Release 1.90.0

Gemfile.lock

@@ -318,7 +318,7 @@ GEM
     multi_xml (0.6.0)
     multipart-post (2.3.0)
     naturally (2.2.1)
-    net-imap (0.5.5)
+    net-imap (0.5.6)
       date
       net-protocol
     net-pop (0.1.2)

app/controllers/application_controller.rb

@@ -22,7 +22,8 @@ class ApplicationController < ActionController::Base
   before_action :get_download_quota
   before_action :get_deployment_notification
   before_action :set_selected_branding_group
-  before_action :check_tos_acceptance
+  # allow users to view privacy policy even if they haven't accepted the ToS yet
+  before_action :check_tos_acceptance, except: :privacy_policy
   before_action :set_ab_test_assignments
 
   rescue_from ActionController::InvalidAuthenticityToken, with: :invalid_csrf

app/controllers/profiles_controller.rb

@@ -96,7 +96,11 @@ def update_firecloud_profile
     end
   end
 
-  def accept_tos; end
+  def accept_tos
+    @previous_acceptance = TosAcceptance.where(
+      email: @user.email, :version.ne => TosAcceptance::CURRENT_VERSION
+    ).order_by(&:version).last
+  end
 
   def record_tos_action
     user_accepted = tos_params[:action] == 'accept'

app/javascript/components/explore/DifferentialExpressionPanel.jsx

@@ -12,7 +12,7 @@ import {
   getCanonicalSize, getCanonicalSignificance
 } from '~/lib/validation/validate-differential-expression'
 import { contactUsLink } from '~/lib/error-utils'
-
+import { getFeatureFlagsWithDefaults } from '~/providers/UserProvider'
 
 import {
   createColumnHelper,
@@ -25,7 +25,8 @@ import {
 
 import DifferentialExpressionModal from '~/components/explore/DifferentialExpressionModal'
 import {
-  OneVsRestDifferentialExpressionGroupPicker, PairwiseDifferentialExpressionGroupPicker
+  OneVsRestDifferentialExpressionGroupPicker, PairwiseDifferentialExpressionGroupPicker,
+  PairwiseDifferentialExpressionGroupLists
 } from '~/components/visualization/controls/DifferentialExpressionGroupPicker'
 
 import {
@@ -725,9 +726,12 @@ export default function DifferentialExpressionPanel({
     setUnfoundGenes(unfoundNames)
   }, [deGenes, searchedGenes, findMode])
 
+  const flags = getFeatureFlagsWithDefaults()
+  const isPairwiseUi = flags?.default_pairwise_de_ui === true
+
   return (
     <>
-      {!hasPairwiseDe &&
+      {!isPairwiseUi && !hasPairwiseDe &&
         <OneVsRestDifferentialExpressionGroupPicker
           bucketId={bucketId}
           clusterName={clusterName}
@@ -745,7 +749,7 @@ export default function DifferentialExpressionPanel({
           significanceMetric={significanceMetric}
         />
       }
-      {hasPairwiseDe &&
+      {!isPairwiseUi && hasPairwiseDe &&
         <PairwiseDifferentialExpressionGroupPicker
           bucketId={bucketId}
           clusterName={clusterName}
@@ -766,6 +770,27 @@ export default function DifferentialExpressionPanel({
         />
       }
 
+      {isPairwiseUi &&
+        <PairwiseDifferentialExpressionGroupLists
+          bucketId={bucketId}
+          clusterName={clusterName}
+          annotation={annotation}
+          setShowDeGroupPicker={setShowDeGroupPicker}
+          deGenes={deGenes}
+          setDeGenes={setDeGenes}
+          deGroup={deGroup}
+          setDeGroup={setDeGroup}
+          countsByLabelForDe={countsByLabelForDe}
+          deObjects={deObjects}
+          setDeFilePath={setDeFilePath}
+          deGroupB={deGroupB}
+          setDeGroupB={setDeGroupB}
+          hasOneVsRestDe={hasOneVsRestDe}
+          sizeMetric={sizeMetric}
+          significanceMetric={significanceMetric}
+        />
+      }
+
       {
         (
           (!hasPairwiseDe && genesToShow) ||

app/javascript/components/explore/ExploreDisplayTabs.jsx

@@ -233,6 +233,9 @@ export default function ExploreDisplayTabs({
   studyAccession, exploreInfo, setExploreInfo, exploreParams, updateExploreParams,
   clearExploreParams, exploreParamsWithDefaults, routerLocation
 }) {
+  const flags = getFeatureFlagsWithDefaults()
+  const hasDefaultPairwiseDeUi = flags?.default_pairwise_de_ui === true
+
   const [, setRenderForcer] = useState({})
   const [dataCache] = useState(createCache())
   // tracks whether the view options controls are open or closed
@@ -250,7 +253,10 @@ export default function ExploreDisplayTabs({
   const [, setShowDeGroupPicker] = useState(false)
   const [deGenes, setDeGenes] = useState(null)
   const [showDifferentialExpressionPanel, setShowDifferentialExpressionPanel] = useState(deGenes !== null)
-  const [showUpstreamDifferentialExpressionPanel, setShowUpstreamDifferentialExpressionPanel] = useState(deGenes !== null)
+
+  const [
+    showUpstreamDifferentialExpressionPanel, setShowUpstreamDifferentialExpressionPanel
+  ] = useState(deGenes !== null)
 
   let initialPanel = 'options'
   if (showDifferentialExpressionPanel || showUpstreamDifferentialExpressionPanel) {
@@ -262,6 +268,10 @@ export default function ExploreDisplayTabs({
 
   // Hash of trace label names to the number of points in that trace
   const [countsByLabelForDe, setCountsByLabelForDe] = useState(null)
+  const showDifferentialExpressionPicker = (
+    hasDefaultPairwiseDeUi &&
+    showViewOptionsControls && initialPanel === 'differential-expression' && deGenes === null
+  )
   const showDifferentialExpressionTable = (showViewOptionsControls && deGenes !== null)
   const plotContainerClass = 'explore-plot-tab-content'
 
@@ -478,12 +488,16 @@ export default function ExploreDisplayTabs({
     let side
     if (showViewOptionsControls) {
       if (
-        (deGenes !== null) ||
-          (hasPairwiseDe && (showDifferentialExpressionPanel || showUpstreamDifferentialExpressionPanel))
+        panelToShow === 'differential-expression'
       ) {
-        // DE table is shown, or pairwise DE is available.  Least horizontal space for plots.
-        main = 'col-md-9'
-        side = 'col-md-3 right-panel'
+        if (hasDefaultPairwiseDeUi && deGenes === null) {
+          main = 'col-md-8'
+          side = 'col-md-4 right-panel'
+        } else {
+          // DE table is shown
+          main = 'col-md-9'
+          side = 'col-md-3 right-panel'
+        }
       } else if (panelToShow === 'cell-filtering') {
         main = 'col-md-10-5'
         side = 'col-md-2-5 right-panel'
@@ -604,6 +618,7 @@ export default function ExploreDisplayTabs({
                     plotPointsSelected,
                     showRelatedGenesIdeogram,
                     showViewOptionsControls,
+                    showDifferentialExpressionPicker,
                     showDifferentialExpressionTable,
                     scatterColor: exploreParamsWithDefaults.scatterColor,
                     setCountsByLabelForDe,
@@ -619,7 +634,8 @@ export default function ExploreDisplayTabs({
                   studyAccession={studyAccession}
                   updateDistributionPlot={distributionPlot => updateExploreParams({ distributionPlot }, false)}
                   dimensions={getPlotDimensions({
-                    showRelatedGenesIdeogram, showViewOptionsControls, showDifferentialExpressionTable
+                    showRelatedGenesIdeogram, showViewOptionsControls,
+                    showDifferentialExpressionPicker, showDifferentialExpressionTable
                   })}
                   cellFaceting={cellFaceting}
                   filteredCells={filteredCells}

app/javascript/components/explore/ScatterTab.jsx

@@ -13,7 +13,8 @@ const MAX_PLOTS = PLOTLY_CONTEXT_NAMES.length
   */
 export default function ScatterTab({
   exploreInfo, exploreParamsWithDefaults, updateExploreParamsWithDefaults, studyAccession, isGene, isMultiGene,
-  plotPointsSelected, isCellSelecting, showRelatedGenesIdeogram, showViewOptionsControls, showDifferentialExpressionTable,
+  plotPointsSelected, isCellSelecting, showRelatedGenesIdeogram, showViewOptionsControls,
+  showDifferentialExpressionPicker, showDifferentialExpressionTable,
   scatterColor, setCountsByLabelForDe, dataCache, filteredCells, cellFilteringSelection
 }) {
   // maintain the map of plotly contexts to the params that generated the corresponding visualization
@@ -61,7 +62,9 @@ export default function ScatterTab({
               dimensionProps={{
                 isMultiRow,
                 isTwoColumn: isTwoColRow,
-                showRelatedGenesIdeogram, showViewOptionsControls,
+                showRelatedGenesIdeogram,
+                showViewOptionsControls,
+                showDifferentialExpressionPicker,
                 showDifferentialExpressionTable
               }}
             />

app/javascript/components/visualization/controls/DifferentialExpressionGroupPicker.jsx

@@ -7,6 +7,10 @@ import { fetchBucketFile } from '~/lib/scp-api'
 import PlotUtils from '~/lib/plot'
 const { getLegendSortedLabels } = PlotUtils
 
+
+// https://stackoverflow.com/questions/37909134/nbsp-jsx-not-working
+const blankSpace = '\u00A0' // How React JSX does  
+
 const basePath = '_scp_internal/differential_expression/'
 
 // Value to show in menu if user has not selected a group for DE
@@ -43,7 +47,7 @@ export function parseDeFile(tsvText, isAuthorDe=false) {
       //
       // TODO: There are usually more columns than size (e.g. logfoldchanges)
       // and significance (e.g. pvals_adj) that may well be of interest.
-      // However, we don't parse those here before there is no UI for them.
+      // However, we don't parse those here because there is no UI for them.
       // If we opt to build a UI for further metrics (e.g. pctNzGroup in Scanpy
       // / pct.1 in Seurat, etc.), we would need to order them canonically
       // across SCP-computed DE results and (Ingest Pipeline-processed) author
@@ -144,6 +148,174 @@ function getMatchingDeOption(
   return matchingDeOption
 }
 
+/** List menu of groups available to select for DE comparison */
+function GroupListMenu({
+  groups, selectedGroups, updateSelectedGroups, setNote, isMenuB=false,
+  hoverAllOthers, setHoverAllOthers
+}) {
+
+  if (isMenuB) {
+    groups.unshift('rest')
+  }
+
+  const groupsIndex = isMenuB ? 1 : 0
+  const otherGroupsIndex = isMenuB ? 0 : 1
+  const otherMenuSelection = selectedGroups[otherGroupsIndex]
+
+  return (
+    <>
+      {groups.map((group, i) => {
+        // If this menu has a selected group and this group isn't it,
+        // then disable this group
+        const isInvalid = group === otherMenuSelection && isMenuB
+
+        if (isInvalid) {return ''}
+
+        const isMenuANull = selectedGroups[0] === null
+
+        const isDisabled = isMenuANull && isMenuB
+        const disabledClass = ''
+        let noteClass = ''
+        let noteText = ''
+        let hoverClass = ''
+
+        const isRest = group === 'rest'
+
+        // TODO (SCP-5912): Integrate DE pairwise comparison availability
+        const isAvailable = isRest
+
+        if (isMenuB) {
+          if (!isDisabled) {
+            if (isAvailable) {
+              if (isRest) {
+                noteText = 'All other groups'
+              } else {
+                noteText = blankSpace
+              }
+              noteClass = 'available'
+            } else {
+              noteText = 'Pick for pairwise DE'
+              noteClass = 'not-yet-available'
+            }
+          }
+
+          if (isDisabled) {
+            noteText = 'Select from left menu first'
+            noteClass = 'disabled'
+          }
+
+          if (hoverAllOthers) {
+            hoverClass = 'hover'
+          }
+        }
+
+        let ariaLabel = ''
+        if (isMenuB) {
+          ariaLabel = (noteText[0].toUpperCase() + noteText.slice(1)).replaceAll('-', ' ')
+        }
+        const labelClass = `de-group-menu-item ${noteClass} ${disabledClass} ${hoverClass}`
+
+        const menuName = `pairwise-menu${isMenuB && '-b'}`
+        const id = `${menuName}-${i}`
+
+        return (
+          <label
+            htmlFor={id}
+            className={labelClass}
+            aria-label={ariaLabel}
+            onMouseEnter={() => {
+              if (isMenuB) {
+                setNote(noteText)
+                if (isRest) {setHoverAllOthers(true)}
+              }
+            }}
+            onMouseLeave={() => {
+              if (isMenuB) {
+                setNote(blankSpace)
+                if (isRest) {setHoverAllOthers(false)}
+              }
+            }}
+            key={i}
+          >
+            <input
+              id={id}
+              type="radio"
+              className="pairwise-menu-input"
+              name={menuName}
+              style={{ marginRight: '4px' }}
+              disabled={isDisabled}
+              onChange={event => {
+                // TODO (SCP-5913): Add downstream views for updated DE picker
+                const radio = event.target
+                const isChecked = radio.checked
+                const groupName = radio.parentElement.innerText
+                const newSelectedGroups = [...selectedGroups]
+
+                const newGroup = isChecked ? groupName : null
+                if (groupsIndex === 0 && newGroup === selectedGroups[1]) {
+                  newSelectedGroups[1] === null
+                }
+
+                newSelectedGroups[groupsIndex] = newGroup
+
+                updateSelectedGroups(newSelectedGroups)
+              }}
+            ></input>
+            {group}
+          </label>
+        )
+      })}
+    </>
+  )
+}
+
+/** Pick groups of cells for pairwise differential expression (DE) */
+export function PairwiseDifferentialExpressionGroupLists({
+  deGenes, countsByLabelForDe
+}) {
+  const groups = getLegendSortedLabels(countsByLabelForDe)
+
+  const [selectedGroups, setSelectedGroups] = useState([null, null])
+  const [note, setNote] = useState(blankSpace)
+  const [hoverAllOthers, setHoverAllOthers] = useState(false)
+
+  /** Set new selection for DE groups to compare */
+  function updateSelectedGroups(newSelectedGroups) {
+    setSelectedGroups(newSelectedGroups)
+  }
+
+  return (
+    <>
+      <div className="differential-expression-picker">
+        <div className="pairwise-menu">
+          <p>Pick groups to compare.</p>
+          <GroupListMenu
+            groups={groups}
+            selectedGroups={selectedGroups}
+            updateSelectedGroups={updateSelectedGroups}
+            hoverAllOthers={hoverAllOthers}
+            setHoverAllOthers={setHoverAllOthers}
+          />
+        </div>
+        <div className="vs-note pairwise-lists">vs. </div>
+        <div className="pairwise-menu pairwise-menu-b">
+          <p><i>{note}</i></p>
+          <GroupListMenu
+            groups={groups}
+            selectedGroups={selectedGroups}
+            updateSelectedGroups={updateSelectedGroups}
+            setNote={setNote}
+            isMenuB={true}
+            hoverAllOthers={hoverAllOthers}
+            setHoverAllOthers={setHoverAllOthers}
+          />
+        </div>
+      </div>
+      {deGenes && <><br/><br/></>}
+    </>
+  )
+}
+
 /** Pick groups of cells for pairwise differential expression (DE) */
 export function PairwiseDifferentialExpressionGroupPicker({
   bucketId, clusterName, annotation, deGenes, deGroup, setDeGroup,