Include date histogram and species multi-select in Geo page (#239)

- Merge #221
- Merge #231

Co-authored-by: Max McCready <75914260+Bluesquare99@users.noreply.github.com>
Co-authored-by: khanzardar <k.zardar@gmail.com>

package.json

@@ -7,6 +7,7 @@
     "dependencies": {
         "@jbrowse/react-linear-genome-view": "^1.3.2",
         "axios": "^0.21.2",
+        "chroma-js": "^2.4.2",
         "d3": "^5.16.0",
         "d3-scale-chromatic": "^2.0.0",
         "fast-xml-parser": "^3.19.0",
@@ -20,7 +21,8 @@
         "react-plotly.js": "^2.5.1",
         "react-router-dom": "^5.2.0",
         "react-scripts": "^4.0.3",
-        "react-select": "^3.1.0"
+        "react-select": "^3.1.0",
+        "react-windowed-select": "^5.1.0"
     },
     "scripts": {
         "build:css": "postcss src/styles/tailwind.css -o src/styles/main.css",
@@ -45,13 +47,16 @@
         ]
     },
     "devDependencies": {
+        "@types/chroma-js": "^2.1.4",
         "@types/d3": "^6.7.3",
         "@types/jest": "^26.0.23",
-        "@types/react": "^17.0.11",
-        "@types/react-helmet": "^6.1.0",
+        "@types/react": "^18.0.14",
+        "@types/react-dom": "^18.0.5",
+        "@types/react-helmet": "^6.1.6",
         "@types/react-plotly.js": "^2.2.4",
         "@types/react-router-dom": "^5.1.7",
         "@types/react-select": "^4.0.16",
+        "@types/react-window": "^1.8.5",
         "@typescript-eslint/eslint-plugin": "^4.28.0",
         "@typescript-eslint/parser": "^4.28.0",
         "autoprefixer": "^9.8.7",

src/components/Geo/Geo.tsx

@@ -1,25 +1,139 @@
 import React from 'react'
 import { Helmet } from 'react-helmet'
-import { MemoizedMapPlot } from './MapPlot'
-import { SelectionInfo } from './SelectionInfo'
-import { RunData } from './types'
+import { MapPlot } from './MapPlot'
+import { ResultsTable } from './ResultsTable'
+import { RunData, RunDataKey } from './types'
 import { helpIcon } from 'common'
+import { fetchPagedGeoMatches } from 'components/Explorer/Base/Result/SerratusApiCalls'
+import {
+    countRunDataByDateAndKey,
+    filterRunDataByGroup,
+    getBioIdsFromRunData,
+    getRunDataFromPaginatedData,
+    groupRunDataByKey,
+    transformToMapPlotData,
+    transformToTimePlotData,
+} from './GeoHelpers'
+import { SpeciesSelect } from './SpeciesSelect'
+import { TimePlot } from './TimePlot'
 
 export const Geo = () => {
-    const [selectedPoints, setSelectedPoints] = React.useState<RunData[]>()
     const [isCollapsed, setIsCollapsed] = React.useState<boolean>(false)
+    const [isFetching, setIsFetching] = React.useState<boolean>(true)
+    const [paginatedRunData, setPaginatedRunData] = React.useState<{
+        [page: string]: RunData[]
+    }>({})
+    const [selectedPoints, setSelectedPoints] = React.useState<RunData[]>([])
+    const [selectedSpecies, setSelectedSpecies] = React.useState<string[]>([])
 
-    const headTags = (
-        <Helmet>
-            <title>Serratus | Planetary RNA Virome</title>
-        </Helmet>
-    )
+    React.useEffect(() => {
+        async function onMount() {
+            fetchRunData()
+        }
+        onMount()
+    }, [])
 
-    return (
-        <div className='mx-4 my-2'>
-            {headTags}
-            <div className='text-center text-xl'>The Planetary RNA Virome</div>
+    function storePaginatedRunData(rows: RunData[], page: number) {
+        if (!rows.length) {
+            return
+        }
+        setPaginatedRunData((prevState) => ({
+            ...prevState,
+            [page]: rows,
+        }))
+    }
+
+    async function fetchRunData() {
+        setIsFetching(true)
+
+        // Fetch first page and get total rows
+        let page = 1
+        const perPage = 20000
+        const searchType = 'rdrp'
+        const { result, total } = await fetchPagedGeoMatches(searchType, page, perPage)
+        storePaginatedRunData(result as RunData[], page)
+
+        // Batch requests for remaining pages
+        const totalPages = Math.ceil(total / perPage)
+        const iterPages = []
+        for (page = page + 1; page <= totalPages; page++) {
+            if (!(page in paginatedRunData)) {
+                iterPages.push(page)
+            }
+        }
+        await Promise.allSettled(
+            iterPages.map(async (page) => {
+                const { result } = await fetchPagedGeoMatches(searchType, page as number, perPage)
+                storePaginatedRunData(result as RunData[], page as number)
+            })
+        )
+        setIsFetching(false)
+    }
+
+    const speciesOptions = React.useMemo(() => {
+        const runData = getRunDataFromPaginatedData(paginatedRunData)
+        const filteredBySelectedPoints = filterRunDataByGroup(
+            runData,
+            getBioIdsFromRunData(selectedPoints),
+            RunDataKey.BiosampleId
+        )
+        const speciesSet = new Set(
+            filteredBySelectedPoints.map((d) => d?.[RunDataKey.ScientificName])
+        )
+        return Array.from(speciesSet).sort()
+    }, [isFetching, selectedPoints, selectedSpecies])
+
+    const filteredAndSelectedRows = React.useMemo(() => {
+        const runData = getRunDataFromPaginatedData(paginatedRunData)
+        if (runData.length === 0) {
+            return []
+        }
+        const filteredBySpecies = filterRunDataByGroup(
+            runData,
+            selectedSpecies,
+            RunDataKey.ScientificName
+        )
+        return filterRunDataByGroup(
+            filteredBySpecies,
+            getBioIdsFromRunData(selectedPoints),
+            RunDataKey.BiosampleId
+        )
+    }, [isFetching, selectedSpecies, selectedPoints])
 
+    const mapData = React.useMemo(() => {
+        const runData = getRunDataFromPaginatedData(paginatedRunData)
+        const filteredBySpecies = filterRunDataByGroup(
+            runData,
+            selectedSpecies,
+            RunDataKey.ScientificName
+        )
+        const groupedRunData =
+            selectedSpecies.length > 0
+                ? groupRunDataByKey(filteredBySpecies, RunDataKey.ScientificName)
+                : {
+                      all: filteredBySpecies,
+                  }
+        return transformToMapPlotData(
+            groupedRunData,
+            selectedSpecies,
+            getBioIdsFromRunData(selectedPoints)
+        )
+    }, [isFetching, selectedSpecies, selectedPoints])
+
+    const timePlotData = React.useMemo(() => {
+        const groupedCounter = countRunDataByDateAndKey(
+            filteredAndSelectedRows,
+            RunDataKey.ScientificName
+        )
+        return transformToTimePlotData(groupedCounter, selectedSpecies)
+    }, [filteredAndSelectedRows])
+
+    return (
+        <div className='mx-14 my-2'>
+            <Helmet>
+                <title>Serratus | Planetary RNA Virome</title>
+            </Helmet>
+            <div className='text-center text-xl my-4'>The Planetary RNA Virome</div>
             <button
                 className='text-left collapse-button'
                 onClick={() => setIsCollapsed(!isCollapsed)}>
@@ -40,17 +154,23 @@ export const Geo = () => {
 
                 <p>A 100-meter randomization is applied to all points to prevent overplotting.</p>
             </div>
-
-            <div className='my-2'>
-                <MemoizedMapPlot setSelectedPoints={setSelectedPoints} />
+            <div className='my-4'>
+                <SpeciesSelect
+                    speciesOptions={speciesOptions}
+                    selectedSpecies={selectedSpecies}
+                    setSelectedSpecies={setSelectedSpecies}
+                />
+            </div>
+            <div className='my-4'>
+                <MapPlot plotData={mapData} setSelectedPoints={setSelectedPoints} />
             </div>
-
             <div className='text-left text-gray-600'>
-                Use <b>`Shift`</b>-click to select multiple points or the <b>`Box Select`</b> or{' '}
-                <b>`Lasso Select`</b> icons in the top-right.
+                Use <b>`Shift`</b> -click to select multiple points or the <b>`Box Select`</b> or{' '}
+                <b>`Lasso Select`</b> icons in the top-right. <b>Double-click</b> to deselect
+                points.
             </div>
-
-            <SelectionInfo selectedPoints={selectedPoints} />
+            <TimePlot plotData={timePlotData} />
+            <ResultsTable rowsToDisplay={filteredAndSelectedRows} />
         </div>
     )
 }