From adac7f14ebe156cbf27c1879a5a05a420506cb57 Mon Sep 17 00:00:00 2001 From: Yukthi Date: Sat, 5 Oct 2024 14:02:25 -0400 Subject: [PATCH] a bunch of changes that aren't working right now --- Eplant/Eplant.tsx | 158 ++++++- Eplant/EplantLayout.tsx | 13 +- Eplant/UI/Layout/ViewContainer/index.tsx | 58 ++- Eplant/UI/Layout/ViewContainer/types.ts | 7 + Eplant/UI/Layout/ViewNotSupported.tsx | 6 +- Eplant/UI/Sidebar.tsx | 5 +- Eplant/{config.ts => config.tsx} | 16 +- Eplant/main.tsx | 37 +- Eplant/util/router/index.ts | 13 + Eplant/views/CellEFP/CellEFP.tsx | 164 +++++++ .../views/CellEFP/CellEFPDataObject/index.tsx | 1 + Eplant/views/CellEFP/index.tsx | 4 +- Eplant/views/CellEFP/types.tsx | 6 + Eplant/views/eFP/Viewer/index.tsx | 2 +- package-lock.json | 432 ++++++++++-------- package.json | 10 +- 16 files changed, 654 insertions(+), 278 deletions(-) create mode 100644 Eplant/UI/Layout/ViewContainer/types.ts rename Eplant/{config.ts => config.tsx} (84%) create mode 100644 Eplant/util/router/index.ts create mode 100644 Eplant/views/CellEFP/CellEFP.tsx diff --git a/Eplant/Eplant.tsx b/Eplant/Eplant.tsx index 01acf77d..38a7ab00 100644 --- a/Eplant/Eplant.tsx +++ b/Eplant/Eplant.tsx @@ -1,40 +1,150 @@ // import useStateWithStorage from '@eplant/util/useStateWithStorage' -import { Route, Routes } from 'react-router-dom' -import { CssBaseline, ThemeProvider } from '@mui/material' +import { useEffect, useState } from 'react' +import { Outlet, useLocation, useNavigate, useParams } from 'react-router-dom' + +import { + Box, + CircularProgress, + CssBaseline, + ThemeProvider, + useTheme, +} from '@mui/material' import { dark, light } from './css/theme' -import Sidebar from './UI/Sidebar' +import { ViewContainer } from './UI/Layout/ViewContainer' +import Sidebar, { collapsedSidebarWidth, sidebarWidth } from './UI/Sidebar' +import { ViewDataError } from './View/viewData' +import FallbackView from './views/FallbackView' import { useConfig } from './config' -import EplantLayout from './EplantLayout' -import { useDarkMode } from './state' +import { + useActiveGeneId, + useActiveViewId, + useDarkMode, + useGeneticElements, + usePageLoad, + useSidebarState, + useSpecies, +} from './state' +import { updateColors } from './updateColors' export type EplantProps = Record -export default function Eplant() { - const { rootPath } = useConfig() - const [darkMode] = useDarkMode() - return ( - - - - - } /> - - - - ) -} /** * The main Eplant component. This is the root of the application. It contains the left nav and the layout. * @returns {JSX.Element} The rendered Eplant component */ +const Eplant = () => { + const [darkMode] = useDarkMode() + const [activeGeneId, setActiveGeneId] = useActiveGeneId() + const [activeViewId, setActiveViewId] = useState('') + const [isCollapse, setIsCollapse] = useSidebarState() + const [genes, setGenes] = useGeneticElements() + const theme = useTheme() + const [globalProgress, loaded] = usePageLoad() + const config = useConfig() + const navigate = useNavigate() + const location = useLocation() + const params = useParams() + const [speciesList] = useSpecies() + useEffect(() => { + if (loaded) { + updateColors(theme) + } + }, [theme, loaded]) + // On app url change, make sure loaded gene and view aligns with URL + useEffect(() => { + const loadGene = async (geneid: string) => { + // TODO: This is super jank, should probably write some better utilities for loading genes + const species = speciesList.find( + (species) => species.name === 'Arabidopsis' + ) + const gene = await species?.api.searchGene(geneid) + if (gene) { + setGenes([...genes, gene]) + } + } + if (params.geneid) { + if (params.geneid !== activeGeneId) { + if (!genes.find((gene) => gene.id === params.geneid)) { + loadGene(params.geneid) + } + setActiveGeneId(params.geneid) + } + } else { + setActiveGeneId('') + } + setActiveViewId(location.pathname.split('/')[1]) + }, [location.pathname]) + + // On active gene change update the gene path segment + useEffect(() => { + const pathSegments = location.pathname.split('/') + const geneid = activeGeneId ? activeGeneId : '' + if (pathSegments.length == 3) { + pathSegments[pathSegments.length - 1] = geneid + } else if (pathSegments.length == 2) { + pathSegments.push(geneid) + } + + const newPath = pathSegments.join('/') + location.search + if (newPath !== location.pathname + location.search) { + navigate(newPath) + } + }, [activeGeneId]) -// SideBar and EplantLayout children -export function MainEplant() { return ( - <> + + - - + ({ + height: `calc(100% - ${theme.spacing(1)})`, + left: `${isCollapse ? collapsedSidebarWidth : sidebarWidth}px`, + right: '0px', + position: 'absolute', + marginTop: '0.5rem', + boxSizing: 'border-box', + transition: 'left 1s ease-out', + backgroundColor: theme.palette.background.paper, + })} + > + +
+ {loaded ? ( + gene.id === activeGeneId) ?? null} + view={ + config.views.find( + (view) => view.id === (activeViewId ?? config.defaultView) + ) ?? FallbackView + } + setView={(viewid) => { + setActiveViewId(viewid) + }} + sx={{ + width: '100%', + height: '100%', + }} + > + ) : ( +
+ +
+ )} + + + ) } +export default Eplant diff --git a/Eplant/EplantLayout.tsx b/Eplant/EplantLayout.tsx index 7695e53f..8c03fe4b 100644 --- a/Eplant/EplantLayout.tsx +++ b/Eplant/EplantLayout.tsx @@ -1,14 +1,5 @@ -import { useContext, useEffect, useRef, useState } from 'react' -import * as FlexLayout from 'flexlayout-react' -import { - Actions, - BorderNode, - ITabSetRenderValues, - Layout, - TabSetNode, -} from 'flexlayout-react' +import { useEffect } from 'react' -import { Add, CallMade, Close } from '@mui/icons-material' import { Box, CircularProgress, IconButton } from '@mui/material' import { useTheme } from '@mui/material/styles' @@ -71,7 +62,7 @@ const EplantLayout = () => { ) ?? FallbackView } setView={(view) => { - setActiveViewId(view.id) + setActiveViewId(view) }} sx={{ width: '100%', diff --git a/Eplant/UI/Layout/ViewContainer/index.tsx b/Eplant/UI/Layout/ViewContainer/index.tsx index cfa2d111..9e59f112 100644 --- a/Eplant/UI/Layout/ViewContainer/index.tsx +++ b/Eplant/UI/Layout/ViewContainer/index.tsx @@ -1,4 +1,5 @@ import { useEffect, useId, useMemo, useState } from 'react' +import { Outlet, useLocation, useNavigate } from 'react-router-dom' import { useConfig } from '@eplant/config' import GeneticElement from '@eplant/GeneticElement' @@ -26,6 +27,7 @@ import Box, { BoxProps } from '@mui/material/Box' import { View } from '../../../View' import LoadingPage from './LoadingPage' +import { ViewContext } from './types' import ViewOptions from './ViewOptions' /** @@ -43,16 +45,19 @@ export function ViewContainer({ ...props }: { view: View - setView: (view: View) => void + setView: (viewid: string) => void gene: GeneticElement | null } & BoxProps) { - const { activeData, error, loading, loadingAmount, dispatch, state } = - useViewData(view, gene) + // const { activeData, error, dispatch, state } = useViewData(view, gene) + const [loading, setLoading] = useState(false) + const [loadAmount, setLoadAmount] = useState(0) const idLabel = useId() const selectId = useId() const [printing, setPrinting] = usePrinting() const [viewingCitations, setViewingCitations] = useState(false) + const navigate = useNavigate() + const location = useLocation() const { userViews, views, genericViews } = useConfig() @@ -64,7 +69,6 @@ export function ViewContainer({ }, 100) } }, [printing]) - const topBar = useMemo( () => ( ({ id={selectId} onChange={(e) => { const view = views.find((view) => view.id == e?.target?.value) - if (view) setView(view) + if (view) { + const pathSegments = location.pathname.split('/') + pathSegments[1] = view.id + const newPath = pathSegments.join('/') + if (newPath !== location.pathname + location.search) { + setView(view.id) + navigate(newPath) + } + } }} sx={{ '& .MuiSelect-select': { @@ -183,7 +195,7 @@ export function ViewContainer({ }} key={view.name} onClick={(e) => { - if (view) setView(view) + if (view) setView(view.id) }} > {view.name} @@ -194,13 +206,13 @@ export function ViewContainer({ - + /> */}
)} diff --git a/Eplant/views/CellEFP/types.tsx b/Eplant/views/CellEFP/types.tsx index a57e1c3f..cbab4b22 100644 --- a/Eplant/views/CellEFP/types.tsx +++ b/Eplant/views/CellEFP/types.tsx @@ -14,3 +14,9 @@ export type CellEFPViewerState = { export type CellEFPViewerAction = | { type: 'reset-transform' } | { type: 'set-transform'; transform: Transform } + +export type CellEFPSearchParams = { + x: string + y: string + zoom: string +} diff --git a/Eplant/views/eFP/Viewer/index.tsx b/Eplant/views/eFP/Viewer/index.tsx index b46b84bd..3fff232b 100644 --- a/Eplant/views/eFP/Viewer/index.tsx +++ b/Eplant/views/eFP/Viewer/index.tsx @@ -482,7 +482,7 @@ export default class EFPViewer > )} diff --git a/package-lock.json b/package-lock.json index 819c43db..470db661 100644 --- a/package-lock.json +++ b/package-lock.json @@ -22,6 +22,7 @@ "@mui/x-data-grid": "^6.15.0", "@mui/x-tree-view": "^7.5.1", "@popperjs/core": "^2.11.8", + "@tanstack/react-query": "^5.53.3", "@types/react-router-dom": "^5.3.3", "axios": "^1.5.1", "color2k": "^2.0.2", @@ -32,8 +33,9 @@ "lodash": "^4.17.21", "react": "^18.2.0", "react-dom": "^18.2.0", - "react-router-dom": "^6.16.0", - "react-window": "^1.8.9" + "react-router-dom": "^6.26.1", + "react-window": "^1.8.9", + "zod": "^3.23.8" }, "devDependencies": { "@eslint/js": "^9.3.0", @@ -62,7 +64,7 @@ "jest": "^29.7.0", "jest-environment-jsdom": "^29.7.0", "jotai-devtools": "^0.7.0", - "msw": "^1.3.1", + "msw": "^0.35.0", "prettier": "3.1.0", "react-draggable": "^4.4.6", "react-transition-group": "^4.4.5", @@ -2325,44 +2327,29 @@ } }, "node_modules/@mswjs/cookies": { - "version": "0.2.2", - "resolved": "https://registry.npmjs.org/@mswjs/cookies/-/cookies-0.2.2.tgz", - "integrity": "sha512-mlN83YSrcFgk7Dm1Mys40DLssI1KdJji2CMKN8eOlBqsTADYzj2+jWzsANsUTFbxDMWPD5e9bfA1RGqBpS3O1g==", + "version": "0.1.7", + "resolved": "https://registry.npmjs.org/@mswjs/cookies/-/cookies-0.1.7.tgz", + "integrity": "sha512-bDg1ReMBx+PYDB4Pk7y1Q07Zz1iKIEUWQpkEXiA2lEWg9gvOZ8UBmGXilCEUvyYoRFlmr/9iXTRR69TrgSwX/Q==", "dev": true, + "license": "MIT", "dependencies": { "@types/set-cookie-parser": "^2.4.0", "set-cookie-parser": "^2.4.6" - }, - "engines": { - "node": ">=14" } }, "node_modules/@mswjs/interceptors": { - "version": "0.17.10", - "resolved": "https://registry.npmjs.org/@mswjs/interceptors/-/interceptors-0.17.10.tgz", - "integrity": "sha512-N8x7eSLGcmUFNWZRxT1vsHvypzIRgQYdG0rJey/rZCy6zT/30qDt8Joj7FxzGNLSwXbeZqJOMqDurp7ra4hgbw==", + "version": "0.12.7", + "resolved": "https://registry.npmjs.org/@mswjs/interceptors/-/interceptors-0.12.7.tgz", + "integrity": "sha512-eGjZ3JRAt0Fzi5FgXiV/P3bJGj0NqsN7vBS0J0FO2AQRQ0jCKQS4lEFm4wvlSgKQNfeuc/Vz6d81VtU3Gkx/zg==", "dev": true, + "license": "MIT", "dependencies": { "@open-draft/until": "^1.0.3", - "@types/debug": "^4.1.7", - "@xmldom/xmldom": "^0.8.3", - "debug": "^4.3.3", - "headers-polyfill": "3.2.5", - "outvariant": "^1.2.1", - "strict-event-emitter": "^0.2.4", - "web-encoding": "^1.1.5" - }, - "engines": { - "node": ">=14" - } - }, - "node_modules/@mswjs/interceptors/node_modules/strict-event-emitter": { - "version": "0.2.8", - "resolved": "https://registry.npmjs.org/strict-event-emitter/-/strict-event-emitter-0.2.8.tgz", - 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"react-router-dom": "^6.16.0", - "react-window": "^1.8.9" + "react-router-dom": "^6.26.1", + "react-window": "^1.8.9", + "zod": "^3.23.8" }, "devDependencies": { "@eslint/js": "^9.3.0", @@ -68,7 +70,7 @@ "jest": "^29.7.0", "jest-environment-jsdom": "^29.7.0", "jotai-devtools": "^0.7.0", - "msw": "^1.3.1", + "msw": "^0.35.0", "prettier": "3.1.0", "react-draggable": "^4.4.6", "react-transition-group": "^4.4.5", @@ -82,4 +84,4 @@ "vite-plugin-eslint": "^1.8.1", "vite-tsconfig-paths": "^4.2.1" } -} \ No newline at end of file +}