Cleaned up un-needed code

BioAnalyticResource · Jan 6, 2025 · c4b85b7 · c4b85b7
1 parent c89c1a3
commit c4b85b7
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Showing 31 changed files with 92 additions and 1,633 deletions.
diff --git a/Eplant/GeneticElement.ts b/Eplant/GeneticElement.ts
@@ -50,12 +50,6 @@ export default class GeneticElement {
 export type SpeciesApi = {
   searchGene: (term: string) => Promise<GeneticElement | null>
   autocomplete: (term: string) => Promise<string[]>
-  loaders: {
-    [key: string]: (
-      gene: GeneticElement,
-      loadEvent: (amount: number) => void
-    ) => Promise<any>
-  }
 }
 
 /**

diff --git a/Eplant/Species/arabidopsis/index.ts b/Eplant/Species/arabidopsis/index.ts
@@ -3,15 +3,9 @@ import axios from 'axios'
 import { Species } from '@eplant/GeneticElement'
 import GeneticElement from '@eplant/GeneticElement'
 
-import GeneInfoViewLoader from './loaders/GeneInfoView'
-import ArabidopsisPublicationViewer from './loaders/PublicationViewer'
 const arabidopsis: Species = new Species('Arabidopsis', {
   autocomplete,
   searchGene,
-  loaders: {
-    'gene-info': GeneInfoViewLoader,
-    'publication-viewer': ArabidopsisPublicationViewer,
-  },
 })
 async function autocomplete(s: string) {
   return (
@@ -39,21 +33,4 @@ async function searchGene(s: string) {
   return gene
 }
 
-async function getGene(s: string) {
-  const data = (
-    await axios.get(
-      'https://bar.utoronto.ca/eplant/cgi-bin/querygene.cgi?species=Arabidopsis_thaliana&term=' +
-        s
-    )
-  ).data
-  if (!data.id || !data.annotation || !data.aliases) return null
-  const gene = new GeneticElement(
-    data.id,
-    data.annotation,
-    arabidopsis,
-    data.aliases
-  )
-  return gene
-}
-
 export default arabidopsis
diff --git a/Eplant/Species/arabidopsis/loaders/GeneInfoView/index.ts b/Eplant/Species/arabidopsis/loaders/GeneInfoView/index.ts
diff --git a/Eplant/Species/arabidopsis/loaders/PublicationViewer/index.ts b/Eplant/Species/arabidopsis/loaders/PublicationViewer/index.ts
diff --git a/Eplant/UI/Layout/ViewContainer/LoadingPage.tsx b/Eplant/UI/Layout/ViewContainer/LoadingPage.tsx
@@ -1,8 +1,7 @@
 import { SVGProps } from 'react'
 
 import GeneticElement from '@eplant/GeneticElement'
-import { View } from '@eplant/View'
-import { ViewDataError } from '@eplant/View/viewData'
+import { View, ViewDataError } from '@eplant/View'
 import { Player } from '@lottiefiles/react-lottie-player'
 import { Box, LinearProgress, Stack, Typography, useTheme } from '@mui/material'
 

diff --git a/Eplant/UI/Layout/ViewContainer/Topbar.tsx b/Eplant/UI/Layout/ViewContainer/Topbar.tsx
@@ -1,9 +1,10 @@
 import { useId } from 'react'
-import { useLocation, useNavigate } from 'react-router-dom'
 
 import { useConfig } from '@eplant/config'
-import { useActiveViewId } from '@eplant/state'
+import { queryClient } from '@eplant/main'
+import { useActiveGeneId, useActiveViewId } from '@eplant/state'
 import { useURLState } from '@eplant/state/URLStateProvider'
+import downloadFile from '@eplant/util/downloadFile'
 import { ActionsPanel } from '@eplant/util/stateUtils/ActionsPanel'
 import { View } from '@eplant/View'
 import {
@@ -19,7 +20,7 @@ import {
 } from '@mui/material'
 
 interface TopBarProps {
-  activeView: View<any, any, any>
+  activeView: View<any, any>
   setViewingCitations: (value: boolean) => void
   loading: boolean
   activeActions: any[]
@@ -32,11 +33,10 @@ export const TopBar = ({
 }: TopBarProps) => {
   const { userViews, views } = useConfig()
   const [activeViewId, setActiveViewId] = useActiveViewId()
+  const [activeGeneId, setActiveGeneId] = useActiveGeneId()
   const { setState } = useURLState<any>()
-  const location = useLocation()
   const idLabel = useId()
   const selectId = useId()
-
   const handleChangeView = (e: any) => {
     const view = views.find((view) => view.id === e.target.value)
     if (view) {
@@ -182,10 +182,21 @@ export const TopBar = ({
           disabled={loading}
           color='secondary'
           onClick={() => {
-            // downloadFile(
-            //   `${activeView.id}${gene ? '-' + gene.id : ''}.json`,
-            //   JSON.stringify(activeData, null, 2)
-            // )
+            let data = queryClient.getQueryData([
+              `${activeView.id}-${activeGeneId}`,
+            ])
+
+            if (!data) {
+              // Some views don't cache based on geneId
+              data = queryClient.getQueryData([activeView.id])
+            }
+            console.log(`${activeView.id}-${activeGeneId}`)
+            console.log(data)
+            console.log(JSON.stringify(data, null, 2))
+            downloadFile(
+              `${activeView.id}${activeGeneId ? '-' + activeGeneId : ''}.json`,
+              JSON.stringify(data, null, 2)
+            )
           }}
         >
           Download data

diff --git a/Eplant/UI/Layout/ViewContainer/index.tsx b/Eplant/UI/Layout/ViewContainer/index.tsx
@@ -12,9 +12,7 @@ import {
 } from '@eplant/state'
 import Modal from '@eplant/UI/Modal'
 import ErrorBoundary from '@eplant/util/ErrorBoundary'
-import { StateAction } from '@eplant/util/stateUtils'
-import { ViewDataError } from '@eplant/View/viewData'
-import CellEFP from '@eplant/views/CellEFP'
+import { StateAction, ViewDataError } from '@eplant/View'
 import GeneInfoView from '@eplant/views/GeneInfoView'
 import {
   Box,
@@ -63,8 +61,6 @@ export function ViewContainer<T, S, A>({
   const activeView =
     views.find((view) => view.id === activeViewId) ?? GeneInfoView
 
-  console.log('activeView', activeView)
-  console.log('activeGene', activeGeneId)
   // On app url change, make sure loaded gene and view aligns with URL
   useEffect(() => {
     const loadGene = async (geneid: string) => {
@@ -81,7 +77,6 @@ export function ViewContainer<T, S, A>({
     }
     if (params.geneid) {
       if (params.geneid !== activeGeneId) {
-        console.log('loading gene', params.geneid)
         if (!genes.find((g) => g.id === params.geneid)) {
           loadGene(params.geneid)
         }
@@ -104,26 +99,27 @@ export function ViewContainer<T, S, A>({
 
   // On active gene change update the gene path segment
   useEffect(() => {
-    console.log('updating path', activeGeneId, location.pathname)
     if (location.pathname !== import.meta.env.BASE_URL) {
       // Only run this after initial redirect
       const pathSegments = location.pathname
         .split('/')
         .filter((segment) => segment !== '')
-      if (pathSegments.length == 2 && activeGeneId) {
+      if (pathSegments.length == 2 && gene) {
         pathSegments[pathSegments.length - 1] = activeGeneId
-      } else if (pathSegments.length == 1 && activeGeneId) {
+      } else if (pathSegments.length == 1 && gene) {
         pathSegments.push(activeGeneId)
         // Will never get here as of now, but if we decide to persist activeGene need
         // to do this.
+      } else {
+        // No gene selected, remove gene path segment
+        pathSegments.pop()
       }
-
       const newPath = '/' + pathSegments.join('/') + '/' + location.search
       if (newPath !== location.pathname + '/' + location.search) {
         navigate(newPath)
       }
     }
-  }, [activeGeneId])
+  }, [activeGeneId, gene])
 
   useEffect(() => {
     const pathSegments = location.pathname.split('/')
@@ -143,8 +139,7 @@ export function ViewContainer<T, S, A>({
         </DialogTitle>
         <DialogContent>
           {activeView.citation ? (
-            // <view.citation state={state} activeData={activeData} gene={gene} />
-            <div></div>
+            <activeView.citation />
           ) : (
             <Box>No information provided for this view</Box>
           )}
@@ -190,14 +185,14 @@ export function ViewContainer<T, S, A>({
         <ErrorBoundary>
           {/* Only show the gene header if a gene is selected and this view belongs to the gene */}
 
-          {activeGeneId === '' ? (
+          {!gene ? (
             <LoadingPage
               loadingAmount={loadAmount}
               gene={gene}
               view={activeView}
               error={ViewDataError.UNSUPPORTED_GENE}
             />
-          ) : (loading && loadAmount < 100) || !gene ? (
+          ) : loading && loadAmount < 100 ? (
             <LoadingPage
               loadingAmount={loadAmount}
               gene={gene}