Merge pull request #2274 from broadinstitute/jb-hca-result-filter

bistline · web-flow · commit 4a33df000531 · 2025-06-16T10:38:02.000-04:00
Adding Options button for search requests
diff --git a/app/controllers/api/v1/search_controller.rb b/app/controllers/api/v1/search_controller.rb
@@ -64,6 +64,14 @@ class SearchController < ApiBaseController
             key :required, false
             key :type, :string
           end
+          parameter do
+            key :name, :external
+            key :in, :query
+            key :description, 'External search services to query in addition to SCP'
+            key :required, false
+            key :type, :string
+            key :enum, %w[hca]
+          end
           parameter do
             key :name, :page
             key :in, :query
@@ -269,10 +277,11 @@ def index
         # convert to array to allow appending external search results (Azul, TDR, etc.)
         @studies = @studies.to_a
 
-        # perform Azul search if there are facets/terms provided by user
+        # perform Azul search if there are facets/terms provided by user, and they requested HCA results
         # run this before inferred search so that they are weighted and sorted correctly
         # skip if user is searching inside a collection or they are performing global gene search
-        if (@facets.present? || @term_list.present?) && (@selected_branding_group.nil? && @search_type == :study)
+        include_azul = params[:external] == 'hca' && @search_type == :study && @selected_branding_group.nil?
+        if (@facets.present? || @term_list.present?) && include_azul
           begin
             azul_results = ::AzulSearchService.append_results_to_studies(@studies,
                                                                          selected_facets: @facets,
diff --git a/app/javascript/components/search/controls/FacetsPanel.jsx b/app/javascript/components/search/controls/FacetsPanel.jsx
@@ -8,6 +8,7 @@ import FacetControl from './FacetControl'
 import CombinedFacetControl from './CombinedFacetControl'
 import MoreFacetsButton from './MoreFacetsButton'
 import { SearchFacetContext } from '~/providers/SearchFacetProvider'
+import OptionsButton from '~/components/search/controls/OptionsButton'
 
 const defaultFacetIds = ['disease', 'species']
 const moreFacetIds = [
@@ -71,6 +72,7 @@ export default function FacetsPanel() {
       }
       <CombinedFacetControl controlDisplayName="cell type" facetIds={['cell_type', 'cell_type__custom']}/>
       <MoreFacetsButton facets={moreFacets} />
+      <OptionsButton />
       <Modal
         show={showSearchHelpModal}
         onHide={() => closeModal(setShowSearchHelpModal)}
diff --git a/app/javascript/components/search/controls/OptionsButton.jsx b/app/javascript/components/search/controls/OptionsButton.jsx
@@ -0,0 +1,41 @@
+import React, { useState, useContext } from 'react'
+import { FontAwesomeIcon } from '@fortawesome/react-fontawesome'
+import { faCogs } from '@fortawesome/free-solid-svg-icons'
+import { Popover, OverlayTrigger } from 'react-bootstrap'
+import { StudySearchContext } from '~/providers/StudySearchProvider'
+
+import OptionsControl from '~/components/search/controls/OptionsControl'
+
+export default function OptionsButton() {
+  const searchContext = useContext(StudySearchContext)
+  const [showOptions, setShowOptions] = useState(false)
+  const configuredOptions = [
+    { searchProp: 'external', value: 'hca', label: 'Include HCA results' }
+  ]
+
+  const optionsPopover = <Popover data-analytics-name='search-options-menu' id='search-options-menu'>
+    <ul className="facet-filter-list">
+      {
+        configuredOptions.map((option) => {
+        return <OptionsControl
+          key={option.searchProp}
+          searchContext={searchContext}
+          searchProp={option.searchProp}
+          value={option.value}
+          label={option.label}/>
+        })
+      }
+    </ul>
+  </Popover>
+
+  return (
+    <OverlayTrigger trigger={['click']} placement='bottom' animation={false} overlay={optionsPopover}>
+    <span id="search-options-button" data-testid="search-options-button"
+          className={`facet ${showOptions ? 'active' : ''}`}>
+      <a onClick={() => setShowOptions(!showOptions)}>
+        <FontAwesomeIcon className="icon-left" icon={faCogs}/>Options
+      </a>
+    </span>
+    </OverlayTrigger>
+  )
+}
diff --git a/app/javascript/components/search/controls/OptionsControl.jsx b/app/javascript/components/search/controls/OptionsControl.jsx
@@ -0,0 +1,21 @@
+import React, { useState } from 'react'
+
+export default function OptionsControl({searchContext, searchProp, value, label}) {
+  const defaultChecked = searchContext.params[searchProp] === value
+  const [isChecked, setIsChecked] = useState(defaultChecked)
+
+  /** toggle state of checkbox */
+  function toggleCheckbox(checked) {
+    setIsChecked(checked)
+    searchContext.updateSearch({ [searchProp] : checked ? value : null })
+  }
+
+  return (
+    <li id={`options-control-${searchProp}`} key={`options-control-${searchProp}`}>
+      <label>
+        <input type="checkbox" checked={isChecked} onChange={() => {toggleCheckbox(!isChecked)}}/>
+          <span onClick={() => {toggleCheckbox(!isChecked)}} >{ label }</span>
+      </label>
+    </li>
+  )
+}
diff --git a/app/javascript/lib/scp-api.jsx b/app/javascript/lib/scp-api.jsx
@@ -898,7 +898,7 @@ export async function fetchSearch(type, searchParams, mock=false) {
 export function buildSearchQueryString(type, searchParams) {
   const facetsParam = buildFacetQueryString(searchParams.facets)
 
-  const params = ['page', 'order', 'terms', 'preset', 'genes', 'genePage']
+  const params = ['page', 'order', 'terms', 'external', 'preset', 'genes', 'genePage']
   let otherParamString = params.map(param => {
     return searchParams[param] ? `&${param}=${searchParams[param]}` : ''
   }).join('')
diff --git a/app/javascript/providers/GeneSearchProvider.jsx b/app/javascript/providers/GeneSearchProvider.jsx
@@ -127,6 +127,7 @@ export function buildParamsFromQuery(query, preset) {
     page: queryParams.genePage ? parseInt(queryParams.genePage) : 1,
     genes: cleanGeneParams,
     terms: queryParams.terms ? queryParams.terms : '',
+    external: queryParams.external ? queryParams.external : '',
     facets: buildFacetsFromQueryString(queryParams.facets),
     preset: preset ? preset : queryString.preset_search
   }
diff --git a/app/javascript/providers/SearchSelectionProvider.jsx b/app/javascript/providers/SearchSelectionProvider.jsx
@@ -43,7 +43,7 @@ export default function SearchSelectionProvider(props) {
   const [selection, setSelection] = useState(
     appliedSelection ?
       appliedSelection :
-      { terms: '', facets: {} })
+      { terms: '', facets: {}, external: '' })
   selection.updateSelection = updateSelection
   selection.updateFacet = updateFacet
   selection.performSearch = performSearch
diff --git a/app/javascript/providers/StudySearchProvider.jsx b/app/javascript/providers/StudySearchProvider.jsx
@@ -17,6 +17,7 @@ const emptySearch = {
   params: {
     terms: '',
     facets: {},
+    external: '',
     page: 1,
     preset_search: undefined,
     order: undefined
@@ -74,6 +75,15 @@ export function useContextStudySearch() {
   return useContext(StudySearchContext)
 }
 
+/** Merges the external parameter into the searchParams object */
+export function mergeExternalParam(searchParams, newParams) {
+  if (Object.keys(newParams).length === 1 && Object.keys(newParams)[0] === 'external') {
+    return newParams.external
+  } else {
+    return searchParams.external
+  }
+}
+
 /**
  * renders a StudySearchContext tied to its props,
  * fires route navigate on changes to params
@@ -97,6 +107,7 @@ export function PropsStudySearchProvider(props) {
     // reset the page to 1 for new searches, unless otherwise specified
     search.page = newParams.page ? newParams.page : 1
     search.preset = undefined // for now, exclude preset from the page URL--it's in the component props instead
+    search.external = mergeExternalParam(searchParams, newParams)
     const mergedParams = Object.assign(buildGeneParamsFromQuery(window.location.search), search)
     const queryString = buildSearchQueryString('study', mergedParams)
     navigate(`?${queryString}`)
@@ -153,6 +164,7 @@ export function buildParamsFromQuery(query, preset) {
     page: queryParams.page ? parseInt(queryParams.page) : 1,
     terms: queryParams.terms ? queryParams.terms : '',
     facets: buildFacetsFromQueryString(queryParams.facets),
+    external: queryParams.external ? queryParams.external : '',
     preset: preset ? preset : queryString.preset_search,
     order: queryParams.order
   }
diff --git a/app/javascript/styles/_search.scss b/app/javascript/styles/_search.scss
@@ -393,3 +393,35 @@ span.text-search {
     background-color: inherit;
   }
 }
+
+#search-options-menu {
+  ul {
+    list-style-type: none;
+    padding-left: 0px;
+  }
+
+  ul.facet-filter-list {
+    max-height: 300px;
+    overflow-y: auto;
+    margin-bottom: 0;
+    label {
+      display: inline-block;
+      white-space: nowrap;
+    }
+    input {
+      font-size: 2em;
+      vertical-align: middle;
+      margin-top: 0px;
+      margin-right: 12px;
+    }
+    label span {
+      vertical-align: middle;
+      font-weight: normal;
+    }
+  }
+
+  li {
+    width: 100%;
+    margin-bottom: 0.5em;
+  }
+}
diff --git a/app/javascript/styles/_searchPanel.scss b/app/javascript/styles/_searchPanel.scss
@@ -6,7 +6,7 @@
     vertical-align: bottom;
   }
 
-  #download-button {
+  #download-button{
     float: right;
   }
 }
diff --git a/test/api/search_controller_test.rb b/test/api/search_controller_test.rb
@@ -335,8 +335,6 @@ class SearchControllerTest < ActionDispatch::IntegrationTest
       assert_includes json['matching_accessions'], accession,
                       "Did not find expected accessions after inferred search, expected #{inferred_accessions} but found #{json['matching_accessions']}"
     end
-    # inferred match will be the last study, but given the number of Azul results present it will note be rendered
-    # as it is likely 20+ pages deep
     assert_equal @other_study.accession, json['matching_accessions'].last
            "Did not mark last search results as inferred_match: #{json['matching_accessions'].last} != #{@other_study.accession}"
   end
@@ -369,23 +367,21 @@ class SearchControllerTest < ActionDispatch::IntegrationTest
     # update other_study to match one filter from facets; should not be inferred since it doesn't meet both criteria
     facet_query = "species:#{HOMO_SAPIENS_FILTER[:id]}#{FACET_DELIM}disease:#{NO_DISEASE_FILTER[:id]}"
     @other_study.study_detail.update(full_description: HOMO_SAPIENS_FILTER[:name])
-    AzulSearchService.stub :get_results, {} do
-      execute_http_request(:get, api_v1_search_path(type: 'study', facets: facet_query))
-      assert_response :success
-      assert_equal @convention_accessions, json['matching_accessions'],
-                   "Did not find expected accessions before inferred search, expected #{@convention_accessions} but found #{json['matching_accessions']}"
+    execute_http_request(:get, api_v1_search_path(type: 'study', facets: facet_query))
+    assert_response :success
+    assert_equal @convention_accessions, json['matching_accessions'],
+                 "Did not find expected accessions before inferred search, expected #{@convention_accessions} but found #{json['matching_accessions']}"
 
-      # update to match both filters; should be inferred
-      double_facet_name = "#{HOMO_SAPIENS_FILTER[:name]} #{NO_DISEASE_FILTER[:name]}"
-      @other_study.study_detail.update(full_description: double_facet_name)
-      execute_http_request(:get, api_v1_search_path(type: 'study', facets: facet_query))
-      assert_response :success
-      inferred_accessions = @convention_accessions + [@other_study.accession]
-      assert_equal inferred_accessions, json['matching_accessions'],
-                   "Did not find expected accessions after inferred search, expected #{inferred_accessions} but found #{json['matching_accessions']}"
-      inferred_study = json['studies'].last
-      assert inferred_study['inferred_match'], "Did not correctly mark #{@other_study.accession} as inferred"
-    end
+    # update to match both filters; should be inferred
+    double_facet_name = "#{HOMO_SAPIENS_FILTER[:name]} #{NO_DISEASE_FILTER[:name]}"
+    @other_study.study_detail.update(full_description: double_facet_name)
+    execute_http_request(:get, api_v1_search_path(type: 'study', facets: facet_query))
+    assert_response :success
+    inferred_accessions = @convention_accessions + [@other_study.accession]
+    assert_equal inferred_accessions, json['matching_accessions'],
+                 "Did not find expected accessions after inferred search, expected #{inferred_accessions} but found #{json['matching_accessions']}"
+    inferred_study = json['studies'].last
+    assert inferred_study['inferred_match'], "Did not correctly mark #{@other_study.accession} as inferred"
   end
 
   test 'should run preset search' do
@@ -506,33 +502,49 @@ class SearchControllerTest < ActionDispatch::IntegrationTest
   end
 
   test 'should support all sorting options' do
-    # use Azul mocks for faster tests
-    # TODO: migrate all other search tests to use Azul mocks (SCP-4328)
-    tcell_json = File.open(Rails.root.join('test/test_data/azul/human_tcell.json')).read
-    human_tcell_response = JSON.parse(tcell_json).with_indifferent_access
-    mock_azul_facets = {
-      genusSpecies: {
-        is: ['Homo sapiens']
-      }
-    }.with_indifferent_access
-
-    # test all 3 sorting options
     ['recent', 'popular', 'foo', nil].each do |sort_order|
-      mock = Minitest::Mock.new
-      mock.expect :format_query_from_facets, mock_azul_facets, [Array]
-      mock.expect :merge_query_objects, mock_azul_facets, [Hash, nil]
-      mock.expect :projects, human_tcell_response, [], query: Hash
-      ApplicationController.stub :hca_azul_client, mock do
-        facet_query = "species:#{HOMO_SAPIENS_FILTER[:id]}"
-        execute_http_request(:get,
-                             api_v1_search_path(
-                               type: 'study',
-                               facets: facet_query,
-                               order: sort_order.to_s
-                             ))
+      facet_query = "species:#{HOMO_SAPIENS_FILTER[:id]}"
+      execute_http_request(:get,
+                           api_v1_search_path(
+                             type: 'study',
+                             facets: facet_query,
+                             order: sort_order.to_s
+                           ))
+      assert_response :success
+    end
+  end
+
+  test 'should query Azul when requested' do
+    facet_query = "species:#{HOMO_SAPIENS_FILTER[:id]}"
+    species_facet = SearchFacet.find_by(identifier: 'species')
+    facet = {
+      id: species_facet.identifier,
+      filters: [HOMO_SAPIENS_FILTER],
+      db_facet: species_facet
+    }
+    mock = Minitest::Mock.new
+    mock.expect(:get_results, {}, [[facet], []])
+    AzulSearchService.stub(:append_results_to_studies, mock) do
+      assert_raises MockExpectationError do
+        execute_http_request(:get, api_v1_search_path(type: 'study', facets: facet_query))
         assert_response :success
         mock.verify
       end
     end
+    studies_by_facet = {
+      @study.accession => {
+        disease: [HOMO_SAPIENS_FILTER],
+        facet_search_weight: 1
+      }
+    }.with_indifferent_access
+    positive_mock = Minitest::Mock.new
+    positive_mock.expect :[], [@study], [:studies]
+    positive_mock.expect :[], studies_by_facet, [:facet_map]
+    positive_mock.expect :[], {}, [:results_matched_by_data]
+    AzulSearchService.stub(:append_results_to_studies, positive_mock) do
+      execute_http_request(:get, api_v1_search_path(type: 'study', facets: facet_query, external: 'hca'))
+      assert_response :success
+      positive_mock.verify
+    end
   end
 end
diff --git a/test/js/search/options-button.test.js b/test/js/search/options-button.test.js
@@ -0,0 +1,28 @@
+import React from 'react'
+import { render, fireEvent } from '@testing-library/react'
+import '@testing-library/jest-dom/extend-expect'
+
+import OptionsButton from '~/components/search/controls/OptionsButton'
+
+describe('OptionsButton component', () => {
+  it('renders the options button with correct icon and text', () => {
+    const { getByText } = render(<OptionsButton />)
+
+    expect(getByText('Options')).toBeInTheDocument()
+  })
+
+  it('toggles options visibility on click', () => {
+    const { getByText, queryByText } = render(<OptionsButton />)
+
+    // Initially, options should not be visible
+    expect(queryByText('Include HCA results')).not.toBeInTheDocument()
+
+    // Click to show options
+    fireEvent.click(getByText('Options'))
+    expect(getByText('Include HCA results')).toBeInTheDocument()
+
+    // Click again to hide options
+    fireEvent.click(getByText('Options'))
+    expect(queryByText('Include HCA results')).not.toBeInTheDocument()
+  })
+})
diff --git a/test/js/search/options-control.test.js b/test/js/search/options-control.test.js

Original file line number	Diff line number	Diff line change
`@@ -127,6 +127,7 @@ export function buildParamsFromQuery(query, preset) {`
`127`	`127`	`page: queryParams.genePage ? parseInt(queryParams.genePage) : 1,`
`128`	`128`	`genes: cleanGeneParams,`
`129`	`129`	`terms: queryParams.terms ? queryParams.terms : '',`
	`130`	`+ external: queryParams.external ? queryParams.external : '',`
`130`	`131`	`facets: buildFacetsFromQueryString(queryParams.facets),`
`131`	`132`	`preset: preset ? preset : queryString.preset_search`
`132`	`133`	`}`
Original file line number	Diff line number	Diff line change
`@@ -6,7 +6,7 @@`
`6`	`6`	`vertical-align: bottom;`
`7`	`7`	`}`
`8`	`8`
`9`		`- #download-button {`
	`9`	`+ #download-button{`
`10`	`10`	`float: right;`
`11`	`11`	`}`
`12`	`12`	`}`