From 34a549da727522c0c3a36d384908217d434764b8 Mon Sep 17 00:00:00 2001 From: Colin Date: Tue, 11 Jul 2023 11:00:19 -0400 Subject: [PATCH 1/5] Delete embedded demos from main repo4 --- embedded_demos/clone_demos.sh | 15 + .../jbrowse-react-app-cra5/.gitignore | 23 - .../jbrowse-react-app-cra5/README.md | 21 - .../jbrowse-react-app-cra5/craco.config.js | 23 - .../jbrowse-react-app-cra5/package.json | 53 - .../jbrowse-react-app-cra5/public/favicon.ico | Bin 3870 -> 0 bytes .../jbrowse-react-app-cra5/public/index.html | 43 - .../jbrowse-react-app-cra5/public/logo192.png | Bin 5347 -> 0 bytes .../jbrowse-react-app-cra5/public/logo512.png | Bin 9664 -> 0 bytes .../public/manifest.json | 25 - .../jbrowse-react-app-cra5/public/robots.txt | 3 - .../jbrowse-react-app-cra5/src/App.tsx | 64 - .../jbrowse-react-app-cra5/src/config.ts | 277 - .../jbrowse-react-app-cra5/src/index.css | 13 - .../jbrowse-react-app-cra5/src/index.tsx | 6 - .../src/react-app-env.d.ts | 1 - 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delete mode 100644 embedded_demos/jbrowse-react-linear-genome-view/src/index.tsx delete mode 100644 embedded_demos/jbrowse-react-linear-genome-view/src/react-app-env.d.ts delete mode 100644 embedded_demos/jbrowse-react-linear-genome-view/src/tracks.ts delete mode 100644 embedded_demos/jbrowse-react-linear-genome-view/tsconfig.json delete mode 100644 embedded_demos/jbrowse-react-linear-genome-view/yarn.lock create mode 100644 embedded_demos/push_demos.sh diff --git a/embedded_demos/clone_demos.sh b/embedded_demos/clone_demos.sh new file mode 100755 index 0000000000..c5e99e5752 --- /dev/null +++ b/embedded_demos/clone_demos.sh @@ -0,0 +1,15 @@ +#!/bin/bash +git clone git@github.com:cmdcolin/jbrowse-react-linear-genome-view-vanillajs +git clone git@github.com:cmdcolin/jbrowse-react-linear-genome-view-cra5 +git clone git@github.com:cmdcolin/jbrowse-react-linear-genome-view-cra4 +git clone git@github.com:cmdcolin/jbrowse-react-linear-genome-view-vite +git clone git@github.com:cmdcolin/jbrowse-react-linear-genome-view-nextjs + +git clone git@github.com:cmdcolin/jbrowse-react-circular-genome-view-vanillajs +git clone git@github.com:cmdcolin/jbrowse-react-circular-genome-view-cra5 +git clone git@github.com:cmdcolin/jbrowse-react-circular-genome-view-cra4 +git clone git@github.com:cmdcolin/jbrowse-react-circular-genome-view-nextjs + +git clone git@github.com:cmdcolin/jbrowse-react-app-nextjs +git clone git@github.com:cmdcolin/jbrowse-react-app-vite +git clone git@github.com:cmdcolin/jbrowse-react-app-cra5 diff --git a/embedded_demos/jbrowse-react-app-cra5/.gitignore b/embedded_demos/jbrowse-react-app-cra5/.gitignore deleted file mode 100644 index 4d29575de8..0000000000 --- a/embedded_demos/jbrowse-react-app-cra5/.gitignore +++ /dev/null @@ -1,23 +0,0 @@ -# See https://help.github.com/articles/ignoring-files/ for more about ignoring files. - -# dependencies -/node_modules -/.pnp -.pnp.js - -# testing -/coverage - -# production -/build - -# misc -.DS_Store -.env.local -.env.development.local -.env.test.local -.env.production.local - -npm-debug.log* -yarn-debug.log* -yarn-error.log* diff --git a/embedded_demos/jbrowse-react-app-cra5/README.md b/embedded_demos/jbrowse-react-app-cra5/README.md deleted file mode 100644 index 823b1ee605..0000000000 --- a/embedded_demos/jbrowse-react-app-cra5/README.md +++ /dev/null @@ -1,21 +0,0 @@ -# jbrowse-react-app-cra5 - -This is a demo of using @jbrowse/react-app installed from NPM with -create-react-app v5 (which uses webpack 5) - -It uses craco to add the webpack NodePolyfillPlugin (used for Buffer polyfill, -etc) - -# Demo of `@jbrowse/react-app` with CRA 5 - -See this app running at https://jbrowse.org/demos/app-cra5/. - -Download this directory from the monorepo using -https://download-directory.github.io/?url=https%3A%2F%2Fgithub.com%2FGMOD%2Fjbrowse-components%2Ftree%2Fmain%2Fembedded_demos%2Fjbrowse-react-app-cra5 - -## Usage - -Run `yarn` and then `yarn start` to start a development instance - -Run `yarn build` which produces a `build` directory that can be deployed to a -static web server diff --git a/embedded_demos/jbrowse-react-app-cra5/craco.config.js b/embedded_demos/jbrowse-react-app-cra5/craco.config.js deleted file mode 100644 index 668feef6a7..0000000000 --- a/embedded_demos/jbrowse-react-app-cra5/craco.config.js +++ /dev/null @@ -1,23 +0,0 @@ -const NodePolyfillPlugin = require('node-polyfill-webpack-plugin') - -module.exports = { - devServer: config => { - config.static.staticOptions = { fallthrough: false } - return config - }, - webpack: { - plugins: [ - new NodePolyfillPlugin({ - excludeAliases: ['console'], - }), - ], - configure: config => { - config.resolve.fallback = { fs: false } - // the 'auto' setting is important for properly resolving the loading of - // worker chunks xref - // https://github.com/webpack/webpack/issues/13791#issuecomment-897579223 - config.output.publicPath = 'auto' - return config - }, - }, -} diff --git a/embedded_demos/jbrowse-react-app-cra5/package.json b/embedded_demos/jbrowse-react-app-cra5/package.json deleted file mode 100644 index 45542001ca..0000000000 --- a/embedded_demos/jbrowse-react-app-cra5/package.json +++ /dev/null @@ -1,53 +0,0 @@ -{ - "name": "jbrowse-react-app-cra5", - "version": "0.1.0", - "license": "MIT", - "private": true, - "dependencies": { - "@craco/craco": "^7.1.0", - "@fontsource/roboto": "^4.5.5", - "@jbrowse/react-app": "^2.0.0", - "@testing-library/jest-dom": "^5.16.4", - "@testing-library/react": "^13.4.0", - "@testing-library/user-event": "^14.4.3", - "@mui/system": "^5.0.0", - "@types/jest": "^29.2.2", - "@types/node": "^18.11.9", - "@types/react": "^18.0.25", - "@types/react-dom": "^18.0.8", - "node-polyfill-webpack-plugin": "^2.0.1", - "react": "^18.0.0", - "react-dom": "^18.0.0", - "react-scripts": "^5.0.1", - "typescript": "^5.0.4", - "web-vitals": "^3.3.1" - }, - "scripts": { - "start": "craco start", - "build": "craco build", - "test": "craco test", - "eject": "craco eject", - "predeploy": "npm run build", - "deploy": "aws s3 sync --delete build s3://jbrowse.org/demos/app-cra5/", - "postdeploy": "aws cloudfront create-invalidation --distribution-id E13LGELJOT4GQO --paths \"/demos/app-cra5/*\"" - }, - "eslintConfig": { - "extends": [ - "react-app", - "react-app/jest" - ] - }, - "browserslist": { - "production": [ - ">0.2%", - "not dead", - "not op_mini all" - ], - "development": [ - "last 1 chrome version", - "last 1 firefox version", - "last 1 safari version" - ] - }, - "homepage": "." -} diff --git a/embedded_demos/jbrowse-react-app-cra5/public/favicon.ico b/embedded_demos/jbrowse-react-app-cra5/public/favicon.ico deleted file mode 100644 index a11777cc471a4344702741ab1c8a588998b1311a..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 3870 zcma);c{J4h9>;%nil|2-o+rCuEF-(I%-F}ijC~o(k~HKAkr0)!FCj~d>`RtpD?8b; 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e9e57dc4d4..0000000000 --- a/embedded_demos/jbrowse-react-app-cra5/public/robots.txt +++ /dev/null @@ -1,3 +0,0 @@ -# https://www.robotstxt.org/robotstxt.html -User-agent: * -Disallow: diff --git a/embedded_demos/jbrowse-react-app-cra5/src/App.tsx b/embedded_demos/jbrowse-react-app-cra5/src/App.tsx deleted file mode 100644 index 24a20eb758..0000000000 --- a/embedded_demos/jbrowse-react-app-cra5/src/App.tsx +++ /dev/null @@ -1,64 +0,0 @@ -import React, { useState, useEffect } from 'react' -import { createViewState, JBrowseApp } from '@jbrowse/react-app' -import makeWorkerInstance from '@jbrowse/react-app/esm/makeWorkerInstance' -import '@fontsource/roboto' - -import config from './config' - -type ViewModel = ReturnType - -function View() { - const [viewState, setViewState] = useState() - const [stateSnapshot, setStateSnapshot] = useState('') - - useEffect(() => { - const state = createViewState({ - config, - makeWorkerInstance, - }) - setViewState(state) - }, []) - - if (!viewState) { - return null - } - - return ( - <> -

JBrowse 2 React App Demo (with create-react-app v5)

- -

Code

- - -

See the state

-
-

- The button below will show you the current session, which includes - things like what region the view is showing and which tracks are open. - This session JSON object can be used in the{' '} - defaultSession of createViewState. -

- -
- -

updates:

- - - diff --git a/embedded_demos/jbrowse-react-circular-genome-view-vanillajs/package.json b/embedded_demos/jbrowse-react-circular-genome-view-vanillajs/package.json deleted file mode 100644 index bc84b3f156..0000000000 --- a/embedded_demos/jbrowse-react-circular-genome-view-vanillajs/package.json +++ /dev/null @@ -1,7 +0,0 @@ -{ - "license": "MIT", - "scripts": { - "deploy": "aws s3 sync --delete . s3://jbrowse.org/demos/cgv-vanillajs/", - "postdeploy": "aws cloudfront create-invalidation --distribution-id E13LGELJOT4GQO --paths \"/demos/cgv-vanillajs/*\"" - } -} diff --git a/embedded_demos/jbrowse-react-circular-genome-view-vanillajs/tracks.js b/embedded_demos/jbrowse-react-circular-genome-view-vanillajs/tracks.js deleted file mode 100644 index b641868fff..0000000000 --- a/embedded_demos/jbrowse-react-circular-genome-view-vanillajs/tracks.js +++ /dev/null @@ -1,24 +0,0 @@ -const tracks = [ - { - type: 'VariantTrack', - trackId: 'pacbio_sv_vcf', - name: 'HG002 Pacbio SV (VCF)', - assemblyNames: ['hg19'], - category: ['GIAB'], - adapter: { - type: 'VcfTabixAdapter', - vcfGzLocation: { - uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/hg19/pacbio/hs37d5.HG002-SequelII-CCS.bnd-only.sv.vcf.gz', - locationType: 'UriLocation', - }, - index: { - location: { - uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/hg19/pacbio/hs37d5.HG002-SequelII-CCS.bnd-only.sv.vcf.gz.tbi', - locationType: 'UriLocation', - }, - }, - }, - }, -] - -export default tracks diff --git a/embedded_demos/jbrowse-react-circular-genome-view-vanillajs/yarn.lock b/embedded_demos/jbrowse-react-circular-genome-view-vanillajs/yarn.lock deleted file mode 100644 index fb57ccd13a..0000000000 --- a/embedded_demos/jbrowse-react-circular-genome-view-vanillajs/yarn.lock +++ /dev/null @@ -1,4 +0,0 @@ -# THIS IS AN AUTOGENERATED FILE. DO NOT EDIT THIS FILE DIRECTLY. -# yarn lockfile v1 - - diff --git a/embedded_demos/jbrowse-react-circular-genome-view/.env b/embedded_demos/jbrowse-react-circular-genome-view/.env deleted file mode 100644 index 6f809cc254..0000000000 --- a/embedded_demos/jbrowse-react-circular-genome-view/.env +++ /dev/null @@ -1 +0,0 @@ -SKIP_PREFLIGHT_CHECK=true diff --git a/embedded_demos/jbrowse-react-circular-genome-view/.gitignore b/embedded_demos/jbrowse-react-circular-genome-view/.gitignore deleted file mode 100644 index 378eac25d3..0000000000 --- a/embedded_demos/jbrowse-react-circular-genome-view/.gitignore +++ /dev/null @@ -1 +0,0 @@ -build diff --git a/embedded_demos/jbrowse-react-circular-genome-view/README.md b/embedded_demos/jbrowse-react-circular-genome-view/README.md deleted file mode 100644 index 3b183c8766..0000000000 --- a/embedded_demos/jbrowse-react-circular-genome-view/README.md +++ /dev/null @@ -1,14 +0,0 @@ -# Demo of `@jbrowse/react-circular-genome-view` - -See this app running at https://jbrowse.org/demos/cgv/. - -This demo is originally by [@garrettjstevens](https://github.com/garrettjstevens/). - -Download this directory from the monorepo using https://download-directory.github.io/?url=https%3A%2F%2Fgithub.com%2FGMOD%2Fjbrowse-components%2Ftree%2Fmain%2Fembedded_demos%2Fjbrowse-react-circular-genome-view - -## Usage - -Run `yarn` and then `yarn start` to start a development instance - -Run `yarn build` which produces a `build` directory that can be deployed to a -static web server diff --git a/embedded_demos/jbrowse-react-circular-genome-view/package.json b/embedded_demos/jbrowse-react-circular-genome-view/package.json deleted file mode 100644 index 190d5e28a6..0000000000 --- a/embedded_demos/jbrowse-react-circular-genome-view/package.json +++ /dev/null @@ -1,62 +0,0 @@ -{ - "name": "jbrowse-react-circular-genome-view-demo", - "version": "0.1.0", - "license": "MIT", - "private": true, - "dependencies": { - "@fontsource/roboto": "^4.5.3", - "@jbrowse/plugin-linear-genome-view": "^2.0.0", - "@jbrowse/react-circular-genome-view": "^2.0.0", - "@testing-library/jest-dom": "^5.11.4", - "@testing-library/react": "^11.1.0", - "@testing-library/user-event": "^12.1.10", - "@types/jest": "^26.0.15", - "@types/node": "^12.0.0", - "@types/react": "^18.0.0", - "@types/react-dom": "^18.0.0", - "react": "^17.0.2", - "react-dom": "^17.0.2", - "react-scripts": "4.0.3", - "typescript": "^4.1.2", - "web-vitals": "^1.0.1" - }, - "scripts": { - "start": "react-scripts start", - "build": "react-scripts build", - "test": "react-scripts test", - "eject": "react-scripts eject", - "predeploy": "npm run build", - "deploy": "aws s3 sync --delete build s3://jbrowse.org/demos/cgv/", - "postdeploy": "aws cloudfront create-invalidation --distribution-id E13LGELJOT4GQO --paths \"/demos/cgv/*\"" - }, - "eslintConfig": { - "extends": [ - "react-app", - "react-app/jest", - "plugin:prettier/recommended" - ] - }, - "prettier": { - "semi": false, - "singleQuote": true, - "trailingComma": "all" - }, - "browserslist": { - "production": [ - ">0.2%", - "not dead", - "not op_mini all" - ], - "development": [ - "last 1 chrome version", - "last 1 firefox version", - "last 1 safari version" - ] - }, - "devDependencies": { - "eslint-config-prettier": "^8.3.0", - "eslint-plugin-prettier": "^3.4.0", - "prettier": "^2.3.0" - }, - "homepage": "." -} diff --git a/embedded_demos/jbrowse-react-circular-genome-view/public/favicon.ico b/embedded_demos/jbrowse-react-circular-genome-view/public/favicon.ico deleted file mode 100644 index 74d9a84d2c98527606656a2ce676207d71864508..0000000000000000000000000000000000000000 GIT binary patch literal 0 HcmV?d00001 literal 15086 zcmd^Gc~q3w6`wRcN&ji_t{fi2BFfLtM{;s<^Zpj~ z)Lu?Z~(9`83;Naj+Cf$iwCJuJOgul_*3k2IEp!4T(E1Z4_GHl$obD}MIY|x*nK6A zuRRA^2zz@FeC@z$vPFaT&-<}s7Ot|IAX$B%UEt`!Y zJ$@_3cve$`vnM?;^Q%`dd(x|LU-1v@+cgXOchAO}Wgo+F+M7^RmgtS4QYo>O{F@c?@xZV9R4T%3!iQ7IDN!h zYTLZz_h&4zm8)3{!*a(+`+%(_?=xMAhZ6JtB#1U1*I#K^Q=$1w@_G|rAg&;8ZDJXx ziQi)BRI=h5F|Bfp*f3X*e60>`6lC=e(|x5GmGP)GJPQ=LkU?4&#-(mCQuL@IKh=8HPM$2NIp zx}jao_jJj9;WQze?P6xO*NX~rwN2Q@c3V7HYqPW6zFeo6n7iR zNfCH(?;Ceb_T%o|Y>Fta#plyBAfBQ+@jCl2fsXK8*0E!3YErN1e?Eve7T%0zrr1R_Ikf%k7K={&XX zL);$cPnOxc@eIrucpj{J7S!GrVi|nq6|y(5d!U_&WwW1xT%@v@#9BW^PnpdBMGaH6 z9ue-BiJgh>5i5v08ZoB3#7@L7>4K-<>~Elx!E-}D6Vf+X2P%2qpC|0nB(n}L5igc1 zp2L#Y(*5?t&GCV(tSn?^W+E*uP56~cOD%S`xBI)Aot>@q%dlUF*$VuY8&9q9kl2?f zVb(31#cWzZvVDf+b)$=0x~{9!#479~rFBLrE-p5ToppL1sIs!sD1ON=?L+S231PsF zL?E;fsJ7i?Z?);*_@uOExMcsPL?eTn{7md`>PG&)rP0#ej#08tgZE9w&c1Q>k1_=p z=wp}sWnPav25wyxN~IEVImHbd-&yuybIeu3ES2o{d)%(Or7mjY*Y)HScaAc|&N@tE z%dG_U5@G2C3oc^B-j?#RU7CS&+{-itM^C{$O}bXXPCwC4=`sY!=!^sa7sM84a`HItc; 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- JBrowse 2 React Circular Genome View Demo (with create-react-app v4) -

- -

Code

-

- The code for this app is available at{' '} - - https://github.com/GMOD/jbrowse-components/tree/main/embedded_demos/jbrowse-react-circular-genome-view - - . -

-

Control the view

-
-

- This is an example of controlling the view from other elements on the - page. Clicking on a button will rotate the view. -

- - -
-

See the state

-
-

- The button below will show you the current session, which includes - things like what region the view is showing and which tracks are open. - This session JSON object can be used in the{' '} - defaultSession of createViewState. -

- -
- -

updates:

- - - diff --git a/embedded_demos/jbrowse-react-linear-genome-view-vanillajs/package.json b/embedded_demos/jbrowse-react-linear-genome-view-vanillajs/package.json deleted file mode 100644 index ea3fe9c080..0000000000 --- a/embedded_demos/jbrowse-react-linear-genome-view-vanillajs/package.json +++ /dev/null @@ -1,7 +0,0 @@ -{ - "license": "MIT", - "scripts": { - "deploy": "aws s3 sync --delete . s3://jbrowse.org/demos/lgv-vanillajs/", - "postdeploy": "aws cloudfront create-invalidation --distribution-id E13LGELJOT4GQO --paths \"/demos/lgv-vanillajs/*\"" - } -} diff --git a/embedded_demos/jbrowse-react-linear-genome-view-vanillajs/tracks.js b/embedded_demos/jbrowse-react-linear-genome-view-vanillajs/tracks.js deleted file mode 100644 index fb6422b271..0000000000 --- a/embedded_demos/jbrowse-react-linear-genome-view-vanillajs/tracks.js +++ /dev/null @@ -1,113 +0,0 @@ -const tracks = [ - { - type: 'FeatureTrack', - trackId: 'genes', - name: 'NCBI RefSeq Genes', - assemblyNames: ['GRCh38'], - category: ['Genes'], - adapter: { - type: 'Gff3TabixAdapter', - gffGzLocation: { - uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/ncbi_refseq/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz', - }, - index: { - location: { - uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/ncbi_refseq/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz.tbi', - }, - }, - }, - textSearching: { - textSearchAdapter: { - type: 'TrixTextSearchAdapter', - textSearchAdapterId: 'gff3tabix_genes-index', - ixFilePath: { - uri: 'https://jbrowse.org/genomes/GRCh38/ncbi_refseq/trix/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz.ix', - }, - ixxFilePath: { - uri: 'https://jbrowse.org/genomes/GRCh38/ncbi_refseq/trix/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz.ixx', - }, - metaFilePath: { - uri: 'https://jbrowse.org/genomes/GRCh38/ncbi_refseq/trix/GCA_000001405.15_GRCh38_full_analysis_set.refseq_annotation.sorted.gff.gz_meta.json', - }, - assemblyNames: ['GRCh38'], - }, - }, - }, - { - type: 'FeatureTrack', - trackId: 'repeats_hg38', - name: 'Repeats', - assemblyNames: ['hg38'], - category: ['Annotation'], - adapter: { - type: 'BigBedAdapter', - bigBedLocation: { - uri: 'https://jbrowse.org/genomes/GRCh38/repeats.bb', - locationType: 'UriLocation', - }, - }, - }, - { - type: 'AlignmentsTrack', - trackId: 'NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome', - name: 'NA12878 Exome', - assemblyNames: ['GRCh38'], - category: ['1000 Genomes', 'Alignments'], - adapter: { - type: 'CramAdapter', - cramLocation: { - uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/alignments/NA12878/NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome.cram', - }, - craiLocation: { - uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/alignments/NA12878/NA12878.alt_bwamem_GRCh38DH.20150826.CEU.exome.cram.crai', - }, - sequenceAdapter: { - type: 'BgzipFastaAdapter', - fastaLocation: { - uri: 'https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz', - }, - faiLocation: { - uri: 'https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.fai', - }, - gziLocation: { - uri: 'https://jbrowse.org/genomes/GRCh38/fasta/hg38.prefix.fa.gz.gzi', - }, - }, - }, - }, - { - type: 'VariantTrack', - trackId: - 'ALL.wgs.shapeit2_integrated_snvindels_v2a.GRCh38.27022019.sites.vcf', - name: '1000 Genomes Variant Calls', - assemblyNames: ['GRCh38'], - category: ['1000 Genomes', 'Variants'], - adapter: { - type: 'VcfTabixAdapter', - vcfGzLocation: { - uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/variants/ALL.wgs.shapeit2_integrated_snvindels_v2a.GRCh38.27022019.sites.vcf.gz', - }, - index: { - location: { - uri: 'https://s3.amazonaws.com/jbrowse.org/genomes/GRCh38/variants/ALL.wgs.shapeit2_integrated_snvindels_v2a.GRCh38.27022019.sites.vcf.gz.tbi', - }, - }, - }, - }, - { - type: 'QuantitativeTrack', - trackId: 'hg38.100way.phyloP100way', - name: 'hg38.100way.phyloP100way', - category: ['Conservation'], - assemblyNames: ['hg38'], - adapter: { - type: 'BigWigAdapter', - bigWigLocation: { - uri: 'https://hgdownload.cse.ucsc.edu/goldenpath/hg38/phyloP100way/hg38.phyloP100way.bw', - locationType: 'UriLocation', - }, - }, - }, -] - -export default tracks diff --git a/embedded_demos/jbrowse-react-linear-genome-view-vanillajs/yarn.lock b/embedded_demos/jbrowse-react-linear-genome-view-vanillajs/yarn.lock deleted file mode 100644 index fb57ccd13a..0000000000 --- a/embedded_demos/jbrowse-react-linear-genome-view-vanillajs/yarn.lock +++ /dev/null @@ -1,4 +0,0 @@ -# THIS IS AN AUTOGENERATED FILE. DO NOT EDIT THIS FILE DIRECTLY. -# yarn lockfile v1 - - diff --git a/embedded_demos/jbrowse-react-linear-genome-view-vite/.gitignore b/embedded_demos/jbrowse-react-linear-genome-view-vite/.gitignore deleted file mode 100644 index d451ff16c1..0000000000 --- a/embedded_demos/jbrowse-react-linear-genome-view-vite/.gitignore +++ /dev/null @@ -1,5 +0,0 @@ -node_modules -.DS_Store -dist -dist-ssr -*.local diff --git a/embedded_demos/jbrowse-react-linear-genome-view-vite/README.md b/embedded_demos/jbrowse-react-linear-genome-view-vite/README.md deleted file mode 100644 index f22011de90..0000000000 --- a/embedded_demos/jbrowse-react-linear-genome-view-vite/README.md +++ /dev/null @@ -1,27 +0,0 @@ -# vite with @jbrowse/react-linear-genome-view - -Based on https://codesandbox.io/s/ylt4t?file=/vite.config.ts:478-540 by -@garrettjstevens - -This is a demo of using the linear genome view with vite (see -https://vitejs.dev/) - -Vite is a build system that is very fast and becoming more popular, using -esbuild and rollup instead of webpack - -This particular demo includes several polyfills that are needed for JBrowse -including the Buffer polyfill - -# Demo of `@jbrowse/react-linear-genome-view` with vite - -See this app running at https://jbrowse.org/demos/lgv-vite/. - -Download this directory from the monorepo using -https://download-directory.github.io/?url=https%3A%2F%2Fgithub.com%2FGMOD%2Fjbrowse-components%2Ftree%2Fmain%2Fembedded_demos%2Fjbrowse-react-linear-genome-view-vite - -## Usage - -Run `yarn` and then `yarn dev` to start a development instance - -Run `yarn build` which produces a `build` directory that can be deployed to a -static web server diff --git a/embedded_demos/jbrowse-react-linear-genome-view-vite/index.html b/embedded_demos/jbrowse-react-linear-genome-view-vite/index.html deleted file mode 100644 index 38f3861103..0000000000 --- a/embedded_demos/jbrowse-react-linear-genome-view-vite/index.html +++ /dev/null @@ -1,13 +0,0 @@ - - - - - - - Vite App - - -
- - - diff --git a/embedded_demos/jbrowse-react-linear-genome-view-vite/package.json b/embedded_demos/jbrowse-react-linear-genome-view-vite/package.json deleted file mode 100644 index fdb3fea547..0000000000 --- a/embedded_demos/jbrowse-react-linear-genome-view-vite/package.json +++ /dev/null @@ -1,31 +0,0 @@ -{ - "name": "vite-react-lgv", - "version": "0.0.0", - "license": "MIT", - "scripts": { - "dev": "vite", - "build": "vite build", - "preview": "vite preview", - "predeploy": "npm run build", - "deploy": "aws s3 sync --delete dist s3://jbrowse.org/demos/lgv-vite/", - "postdeploy": "aws cloudfront create-invalidation --distribution-id E13LGELJOT4GQO --paths \"/demos/lgv-vite/*\"" - }, - "dependencies": { - "@esbuild-plugins/node-modules-polyfill": "^0.2.2", - "@fontsource/roboto": "^5.0.3", - "@jbrowse/core": "^2.0.0", - "@jbrowse/react-linear-genome-view": "^2.0.0", - "@types/node": "^20.3.3", - "react": "^18.2.0", - "react-dom": "^18.2.0" - }, - "devDependencies": { - "@types/react": "^18.0.26", - "@types/react-dom": "^18.0.9", - "@vitejs/plugin-react": "^4.0.1", - "buffer": "^6.0.3", - "stream-browserify": "^3.0.0", - "typescript": "^5.1.6", - "vite": "^4.0.0" - } -} diff --git a/embedded_demos/jbrowse-react-linear-genome-view-vite/src/App.tsx b/embedded_demos/jbrowse-react-linear-genome-view-vite/src/App.tsx deleted file mode 100644 index 11cd54243e..0000000000 --- a/embedded_demos/jbrowse-react-linear-genome-view-vite/src/App.tsx +++ /dev/null @@ -1,105 +0,0 @@ -import React, { useState, useEffect } from 'react' -import '@fontsource/roboto' -import { - createViewState, - JBrowseLinearGenomeView, -} from '@jbrowse/react-linear-genome-view' - -import assembly from './assembly' -import tracks from './tracks' -import defaultSession from './defaultSession' - -type ViewModel = ReturnType - -function View() { - const [viewState, setViewState] = useState() - const [patches, setPatches] = useState('') - const [stateSnapshot, setStateSnapshot] = useState('') - - useEffect(() => { - const state = createViewState({ - assembly, - tracks, - defaultSession, - onChange: patch => { - setPatches(previous => previous + JSON.stringify(patch) + '\n') - }, - }) - setViewState(state) - }, []) - - if (!viewState) { - return null - } - - return ( - <> -

JBrowse 2 React Linear Genome View Demo w/ vite

- -

Code

-

- The code for this app is available at{' '} - - https://github.com/GMOD/jbrowse-components/tree/main/embedded_demos/jbrowse-react-linear-genome-view-vite - - . -

-

Control the view

-
-

- This is an example of controlling the view from other elements on the - page. Clicking on a button will navigate the view to the location of - that gene. -

- - -
-

See the state

-
-

- The button below will show you the current session, which includes - things like what region the view is showing and which tracks are open. - This session JSON object can be used in the{' '} - defaultSession of createViewState. -

- -
-

- The code for this app is available at{' '} - - https://github.com/GMOD/jbrowse-components/tree/main/embedded_demos/jbrowse-react-app-cra5 - - . -