Merge pull request #1894 from broadinstitute/development

Release 1.56.0
broadinstitute · Oct 4, 2023 · ba5c496 · ba5c496
2 parents 14b0e8b + 583d3ed
commit ba5c496
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Showing 55 changed files with 1,686 additions and 527 deletions.
diff --git a/app/controllers/api/v1/study_files_controller.rb b/app/controllers/api/v1/study_files_controller.rb
@@ -747,7 +747,9 @@ def study_file_params
             data_fragments: AnnDataFileInfo::DATA_FRAGMENT_PARAMS
           ],
           differential_expression_file_info_attributes: [
-            :_id, :clustering_association, :annotation_name, :annotation_scope, :computational_method
+            :_id, :clustering_association, :annotation_name, :annotation_scope, :computational_method,
+            :gene_header, :group_header, :comparison_group_header,
+            :size_metric, :significance_metric
           ],
         )
       end

diff --git a/app/controllers/api/v1/visualization/annotations_controller.rb b/app/controllers/api/v1/visualization/annotations_controller.rb
@@ -241,19 +241,24 @@ def cell_values
         def facets
           cluster = ClusterVizService.get_cluster_group(@study, params)
           if cluster.nil?
-            render json: { error: "Cannot find cluster: #{params[:cluster]}" }, status: :not_found and return
+            render json: { error: "Cannot find clustering: #{params[:cluster]}" }, status: :not_found and return
           end
 
           # need to check for presence as some clusters will not have them if cells were not found in all_cells_array
           unless cluster.indexed
-            render json: { error: 'Cluster is not indexed' }, status: :bad_request and return
+            render json: { error: 'Clustering is not indexed' }, status: :bad_request and return
           end
 
+          # annotation validation
           if params[:annotations].include?('--numeric--')
             render json: { error: 'Cannot use numeric annotations for facets' }, status: :bad_request and return
           end
 
           annotations = self.class.get_facet_annotations(@study, cluster, params[:annotations])
+          if annotations.empty? && params[:annotations].blank?
+            render json: { error: 'Must provide at least one annotation' }, status: :bad_request and return
+          end
+
           missing = self.class.find_missing_annotations(annotations, params[:annotations])
           if missing.any?
             render json: { error: "Cannot find annotations: #{missing.join(', ')}" }, status: :not_found and return

diff --git a/app/controllers/api/v1/visualization/expression_controller.rb b/app/controllers/api/v1/visualization/expression_controller.rb
@@ -202,8 +202,7 @@ def set_selected_annotation
                                                                      cluster: @cluster,
                                                                      annot_name: params[:annotation_name],
                                                                      annot_type: params[:annotation_type],
-                                                                     annot_scope: params[:annotation_scope],
-                                                                     fallback: false)
+                                                                     annot_scope: params[:annotation_scope])
         end
 
         def set_subsampling_threshold

diff --git a/app/controllers/site_controller.rb b/app/controllers/site_controller.rb
@@ -165,7 +165,6 @@ def study
     # normally we would do this in React but the tab display is in the Rails HTML view
     # we need to check server-side since we have to account for @study.can_visualize? as well
     @explore_tab_default = @study.can_visualize?
-    @show_appcue_pin = FeatureFlaggable.feature_flags_for_instances(current_user).[](:show_appcue_viz_tour)
   end
 
   def record_download_acceptance

diff --git a/app/controllers/studies_controller.rb b/app/controllers/studies_controller.rb
@@ -997,7 +997,11 @@ def study_file_params
                                        expression_file_info_attributes: [:id, :library_preparation_protocol, :units,
                                                                          :biosample_input_type, :modality, :is_raw_counts,
                                                                          raw_counts_associations: []],
-                                       differential_expression_file_info_attributes: [:_id, :clustering_association, :annotation_association, :computational_method]
+                                       differential_expression_file_info_attributes: [
+                                          :_id, :clustering_association, :annotation_association, :computational_method,
+                                          :gene_header, :group_header, :comparison_group_header,
+                                          :size_metric, :significance_metric
+                                        ]
                                        )
   end
 

diff --git a/app/javascript/components/HomePageContent.jsx b/app/javascript/components/HomePageContent.jsx
@@ -10,7 +10,7 @@ import ResultsPanel from '~/components/search/results/ResultsPanel'
 import StudyDetails from '~/components/search/results/StudySearchResult'
 import StudySearchProvider, { StudySearchContext } from '~/providers/StudySearchProvider'
 import SearchFacetProvider from '~/providers/SearchFacetProvider'
-import UserProvider, { getFeatureFlagsWithDefaults } from '~/providers/UserProvider'
+import UserProvider from '~/providers/UserProvider'
 import ErrorBoundary from '~/lib/ErrorBoundary'
 
 /** include search controls and results */
@@ -30,8 +30,6 @@ const LinkableSearchTabs = function(props) {
   const location = useLocation()
   const basePath = location.pathname.includes('covid19') ? '/single_cell/covid19' : '/single_cell'
   const showGenesTab = location.pathname.includes('/app/genes')
-  const featureFlags = getFeatureFlagsWithDefaults()
-  const showVizAppcue = featureFlags && featureFlags?.show_appcue_viz_tour
 
   // the queryParams object does not support the more typical hasOwnProperty test
   return (
@@ -45,13 +43,6 @@ const LinkableSearchTabs = function(props) {
           className={showGenesTab ? 'active' : ''}>
           <span className="fas fa-dna"></span> Search genes
         </Link>
-        { showVizAppcue &&
-          <a className='btn btn-primary appcue-pin'
-             href='https://singlecell.broadinstitute.org/single_cell/study/SCP2271'
-             data-analytics-name='appcue-viz-demo'>
-            Demo of SCP visualization tools
-          </a>
-        }
       </nav>
       <div className="tab-content top-pad">
         <Router basepath={basePath}>

diff --git a/app/javascript/components/explore/DifferentialExpressionFilters.jsx b/app/javascript/components/explore/DifferentialExpressionFilters.jsx
@@ -10,6 +10,7 @@ function MetricDisplayValue({ metric }) {
     <>
       {metric === 'log2FoldChange' && <>log<sub>2</sub>(FC)</>}
       {metric === 'pvalAdj' && <>Adj. p-value</>}
+      {metric === 'pval' && <>p-value</>}
       {metric === 'qval' && <>q-value</>}
     </>
   )
@@ -18,28 +19,28 @@ function MetricDisplayValue({ metric }) {
 /**
   * Adds slider widget for a numerical metric
   **/
-function SliderContainer({ metric, toggleDeFacet, isActive }) {
+function SliderContainer({ metricHeader, metric, toggleDeFacet, isActive }) {
   return (
     <div className={`de-slider-container ${isActive ? '' : 'inactive'}`}>
       <div className="de-slider-checkbox-container">
         <input
           type="checkbox"
           checked={isActive}
-          className={`slider-checkbox slider-checkbox-${metric}`}
-          onChange={() => {toggleDeFacet(metric)}}
+          className={`slider-checkbox slider-checkbox-${metricHeader}`}
+          onChange={() => {toggleDeFacet(metricHeader)}}
         />
-        <label htmlFor={`slider-checkbox-${metric}`} >
+        <label htmlFor={`slider-checkbox-${metricHeader}`} >
           <MetricDisplayValue metric={metric} />
         </label>
       </div>
-      <div className={`de-slider de-slider-${metric}`} data-metric={metric}></div>
+      <div className={`de-slider de-slider-${metricHeader}`} data-metric-header={metricHeader}></div>
       <br/>
     </div>
   )
 }
 
 const defaultSliderConfigProps = {
-  'pvalAdj': {
+  'significance': {
     range: {
       'min': [0, 0.001],
       '50%': [0.05, 0.01],
@@ -52,20 +53,7 @@ const defaultSliderConfigProps = {
     values: [0, 25, 50, 73.5, 100],
     density: 4
   },
-  'qval': {
-    range: {
-      'min': [0, 0.001],
-      '50%': [0.05, 0.01],
-      'max': 1
-    },
-    start: [0, 0.05],
-    sliderDecimals: 3,
-    pipDecimals: 3,
-    connect: true,
-    values: [0, 25, 50, 73.5, 100],
-    density: 4
-  },
-  'log2FoldChange': {
+  'size': {
     range: {
       'min': [-1.5],
       'max': 1.5
@@ -83,12 +71,12 @@ const defaultSliderConfigProps = {
 *
 * noUiSlider docs: https://refreshless.com/nouislider/
 **/
-function getSliderConfig(metric) {
-  const defaultProps = defaultSliderConfigProps[metric]
+function getSliderConfig(metricHeader) {
+  const defaultProps = defaultSliderConfigProps[metricHeader]
 
   let configRange
   let configStart
-  if (['pvalAdj', 'qval'].includes(metric)) {
+  if (metricHeader === 'significance') {
     configRange = {
       'min': [0, 0.001],
       '50%': [0.05, 0.01],
@@ -135,19 +123,20 @@ function getSliderConfig(metric) {
 
 /** Range filters for DE table */
 export default function DifferentialExpressionFilters({
-  deFacets, activeFacets, updateDeFacets, toggleDeFacet, isAuthorDe
+  deFacets, activeFacets, updateDeFacets, toggleDeFacet,
+  hasPairwiseDe, sizeMetric, significanceMetric
 }) {
-  const fdrMetric = isAuthorDe ? 'qval' : 'pvalAdj'
-  const metrics = ['log2FoldChange', fdrMetric]
+  const metricHeaders = ['size', 'significance']
+  const metrics = [sizeMetric, significanceMetric]
 
   /** Update DE facets upon changing range filter selection */
   function onUpdateDeFacets(range) {
     // eslint-disable-next-line no-invalid-this
     const slider = this
-    const metric = slider.target.dataset['metric']
+    const metricHeader = slider.target.dataset['metricHeader']
 
     range = range.map(d => parseFloat(d))
-    if (metric === 'log2FoldChange') {
+    if (metricHeader === 'size') {
       range = range.map(v => {
         if (v === -1.5) {return -Infinity}
         if (v === 1.5) {return Infinity}
@@ -157,20 +146,20 @@ export default function DifferentialExpressionFilters({
     } else {
       range = [{ min: range[0], max: range[1] }]
     }
-    deFacets[metric] = range
+    deFacets[metricHeader] = range
 
-    updateDeFacets(deFacets, metric)
+    updateDeFacets(deFacets, metricHeader)
   }
 
   useEffect(() => {
-    metrics.forEach(metric => {
-      const sliderSelector = `.de-slider-${metric}`
+    metricHeaders.forEach(metricHeader => {
+      const sliderSelector = `.de-slider-${metricHeader}`
       const slider = document.querySelector(sliderSelector)
 
       if (!slider.noUiSlider) {
-        const config = getSliderConfig(metric)
+        const config = getSliderConfig(metricHeader)
         noUiSlider.create(slider, config)
-        if (metric === 'log2FoldChange') {
+        if (metricHeader === 'size') {
           const val1 = document.querySelector(`${sliderSelector} .noUi-value:nth-child(2)`)
           val1.innerHTML = `≤ ${ val1.innerHTML}`
           const val2 = document.querySelector(`${sliderSelector} .noUi-value:last-child`)
@@ -183,13 +172,14 @@ export default function DifferentialExpressionFilters({
 
   return (
     <div>
-      {!isAuthorDe && <br/>}
-      {metrics.map(metric =>
+      {!hasPairwiseDe && <br/>}
+      {metricHeaders.map((metricHeader, i) =>
         <SliderContainer
-          metric={metric}
-          key={metric}
+          metricHeader={metricHeader}
+          metric={metrics[i]}
+          key={metricHeader}
           toggleDeFacet={toggleDeFacet}
-          isActive={activeFacets[metric]}
+          isActive={activeFacets[metricHeader]}
         />
       )}
     </div>