Merge pull request #1068 from griffithlab/improved-quicksearch

Quicksearch improvements

client/src/app/components/layout/quicksearch/quicksearch-component.html

@@ -8,14 +8,15 @@
   nzPlaceHolder="Search CIViC"
   [nzOptionHeightPx]="28"
   [nzShowArrow]="false"
+  [nzDropdownRender]="searchEntities"
   [nzDropdownMatchSelectWidth]="false">
   <nz-option
     *ngFor="let o of (option$ | ngrxPush)"
     nzCustomContent
     [nzValue]="o.result">
     <i
       nz-icon
-      style="margin-right: 0.5em;"
+      style="margin-right: 0.5em"
       nzTheme="twotone"
       [nzTwotoneColor]="converter(o.result.resultType) | entityColor"
       [nzType]="o.result.resultType | iconNameForSubscribableEntity"></i>
@@ -39,3 +40,26 @@
     Loading Data...
   </nz-option>
 </nz-select>
+
+<ng-template #searchEntities>
+  <hr />
+  <nz-checkbox-wrapper (nzOnChange)="selectedEntitiesChanged($event)">
+    <div class="entity-select">
+      @for(entity of searchableEntities; track entity) {
+      <label
+        nz-checkbox
+        [nzValue]="entity"
+        nz-tooltip
+        [nzTooltipTitle]="entity"
+        [ngModel]="isSelected(entity)">
+        <i
+          nz-icon
+          nzTheme="twotone"
+          nzTool
+          [nzTwotoneColor]="entity | entityColor"
+          [nzType]="entity | iconNameForSubscribableEntity"></i>
+      </label>
+      }
+    </div>
+  </nz-checkbox-wrapper>
+</ng-template>

client/src/app/components/layout/quicksearch/quicksearch-component.less

@@ -5,3 +5,13 @@
 nz-select {
   width: 100%;
 }
+
+hr {
+  border-color: #6666
+}
+
+.entity-select {
+  margin-right: 10px;
+  margin-left: 10px;
+
+}

client/src/app/components/layout/quicksearch/quicksearch-component.ts

@@ -49,6 +49,10 @@ export class CvcQuicksearchComponent {
   @ViewChild(NzSelectComponent, { static: true })
   selectNode!: NzSelectComponent
 
+  selectedEntities: SearchableEntities[] = Object.values(SearchableEntities)
+  searchableEntities = Object.keys(SearchableEntities)
+  currentSearchTerm?: string
+
   // SOURCE STREAMS
   onSearch$: Subject<string>
   onSelect$: Subject<void>
@@ -62,25 +66,29 @@ export class CvcQuicksearchComponent {
   option$: Observable<QuicksearchOption[]>
   isLoading$: Observable<boolean>
 
-
   converter = entityTypeToTypename
 
-  constructor(private gql: QuicksearchGQL, private router: Router) {
+  constructor(
+    private gql: QuicksearchGQL,
+    private router: Router
+  ) {
     this.onSearch$ = new Subject<string>()
     this.onSelect$ = new Subject<void>()
 
     this.response$ = this.onSearch$.pipe(
       skip(1), // drop initial empty string from input init
       throttleTime(300, asyncScheduler, { leading: false, trailing: true }),
       switchMap((str: string) => {
+        this.currentSearchTerm = str
+        let selectedEntities = this.selectedEntities
         // if queryRef doesn't exist, create it with watchQuery observable
         // if it does, refetch with fetchQuery observable.
         // using defer() ensures functions are not called until
         // values are emitted. otherwise they'll be called on subscribe.
         return iif(
           () => this.queryRef === undefined, // predicate
-          defer(() => watchQuery(str)), // true
-          defer(() => fetchQuery(str))
+          defer(() => watchQuery(str, selectedEntities)), // true
+          defer(() => fetchQuery(str, selectedEntities))
         ) // false
       })
     )
@@ -114,14 +122,19 @@ export class CvcQuicksearchComponent {
     })
 
     // set queryRef with watch(), return its valueChanges observable
-    const watchQuery = (str: string) => {
-      this.queryRef = this.gql.watch({ query: str, highlightMatches: true })
+    const watchQuery = (str: string, entities: Maybe<SearchableEntities[]>) => {
+      this.queryRef = this.gql.watch({
+        query: str,
+        highlightMatches: true,
+        types: entities,
+      })
       return this.queryRef.valueChanges
     }
 
     // return observable from refetch() promise
-    const fetchQuery = (str: string) =>
-      from(this.queryRef.refetch({ query: str }))
+    const fetchQuery = (str: string, entities: Maybe<SearchableEntities[]>) => {
+      return from(this.queryRef.refetch({ query: str, types: entities }))
+    }
   }
 
   urlForResult(res: SearchResult): string {
@@ -136,10 +149,28 @@ export class CvcQuicksearchComponent {
       case SearchableEntities.MolecularProfile:
         name = 'molecular-profiles'
         break
+      case SearchableEntities.Therapy:
+        name = 'therapies'
+        break
       default:
         name = `${res.resultType.toLowerCase()}s`
     }
 
     return `/${name}/${res.id}/summary`
   }
+
+  selectedEntitiesChanged(selectedEntities: string[]) {
+    this.selectedEntities = selectedEntities.map(
+      (x) => SearchableEntities[x as keyof typeof SearchableEntities]
+    )
+
+    if (this.currentSearchTerm) {
+      this.onSearch$.next(this.currentSearchTerm)
+    }
+  }
+
+  isSelected(entity: string): boolean {
+    const x = SearchableEntities[entity as keyof typeof SearchableEntities]
+    return this.selectedEntities.includes(x)
+  }
 }

client/src/app/components/layout/quicksearch/quicksearch.module.ts

@@ -11,6 +11,8 @@ import { FormsModule } from '@angular/forms'
 import { NzSelectModule } from 'ng-zorro-antd/select'
 import { NzTypographyModule } from 'ng-zorro-antd/typography'
 import { CvcPipesModule } from '@app/core/pipes/pipes.module'
+import { NzCheckboxModule } from 'ng-zorro-antd/checkbox'
+import { NzToolTipModule } from 'ng-zorro-antd/tooltip'
 
 @NgModule({
   declarations: [CvcQuicksearchComponent],
@@ -27,6 +29,8 @@ import { CvcPipesModule } from '@app/core/pipes/pipes.module'
     NzFormModule,
     NzIconModule,
     NzAutocompleteModule,
+    NzCheckboxModule,
+    NzToolTipModule,
   ],
   exports: [CvcQuicksearchComponent],
 })

client/src/app/core/pipes/icon-name-for-subscribable-entity.ts

@@ -31,11 +31,17 @@ export class IconNameForSubscribableEntity implements PipeTransform {
       case SubscribableEntities.VariantGroup:
       case 'VARIANT_GROUP':
       case 'VariantGroup':
-        return 'civic-variant-group'
+        return 'civic-variantgroup'
       case SubscribableEntities.MolecularProfile:
       case 'MOLECULAR_PROFILE':
       case 'MolecularProfile':
         return 'civic-molecularprofile'
+      case 'THERAPY':
+      case 'Therapy':
+        return 'civic-therapy'
+      case 'DISEASE':
+      case 'Disease':
+        return 'civic-disease'
       default:
         console.log('String No icon name found for ' + e)
         return 'border-outer'

client/src/app/generated/civic.apollo.ts

@@ -5195,10 +5195,12 @@ export type SearchResult = {
 
 export enum SearchableEntities {
   Assertion = 'ASSERTION',
+  Disease = 'DISEASE',
   EvidenceItem = 'EVIDENCE_ITEM',
   Feature = 'FEATURE',
   MolecularProfile = 'MOLECULAR_PROFILE',
   Revision = 'REVISION',
+  Therapy = 'THERAPY',
   Variant = 'VARIANT',
   VariantGroup = 'VARIANT_GROUP'
 }

client/src/app/generated/server.model.graphql

@@ -8763,10 +8763,12 @@ type SearchResult {
 
 enum SearchableEntities {
   ASSERTION
+  DISEASE
   EVIDENCE_ITEM
   FEATURE
   MOLECULAR_PROFILE
   REVISION
+  THERAPY
   VARIANT
   VARIANT_GROUP
 }

client/src/app/generated/server.schema.json

@@ -40478,6 +40478,18 @@
               "description": null,
               "isDeprecated": false,
               "deprecationReason": null
+            },
+            {
+              "name": "THERAPY",
+              "description": null,
+              "isDeprecated": false,
+              "deprecationReason": null
+            },
+            {
+              "name": "DISEASE",
+              "description": null,
+              "isDeprecated": false,
+              "deprecationReason": null
             }
           ],
           "possibleTypes": null

server/app/graphql/resolvers/quicksearch.rb

@@ -16,7 +16,9 @@ def resolve(query:, types: nil, highlight_matches: false)
                        Assertion,
                        VariantGroup,
                        Revision,
-                       MolecularProfile
+                       MolecularProfile,
+                       Therapy,
+                       Disease
                       ]
                     else
                       types
@@ -33,8 +35,15 @@ def resolve(query:, types: nil, highlight_matches: false)
                   models: query_targets,
                   highlight: tag,
                   limit: 10,
-                  fields: ['id^10', 'name', 'aliases', 'feature', 'feature_type']
-                ).with_highlights(multiple: true)
+                  fields: [
+                    {'id^10' => :word },
+                    {'ncit_id' => :word },
+                    {'doid' => :word },
+                    {'name^10' => :word },
+                    {'aliases' => :word_start },
+                    {'feature' => :word },
+                    {'feature_type' => :word }
+                  ]).with_highlights(multiple: true)
 
     results.map do |res, highlights|
       {
@@ -59,7 +68,7 @@ def format_name(name, highlights)
   def format_highlights(highlights)
     rows = highlights.map do |field_name, matches|
       next if field_name == :name
-      name = field_name.to_s.titleize
+    name = field_name.to_s.split(".").first&.titleize
       match_string = matches.join(', ')
       "#{name}: #{match_string}"
     end

server/app/graphql/resolvers/top_level_therapies.rb

@@ -9,11 +9,11 @@ class Resolvers::TopLevelTherapies < GraphQL::Schema::Resolver
   description 'List and filter Therapies from the NCI Thesaurus.'
 
   scope do
-    Therapy.select('therapies.id, therapies.name, max(therapies.ncit_id) as ncit_id, count(distinct(assertions.id)) as assertion_count, count(distinct(evidence_items.id)) as evidence_count')
+    Therapy.select('therapies.id, therapies.name, therapies.deprecated, max(therapies.ncit_id) as ncit_id, count(distinct(assertions.id)) as assertion_count, count(distinct(evidence_items.id)) as evidence_count')
       .left_outer_joins(:assertions, :evidence_items)
       .where("evidence_items.status != 'rejected' OR assertions.status != 'rejected'")
       .where(deprecated: false)
-      .group('therapies.id, therapies.name')
+      .group('therapies.id, therapies.name, therapies.deprecated')
       .having('COUNT(evidence_items.id) > 0 OR COUNT(assertions.id) > 0')
       .order('evidence_count DESC', :id)
   end

server/app/graphql/types/quicksearch/searchable_entities.rb

@@ -7,5 +7,7 @@ class SearchableEntities < Types::BaseEnum
     value 'VARIANT_GROUP', value: VariantGroup
     value 'REVISION', value: Revision
     value 'MOLECULAR_PROFILE', value: MolecularProfile
+    value 'THERAPY', value: Therapy
+    value 'DISEASE', value: Disease
   end
 end

server/app/models/disease.rb

@@ -9,6 +9,22 @@ class Disease < ApplicationRecord
   has_many :source_suggestions
   has_and_belongs_to_many :disease_aliases
 
+  searchkick highlight: [:name, :aliases], callbacks: :async, word_start: [:name, :aliases]
+  scope :search_import, -> { includes(:disease_aliases) }
+
+  def search_data
+    {
+      name: name,
+      doid: "DOID:#{doid}",
+      aliases: disease_aliases.map(&:name)
+    }
+  end
+
+  def should_index?
+    evidence_items.any?
+  end
+
+
   def disease_url
     Disease.url_for_doid(doid)
   end

server/app/models/therapy.rb

@@ -10,6 +10,21 @@ class Therapy < ApplicationRecord
 
   validates :ncit_id, uniqueness: true, allow_nil: true
 
+  searchkick highlight: [:name, :aliases], callbacks: :async, word_start: [:name, :aliases]
+  scope :search_import, -> { includes(:therapy_aliases) }
+
+  def search_data
+    {
+      name: name,
+      ncit_id: ncit_id,
+      aliases: therapy_aliases.map(&:name)
+    }
+  end
+
+  def should_index?
+    evidence_items.any?
+  end
+
   def self.url_for(ncit_id:)
     if ncit_id.nil?
       nil