Merge pull request #2344 from broadinstitute/development

Release 1.107.0

Author: eweitz

app/javascript/components/explore/ExploreDisplayTabs.jsx

@@ -11,7 +11,7 @@ import PlotUtils from '~/lib/plot'
 const getPlotDimensions = PlotUtils.getPlotDimensions
 import ScatterPlot from '~/components/visualization/ScatterPlot'
 import StudyViolinPlot from '~/components/visualization/StudyViolinPlot'
-import DotPlot from '~/components/visualization/DotPlot'
+import DotPlot, { shouldUsePreprocessedData } from '~/components/visualization/DotPlot'
 import Heatmap from '~/components/visualization/Heatmap'
 import Pathway from '~/components/visualization/Pathway'
 import GeneListHeatmap from '~/components/visualization/GeneListHeatmap'
@@ -279,6 +279,9 @@ export default function ExploreDisplayTabs({
   const referencePlotDataParams = _clone(exploreParams)
   referencePlotDataParams.genes = []
 
+  // disable 50-gene query limit if study has preprocessed dotplot data
+  const disableGeneQueryLimit = shouldUsePreprocessedData(flags, exploreInfo)
+
   // TODO (SCP-5760): Refactor pathway diagrams into independent component where
   // React state can be propagated conventionally, then remove this
   window.SCP.exploreParamsWithDefaults = exploreParamsWithDefaults
@@ -539,6 +542,7 @@ export default function ExploreDisplayTabs({
               isLoading={!exploreInfo}
               speciesList={exploreInfo ? exploreInfo.taxonNames : []}
               selectedAnnotation={selectedAnnotation}
+              disableGeneQueryLimit={disableGeneQueryLimit}
             />
             { // show if this is gene search || gene list
               (isGene || isGeneList || hasIdeogramOutputs || isPathway) &&

app/javascript/components/explore/StudyGeneField.jsx

@@ -98,9 +98,11 @@ function getQueryArrayFromSearchOptions(searchOptions, speciesList, selectedAnno
 * @param queryFn Function to call to execute the API search
 * @param allGenes String array of valid genes in the study
 * @param speciesList String array of species scientific names
+* @param isLoading boolean flag for disabling search while loading
+* @param disableGeneQueryLimit boolean flag for allowing searches larger than 50 genes for preprocessed data
 */
 export default function StudyGeneField({
-  queries, queryFn, allGenes, speciesList, selectedAnnotation, isLoading=false
+  queries, queryFn, allGenes, speciesList, selectedAnnotation, isLoading=false, disableGeneQueryLimit = false
 }) {
   const [inputText, setInputText] = useState('')
 
@@ -158,7 +160,7 @@ export default function StudyGeneField({
     } else if (newQueryArray && newQueryArray.length) {
       const newQueries = getQueriesFromSearchOptions(newQueryArray, speciesList, selectedAnnotation)
       const queries = newQueries
-      if (queries.length > window.MAX_GENE_SEARCH) {
+      if (queries.length > window.MAX_GENE_SEARCH && !disableGeneQueryLimit) {
         log('search-too-many-genes', { numGenes: queries.length })
         setShowTooManyGenesModal(true)
       } else {

app/javascript/components/visualization/DotPlot.jsx

@@ -325,7 +325,7 @@ export function renderDotPlot({
     focus: null,
     tabManager: morpheusTabManager($target),
     tools,
-    loadedCallback: () => logMorpheusPerfTime(target, 'dotplot', genes)
+    loadedCallback: () => logMorpheusPerfTime(target, 'dotplot', genes, isPrecomputed)
   }
 
   // For pre-computed data, tell Morpheus to display series 0 for color
@@ -466,14 +466,14 @@ export function morpheusTabManager($target) {
 }
 
 /** Log render performance timing for Morpheus dot plots and heatmaps */
-export function logMorpheusPerfTime(target, plotType, genes) {
+export function logMorpheusPerfTime(target, plotType, genes, isPrecomputed) {
   const graphId = target.slice(1) // e.g. #dotplot-1 -> dotplot-1
   performance.measure(graphId, `perfTimeStart-${graphId}`)
   const perfTime = Math.round(
     performance.getEntriesByName(graphId)[0].duration
   )
 
-  log(`plot:${plotType}`, { perfTime, genes })
+  log(`plot:${plotType}`, { perfTime, genes, isPrecomputed })
 }
 
 /** Log performance of loading JSON datasets for Morpheus */

app/javascript/components/visualization/Heatmap.jsx

@@ -24,24 +24,29 @@ function RawHeatmap({
   const [graphId] = useState(_uniqueId('heatmap-'))
   const [dataset, setDataset] = useState(morpheusData)
   const morpheusHeatmap = useRef(null)
-  const { ErrorComponent, setShowError, setErrorContent } = useErrorMessage()
+  const { ErrorComponent, showError, setShowError, setError } = useErrorMessage()
 
   // Fetch dataset if not provided via morpheusData prop, but only when tab is visible
   useEffect(() => {
     async function fetchDataset() {
       if (isVisible && !morpheusData && cluster && annotation.name && genes.length > 0) {
-        const [data] = await fetchMorpheusJson(
-          studyAccession,
-          genes,
-          cluster,
-          annotation.name,
-          annotation.type,
-          annotation.scope,
-          subsample,
-          false, // mock
-          false // usePreprocessed - always use full morpheus data for heatmaps
-        )
-        setDataset(data)
+        try {
+          const [data] = await fetchMorpheusJson(
+            studyAccession,
+            genes,
+            cluster,
+            annotation.name,
+            annotation.type,
+            annotation.scope,
+            subsample,
+            false, // mock
+            false // usePreprocessed - always use full morpheus data for heatmaps
+          )
+          setDataset(data)
+        } catch (error) {
+          setError(error.message)
+          setShowError(true)
+        }
       } else if (morpheusData) {
         setDataset(morpheusData)
       }
@@ -70,7 +75,7 @@ function RawHeatmap({
         rowCentering: heatmapRowCentering,
         sortColumns: true,
         setShowError,
-        setErrorContent,
+        setError,
         genes
       })
     }
@@ -92,7 +97,7 @@ function RawHeatmap({
     <div>
       <div className="plot">
         { ErrorComponent }
-        <LoadingSpinner isLoading={!canRender}>
+        <LoadingSpinner isLoading={!canRender && !showError}>
           <div id={graphId} className="heatmap-graph" style={{ minWidth: '80vw' }}></div>
         </LoadingSpinner>
       </div>

app/lib/study_search_service.rb

@@ -2,8 +2,9 @@
 class StudySearchService
 
   MAX_GENE_SEARCH = 50
-  MAX_GENE_SEARCH_MSG = "For performance reasons, gene search is limited to #{MAX_GENE_SEARCH} genes. Please use " \
-                        'multiple searches to view more genes.'.freeze
+  MAX_GENE_SEARCH_MSG = "For performance reasons, gene search is limited to #{MAX_GENE_SEARCH} genes, except for  " \
+                        'pre-processed dot plots (where available). ' \
+                        'Please use multiple searches to view more genes.'.freeze
 
   # list of common 'stop words' to scrub from term-based search requests
   # these are unhelpful in search contexts as they artificially inflate irrelevant results