate.'); + return; + } -const plugins = JSON.parse( - fs - .readFileSync(path.join(process.cwd(), 'config', 'plugins.json')) - .toString('utf-8'), -); -const imports = plugins - .map( - (plugin) => - `import { registerApp as registerApp${plugin.name} } from "${plugin.module}";`, - ) - .join('\n'); -const register = plugins - .map((plugin) => `registerApp${plugin.name}();`) - .join('\n'); -fs.writeFileSync( - path.join(process.cwd(), 'config', 'registerSitePlugins.js'), - `${imports} + console.log('Generating plugins...'); + + const plugins = JSON.parse( + fs + .readFileSync(path.join(process.cwd(), 'config', 'plugins.json')) + .toString('utf-8'), + ); + const imports = plugins + .map( + (plugin) => + `import { registerApp as registerApp${plugin.name} } from "${plugin.module}";`, + ) + .join('\n'); + const register = plugins + .map((plugin) => `registerApp${plugin.name}();`) + .join('\n'); + fs.writeFileSync( + path.join(process.cwd(), 'config', 'registerSitePlugins.js'), + `${imports} export const registerSitePlugins = () => { ${register} }; `, -); + ); +}; + +main(); diff --git a/src/pages/AISearch.tsx b/src/pages/AISearch.tsx new file mode 100644 index 0000000..5dacef7 --- /dev/null +++ b/src/pages/AISearch.tsx @@ -0,0 +1,9 @@ +import { + AiSearchPage, + AISearchPageGetServerSideProps as getServerSideProps, +} from '@gen3/frontend'; + + +export default AiSearchPage; + +export { getServerSideProps }; diff --git a/src/pages/Explorer.tsx b/src/pages/Explorer.tsx index 8322e2c..fc6f278 100644 --- a/src/pages/Explorer.tsx +++ b/src/pages/Explorer.tsx @@ -3,7 +3,7 @@ import { ExplorerPageGetServerSideProps as getServerSideProps, } from '@gen3/frontend'; -import { registerCohortTableCustomCellRenderers } from "@/lib/CohortBuilder/CustomCellRenderers"; +import { registerCohortTableCustomCellRenderers } from '@/lib/CohortBuilder/CustomCellRenderers'; registerCohortTableCustomCellRenderers(); diff --git a/src/pages/SamplePage.tsx b/src/pages/SamplePage.tsx index 7fe48bb..1124364 100644 --- a/src/pages/SamplePage.tsx +++ b/src/pages/SamplePage.tsx @@ -26,7 +26,7 @@ const SamplePage = ({ headerProps, footerProps }: NavPageLayoutProps) => { export const getServerSideProps: GetServerSideProps< NavPageLayoutProps -> = async (_context) => { +> = async () => { return { props: { ...(await getNavPageLayoutPropsFromConfig()), diff --git a/src/pages/Submission.tsx b/src/pages/Submission.tsx new file mode 100644 index 0000000..f6e0969 --- /dev/null +++ b/src/pages/Submission.tsx @@ -0,0 +1,7 @@ +import { + SubmissionPage, + SubmissionPageGetServerSideProps as getServerSideProps, +} from '@gen3/frontend'; +export default SubmissionPage; + +export { getServerSideProps }; diff --git a/src/pages/Workspaces.tsx b/src/pages/Workspace.tsx similarity index 100% rename from src/pages/Workspaces.tsx rename to src/pages/Workspace.tsx diff --git a/src/pages/_app.tsx b/src/pages/_app.tsx index 85551da..6b1c2ed 100644 --- a/src/pages/_app.tsx +++ b/src/pages/_app.tsx @@ -1,32 +1,39 @@ -import type { AppProps } from 'next/app'; +import App, { AppProps, AppContext, AppInitialProps } from 'next/app'; import { useEffect } from 'react'; -import { Gen3Provider, TenStringArray, type ModalsConfig } from '@gen3/frontend'; -import themeColors from '../../config/themeColors.json'; -import themeFonts from '../../config/themeFonts.json'; -import icons from '../../config/icons/gen3.json'; +import { + Gen3Provider, + TenStringArray, + type ModalsConfig, + ContentSource, + RegisteredIcons, + Fonts, + SessionConfiguration, +} from '@gen3/frontend'; import '../styles/globals.css'; import 'graphiql/graphiql.css'; import '@graphiql/react/dist/style.css'; -import { setDRSHostnames } from '@gen3/core'; - - -// TODO: This can be done in a better way using newer NextJS features -import sessionConfig from '../../config/session.json'; -import modalsConfig from '../../config/modals.json'; +import { GEN3_COMMONS_NAME, setDRSHostnames } from '@gen3/core'; import drsHostnames from '../../config/drsHostnames.json'; -const colors = Object.fromEntries( - Object.entries(themeColors).map(([key, values]) => [ - key, - Object.values(values) as TenStringArray, - ]), -); - -export default function App({ Component, pageProps }: AppProps) { +interface Gen3AppProps { + colors: Record; + icons: RegisteredIcons; + themeFonts: Fonts; + modalsConfig: ModalsConfig; + sessionConfig: SessionConfiguration; +} +const Gen3App = ({ + Component, + pageProps, + colors, + icons, + themeFonts, + sessionConfig, + modalsConfig, +}: AppProps & Gen3AppProps) => { useEffect(() => { setDRSHostnames(drsHostnames); - }, []); return ( @@ -34,10 +41,75 @@ export default function App({ Component, pageProps }: AppProps) { colors={colors} icons={icons} fonts={themeFonts} - sessionConfig={sessionConfig.sessionConfig} - modalsConfig={modalsConfig as ModalsConfig} + sessionConfig={sessionConfig} + modalsConfig={modalsConfig} > ); -} +}; + +// TODO: replace with page router +Gen3App.getInitialProps = async ( + context: AppContext, +): Promise => { + const ctx = await App.getInitialProps(context); + + try { + const modals = await ContentSource.get( + `config/${GEN3_COMMONS_NAME}/modals.json`, + ); + const session = await ContentSource.get( + `config/${GEN3_COMMONS_NAME}/session.json`, + ); + + const fonts = await ContentSource.get( + `config/${GEN3_COMMONS_NAME}/themeFonts.json`, + ); + + const themeColors = await ContentSource.get( + `config/${GEN3_COMMONS_NAME}/themeColors.json`, + ); + + const colors = Object.fromEntries( + Object.entries(themeColors).map(([key, values]) => [ + key, + Object.values(values) as TenStringArray, + ]), + ); + + const icons = await ContentSource.get('config/icons/gen3.json'); + return { + ...ctx, + modalsConfig: modals, + sessionConfig: session, + themeFonts: fonts as Fonts, + colors: colors, + icons: icons as RegisteredIcons, + }; + } catch (error: unknown) { + if (error instanceof Error) { + console.error('Provider Wrapper error loading config', error.toString()); + } else console.error('Provider wrapper: unknown error'); + } + // return default + return { + ...ctx, + colors: {}, + themeFonts: { + heading: ['Poppins', 'sans-serif'], + content: ['Poppins', 'sans-serif'], + fontFamily: 'Poppins', + }, + icons: { + prefix: 'gen3', + lastModified: 0, + icons: {}, + width: 0, + height: 0, + }, + modalsConfig: {}, + sessionConfig: {}, + }; +}; +export default Gen3App; diff --git a/tailwind.config.js b/tailwind.config.js index f49e613..142084b 100644 --- a/tailwind.config.js +++ b/tailwind.config.js @@ -2,12 +2,13 @@ /* eslint-disable @typescript-eslint/no-var-requires */ const plugin = require('tailwindcss/plugin'); -const themeColors = require('./config/themeColors.json'); -const themeFonts = require('./config/themeFonts.json'); +/* eslint-disable @typescript-eslint/no-var-requires */ +const { GEN3_COMMONS_NAME } = require('@gen3/core'); +const themeColors = require(`./config/${GEN3_COMMONS_NAME}/themeColors.json`); +const themeFonts = require(`./config/${GEN3_COMMONS_NAME}/themeFonts.json`); module.exports = { presets: [require('@gen3/frontend/tailwind')], - // important: '#__next', // Uncommenting this affects tailwind styling in Modals content: [ './src/pages/**/*.{js,ts,jsx,tsx}', './src/components/**/*.{js,ts,jsx,tsx}', From e83cb6f609ae2cc85cf64bc3eeecc41e7156b11c Mon Sep 17 00:00:00 2001 From: Craig Barnes Date: Mon, 24 Jun 2024 09:23:43 -0500 Subject: [PATCH 06/22] Chore/patch 0 10 31 (#36) * update config and dependencies * update config/package.json * add eslint/prettier * update typescript esplugin * update github ci * update Dockerfile * update to 0.10.31 * update to 0.10.31 * update dockerfile * update dockerfile * update dockerfile * update dockerfile * update dockerfile * update docker * testing update build ci * testing update build ci * Delete .idea directory * update docker * Update Dockerfile * update Docker --- Dockerfile | 4 +- config/gen3/dictionary.json | 4 + config/gen3/explorer.json | 6 + .../dictionary_icon_administrative.svg | 16 ++ .../dictionary_icon_analysis.svg | 13 ++ .../dictionary_icon_biospecimen.svg | 11 ++ .../dictionary_icon_clinical.svg | 13 ++ .../dictionary_icon_clinical_assessment.svg | 20 ++ .../dictionary_icon_data_file.svg | 15 ++ .../dictionary_icon_data_observations.svg | 14 ++ .../dictionary_icon_default.svg | 16 ++ .../dictionary_icon_experimental_methods.svg | 11 ++ .../dictionary_icon_imaging.svg | 11 ++ .../dictionary_icon_index_file.svg | 16 ++ .../dictionary_icon_medical_history.svg | 13 ++ .../dictionary_icon_metadata.svg | 16 ++ .../dictionary_icon_notation.svg | 12 ++ .../dictionary_icon_study_administration.svg | 16 ++ ...ictionary_icon_subject_characteristics.svg | 14 ++ config/icons/gen3.json | 71 +++++++- package-lock.json | 36 ++-- package.json | 8 +- src/lib/CohortBuilder/FileDetailsPanel.tsx | 171 ++++++++++++++++++ src/pages/DataDictionary.tsx | 6 +- src/pages/Explorer.tsx | 6 +- 25 files changed, 506 insertions(+), 33 deletions(-) create mode 100644 config/gen3/dictionary.json create mode 100755 config/icons/dataDictionary/dictionary_icon_administrative.svg create mode 100755 config/icons/dataDictionary/dictionary_icon_analysis.svg create mode 100755 config/icons/dataDictionary/dictionary_icon_biospecimen.svg create mode 100755 config/icons/dataDictionary/dictionary_icon_clinical.svg create mode 100755 config/icons/dataDictionary/dictionary_icon_clinical_assessment.svg create mode 100755 config/icons/dataDictionary/dictionary_icon_data_file.svg create mode 100644 config/icons/dataDictionary/dictionary_icon_data_observations.svg create mode 100644 config/icons/dataDictionary/dictionary_icon_default.svg create mode 100644 config/icons/dataDictionary/dictionary_icon_experimental_methods.svg create mode 100644 config/icons/dataDictionary/dictionary_icon_imaging.svg create mode 100644 config/icons/dataDictionary/dictionary_icon_index_file.svg create mode 100755 config/icons/dataDictionary/dictionary_icon_medical_history.svg create mode 100755 config/icons/dataDictionary/dictionary_icon_metadata.svg create mode 100755 config/icons/dataDictionary/dictionary_icon_notation.svg create mode 100644 config/icons/dataDictionary/dictionary_icon_study_administration.svg create mode 100644 config/icons/dataDictionary/dictionary_icon_subject_characteristics.svg create mode 100644 src/lib/CohortBuilder/FileDetailsPanel.tsx diff --git a/Dockerfile b/Dockerfile index e04c407..928e5c0 100644 --- a/Dockerfile +++ b/Dockerfile @@ -3,12 +3,10 @@ # for Macbook silicon M1/m2 uncomment the following lines and comment quay.io/cdis/ubuntu:20.04: #FROM arm64v8/ubuntu:20.04 as build -FROM quay.io/cdis/ubuntu:20.04 as build +FROM quay.io/cdis/ubuntu:20.04 AS build ARG NODE_VERSION=20 -ENV DEBIAN_FRONTEND=noninteractive - ARG BASE_PATH ARG NEXT_PUBLIC_PORTAL_BASENAME ENV NPM_CONFIG_PREFIX=/home/node/.npm-global diff --git a/config/gen3/dictionary.json b/config/gen3/dictionary.json new file mode 100644 index 0000000..9e29f7c --- /dev/null +++ b/config/gen3/dictionary.json @@ -0,0 +1,4 @@ +{ +"showGraph": false, +"showDownloads": false +} diff --git a/config/gen3/explorer.json b/config/gen3/explorer.json index afee5ea..fe821a2 100644 --- a/config/gen3/explorer.json +++ b/config/gen3/explorer.json @@ -76,6 +76,12 @@ }, "table": { "enabled": true, + "detailsConfig": { + "panel": "default", + "mode" : "click", + "idField": "submitter_id", + "title": "Details" + }, "fields": [ "submitter_id", "sex", diff --git a/config/icons/dataDictionary/dictionary_icon_administrative.svg b/config/icons/dataDictionary/dictionary_icon_administrative.svg new file mode 100755 index 0000000..34b2184 --- /dev/null +++ b/config/icons/dataDictionary/dictionary_icon_administrative.svg @@ -0,0 +1,16 @@ + + + + icon-administrative + Created with Sketch. + + + + + + + + + + + diff --git a/config/icons/dataDictionary/dictionary_icon_analysis.svg b/config/icons/dataDictionary/dictionary_icon_analysis.svg new file mode 100755 index 0000000..df8b2ec --- /dev/null +++ b/config/icons/dataDictionary/dictionary_icon_analysis.svg @@ -0,0 +1,13 @@ + + + + icon_analysis + Created with Sketch. + + + + + + + + diff --git a/config/icons/dataDictionary/dictionary_icon_biospecimen.svg b/config/icons/dataDictionary/dictionary_icon_biospecimen.svg new file mode 100755 index 0000000..bdeea3b --- /dev/null +++ b/config/icons/dataDictionary/dictionary_icon_biospecimen.svg @@ -0,0 +1,11 @@ + + + + icon_Biospecimen + Created with Sketch. + + + + + + diff --git a/config/icons/dataDictionary/dictionary_icon_clinical.svg b/config/icons/dataDictionary/dictionary_icon_clinical.svg new file mode 100755 index 0000000..69d2882 --- /dev/null +++ b/config/icons/dataDictionary/dictionary_icon_clinical.svg @@ -0,0 +1,13 @@ + + + + hospital + Created with Sketch. + + + + + + + + diff --git a/config/icons/dataDictionary/dictionary_icon_clinical_assessment.svg b/config/icons/dataDictionary/dictionary_icon_clinical_assessment.svg new file mode 100755 index 0000000..49756c8 --- /dev/null +++ b/config/icons/dataDictionary/dictionary_icon_clinical_assessment.svg @@ -0,0 +1,20 @@ + + + + icon_clinical_assessment + Created with Sketch. + + + + + + + + + + + + + + + diff --git a/config/icons/dataDictionary/dictionary_icon_data_file.svg b/config/icons/dataDictionary/dictionary_icon_data_file.svg new file mode 100755 index 0000000..0284e37 --- /dev/null +++ b/config/icons/dataDictionary/dictionary_icon_data_file.svg @@ -0,0 +1,15 @@ + + + + icon_data_file + Created with Sketch. + + + + + + + + + + diff --git a/config/icons/dataDictionary/dictionary_icon_data_observations.svg b/config/icons/dataDictionary/dictionary_icon_data_observations.svg new file mode 100644 index 0000000..5b80e47 --- /dev/null +++ b/config/icons/dataDictionary/dictionary_icon_data_observations.svg @@ -0,0 +1,14 @@ + + + + Group 22 + Created with Sketch. + + + + + + + + + diff --git a/config/icons/dataDictionary/dictionary_icon_default.svg b/config/icons/dataDictionary/dictionary_icon_default.svg new file mode 100644 index 0000000..90f8248 --- /dev/null +++ b/config/icons/dataDictionary/dictionary_icon_default.svg @@ -0,0 +1,16 @@ + + + + Group 47 + Created with Sketch. + + + + + + + + + + + diff --git a/config/icons/dataDictionary/dictionary_icon_experimental_methods.svg b/config/icons/dataDictionary/dictionary_icon_experimental_methods.svg new file mode 100644 index 0000000..cc0b4fc --- /dev/null +++ b/config/icons/dataDictionary/dictionary_icon_experimental_methods.svg @@ -0,0 +1,11 @@ + + + + Group 23 + Created with Sketch. + + + + + + diff --git a/config/icons/dataDictionary/dictionary_icon_imaging.svg b/config/icons/dataDictionary/dictionary_icon_imaging.svg new file mode 100644 index 0000000..8a96d61 --- /dev/null +++ b/config/icons/dataDictionary/dictionary_icon_imaging.svg @@ -0,0 +1,11 @@ + + + + Group 19 + Created with Sketch. + + + + + + diff --git a/config/icons/dataDictionary/dictionary_icon_index_file.svg b/config/icons/dataDictionary/dictionary_icon_index_file.svg new file mode 100644 index 0000000..dab9dd4 --- /dev/null +++ b/config/icons/dataDictionary/dictionary_icon_index_file.svg @@ -0,0 +1,16 @@ + + + + Group + Created with Sketch. + + + + + + + + + + + diff --git a/config/icons/dataDictionary/dictionary_icon_medical_history.svg b/config/icons/dataDictionary/dictionary_icon_medical_history.svg new file mode 100755 index 0000000..69d2882 --- /dev/null +++ b/config/icons/dataDictionary/dictionary_icon_medical_history.svg @@ -0,0 +1,13 @@ + + + + hospital + Created with Sketch. + + + + + + + + diff --git a/config/icons/dataDictionary/dictionary_icon_metadata.svg b/config/icons/dataDictionary/dictionary_icon_metadata.svg new file mode 100755 index 0000000..5f40962 --- /dev/null +++ b/config/icons/dataDictionary/dictionary_icon_metadata.svg @@ -0,0 +1,16 @@ + + + + icon_metadata + Created with Sketch. + + + + + + + + + + + diff --git a/config/icons/dataDictionary/dictionary_icon_notation.svg b/config/icons/dataDictionary/dictionary_icon_notation.svg new file mode 100755 index 0000000..d546f7d --- /dev/null +++ b/config/icons/dataDictionary/dictionary_icon_notation.svg @@ -0,0 +1,12 @@ + + + + icon_notation + Created with Sketch. + + + + + + + diff --git a/config/icons/dataDictionary/dictionary_icon_study_administration.svg b/config/icons/dataDictionary/dictionary_icon_study_administration.svg new file mode 100644 index 0000000..3fce02a --- /dev/null +++ b/config/icons/dataDictionary/dictionary_icon_study_administration.svg @@ -0,0 +1,16 @@ + + + + Group 21 + Created with Sketch. + + + + + + + + + + + diff --git a/config/icons/dataDictionary/dictionary_icon_subject_characteristics.svg b/config/icons/dataDictionary/dictionary_icon_subject_characteristics.svg new file mode 100644 index 0000000..3da1d98 --- /dev/null +++ b/config/icons/dataDictionary/dictionary_icon_subject_characteristics.svg @@ -0,0 +1,14 @@ + + + + Group 20 + Created with Sketch. + + + + + + + + + diff --git a/config/icons/gen3.json b/config/icons/gen3.json index 95fbc67..21bf7fd 100644 --- a/config/icons/gen3.json +++ b/config/icons/gen3.json @@ -1,6 +1,6 @@ { "prefix": "gen3", - "lastModified": 1708125912, + "lastModified": 1718898014, "icons": { "analysis": { "body": "", @@ -29,13 +29,65 @@ "width": 489.709, "height": 489.709 }, + "dictionary-icon-administrative": { + "body": "" + }, + "dictionary-icon-analysis": { + "body": "", + "height": 21 + }, + "dictionary-icon-biospecimen": { + "body": "" + }, + "dictionary-icon-clinical": { + "body": "" + }, + "dictionary-icon-clinical-assessment": { + "body": "" + }, + "dictionary-icon-data-file": { + "body": "" + }, + "dictionary-icon-data-observations": { + "body": "" + }, + "dictionary-icon-default": { + "body": "", + "height": 21 + }, + "dictionary-icon-experimental-methods": { + "body": "" + }, + "dictionary-icon-imaging": { + "body": "" + }, + "dictionary-icon-index-file": { + "body": "" + }, + "dictionary-icon-medical-history": { + "body": "" + }, + "dictionary-icon-metadata": { + "body": "" + }, + "dictionary-icon-notation": { + "body": "" + }, + "dictionary-icon-study-administration": { + "body": "" + }, + "dictionary-icon-subject-characteristics": { + "body": "" + }, "download": { "body": "", "width": 24, "height": 24 }, "exploration": { - "body": "" + "body": "", + "width": 512, + "height": 512 }, "gen3": { "body": "", @@ -63,16 +115,21 @@ "height": 511.999 }, "upload": { - "body": "" + "body": "", + "width": 512, + "height": 512 }, "user": { "body": "", - "width": 448 + "width": 448, + "height": 512 }, "workspace": { - "body": "" + "body": "", + "width": 512, + "height": 512 } }, - "width": 512, - "height": 512 + "width": 20, + "height": 20 } diff --git a/package-lock.json b/package-lock.json index 9dc48d6..947a9e1 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,14 +1,14 @@ { "name": "@gen3/commons-portal-app-base", - "version": "0.10.30", + "version": "0.10.31", "lockfileVersion": 3, "requires": true, "packages": { "": { "name": "@gen3/commons-portal-app-base", - "version": "0.10.30", + "version": "0.10.31", "dependencies": { - "@gen3/frontend": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-frontend-0.10.30.tgz", + "@gen3/frontend": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-frontend-0.10.31.tgz", "@mantine/core": "^6.0.21", "@mdx-js/loader": "^3.0.0", "@mdx-js/react": "^3.0.0", @@ -17,7 +17,7 @@ "cookies-next": "^4.1.1" }, "devDependencies": { - "@gen3/toolsff": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-toolsff-0.10.30.tgz", + "@gen3/toolsff": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-toolsff-0.10.31.tgz", "@tailwindcss/aspect-ratio": "^0.4.2", "@tailwindcss/forms": "^0.5.3", "@tailwindcss/line-clamp": "^0.4.2", @@ -50,7 +50,7 @@ "npm": ">=10.2.3" }, "peerDependencies": { - "@gen3/core": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-core-0.10.30.tgz", + "@gen3/core": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-core-0.10.31.tgz", "react": "^18.2.0", "react-dom": "^18.2.0" } @@ -1852,9 +1852,9 @@ "integrity": "sha512-f7iw44q1EjBv3MNcHCGAgrW/QVyweaEouFsJzykPhTOGnZFSwFJRISToXornOmuAy7xUUGiVdqOLiykgZoYB8A==" }, "node_modules/@gen3/core": { - "version": "0.10.30", - "resolved": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-core-0.10.30.tgz", - "integrity": "sha512-BuDm4FiHzfO3eALi21b226M6nXT7du53bx44YUPK+jDKcZxO5dgfpeQFfyyJoK0CpWehiuhjMrgum+pY8Zw7ZA==", + "version": "0.10.31", + "resolved": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-core-0.10.31.tgz", + "integrity": "sha512-fxaBN7B9y5WuuZKtLcs0owDqotPhc8QUFv9B8vCl0sZPRdMiKqezDV8PlFDK7WPBJUypDf4vYizS74OXADZpsA==", "peer": true, "dependencies": { "@reduxjs/toolkit": "1.9.5", @@ -1875,9 +1875,9 @@ } }, "node_modules/@gen3/frontend": { - "version": "0.10.30", - "resolved": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-frontend-0.10.30.tgz", - "integrity": "sha512-CC/DF22dao1hoI+RAo8OzhygW3G0OJuhgOpkO5Nubab6u7Xz029J7jCIaMXYwbb0KPaiFfjsZbATpd+0nRfMhw==", + "version": "0.10.31", + "resolved": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-frontend-0.10.31.tgz", + "integrity": "sha512-tAujRvtwHM7ptrwp03Jgul5BygRu1kZhCDDNtdKCOXx9IKodmfadK6vFPXsynHtXkK5bW416Hgr3VdErfC57GA==", "dependencies": { "@fontsource/montserrat": "^4.5.12", "@fontsource/source-sans-pro": "^4.5.11", @@ -1899,6 +1899,7 @@ "@tailwindcss/typography": "^0.5.7", "@types/dompurify": "^3.0.3", "chart.js": "^4.0.1", + "colorette": "^2.0.20", "cookies-next": "^2.1.1", "default-composer": "^0.6.0", "dompurify": "^3.0.5", @@ -1913,7 +1914,7 @@ "jose": "^4.13.1", "js-cookie": "^3.0.5", "jsonpath-plus": "^8.0.0", - "mantine-react-table": "^1.3.3", + "mantine-react-table": "^1.3.4", "minisearch": "^6.3.0", "next": "^14.2.3", "next-compose-plugins": "^2.2.1", @@ -2087,9 +2088,9 @@ "integrity": "sha512-ARDJmphmdvUk6Glw7y9DQ2bFkKBHwQHLi2lsaH6PPmz/Ka9sFOBsBluozhDltWmnv9u/cF6Rt87znRTPV+yp/A==" }, "node_modules/@gen3/toolsff": { - "version": "0.10.30", - "resolved": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-toolsff-0.10.30.tgz", - "integrity": "sha512-P4i9JKIzTP5ZxwnDPLkqTzTtQPLEcK6VegSfjqrfK9GVFpVLgEIBxaJs1odKnjiDDkPWDYoa4ux7xYh3apQjYA==", + "version": "0.10.31", + "resolved": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-toolsff-0.10.31.tgz", + "integrity": "sha512-Oaqf9RcS+XmDA+Julit9e/MaZ2LCRIEUaBfqruceF0XNT5e+8iA0UroO157D3dcJFRLgCjliBHK9PpPWCwXQDw==", "dev": true, "dependencies": { "@iconify/tools": "^2.1.2", @@ -8468,6 +8469,11 @@ "simple-swizzle": "^0.2.2" } }, + "node_modules/colorette": { + "version": "2.0.20", + "resolved": "https://registry.npmjs.org/colorette/-/colorette-2.0.20.tgz", + "integrity": "sha512-IfEDxwoWIjkeXL1eXcDiow4UbKjhLdq6/EuSVR9GMN7KVH3r9gQ83e73hsz1Nd1T3ijd5xv1wcWRYO+D6kCI2w==" + }, "node_modules/combined-stream": { "version": "1.0.8", "resolved": "https://registry.npmjs.org/combined-stream/-/combined-stream-1.0.8.tgz", diff --git a/package.json b/package.json index 82e03b5..067316f 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "@gen3/commons-portal-app-base", - "version": "0.10.30", + "version": "0.10.31", "private": "true", "engines": { "npm": ">=10.2.3", @@ -18,7 +18,7 @@ "getDRSToHostname": "node ./node_modules/@gen3/toolsff/dist/getDRSToHostname.esm.js --out=config/" }, "dependencies": { - "@gen3/frontend": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-frontend-0.10.30.tgz", + "@gen3/frontend": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-frontend-0.10.31.tgz", "@mantine/core": "^6.0.21", "@mdx-js/loader": "^3.0.0", "@mdx-js/react": "^3.0.0", @@ -27,7 +27,7 @@ "cookies-next": "^4.1.1" }, "devDependencies": { - "@gen3/toolsff": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-toolsff-0.10.30.tgz", + "@gen3/toolsff": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-toolsff-0.10.31.tgz", "@tailwindcss/aspect-ratio": "^0.4.2", "@tailwindcss/forms": "^0.5.3", "@tailwindcss/line-clamp": "^0.4.2", @@ -56,7 +56,7 @@ "@typescript-eslint/eslint-plugin": "^7.12.0" }, "peerDependencies": { - "@gen3/core": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-core-0.10.30.tgz", + "@gen3/core": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-core-0.10.31.tgz", "react": "^18.2.0", "react-dom": "^18.2.0" } diff --git a/src/lib/CohortBuilder/FileDetailsPanel.tsx b/src/lib/CohortBuilder/FileDetailsPanel.tsx new file mode 100644 index 0000000..11323b5 --- /dev/null +++ b/src/lib/CohortBuilder/FileDetailsPanel.tsx @@ -0,0 +1,171 @@ +/* eslint-disable @typescript-eslint/no-explicit-any */ // TODO remove use of any +import { + Anchor, + Group, + LoadingOverlay, + Stack, + Table, + Text, + CopyButton, + ActionIcon, + Tooltip, + Button, +} from '@mantine/core'; +import { useGeneralGQLQuery, GEN3_FENCE_API } from '@gen3/core'; +import { + ErrorCard, + type TableDetailsPanelProps, + ExplorerTableDetailsPanelFactory, +} from '@gen3/frontend'; +import { + MdContentCopy as IconCopy, + MdCheck as IconCheck, +} from 'react-icons/md'; + +// a definition of the query response +interface QueryResponse { + data?: Record>; +} + +/** + * Checks if the given object is a QueryResponse. + * + * @param {any} obj - The object to be checked. + * @returns {boolean} Returns true if the object is a QueryResponse, false otherwise. + */ +const isQueryResponse = (obj: any): obj is QueryResponse => { + // Considering that the data property can be optional + return ( + typeof obj === 'object' && + (obj.data === undefined || typeof obj.data === 'object') + ); +}; + +/** + * Extracts data from a QueryResponse object based on an index. + * + * @param {QueryResponse} data - The QueryResponse object containing the data. + * @param {string} index - The index to extract the data from. + * @returns {Record} - The extracted data as a key-value pair object. + */ +const extractData = ( + data: QueryResponse, + index: string, +): Record => { + if (data === undefined || data === null) return {}; + if (data.data === undefined || data.data === null) return {}; + + return Array.isArray(data.data[index]) && data.data[index].length > 0 + ? data.data[index][0] + : {}; +}; + +export const FileDetailsPanel = ({ + id, + index, + tableConfig, + onClose, +}: TableDetailsPanelProps) => { + // get the idField from the configuration + const idField = tableConfig.detailsConfig?.idField; + // call the general Guppy GQL which takes an object { query: string, variables: object } + const { data, isLoading, isError } = useGeneralGQLQuery({ + query: `query ($filter: JSON) { + ${index} (filter: $filter, accessibility: all) { + ${tableConfig.fields} + } + }`, + variables: { + filter: { + AND: [ + { + IN: { + [idField ?? 0]: [id], + }, + }, + ], + }, + }, + }); + + // handle misconfiguration + if (!idField) { + return ( + + ); + } + // show data error if graphql fails + if (isError) { + return ; + } + + // process guppy response + const queryData = isQueryResponse(data) ? extractData(data, index) : {}; + + // create the rows for the table + const rows = Object.entries(queryData).map(([field, value]) => ( + + + {field} + + + {/* + if field is one that we want a link for make it an Anchor otherwise + render as text. + */} + {field === 'object_id' ? ( + + {value ? (value as string) : ''} + + ) : ( + {value ? (value as string) : ''} + )} + + + )); + return ( + + + Results for {id} + + + + + + + + {rows} +
FieldValue
+ + + {({ copied, copy }) => ( + + + {copied ? : } + + + )} + + + + + ); +}; + +export const registerCustomExplorerDetailsPanels = () => { + ExplorerTableDetailsPanelFactory().registerRendererCatalog({ + // NOTE: The catalog name must be tableDetails + tableDetails: { fileDetails: FileDetailsPanel }, // TODO: add simpler registration function that ensures the catalog name is tableDetails + }); +}; diff --git a/src/pages/DataDictionary.tsx b/src/pages/DataDictionary.tsx index 274b3b1..0302c07 100644 --- a/src/pages/DataDictionary.tsx +++ b/src/pages/DataDictionary.tsx @@ -1,7 +1,7 @@ import { - DataDictionaryPage, - DataDictionaryPageGetServerSideProps as getServerSideProps, + DictionaryPage, + DictionaryPageGetServerSideProps as getServerSideProps, } from '@gen3/frontend'; -export default DataDictionaryPage; +export default DictionaryPage; export { getServerSideProps }; diff --git a/src/pages/Explorer.tsx b/src/pages/Explorer.tsx index fc6f278..9923b56 100644 --- a/src/pages/Explorer.tsx +++ b/src/pages/Explorer.tsx @@ -3,9 +3,13 @@ import { ExplorerPageGetServerSideProps as getServerSideProps, } from '@gen3/frontend'; -import { registerCohortTableCustomCellRenderers } from '@/lib/CohortBuilder/CustomCellRenderers'; +import { registerCohortTableCustomCellRenderers +} from '@/lib/CohortBuilder/CustomCellRenderers'; + +import { registerCustomExplorerDetailsPanels } from '@/lib/CohortBuilder/FileDetailsPanel'; registerCohortTableCustomCellRenderers(); +registerCustomExplorerDetailsPanels(); export default ExplorerPage; From 7fda838a6d7147f83f0feecba9d50e1a2693b0ea Mon Sep 17 00:00:00 2001 From: Craig Barnes Date: Mon, 9 Sep 2024 09:36:55 -0500 Subject: [PATCH 07/22] Update to 0.10.44 (#41) * update to 0.10.44 * update to 0.10.44 * update mantine and style for tailwind --- .eslintignore | 2 + .eslintrc.js | 1 + config/gen3/alternate_colors/dark.json | 9 + config/gen3/alternate_colors/pallet2.json | 11 + config/gen3/alternate_colors/urban.json | 9 + config/gen3/colors.json | 12 +- config/gen3/crosswalk.json | 29 + config/gen3/discovery.json | 454 +-- config/gen3/explorer.json | 778 +----- config/gen3/footer.json | 4 +- config/gen3/login.json | 6 +- config/gen3/navigation.json | 5 +- config/gen3/profile.json | 1 + config/gen3/session.json | 2 +- config/gen3/submission.json | 30 + config/gen3/themeColors.json | 134 +- config/gen3/themeFonts.json | 6 +- config/gen3/workspaces.json | 3 + package-lock.json | 2439 +++++++---------- package.json | 32 +- src/lib/CohortBuilder/CustomCellRenderers.tsx | 20 +- src/lib/CohortBuilder/FileDetailsPanel.tsx | 11 +- src/lib/Discovery/CustomRowRenderers.tsx | 121 +- src/lib/Discovery/Filemap.tsx | 2 +- src/pages/Crosswalk.tsx | 7 + src/pages/DataDictionary.tsx | 1 + src/pages/Explorer.tsx | 4 +- src/pages/SamplePage.tsx | 31 +- src/pages/_app.tsx | 25 +- src/pages/_document.tsx | 30 +- src/styles/globals.css | 85 +- tailwind.config.js | 1 - 32 files changed, 1679 insertions(+), 2626 deletions(-) create mode 100644 .eslintignore create mode 100644 config/gen3/alternate_colors/dark.json create mode 100644 config/gen3/alternate_colors/pallet2.json create mode 100644 config/gen3/alternate_colors/urban.json create mode 100644 config/gen3/crosswalk.json create mode 100644 config/gen3/submission.json create mode 100644 config/gen3/workspaces.json create mode 100644 src/pages/Crosswalk.tsx diff --git a/.eslintignore b/.eslintignore new file mode 100644 index 0000000..905cb7e --- /dev/null +++ b/.eslintignore @@ -0,0 +1,2 @@ +*.css +node_modules diff --git a/.eslintrc.js b/.eslintrc.js index edf6734..f0f9465 100644 --- a/.eslintrc.js +++ b/.eslintrc.js @@ -23,6 +23,7 @@ module.exports = { }, plugins: ['jsx-a11y', 'react', 'react-hooks', '@typescript-eslint'], rules: { + '@typescript-eslint/no-explicit-any':['warn'], 'no-underscore-dangle': 'off', 'import/prefer-default-export': 'off', 'linebreak-style': ['error', 'unix'], diff --git a/config/gen3/alternate_colors/dark.json b/config/gen3/alternate_colors/dark.json new file mode 100644 index 0000000..492038e --- /dev/null +++ b/config/gen3/alternate_colors/dark.json @@ -0,0 +1,9 @@ +{ + "primary": "#009688", + "secondary": "#465451", + "accent": "#cba12c", + "base": "#111111", + "accentWarm": "#892115", + "accentCool": "#255990", + "chart": "#0d95A1" +} diff --git a/config/gen3/alternate_colors/pallet2.json b/config/gen3/alternate_colors/pallet2.json new file mode 100644 index 0000000..b3fb0a1 --- /dev/null +++ b/config/gen3/alternate_colors/pallet2.json @@ -0,0 +1,11 @@ + + +{ +"primary": "#edae49", +"secondary": "#772b38", +"accent": "#00798c", +"base": "#7a7a7a", +"accentWarm": "#30638e", +"accentCool": "#003d5b", +"chart": "#0d95A1" +} diff --git a/config/gen3/alternate_colors/urban.json b/config/gen3/alternate_colors/urban.json new file mode 100644 index 0000000..3d83f54 --- /dev/null +++ b/config/gen3/alternate_colors/urban.json @@ -0,0 +1,9 @@ +{ + "primary": "#2C2C54", + "secondary": "#AAABB8", + "accent": "#474787", + "base": "#ECECEC", + "accentWarm": "#892115", + "accentCool": "#255990", + "chart": "#0d95A1" +} diff --git a/config/gen3/colors.json b/config/gen3/colors.json index 9ac464a..3d83f54 100644 --- a/config/gen3/colors.json +++ b/config/gen3/colors.json @@ -1,9 +1,9 @@ { - "primary": "#345948", - "secondary": "#BF7E06", - "accent": "#8C0404", - "base": "#CCCCCC", - "accentWarm": "#594B04", - "accentCool": "#908719", + "primary": "#2C2C54", + "secondary": "#AAABB8", + "accent": "#474787", + "base": "#ECECEC", + "accentWarm": "#892115", + "accentCool": "#255990", "chart": "#0d95A1" } diff --git a/config/gen3/crosswalk.json b/config/gen3/crosswalk.json new file mode 100644 index 0000000..194bd51 --- /dev/null +++ b/config/gen3/crosswalk.json @@ -0,0 +1,29 @@ +{ + "mapping" : { + "source" : { + "id": "prom", + "label": "Prometheus", + "description" : "PROject for Military Exposures and Toxin History Evaluation in US Service Members" + }, + "external" : [ + { + "id": "GDC", + "label": "Genomic Data Commons", + "dataPath": "crosswalk->subject->https://portal.gdc.cancer.gov->case.case_id->value", + "description": "A repository and computational platform for cancer researchers who need to understand cancer, its clinical progression, and response to therapy." + }, + { + "id": "VPOC", + "label": "VPOC", + "dataPath": "crosswalk->subject->https://vpodc.data-commons.org->case.submitter_id->value", + "description": "Veterans Precision Oncology Data Commons® (VPOC) The Veterans Data Commons supports the management, analysis and sharing of veteran oncologic data for the research community and aims to accelerate discovery and development of therapies, diagnostic tests, and other technologies for precision oncology" + }, + { + "id": "TCIA", + "label": "TCIA", + "dataPath": "crosswalk->subject->https://www.cancerimagingarchive.net->subject.subject_id->value", + "description": "The Cancer Imaging Archive (TCIA) is a service which de-identifies and hosts a large archive of medical images of cancer accessible for public download" + } + ] + } +} diff --git a/config/gen3/discovery.json b/config/gen3/discovery.json index 45c2750..69175ca 100644 --- a/config/gen3/discovery.json +++ b/config/gen3/discovery.json @@ -1,248 +1,252 @@ { - "tableConfig": { - "selectableRows": true, - "expandableRows": true - }, - "features": { - "advSearchFilters": { - "enabled": false, - "field": "advSearchFilters", - "displayName": "Filters", - "filters": [ + "metadataConfig": [ + { + "tableConfig": { + "selectableRows": true, + "expandableRows": true + }, + "features": { + "advSearchFilters": { + "enabled": false, + "field": "advSearchFilters", + "displayName": "Filters", + "filters": [ + { + "key": "Study Type" + }, + { + "key": "Data Type" + }, + { + "key": "Subject Type" + }, + { + "key": "Gender" + }, + { + "key": "Age" + } + ] + }, + "tagsColumn": { + "enabled": false + }, + "tagsInDescription": { + "enabled": true + }, + "exportToWorkspace": { + "enabled": true, + "manifestFieldName": "__manifest", + "enableDownloadManifest": true, + "enableDownloadZip": true, + "downloadZipButtonText": "Download Zip", + "downloadManifestButtonText": "Download Manifest", + "documentationLinks": { + "gen3Client": "https://gen3.org/resources/user/gen3-client/", + "gen3Workspaces": "https://gen3.org/resources/user/analyze-data/" + }, + "verifyExternalLogins": true + }, + "pageTitle": { + "enabled": true, + "title": "Discover Datasets" + }, + "search": { + "searchBar": { + "enabled": true, + "inputSubtitle": "Search studies by keywords", + "searchableTextFields": [ + "study_description", + "_unique_id", + "full_name" + ] + }, + "tagSearchDropdown": { + "enabled": true, + "collapsibleButtonText": "Data Repository" + } + }, + "authorization": { + "enabled": true, + "columnTooltip": "Filter by data access", + "supportedValues": { + "accessible": { + "enabled": true, + "menuText": "Available" + }, + "unaccessible": { + "enabled": false, + "menuText": "Not Accessible" + }, + "pending": { + "enabled": true, + "menuText": "Pending" + }, + "notAvailable": { + "enabled": true, + "menuText": "Not Available" + } + } + } + }, + "aggregations": [ + { + "name": "Studies", + "field": "_unique_id", + "type": "count" + } + ], + "tagSelector": { + "showTagCategoryNames": true + }, + "studies": [], + "studyColumns": [ { - "key": "Study Type" + "name": "Study ID", + "field": "_unique_id", + "contentType": "string", + "errorIfNotAvailable": false, + "valueIfNotAvailable": "n/a" }, { - "key": "Data Type" + "name": "Study Name", + "field": "full_name", + "contentType": "string", + "errorIfNotAvailable": false, + "valueIfNotAvailable": "n/a" }, { - "key": "Subject Type" + "name": "Study Title", + "field": "study_title", + "contentType": "string", + "errorIfNotAvailable": false, + "valueIfNotAvailable": "n/a" }, { - "key": "Gender" + "name": "Source", + "field": "source", + "contentType": "string", + "errorIfNotAvailable": false, + "valueIfNotAvailable": "n/a" }, { - "key": "Age" + "name": "Data Files", + "field": "__manifest", + "contentType": "manifest", + "errorIfNotAvailable": false, + "valueIfNotAvailable": "n/a" + }, + { + "name": "Subjects", + "field": "subjects_count", + "contentType": "string", + "errorIfNotAvailable": false, + "valueIfNotAvailable": "n/a" } - ] - }, - "tagsColumn": { - "enabled": false - }, - "tagsInDescription": { - "enabled": true - }, - "exportToWorkspace": { - "enabled": true, - "manifestFieldName": "__manifest", - "enableDownloadManifest": true, - "enableDownloadZip": true, - "downloadZipButtonText": "Download Zip", - "downloadManifestButtonText": "Download Manifest", - "documentationLinks": { - "gen3Client": "https://gen3.org/resources/user/gen3-client/", - "gen3Workspaces": "https://gen3.org/resources/user/analyze-data/" - }, - "verifyExternalLogins": true - }, - "pageTitle": { - "enabled": true, - "title": "Discover Datasets" - }, - "search": { - "searchBar": { - "enabled": true, - "inputSubtitle": "Search studies by keywords", - "searchableTextFields": [ - "study_description", - "_unique_id", - "full_name" - ] + ], + "studyPreviewField": { + "name": "Study Description", + "field": "study_description", + "contentType": "string", + "includeName": true, + "includeIfNotAvailable": false, + "valueIfNotAvailable": "No summary has been provided for this study." }, - "tagSearchDropdown": { - "enabled": true, - "collapsibleButtonText": "Data Repository" - } - }, - "authorization": { - "enabled": true, - "columnTooltip": "Filter by data access", - "supportedValues": { - "accessible": { - "enabled": true, - "menuText": "Available" - }, - "unaccessible": { - "enabled": false, - "menuText": "Not Accessible" + "simpleDetailsView": { + "header": { + "field": "study_title" }, - "pending": { - "enabled": true, - "menuText": "Pending" + "downloadLinks": { + "field": "data_download_links" }, - "notAvailable": { - "enabled": true, - "menuText": "Not Available" - } - } - } - }, - "aggregations": [ - { - "name": "Studies", - "field": "_unique_id", - "type": "count" - } - ], - "tagSelector": { - "showTagCategoryNames": true - }, - "studies": [], - "studyColumns": [ - { - "name": "Study ID", - "field": "_unique_id", - "contentType": "string", - "errorIfNotAvailable": false, - "valueIfNotAvailable": "n/a" - }, - { - "name": "Study Name", - "field": "full_name", - "contentType": "string", - "errorIfNotAvailable": false, - "valueIfNotAvailable": "n/a" - }, - { - "name": "Study Title", - "field": "study_title", - "contentType": "string", - "errorIfNotAvailable": false, - "valueIfNotAvailable": "n/a" - }, - { - "name": "Source", - "field": "source", - "contentType": "string", - "errorIfNotAvailable": false, - "valueIfNotAvailable": "n/a" - }, - { - "name": "Data Files", - "field": "__manifest", - "contentType": "manifest", - "errorIfNotAvailable": false, - "valueIfNotAvailable": "n/a" - }, - { - "name": "Subjects", - "field": "subjects_count", - "contentType": "string", - "errorIfNotAvailable": false, - "valueIfNotAvailable": "n/a" - } - ], - "studyPreviewField": { - "name": "Study Description", - "field": "study_description", - "contentType": "string", - "includeName": true, - "includeIfNotAvailable": false, - "valueIfNotAvailable": "No summary has been provided for this study." - }, - "simpleDetailsView": { - "header": { - "field": "study_title" - }, - "downloadLinks": { - "field": "data_download_links" - }, - "fieldsToShow": [ - { - "groupWidth": "half", - "fields": [ - { - "name": "Study Name", - "field": "full_name", - "contentType": "string", - "includeIfNotAvailable": false - }, - { - "name": "Study Title", - "field": "study_title", - "contentType": "string", - "includeIfNotAvailable": false - }, - { - "name": "Funding", - "field": "funding", - "contentType": "string", - "includeIfNotAvailable": false - }, - { - "name": "Source", - "field": "source", - "contentType": "string", - "includeIfNotAvailable": false - }, - { - "name": "Data Files", - "field": "data_files_count", - "contentType": "string", - "includeIfNotAvailable": false - }, - { - "name": "Subjects", - "field": "subjects_count", - "contentType": "string", - "includeIfNotAvailable": false - }, + "fieldsToShow": [ { - "name": "Project ID", - "field": "project_id", - "contentType": "string", - "includeIfNotAvailable": false + "groupWidth": "half", + "fields": [ + { + "name": "Study Name", + "field": "full_name", + "contentType": "string", + "includeIfNotAvailable": false + }, + { + "name": "Study Title", + "field": "study_title", + "contentType": "string", + "includeIfNotAvailable": false + }, + { + "name": "Funding", + "field": "funding", + "contentType": "string", + "includeIfNotAvailable": false + }, + { + "name": "Source", + "field": "source", + "contentType": "string", + "includeIfNotAvailable": false + }, + { + "name": "Data Files", + "field": "data_files_count", + "contentType": "string", + "includeIfNotAvailable": false + }, + { + "name": "Subjects", + "field": "subjects_count", + "contentType": "string", + "includeIfNotAvailable": false + }, + { + "name": "Project ID", + "field": "project_id", + "contentType": "string", + "includeIfNotAvailable": false + }, + { + "name": "Link", + "field": "link", + "contentType": "link", + "includeIfNotAvailable": false + } + ] }, { - "name": "Link", - "field": "link", - "contentType": "link", - "includeIfNotAvailable": false + "groupWidth": "half", + "fields": [ + { + "name": "Study Description", + "field": "study_description", + "contentType": "paragraph", + "includeIfNotAvailable": false, + "valueIfNotAvailable": "No summary has been provided for this study." + } + ] } ] }, - { - "groupWidth": "half", - "fields": [ - { - "name": "Study Description", - "field": "study_description", - "contentType": "paragraph", - "includeIfNotAvailable": false, - "valueIfNotAvailable": "No summary has been provided for this study." - } - ] - } - ] - }, - "tagsDisplayName": "Study Filters", - "tagColumnWidth": "500px", - "minimalFieldMapping": { - "authzField": "authz", - "tagsListFieldName": "tags", - "dataAvailabilityField": "data_availability", - "uid": "_hdp_uid" - }, - "tagCategories": [ - { - "name": "Condition", - "color": "#532565", - "display": false - }, - { - "name": "Data Type", - "color": "#982568", - "display": false + "tagsDisplayName": "Study Filters", + "tagColumnWidth": "500px", + "minimalFieldMapping": { + "authzField": "authz", + "tagsListFieldName": "tags", + "dataAvailabilityField": "data_availability", + "uid": "_hdp_uid" + }, + "tagCategories": [ + { + "name": "Condition", + "color": "#532565", + "display": false + }, + { + "name": "Data Type", + "color": "#982568", + "display": false + } + ] } ] } diff --git a/config/gen3/explorer.json b/config/gen3/explorer.json index fe821a2..63f00f3 100644 --- a/config/gen3/explorer.json +++ b/config/gen3/explorer.json @@ -2,75 +2,40 @@ { "tabTitle": "Cases", "charts": { - "covid19_positive": { - "chartType": "fullPie", - "title": "COVID-19 Positive" - }, - "sex": { - "chartType": "fullPie", - "title": "Sex" - }, "race": { "chartType": "fullPie", "title": "Race" + }, + "ethnicity": { + "chartType": "horizontalStacked", + "title": "Ethnicity" + }, + "gender": { + "chartType": "bar", + "title": "Gender" } }, "filters": { "tabs": [ { - "title": "Demographics", - "fields": [ - "sex", - "race", - "ethnicity", - "age_at_index", - "index_event", - "zip", - "covid19_positive", - "project_id" - ] - }, - { - "title": "COVID Tests", - "fields": [ - "measurements.test_name", - "measurements.test_result_text", - "measurements.test_method", - "measurements.test_days_from_index" - ] - }, - { - "title": "Medications", - "fields": [ - "medications.days_to_medication_start", - "medications.days_to_medication_end", - "medications.dose_sequence_number", - "medications.medication_code", - "medications.medication_code_system", - "medications.medication_manufacturer", - "medications.medication_name", - "medications.medication_status", - "medications.medication_type" - ] + "title": "Study Selection", + "fields": ["project"] }, { - "title": "Procedures", + "title": "Subjects", "fields": [ - "procedures.breathing_support_type", - "procedures.days_to_procedure_start", - "procedures.days_to_procedure_end", - "procedures.procedure_name" - ] - }, - { - "title": "Conditions", - "fields": [ - "conditions.condition_name", - "conditions.condition_code_system", - "conditions.condition_code", - "conditions.days_to_condition_start", - "conditions.days_to_condition_end" - ] + "study", + "gender", + "race", + "ethnicity", + "vital_status", + "whatever_lab_result_value" + ], + "fieldsConfig": { + "gender" : { + "type" : "multiselect" + } + } } ] }, @@ -82,71 +47,52 @@ "idField": "submitter_id", "title": "Details" }, + "pageLimit": { + "limit": 10000 + }, "fields": [ - "submitter_id", - "sex", - "age_at_index", - "index_event", + "project", + "gender", "race", "ethnicity", - "zip", - "covid19_positive", - "measurements.test_name", - "measurements.test_result_text", - "measurements.test_method", - "measurements.test_days_from_index", - "medications.days_to_medication_start", - "medications.days_to_medication_end", - "medications.dose_sequence_number", - "medications.medication_code", - "medications.medication_code_system", - "medications.medication_manufacturer", - "medications.medication_name", - "medications.medication_status", - "medications.medication_type", - "procedures.breathing_support_type", - "procedures.days_to_procedure_start", - "procedures.days_to_procedure_end", - "procedures.procedure_name", - "conditions.condition_name", - "conditions.condition_code_system", - "conditions.condition_code", - "conditions.days_to_condition_start", - "conditions.days_to_condition_end", - "_imaging_studies_count", - "_ct_series_file_count", - "_dx_series_file_count", - "_cr_series_file_count", - "_mr_series_file_count", - "project_id" + "whatever_lab_result_value" ], "columns": { - "measurements.test_name": { - "title": "Test Name", - "type": "array", - "accessorPath": "measurements[*].test_name" - }, - "measurements.test_result_text": { - "title": "Test Results Text", - "type": "array", - "accessorPath": "measurements[*].test_result_text", - "cellRenderFunction": "NegativePositive" - }, - "measurements.test_method": { - "title": "Test Method", - "type": "array", - "accessorPath": "measurements[*].test_method" - }, - "measurements.test_days_from_index": { - "title": "Test Days from Index", - "type": "array", - "accessorPath": "measurements[*].test_days_from_index" + "whatever_lab_result_value": { + "sortable": false } } }, "dropdowns": { "download-table": { - "title": "Download Case Metadata Table" + "title": "Download Table", + "leftIcon": "gen3:download", + "rightIcon": "gen3:chevron-down", + "dropdownItems": [ + { + "enabled": true, + "type": "data-json", + "title": "JSON", + "leftIcon": "datafile", + "rightIcon": "download", + "action": "data-json", + "actionArgs" : { + "filename": "MIDRC_Series_table.json", + "rootPath": "gen3_discovery" + } + }, + { + "enabled": true, + "type": "data-csv", + "title": "CSV", + "leftIcon": "datafile", + "rightIcon": "download", + "action": "data-csv", + "actionArgs" : { + "filename": "data_table.csv" + } + } + ] } }, "buttons": [ @@ -157,7 +103,9 @@ "dropdownId": "download-table", "leftIcon": "datafile", "rightIcon": "download", - "fileName": "MIDRC_Cases_table.json" + "actionArgs": { + "filename": "data_table.json" + } }, { "enabled": true, @@ -166,7 +114,9 @@ "dropdownId": "download-table", "leftIcon": "datafile", "rightIcon": "download", - "fileName": "MIDRC_Cases_table.tsv" + "actionArgs": { + "filename": "data_table.tsv" + } }, { "enabled": true, @@ -175,549 +125,111 @@ "dropdownId": "download-table", "leftIcon": "datafile", "rightIcon": "download", - "fileName": "MIDRC_Cases_table.csv" + "actionArgs": { + "filename": "data_table.csv" + } }, { "enabled": true, "type": "manifest", + "action": "manifest", "title": "Download File Manifest for Cases", "leftIcon": "datafile", "rightIcon": "download", - "fileName": "MIDRC_case_manifest.json" - }, - { - "enabled": false, - "type": "export-to-workspace", - "title": "Export to Workspace", - "leftIcon": "datafile", - "rightIcon": "download" + "fileName": "case_manifest.json", + "actionArgs": { + "resourceIndexType": "file", + "resourceIdField": "object_id", + "referenceIdFieldInResourceIndex": "project_id", + "referenceIdFieldInDataIndex": "project_id", + "fileFields": ["file_name", "file_size", "md5sum", "object_id"] + } } ], - "loginForDownload": true, + "loginForDownload": false, "guppyConfig": { - "dataType": "case", - "nodeCountTitle": "Cases", + "dataType": "subject", + "nodeCountTitle": "Subjects", "fieldMapping": [ { - "field": "project_id", - "name": "Project ID" - }, - { - "field": "submitter_id", - "name": "Case ID" + "field": "_samples_count", + "name": "Samples Count" }, { - "field": "_imaging_studies_count", - "name": "Imaging Studies Count" + "field": "_imaging_files_count", + "name": "Imaging Files Count" }, { - "field": "_ct_series_file_count", - "name": "CT Series Count" + "field": "_unaligned_reads_files_count", + "name": "Unaligned Reads Count" }, { - "field": "_dx_series_file_count", - "name": "DX Series Count" + "field": "_aligned_reads_files_count", + "name": "Aligned Reads Count" }, { - "field": "_cr_series_file_count", - "name": "CR Series Count" - }, - { - "field": "_mr_series_file_count", - "name": "MR Series Count" + "field": "_expression_arrays_count", + "name": "Expression Arrays Count" } ], "manifestMapping": { - "resourceIndexType": "imaging_data_file", + "resourceIndexType": "file", "resourceIdField": "object_id", - "referenceIdFieldInResourceIndex": "_case_id", - "referenceIdFieldInDataIndex": "_case_id" + "referenceIdFieldInResourceIndex": "subject_id", + "referenceIdFieldInDataIndex": "subject_id" }, - "accessibleFieldCheckList": [ - "project_id" - ], - "accessibleValidationField": "project_id" + "accessibleFieldCheckList": ["project"], + "accessibleValidationField": "project" } }, { - "tabTitle": "Measurements", + "tabTitle": "Data Files", "charts": { - "test_method": { - "chartType": "fullPie", - "title": "Test Method" + "file_type": { + "chartType": "stackedBar", + "title": "File Type" }, - "test_result_text": { - "chartType": "fullPie", - "title": "COVID-19 Test Result" - }, - "test_name": { - "chartType": "donut", - "title": "Test Name" + "file_format": { + "chartType": "stackedBar", + "title": "File Format" } }, "filters": { "tabs": [ { - "title": "COVID-19 Tests", - "fields": [ - "test_method", - "test_result_text", - "test_name", - "test_days_from_index", - "project_id" - ] + "title": "File", + "fields": ["subject_id"] } ] }, "table": { "enabled": true, - "fields": [ - "case_ids", - "test_method", - "test_result_text", - "test_name", - "test_days_from_index", - "submitter_id", - "project_id" - ] - }, - "dropdowns": { - "download-table": { - "title": "Download Measurements Metadata Table" - } - }, - "buttons": [ - { - "enabled": true, - "type": "data-json", - "title": "JSON", - "dropdownId": "download-table", - "leftIcon": "datafile", - "rightIcon": "download", - "fileName": "MIDRC_Measurements_table.json" - }, - { - "enabled": true, - "type": "data-tsv", - "title": "TSV", - "dropdownId": "download-table", - "leftIcon": "datafile", - "rightIcon": "download", - "fileName": "MIDRC_Measurements_table.tsv" - }, - { - "enabled": true, - "type": "data-csv", - "title": "CSV", - "dropdownId": "download-table", - "leftIcon": "datafile", - "rightIcon": "download", - "fileName": "MIDRC_Measurements_table.csv" - } - ], - "loginForDownload": true, - "guppyConfig": { - "dataType": "measurement", - "nodeCountTitle": "Measurements", - "fieldMapping": [ - { - "field": "project_id", - "name": "Project ID" - }, - { - "field": "submitter_id", - "name": "Measurement ID" - }, - { - "field": "case_ids", - "name": "Case ID" - } - ], - "accessibleFieldCheckList": [ - "project_id" - ], - "accessibleValidationField": "project_id" - } - }, - { - "tabTitle": "Imaging Studies", - "charts": { - "study_modality": { - "chartType": "fullPie", - "title": "Study Modality" + "detailsConfig": { + "panel": "fileDetails", + "mode": "click", + "idField": "file_name", + "title": "File Details" }, - "sex": { - "chartType": "fullPie", - "title": "Case Sex" - } - }, - "filters": { - "tabs": [ - { - "title": "Study Properties", - "fields": [ - "study_modality", - "study_description", - "age_at_imaging", - "study_year", - "study_year_shifted", - "body_part_examined", - "study_location", - "days_from_study_to_pos_covid_test", - "days_from_study_to_neg_covid_test", - "project_id" - ] - }, - { - "title": "LOINC Properties", - "fields": [ - "loinc_long_common_name", - "loinc_method", - "loinc_system", - "loinc_contrast", - "loinc_code" - ] - }, - { - "title": "Imaging Properties", - "fields": [ - "data_format", - "data_category", - "data_type" - ] - }, - { - "title": "Case Demographics", - "fields": [ - "covid19_positive", - "age_at_index", - "sex", - "race", - "ethnicity", - "zip", - "index_event" - ] - } - ] + "fields": ["subject_id", "file_type", "file_size", "object_id"] }, - "table": { - "enabled": true, - "fields": [ - "submitter_id", - "study_modality", - "study_description", - "body_part_examined", - "age_at_imaging", - "days_to_study", - "study_year", - "study_year_shifted", - "loinc_long_common_name", - "loinc_method", - "loinc_system", - "loinc_contrast", - "loinc_code", - "days_from_study_to_pos_covid_test", - "days_from_study_to_neg_covid_test", - "covid19_positive", - "age_at_index", - "index_event", - "sex", - "race", - "ethnicity", - "zip", - "_ct_series_file_count", - "_dx_series_file_count", - "_cr_series_file_count", - "_mr_series_file_count", - "data_format", - "data_category", - "data_type", - "study_uid", - "case_ids", - "object_id", - "project_id" - ], - "dicomViewerId": "submitter_id", - "linkFields": [ - "submitter_id" - ] - }, - "dropdowns": { - "download-table": { - "title": "Download Imaging Studies Table" - } - }, - "buttons": [ - { - "enabled": true, - "type": "data-json", - "title": "JSON", - "dropdownId": "download-table", - "leftIcon": "datafile", - "rightIcon": "download", - "fileName": "MIDRC_Imaging_Studies_table.json" - }, - { - "enabled": true, - "type": "data-tsv", - "title": "TSV", - "dropdownId": "download-table", - "leftIcon": "datafile", - "rightIcon": "download", - "fileName": "MIDRC_Imaging_Studies_table.tsv" - }, - { - "enabled": true, - "type": "data-csv", - "title": "CSV", - "dropdownId": "download-table", - "leftIcon": "datafile", - "rightIcon": "download", - "fileName": "MIDRC_Imaging_Studies_table.csv" - }, - { - "enabled": true, - "type": "manifest", - "title": "Download File Manifest for Imaging Studies", - "leftIcon": "datafile", - "rightIcon": "download", - "fileName": "MIDRC_imaging_study_manifest.json" - }, - { - "enabled": false, - "type": "export-to-workspace", - "title": "Export to Workspace", - "leftIcon": "datafile", - "rightIcon": "download" - } - ], - "loginForDownload": true, "guppyConfig": { - "dataType": "imaging_study", - "nodeCountTitle": "Imaging Studies", + "dataType": "file", "fieldMapping": [ { - "field": "project_id", - "name": "Project ID" - }, - { - "field": "submitter_id", - "name": "Browse in DICOM viewer" - }, - { - "field": "case_ids", - "name": "Patient ID" - }, - { - "field": "_ct_series_file_count", - "name": "CT Series Count" - }, - { - "field": "_dx_series_file_count", - "name": "DX Series Count" - }, - { - "field": "_cr_series_file_count", - "name": "CR Series Count" - }, - { - "field": "_mr_series_file_count", - "name": "MR Series Count" - }, - { - "field": "loinc_long_common_name", - "name": "Long Common Name (Study description)" - }, - { - "field": "loinc_contrast", - "name": "Contrast" - }, - { - "field": "loinc_code", - "name": "LOINC Code" - }, - { - "field": "loinc_method", - "name": "Method (Modality)" - }, - { - "field": "loinc_system", - "name": "System (Body region)" + "field": "file_id", + "name": "GUID" } ], + "nodeCountTitle": "Files", "manifestMapping": { - "resourceIndexType": "imaging_data_file", - "resourceIdField": "object_id", - "referenceIdFieldInResourceIndex": "_imaging_study_id", - "referenceIdFieldInDataIndex": "_imaging_study_id", - "useFilterForCounts": true - }, - "accessibleFieldCheckList": [ - "project_id" - ], - "accessibleValidationField": "project_id" - } - }, - { - "tabTitle": "Imaging Series", - "charts": { - "sex": { - "chartType": "fullPie", - "title": "Case Sex" - }, - "covid19_positive": { - "chartType": "fullPie", - "title": "Cases that ever had COVID-19" - } - }, - "filters": { - "tabs": [ - { - "title": "Study Properties", - "fields": [ - "study_description", - "age_at_imaging", - "study_year", - "study_year_shifted", - "study_location", - "days_from_study_to_pos_covid_test", - "days_from_study_to_neg_covid_test", - "project_id" - ] - }, - { - "title": "Series Properties", - "fields": [ - "acquisition_type", - "angio_flag", - "contrast_bolus_agent", - "convolution_kernel", - "detector_type", - "diffusion_b_value", - "diffusion_gradient_orientation", - "echo_number", - "echo_time", - "echo_train_length", - "exposure_modulation_type", - "image_type", - "imaged_nucleus", - "imager_pixel_spacing", - "lossy_image_compression", - "manufacturer", - "manufacturer_model_name", - "modality", - "multiframe_images", - "number_of_temporal_positions", - "patient_position", - "pixel_spacing", - "radiopharmaceutical", - "repetition_time", - "scan_options", - "sequence_variant", - "series_description", - "slice_thickness", - "software_version", - "spacing_between_slices", - "spatial_resolution", - "transducer_type", - "view_position", - "data_format", - "data_category", - "data_type" - ] - }, - { - "title": "Case Demographics", - "fields": [ - "covid19_positive", - "age_at_index", - "sex", - "race", - "zip", - "index_event" - ] - } - ] - }, - "table": { - "enabled": true, - "fields": [ - "acquisition_type", - "angio_flag", - "contrast_bolus_agent", - "convolution_kernel", - "detector_type", - "diffusion_b_value", - "diffusion_gradient_orientation", - "echo_number", - "echo_time", - "echo_train_length", - "exposure_modulation_type", - "image_type", - "imaged_nucleus", - "imager_pixel_spacing", - "lossy_image_compression", - "manufacturer", - "manufacturer_model_name", - "modality", - "multiframe_images", - "number_of_temporal_positions", - "patient_position", - "pixel_spacing", - "radiopharmaceutical", - "repetition_time", - "scan_options", - "sequence_variant", - "series_description", - "slice_thickness", - "software_version", - "spacing_between_slices", - "spatial_resolution", - "transducer_type", - "view_position", - "study_description", - "age_at_imaging", - "days_to_study", - "study_year", - "study_year_shifted", - "days_from_study_to_pos_covid_test", - "days_from_study_to_neg_covid_test", - "data_format", - "covid19_positive", - "age_at_index", - "index_event", - "sex", - "race", - "zip", - "data_format", - "data_category", - "data_type", - "series_uid", - "study_uid", - "case_ids", - "object_id", - "submitter_id", - "project_id" - ], - "columns": { - "object_id": { - "title": "Object Id2", - "type": "link", - "accessorPath": "object_id", - "params": { - "baseURL": "/browse/series/" - } - } + "resourceIndexType": "subject", + "resourceIdField": "subject_id", + "referenceIdFieldInResourceIndex": "object_id", + "referenceIdFieldInDataIndex": "object_id" }, - "dicomViewerId": "submitter_id", - "linkFields": [ - "submitter_id" - ] - }, - "dropdowns": { - "download-table": { - "title": "Download Table" - } + "accessibleFieldCheckList": ["subject_id"], + "accessibleValidationField": "subject_id", + "downloadAccessor": "subject_id" }, "buttons": [ { @@ -727,7 +239,9 @@ "dropdownId": "download-table", "leftIcon": "datafile", "rightIcon": "download", - "fileName": "MIDRC_Imaging_Series_table.json" + "actionArgs": { + "filename": "data_table.json" + } }, { "enabled": true, @@ -736,7 +250,9 @@ "dropdownId": "download-table", "leftIcon": "datafile", "rightIcon": "download", - "fileName": "MIDRC_Imaging_Series_table.tsv" + "actionArgs": { + "filename": "data_table.tsv" + } }, { "enabled": true, @@ -745,7 +261,9 @@ "dropdownId": "download-table", "leftIcon": "datafile", "rightIcon": "download", - "fileName": "MIDRC_Imaging_Series_table.csv" + "actionArgs": { + "filename": "data_table.csv" + } }, { "enabled": true, @@ -753,39 +271,11 @@ "title": "Download File Manifest", "leftIcon": "datafile", "rightIcon": "download", - "fileName": "MIDRC_Imaging_Series_manifest.json" - }, - { - "enabled": false, - "type": "export-to-workspace", - "title": "Export to Workspace", - "leftIcon": "datafile", - "rightIcon": "download" + "actionArgs": { + "filename": "data_table_manifest.csv" + } } ], - "loginForDownload": true, - "guppyConfig": { - "dataType": "imaging_data_file", - "nodeCountTitle": "Imaging Series", - "fieldMapping": [ - { - "field": "project_id", - "name": "Project ID" - }, - { - "field": "case_ids", - "name": "Patient ID" - } - ], - "manifestMapping": { - "referenceIdFieldInResourceIndex": "object_id", - "referenceIdFieldInDataIndex": "object_id" - }, - "downloadAccessor": "object_id", - "accessibleFieldCheckList": [ - "project_id" - ], - "accessibleValidationField": "project_id" - } + "loginForDownload": true } ] diff --git a/config/gen3/footer.json b/config/gen3/footer.json index 2429d38..0985b5a 100644 --- a/config/gen3/footer.json +++ b/config/gen3/footer.json @@ -2,13 +2,13 @@ "footerRightLogos": [ [ { - "logo": "/icons/gen3.png", + "logo": "/images/gen3.png", "width": 132, "height": 60, "description": "Gen3 Logo" }, { - "logo": "/icons/createdby.png", + "logo": "/images/createdby.png", "width": 170, "height": 60, "description": "Created by CTDS" diff --git a/config/gen3/login.json b/config/gen3/login.json index 8ea514a..4893104 100644 --- a/config/gen3/login.json +++ b/config/gen3/login.json @@ -11,9 +11,11 @@ ], "bottomContent": [ { - "text": "If you have any questions about access or the registration process, please contact gen3@datacommons.io.", + "text": "If you have any questions about access or the registration process, please contact", + "email": "gen3@datacommons.io", "className": "text-center text-sm" } ], - "image": "images/sideTexture.png" + "image": "images/gene_side_texture.svg", + "showCredentialsLogin" : true } diff --git a/config/gen3/navigation.json b/config/gen3/navigation.json index a6ba423..5f5de63 100644 --- a/config/gen3/navigation.json +++ b/config/gen3/navigation.json @@ -1,5 +1,4 @@ { - "type": "horizontal", "navigation": { "classNames": { "root": "pl-1 mr-6 bg-base-max text-primary opacity-100 hover:opacity-100", @@ -44,7 +43,7 @@ }, { "icon": "gen3:workspace", - "href": "/Workspace", + "href": "/#hostname#workspace/", "name": "Workspace", "tooltip": "Gen3 workspaces are secure data analysis environments in the cloud that can access data from one or more data resources." }, @@ -68,6 +67,6 @@ "name": "Documentation" } ], - "showLogin": true + "loginButtonVisibility": "visible" } } diff --git a/config/gen3/profile.json b/config/gen3/profile.json index df4c924..ab234cf 100644 --- a/config/gen3/profile.json +++ b/config/gen3/profile.json @@ -1,4 +1,5 @@ { + "hasExternalLogins" : true, "resourceTable": { "serviceColors": { "guppy": { diff --git a/config/gen3/session.json b/config/gen3/session.json index fd92023..07a6273 100644 --- a/config/gen3/session.json +++ b/config/gen3/session.json @@ -2,6 +2,6 @@ "sessionConfig" : { "updateSessionTime": 5, "inactiveTimeLimit": 20, - "logoutInactiveUsers": true + "logoutInactiveUsers": false } } diff --git a/config/gen3/submission.json b/config/gen3/submission.json new file mode 100644 index 0000000..18f6c32 --- /dev/null +++ b/config/gen3/submission.json @@ -0,0 +1,30 @@ +{ + "projectTable": { + "columns": [ + { + "name": "Subjects", + "field": "_subject_count", + "errorIfNotAvailable": false, + "valueIfNotAvailable": "n/a" + }, + { + "name": "Studies", + "field": "_study_count", + "errorIfNotAvailable": false, + "valueIfNotAvailable": "n/a" + }, + { + "name": "Aliquots", + "field": "_aliquot_count", + "errorIfNotAvailable": false, + "valueIfNotAvailable": "n/a" + }, + { + "name": "Files", + "field": "_genotyping_array_count", + "errorIfNotAvailable": false, + "valueIfNotAvailable": "n/a" + } + ] + } +} diff --git a/config/gen3/themeColors.json b/config/gen3/themeColors.json index aaa8efd..1376bc3 100644 --- a/config/gen3/themeColors.json +++ b/config/gen3/themeColors.json @@ -1,21 +1,21 @@ { "primary": { - "max": "#ebeeed", - "lightest": "#bdc9c4", - "lighter": "#8fa49a", - "light": "#627e71", - "DEFAULT": "#345948", - "vivid": "#2d6049", - "dark": "#284538", - "darker": "#1d3128", - "darkest": "#111d17", - "min": "#050907" + "max": "#eaeaee", + "lightest": "#babac7", + "lighter": "#8b8ba1", + "light": "#5b5b7a", + "DEFAULT": "#2C2C54", + "vivid": "#26265a", + "dark": "#222241", + "darker": "#18182e", + "darkest": "#0e0e1b", + "min": "#040408" }, "primary-contrast": { "max": "#111111", "lightest": "#111111", "lighter": "#111111", - "light": "#000000", + "light": "#fefefe", "DEFAULT": "#fefefe", "vivid": "#fefefe", "dark": "#fefefe", @@ -24,16 +24,16 @@ "min": "#fefefe" }, "secondary": { - "max": "#f9f2e6", - "lightest": "#ead5ae", - "lighter": "#dcb876", - "light": "#cd9b3e", - "DEFAULT": "#BF7E06", - "vivid": "#c58000", - "dark": "#946205", - "darker": "#694503", - "darkest": "#3e2902", - "min": "#130d99" + "max": "#f7f7f8", + "lightest": "#e3e4e8", + "lighter": "#d0d1d8", + "light": "#bdbec8", + "DEFAULT": "#AAABB8", + "vivid": "#a2a4c0", + "dark": "#84858f", + "darker": "#5e5e65", + "darkest": "#37383c", + "min": "#111112" }, "secondary-contrast": { "max": "#111111", @@ -42,22 +42,22 @@ "light": "#111111", "DEFAULT": "#111111", "vivid": "#111111", - "dark": "#fefefe", + "dark": "#111111", "darker": "#fefefe", "darkest": "#fefefe", "min": "#fefefe" }, "accent": { - "max": "#f4e6e6", - "lightest": "#daadad", - "lighter": "#c07575", - "light": "#a63c3c", - "DEFAULT": "#8C0404", - "vivid": "#900000", - "dark": "#6d0303", - "darker": "#4d0202", - "darkest": "#2d0101", - "min": "#0e6666" + "max": "#ededf3", + "lightest": "#c3c3d8", + "lighter": "#9a9abd", + "light": "#7070a2", + "DEFAULT": "#474787", + "vivid": "#3d3d91", + "dark": "#373769", + "darker": "#27274a", + "darkest": "#17172c", + "min": "#07070d" }, "accent-contrast": { "max": "#111111", @@ -72,16 +72,16 @@ "min": "#fefefe" }, "accent-warm": { - "max": "#eeede6", - "lightest": "#c9c5ad", - "lighter": "#a49c75", - "light": "#7e743c", - "DEFAULT": "#594B04", - "vivid": "#5d4e00", - "dark": "#453a03", - "darker": "#312902", - "darkest": "#1d1801", - "min": "#090766" + "max": "#f3e9e8", + "lightest": "#d9b7b3", + "lighter": "#be857e", + "light": "#a4534a", + "DEFAULT": "#892115", + "vivid": "#911b0d", + "dark": "#6a1a10", + "darker": "#4b120c", + "darkest": "#2d0b07", + "min": "#0e0302" }, "accent-warm-contrast": { "max": "#111111", @@ -96,40 +96,40 @@ "min": "#fefefe" }, "accent-cool": { - "max": "#f4f3e8", - "lightest": "#dbd8b4", - "lighter": "#c2bd81", - "light": "#a9a24d", - "DEFAULT": "#908719", - "vivid": "#988e11", - "dark": "#706913", - "darker": "#4f4a0e", - "darkest": "#2f2c08", - "min": "#0e0d02" + "max": "#e9eef4", + "lightest": "#b8c9db", + "lighter": "#87a4c2", + "light": "#567ea9", + "DEFAULT": "#255990", + "vivid": "#1c5999", + "dark": "#1d4570", + "darker": "#14314f", + "darkest": "#0c1d2f", + "min": "#04090e" }, "accent-cool-contrast": { "max": "#111111", "lightest": "#111111", "lighter": "#111111", - "light": "#111111", - "DEFAULT": "#111111", - "vivid": "#111111", + "light": "#000000", + "DEFAULT": "#fefefe", + "vivid": "#fefefe", "dark": "#fefefe", "darker": "#fefefe", "darkest": "#fefefe", "min": "#fefefe" }, "base": { - "max": "#fafafa", - "lightest": "#eeeeee", - "lighter": "#e3e3e3", - "light": "#d7d7d7", - "DEFAULT": "#CCCCCC", - "vivid": "#d1c7c7", - "dark": "#9e9e9e", - "darker": "#707070", - "darkest": "#424242", - "min": "#141414" + "max": "#fdfdfd", + "lightest": "#f9f9f9", + "lighter": "#f5f5f5", + "light": "#f0f0f0", + "DEFAULT": "#ECECEC", + "vivid": "#eeeaea", + "dark": "#b7b7b7", + "darker": "#828282", + "darkest": "#4d4d4d", + "min": "#181818" }, "base-contrast": { "max": "#111111", @@ -139,7 +139,7 @@ "DEFAULT": "#111111", "vivid": "#111111", "dark": "#111111", - "darker": "#fefefe", + "darker": "#111111", "darkest": "#fefefe", "min": "#fefefe" }, @@ -203,7 +203,7 @@ "darkest": "#535353", "min": "#191919" }, - "tablePallet-contrast": { + "table-contrast": { "max": "#111111", "lightest": "#111111", "lighter": "#111111", diff --git a/config/gen3/themeFonts.json b/config/gen3/themeFonts.json index 1a5a722..f40ccb8 100644 --- a/config/gen3/themeFonts.json +++ b/config/gen3/themeFonts.json @@ -1,5 +1,5 @@ { - "heading": ["Montserrat", "sans-serif"], - "content": ["Noto Sans", "sans-serif"], - "fontFamily": "Montserrat" + "heading": ["Poppins", "sans-serif"], + "content": ["Poppins", "sans-serif"], + "fontFamily": "Poppins" } diff --git a/config/gen3/workspaces.json b/config/gen3/workspaces.json new file mode 100644 index 0000000..0db3279 --- /dev/null +++ b/config/gen3/workspaces.json @@ -0,0 +1,3 @@ +{ + +} diff --git a/package-lock.json b/package-lock.json index 947a9e1..2d0ad96 100644 --- a/package-lock.json +++ b/package-lock.json @@ -8,16 +8,25 @@ "name": "@gen3/commons-portal-app-base", "version": "0.10.31", "dependencies": { - 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"resolved": "https://registry.npmjs.org/uc.micro/-/uc.micro-1.0.6.tgz", - "integrity": "sha512-8Y75pvTYkLJW2hWQHXxoqRgV7qb9B+9vFEtidML+7koHUFapnVJAZ6cKs+Qjz5Aw3aZWHMC6u0wJE3At+nSGwA==" + "version": "2.1.0", + "resolved": "https://registry.npmjs.org/uc.micro/-/uc.micro-2.1.0.tgz", + "integrity": "sha512-ARDJmphmdvUk6Glw7y9DQ2bFkKBHwQHLi2lsaH6PPmz/Ka9sFOBsBluozhDltWmnv9u/cF6Rt87znRTPV+yp/A==", + "license": "MIT" }, "node_modules/ufo": { "version": "1.4.0", @@ -25783,9 +25281,10 @@ } }, "node_modules/use-callback-ref": { - "version": "1.3.1", - "resolved": "https://registry.npmjs.org/use-callback-ref/-/use-callback-ref-1.3.1.tgz", - "integrity": "sha512-Lg4Vx1XZQauB42Hw3kK7JM6yjVjgFmFC5/Ab797s79aARomD2nEErc4mCgM8EZrARLmmbWpi5DGCadmK50DcAQ==", + "version": "1.3.2", + "resolved": "https://registry.npmjs.org/use-callback-ref/-/use-callback-ref-1.3.2.tgz", + "integrity": "sha512-elOQwe6Q8gqZgDA8mrh44qRTQqpIHDcZ3hXTLjBe1i4ph8XpNJnO+aQf3NaG+lriLopI4HMx9VjQLfPQ6vhnoA==", + "license": "MIT", "dependencies": { "tslib": "^2.0.0" }, @@ -25806,6 +25305,7 @@ "version": "1.3.0", "resolved": "https://registry.npmjs.org/use-composed-ref/-/use-composed-ref-1.3.0.tgz", "integrity": "sha512-GLMG0Jc/jiKov/3Ulid1wbv3r54K9HlMW29IWcDFPEqFkSO2nS0MuefWgMJpeHQ9YJeXDL3ZUF+P3jdXlZX/cQ==", + "license": "MIT", "peerDependencies": { "react": "^16.8.0 || ^17.0.0 || ^18.0.0" } @@ -25825,6 +25325,7 @@ "version": "1.1.2", "resolved": "https://registry.npmjs.org/use-isomorphic-layout-effect/-/use-isomorphic-layout-effect-1.1.2.tgz", "integrity": "sha512-49L8yCO3iGT/ZF9QttjwLF/ZD9Iwto5LnH5LmEdk/6cFmXddqi2ulF0edxTwjj+7mqvpVVGQWvbXZdn32wRSHA==", + "license": "MIT", "peerDependencies": { "react": "^16.8.0 || ^17.0.0 || ^18.0.0" }, @@ -25838,6 +25339,7 @@ "version": "1.2.1", "resolved": "https://registry.npmjs.org/use-latest/-/use-latest-1.2.1.tgz", "integrity": "sha512-xA+AVm/Wlg3e2P/JiItTziwS7FK92LWrDB0p+hgXloIMuVCeJJ8v6f0eeHyPZaJrM+usM1FkFfbNCrJGs8A/zw==", + "license": "MIT", "dependencies": { "use-isomorphic-layout-effect": "^1.1.1" }, @@ -25854,6 +25356,7 @@ "version": "1.1.2", "resolved": "https://registry.npmjs.org/use-sidecar/-/use-sidecar-1.1.2.tgz", "integrity": "sha512-epTbsLuzZ7lPClpz2TyryBfztm7m+28DlEv2ZCQ3MDr5ssiwyOwGH/e5F9CkfWjJ1t4clvI58yF822/GUkjjhw==", + "license": "MIT", "dependencies": { "detect-node-es": "^1.1.0", "tslib": "^2.0.0" @@ -25872,9 +25375,10 @@ } }, "node_modules/use-sync-external-store": { - "version": "1.2.0", - "resolved": "https://registry.npmjs.org/use-sync-external-store/-/use-sync-external-store-1.2.0.tgz", - "integrity": "sha512-eEgnFxGQ1Ife9bzYs6VLi8/4X6CObHMw9Qr9tPY43iKwsPw8xE8+EFsf/2cFZ5S3esXgpWgtSCtLNS41F+sKPA==", + "version": "1.2.2", + "resolved": "https://registry.npmjs.org/use-sync-external-store/-/use-sync-external-store-1.2.2.tgz", + "integrity": "sha512-PElTlVMwpblvbNqQ82d2n6RjStvdSoNe9FG28kNfz3WiXilJm4DdNkEzRhCZuIDwY8U08WVihhGR5iRqAwfDiw==", + "license": "MIT", "peerDependencies": { "react": "^16.8.0 || ^17.0.0 || ^18.0.0" } @@ -25892,6 +25396,7 @@ "https://github.com/sponsors/broofa", "https://github.com/sponsors/ctavan" ], + "license": "MIT", "peer": true, "bin": { "uuid": "dist/bin/uuid" @@ -26451,7 +25956,8 @@ "node_modules/vscode-languageserver-types": { "version": "3.17.5", "resolved": "https://registry.npmjs.org/vscode-languageserver-types/-/vscode-languageserver-types-3.17.5.tgz", - "integrity": "sha512-Ld1VelNuX9pdF39h2Hgaeb5hEZM2Z3jUrrMgWQAu82jMtZp7p3vJT3BzToKtZI7NgQssZje5o0zryOrhQvzQAg==" + "integrity": "sha512-Ld1VelNuX9pdF39h2Hgaeb5hEZM2Z3jUrrMgWQAu82jMtZp7p3vJT3BzToKtZI7NgQssZje5o0zryOrhQvzQAg==", + "license": "MIT" }, "node_modules/vt-pbf": { "version": "3.1.3", @@ -26468,6 +25974,7 @@ "version": "2.2.8", "resolved": "https://registry.npmjs.org/w3c-keyname/-/w3c-keyname-2.2.8.tgz", "integrity": "sha512-dpojBhNsCNN7T82Tm7k26A6G9ML3NkhDsnw9n/eoxSRlVBB4CEtIQ/KTCLI2Fwf3ataSXRhYFkQi3SlnFwPvPQ==", + "license": "MIT", "peer": true }, "node_modules/walker": { @@ -26842,9 +26349,10 @@ } }, "node_modules/zrender": { - "version": "5.5.0", - "resolved": "https://registry.npmjs.org/zrender/-/zrender-5.5.0.tgz", - "integrity": "sha512-O3MilSi/9mwoovx77m6ROZM7sXShR/O/JIanvzTwjN3FORfLSr81PsUGd7jlaYOeds9d8tw82oP44+3YucVo+w==", + "version": "5.6.0", + "resolved": "https://registry.npmjs.org/zrender/-/zrender-5.6.0.tgz", + "integrity": "sha512-uzgraf4njmmHAbEUxMJ8Oxg+P3fT04O+9p7gY+wJRVxo8Ge+KmYv0WJev945EH4wFuc4OY2NLXz46FZrWS9xJg==", + "license": "BSD-3-Clause", "dependencies": { "tslib": "2.3.0" } @@ -26852,7 +26360,8 @@ "node_modules/zrender/node_modules/tslib": { "version": "2.3.0", "resolved": "https://registry.npmjs.org/tslib/-/tslib-2.3.0.tgz", - "integrity": "sha512-N82ooyxVNm6h1riLCoyS9e3fuJ3AMG2zIZs2Gd1ATcSFjSA23Q0fzjjZeh0jbJvWVDZ0cJT8yaNNaaXHzueNjg==" + "integrity": "sha512-N82ooyxVNm6h1riLCoyS9e3fuJ3AMG2zIZs2Gd1ATcSFjSA23Q0fzjjZeh0jbJvWVDZ0cJT8yaNNaaXHzueNjg==", + "license": "0BSD" }, "node_modules/zwitch": { "version": "2.0.4", diff --git a/package.json b/package.json index 067316f..e65bcaf 100644 --- a/package.json +++ b/package.json @@ -18,16 +18,25 @@ "getDRSToHostname": "node ./node_modules/@gen3/toolsff/dist/getDRSToHostname.esm.js --out=config/" }, "dependencies": { - "@gen3/frontend": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-frontend-0.10.31.tgz", - "@mantine/core": "^6.0.21", + "@fontsource/montserrat": "^5.0.19", + "@fontsource/source-sans-pro": "^5.0.8", + "@fontsource/poppins": "^5.0.15", + "@gen3/frontend": "^0.10.44", + "@mantine/core": "^7.12.1", + "@mantine/form": "^7.12.1", + "@mantine/hooks": "^7.12.1", + "@mantine/modals": "^7.12.1", + "@mantine/notifications": "^7.12.1", "@mdx-js/loader": "^3.0.0", "@mdx-js/react": "^3.0.0", - "@next/mdx": "^14.2.3", + "@next/mdx": "^14.2.8", "@types/mdx": "^2.0.11", - "cookies-next": "^4.1.1" + "cookies-next": "^4.1.1", + "swr": "^2.2.5", + "@axe-core/react": "^4.10.0" }, "devDependencies": { - "@gen3/toolsff": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-toolsff-0.10.31.tgz", + "@gen3/toolsff": "^0.10.44", "@tailwindcss/aspect-ratio": "^0.4.2", "@tailwindcss/forms": "^0.5.3", "@tailwindcss/line-clamp": "^0.4.2", @@ -42,22 +51,17 @@ "eslint-plugin-react": "^7.30.1", "eslint-plugin-react-hooks": "^4.6.0", "eslint-config-next": "14.2.3", - "next": "^14.2.3", + "next": "^14.2.8", "postcss": "^8.4.29", "postcss-loader": "^7.3.2", "postcss-preset-env": "^8.4.2", "prettier": "^2.7.1", "react": "^18.2.0", "react-dom": "18.2.0", - "tailwindcss": "^3.3.7", - "ts-jest": "^29.0.3", + "tailwindcss": "^3.4.10", + "ts-jest": "^29.1.2", "ts-node": "^10.9.1", - "typescript": "5.0.2", + "typescript": "5.5.4", "@typescript-eslint/eslint-plugin": "^7.12.0" - }, - "peerDependencies": { - "@gen3/core": "https://github.com/uc-cdis/gen3-frontend-framework/releases/download/v0.10.0-alpha/gen3-core-0.10.31.tgz", - "react": "^18.2.0", - "react-dom": "^18.2.0" } } diff --git a/src/lib/CohortBuilder/CustomCellRenderers.tsx b/src/lib/CohortBuilder/CustomCellRenderers.tsx index 01e3c9b..c211e92 100644 --- a/src/lib/CohortBuilder/CustomCellRenderers.tsx +++ b/src/lib/CohortBuilder/CustomCellRenderers.tsx @@ -3,26 +3,26 @@ import { type CellRendererFunctionProps, } from '@gen3/frontend'; import { ActionIcon } from '@mantine/core'; -import React from 'react'; +import React from 'react'; import { FaExternalLinkAlt } from 'react-icons/fa'; - const RenderDiacomLink = ({ cell }: CellRendererFunctionProps) => { - if (cell.getValue() === undefined || cell.getValue() === '') { + if (!cell?.getValue() || cell?.getValue() === '') { return ; } else return ( - - - - - + + + + + ); }; export const registerCohortTableCustomCellRenderers = () => { ExplorerTableCellRendererFactory().registerRenderer( - 'link', 'DiacomLink' , - RenderDiacomLink, + 'link', + 'DiacomLink', + RenderDiacomLink, ); }; diff --git a/src/lib/CohortBuilder/FileDetailsPanel.tsx b/src/lib/CohortBuilder/FileDetailsPanel.tsx index 11323b5..0721c01 100644 --- a/src/lib/CohortBuilder/FileDetailsPanel.tsx +++ b/src/lib/CohortBuilder/FileDetailsPanel.tsx @@ -1,4 +1,3 @@ -/* eslint-disable @typescript-eslint/no-explicit-any */ // TODO remove use of any import { Anchor, Group, @@ -51,7 +50,7 @@ const isQueryResponse = (obj: any): obj is QueryResponse => { const extractData = ( data: QueryResponse, index: string, -): Record => { +): Record => { if (data === undefined || data === null) return {}; if (data.data === undefined || data.data === null) return {}; @@ -106,7 +105,7 @@ export const FileDetailsPanel = ({ const rows = Object.entries(queryData).map(([field, value]) => ( - {field} + {field} {/* @@ -131,8 +130,8 @@ export const FileDetailsPanel = ({ return ( - Results for {id} - + Results for {id} +
@@ -141,7 +140,7 @@ export const FileDetailsPanel = ({ {rows}
Field
- + {({ copied, copy }) => ( { + const { discoveryConfig: config } = useDiscoveryContext(); -interface TagData { - name: string; - category: string; -} + if (!studyPreviewConfig) { + return ; + } + const value = + JSONPath({ + json: row.original, + path: studyPreviewConfig.field, + }) ?? + config?.studyPreviewField?.valueIfNotAvailable ?? + ''; -const DetailsWithTagsRowRenderer = - ( - { row } : RowRenderFunctionParams, - studyPreviewConfig?: StudyDetailsField, - ): ReactElement => { - const { discoveryConfig: config, setStudyDetails } = useDiscoveryContext(); + return ( + +
+ + {value} + - if (!studyPreviewConfig) { - return ; - } - const value = - JSONPath({ - json: row.original, - path: studyPreviewConfig.field, - }) ?? - config?.studyPreviewField?.valueIfNotAvailable ?? - ''; +
+ {row.original?.tags.map((tagInfo: TagData) => { + const { color, display, label } = getTagInfo(tagInfo, config.tags); - return ( - { - setStudyDetails(() => { - return { ...row.original }; - }); - }} - > -
- - {value} - - -
- {row.original?.tags.map(({ name, category }: TagData) => { - const color = getTagColor(category, config.tagCategories); - if (name === '') return null; // no tag - return ( - - {name} - - ); - })} -
+ if (tagInfo.name === '') return null; // no tag + if (!display) return null; + return ( + + {label} + + ); + })}
- - ); - }; +
+ + ); +}; export default DetailsWithTagsRowRenderer; diff --git a/src/lib/Discovery/Filemap.tsx b/src/lib/Discovery/Filemap.tsx index 8c859c2..a7fde6d 100644 --- a/src/lib/Discovery/Filemap.tsx +++ b/src/lib/Discovery/Filemap.tsx @@ -151,7 +151,7 @@ export const FilemapPopup = ({ value }: CellRenderFunctionProps) => { {value[0].length} - +
diff --git a/src/pages/Crosswalk.tsx b/src/pages/Crosswalk.tsx new file mode 100644 index 0000000..6474055 --- /dev/null +++ b/src/pages/Crosswalk.tsx @@ -0,0 +1,7 @@ +import { + CrosswalkPage, + CrosswalkPageGetServerSideProps as getServerSideProps, +} from '@gen3/frontend'; +export default CrosswalkPage; + +export { getServerSideProps }; diff --git a/src/pages/DataDictionary.tsx b/src/pages/DataDictionary.tsx index 0302c07..8f1a9ca 100644 --- a/src/pages/DataDictionary.tsx +++ b/src/pages/DataDictionary.tsx @@ -2,6 +2,7 @@ import { DictionaryPage, DictionaryPageGetServerSideProps as getServerSideProps, } from '@gen3/frontend'; + export default DictionaryPage; export { getServerSideProps }; diff --git a/src/pages/Explorer.tsx b/src/pages/Explorer.tsx index 9923b56..631cff0 100644 --- a/src/pages/Explorer.tsx +++ b/src/pages/Explorer.tsx @@ -3,9 +3,7 @@ import { ExplorerPageGetServerSideProps as getServerSideProps, } from '@gen3/frontend'; -import { registerCohortTableCustomCellRenderers -} from '@/lib/CohortBuilder/CustomCellRenderers'; - +import { registerCohortTableCustomCellRenderers } from '@/lib/CohortBuilder/CustomCellRenderers'; import { registerCustomExplorerDetailsPanels } from '@/lib/CohortBuilder/FileDetailsPanel'; registerCohortTableCustomCellRenderers(); diff --git a/src/pages/SamplePage.tsx b/src/pages/SamplePage.tsx index 1124364..9b652e1 100644 --- a/src/pages/SamplePage.tsx +++ b/src/pages/SamplePage.tsx @@ -1,5 +1,5 @@ import React from 'react'; -import { Text, Paper } from '@mantine/core'; +import { Center, Text, Paper } from '@mantine/core'; import { NavPageLayout, NavPageLayoutProps, @@ -9,21 +9,30 @@ import { GetServerSideProps } from 'next'; const SamplePage = ({ headerProps, footerProps }: NavPageLayoutProps) => { return ( - -
- - This is a example custom page in Gen3 - - You can add your own content here, and add a link to this page in - the navigation bar by editing the config file in{' '} - COMMONSNAME/navigation.json - - + +
+
+ + This is a example custom page in Gen3 + + You can add your own content here, and add a link to this page in + the navigation bar by editing the config file in navigation.json + + +
); }; +// TODO: replace this with a custom getServerSideProps function export const getServerSideProps: GetServerSideProps< NavPageLayoutProps > = async () => { diff --git a/src/pages/_app.tsx b/src/pages/_app.tsx index 6b1c2ed..a0896dc 100644 --- a/src/pages/_app.tsx +++ b/src/pages/_app.tsx @@ -1,5 +1,6 @@ import App, { AppProps, AppContext, AppInitialProps } from 'next/app'; -import { useEffect } from 'react'; +import React, { useEffect } from 'react'; + import { Gen3Provider, TenStringArray, @@ -10,11 +11,23 @@ import { SessionConfiguration, } from '@gen3/frontend'; import '../styles/globals.css'; -import 'graphiql/graphiql.css'; -import '@graphiql/react/dist/style.css'; +// import 'graphiql/graphiql.css'; +//import '@graphiql/react/dist/style.css'; +import '@fontsource/montserrat'; +import '@fontsource/source-sans-pro'; +import '@fontsource/poppins'; + import { GEN3_COMMONS_NAME, setDRSHostnames } from '@gen3/core'; import drsHostnames from '../../config/drsHostnames.json'; +if (typeof window !== 'undefined' && process.env.NODE_ENV !== 'production') { + // eslint-disable-next-line @typescript-eslint/no-var-requires + const ReactDOM = require('react-dom'); + // eslint-disable-next-line @typescript-eslint/no-var-requires + const axe = require('@axe-core/react'); + axe(React, ReactDOM, 1000); +} + interface Gen3AppProps { colors: Record; icons: RegisteredIcons; @@ -87,10 +100,8 @@ Gen3App.getInitialProps = async ( colors: colors, icons: icons as RegisteredIcons, }; - } catch (error: unknown) { - if (error instanceof Error) { - console.error('Provider Wrapper error loading config', error.toString()); - } else console.error('Provider wrapper: unknown error'); + } catch (error: any) { + console.error('Provider Wrapper error loading config', error.toString()); } // return default return { diff --git a/src/pages/_document.tsx b/src/pages/_document.tsx index e1e9cbb..1f1c64a 100644 --- a/src/pages/_document.tsx +++ b/src/pages/_document.tsx @@ -1,13 +1,21 @@ -import { Html, Head, Main, NextScript } from 'next/document'; +import Document, { DocumentContext, DocumentInitialProps } from 'next/document'; +import { ColorSchemeScript } from '@mantine/core'; -export default function Document() { - return ( - - - -
- - - - ); +class Gen3Document extends Document { + static async getInitialProps( + ctx: DocumentContext, + ): Promise { + const initialProps = await Document.getInitialProps(ctx); + return { + ...initialProps, + styles: ( + <> + {initialProps.styles} + + + ), + }; + } } + +export default Gen3Document; diff --git a/src/styles/globals.css b/src/styles/globals.css index 4bc9d67..fd79e06 100644 --- a/src/styles/globals.css +++ b/src/styles/globals.css @@ -1,89 +1,16 @@ -@tailwind base; -@tailwind components; -@tailwind utilities; +@import "tailwindcss/base"; +@import "tailwindcss/components"; -@import '~@fontsource/montserrat/700.css'; -@import '~@fontsource/montserrat/400-italic.css'; -@import '~@fontsource/montserrat/index.css'; -@import '~@fontsource/montserrat/600.css'; -@import '~@fontsource/montserrat/700-italic.css'; -@import '~@fontsource/source-sans-pro/index.css'; +@import '@mantine/core/styles.css'; +@import 'mantine-react-table/styles.css'; -.tooltip { - position: relative; - display: inline-block; - font-size: 0.875rem; - font-weight: normal; - line-height: 1.6em; - letter-spacing: 0.02rem; -} - -.has-tooltip .tooltip { - visibility: hidden; - position: absolute; - z-index: 1000; - top: 90%; - vertical-align: middle; - transform: translateX(-75%); -} - -.has-tooltip .tooltip::before { - content: ''; - position: absolute; - bottom: 100%; - left: 50%; - margin-left: 35%; - border-width: 10px; - border-style: solid; - border-color: transparent transparent gray transparent; -} - -.has-tooltip .tooltip::after { - content: ''; - position: absolute; - bottom: 100%; - left: 50%; - margin-left: 35%; - transform: translateY(1px); - border-width: 10px; - border-style: solid; - border-color: transparent transparent white transparent; -} - -.has-tooltip:hover .tooltip { - visibility: visible; -} - -.h3-typo { - font-size: 1.125rem; - font-weight: 700; - letter-spacing: 0.02rem; -} - -.body-typo { - font-size: 0.875rem; - font-weight: normal; - line-height: 1.6em; - letter-spacing: 0.02rem; -} +@import "tailwindcss/utilities"; +@import '@gen3/frontend/dist/styles.css'; -.navbutton-type { - font-size: 1.125rem; - font-weight: 700; - letter-spacing: 0.02rem; -} @layer base { html { @apply font-heading; } } -.mantine-TableBodyCell-DetailPanel { - border-color: aqua; - border-top: hidden; - padding: 16px; - margin: 16px 0; -} - -@tailwind utilities; @tailwind variants; diff --git a/tailwind.config.js b/tailwind.config.js index 142084b..15fe3cd 100644 --- a/tailwind.config.js +++ b/tailwind.config.js @@ -8,7 +8,6 @@ const themeColors = require(`./config/${GEN3_COMMONS_NAME}/themeColors.json`); const themeFonts = require(`./config/${GEN3_COMMONS_NAME}/themeFonts.json`); module.exports = { - presets: [require('@gen3/frontend/tailwind')], content: [ './src/pages/**/*.{js,ts,jsx,tsx}', './src/components/**/*.{js,ts,jsx,tsx}', From ead264e46050ad354fbd2d54ee69da19f5f7ab26 Mon Sep 17 00:00:00 2001 From: Craig Barnes Date: Wed, 6 Nov 2024 17:56:44 +0100 Subject: [PATCH 08/22] update changed to support v0.10.48 (#46) * update changed to support v0.10.48 * update changed to support v0.10.50 * add next js config flags --- config/gen3/apps/CohortDiscovery.json | 33 + config/gen3/apps/CohortDiversity.json | 53 + config/gen3/explorer.json | 2 +- config/gen3/footer.json | 38 +- config/gen3/navigation.json | 9 +- config/gen3/themeColors.json | 11 +- next.config.js | 13 +- package-lock.json | 2052 ++++++++++++++----------- package.json | 44 +- src/lib/Grafana/grafana.ts | 43 + src/pages/_app.tsx | 25 +- src/pages/_document.tsx | 31 +- src/pages/app/[appName].tsx | 78 + src/styles/globals.css | 3 + 14 files changed, 1491 insertions(+), 944 deletions(-) create mode 100644 config/gen3/apps/CohortDiscovery.json create mode 100644 config/gen3/apps/CohortDiversity.json create mode 100644 src/lib/Grafana/grafana.ts create mode 100644 src/pages/app/[appName].tsx diff --git a/config/gen3/apps/CohortDiscovery.json b/config/gen3/apps/CohortDiscovery.json new file mode 100644 index 0000000..bdb8c75 --- /dev/null +++ b/config/gen3/apps/CohortDiscovery.json @@ -0,0 +1,33 @@ +{ + "name": "CohortDiscovery", + "dataIndexes": [ + { + "dataConfig": { + "dataType": "subject", + "nodeCountTitle": "Cases" + }, + "tabTitle": "Cases", + "tabs": [ + { + "title": "Demographic", + "fields": [ + "gender", + "race", + "ethnicity", + "vital_status" + ] + }, + { + "title": "Study", + "fields": [ + "gender", + "race", + "ethnicity", + "vital_status", + "project" + ] + } + ] + } + ] +} diff --git a/config/gen3/apps/CohortDiversity.json b/config/gen3/apps/CohortDiversity.json new file mode 100644 index 0000000..a56f13a --- /dev/null +++ b/config/gen3/apps/CohortDiversity.json @@ -0,0 +1,53 @@ +{ + "datasets": { + "ground": { + "dataset": "census", + "label": "Census" + }, + "comparison": [ + { + "dataset": "MIDRC", + "label": "MIDRC Data Commons" + } + ] + }, + "fields": [ + "age_at_index", + "sex", + "race", + "ethnicity" + ], + "fieldsConfig": { + "Age_at_Index": { + "title": "Age at Index" + } + }, + "charts": { + "age_at_index": { + "chartType": "bar" + }, + "sex": { + "chartType": "bar" + }, + "race": { + "chartType": "bar" + }, + "ethnicity": { + "chartType": "bar" + } + }, + "comparisonCharts": { + "age_at_index": { + "chartType": "radarComparison" + }, + "sex": { + "chartType": "barComparison" + }, + "race": { + "chartType": "barComparison" + }, + "ethnicity": { + "chartType": "barComparison" + } + } +} diff --git a/config/gen3/explorer.json b/config/gen3/explorer.json index 63f00f3..f856dbf 100644 --- a/config/gen3/explorer.json +++ b/config/gen3/explorer.json @@ -45,7 +45,7 @@ "panel": "default", "mode" : "click", "idField": "submitter_id", - "title": "Details" + "title": "Row Details" }, "pageLimit": { "limit": 10000 diff --git a/config/gen3/footer.json b/config/gen3/footer.json index 0985b5a..4dd0f19 100644 --- a/config/gen3/footer.json +++ b/config/gen3/footer.json @@ -1,18 +1,34 @@ { - "footerRightLogos": [ - [ + "classNames": { + "root": "bg-base-darker", + "layout": "flex items-center justify-end" + }, + "rightSection": { + "columns": [ { - "logo": "/images/gen3.png", - "width": 132, - "height": 60, - "description": "Gen3 Logo" + "rows": [ + { + "Icon": { + "logo": "/icons/gen3.png", + "width": 132, + "height": 60, + "description": "Gen3 Logo" + } + } + ] }, { - "logo": "/images/createdby.png", - "width": 170, - "height": 60, - "description": "Created by CTDS" + "rows": [ + { + "Icon": { + "logo": "/icons/createdby.png", + "width": 170, + "height": 60, + "description": "Created by CTDS" + } + } + ] } ] - ] + } } diff --git a/config/gen3/navigation.json b/config/gen3/navigation.json index 5f5de63..d04260e 100644 --- a/config/gen3/navigation.json +++ b/config/gen3/navigation.json @@ -7,7 +7,8 @@ }, "logo": { "src": "/icons/gen3-dark.svg", - "height": 128, + "width": 120, + "height": 60, "href": "/" }, "items": [ @@ -52,6 +53,12 @@ "href": "/Profile", "name": "Profile", "tooltip": "Create API keys for programmatic data access, and review your authorization privileges to datasets and services." + }, + { + "icon": "gen3:profile", + "href": "/DataLibrary", + "name": "Data Library", + "tooltip": "library of data" } ] }, diff --git a/config/gen3/themeColors.json b/config/gen3/themeColors.json index 1376bc3..8d96529 100644 --- a/config/gen3/themeColors.json +++ b/config/gen3/themeColors.json @@ -214,5 +214,14 @@ "darker": "#111111", "darkest": "#fefefe", "min": "#fefefe" - } + }, + "navigation": { + "footer": "#373A3C", + "topbar_hover": "#FFFFFF", + "light": "#111111", + "DEFAULT": "#111111", + "dark": "#111111", + "darker": "#111111", + "darkest": "#111111", + "min": "#111111"} } diff --git a/next.config.js b/next.config.js index 802ea3b..505bc63 100644 --- a/next.config.js +++ b/next.config.js @@ -17,7 +17,6 @@ const withMDX = require('@next/mdx')({ }, }); - // Next configuration with support for rewrting API to existing common services const nextConfig = { output: 'standalone', @@ -27,18 +26,22 @@ const nextConfig = { transpilePackages: ['@gen3/core', '@gen3/frontend'], webpack: (config) => { config.infrastructureLogging = { - level: "error", + level: 'error', }; return config; }, + experimental: { + esmExternals: true, + instrumentationHook: true, + }, async headers() { return [ { - source: "/(.*)?", // Matches all pages + source: '/(.*)?', // Matches all pages headers: [ { - key: "X-Frame-Options", - value: "SAMEORIGIN", + key: 'X-Frame-Options', + value: 'SAMEORIGIN', }, ], }, diff --git a/package-lock.json b/package-lock.json index 2d0ad96..52b296f 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,37 +1,44 @@ { "name": "@gen3/commons-portal-app-base", - "version": "0.10.31", + "version": "0.10.50", "lockfileVersion": 3, "requires": true, "packages": { "": { "name": "@gen3/commons-portal-app-base", - "version": "0.10.31", + "version": "0.10.50", "dependencies": { - "@axe-core/react": "^4.10.0", "@fontsource/montserrat": "^5.0.19", "@fontsource/poppins": "^5.0.15", "@fontsource/source-sans-pro": "^5.0.8", - "@gen3/frontend": "^0.10.44", - "@mantine/core": "^7.12.1", - "@mantine/form": "^7.12.1", - "@mantine/hooks": "^7.12.1", - "@mantine/modals": "^7.12.1", - "@mantine/notifications": "^7.12.1", + "@gen3/core": "^0.10.50", + "@gen3/frontend": "^0.10.50", + "@grafana/faro-react": "^1.9.1", + "@grafana/faro-web-sdk": "^1.9.1", + "@grafana/faro-web-tracing": "^1.9.1", + "@mantine/core": "^7.13.3", + "@mantine/dates": "^7.13.3", + "@mantine/form": "^7.13.3", + "@mantine/hooks": "^7.13.3", + "@mantine/modals": "^7.13.3", + "@mantine/notifications": "^7.13.3", "@mdx-js/loader": "^3.0.0", "@mdx-js/react": "^3.0.0", - "@next/mdx": "^14.2.8", - "@types/mdx": "^2.0.11", + "@next/mdx": "^14.2.15", "cookies-next": "^4.1.1", + "react": "^18.2.0", + "react-dom": "18.2.0", "swr": "^2.2.5" }, "devDependencies": { - "@gen3/toolsff": "^0.10.44", + "@axe-core/react": "^4.10.0", + "@gen3/toolsff": "^0.10.50", "@tailwindcss/aspect-ratio": "^0.4.2", "@tailwindcss/forms": "^0.5.3", "@tailwindcss/line-clamp": "^0.4.2", "@tailwindcss/typography": "^0.5.7", "@types/lodash": "^4.14.202", + "@types/mdx": "^2.0.11", "@types/react": "^18.2.21", "@types/react-dom": "^18.2.7", "@typescript-eslint/eslint-plugin": "^7.12.0", @@ -42,17 +49,20 @@ "eslint-plugin-jsx-a11y": "^6.6.1", "eslint-plugin-react": "^7.30.1", "eslint-plugin-react-hooks": "^4.6.0", - "next": "^14.2.8", + "next": "^14.2.15", "postcss": "^8.4.29", + "postcss-import": "^16.1.0", "postcss-loader": "^7.3.2", + "postcss-modules": "^6.0.0", "postcss-preset-env": "^8.4.2", + "postcss-preset-mantine": "^1.17.0", "prettier": "^2.7.1", "react": "^18.2.0", "react-dom": "18.2.0", "tailwindcss": "^3.4.10", "ts-jest": "^29.1.2", "ts-node": "^10.9.1", - "typescript": "5.5.4" + "typescript": "^5.6.2" }, "engines": { "node": ">=20.11.0", @@ -110,6 +120,7 @@ "version": "4.10.0", "resolved": "https://registry.npmjs.org/@axe-core/react/-/react-4.10.0.tgz", "integrity": "sha512-gpFj1+G0zabbd0ZDum1N5FPJtUOfPIfslXNH58WuR7opSK0WTwPJ49ZlYr/Wg2fA4VGI5lfkG5fAZSG9p8ecKw==", + "dev": true, "license": "MPL-2.0", "dependencies": { "axe-core": "~4.10.0", @@ -120,6 +131,7 @@ "version": "4.10.0", "resolved": "https://registry.npmjs.org/axe-core/-/axe-core-4.10.0.tgz", "integrity": "sha512-Mr2ZakwQ7XUAjp7pAwQWRhhK8mQQ6JAaNWSjmjxil0R8BPioMtQsTLOolGYkji1rcL++3dCqZA3zWqpT+9Ew6g==", + "dev": true, "license": "MPL-2.0", "engines": { "node": ">=4" @@ -713,9 +725,10 @@ } }, "node_modules/@babel/runtime": { - "version": "7.24.4", - "resolved": "https://registry.npmjs.org/@babel/runtime/-/runtime-7.24.4.tgz", - "integrity": "sha512-dkxf7+hn8mFBwKjs9bvBlArzLVxVbS8usaPUDd5p2a9JCL9tB8OaOVN1isD4+Xyk4ns89/xeOmbQvgdK7IIVdA==", + "version": "7.25.7", + "resolved": "https://registry.npmjs.org/@babel/runtime/-/runtime-7.25.7.tgz", + "integrity": "sha512-FjoyLe754PMiYsFaN5C94ttGiOmBNYTf6pLr4xXHAT5uctHb092PBszndLDR5XA/jghQvn4n7JMHl7dmTgbm9w==", + "license": "MIT", "dependencies": { "regenerator-runtime": "^0.14.0" }, @@ -1563,15 +1576,6 @@ "postcss": "^8.4" } }, - "node_modules/@emnapi/runtime": { - "version": "0.45.0", - "resolved": "https://registry.npmjs.org/@emnapi/runtime/-/runtime-0.45.0.tgz", - "integrity": "sha512-Txumi3td7J4A/xTTwlssKieHKTGl3j4A1tglBx72auZ49YK7ePY6XZricgIg9mnZT4xPfA+UPCUdnhRuEFDL+w==", - "optional": true, - "dependencies": { - "tslib": "^2.4.0" - } - }, "node_modules/@emotion/is-prop-valid": { "version": "0.8.8", "resolved": "https://registry.npmjs.org/@emotion/is-prop-valid/-/is-prop-valid-0.8.8.tgz", @@ -1710,13 +1714,13 @@ } }, "node_modules/@floating-ui/react": { - "version": "0.26.23", - "resolved": "https://registry.npmjs.org/@floating-ui/react/-/react-0.26.23.tgz", - "integrity": "sha512-9u3i62fV0CFF3nIegiWiRDwOs7OW/KhSUJDNx2MkQM3LbE5zQOY01sL3nelcVBXvX7Ovvo3A49I8ql+20Wg/Hw==", + "version": "0.26.25", + "resolved": "https://registry.npmjs.org/@floating-ui/react/-/react-0.26.25.tgz", + "integrity": "sha512-hZOmgN0NTOzOuZxI1oIrDu3Gcl8WViIkvPMpB4xdd4QD6xAMtwgwr3VPoiyH/bLtRcS1cDnhxLSD1NsMJmwh/A==", "license": "MIT", "dependencies": { - "@floating-ui/react-dom": "^2.1.1", - "@floating-ui/utils": "^0.2.7", + "@floating-ui/react-dom": "^2.1.2", + "@floating-ui/utils": "^0.2.8", "tabbable": "^6.0.0" }, "peerDependencies": { @@ -1725,9 +1729,9 @@ } }, "node_modules/@floating-ui/react-dom": { - "version": "2.1.1", - "resolved": "https://registry.npmjs.org/@floating-ui/react-dom/-/react-dom-2.1.1.tgz", - "integrity": "sha512-4h84MJt3CHrtG18mGsXuLCHMrug49d7DFkU0RMIyshRveBeyV2hmV/pDaF2Uxtu8kgq5r46llp5E5FQiR0K2Yg==", + "version": "2.1.2", + "resolved": "https://registry.npmjs.org/@floating-ui/react-dom/-/react-dom-2.1.2.tgz", + "integrity": "sha512-06okr5cgPzMNBy+Ycse2A6udMi4bqwW/zgBF/rwjcNqWkyr82Mcg8b0vjX8OJpZFy/FKjJmw6wV7t44kK6kW7A==", "license": "MIT", "dependencies": { "@floating-ui/dom": "^1.0.0" @@ -1738,9 +1742,9 @@ } }, "node_modules/@floating-ui/utils": { - "version": "0.2.7", - "resolved": "https://registry.npmjs.org/@floating-ui/utils/-/utils-0.2.7.tgz", - "integrity": "sha512-X8R8Oj771YRl/w+c1HqAC1szL8zWQRwFvgDwT129k9ACdBoud/+/rX9V0qiMl6LWUdP9voC2nDVZYPMQQsb6eA==", + "version": "0.2.8", + "resolved": "https://registry.npmjs.org/@floating-ui/utils/-/utils-0.2.8.tgz", + "integrity": "sha512-kym7SodPp8/wloecOpcmSnWJsK7M0E5Wg8UcFA+uO4B9s5d0ywXOEro/8HM9x0rW+TljRzul/14UYz3TleT3ig==", "license": "MIT" }, "node_modules/@fontsource/montserrat": { @@ -1762,18 +1766,19 @@ "license": "OFL-1.1" }, "node_modules/@gen3/core": { - "version": "0.10.44", - "resolved": "https://registry.npmjs.org/@gen3/core/-/core-0.10.44.tgz", - "integrity": "sha512-V0JOPQnzutViOBfwciGMXvxnE+zR3Vhcut3B0+qtLZRCdY+TEaugtlmYM2q1ykmOrxlOimajs1aPFlcn0mLE0g==", + "version": "0.10.50", + "resolved": "https://registry.npmjs.org/@gen3/core/-/core-0.10.50.tgz", + "integrity": "sha512-EFeGMx5YU02zQAQ7UOsYjLbu6ZAWdGU8CAo9kJHInWxzDvi5vWiWu4gfI99/4/JTppjJ0iZQR4NpNhfrIFl/ew==", "license": "Apache-2.0", - "peer": true, "dependencies": { - "@reduxjs/toolkit": "1.9.5", + "@reduxjs/toolkit": "^2.2.8", "flat": "^6.0.1", "papaparse": "^5.4.1", "queue": "6.0.2", - "react-redux": "^8.1.0", + "react-redux": "^9.1.2", + "redux": "^5.0.1", "redux-persist": "^6.0.0", + "swr": "^2.2.5", "uuid": "^9.0.1" }, "engines": { @@ -1785,23 +1790,49 @@ "react-dom": "^18.2.0" } }, + "node_modules/@gen3/core/node_modules/react-redux": { + "version": "9.1.2", + "resolved": "https://registry.npmjs.org/react-redux/-/react-redux-9.1.2.tgz", + "integrity": "sha512-0OA4dhM1W48l3uzmv6B7TXPCGmokUU4p1M44DGN2/D9a1FjVPukVjER1PcPX97jIg6aUeLq1XJo1IpfbgULn0w==", + "license": "MIT", + "dependencies": { + "@types/use-sync-external-store": "^0.0.3", + "use-sync-external-store": "^1.0.0" + }, + "peerDependencies": { + "@types/react": "^18.2.25", + "react": "^18.0", + "redux": "^5.0.0" + }, + "peerDependenciesMeta": { + "@types/react": { + "optional": true + }, + "redux": { + "optional": true + } + } + }, "node_modules/@gen3/frontend": { - "version": "0.10.44", - "resolved": "https://registry.npmjs.org/@gen3/frontend/-/frontend-0.10.44.tgz", - "integrity": "sha512-E1vrR1BK8tjcXhlVTDm9BssR/Avcv3ucdJUhPCxLDzGiybh46xfcCMUWMEj/rINYXkFM7z5sAlY+LJsev95/KQ==", + "version": "0.10.50", + "resolved": "https://registry.npmjs.org/@gen3/frontend/-/frontend-0.10.50.tgz", + "integrity": "sha512-2aVLgWcBUBB4tjPGBNMHKVY4zIB4IqrlDOVVR8mTjIlgJ3OH63SMUDy8Lc2LdpFv0rfVWJ5U3KbsF8TgUmMEqA==", "license": "Apache-2.0", "dependencies": { "@graphiql/react": "^0.23.1", "@iconify/react": "^4.0.1", - "@mantine/core": "^7.12.1", - "@mantine/form": "^7.12.1", - "@mantine/hooks": "^7.12.1", - "@mantine/modals": "^7.12.1", - "@mantine/notifications": "^7.12.1", + "@kbox-labs/react-echarts": "^1.4.0", + "@mantine/core": "^7.13.3", + "@mantine/dates": "^7.13.3", + "@mantine/form": "^7.13.3", + "@mantine/hooks": "^7.13.3", + "@mantine/modals": "^7.13.3", + "@mantine/notifications": "^7.13.3", "@mdx-js/loader": "^2.1.5", "@mdx-js/mdx": "^2.1.5", "@next/mdx": "^14.1.1", - "@reduxjs/toolkit": "^1.9.5", + "@reduxjs/toolkit": "^2.2.8", + "@tabler/icons-react": "^3.19.0", "@tailwindcss/aspect-ratio": "^0.4.2", "@tailwindcss/forms": "^0.5.3", "@tailwindcss/line-clamp": "^0.4.2", @@ -1816,14 +1847,15 @@ "fetch-retry": "^5.0.6", "file-saver": "^2.0.5", "filesize": "^10.1.1", - "graphiql": "^3.4.1", - "graphql": "^16.8.0", + "graphiql": "^3.7.1", + "graphql": "^16.9.0", "graphql-ws": "^5.14.0", "gray-matter": "^4.0.3", "jose": "^4.15.9", "js-cookie": "^3.0.5", "jsonpath-plus": "^8.0.0", - "mantine-react-table": "^2.0.0-beta.6", + "mantine-react-table": "^2.0.0-beta.7", + "mathjs": "^13.1.1", "minisearch": "^6.3.0", "next": "^14.2.8", "next-compose-plugins": "^2.2.1", @@ -1842,9 +1874,8 @@ "react-table": "^7.8.0", "recharts": "^2.4.3", "remark-gfm": "^4.0.0", - "sharp": "^0.33.2", 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"license": "MIT" + }, "node_modules/tiny-invariant": { "version": "1.3.3", "resolved": "https://registry.npmjs.org/tiny-invariant/-/tiny-invariant-1.3.3.tgz", @@ -24995,6 +25233,15 @@ "url": "https://github.com/sponsors/ljharb" } }, + "node_modules/typed-function": { + "version": "4.2.1", + "resolved": "https://registry.npmjs.org/typed-function/-/typed-function-4.2.1.tgz", + "integrity": "sha512-EGjWssW7Tsk4DGfE+5yluuljS1OGYWiI1J6e8puZz9nTMM51Oug8CD5Zo4gWMsOhq5BI+1bF+rWTm4Vbj3ivRA==", + "license": "MIT", + "engines": { + "node": ">= 18" + } + }, "node_modules/typedarray": { "version": "0.0.6", "resolved": "https://registry.npmjs.org/typedarray/-/typedarray-0.0.6.tgz", @@ -25012,9 +25259,9 @@ } }, "node_modules/typescript": { - "version": "5.5.4", - "resolved": "https://registry.npmjs.org/typescript/-/typescript-5.5.4.tgz", - "integrity": "sha512-Mtq29sKDAEYP7aljRgtPOpTvOfbwRWlS6dPRzwjdE+C0R4brX/GUyhHSecbHMFLNBLcJIPt9nl9yG5TZ1weH+Q==", + "version": "5.6.3", + "resolved": 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"https://registry.npmjs.org/uc.micro/-/uc.micro-2.1.0.tgz", @@ -25397,7 +25670,6 @@ "https://github.com/sponsors/ctavan" ], "license": "MIT", - "peer": true, "bin": { "uuid": "dist/bin/uuid" } @@ -26006,6 +26278,12 @@ "integrity": "sha512-lNR9aAefbGPpHO7AEnY0hCFjz1eTkWCXYvkTRrTHs9qv8zJp+SkVYpzfLIFXQQiG3tVvbNFQgVg2bQS8YGgxyw==", "peer": true }, + "node_modules/web-vitals": { + "version": "4.2.3", + "resolved": "https://registry.npmjs.org/web-vitals/-/web-vitals-4.2.3.tgz", + "integrity": "sha512-/CFAm1mNxSmOj6i0Co+iGFJ58OS4NRGVP+AWS/l509uIK5a1bSoIVaHz/ZumpHTfHSZBpgrJ+wjfpAOrTHok5Q==", + "license": "Apache-2.0" + }, "node_modules/webgl-context": { "version": "2.2.0", "resolved": "https://registry.npmjs.org/webgl-context/-/webgl-context-2.2.0.tgz", @@ -26348,6 +26626,12 @@ "url": "https://github.com/sponsors/sindresorhus" } }, + "node_modules/zone.js": { + "version": "0.14.10", + "resolved": "https://registry.npmjs.org/zone.js/-/zone.js-0.14.10.tgz", + "integrity": "sha512-YGAhaO7J5ywOXW6InXNlLmfU194F8lVgu7bRntUF3TiG8Y3nBK0x1UJJuHUP/e8IyihkjCYqhCScpSwnlaSRkQ==", + "license": "MIT" + }, "node_modules/zrender": { "version": "5.6.0", "resolved": "https://registry.npmjs.org/zrender/-/zrender-5.6.0.tgz", diff --git a/package.json b/package.json index e65bcaf..d7ebe6c 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "@gen3/commons-portal-app-base", - "version": "0.10.31", + "version": "0.10.50", "private": "true", "engines": { "npm": ">=10.2.3", @@ -19,24 +19,30 @@ }, "dependencies": { "@fontsource/montserrat": "^5.0.19", - "@fontsource/source-sans-pro": "^5.0.8", "@fontsource/poppins": "^5.0.15", - "@gen3/frontend": "^0.10.44", - "@mantine/core": "^7.12.1", - "@mantine/form": "^7.12.1", - "@mantine/hooks": "^7.12.1", - "@mantine/modals": "^7.12.1", - "@mantine/notifications": "^7.12.1", + "@fontsource/source-sans-pro": "^5.0.8", + "@gen3/core": "^0.10.50", + "@gen3/frontend": "^0.10.50", + "@grafana/faro-react": "^1.9.1", + "@grafana/faro-web-sdk": "^1.9.1", + "@grafana/faro-web-tracing": "^1.9.1", + "@mantine/core": "^7.13.3", + "@mantine/form": "^7.13.3", + "@mantine/hooks": "^7.13.3", + "@mantine/modals": "^7.13.3", + "@mantine/dates": "^7.13.3", + "@mantine/notifications": "^7.13.3", "@mdx-js/loader": "^3.0.0", "@mdx-js/react": "^3.0.0", - "@next/mdx": "^14.2.8", - "@types/mdx": "^2.0.11", + "@next/mdx": "^14.2.15", "cookies-next": "^4.1.1", - "swr": "^2.2.5", - "@axe-core/react": "^4.10.0" + "react": "^18.2.0", + "react-dom": "18.2.0", + "swr": "^2.2.5" }, "devDependencies": { - "@gen3/toolsff": "^0.10.44", + "@axe-core/react": "^4.10.0", + "@gen3/toolsff": "^0.10.50", "@tailwindcss/aspect-ratio": "^0.4.2", "@tailwindcss/forms": "^0.5.3", "@tailwindcss/line-clamp": "^0.4.2", @@ -44,24 +50,28 @@ "@types/lodash": "^4.14.202", "@types/react": "^18.2.21", "@types/react-dom": "^18.2.7", + "@types/mdx": "^2.0.11", + "@typescript-eslint/eslint-plugin": "^7.12.0", "eslint": "8.57.0", + "eslint-config-next": "14.2.3", "eslint-config-prettier": "^8.8.0", "eslint-plugin-import": "^2.27.5", "eslint-plugin-jsx-a11y": "^6.6.1", "eslint-plugin-react": "^7.30.1", "eslint-plugin-react-hooks": "^4.6.0", - "eslint-config-next": "14.2.3", - "next": "^14.2.8", + "next": "^14.2.15", "postcss": "^8.4.29", + "postcss-import": "^16.1.0", "postcss-loader": "^7.3.2", + "postcss-modules": "^6.0.0", "postcss-preset-env": "^8.4.2", + "postcss-preset-mantine": "^1.17.0", "prettier": "^2.7.1", "react": "^18.2.0", "react-dom": "18.2.0", "tailwindcss": "^3.4.10", "ts-jest": "^29.1.2", "ts-node": "^10.9.1", - "typescript": "5.5.4", - "@typescript-eslint/eslint-plugin": "^7.12.0" + "typescript": "^5.6.2" } } diff --git a/src/lib/Grafana/grafana.ts b/src/lib/Grafana/grafana.ts new file mode 100644 index 0000000..cc0aa51 --- /dev/null +++ b/src/lib/Grafana/grafana.ts @@ -0,0 +1,43 @@ +import { + getWebInstrumentations, + initializeFaro, + ReactIntegration, +} from '@grafana/faro-react'; +import { TracingInstrumentation } from '@grafana/faro-web-tracing'; + +// Get the current, runtime version of the App to surface to Faro +// import packageJson from "../../package.json"; + +export const initGrafanaFaro = () => { + return initializeFaro({ + url: 'https://faro.planx-pla.net/collect', + + app: { + // TODO: Populate with real values. + name: 'gen3-frontend-framework', + // version: packageJson.version, + version: '10.0.0', + environment: 'local', + }, + + instrumentations: [ + // load the mandatory web instrumentation + ...getWebInstrumentations({ + captureConsole: true, + }), + + // add tracing instrumentation which should include the React Profiler + new TracingInstrumentation(), + + new ReactIntegration({ + // In the future, we may choose to integrate with React router instrumentation to + // get deeper metrics on matched routes, navigation types, etc. + // Next/router doesn't seem to be supported which won't give us route metrics. + // + // Reference: https://github.com/grafana/faro-web-sdk/tree/main/packages/react + // + // router: {} + }), + ], + }); +}; diff --git a/src/pages/_app.tsx b/src/pages/_app.tsx index a0896dc..16dfe42 100644 --- a/src/pages/_app.tsx +++ b/src/pages/_app.tsx @@ -1,6 +1,6 @@ import App, { AppProps, AppContext, AppInitialProps } from 'next/app'; -import React, { useEffect } from 'react'; - +import React, { useEffect, useRef } from 'react'; +import { Faro, FaroErrorBoundary, withFaroProfiler } from '@grafana/faro-react'; import { Gen3Provider, TenStringArray, @@ -11,12 +11,10 @@ import { SessionConfiguration, } from '@gen3/frontend'; import '../styles/globals.css'; -// import 'graphiql/graphiql.css'; -//import '@graphiql/react/dist/style.css'; import '@fontsource/montserrat'; import '@fontsource/source-sans-pro'; import '@fontsource/poppins'; - +import { initGrafanaFaro } from '../lib/Grafana/grafana'; import { GEN3_COMMONS_NAME, setDRSHostnames } from '@gen3/core'; import drsHostnames from '../../config/drsHostnames.json'; @@ -49,7 +47,21 @@ const Gen3App = ({ setDRSHostnames(drsHostnames); }, []); + const faroRef = useRef(null); + + useEffect(() => { + // if ( + // process.env.NEXT_PUBLIC_FARO_COLLECTOR_URL && + // process.env.NEXT_PUBLIC_FARO_APP_ENVIRONMENT != "local" && + // !faroRef.current + // ) { + if (!faroRef.current) faroRef.current = initGrafanaFaro(); + // } + }, []); + + return ( + + ); }; @@ -123,4 +136,4 @@ Gen3App.getInitialProps = async ( sessionConfig: {}, }; }; -export default Gen3App; +export default withFaroProfiler(Gen3App); diff --git a/src/pages/_document.tsx b/src/pages/_document.tsx index 1f1c64a..53ff867 100644 --- a/src/pages/_document.tsx +++ b/src/pages/_document.tsx @@ -1,21 +1,16 @@ -import Document, { DocumentContext, DocumentInitialProps } from 'next/document'; +import { Head, Html, Main, NextScript } from 'next/document'; import { ColorSchemeScript } from '@mantine/core'; -class Gen3Document extends Document { - static async getInitialProps( - ctx: DocumentContext, - ): Promise { - const initialProps = await Document.getInitialProps(ctx); - return { - ...initialProps, - styles: ( - <> - {initialProps.styles} - - - ), - }; - } +export default function Document() { + return ( + + + + + +
+ + + + ); } - -export default Gen3Document; diff --git a/src/pages/app/[appName].tsx b/src/pages/app/[appName].tsx new file mode 100644 index 0000000..6ac5ce6 --- /dev/null +++ b/src/pages/app/[appName].tsx @@ -0,0 +1,78 @@ +import React from 'react'; +import { + useCoreSelector, + selectGen3AppByName, + GEN3_COMMONS_NAME, +} from '@gen3/core'; +import { GetServerSideProps } from 'next'; +import { NextRouter, useRouter } from 'next/dist/client/router'; + +import { + NavPageLayout, + NavPageLayoutProps, + getNavPageLayoutPropsFromConfig, + ContentSource, +} from '@gen3/frontend'; + +interface AppConfig extends NavPageLayoutProps { + config?: object; +} + +const AppsPage = ({ headerProps, footerProps, config }: AppConfig) => { + const router = useRouter(); + const appName = getAppName(router); + + const GdcApp = useCoreSelector( + () => selectGen3AppByName(appName), // TODO update ById to ByName + ) as React.ElementType; + + return ( + + {GdcApp && } + + ); +}; + +const getAppName = (router: NextRouter): string => { + const { appName } = router.query; + if (typeof appName === 'string') return appName; + else if (typeof appName === 'object') return appName[0]; + + return 'UNKNOWN_APP_ID'; +}; + +export const getServerSideProps: GetServerSideProps< + NavPageLayoutProps +> = async (context) => { + const appName = context.query.appName as string; + + try { + const config: any = await ContentSource.get( + `config/${GEN3_COMMONS_NAME}/apps/${appName}.json`, + ); + + return { + props: { + ...(await getNavPageLayoutPropsFromConfig()), + config: config, + }, + }; + } catch (err) { + console.error(err); + return { + props: { + ...(await getNavPageLayoutPropsFromConfig()), + config: undefined, + }, + }; + } +}; + +export default AppsPage; diff --git a/src/styles/globals.css b/src/styles/globals.css index fd79e06..94981ea 100644 --- a/src/styles/globals.css +++ b/src/styles/globals.css @@ -7,6 +7,9 @@ @import "tailwindcss/utilities"; @import '@gen3/frontend/dist/styles.css'; +@import 'graphiql/graphiql.css'; +@import '@graphiql/react/dist/style.css'; + @layer base { html { @apply font-heading; From 60e349a70ec80645bf7e6b99a0baafd74f14e027 Mon Sep 17 00:00:00 2001 From: Craig Barnes Date: Wed, 13 Nov 2024 21:19:57 +0100 Subject: [PATCH 09/22] Chore/0.10.51 (#49) * update v0.10.51 * update version to v0.10.51 * update Dockerfile --- .env.production | 3 - Dockerfile | 9 +- config/icons/color.json | 28 +++++++ config/icons/color/analysis.svg | 1 + config/icons/color/discovery.svg | 1 + config/icons/color/explorer.svg | 1 + config/icons/color/profile.svg | 1 + config/icons/color/workspaces.svg | 1 + config/icons/dataDictionary.json | 58 +++++++++++++ config/icons/download.svg | 1 - config/icons/gen3.json | 55 ++++++++++-- config/icons/gen3/aiSearch.svg | 3 + config/icons/{ => gen3}/analysis.svg | 0 config/icons/{ => gen3}/bar-chart.svg | 0 config/icons/gen3/chevron-contract.svg | 1 + config/icons/{ => gen3}/chevron-down.svg | 0 config/icons/gen3/chevron-expand.svg | 1 + config/icons/gen3/comparison.svg | 1 + config/icons/{ => gen3}/datafile.svg | 0 config/icons/{ => gen3}/dictionary.svg | 0 config/icons/gen3/download.svg | 1 + config/icons/{ => gen3}/exploration.svg | 0 config/icons/{ => gen3}/gen3-dark.svg | 0 config/icons/{ => gen3}/gen3.svg | 0 config/icons/gen3/jupyter.svg | 90 ++++++++++++++++++++ config/icons/gen3/loginArrowCircle.svg | 1 + config/icons/{ => gen3}/loginCircle.svg | 0 config/icons/gen3/not-found.svg | 94 +++++++++++++++++++++ config/icons/gen3/notebook.svg | 92 +++++++++++++++++++++ config/icons/gen3/open_in_modal.svg | 3 + config/icons/{ => gen3}/profile.svg | 0 config/icons/{ => gen3}/query.svg | 0 config/icons/gen3/upload.svg | 1 + config/icons/{ => gen3}/user.svg | 0 config/icons/{ => gen3}/workspace.svg | 0 config/icons/upload.svg | 17 ---- config/icons/workspace.json | 24 ++++++ config/icons/workspace/galaxy.svg | 19 +++++ config/icons/workspace/jupyter.svg | 90 ++++++++++++++++++++ config/icons/workspace/rlogo.svg | 17 ++++ config/icons/workspace/rstudio.svg | 12 +++ package-lock.json | 101 +++++++++++++++++++---- package.json | 8 +- src/lib/content/loadContent.ts | 40 +++++++++ src/pages/Analysis.tsx | 7 ++ src/pages/NotebookLite.tsx | 7 ++ src/pages/Workspace.tsx | 6 +- src/pages/_app.tsx | 98 +++++++++++----------- src/pages/no-workspace-access.tsx | 7 ++ 49 files changed, 794 insertions(+), 106 deletions(-) delete mode 100644 .env.production create mode 100644 config/icons/color.json create mode 100644 config/icons/color/analysis.svg create mode 100644 config/icons/color/discovery.svg create mode 100644 config/icons/color/explorer.svg create mode 100644 config/icons/color/profile.svg create mode 100644 config/icons/color/workspaces.svg create mode 100644 config/icons/dataDictionary.json delete mode 100644 config/icons/download.svg create mode 100644 config/icons/gen3/aiSearch.svg rename config/icons/{ => gen3}/analysis.svg (100%) rename config/icons/{ => gen3}/bar-chart.svg (100%) create mode 100644 config/icons/gen3/chevron-contract.svg rename config/icons/{ => gen3}/chevron-down.svg (100%) create mode 100644 config/icons/gen3/chevron-expand.svg create mode 100644 config/icons/gen3/comparison.svg rename config/icons/{ => gen3}/datafile.svg (100%) rename config/icons/{ => gen3}/dictionary.svg (100%) create mode 100644 config/icons/gen3/download.svg rename config/icons/{ => gen3}/exploration.svg (100%) rename config/icons/{ => gen3}/gen3-dark.svg (100%) rename config/icons/{ => gen3}/gen3.svg (100%) create mode 100644 config/icons/gen3/jupyter.svg create mode 100644 config/icons/gen3/loginArrowCircle.svg rename config/icons/{ => gen3}/loginCircle.svg (100%) create mode 100644 config/icons/gen3/not-found.svg create mode 100644 config/icons/gen3/notebook.svg create mode 100644 config/icons/gen3/open_in_modal.svg rename config/icons/{ => gen3}/profile.svg (100%) rename config/icons/{ => gen3}/query.svg (100%) create mode 100755 config/icons/gen3/upload.svg rename config/icons/{ => gen3}/user.svg (100%) rename config/icons/{ => gen3}/workspace.svg (100%) delete mode 100755 config/icons/upload.svg create mode 100644 config/icons/workspace.json create mode 100644 config/icons/workspace/galaxy.svg create mode 100644 config/icons/workspace/jupyter.svg create mode 100644 config/icons/workspace/rlogo.svg create mode 100644 config/icons/workspace/rstudio.svg create mode 100644 src/lib/content/loadContent.ts create mode 100644 src/pages/Analysis.tsx create mode 100644 src/pages/NotebookLite.tsx create mode 100644 src/pages/no-workspace-access.tsx diff --git a/.env.production b/.env.production deleted file mode 100644 index fa20fe4..0000000 --- a/.env.production +++ /dev/null @@ -1,3 +0,0 @@ -GEN3_COMMONS_NAME=gen3 -NEXT_PUBLIC_GEN3_API=https://localhost/ -NEXT_PUBLIC_GEN3_DOMAIN=https://localhost/ diff --git a/Dockerfile b/Dockerfile index 928e5c0..3b80b98 100644 --- a/Dockerfile +++ b/Dockerfile @@ -31,17 +31,10 @@ RUN apt-get update && apt-get install -y --no-install-recommends \ && npm install -g npm@10.5.2 RUN addgroup --system --gid 1001 nextjs && adduser --system --uid 1001 nextjs -COPY ./package.json ./package-lock.json ./ -COPY ./package-lock.json ./ +COPY ./package.json ./package-lock.json ./next.config.js ./tsconfig.json ./.env.development ./tailwind.config.js ./postcss.config.js ./ COPY ./src ./src COPY ./public ./public COPY ./config ./config -COPY ./next.config.js ./ -COPY ./tsconfig.json ./ -COPY ./.env.development ./ -COPY ./.env.production ./ -COPY ./tailwind.config.js ./ -COPY ./postcss.config.js ./ RUN npm ci RUN npm install \ "@swc/core" \ diff --git a/config/icons/color.json b/config/icons/color.json new file mode 100644 index 0000000..852e13a --- /dev/null +++ b/config/icons/color.json @@ -0,0 +1,28 @@ +{ + "prefix": "color", + "lastModified": 1724107947, + "icons": { + "analysis": { + "body": "", + "width": 64, + "height": 64 + }, + "discovery": { + "body": "", + "top": -13 + }, + "explorer": { + "body": "", + "left": -30, + "width": 511 + }, + "profile": { + "body": "" + }, + "workspaces": { + "body": "" + } + }, + "width": 512, + "height": 512 +} diff --git a/config/icons/color/analysis.svg b/config/icons/color/analysis.svg new file mode 100644 index 0000000..877872c --- /dev/null +++ b/config/icons/color/analysis.svg @@ -0,0 +1 @@ + diff --git a/config/icons/color/discovery.svg b/config/icons/color/discovery.svg new file mode 100644 index 0000000..2fe223a --- /dev/null +++ b/config/icons/color/discovery.svg @@ -0,0 +1 @@ + diff --git a/config/icons/color/explorer.svg b/config/icons/color/explorer.svg new file mode 100644 index 0000000..7cfe2d0 --- /dev/null +++ b/config/icons/color/explorer.svg @@ -0,0 +1 @@ + diff --git a/config/icons/color/profile.svg b/config/icons/color/profile.svg new file mode 100644 index 0000000..0fb33c8 --- /dev/null +++ b/config/icons/color/profile.svg @@ -0,0 +1 @@ + diff --git a/config/icons/color/workspaces.svg b/config/icons/color/workspaces.svg new file mode 100644 index 0000000..d073469 --- /dev/null +++ b/config/icons/color/workspaces.svg @@ -0,0 +1 @@ + diff --git a/config/icons/dataDictionary.json b/config/icons/dataDictionary.json new file mode 100644 index 0000000..7bf0508 --- /dev/null +++ b/config/icons/dataDictionary.json @@ -0,0 +1,58 @@ +{ + "prefix": "dataDictionary", + "lastModified": 1724107947, + "icons": { + "dictionary-icon-administrative": { + "body": "" + }, + "dictionary-icon-analysis": { + "body": "", + "height": 21 + }, + "dictionary-icon-biospecimen": { + "body": "" + }, + "dictionary-icon-clinical": { + "body": "" + }, + "dictionary-icon-clinical-assessment": { + "body": "" + }, + "dictionary-icon-data-file": { + "body": "" + }, + "dictionary-icon-data-observations": { + "body": "" + }, + "dictionary-icon-default": { + "body": "", + "height": 21 + }, + "dictionary-icon-experimental-methods": { + "body": "" + }, + "dictionary-icon-imaging": { + "body": "" + }, + "dictionary-icon-index-file": { + "body": "" + }, + "dictionary-icon-medical-history": { + "body": "" + }, + "dictionary-icon-metadata": { + "body": "" + }, + "dictionary-icon-notation": { + "body": "" + }, + "dictionary-icon-study-administration": { + "body": "" + }, + "dictionary-icon-subject-characteristics": { + "body": "" + } + }, + "width": 20, + "height": 20 +} diff --git a/config/icons/download.svg b/config/icons/download.svg deleted file mode 100644 index 22a2656..0000000 --- a/config/icons/download.svg +++ /dev/null @@ -1 +0,0 @@ - diff --git a/config/icons/gen3.json b/config/icons/gen3.json index 21bf7fd..26d4c6a 100644 --- a/config/icons/gen3.json +++ b/config/icons/gen3.json @@ -1,7 +1,12 @@ { "prefix": "gen3", - "lastModified": 1718898014, + "lastModified": 1730144270, "icons": { + "aisearch": { + "body": "", + "width": 682.67, + "height": 682.67 + }, "analysis": { "body": "", "width": 35, @@ -14,11 +19,26 @@ "width": 315.67, "height": 294.22 }, + "chevron-contract": { + "body": "", + "width": 16, + "height": 16 + }, "chevron-down": { "body": "", "width": 58.026, "height": 58.026 }, + "chevron-expand": { + "body": "", + "width": 512, + "height": 512 + }, + "comparison": { + "body": "", + "width": 512, + "height": 512 + }, "datafile": { "body": "", "width": 60, @@ -79,8 +99,13 @@ "dictionary-icon-subject-characteristics": { "body": "" }, + "dot": { + "body": "", + "width": 256, + "height": 256 + }, "download": { - "body": "", + "body": "", "width": 24, "height": 24 }, @@ -99,11 +124,31 @@ "width": 195, "height": 89 }, + "jupyter": { + "body": "", + "width": 44, + "height": 51 + }, + "loginarrowcircle": { + "body": "", + "width": 30, + "height": 30 + }, "logincircle": { "body": "", "width": 24, "height": 24 }, + "open-in-modal": { + "body": "", + "width": 24, + "height": 24 + }, + "notebook": { + "body": "", + "width": 682.667, + "height": 682.667 + }, "profile": { "body": "", "width": 512.001, @@ -115,9 +160,9 @@ "height": 511.999 }, "upload": { - "body": "", - "width": 512, - "height": 512 + "body": "", + "width": 24, + "height": 24 }, "user": { "body": "", diff --git a/config/icons/gen3/aiSearch.svg b/config/icons/gen3/aiSearch.svg new file mode 100644 index 0000000..593075d --- /dev/null +++ b/config/icons/gen3/aiSearch.svg @@ -0,0 +1,3 @@ + + + diff --git a/config/icons/analysis.svg b/config/icons/gen3/analysis.svg similarity index 100% rename from config/icons/analysis.svg rename to config/icons/gen3/analysis.svg diff --git a/config/icons/bar-chart.svg b/config/icons/gen3/bar-chart.svg similarity index 100% rename from config/icons/bar-chart.svg rename to config/icons/gen3/bar-chart.svg diff --git a/config/icons/gen3/chevron-contract.svg b/config/icons/gen3/chevron-contract.svg new file mode 100644 index 0000000..7b16d84 --- /dev/null +++ b/config/icons/gen3/chevron-contract.svg @@ -0,0 +1 @@ + diff --git a/config/icons/chevron-down.svg b/config/icons/gen3/chevron-down.svg similarity index 100% rename from config/icons/chevron-down.svg rename to config/icons/gen3/chevron-down.svg diff --git a/config/icons/gen3/chevron-expand.svg b/config/icons/gen3/chevron-expand.svg new file mode 100644 index 0000000..3a62aae --- /dev/null +++ b/config/icons/gen3/chevron-expand.svg @@ -0,0 +1 @@ + diff --git a/config/icons/gen3/comparison.svg b/config/icons/gen3/comparison.svg new file mode 100644 index 0000000..114deb8 --- /dev/null +++ b/config/icons/gen3/comparison.svg @@ -0,0 +1 @@ + diff --git a/config/icons/datafile.svg b/config/icons/gen3/datafile.svg similarity index 100% rename from config/icons/datafile.svg rename to config/icons/gen3/datafile.svg diff --git a/config/icons/dictionary.svg b/config/icons/gen3/dictionary.svg similarity index 100% rename from config/icons/dictionary.svg rename to config/icons/gen3/dictionary.svg diff --git a/config/icons/gen3/download.svg b/config/icons/gen3/download.svg new file mode 100644 index 0000000..cab0abb --- /dev/null +++ b/config/icons/gen3/download.svg @@ -0,0 +1 @@ + diff --git a/config/icons/exploration.svg b/config/icons/gen3/exploration.svg similarity index 100% rename from config/icons/exploration.svg rename to config/icons/gen3/exploration.svg diff --git a/config/icons/gen3-dark.svg b/config/icons/gen3/gen3-dark.svg similarity index 100% rename from config/icons/gen3-dark.svg rename to config/icons/gen3/gen3-dark.svg diff --git a/config/icons/gen3.svg b/config/icons/gen3/gen3.svg similarity index 100% rename from config/icons/gen3.svg rename to config/icons/gen3/gen3.svg diff --git a/config/icons/gen3/jupyter.svg b/config/icons/gen3/jupyter.svg new file mode 100644 index 0000000..d0fa7e4 --- /dev/null +++ b/config/icons/gen3/jupyter.svg @@ -0,0 +1,90 @@ + +Group.svg +Created using Figma 0.90 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/config/icons/gen3/loginArrowCircle.svg b/config/icons/gen3/loginArrowCircle.svg new file mode 100644 index 0000000..1fed0b6 --- /dev/null +++ b/config/icons/gen3/loginArrowCircle.svg @@ -0,0 +1 @@ + diff --git a/config/icons/loginCircle.svg b/config/icons/gen3/loginCircle.svg similarity index 100% rename from config/icons/loginCircle.svg rename to config/icons/gen3/loginCircle.svg diff --git a/config/icons/gen3/not-found.svg b/config/icons/gen3/not-found.svg new file mode 100644 index 0000000..68b0144 --- /dev/null +++ b/config/icons/gen3/not-found.svg @@ -0,0 +1,94 @@ + + + + 404 + Created with Sketch. + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/config/icons/gen3/notebook.svg b/config/icons/gen3/notebook.svg new file mode 100644 index 0000000..db56476 --- /dev/null +++ b/config/icons/gen3/notebook.svg @@ -0,0 +1,92 @@ + + + + diff --git a/config/icons/gen3/open_in_modal.svg b/config/icons/gen3/open_in_modal.svg new file mode 100644 index 0000000..3462c34 --- /dev/null +++ b/config/icons/gen3/open_in_modal.svg @@ -0,0 +1,3 @@ + + + diff --git a/config/icons/profile.svg b/config/icons/gen3/profile.svg similarity index 100% rename from config/icons/profile.svg rename to config/icons/gen3/profile.svg diff --git a/config/icons/query.svg b/config/icons/gen3/query.svg similarity index 100% rename from config/icons/query.svg rename to config/icons/gen3/query.svg diff --git a/config/icons/gen3/upload.svg b/config/icons/gen3/upload.svg new file mode 100755 index 0000000..8859cfc --- /dev/null +++ b/config/icons/gen3/upload.svg @@ -0,0 +1 @@ + diff --git a/config/icons/user.svg b/config/icons/gen3/user.svg similarity index 100% rename from config/icons/user.svg rename to config/icons/gen3/user.svg diff --git a/config/icons/workspace.svg b/config/icons/gen3/workspace.svg similarity index 100% rename from config/icons/workspace.svg rename to config/icons/gen3/workspace.svg diff --git a/config/icons/upload.svg b/config/icons/upload.svg deleted file mode 100755 index c2e2c5f..0000000 --- a/config/icons/upload.svg +++ /dev/null @@ -1,17 +0,0 @@ - - - - - - - - - - - - - - diff --git a/config/icons/workspace.json b/config/icons/workspace.json new file mode 100644 index 0000000..8cd2718 --- /dev/null +++ b/config/icons/workspace.json @@ -0,0 +1,24 @@ +{ + "prefix": "workspace", + "lastModified": 1724107947, + "icons": { + "galaxy": { + "body": "", + "width": 66 + }, + "jupyter": { + "body": "", + "width": 44, + "height": 51 + }, + "rlogo": { + "body": "", + "width": 75 + }, + "rstudio": { + "body": "", + "width": 50 + } + }, + "height": 50 +} diff --git a/config/icons/workspace/galaxy.svg b/config/icons/workspace/galaxy.svg new file mode 100644 index 0000000..3f743b7 --- /dev/null +++ b/config/icons/workspace/galaxy.svg @@ -0,0 +1,19 @@ + + + + Group Copy + Created with Sketch. + + + + + + + + + + + + + + diff --git a/config/icons/workspace/jupyter.svg b/config/icons/workspace/jupyter.svg new file mode 100644 index 0000000..ce0006b --- /dev/null +++ b/config/icons/workspace/jupyter.svg @@ -0,0 +1,90 @@ + +Group.svg +Created using Figma 0.90 + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/config/icons/workspace/rlogo.svg b/config/icons/workspace/rlogo.svg new file mode 100644 index 0000000..712b113 --- /dev/null +++ b/config/icons/workspace/rlogo.svg @@ -0,0 +1,17 @@ + + + + + + + + + + + + + + + + + diff --git a/config/icons/workspace/rstudio.svg b/config/icons/workspace/rstudio.svg new file mode 100644 index 0000000..32930f9 --- /dev/null +++ b/config/icons/workspace/rstudio.svg @@ -0,0 +1,12 @@ + + + + RStudio-Logo-flat + Created with Sketch. + + + + + + + diff --git a/package-lock.json b/package-lock.json index 52b296f..c2a6121 100644 --- a/package-lock.json +++ b/package-lock.json @@ -11,8 +11,8 @@ "@fontsource/montserrat": "^5.0.19", "@fontsource/poppins": "^5.0.15", "@fontsource/source-sans-pro": "^5.0.8", - "@gen3/core": "^0.10.50", - "@gen3/frontend": "^0.10.50", + "@gen3/core": "^0.10.51", + "@gen3/frontend": "^0.10.51", "@grafana/faro-react": "^1.9.1", "@grafana/faro-web-sdk": "^1.9.1", "@grafana/faro-web-tracing": "^1.9.1", @@ -32,7 +32,7 @@ }, "devDependencies": { "@axe-core/react": "^4.10.0", - "@gen3/toolsff": "^0.10.50", + "@gen3/toolsff": "^0.10.51", "@tailwindcss/aspect-ratio": "^0.4.2", "@tailwindcss/forms": "^0.5.3", "@tailwindcss/line-clamp": "^0.4.2", @@ -1766,9 +1766,9 @@ "license": "OFL-1.1" }, "node_modules/@gen3/core": { - "version": "0.10.50", - "resolved": "https://registry.npmjs.org/@gen3/core/-/core-0.10.50.tgz", - "integrity": "sha512-EFeGMx5YU02zQAQ7UOsYjLbu6ZAWdGU8CAo9kJHInWxzDvi5vWiWu4gfI99/4/JTppjJ0iZQR4NpNhfrIFl/ew==", + "version": "0.10.51", + "resolved": "https://registry.npmjs.org/@gen3/core/-/core-0.10.51.tgz", + "integrity": "sha512-F8SGoJld8j61t4Pn/gXLDVnKy+iR3+4fUTpDVk8v8Y22JyziTkGaldDX8FjswPaLS0ZPPpu4Lx+qPSNQquxclw==", "license": "Apache-2.0", "dependencies": { "@reduxjs/toolkit": "^2.2.8", @@ -1783,7 +1783,7 @@ }, "engines": { "node": ">=20.11.0", - "npm": ">=10.2.3" + "npm": ">=10.8.2" }, "peerDependencies": { "react": "^18.2.0", @@ -1814,12 +1814,13 @@ } }, "node_modules/@gen3/frontend": { - "version": "0.10.50", - "resolved": "https://registry.npmjs.org/@gen3/frontend/-/frontend-0.10.50.tgz", - "integrity": "sha512-2aVLgWcBUBB4tjPGBNMHKVY4zIB4IqrlDOVVR8mTjIlgJ3OH63SMUDy8Lc2LdpFv0rfVWJ5U3KbsF8TgUmMEqA==", + "version": "0.10.51", + "resolved": "https://registry.npmjs.org/@gen3/frontend/-/frontend-0.10.51.tgz", + "integrity": "sha512-R9+LrlIM21JvaBsCHb9rGKQPHkWCumFk7Z9guPoWbTQSIpdvzPxDtijSSHUpMUxFuoeYmcC3lqNB8w6DPNJjmw==", "license": "Apache-2.0", "dependencies": { "@graphiql/react": "^0.23.1", + "@hello-pangea/dnd": "^17.0.0", "@iconify/react": "^4.0.1", "@kbox-labs/react-echarts": "^1.4.0", "@mantine/core": "^7.13.3", @@ -1956,9 +1957,9 @@ } }, "node_modules/@gen3/toolsff": { - "version": "0.10.50", - "resolved": "https://registry.npmjs.org/@gen3/toolsff/-/toolsff-0.10.50.tgz", - "integrity": "sha512-7U3KT/vR6tQ1FfPPDv+1EIcu13ydTACImlt1W+kqFOalrUbGTuJGIVWhsn05U3Rde8nb/KpwYXkDlwNfB+eI+g==", + "version": "0.10.51", + "resolved": "https://registry.npmjs.org/@gen3/toolsff/-/toolsff-0.10.51.tgz", + "integrity": "sha512-EIYWazQmjLoH30/Pmcr5LkV4ICf3Rvw7SxFi/RzsVLrmzc/T6xxee9lNBiY1O6JaCjQ1G5aaK2JmPVLeUTbQAA==", "dev": true, "license": "Apache-2.0", "dependencies": { @@ -1973,7 +1974,7 @@ }, "engines": { "node": ">=20.11.0", - "npm": ">=10.2.3" + "npm": ">=10.8.2" }, "peerDependencies": { "ts-node": "^10.9.2" @@ -2117,6 +2118,48 @@ "react-dom": "^16 || ^17 || ^18" } }, + "node_modules/@hello-pangea/dnd": { + "version": "17.0.0", + "resolved": "https://registry.npmjs.org/@hello-pangea/dnd/-/dnd-17.0.0.tgz", + "integrity": "sha512-LDDPOix/5N0j5QZxubiW9T0M0+1PR0rTDWeZF5pu1Tz91UQnuVK4qQ/EjY83Qm2QeX0eM8qDXANfDh3VVqtR4Q==", + "license": "Apache-2.0", + "dependencies": { + "@babel/runtime": "^7.25.6", + "css-box-model": "^1.2.1", + "memoize-one": "^6.0.0", + "raf-schd": "^4.0.3", + "react-redux": "^9.1.2", + "redux": "^5.0.1", + "use-memo-one": "^1.1.3" + }, + "peerDependencies": { + "react": "^18.0.0", + "react-dom": "^18.0.0" + } + }, + "node_modules/@hello-pangea/dnd/node_modules/react-redux": { + "version": "9.1.2", + "resolved": "https://registry.npmjs.org/react-redux/-/react-redux-9.1.2.tgz", + "integrity": "sha512-0OA4dhM1W48l3uzmv6B7TXPCGmokUU4p1M44DGN2/D9a1FjVPukVjER1PcPX97jIg6aUeLq1XJo1IpfbgULn0w==", + "license": "MIT", + "dependencies": { + "@types/use-sync-external-store": "^0.0.3", + "use-sync-external-store": "^1.0.0" + }, + "peerDependencies": { + "@types/react": "^18.2.25", + "react": "^18.0", + "redux": "^5.0.0" + }, + "peerDependenciesMeta": { + "@types/react": { + "optional": true + }, + "redux": { + "optional": true + } + } + }, "node_modules/@humanwhocodes/config-array": { "version": "0.11.14", "resolved": "https://registry.npmjs.org/@humanwhocodes/config-array/-/config-array-0.11.14.tgz", @@ -8375,6 +8418,15 @@ "postcss": "^8.4" } }, + "node_modules/css-box-model": { + "version": "1.2.1", + "resolved": "https://registry.npmjs.org/css-box-model/-/css-box-model-1.2.1.tgz", + "integrity": "sha512-a7Vr4Q/kd/aw96bnJG332W9V9LkJO69JRcaCYDUqjp6/z0w6VcZjgAcTbgFxEPfBgdnAwlh3iwu+hLopa+flJw==", + "license": "MIT", + "dependencies": { + "tiny-invariant": "^1.0.6" + } + }, "node_modules/css-font": { "version": "1.2.0", "resolved": "https://registry.npmjs.org/css-font/-/css-font-1.2.0.tgz", @@ -17622,6 +17674,12 @@ "integrity": "sha512-Lf+9+2r+Tdp5wXDXC4PcIBjTDtq4UKjCPMQhKIuzpJNW0b96kVqSwW0bT7FhRSfmAiFYgP+SCRvdrDozfh0U5w==", "license": "MIT" }, + "node_modules/memoize-one": { + "version": "6.0.0", + "resolved": "https://registry.npmjs.org/memoize-one/-/memoize-one-6.0.0.tgz", + "integrity": "sha512-rkpe71W0N0c0Xz6QD0eJETuWAJGnJ9afsl1srmwPrI+yBCkge5EycXXbYRyvL29zZVUWQCY7InPRCv3GDXuZNw==", + "license": "MIT" + }, "node_modules/merge-stream": { "version": "2.0.0", "resolved": "https://registry.npmjs.org/merge-stream/-/merge-stream-2.0.0.tgz", @@ -21435,6 +21493,12 @@ "performance-now": "^2.1.0" } }, + "node_modules/raf-schd": { + "version": "4.0.3", + "resolved": "https://registry.npmjs.org/raf-schd/-/raf-schd-4.0.3.tgz", + "integrity": "sha512-tQkJl2GRWh83ui2DiPTJz9wEiMN20syf+5oKfB03yYP7ioZcJwsIK8FjrtLwH1m7C7e+Tt2yYBlrOpdT+dyeIQ==", + "license": "MIT" + }, "node_modules/randombytes": { "version": "2.1.0", "resolved": "https://registry.npmjs.org/randombytes/-/randombytes-2.1.0.tgz", @@ -25625,6 +25689,15 @@ } } }, + "node_modules/use-memo-one": { + "version": "1.1.3", + "resolved": "https://registry.npmjs.org/use-memo-one/-/use-memo-one-1.1.3.tgz", + "integrity": "sha512-g66/K7ZQGYrI6dy8GLpVcMsBp4s17xNkYJVSMvTEevGy3nDxHOfE6z8BVE22+5G5x7t3+bhzrlTDB7ObrEE0cQ==", + "license": "MIT", + "peerDependencies": { + "react": "^16.8.0 || ^17.0.0 || ^18.0.0" + } + }, "node_modules/use-sidecar": { "version": "1.1.2", "resolved": "https://registry.npmjs.org/use-sidecar/-/use-sidecar-1.1.2.tgz", diff --git a/package.json b/package.json index d7ebe6c..8198464 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "@gen3/commons-portal-app-base", - "version": "0.10.50", + "version": "0.10.51", "private": "true", "engines": { "npm": ">=10.2.3", @@ -21,8 +21,8 @@ "@fontsource/montserrat": "^5.0.19", "@fontsource/poppins": "^5.0.15", "@fontsource/source-sans-pro": "^5.0.8", - "@gen3/core": "^0.10.50", - "@gen3/frontend": "^0.10.50", + "@gen3/core": "^0.10.51", + "@gen3/frontend": "^0.10.51", "@grafana/faro-react": "^1.9.1", "@grafana/faro-web-sdk": "^1.9.1", "@grafana/faro-web-tracing": "^1.9.1", @@ -42,7 +42,7 @@ }, "devDependencies": { "@axe-core/react": "^4.10.0", - "@gen3/toolsff": "^0.10.50", + "@gen3/toolsff": "^0.10.51", "@tailwindcss/aspect-ratio": "^0.4.2", "@tailwindcss/forms": "^0.5.3", "@tailwindcss/line-clamp": "^0.4.2", diff --git a/src/lib/content/loadContent.ts b/src/lib/content/loadContent.ts new file mode 100644 index 0000000..d4c2c8d --- /dev/null +++ b/src/lib/content/loadContent.ts @@ -0,0 +1,40 @@ +import { + ContentSource, + Fonts, + RegisteredIcons, + TenStringArray, +} from '@gen3/frontend'; +import { GEN3_COMMONS_NAME } from '@gen3/core'; + +export const loadContent = async () => { + const modals = await ContentSource.get( + `config/${GEN3_COMMONS_NAME}/modals.json`, + ); + const session = await ContentSource.get( + `config/${GEN3_COMMONS_NAME}/session.json`, + ); + + const fonts = await ContentSource.get( + `config/${GEN3_COMMONS_NAME}/themeFonts.json`, + ); + + const themeColors = await ContentSource.get( + `config/${GEN3_COMMONS_NAME}/themeColors.json`, + ); + + const colors = Object.fromEntries( + Object.entries(themeColors).map(([key, values]) => [ + key, + Object.values(values) as TenStringArray, + ]), + ); + + const icons = await ContentSource.getAll(`config/icons/`, '\\.json'); + return { + modalsConfig: modals, + sessionConfig: session, + themeFonts: fonts as Fonts, + colors: colors, + icons: icons as RegisteredIcons[], + }; +}; diff --git a/src/pages/Analysis.tsx b/src/pages/Analysis.tsx new file mode 100644 index 0000000..21e809d --- /dev/null +++ b/src/pages/Analysis.tsx @@ -0,0 +1,7 @@ +import { + AnalysisPage, + AnalysisPageGetServerSideProps as getServerSideProps, + } from '@gen3/frontend'; + export default AnalysisPage; + + export { getServerSideProps }; diff --git a/src/pages/NotebookLite.tsx b/src/pages/NotebookLite.tsx new file mode 100644 index 0000000..6c163d2 --- /dev/null +++ b/src/pages/NotebookLite.tsx @@ -0,0 +1,7 @@ +import { + NotebookLitePage, + NotebookLitePageGetStaticProps as getStaticProps, +} from '@gen3/frontend'; + +export default NotebookLitePage; +export { getStaticProps }; diff --git a/src/pages/Workspace.tsx b/src/pages/Workspace.tsx index e4578be..96f172e 100644 --- a/src/pages/Workspace.tsx +++ b/src/pages/Workspace.tsx @@ -1,7 +1,7 @@ import { - WorkspacesPage, - WorkspacesPageGetServerSideProps as getServerSideProps, + WorkspacePage, + WorkspacePageGetServerSideProps as getServerSideProps, } from '@gen3/frontend'; -export default WorkspacesPage; +export default WorkspacePage; export { getServerSideProps }; diff --git a/src/pages/_app.tsx b/src/pages/_app.tsx index 16dfe42..e4b1b57 100644 --- a/src/pages/_app.tsx +++ b/src/pages/_app.tsx @@ -1,34 +1,48 @@ import App, { AppProps, AppContext, AppInitialProps } from 'next/app'; import React, { useEffect, useRef } from 'react'; + import { Faro, FaroErrorBoundary, withFaroProfiler } from '@grafana/faro-react'; + +import { initGrafanaFaro } from '../lib/Grafana/grafana'; + import { Gen3Provider, TenStringArray, type ModalsConfig, - ContentSource, RegisteredIcons, Fonts, SessionConfiguration, + registerCohortDiscoveryApp, + registerCohortDiversityApp, + registerCohortBuilderDefaultPreviewRenderers, + registerExplorerDefaultCellRenderers, } from '@gen3/frontend'; + +import { registerCohortTableCustomCellRenderers } from '@/lib/CohortBuilder/CustomCellRenderers'; +import { registerCustomExplorerDetailsPanels } from '@/lib/CohortBuilder/FileDetailsPanel'; + import '../styles/globals.css'; import '@fontsource/montserrat'; import '@fontsource/source-sans-pro'; import '@fontsource/poppins'; -import { initGrafanaFaro } from '../lib/Grafana/grafana'; -import { GEN3_COMMONS_NAME, setDRSHostnames } from '@gen3/core'; + +import { setDRSHostnames } from '@gen3/core'; import drsHostnames from '../../config/drsHostnames.json'; +import { loadContent } from '../lib/content/loadContent'; if (typeof window !== 'undefined' && process.env.NODE_ENV !== 'production') { - // eslint-disable-next-line @typescript-eslint/no-var-requires + // eslint-disable-next-line @typescript-eslint/no-var-requires, @typescript-eslint/no-require-imports const ReactDOM = require('react-dom'); - // eslint-disable-next-line @typescript-eslint/no-var-requires + // eslint-disable-next-line @typescript-eslint/no-var-requires, @typescript-eslint/no-require-imports const axe = require('@axe-core/react'); axe(React, ReactDOM, 1000); } +// TODO fix app registration + interface Gen3AppProps { colors: Record; - icons: RegisteredIcons; + icons: Array; themeFonts: Fonts; modalsConfig: ModalsConfig; sessionConfig: SessionConfiguration; @@ -50,27 +64,33 @@ const Gen3App = ({ const faroRef = useRef(null); useEffect(() => { + // one time init // if ( // process.env.NEXT_PUBLIC_FARO_COLLECTOR_URL && // process.env.NEXT_PUBLIC_FARO_APP_ENVIRONMENT != "local" && // !faroRef.current // ) { if (!faroRef.current) faroRef.current = initGrafanaFaro(); + registerCohortDiscoveryApp(); + registerCohortDiversityApp(); + registerExplorerDefaultCellRenderers(); + registerCohortBuilderDefaultPreviewRenderers(); + registerCohortTableCustomCellRenderers(); + registerCustomExplorerDetailsPanels(); // } }, []); - return ( - - - + + + ); }; @@ -82,36 +102,10 @@ Gen3App.getInitialProps = async ( const ctx = await App.getInitialProps(context); try { - const modals = await ContentSource.get( - `config/${GEN3_COMMONS_NAME}/modals.json`, - ); - const session = await ContentSource.get( - `config/${GEN3_COMMONS_NAME}/session.json`, - ); - - const fonts = await ContentSource.get( - `config/${GEN3_COMMONS_NAME}/themeFonts.json`, - ); - - const themeColors = await ContentSource.get( - `config/${GEN3_COMMONS_NAME}/themeColors.json`, - ); - - const colors = Object.fromEntries( - Object.entries(themeColors).map(([key, values]) => [ - key, - Object.values(values) as TenStringArray, - ]), - ); - - const icons = await ContentSource.get('config/icons/gen3.json'); + const res = await loadContent(); return { ...ctx, - modalsConfig: modals, - sessionConfig: session, - themeFonts: fonts as Fonts, - colors: colors, - icons: icons as RegisteredIcons, + ...res, }; } catch (error: any) { console.error('Provider Wrapper error loading config', error.toString()); @@ -125,13 +119,15 @@ Gen3App.getInitialProps = async ( content: ['Poppins', 'sans-serif'], fontFamily: 'Poppins', }, - icons: { - prefix: 'gen3', - lastModified: 0, - icons: {}, - width: 0, - height: 0, - }, + icons: [ + { + prefix: 'gen3', + lastModified: 0, + icons: {}, + width: 0, + height: 0, + }, + ], modalsConfig: {}, sessionConfig: {}, }; diff --git a/src/pages/no-workspace-access.tsx b/src/pages/no-workspace-access.tsx new file mode 100644 index 0000000..b9c9aa9 --- /dev/null +++ b/src/pages/no-workspace-access.tsx @@ -0,0 +1,7 @@ +import { + WorkspaceNoAccessPage, + WorkspaceNoAccessPageServerSideProps as getServerSideProps, +} from '@gen3/frontend'; +export default WorkspaceNoAccessPage; + +export { getServerSideProps }; From f55e1884c64238f2516642fb861c86f5d257cf1a Mon Sep 17 00:00:00 2001 From: Craig Barnes Date: Sun, 8 Dec 2024 12:21:38 -0500 Subject: [PATCH 10/22] Update to Gen3.2 Release 0.10.55 (#53) Update to Gen3.2 v0.10.55 --- .nvmrc | 2 +- package-lock.json | 661 +++++++++++++++++++++++++------------- package.json | 10 +- src/pages/DataLibrary.tsx | 8 + src/pages/_app.tsx | 22 +- 5 files changed, 454 insertions(+), 249 deletions(-) create mode 100644 src/pages/DataLibrary.tsx diff --git a/.nvmrc b/.nvmrc index 209e3ef..016e34b 100644 --- a/.nvmrc +++ b/.nvmrc @@ -1 +1 @@ -20 +v20.17.0 diff --git a/package-lock.json b/package-lock.json index c2a6121..f1f0c52 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,18 +1,18 @@ { "name": "@gen3/commons-portal-app-base", - "version": "0.10.50", + "version": "0.10.55", "lockfileVersion": 3, "requires": true, "packages": { "": { "name": "@gen3/commons-portal-app-base", - "version": "0.10.50", + "version": "0.10.55", "dependencies": { "@fontsource/montserrat": "^5.0.19", "@fontsource/poppins": "^5.0.15", "@fontsource/source-sans-pro": "^5.0.8", - "@gen3/core": "^0.10.51", - "@gen3/frontend": "^0.10.51", + "@gen3/core": "^0.10.55", + "@gen3/frontend": "^0.10.55", "@grafana/faro-react": "^1.9.1", "@grafana/faro-web-sdk": "^1.9.1", "@grafana/faro-web-tracing": "^1.9.1", @@ -26,13 +26,15 @@ "@mdx-js/react": "^3.0.0", "@next/mdx": "^14.2.15", "cookies-next": "^4.1.1", + "idb": "^8.0.0", + "jsonpath-plus": "^10.2.0", "react": "^18.2.0", "react-dom": "18.2.0", "swr": "^2.2.5" }, "devDependencies": { "@axe-core/react": "^4.10.0", - "@gen3/toolsff": "^0.10.51", + "@gen3/toolsff": "^0.10.55", "@tailwindcss/aspect-ratio": "^0.4.2", "@tailwindcss/forms": "^0.5.3", "@tailwindcss/line-clamp": "^0.4.2", @@ -95,23 +97,25 @@ } }, "node_modules/@antfu/install-pkg": { - "version": "0.1.1", - "resolved": "https://registry.npmjs.org/@antfu/install-pkg/-/install-pkg-0.1.1.tgz", - "integrity": "sha512-LyB/8+bSfa0DFGC06zpCEfs89/XoWZwws5ygEa5D+Xsm3OfI+aXQ86VgVG7Acyef+rSZ5HE7J8rrxzrQeM3PjQ==", + "version": "0.4.1", + "resolved": "https://registry.npmjs.org/@antfu/install-pkg/-/install-pkg-0.4.1.tgz", + "integrity": "sha512-T7yB5QNG29afhWVkVq7XeIMBa5U/vs9mX69YqayXypPRmYzUmzwnYltplHmPtZ4HPCn+sQKeXW8I47wCbuBOjw==", "dev": true, + "license": "MIT", "dependencies": { - "execa": "^5.1.1", - "find-up": "^5.0.0" + "package-manager-detector": "^0.2.0", + "tinyexec": "^0.3.0" }, "funding": { "url": "https://github.com/sponsors/antfu" } }, "node_modules/@antfu/utils": { - "version": "0.7.7", - "resolved": "https://registry.npmjs.org/@antfu/utils/-/utils-0.7.7.tgz", - "integrity": "sha512-gFPqTG7otEJ8uP6wrhDv6mqwGWYZKNvAcCq6u9hOj0c+IKCEsY4L1oC9trPq2SaWIzAfHvqfBDxF591JkMf+kg==", + "version": "0.7.10", + "resolved": "https://registry.npmjs.org/@antfu/utils/-/utils-0.7.10.tgz", + "integrity": "sha512-+562v9k4aI80m1+VuMHehNJWLOFjBnXn3tdOitzD0il5b7smkSBal4+a3oKiQTbrwMmN/TBUMDvbdoWDehgOww==", "dev": true, + "license": "MIT", "funding": { "url": "https://github.com/sponsors/antfu" } @@ -1766,9 +1770,9 @@ 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+24909,8 @@ "version": "4.0.0", "resolved": "https://registry.npmjs.org/yallist/-/yallist-4.0.0.tgz", "integrity": "sha512-3wdGidZyq5PB084XLES5TpOSRA3wjXAlIWMhum2kRcv/41Sn2emQ0dycQW4uZXLejwKvg6EsvbdlVL+FYEct7A==", - "dev": true + "dev": true, + "license": "ISC" }, "node_modules/terser": { "version": "5.28.1", @@ -24910,6 +25074,13 @@ "resolved": "https://registry.npmjs.org/tinycolor2/-/tinycolor2-1.6.0.tgz", "integrity": "sha512-XPaBkWQJdsf3pLKJV9p4qN/S+fm2Oj8AIPo1BTUhg5oxkvm9+SVEGFdhyOz7tTdUTfvxMiAs4sp6/eZO2Ew+pw==" }, + "node_modules/tinyexec": { + "version": "0.3.1", + "resolved": "https://registry.npmjs.org/tinyexec/-/tinyexec-0.3.1.tgz", + "integrity": "sha512-WiCJLEECkO18gwqIp6+hJg0//p23HXp4S+gGtAKu3mI2F2/sXC4FvHvXvB0zJVVaTPhx1/tOwdbRsa1sOBIKqQ==", + "dev": true, + "license": "MIT" + }, "node_modules/tinyqueue": { "version": "2.0.3", "resolved": "https://registry.npmjs.org/tinyqueue/-/tinyqueue-2.0.3.tgz", @@ -24979,12 +25150,6 @@ "topoquantize": "bin/topoquantize" } }, - "node_modules/tr46": { - "version": "0.0.3", - "resolved": "https://registry.npmjs.org/tr46/-/tr46-0.0.3.tgz", - "integrity": "sha512-N3WMsuqV66lT30CrXNbEjx4GEwlow3v6rr4mCcv6prnfwhS01rkgyFdjPNBYd9br7LpXV1+Emh01fHnq2Gdgrw==", - "dev": true - }, "node_modules/trim-lines": { "version": "3.0.1", "resolved": "https://registry.npmjs.org/trim-lines/-/trim-lines-3.0.1.tgz", @@ -25369,10 +25534,11 @@ "license": "MIT" }, "node_modules/ufo": { - "version": "1.4.0", - "resolved": "https://registry.npmjs.org/ufo/-/ufo-1.4.0.tgz", - "integrity": "sha512-Hhy+BhRBleFjpJ2vchUNN40qgkh0366FWJGqVLYBHev0vpHTrXSA0ryT+74UiW6KWsldNurQMKGqCm1M2zBciQ==", - "dev": true + "version": "1.5.4", + "resolved": "https://registry.npmjs.org/ufo/-/ufo-1.5.4.tgz", + "integrity": "sha512-UsUk3byDzKd04EyoZ7U4DOlxQaD14JUKQl6/P7wiX4FNvUfm3XL246n9W5AmqwW5RSFJ27NAuM0iLscAOYUiGQ==", + "dev": true, + "license": "MIT" }, "node_modules/unbox-primitive": { "version": "1.0.2", @@ -25389,6 +25555,16 @@ "url": "https://github.com/sponsors/ljharb" } }, + "node_modules/undici": { + "version": "6.21.0", + "resolved": "https://registry.npmjs.org/undici/-/undici-6.21.0.tgz", + "integrity": "sha512-BUgJXc752Kou3oOIuU1i+yZZypyZRqNPW0vqoMPl8VaoalSfeR0D8/t4iAS3yirs79SSMTxTag+ZC86uswv+Cw==", + "dev": true, + "license": "MIT", + "engines": { + "node": ">=18.17" + } + }, "node_modules/undici-types": { "version": "5.26.5", "resolved": "https://registry.npmjs.org/undici-types/-/undici-types-5.26.5.tgz", @@ -26366,12 +26542,6 @@ "get-canvas-context": "^1.0.1" } }, - "node_modules/webidl-conversions": { - "version": "3.0.1", - "resolved": "https://registry.npmjs.org/webidl-conversions/-/webidl-conversions-3.0.1.tgz", - "integrity": "sha512-2JAn3z8AR6rjK8Sm8orRC0h/bcl/DqL7tRPdGZ4I1CjdF+EaMLmYxBHyXuKL849eucPFhvBoxMsflfOb8kxaeQ==", - "dev": true - }, "node_modules/webpack": { "version": "5.90.3", "resolved": "https://registry.npmjs.org/webpack/-/webpack-5.90.3.tgz", @@ -26428,14 +26598,40 @@ "node": ">=10.13.0" } }, - "node_modules/whatwg-url": { - "version": "5.0.0", - "resolved": "https://registry.npmjs.org/whatwg-url/-/whatwg-url-5.0.0.tgz", - "integrity": "sha512-saE57nupxk6v3HY35+jzBwYa0rKSy0XR8JSxZPwgLr7ys0IBzhGviA1/TUGJLmSVqs8pb9AnvICXEuOHLprYTw==", + "node_modules/whatwg-encoding": { + "version": "3.1.1", + "resolved": "https://registry.npmjs.org/whatwg-encoding/-/whatwg-encoding-3.1.1.tgz", + "integrity": "sha512-6qN4hJdMwfYBtE3YBTTHhoeuUrDBPZmbQaxWAqSALV/MeEnR5z1xd8UKud2RAkFoPkmB+hli1TZSnyi84xz1vQ==", + "dev": true, + "license": "MIT", + "dependencies": { + "iconv-lite": "0.6.3" + }, + "engines": { + "node": ">=18" + } + }, + "node_modules/whatwg-encoding/node_modules/iconv-lite": { + "version": "0.6.3", + "resolved": "https://registry.npmjs.org/iconv-lite/-/iconv-lite-0.6.3.tgz", + "integrity": "sha512-4fCk79wshMdzMp2rH06qWrJE4iolqLhCUH+OiuIgU++RB0+94NlDL81atO7GX55uUKueo0txHNtvEyI6D7WdMw==", "dev": true, + "license": "MIT", "dependencies": { - "tr46": "~0.0.3", - "webidl-conversions": "^3.0.0" + "safer-buffer": ">= 2.1.2 < 3.0.0" + }, + "engines": { + "node": ">=0.10.0" + } + }, + "node_modules/whatwg-mimetype": { + "version": "4.0.0", + "resolved": "https://registry.npmjs.org/whatwg-mimetype/-/whatwg-mimetype-4.0.0.tgz", + "integrity": "sha512-QaKxh0eNIi2mE9p2vEdzfagOKHCcj1pJ56EEHGQOVxp8r9/iszLUUV7v89x9O1p/T+NlTM5W7jW6+cz4Fq1YVg==", + "dev": true, + "license": "MIT", + "engines": { + "node": ">=18" } }, "node_modules/which": { @@ -26673,6 +26869,7 @@ "resolved": "https://registry.npmjs.org/yauzl/-/yauzl-2.10.0.tgz", "integrity": "sha512-p4a9I6X6nu6IhoGmBqAcbJy1mlC4j27vEPZX9F4L4/vZT3Lyq1VkFHw/V/PUcB9Buo+DG3iHkT0x3Qya58zc3g==", "dev": true, + "license": "MIT", "dependencies": { "buffer-crc32": "~0.2.3", "fd-slicer": "~1.1.0" diff --git a/package.json b/package.json index 8198464..d1fb732 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "@gen3/commons-portal-app-base", - "version": "0.10.51", + "version": "0.10.55", "private": "true", "engines": { "npm": ">=10.2.3", @@ -21,11 +21,13 @@ "@fontsource/montserrat": "^5.0.19", "@fontsource/poppins": "^5.0.15", "@fontsource/source-sans-pro": "^5.0.8", - "@gen3/core": "^0.10.51", - "@gen3/frontend": "^0.10.51", + "jsonpath-plus": "^10.2.0", + "@gen3/core": "^0.10.55", + "@gen3/frontend": "^0.10.55", "@grafana/faro-react": "^1.9.1", "@grafana/faro-web-sdk": "^1.9.1", "@grafana/faro-web-tracing": "^1.9.1", + "idb": "^8.0.0", "@mantine/core": "^7.13.3", "@mantine/form": "^7.13.3", "@mantine/hooks": "^7.13.3", @@ -42,7 +44,7 @@ }, "devDependencies": { "@axe-core/react": "^4.10.0", - "@gen3/toolsff": "^0.10.51", + "@gen3/toolsff": "^0.10.55", "@tailwindcss/aspect-ratio": "^0.4.2", "@tailwindcss/forms": "^0.5.3", "@tailwindcss/line-clamp": "^0.4.2", diff --git a/src/pages/DataLibrary.tsx b/src/pages/DataLibrary.tsx new file mode 100644 index 0000000..23c665c --- /dev/null +++ b/src/pages/DataLibrary.tsx @@ -0,0 +1,8 @@ +import { + DataLibraryPage, + DataLibraryPageGetServerSideProps as getServerSideProps, +} from '@gen3/frontend'; + +export default DataLibraryPage; + +export { getServerSideProps }; diff --git a/src/pages/_app.tsx b/src/pages/_app.tsx index e4b1b57..9b45c99 100644 --- a/src/pages/_app.tsx +++ b/src/pages/_app.tsx @@ -12,7 +12,7 @@ import { RegisteredIcons, Fonts, SessionConfiguration, - registerCohortDiscoveryApp, + // registerCohortDiscoveryApp, registerCohortDiversityApp, registerCohortBuilderDefaultPreviewRenderers, registerExplorerDefaultCellRenderers, @@ -38,8 +38,6 @@ if (typeof window !== 'undefined' && process.env.NODE_ENV !== 'production') { axe(React, ReactDOM, 1000); } -// TODO fix app registration - interface Gen3AppProps { colors: Record; icons: Array; @@ -49,14 +47,14 @@ interface Gen3AppProps { } const Gen3App = ({ - Component, - pageProps, - colors, - icons, - themeFonts, - sessionConfig, - modalsConfig, -}: AppProps & Gen3AppProps) => { + Component, + pageProps, + colors, + icons, + themeFonts, + sessionConfig, + modalsConfig, + }: AppProps & Gen3AppProps) => { useEffect(() => { setDRSHostnames(drsHostnames); }, []); @@ -71,7 +69,7 @@ const Gen3App = ({ // !faroRef.current // ) { if (!faroRef.current) faroRef.current = initGrafanaFaro(); - registerCohortDiscoveryApp(); + // registerCohortDiscoveryApp(); registerCohortDiversityApp(); registerExplorerDefaultCellRenderers(); registerCohortBuilderDefaultPreviewRenderers(); From 496e95eace47d425b4c3ea156879b5c60b9fab77 Mon Sep 17 00:00:00 2001 From: Albert Snow Date: Sun, 8 Dec 2024 11:22:00 -0600 Subject: [PATCH 11/22] Update CustomCellRenderers.tsx to DicomLink (#52) --- src/lib/CohortBuilder/CustomCellRenderers.tsx | 6 +++--- 1 file changed, 3 insertions(+), 3 deletions(-) diff --git a/src/lib/CohortBuilder/CustomCellRenderers.tsx b/src/lib/CohortBuilder/CustomCellRenderers.tsx index c211e92..0258645 100644 --- a/src/lib/CohortBuilder/CustomCellRenderers.tsx +++ b/src/lib/CohortBuilder/CustomCellRenderers.tsx @@ -6,7 +6,7 @@ import { ActionIcon } from '@mantine/core'; import React from 'react'; import { FaExternalLinkAlt } from 'react-icons/fa'; -const RenderDiacomLink = ({ cell }: CellRendererFunctionProps) => { +const RenderDicomLink = ({ cell }: CellRendererFunctionProps) => { if (!cell?.getValue() || cell?.getValue() === '') { return ; } else @@ -22,7 +22,7 @@ const RenderDiacomLink = ({ cell }: CellRendererFunctionProps) => { export const registerCohortTableCustomCellRenderers = () => { ExplorerTableCellRendererFactory().registerRenderer( 'link', - 'DiacomLink', - RenderDiacomLink, + 'DicomLink', + RenderDicomLink, ); }; From 6dd0e8c3da4afec8f8f025bf948595e948bc5151 Mon Sep 17 00:00:00 2001 From: Shawn O'Connor Date: Tue, 17 Dec 2024 09:27:18 -0600 Subject: [PATCH 12/22] update git workflows node version, remove automated npm update (#55) Co-authored-by: Shawn O'Connor --- .github/workflows/ci.yaml | 6 ++---- 1 file changed, 2 insertions(+), 4 deletions(-) diff --git a/.github/workflows/ci.yaml b/.github/workflows/ci.yaml index 642f40d..cbfff44 100644 --- a/.github/workflows/ci.yaml +++ b/.github/workflows/ci.yaml @@ -5,11 +5,9 @@ jobs: runs-on: ubuntu-latest steps: - uses: actions/checkout@v2 - - uses: actions/setup-node@v3.4.1 + - uses: actions/setup-node@v4.1.0 with: - node-version: 20.11.0 - - name: install npm version - run: npm install -g npm + node-version: 20.17.0 - name: Get Version run: npm -v - name: Install modules From b63788d784cd94537983072bc29ff433a118d613 Mon Sep 17 00:00:00 2001 From: Craig Barnes Date: Thu, 19 Dec 2024 16:47:24 -0600 Subject: [PATCH 13/22] Update/release 0 10 67 (#57) * update version to v0.10.61 * update version to v0.10.67 * update version to v0.10.67 * Update ci.yaml --- .gitignore | 1 + Dockerfile | 60 +- package-lock.json | 19352 +++++++++++++++++++++++---------------- package.json | 10 +- src/pages/_app.tsx | 1 - src/styles/globals.css | 1 + 6 files changed, 11623 insertions(+), 7802 deletions(-) diff --git a/.gitignore b/.gitignore index 8f322f0..7fb7b63 100644 --- a/.gitignore +++ b/.gitignore @@ -18,6 +18,7 @@ # misc .DS_Store *.pem +.idea # debug npm-debug.log* diff --git a/Dockerfile b/Dockerfile index 3b80b98..a513973 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,44 +1,30 @@ -# docker build -t gen3ff . -# docker run -p 3000:3000 -it gen3ff -# for Macbook silicon M1/m2 uncomment the following lines and comment quay.io/cdis/ubuntu:20.04: -#FROM arm64v8/ubuntu:20.04 as build - -FROM quay.io/cdis/ubuntu:20.04 AS build - -ARG NODE_VERSION=20 - -ARG BASE_PATH -ARG NEXT_PUBLIC_PORTAL_BASENAME -ENV NPM_CONFIG_PREFIX=/home/node/.npm-global -ENV PATH=$PATH:/home/node/.npm-global/bin +# Build stage +FROM node:20-slim AS builder WORKDIR /gen3 -RUN apt-get update && apt-get install -y --no-install-recommends \ - build-essential \ - libssl1.1 \ - libgnutls30 \ - ca-certificates \ - curl \ - git \ - gnupg \ - && mkdir -p /etc/apt/keyrings \ - && curl -fsSL https://deb.nodesource.com/gpgkey/nodesource-repo.gpg.key | gpg --dearmor -o /etc/apt/keyrings/nodesource.gpg \ - && echo "deb [signed-by=/etc/apt/keyrings/nodesource.gpg] https://deb.nodesource.com/node_$NODE_VERSION.x nodistro main" | tee /etc/apt/sources.list.d/nodesource.list \ - && apt-get update \ - && apt-get install -y nodejs \ - && apt-get clean \ - && npm install -g npm@10.5.2 - -RUN addgroup --system --gid 1001 nextjs && adduser --system --uid 1001 nextjs COPY ./package.json ./package-lock.json ./next.config.js ./tsconfig.json ./.env.development ./tailwind.config.js ./postcss.config.js ./ +RUN npm ci COPY ./src ./src COPY ./public ./public COPY ./config ./config -RUN npm ci -RUN npm install \ - "@swc/core" \ - "@napi-rs/magic-string" -RUN npm run build -ENV PORT=80 -CMD ["npm", "run", "start"] +RUN npm install @swc/core @napi-rs/magic-string && \ + npm run build + +# Production stage +FROM node:20-slim AS runner + +WORKDIR /gen3 +ENV PORT=3000 + +RUN addgroup --system --gid 1001 nextjs && \ + adduser --system --uid 1001 nextjs + +COPY --from=builder /gen3/config ./config +COPY --from=builder /gen3/public ./public +COPY --from=builder /gen3/.next/standalone ./ +COPY --from=builder /gen3/.next/static ./.next/static + +USER nextjs +ENV PORT=3000 +CMD ["node", "server.js"] diff --git a/package-lock.json b/package-lock.json index f1f0c52..bb5632f 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,18 +1,18 @@ { "name": "@gen3/commons-portal-app-base", - "version": "0.10.55", + "version": "0.10.67", "lockfileVersion": 3, "requires": true, "packages": { "": { "name": "@gen3/commons-portal-app-base", - "version": "0.10.55", + "version": "0.10.67", "dependencies": { "@fontsource/montserrat": "^5.0.19", "@fontsource/poppins": "^5.0.15", "@fontsource/source-sans-pro": "^5.0.8", - "@gen3/core": "^0.10.55", - "@gen3/frontend": "^0.10.55", + "@gen3/core": "^0.10.67", + "@gen3/frontend": "^0.10.67", "@grafana/faro-react": "^1.9.1", "@grafana/faro-web-sdk": "^1.9.1", "@grafana/faro-web-tracing": "^1.9.1", @@ -25,7 +25,7 @@ "@mdx-js/loader": "^3.0.0", "@mdx-js/react": "^3.0.0", "@next/mdx": "^14.2.15", - "cookies-next": "^4.1.1", + "cookies-next": "^4.3.0", "idb": "^8.0.0", "jsonpath-plus": "^10.2.0", "react": "^18.2.0", @@ -34,7 +34,7 @@ }, "devDependencies": { "@axe-core/react": "^4.10.0", - "@gen3/toolsff": "^0.10.55", + "@gen3/toolsff": "^0.10.67", "@tailwindcss/aspect-ratio": "^0.4.2", "@tailwindcss/forms": "^0.5.3", "@tailwindcss/line-clamp": "^0.4.2", @@ -75,6 +75,7 @@ "version": "5.2.0", "resolved": "https://registry.npmjs.org/@alloc/quick-lru/-/quick-lru-5.2.0.tgz", "integrity": "sha512-UrcABB+4bUrFABwbluTIBErXwvbsU/V7TZWfmbgJfbkwiBuziS9gxdODUyuiecfdGQ85jglMW6juS3+z5TsKLw==", + "license": "MIT", "engines": { "node": ">=10" }, @@ -83,14 +84,15 @@ } }, "node_modules/@ampproject/remapping": { - "version": "2.2.1", - "resolved": "https://registry.npmjs.org/@ampproject/remapping/-/remapping-2.2.1.tgz", - "integrity": 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+ "node": ">=12" + }, + "funding": { + "url": "https://github.com/chalk/ansi-styles?sponsor=1" + } + }, + "node_modules/wrap-ansi/node_modules/strip-ansi": { + "version": "7.1.0", + "resolved": "https://registry.npmjs.org/strip-ansi/-/strip-ansi-7.1.0.tgz", + "integrity": "sha512-iq6eVVI64nQQTRYq2KtEg2d2uU7LElhTJwsH4YzIHZshxlgZms/wIc4VoDQTlG/IvVIrBKG06CrZnp0qv7hkcQ==", + "license": "MIT", + "dependencies": { + "ansi-regex": "^6.0.1" + }, + "engines": { + "node": ">=12" + }, + "funding": { + "url": "https://github.com/chalk/strip-ansi?sponsor=1" + } + }, "node_modules/wrappy": { "version": "1.0.2", "resolved": "https://registry.npmjs.org/wrappy/-/wrappy-1.0.2.tgz", - "integrity": "sha512-l4Sp/DRseor9wL6EvV2+TuQn63dMkPjZ/sp9XkghTEbV9KlPS1xUsZ3u7/IQO4wxtcFB4bgpQPRcR3QCvezPcQ==" + "integrity": "sha512-l4Sp/DRseor9wL6EvV2+TuQn63dMkPjZ/sp9XkghTEbV9KlPS1xUsZ3u7/IQO4wxtcFB4bgpQPRcR3QCvezPcQ==", + "license": "ISC" }, "node_modules/write-file-atomic": { "version": "4.0.2", "resolved": 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"resolved": "https://registry.npmjs.org/y18n/-/y18n-5.0.8.tgz", "integrity": "sha512-0pfFzegeDWJHJIAmTLRP2DwHjdF5s7jo9tuztdQxAhINCdvS+3nGINqPd00AphqJR/0LhANUS6/+7SCb98YOfA==", "dev": true, + "license": "ISC", "peer": true, "engines": { "node": ">=10" @@ -26823,12 +30626,14 @@ "resolved": "https://registry.npmjs.org/yallist/-/yallist-3.1.1.tgz", "integrity": "sha512-a4UGQaWPH59mOXUYnAG2ewncQS4i4F43Tv3JoAM+s2VDAmS9NsK8GpDMLrCHPksFT7h3K6TOoUNn2pb7RoXx4g==", "dev": true, + "license": "ISC", "peer": true }, "node_modules/yaml": { - "version": "2.4.0", - "resolved": "https://registry.npmjs.org/yaml/-/yaml-2.4.0.tgz", - "integrity": "sha512-j9iR8g+/t0lArF4V6NE/QCfT+CO7iLqrXAHZbJdo+LfjqP1vR8Fg5bSiaq6Q2lOD1AUEVrEVIgABvBFYojJVYQ==", + "version": "2.6.1", + "resolved": "https://registry.npmjs.org/yaml/-/yaml-2.6.1.tgz", + "integrity": "sha512-7r0XPzioN/Q9kXBro/XPnA6kznR73DHq+GXh5ON7ZozRO6aMjbmiBuKste2wslTFkC5d1dw0GooOCepZXJ2SAg==", + "license": "ISC", "bin": { "yaml": "bin.mjs" }, @@ -26841,6 +30646,7 @@ "resolved": "https://registry.npmjs.org/yargs/-/yargs-17.7.2.tgz", "integrity": "sha512-7dSzzRQ++CKnNI/krKnYRV7JKKPUXMEh61soaHKg9mrWEhzFWhFnxPxGl+69cD1Ou63C13NUPCnmIcrvqCuM6w==", "dev": true, + "license": "MIT", "peer": true, "dependencies": { "cliui": "^8.0.1", @@ -26860,10 +30666,35 @@ "resolved": "https://registry.npmjs.org/yargs-parser/-/yargs-parser-21.1.1.tgz", "integrity": "sha512-tVpsJW7DdjecAiFpbIB1e3qxIQsE6NoPc5/eTdrbbIC4h0LVsWhnoa3g+m2HclBIujHzsxZ4VJVA+GUuc2/LBw==", "dev": true, + "license": "ISC", "engines": { "node": ">=12" } }, + "node_modules/yargs/node_modules/emoji-regex": { + "version": "8.0.0", + "resolved": "https://registry.npmjs.org/emoji-regex/-/emoji-regex-8.0.0.tgz", + "integrity": "sha512-MSjYzcWNOA0ewAHpz0MxpYFvwg6yjy1NG3xteoqz644VCo/RPgnr1/GGt+ic3iJTzQ8Eu3TdM14SawnVUmGE6A==", + "dev": true, + "license": "MIT", + "peer": true + }, + "node_modules/yargs/node_modules/string-width": { + "version": "4.2.3", + "resolved": "https://registry.npmjs.org/string-width/-/string-width-4.2.3.tgz", + "integrity": "sha512-wKyQRQpjJ0sIp62ErSZdGsjMJWsap5oRNihHhu6G7JVO/9jIB6UyevL+tXuOqrng8j/cxKTWyWUwvSTriiZz/g==", + "dev": true, + "license": "MIT", + "peer": true, + "dependencies": { + "emoji-regex": "^8.0.0", + "is-fullwidth-code-point": "^3.0.0", + "strip-ansi": "^6.0.1" + }, + "engines": { + "node": ">=8" + } + }, "node_modules/yauzl": { "version": "2.10.0", "resolved": "https://registry.npmjs.org/yauzl/-/yauzl-2.10.0.tgz", @@ -26880,6 +30711,7 @@ "resolved": "https://registry.npmjs.org/yn/-/yn-3.1.1.tgz", "integrity": "sha512-Ux4ygGWsu2c7isFWe8Yu1YluJmqVhxqK2cLXNQA5AcC3QfbGNpM7fu0Y8b/z16pXLnFxZYvWhd3fhBY9DLmC6Q==", "devOptional": true, + "license": "MIT", "engines": { "node": ">=6" } @@ -26889,6 +30721,7 @@ "resolved": "https://registry.npmjs.org/yocto-queue/-/yocto-queue-0.1.0.tgz", "integrity": "sha512-rVksvsnNCdJ/ohGc6xgPwyN8eheCxsiLM8mxuE/t/mOVqJewPuO1miLpTHQiRgTKCLexL4MeAFVagts7HmNZ2Q==", "dev": true, + "license": "MIT", "engines": { "node": ">=10" }, @@ -26921,6 +30754,7 @@ "version": "2.0.4", "resolved": "https://registry.npmjs.org/zwitch/-/zwitch-2.0.4.tgz", "integrity": "sha512-bXE4cR/kVZhKZX/RjPEflHaKVhUVl85noU3v6b8apfQEc1x4A+zBxjZ4lN8LqGd6WZ3dl98pY4o717VFmoPp+A==", + "license": "MIT", "funding": { "type": "github", "url": "https://github.com/sponsors/wooorm" diff --git a/package.json b/package.json index d1fb732..854fdfb 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "@gen3/commons-portal-app-base", - "version": "0.10.55", + "version": "0.10.67", "private": "true", "engines": { "npm": ">=10.2.3", @@ -22,8 +22,8 @@ "@fontsource/poppins": "^5.0.15", "@fontsource/source-sans-pro": "^5.0.8", "jsonpath-plus": "^10.2.0", - "@gen3/core": "^0.10.55", - "@gen3/frontend": "^0.10.55", + "@gen3/core": "^0.10.67", + "@gen3/frontend": "^0.10.67", "@grafana/faro-react": "^1.9.1", "@grafana/faro-web-sdk": "^1.9.1", "@grafana/faro-web-tracing": "^1.9.1", @@ -37,14 +37,14 @@ "@mdx-js/loader": "^3.0.0", "@mdx-js/react": "^3.0.0", "@next/mdx": "^14.2.15", - "cookies-next": "^4.1.1", + "cookies-next": "^4.3.0", "react": "^18.2.0", "react-dom": "18.2.0", "swr": "^2.2.5" }, "devDependencies": { "@axe-core/react": "^4.10.0", - "@gen3/toolsff": "^0.10.55", + "@gen3/toolsff": "^0.10.67", "@tailwindcss/aspect-ratio": "^0.4.2", "@tailwindcss/forms": "^0.5.3", "@tailwindcss/line-clamp": "^0.4.2", diff --git a/src/pages/_app.tsx b/src/pages/_app.tsx index 9b45c99..d7380a8 100644 --- a/src/pages/_app.tsx +++ b/src/pages/_app.tsx @@ -12,7 +12,6 @@ import { RegisteredIcons, Fonts, SessionConfiguration, - // registerCohortDiscoveryApp, registerCohortDiversityApp, registerCohortBuilderDefaultPreviewRenderers, registerExplorerDefaultCellRenderers, diff --git a/src/styles/globals.css b/src/styles/globals.css index 94981ea..e941002 100644 --- a/src/styles/globals.css +++ b/src/styles/globals.css @@ -2,6 +2,7 @@ @import "tailwindcss/components"; @import '@mantine/core/styles.css'; +@import '@mantine/notifications/styles.css'; @import 'mantine-react-table/styles.css'; @import "tailwindcss/utilities"; From e6c754320e8f9fb9ef6fd51cc64af4f89a1e0127 Mon Sep 17 00:00:00 2001 From: Shawn O'Connor Date: Fri, 20 Dec 2024 14:54:07 -0600 Subject: [PATCH 14/22] update build to use start.sh for automation (#59) Co-authored-by: Shawn O'Connor --- Dockerfile | 3 ++- start.sh | 5 +++++ 2 files changed, 7 insertions(+), 1 deletion(-) create mode 100644 start.sh diff --git a/Dockerfile b/Dockerfile index a513973..89c6ec0 100644 --- a/Dockerfile +++ b/Dockerfile @@ -8,6 +8,7 @@ RUN npm ci COPY ./src ./src COPY ./public ./public COPY ./config ./config +COPY ./start.sh ./ RUN npm install @swc/core @napi-rs/magic-string && \ npm run build @@ -27,4 +28,4 @@ COPY --from=builder /gen3/.next/static ./.next/static USER nextjs ENV PORT=3000 -CMD ["node", "server.js"] +CMD bash ./start.sh diff --git a/start.sh b/start.sh new file mode 100644 index 0000000..5cf0f39 --- /dev/null +++ b/start.sh @@ -0,0 +1,5 @@ +#!/bin/bash + +set -e +echo "starting server" +npm run start From 740ce37d8ee1664f8d2ed34c5c18e60dcc6818f5 Mon Sep 17 00:00:00 2001 From: Craig Barnes Date: Wed, 15 Jan 2025 10:12:52 -0600 Subject: [PATCH 15/22] update to 0.10.73 (#63) --- .env.development | 6 +- package-lock.json | 321 +++++++++++------------ package.json | 28 +- src/lib/Discovery/CustomRowRenderers.tsx | 2 +- src/pages/_app.tsx | 36 +-- src/pages/_document.tsx | 4 +- 6 files changed, 184 insertions(+), 213 deletions(-) diff --git a/.env.development b/.env.development index 52a3fdf..e273d02 100644 --- a/.env.development +++ b/.env.development @@ -1,6 +1,2 @@ -GEN3_COMMONS_NAME=gen3 +GEN3_COMMONS_NAME=prom NEXT_PUBLIC_GEN3_API=https://localhost:3010 -NEXT_PUBLIC_GEN3_DOMAIN=https://localhost:3010 - -# set these if you want to use different endpoints -#NEXT_PUBLIC_GEN3_GUPPY_API= diff --git a/package-lock.json b/package-lock.json index bb5632f..76f0af0 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,40 +1,40 @@ { "name": "@gen3/commons-portal-app-base", - "version": "0.10.67", + "version": "0.10.71", "lockfileVersion": 3, "requires": true, "packages": { "": { "name": "@gen3/commons-portal-app-base", - "version": "0.10.67", + "version": "0.10.71", "dependencies": { "@fontsource/montserrat": "^5.0.19", "@fontsource/poppins": "^5.0.15", "@fontsource/source-sans-pro": "^5.0.8", - "@gen3/core": "^0.10.67", - "@gen3/frontend": "^0.10.67", + "@gen3/core": "^0.10.73", + "@gen3/frontend": "^0.10.73", "@grafana/faro-react": "^1.9.1", "@grafana/faro-web-sdk": "^1.9.1", "@grafana/faro-web-tracing": "^1.9.1", - "@mantine/core": "^7.13.3", - "@mantine/dates": "^7.13.3", - "@mantine/form": "^7.13.3", - "@mantine/hooks": "^7.13.3", - "@mantine/modals": "^7.13.3", - "@mantine/notifications": "^7.13.3", + "@mantine/core": "^7.16.0", + "@mantine/dates": "^7.16.0", + "@mantine/form": "^7.16.0", + "@mantine/hooks": "^7.16.0", + "@mantine/modals": "^7.16.0", + "@mantine/notifications": "^7.16.0", "@mdx-js/loader": "^3.0.0", "@mdx-js/react": "^3.0.0", "@next/mdx": "^14.2.15", "cookies-next": "^4.3.0", "idb": "^8.0.0", "jsonpath-plus": "^10.2.0", - "react": "^18.2.0", - "react-dom": "18.2.0", + "react": "^18.3.1", + "react-dom": "18.3.1", "swr": "^2.2.5" }, "devDependencies": { "@axe-core/react": "^4.10.0", - "@gen3/toolsff": "^0.10.67", + "@gen3/toolsff": "^0.10.73", "@tailwindcss/aspect-ratio": "^0.4.2", "@tailwindcss/forms": "^0.5.3", "@tailwindcss/line-clamp": "^0.4.2", @@ -51,7 +51,7 @@ "eslint-plugin-jsx-a11y": "^6.6.1", "eslint-plugin-react": "^7.30.1", "eslint-plugin-react-hooks": "^4.6.0", - "next": "^14.2.15", + "next": "^14.2.23", "postcss": "^8.4.29", "postcss-import": "^16.1.0", "postcss-loader": "^7.3.2", @@ -59,8 +59,6 @@ "postcss-preset-env": "^8.4.2", "postcss-preset-mantine": "^1.17.0", "prettier": "^2.7.1", - "react": "^18.2.0", - "react-dom": "18.2.0", "tailwindcss": "^3.4.10", "ts-jest": "^29.1.2", "ts-node": "^10.9.1", @@ -1719,19 +1717,19 @@ "license": "OFL-1.1" }, "node_modules/@gen3/core": { - "version": "0.10.67", - "resolved": "https://registry.npmjs.org/@gen3/core/-/core-0.10.67.tgz", - "integrity": "sha512-gWSiC5Ddm5GG/CR2dML0mjaRE1H8cMMLuCp2K2X6oEVaZlgpOIJhX0UVc4qfS+kTOX98OTcI+ZAa998+93FvTw==", + "version": "0.10.73", + "resolved": "https://registry.npmjs.org/@gen3/core/-/core-0.10.73.tgz", + "integrity": "sha512-znA2hcp+NmUzser6JGLNJQhtJRpalIXDDEzKAPQm11IMW5EhFehrp47bbcKfVuF1PCBHJaec5Nmh804NHlZZNA==", "license": "Apache-2.0", "dependencies": { - "@reduxjs/toolkit": "^2.2.8", + "@reduxjs/toolkit": "^2.5.0", "flat": "^6.0.1", "papaparse": "^5.4.1", "queue": "6.0.2", - "react-redux": "^9.1.2", + "react-redux": "^9.2.0", "redux": "^5.0.1", "redux-persist": "^6.0.0", - "swr": "^2.2.5", + "swr": "^2.3.0", "uuid": "^9.0.1" }, "engines": { @@ -1739,31 +1737,32 @@ "npm": ">=10.8.2" }, "peerDependencies": { - "react": "^18.2.0", + "react": "^18.3.1", "react-cookie": "^7.2.2", - "react-dom": "^18.2.0" + "react-dom": "^18.3.1" } }, "node_modules/@gen3/frontend": { - "version": "0.10.67", - "resolved": "https://registry.npmjs.org/@gen3/frontend/-/frontend-0.10.67.tgz", - "integrity": "sha512-/mY2b6lOc2oStftXQu0h7eUeMkN9Rd4CNXEUd1Af9YHkuB/+8DL/gELpUyEi5r53nC2V6bohfDFhrFa4XEAL4Q==", + "version": "0.10.73", + "resolved": "https://registry.npmjs.org/@gen3/frontend/-/frontend-0.10.73.tgz", + "integrity": "sha512-pann8x1nzbytTxcfrGNVEp92y3eiTUzOVsmXkeWOOCU2/Cb2jO0yG0XEMbpWheiln8ich8lStOt8Jl8Ip03Peg==", "license": "Apache-2.0", "dependencies": { + "@gen3/core": "^0.10.73", "@graphiql/react": "^0.23.1", "@hello-pangea/dnd": "^17.0.0", "@iconify/react": "^5.0.2", "@kbox-labs/react-echarts": "^1.4.0", - "@mantine/core": "^7.13.3", - "@mantine/dates": "^7.13.3", - "@mantine/form": "^7.13.3", - "@mantine/hooks": "^7.13.3", - "@mantine/modals": "^7.13.3", - "@mantine/notifications": "^7.13.3", + "@mantine/core": "^7.16.0", + "@mantine/dates": "^7.16.0", + 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"sha512-mjN3fE6u/tynneLiEg56XnthzuYw+kD7mCujgVqioxyPqbmiotUCGJpIZGS/VaPg3ZDT1tvWxiVyRzeqJFm/kw==", "license": "MIT", "dependencies": { - "@next/env": "14.2.21", + "@next/env": "14.2.23", "@swc/helpers": "0.5.5", "busboy": "1.6.0", "caniuse-lite": "^1.0.30001579", @@ -21682,15 +21653,15 @@ "node": ">=18.17.0" }, "optionalDependencies": { - "@next/swc-darwin-arm64": "14.2.21", - "@next/swc-darwin-x64": "14.2.21", - "@next/swc-linux-arm64-gnu": "14.2.21", - "@next/swc-linux-arm64-musl": "14.2.21", - "@next/swc-linux-x64-gnu": "14.2.21", - "@next/swc-linux-x64-musl": "14.2.21", - "@next/swc-win32-arm64-msvc": "14.2.21", - "@next/swc-win32-ia32-msvc": "14.2.21", - "@next/swc-win32-x64-msvc": "14.2.21" + "@next/swc-darwin-arm64": "14.2.23", + "@next/swc-darwin-x64": "14.2.23", + "@next/swc-linux-arm64-gnu": "14.2.23", + "@next/swc-linux-arm64-musl": "14.2.23", + "@next/swc-linux-x64-gnu": "14.2.23", + "@next/swc-linux-x64-musl": "14.2.23", + "@next/swc-win32-arm64-msvc": "14.2.23", + "@next/swc-win32-ia32-msvc": "14.2.23", + "@next/swc-win32-x64-msvc": "14.2.23" }, "peerDependencies": { "@opentelemetry/api": "^1.1.0", @@ -23874,16 +23845,16 @@ } }, "node_modules/react-dom": { - "version": "18.2.0", - "resolved": "https://registry.npmjs.org/react-dom/-/react-dom-18.2.0.tgz", - "integrity": "sha512-6IMTriUmvsjHUjNtEDudZfuDQUoWXVxKHhlEGSk81n4YFS+r/Kl99wXiwlVXtPBtJenozv2P+hxDsw9eA7Xo6g==", + "version": "18.3.1", + "resolved": "https://registry.npmjs.org/react-dom/-/react-dom-18.3.1.tgz", + "integrity": "sha512-5m4nQKp+rZRb09LNH59GM4BxTh9251/ylbKIbpe7TpGxfJ+9kv6BLkLBXIjjspbgbnIBNqlI23tRnTWT0snUIw==", "license": "MIT", "dependencies": { "loose-envify": "^1.1.0", - "scheduler": "^0.23.0" + "scheduler": "^0.23.2" }, "peerDependencies": { - "react": "^18.2.0" + "react": "^18.3.1" } }, "node_modules/react-fast-compare": { @@ -24566,13 +24537,13 @@ } }, "node_modules/react-number-format": { - "version": "5.4.2", - "resolved": "https://registry.npmjs.org/react-number-format/-/react-number-format-5.4.2.tgz", - "integrity": "sha512-cg//jVdS49PYDgmcYoBnMMHl4XNTMuV723ZnHD2aXYtWWWqbVF3hjQ8iB+UZEuXapLbeA8P8H+1o6ZB1lcw3vg==", + "version": "5.4.3", + "resolved": "https://registry.npmjs.org/react-number-format/-/react-number-format-5.4.3.tgz", + "integrity": "sha512-VCY5hFg/soBighAoGcdE+GagkJq0230qN6jcS5sp8wQX1qy1fYN/RX7/BXkrs0oyzzwqR8/+eSUrqXbGeywdUQ==", "license": "MIT", "peerDependencies": { - "react": "^0.14 || ^15.0.0 || ^16.0.0 || ^17.0.0 || ^18.0.0", - "react-dom": "^0.14 || ^15.0.0 || ^16.0.0 || ^17.0.0 || ^18.0.0" + "react": "^0.14 || ^15.0.0 || ^16.0.0 || ^17.0.0 || ^18.0.0 || ^19.0.0", + "react-dom": "^0.14 || ^15.0.0 || ^16.0.0 || ^17.0.0 || ^18.0.0 || ^19.0.0" } }, "node_modules/react-plotly.js": { @@ -24709,9 +24680,9 @@ } }, "node_modules/react-textarea-autosize": { - "version": "8.5.5", - "resolved": "https://registry.npmjs.org/react-textarea-autosize/-/react-textarea-autosize-8.5.5.tgz", - "integrity": "sha512-CVA94zmfp8m4bSHtWwmANaBR8EPsKy2aZ7KwqhoS4Ftib87F9Kvi7XQhOixypPLMc6kVYgOXvKFuuzZDpHGRPg==", + "version": "8.5.6", + "resolved": "https://registry.npmjs.org/react-textarea-autosize/-/react-textarea-autosize-8.5.6.tgz", + "integrity": "sha512-aT3ioKXMa8f6zHYGebhbdMD2L00tKeRX1zuVuDx9YQK/JLLRSaSxq3ugECEmUB9z2kvk6bFSIoRHLkkUv0RJiw==", "license": "MIT", "dependencies": { "@babel/runtime": "^7.20.13", @@ -24722,7 +24693,7 @@ "node": ">=10" }, "peerDependencies": { - "react": "^16.8.0 || ^17.0.0 || ^18.0.0" + "react": "^16.8.0 || ^17.0.0 || ^18.0.0 || ^19.0.0" } }, "node_modules/react-transition-group": { @@ -28227,16 +28198,16 @@ } }, "node_modules/swr": { - "version": "2.2.5", - "resolved": "https://registry.npmjs.org/swr/-/swr-2.2.5.tgz", - "integrity": "sha512-QtxqyclFeAsxEUeZIYmsaQ0UjimSq1RZ9Un7I68/0ClKK/U3LoyQunwkQfJZr2fc22DfIXLNDc2wFyTEikCUpg==", + "version": "2.3.0", + "resolved": "https://registry.npmjs.org/swr/-/swr-2.3.0.tgz", + "integrity": "sha512-NyZ76wA4yElZWBHzSgEJc28a0u6QZvhb6w0azeL2k7+Q1gAzVK+IqQYXhVOC/mzi+HZIozrZvBVeSeOZNR2bqA==", "license": "MIT", "dependencies": { - "client-only": "^0.0.1", - "use-sync-external-store": "^1.2.0" + "dequal": "^2.0.3", + "use-sync-external-store": "^1.4.0" }, "peerDependencies": { - "react": "^16.11.0 || ^17.0.0 || ^18.0.0" + "react": "^16.11.0 || ^17.0.0 || ^18.0.0 || ^19.0.0" } }, "node_modules/tabbable": { diff --git a/package.json b/package.json index 854fdfb..8ae8be2 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "@gen3/commons-portal-app-base", - "version": "0.10.67", + "version": "0.10.73", "private": "true", "engines": { "npm": ">=10.2.3", @@ -22,29 +22,29 @@ "@fontsource/poppins": "^5.0.15", "@fontsource/source-sans-pro": "^5.0.8", "jsonpath-plus": "^10.2.0", - "@gen3/core": "^0.10.67", - "@gen3/frontend": "^0.10.67", + "@gen3/core": "^0.10.73", + "@gen3/frontend": "^0.10.73", "@grafana/faro-react": "^1.9.1", "@grafana/faro-web-sdk": "^1.9.1", "@grafana/faro-web-tracing": "^1.9.1", "idb": "^8.0.0", - "@mantine/core": "^7.13.3", - "@mantine/form": "^7.13.3", - "@mantine/hooks": "^7.13.3", - "@mantine/modals": "^7.13.3", - "@mantine/dates": "^7.13.3", - "@mantine/notifications": "^7.13.3", + "@mantine/core": "^7.16.0", + "@mantine/dates": "^7.16.0", + "@mantine/form": "^7.16.0", + "@mantine/hooks": "^7.16.0", + "@mantine/modals": "^7.16.0", + "@mantine/notifications": "^7.16.0", "@mdx-js/loader": "^3.0.0", "@mdx-js/react": "^3.0.0", "@next/mdx": "^14.2.15", "cookies-next": "^4.3.0", - "react": "^18.2.0", - "react-dom": "18.2.0", + "react": "^18.3.1", + "react-dom": "18.3.1", "swr": "^2.2.5" }, "devDependencies": { "@axe-core/react": "^4.10.0", - "@gen3/toolsff": "^0.10.67", + "@gen3/toolsff": "^0.10.73", "@tailwindcss/aspect-ratio": "^0.4.2", "@tailwindcss/forms": "^0.5.3", "@tailwindcss/line-clamp": "^0.4.2", @@ -61,7 +61,7 @@ "eslint-plugin-jsx-a11y": "^6.6.1", "eslint-plugin-react": "^7.30.1", "eslint-plugin-react-hooks": "^4.6.0", - "next": "^14.2.15", + "next": "^14.2.23", "postcss": "^8.4.29", "postcss-import": "^16.1.0", "postcss-loader": "^7.3.2", @@ -69,8 +69,6 @@ "postcss-preset-env": "^8.4.2", "postcss-preset-mantine": "^1.17.0", "prettier": "^2.7.1", - "react": "^18.2.0", - "react-dom": "18.2.0", "tailwindcss": "^3.4.10", "ts-jest": "^29.1.2", "ts-node": "^10.9.1", diff --git a/src/lib/Discovery/CustomRowRenderers.tsx b/src/lib/Discovery/CustomRowRenderers.tsx index f785432..3c393c5 100644 --- a/src/lib/Discovery/CustomRowRenderers.tsx +++ b/src/lib/Discovery/CustomRowRenderers.tsx @@ -41,7 +41,7 @@ const DetailsWithTagsRowRenderer = (
- {row.original?.tags.map((tagInfo: TagData) => { + {row.original?.tags?.map((tagInfo: TagData) => { const { color, display, label } = getTagInfo(tagInfo, config.tags); if (tagInfo.name === '') return null; // no tag diff --git a/src/pages/_app.tsx b/src/pages/_app.tsx index d7380a8..4396ec6 100644 --- a/src/pages/_app.tsx +++ b/src/pages/_app.tsx @@ -1,8 +1,7 @@ import App, { AppProps, AppContext, AppInitialProps } from 'next/app'; -import React, { useEffect, useRef } from 'react'; - +import React, { useEffect, useMemo, useRef } from 'react'; +import { MantineProvider } from '@mantine/core'; import { Faro, FaroErrorBoundary, withFaroProfiler } from '@grafana/faro-react'; - import { initGrafanaFaro } from '../lib/Grafana/grafana'; import { @@ -11,10 +10,12 @@ import { type ModalsConfig, RegisteredIcons, Fonts, + createMantineTheme, SessionConfiguration, + // registerCohortDiscoveryApp, registerCohortDiversityApp, registerCohortBuilderDefaultPreviewRenderers, - registerExplorerDefaultCellRenderers, + registerMetadataSchemaApp, } from '@gen3/frontend'; import { registerCohortTableCustomCellRenderers } from '@/lib/CohortBuilder/CustomCellRenderers'; @@ -27,7 +28,7 @@ import '@fontsource/poppins'; import { setDRSHostnames } from '@gen3/core'; import drsHostnames from '../../config/drsHostnames.json'; -import { loadContent } from '../lib/content/loadContent'; +import { loadContent } from '@/lib/content/loadContent'; if (typeof window !== 'undefined' && process.env.NODE_ENV !== 'production') { // eslint-disable-next-line @typescript-eslint/no-var-requires, @typescript-eslint/no-require-imports @@ -70,24 +71,29 @@ const Gen3App = ({ if (!faroRef.current) faroRef.current = initGrafanaFaro(); // registerCohortDiscoveryApp(); registerCohortDiversityApp(); - registerExplorerDefaultCellRenderers(); + registerMetadataSchemaApp(); registerCohortBuilderDefaultPreviewRenderers(); registerCohortTableCustomCellRenderers(); registerCustomExplorerDetailsPanels(); // } }, []); + const theme = useMemo( + () => createMantineTheme(themeFonts, colors), + [themeFonts, colors], + ); + return ( - - - + + + + + ); }; diff --git a/src/pages/_document.tsx b/src/pages/_document.tsx index 53ff867..f6b2267 100644 --- a/src/pages/_document.tsx +++ b/src/pages/_document.tsx @@ -1,9 +1,9 @@ import { Head, Html, Main, NextScript } from 'next/document'; -import { ColorSchemeScript } from '@mantine/core'; +import { ColorSchemeScript, mantineHtmlProps } from '@mantine/core'; export default function Document() { return ( - + From 337e53a872202f31812b77624510eea29e64dacc Mon Sep 17 00:00:00 2001 From: Craig Barnes Date: Wed, 15 Jan 2025 11:33:29 -0600 Subject: [PATCH 16/22] Chore/update docker (#64) * update Dockerfile * update .env files --- .env.development | 2 +- .env.production | 1 + Dockerfile | 10 +++++++--- 3 files changed, 9 insertions(+), 4 deletions(-) create mode 100644 .env.production diff --git a/.env.development b/.env.development index e273d02..64a2760 100644 --- a/.env.development +++ b/.env.development @@ -1,2 +1,2 @@ -GEN3_COMMONS_NAME=prom +GEN3_COMMONS_NAME=gen3 NEXT_PUBLIC_GEN3_API=https://localhost:3010 diff --git a/.env.production b/.env.production new file mode 100644 index 0000000..0a10ad9 --- /dev/null +++ b/.env.production @@ -0,0 +1 @@ +GEN3_COMMONS_NAME=gen3 diff --git a/Dockerfile b/Dockerfile index 89c6ec0..3a49e45 100644 --- a/Dockerfile +++ b/Dockerfile @@ -1,9 +1,11 @@ +# docker build -t ff . +# docker run -p 3000:3000 -it ff # Build stage FROM node:20-slim AS builder WORKDIR /gen3 -COPY ./package.json ./package-lock.json ./next.config.js ./tsconfig.json ./.env.development ./tailwind.config.js ./postcss.config.js ./ +COPY ./package.json ./package-lock.json ./next.config.js ./tsconfig.json ./.env.development ./tailwind.config.js ./postcss.config.js ./start.sh ./.env.production ./ RUN npm ci COPY ./src ./src COPY ./public ./public @@ -16,7 +18,6 @@ RUN npm install @swc/core @napi-rs/magic-string && \ FROM node:20-slim AS runner WORKDIR /gen3 -ENV PORT=3000 RUN addgroup --system --gid 1001 nextjs && \ adduser --system --uid 1001 nextjs @@ -25,7 +26,10 @@ COPY --from=builder /gen3/config ./config COPY --from=builder /gen3/public ./public COPY --from=builder /gen3/.next/standalone ./ COPY --from=builder /gen3/.next/static ./.next/static +COPY --from=builder /gen3/start.sh ./start.sh +RUN chown nextjs:nextjs /gen3/.next +VOLUME /gen3/.next -USER nextjs +USER nextjs:nextjs ENV PORT=3000 CMD bash ./start.sh From 08029b02cacdb856a4bdfb7e0720e1ea64fe2071 Mon Sep 17 00:00:00 2001 From: Craig Barnes Date: Fri, 24 Jan 2025 09:03:16 -0600 Subject: [PATCH 17/22] Chore/update 0.10.74 (#66) * update Dockerfile * update .env files * update to gen3.2 0.10.74 --- package-lock.json | 30 +++++++++++++++--------------- package.json | 6 +++--- 2 files changed, 18 insertions(+), 18 deletions(-) diff --git a/package-lock.json b/package-lock.json index 76f0af0..eba35b1 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,18 +1,18 @@ { "name": "@gen3/commons-portal-app-base", - "version": "0.10.71", + "version": "0.10.73", "lockfileVersion": 3, "requires": true, "packages": { "": { "name": "@gen3/commons-portal-app-base", - "version": "0.10.71", + "version": "0.10.73", "dependencies": { "@fontsource/montserrat": "^5.0.19", "@fontsource/poppins": "^5.0.15", "@fontsource/source-sans-pro": "^5.0.8", - "@gen3/core": "^0.10.73", - "@gen3/frontend": "^0.10.73", + "@gen3/core": "^0.10.74", + "@gen3/frontend": "^0.10.74", "@grafana/faro-react": "^1.9.1", "@grafana/faro-web-sdk": "^1.9.1", "@grafana/faro-web-tracing": "^1.9.1", @@ -34,7 +34,7 @@ }, "devDependencies": { "@axe-core/react": "^4.10.0", - "@gen3/toolsff": "^0.10.73", + "@gen3/toolsff": "^0.10.74", "@tailwindcss/aspect-ratio": "^0.4.2", "@tailwindcss/forms": "^0.5.3", "@tailwindcss/line-clamp": "^0.4.2", @@ -1717,9 +1717,9 @@ "license": "OFL-1.1" }, "node_modules/@gen3/core": { - "version": "0.10.73", - "resolved": "https://registry.npmjs.org/@gen3/core/-/core-0.10.73.tgz", - "integrity": "sha512-znA2hcp+NmUzser6JGLNJQhtJRpalIXDDEzKAPQm11IMW5EhFehrp47bbcKfVuF1PCBHJaec5Nmh804NHlZZNA==", + "version": "0.10.74", + "resolved": "https://registry.npmjs.org/@gen3/core/-/core-0.10.74.tgz", + "integrity": "sha512-E8MsoiPexPmuZQYg0JBkuOG4EswF8fAEPFAQMx/xj9Y7EwHYq8GMzAOYDH58gc02EeB9JaMPwXpMdSn/BHLJIA==", "license": "Apache-2.0", "dependencies": { "@reduxjs/toolkit": "^2.5.0", @@ -1743,12 +1743,12 @@ } }, "node_modules/@gen3/frontend": { - "version": "0.10.73", - "resolved": "https://registry.npmjs.org/@gen3/frontend/-/frontend-0.10.73.tgz", - "integrity": "sha512-pann8x1nzbytTxcfrGNVEp92y3eiTUzOVsmXkeWOOCU2/Cb2jO0yG0XEMbpWheiln8ich8lStOt8Jl8Ip03Peg==", + "version": "0.10.74", + "resolved": "https://registry.npmjs.org/@gen3/frontend/-/frontend-0.10.74.tgz", + "integrity": "sha512-VSBeneqSkgLadU3FNRVduOAElIk06cHVRJ2lU5E0dm1Eh/DkqQ2lqF8VRnMt3mrW5zP2QvlADZ/o+vzYvs9FPA==", "license": "Apache-2.0", "dependencies": { - "@gen3/core": "^0.10.73", + "@gen3/core": "^0.10.74", "@graphiql/react": "^0.23.1", "@hello-pangea/dnd": "^17.0.0", "@iconify/react": "^5.0.2", @@ -1892,9 +1892,9 @@ } }, "node_modules/@gen3/toolsff": { - "version": "0.10.73", - "resolved": "https://registry.npmjs.org/@gen3/toolsff/-/toolsff-0.10.73.tgz", - "integrity": "sha512-gsNCRr6y6lxZNT4N3iOw7vLXmQpdRXpmdWo4m0m+Xq36EVjsn0yLD5OP/aWnzTqGS9ztDjqXraUCAsFk107wMg==", + "version": "0.10.74", + "resolved": "https://registry.npmjs.org/@gen3/toolsff/-/toolsff-0.10.74.tgz", + "integrity": "sha512-DR8jVt00PPal/XvE3j5R8Gz66Jn8G5DeVyF1bTI33euEji2yV0zFJX5hggjTZFG2JZA1t/rklmzogNQvEPL3Mg==", "dev": true, "license": "Apache-2.0", "dependencies": { diff --git a/package.json b/package.json index 8ae8be2..bfa9474 100644 --- a/package.json +++ b/package.json @@ -22,8 +22,8 @@ "@fontsource/poppins": "^5.0.15", "@fontsource/source-sans-pro": "^5.0.8", "jsonpath-plus": "^10.2.0", - "@gen3/core": "^0.10.73", - "@gen3/frontend": "^0.10.73", + "@gen3/core": "^0.10.74", + "@gen3/frontend": "^0.10.74", "@grafana/faro-react": "^1.9.1", "@grafana/faro-web-sdk": "^1.9.1", "@grafana/faro-web-tracing": "^1.9.1", @@ -44,7 +44,7 @@ }, "devDependencies": { "@axe-core/react": "^4.10.0", - "@gen3/toolsff": "^0.10.73", + "@gen3/toolsff": "^0.10.74", "@tailwindcss/aspect-ratio": "^0.4.2", "@tailwindcss/forms": "^0.5.3", "@tailwindcss/line-clamp": "^0.4.2", From de73530c1cdd62fa4e54a5321d5513b80975b2df Mon Sep 17 00:00:00 2001 From: Advaith Mahendrakar <120632885+AdvaithMahendrakar12@users.noreply.github.com> Date: Fri, 24 Jan 2025 20:34:28 +0530 Subject: [PATCH 18/22] Added Loading.tsx component and integrated Suspense (#65) * Added Loading.tsx component and integrated Suspense * Moved Loading.tsx to components folder and updated _app.tsx --- src/components/Loading.tsx | 12 +++++++++++ src/pages/_app.tsx | 41 +++++++++++++++++++++++++++----------- 2 files changed, 41 insertions(+), 12 deletions(-) create mode 100644 src/components/Loading.tsx diff --git a/src/components/Loading.tsx b/src/components/Loading.tsx new file mode 100644 index 0000000..129771a --- /dev/null +++ b/src/components/Loading.tsx @@ -0,0 +1,12 @@ + +import React from 'react'; + +const Loading = () => { + return ( +
+
+
+ ); +}; +export default Loading; + diff --git a/src/pages/_app.tsx b/src/pages/_app.tsx index 4396ec6..ed240fc 100644 --- a/src/pages/_app.tsx +++ b/src/pages/_app.tsx @@ -1,9 +1,10 @@ import App, { AppProps, AppContext, AppInitialProps } from 'next/app'; -import React, { useEffect, useMemo, useRef } from 'react'; +import React, { useState,useEffect, useMemo, useRef ,Suspense} from 'react'; import { MantineProvider } from '@mantine/core'; import { Faro, FaroErrorBoundary, withFaroProfiler } from '@grafana/faro-react'; import { initGrafanaFaro } from '../lib/Grafana/grafana'; + import { Gen3Provider, TenStringArray, @@ -29,6 +30,7 @@ import '@fontsource/poppins'; import { setDRSHostnames } from '@gen3/core'; import drsHostnames from '../../config/drsHostnames.json'; import { loadContent } from '@/lib/content/loadContent'; +import Loading from '../components/Loading'; if (typeof window !== 'undefined' && process.env.NODE_ENV !== 'production') { // eslint-disable-next-line @typescript-eslint/no-var-requires, @typescript-eslint/no-require-imports @@ -78,26 +80,41 @@ const Gen3App = ({ // } }, []); + const theme = useMemo( () => createMantineTheme(themeFonts, colors), [themeFonts, colors], ); + const [isClient, setIsClient] = useState(false); + useEffect(() => { + setIsClient(true); // Only on client-side + }, []); return ( - - - - - - - + <> + {isClient ? ( + }> + + + + + + + + + ) : ( + // Show some fallback UI while waiting for the client to load + + )} + ); }; + // TODO: replace with page router Gen3App.getInitialProps = async ( context: AppContext, From 2a1c7732a6228db7998124ed24e624650971f505 Mon Sep 17 00:00:00 2001 From: Craig Barnes Date: Mon, 27 Jan 2025 15:56:43 -0600 Subject: [PATCH 19/22] update to 0.10.77 (#67) --- package-lock.json | 26 +++++++++++++------------- package.json | 6 +++--- 2 files changed, 16 insertions(+), 16 deletions(-) diff --git a/package-lock.json b/package-lock.json index eba35b1..dc0ddcb 100644 --- a/package-lock.json +++ b/package-lock.json @@ -11,8 +11,8 @@ "@fontsource/montserrat": "^5.0.19", "@fontsource/poppins": "^5.0.15", "@fontsource/source-sans-pro": "^5.0.8", - "@gen3/core": "^0.10.74", - "@gen3/frontend": "^0.10.74", + "@gen3/core": "^0.10.77", + "@gen3/frontend": "^0.10.77", "@grafana/faro-react": "^1.9.1", "@grafana/faro-web-sdk": "^1.9.1", "@grafana/faro-web-tracing": "^1.9.1", @@ -34,7 +34,7 @@ }, "devDependencies": { "@axe-core/react": "^4.10.0", - "@gen3/toolsff": "^0.10.74", + "@gen3/toolsff": "^0.10.77", "@tailwindcss/aspect-ratio": "^0.4.2", "@tailwindcss/forms": "^0.5.3", "@tailwindcss/line-clamp": "^0.4.2", @@ -1717,9 +1717,9 @@ "license": "OFL-1.1" }, "node_modules/@gen3/core": { - "version": "0.10.74", - "resolved": "https://registry.npmjs.org/@gen3/core/-/core-0.10.74.tgz", - "integrity": "sha512-E8MsoiPexPmuZQYg0JBkuOG4EswF8fAEPFAQMx/xj9Y7EwHYq8GMzAOYDH58gc02EeB9JaMPwXpMdSn/BHLJIA==", + "version": "0.10.77", + "resolved": "https://registry.npmjs.org/@gen3/core/-/core-0.10.77.tgz", + "integrity": "sha512-qhnwYVm6SNxAd8eihIR4uyDOS4es75VILJeD2qM/8tHaC8fNWDqm9neC+EnFlzdYHpDpxpaIinZTYyEg/Co62Q==", "license": "Apache-2.0", "dependencies": { "@reduxjs/toolkit": "^2.5.0", @@ -1743,12 +1743,12 @@ } }, "node_modules/@gen3/frontend": { - "version": "0.10.74", - "resolved": "https://registry.npmjs.org/@gen3/frontend/-/frontend-0.10.74.tgz", - "integrity": "sha512-VSBeneqSkgLadU3FNRVduOAElIk06cHVRJ2lU5E0dm1Eh/DkqQ2lqF8VRnMt3mrW5zP2QvlADZ/o+vzYvs9FPA==", + "version": "0.10.77", + "resolved": "https://registry.npmjs.org/@gen3/frontend/-/frontend-0.10.77.tgz", + "integrity": "sha512-8XVsoIrGThWtq6ZdWd5eBoPeOWbCTmG0LxTtSDGVdkoGU1GeUg6SD6dkKkWHQG5UvKJqltt9ZUrxHrP9YTJg5A==", "license": "Apache-2.0", "dependencies": { - "@gen3/core": "^0.10.74", + "@gen3/core": "^0.10.77", "@graphiql/react": "^0.23.1", "@hello-pangea/dnd": "^17.0.0", "@iconify/react": "^5.0.2", @@ -1892,9 +1892,9 @@ } }, "node_modules/@gen3/toolsff": { - "version": "0.10.74", - "resolved": "https://registry.npmjs.org/@gen3/toolsff/-/toolsff-0.10.74.tgz", - "integrity": "sha512-DR8jVt00PPal/XvE3j5R8Gz66Jn8G5DeVyF1bTI33euEji2yV0zFJX5hggjTZFG2JZA1t/rklmzogNQvEPL3Mg==", + "version": "0.10.77", + "resolved": "https://registry.npmjs.org/@gen3/toolsff/-/toolsff-0.10.77.tgz", + "integrity": "sha512-O4ajaSVLsDezwfPv92mfKBc3U1ZEvB4LljT0GMOQZZKSE3Mql5KTKUEtSKdwRzEDrp2AYcmCNJQZbOdJ7U3WJg==", "dev": true, "license": "Apache-2.0", "dependencies": { diff --git a/package.json b/package.json index bfa9474..acca839 100644 --- a/package.json +++ b/package.json @@ -22,8 +22,8 @@ "@fontsource/poppins": "^5.0.15", "@fontsource/source-sans-pro": "^5.0.8", "jsonpath-plus": "^10.2.0", - "@gen3/core": "^0.10.74", - "@gen3/frontend": "^0.10.74", + "@gen3/core": "^0.10.77", + "@gen3/frontend": "^0.10.77", "@grafana/faro-react": "^1.9.1", "@grafana/faro-web-sdk": "^1.9.1", "@grafana/faro-web-tracing": "^1.9.1", @@ -44,7 +44,7 @@ }, "devDependencies": { "@axe-core/react": "^4.10.0", - "@gen3/toolsff": "^0.10.74", + "@gen3/toolsff": "^0.10.77", "@tailwindcss/aspect-ratio": "^0.4.2", "@tailwindcss/forms": "^0.5.3", "@tailwindcss/line-clamp": "^0.4.2", From fa7564722b2c0e9c27c0012a68a391871a07740d Mon Sep 17 00:00:00 2001 From: Craig Barnes Date: Tue, 28 Jan 2025 12:46:31 -0600 Subject: [PATCH 20/22] update to 0.10.78 (#68) --- package-lock.json | 30 +++++++++++++++--------------- package.json | 8 ++++---- 2 files changed, 19 insertions(+), 19 deletions(-) diff --git a/package-lock.json b/package-lock.json index dc0ddcb..36871e5 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,18 +1,18 @@ { "name": "@gen3/commons-portal-app-base", - "version": "0.10.73", + "version": "0.10.78", "lockfileVersion": 3, "requires": true, "packages": { "": { "name": "@gen3/commons-portal-app-base", - "version": "0.10.73", + "version": "0.10.78", "dependencies": { "@fontsource/montserrat": "^5.0.19", "@fontsource/poppins": "^5.0.15", "@fontsource/source-sans-pro": "^5.0.8", - "@gen3/core": "^0.10.77", - "@gen3/frontend": "^0.10.77", + "@gen3/core": "^0.10.78", + "@gen3/frontend": "^0.10.78", "@grafana/faro-react": "^1.9.1", "@grafana/faro-web-sdk": "^1.9.1", "@grafana/faro-web-tracing": "^1.9.1", @@ -34,7 +34,7 @@ }, "devDependencies": { "@axe-core/react": "^4.10.0", - "@gen3/toolsff": "^0.10.77", + "@gen3/toolsff": "^0.10.78", "@tailwindcss/aspect-ratio": "^0.4.2", "@tailwindcss/forms": "^0.5.3", "@tailwindcss/line-clamp": "^0.4.2", @@ -1717,9 +1717,9 @@ "license": "OFL-1.1" }, "node_modules/@gen3/core": { - "version": "0.10.77", - "resolved": "https://registry.npmjs.org/@gen3/core/-/core-0.10.77.tgz", - "integrity": "sha512-qhnwYVm6SNxAd8eihIR4uyDOS4es75VILJeD2qM/8tHaC8fNWDqm9neC+EnFlzdYHpDpxpaIinZTYyEg/Co62Q==", + "version": "0.10.78", + "resolved": "https://registry.npmjs.org/@gen3/core/-/core-0.10.78.tgz", + "integrity": "sha512-4cRQ85wQ/HMDOgI2l/FUZe0ZDUB5eZP7ZLT8bHjFyqz1SbZtgBGd60KrQeUz0HGUXEqKaJyTV3UVxIUvxOgXdw==", "license": "Apache-2.0", "dependencies": { "@reduxjs/toolkit": "^2.5.0", @@ -1743,12 +1743,12 @@ } }, "node_modules/@gen3/frontend": { - "version": "0.10.77", - "resolved": "https://registry.npmjs.org/@gen3/frontend/-/frontend-0.10.77.tgz", - "integrity": "sha512-8XVsoIrGThWtq6ZdWd5eBoPeOWbCTmG0LxTtSDGVdkoGU1GeUg6SD6dkKkWHQG5UvKJqltt9ZUrxHrP9YTJg5A==", + "version": "0.10.78", + "resolved": "https://registry.npmjs.org/@gen3/frontend/-/frontend-0.10.78.tgz", + "integrity": "sha512-uvyuFrnnNhZn35V2ky5DkrzrswlmOwfXs4fireWnKUP+O6P0Ecscr8x21JKUICIH8I/UMaE77xYPhICduTX9nQ==", "license": "Apache-2.0", "dependencies": { - "@gen3/core": "^0.10.77", + "@gen3/core": "^0.10.78", "@graphiql/react": "^0.23.1", "@hello-pangea/dnd": "^17.0.0", "@iconify/react": "^5.0.2", @@ -1892,9 +1892,9 @@ } }, "node_modules/@gen3/toolsff": { - "version": "0.10.77", - "resolved": "https://registry.npmjs.org/@gen3/toolsff/-/toolsff-0.10.77.tgz", - "integrity": "sha512-O4ajaSVLsDezwfPv92mfKBc3U1ZEvB4LljT0GMOQZZKSE3Mql5KTKUEtSKdwRzEDrp2AYcmCNJQZbOdJ7U3WJg==", + "version": "0.10.78", + "resolved": "https://registry.npmjs.org/@gen3/toolsff/-/toolsff-0.10.78.tgz", + "integrity": "sha512-iFF+VlXGNKuOwZ/Jg7gh0RCygUS3S+FDu3G+3qHNnmrpN/KEZvL4yscdxiRSQmCjin99QpuJzla4FNt4raTx/A==", "dev": true, "license": "Apache-2.0", "dependencies": { diff --git a/package.json b/package.json index acca839..08ef956 100644 --- a/package.json +++ b/package.json @@ -1,6 +1,6 @@ { "name": "@gen3/commons-portal-app-base", - "version": "0.10.73", + "version": "0.10.78", "private": "true", "engines": { "npm": ">=10.2.3", @@ -22,8 +22,8 @@ "@fontsource/poppins": "^5.0.15", "@fontsource/source-sans-pro": "^5.0.8", "jsonpath-plus": "^10.2.0", - "@gen3/core": "^0.10.77", - "@gen3/frontend": "^0.10.77", + "@gen3/core": "^0.10.78", + "@gen3/frontend": "^0.10.78", "@grafana/faro-react": "^1.9.1", "@grafana/faro-web-sdk": "^1.9.1", "@grafana/faro-web-tracing": "^1.9.1", @@ -44,7 +44,7 @@ }, "devDependencies": { "@axe-core/react": "^4.10.0", - "@gen3/toolsff": "^0.10.77", + "@gen3/toolsff": "^0.10.78", "@tailwindcss/aspect-ratio": "^0.4.2", "@tailwindcss/forms": "^0.5.3", "@tailwindcss/line-clamp": "^0.4.2", From c0e2bd2ade2c255b6c099a35c0a1887b14adf3af Mon Sep 17 00:00:00 2001 From: craigrbarnes Date: Tue, 28 Jan 2025 13:50:13 -0600 Subject: [PATCH 21/22] add package lock --- package-lock.json | 89 ++++++----------------------------------------- 1 file changed, 11 insertions(+), 78 deletions(-) diff --git a/package-lock.json b/package-lock.json index 36871e5..3d78ee9 100644 --- a/package-lock.json +++ b/package-lock.json @@ -1,12 +1,12 @@ { - "name": "@gen3/commons-portal-app-base", - "version": "0.10.78", + "name": "@gen3/bih-data-portal", + "version": "0.1.3", "lockfileVersion": 3, "requires": true, "packages": { "": { - "name": "@gen3/commons-portal-app-base", - "version": "0.10.78", + "name": "@gen3/bih-data-portal", + "version": "0.1.3", "dependencies": { "@fontsource/montserrat": "^5.0.19", "@fontsource/poppins": "^5.0.15", @@ -53,9 +53,7 @@ "eslint-plugin-react-hooks": "^4.6.0", "next": "^14.2.23", "postcss": "^8.4.29", - "postcss-import": "^16.1.0", "postcss-loader": "^7.3.2", - "postcss-modules": "^6.0.0", "postcss-preset-env": "^8.4.2", "postcss-preset-mantine": "^1.17.0", "prettier": "^2.7.1", @@ -11546,26 +11544,6 @@ "url": "https://github.com/sponsors/ljharb" } }, - "node_modules/generic-names": { - "version": "4.0.0", - "resolved": "https://registry.npmjs.org/generic-names/-/generic-names-4.0.0.tgz", - "integrity": "sha512-ySFolZQfw9FoDb3ed9d80Cm9f0+r7qj+HJkWjeD9RBfpxEVTlVhol+gvaQB/78WbwYfbnNh8nWHHBSlg072y6A==", - "dev": true, - "license": "MIT", - "dependencies": { - "loader-utils": "^3.2.0" - } - }, - "node_modules/generic-names/node_modules/loader-utils": { - "version": "3.3.1", - "resolved": "https://registry.npmjs.org/loader-utils/-/loader-utils-3.3.1.tgz", - "integrity": "sha512-FMJTLMXfCLMLfJxcX9PFqX5qD88Z5MRGaZCVzfuqeZSPsyiBzs+pahDQjbIWz2QIzPZz0NX9Zy4FX3lmK6YHIg==", - "dev": true, - "license": "MIT", - "engines": { - "node": ">= 12.13.0" - } - }, "node_modules/gensync": { "version": "1.0.0-beta.2", "resolved": "https://registry.npmjs.org/gensync/-/gensync-1.0.0-beta.2.tgz", @@ -13240,6 +13218,7 @@ "resolved": "https://registry.npmjs.org/icss-utils/-/icss-utils-5.1.0.tgz", "integrity": "sha512-soFhflCVWLfRNOPU3iv5Z9VUdT44xFRbzjLsEzSr5AQmgqPMTHdU3PMT1Cf1ssx8fLNJDA1juftYl+PUcv3MqA==", "license": "ISC", + "peer": true, "engines": { "node": "^10 || ^12 || >= 14" }, @@ -15298,13 +15277,6 @@ "integrity": "sha512-v2kDEe57lecTulaDIuNTPy3Ry4gLGJ6Z1O3vE1krgXZNrsQ+LFTGHVxVjcXPs17LhbZVGedAJv8XZ1tvj5FvSg==", "license": "MIT" }, - "node_modules/lodash.camelcase": { - "version": "4.3.0", - "resolved": "https://registry.npmjs.org/lodash.camelcase/-/lodash.camelcase-4.3.0.tgz", - "integrity": "sha512-TwuEnCnxbc3rAvhf/LbG7tJUDzhqXyFnv3dtzLOPgCG/hODL7WFnsbwktkD7yUV0RrreP/l1PALq/YSg6VvjlA==", - "dev": true, - "license": "MIT" - }, "node_modules/lodash.castarray": { "version": "4.4.0", "resolved": "https://registry.npmjs.org/lodash.castarray/-/lodash.castarray-4.4.0.tgz", @@ -22913,24 +22885,6 @@ "postcss": "^8.4" } }, - "node_modules/postcss-import": { - "version": "16.1.0", - "resolved": "https://registry.npmjs.org/postcss-import/-/postcss-import-16.1.0.tgz", - "integrity": "sha512-7hsAZ4xGXl4MW+OKEWCnF6T5jqBw80/EE9aXg1r2yyn1RsVEU8EtKXbijEODa+rg7iih4bKf7vlvTGYR4CnPNg==", - "dev": true, - "license": "MIT", - "dependencies": { - "postcss-value-parser": "^4.0.0", - "read-cache": "^1.0.0", - "resolve": "^1.1.7" - }, - "engines": { - "node": ">=18.0.0" - }, - "peerDependencies": { - "postcss": "^8.0.0" - } - }, "node_modules/postcss-initial": { "version": "4.0.1", "resolved": "https://registry.npmjs.org/postcss-initial/-/postcss-initial-4.0.1.tgz", @@ -23092,31 +23046,12 @@ "postcss": "^8.2.14" } }, - "node_modules/postcss-modules": { - "version": "6.0.1", - "resolved": "https://registry.npmjs.org/postcss-modules/-/postcss-modules-6.0.1.tgz", - "integrity": "sha512-zyo2sAkVvuZFFy0gc2+4O+xar5dYlaVy/ebO24KT0ftk/iJevSNyPyQellsBLlnccwh7f6V6Y4GvuKRYToNgpQ==", - "dev": true, - "license": "MIT", - "dependencies": { - "generic-names": "^4.0.0", - "icss-utils": "^5.1.0", - "lodash.camelcase": "^4.3.0", - "postcss-modules-extract-imports": "^3.1.0", - "postcss-modules-local-by-default": "^4.0.5", - "postcss-modules-scope": "^3.2.0", - "postcss-modules-values": "^4.0.0", - "string-hash": "^1.1.3" - }, - "peerDependencies": { - "postcss": "^8.0.0" - } - }, "node_modules/postcss-modules-extract-imports": { "version": "3.1.0", "resolved": "https://registry.npmjs.org/postcss-modules-extract-imports/-/postcss-modules-extract-imports-3.1.0.tgz", "integrity": "sha512-k3kNe0aNFQDAZGbin48pL2VNidTF0w4/eASDsxlyspobzU3wZQLOGj7L9gfRe0Jo9/4uud09DsjFNH7winGv8Q==", "license": "ISC", + "peer": true, "engines": { "node": "^10 || ^12 || >= 14" }, @@ -23129,6 +23064,7 @@ "resolved": "https://registry.npmjs.org/postcss-modules-local-by-default/-/postcss-modules-local-by-default-4.2.0.tgz", "integrity": "sha512-5kcJm/zk+GJDSfw+V/42fJ5fhjL5YbFDl8nVdXkJPLLW+Vf9mTD5Xe0wqIaDnLuL2U6cDNpTr+UQ+v2HWIBhzw==", "license": "MIT", + "peer": true, "dependencies": { "icss-utils": "^5.0.0", "postcss-selector-parser": "^7.0.0", @@ -23146,6 +23082,7 @@ "resolved": "https://registry.npmjs.org/postcss-selector-parser/-/postcss-selector-parser-7.0.0.tgz", "integrity": "sha512-9RbEr1Y7FFfptd/1eEdntyjMwLeghW1bHX9GWjXo19vx4ytPQhANltvVxDggzJl7mnWM+dX28kb6cyS/4iQjlQ==", "license": "MIT", + "peer": true, "dependencies": { "cssesc": "^3.0.0", "util-deprecate": "^1.0.2" @@ -23159,6 +23096,7 @@ "resolved": "https://registry.npmjs.org/postcss-modules-scope/-/postcss-modules-scope-3.2.1.tgz", "integrity": "sha512-m9jZstCVaqGjTAuny8MdgE88scJnCiQSlSrOWcTQgM2t32UBe+MUmFSO5t7VMSfAf/FJKImAxBav8ooCHJXCJA==", "license": "ISC", + "peer": true, "dependencies": { "postcss-selector-parser": "^7.0.0" }, @@ -23174,6 +23112,7 @@ "resolved": "https://registry.npmjs.org/postcss-selector-parser/-/postcss-selector-parser-7.0.0.tgz", "integrity": "sha512-9RbEr1Y7FFfptd/1eEdntyjMwLeghW1bHX9GWjXo19vx4ytPQhANltvVxDggzJl7mnWM+dX28kb6cyS/4iQjlQ==", "license": "MIT", + "peer": true, "dependencies": { "cssesc": "^3.0.0", "util-deprecate": "^1.0.2" @@ -23187,6 +23126,7 @@ "resolved": "https://registry.npmjs.org/postcss-modules-values/-/postcss-modules-values-4.0.0.tgz", "integrity": "sha512-RDxHkAiEGI78gS2ofyvCsu7iycRv7oqw5xMWn9iMoR0N/7mf9D50ecQqUo5BZ9Zh2vH4bCUR/ktCqbB9m8vJjQ==", "license": "ISC", + "peer": true, "dependencies": { "icss-utils": "^5.0.0" }, @@ -27655,13 +27595,6 @@ "license": "MIT", "peer": true }, - "node_modules/string-hash": { - "version": "1.1.3", - "resolved": "https://registry.npmjs.org/string-hash/-/string-hash-1.1.3.tgz", - "integrity": "sha512-kJUvRUFK49aub+a7T1nNE66EJbZBMnBgoC1UbCZ5n6bsZKBRga4KgBRTMn/pFkeCZSYtNeSyMxPDM0AXWELk2A==", - "dev": true, - "license": "CC0-1.0" - }, "node_modules/string-length": { "version": "4.0.2", "resolved": "https://registry.npmjs.org/string-length/-/string-length-4.0.2.tgz", From 176fa85440dca1af9221fd0fa10a4201aa5be259 Mon Sep 17 00:00:00 2001 From: craigrbarnes Date: Tue, 28 Jan 2025 13:55:09 -0600 Subject: [PATCH 22/22] update Diacom to Dicom --- config/bih/explorer.json | 2 +- src/lib/CohortBuilder/CustomCellRenderers.tsx | 3 +-- 2 files changed, 2 insertions(+), 3 deletions(-) diff --git a/config/bih/explorer.json b/config/bih/explorer.json index b514b25..f590a9b 100644 --- a/config/bih/explorer.json +++ b/config/bih/explorer.json @@ -495,7 +495,7 @@ "title": "DICOM Viewer URL", "type": "link", "width" : "32px", - "cellRenderFunction": "DiacomLink" + "cellRenderFunction": "DicomLink" }, "subject_id": { "title": "Subject ID" diff --git a/src/lib/CohortBuilder/CustomCellRenderers.tsx b/src/lib/CohortBuilder/CustomCellRenderers.tsx index 331da16..e759f7d 100644 --- a/src/lib/CohortBuilder/CustomCellRenderers.tsx +++ b/src/lib/CohortBuilder/CustomCellRenderers.tsx @@ -25,8 +25,7 @@ const RenderLinkCell = ( }; -const RenderDicomLink = ({ cell }: CellRendererFunctionProps) => { - if (!cell.getValue() || cell.getValue() === '') { + const RenderDicomLink = ({ cell }: CellRendererFunctionProps) => { if (!cell?.getValue() || cell?.getValue() === '') { return ;