diff --git a/packages/sites/genomics-site/package.json b/packages/sites/genomics-site/package.json index 8f1a4417fe..c245f2d478 100644 --- a/packages/sites/genomics-site/package.json +++ b/packages/sites/genomics-site/package.json @@ -94,5 +94,8 @@ }, "files": [ "dist" - ] + ], + "dependencies": { + "@jbrowse/react-linear-genome-view": "^2.16.1" + } } diff --git a/packages/sites/genomics-site/webapp/wdkCustomization/js/client/components/common/Gbrowse.jsx b/packages/sites/genomics-site/webapp/wdkCustomization/js/client/components/common/Gbrowse.jsx index 69962ecd0f..05ff4aa5a9 100644 --- a/packages/sites/genomics-site/webapp/wdkCustomization/js/client/components/common/Gbrowse.jsx +++ b/packages/sites/genomics-site/webapp/wdkCustomization/js/client/components/common/Gbrowse.jsx @@ -3,7 +3,7 @@ import { once, debounce } from 'lodash'; import PropTypes from 'prop-types'; import React, { PureComponent } from 'react'; import { httpGet } from '@veupathdb/web-common/lib/util/http'; -import { JbrowseIframe } from '@veupathdb/web-common/lib/components/JbrowseIframe'; +import JbrowseIframe from './JBrowse2'; // stand-in for iframe component - it's not an iframe any more import { Loading } from '@veupathdb/wdk-client/lib/Components'; import newFeatureImage from '@veupathdb/wdk-client/lib/Core/Style/images/new-feature.png'; diff --git a/packages/sites/genomics-site/webapp/wdkCustomization/js/client/components/common/JBrowse2.tsx b/packages/sites/genomics-site/webapp/wdkCustomization/js/client/components/common/JBrowse2.tsx new file mode 100644 index 0000000000..4eee2a57ec --- /dev/null +++ b/packages/sites/genomics-site/webapp/wdkCustomization/js/client/components/common/JBrowse2.tsx @@ -0,0 +1,73 @@ +import React, { useEffect, useState } from 'react'; +import { Loading } from '@veupathdb/wdk-client/lib/Components'; +import { + createViewState, + JBrowseLinearGenomeView, +} from '@jbrowse/react-linear-genome-view'; + +interface JBrowseConfig { + assemblies: { name: string }[]; + tracks: any[]; +} + +interface Props { + jbrowseUrl: string; + height: number; +} + +export default function JBrowse2LinearView({ + jbrowseUrl, + height = 400, +}: Props) { + // const url = new URL(jbrowseUrl, 'https://example.com'); + // const params = url.searchParams; + const assemblyId = 'agamPEST'; // (params.get('data') ?? '').split('/').pop(); // TO DO: better fallback + const location = 'AgamP4_2L'; // params.get('loc'); + // const tracks = params.get('tracks'); // comma-delimited track ids + + const [config, setConfig] = useState(); + const [loading, setLoading] = useState(true); + + // Could use wdk usePromise? or react-query? + useEffect(() => { + // Fetch the config JSON + fetch('/jbrowse2/config.json') + .then((response) => { + if (!response.ok) { + throw new Error(`Error: ${response.status}`); + } + return response.json(); + }) + .then((data) => { + setConfig(data); + setLoading(false); + }) + .catch((error) => { + console.error('Failed to load JSON config:', error); + setLoading(false); // Set to false to avoid infinite loading + }); + }, []); + + if (loading) { + return ; + } + + if (!config) { + return
Error loading configuration
; // Error handling fallback - TO DO add contact-us etc + } + + const assembly = config.assemblies.find(({ name }) => name === assemblyId); + + if (!assembly) { + return
Error finding assembly '{assemblyId}'
; + } + const { tracks } = config; + + const viewState = createViewState({ + assembly, + tracks, + location, + }); + + return ; +} diff --git a/packages/sites/genomics-site/webpack.config.local.mjs b/packages/sites/genomics-site/webpack.config.local.mjs index 31da24b884..fe352b8a76 100644 --- a/packages/sites/genomics-site/webpack.config.local.mjs +++ b/packages/sites/genomics-site/webpack.config.local.mjs @@ -17,6 +17,8 @@ export default configure({ ...makeCommonDevServerConfig({ rootClientUrl: process.env.ROOT_URL, proxies: { + [process.env.JBROWSE2_DATA_ENDPOINT]: process.env.JBROWSE2_DATA_URL, + [process.env.JBROWSE2_ENDPOINT]: process.env.JBROWSE2_URL, [process.env.WDK_SERVICE_ENDPOINT]: process.env.WDK_SERVICE_URL, [process.env.VDI_SERVICE_ENDPOINT]: process.env.VDI_SERVICE_URL, [process.env.SITE_SEARCH_SERVICE_ENDPOINT]: process.env.SITE_SEARCH_SERVICE_URL, diff --git a/yarn.lock b/yarn.lock index f11d63216a..3fff438f5f 100644 --- a/yarn.lock +++ b/yarn.lock @@ -1754,6 +1754,15 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