Merge branch 'enh-codespell' of github.com:yarikoptic/civic-v2 into y…

…arikoptic-enh-codespell

.codespellrc

@@ -0,0 +1,8 @@
+[codespell]
+# Ref: https://github.com/codespell-project/codespell#using-a-config-file
+# generated/ was excluded but might need to be fixed as well!
+skip = .git*,*.svg,*.lock,*.css,.codespellrc,*.js,generated,assets,variants-summary.page.html
+check-hidden = true
+# Ignore super long lines -- must be minimized etc
+ignore-regex = ^.{120,}|\b(AllTime|allTime)\b
+ignore-words-list = iif

.github/workflows/codespell.yml

@@ -0,0 +1,23 @@
+# Codespell configuration is within .codespellrc
+---
+name: Codespell
+
+on:
+  push:
+    branches: [main]
+  pull_request:
+    branches: [main]
+
+permissions:
+  contents: read
+
+jobs:
+  codespell:
+    name: Check for spelling errors
+    runs-on: ubuntu-latest
+
+    steps:
+      - name: Checkout
+        uses: actions/checkout@v4
+      - name: Codespell
+        uses: codespell-project/actions-codespell@v2

README.md

@@ -11,7 +11,7 @@ All content created in CIViC is, and will continue to be, freely available, with
 ## Getting Started
 CIViC is a Rails backend serving a GraphQL API to an Angular frontend. The same API that powers the frontend is available for anyone to use. The easiest way to get started is to experiment in the [GraphiQL user interface](https://civicdb.org/api/graphiql). You can also browse autogenerated documentation [here](https://griffithlab.github.io/civic-v2/).
 ### Dependencies
-* Ruby >= 3.0 (recomended install via rbenv)
+* Ruby >= 3.0 (recommended install via rbenv)
 * PostgreSQL >= 14
 * Node >= 14
 

client/src/app/components/evidence/evidence-table/evidence-table.component.html

@@ -402,7 +402,7 @@
               nzLabel="Combined"></nz-option>
             <nz-option
               nzValue="UNKNOWN"
-              nzLabel="Unkown"></nz-option>
+              nzLabel="Unknown"></nz-option>
             <nz-option
               nzValue="NA"
               nzLabel="N/A"></nz-option>

client/src/app/components/therapies/my-chem-info/my-chem-info.component.html

@@ -9,7 +9,7 @@
                 {{chemInfo.chebiDefinition}}
               </ng-container>
             </nz-descriptions-item>
-            <nz-descriptions-item nzTitle="Inidications" [nzSpan]="2">
+            <nz-descriptions-item nzTitle="Indications" [nzSpan]="2">
               <ng-container *ngIf="chemInfo.indications.length > 0; else noValue">
                 <cvc-tag-list>
                   <nz-tag *ngFor="let i of chemInfo.indications">{{i}}</nz-tag>

client/src/app/core/utilities/closeable-tag-base.ts

@@ -8,7 +8,7 @@ export abstract class BaseCloseableTag implements OnInit {
   popoverVisible = false
   abstract idFunction(): number
 
-  // TODO: implement as getter/setters to remove ngOnInit depdendency for virtual scroll cache
+  // TODO: implement as getter/setters to remove ngOnInit dependency for virtual scroll cache
   // Low priority as closable tags are not currently used in virtual scroll viewports.
   ngOnInit(): void {
     if (this.onCloseClicked) {

client/src/app/core/utilities/enum-tooltips/get-evidence-enum-tooltip.ts

@@ -83,7 +83,7 @@ export const tooltips: tooltipMap = {
   },
 }
 
-// a map of tooltips that differ based on their display context (entity type, evidence/asssertion type)
+// a map of tooltips that differ based on their display context (entity type, evidence/assertion type)
 export type ContextualTooltipMap = {
   [key: string | symbol]: {
     // TODO: type as [key in ContextualAttribute]?: {

client/src/app/forms/components/form-errors-alert/form-errors-alert.component.html

@@ -8,7 +8,7 @@
   *ngIf="errors.length > 1"
   [nzDescription]="errorList"
   nzShowIcon
-  nzMessage="Submit Errors Occured"></nz-alert>
+  nzMessage="Submit Errors Occurred"></nz-alert>
 
 <ng-template
   #errorList

client/src/app/forms/mixins/entity-select-field.mixin.ts

@@ -88,7 +88,7 @@ export interface EntitySelectFieldOptions<
  * TAF = typeahead query optional parameters fragment
  * TQ  = tag query
  * TV  = tag query variables
- * TAP = optional typeahead query paramters type
+ * TAP = optional typeahead query parameters type
  * */
 
 export function EntitySelectField<

client/src/app/forms/mixins/string-select-field.mixin.ts

@@ -68,7 +68,7 @@ export interface StringSelectFieldOptions<
  * TAQ = typeahead query
  * TAV = typeahead query variables
  * TAF = typeahead query optional parameters fragment
- * TAP = optional typeahead query paramters type
+ * TAP = optional typeahead query parameters type
  * */
 
 export function StringSelectField<

client/src/app/forms/test-pages/tags-test/tags-test.page.html

@@ -11,7 +11,7 @@
         <th>Popover</th>
         <th>Closeable</th>
         <th>Checkable</th>
-        <th>Trucate</th>
+        <th>Truncate</th>
         <th>Group</th>
         <th>Unlinked</th>
       </tr>

client/src/app/forms/types/evidence-select/evidence-manager/evidence-manager.config.ts

@@ -45,7 +45,7 @@ export const columnKeyToQueryVariableMap: EvidenceManagerColQueryMap = {
   therapies: 'therapyName',
   evidenceItem: 'id',
 }
-// colum keys included here will be hidden in preference panel, preventing
+// column keys included here will be hidden in preference panel, preventing
 // defaults from being changed by the user
 export const omittedFromPrefs: EvidenceManagerColKey[] = ['selected', 'id']
 

client/src/app/forms/types/evidence-select/evidence-manager/evidence-manager.types.ts

@@ -177,7 +177,7 @@ interface TagConfig {
 // most entity tag cols can be customized using TagConfig.
 // if showStatus set to true, tag will display status styles.
 // NOTE: use BaseColumnConfig's 'context' option if it's necessary
-// to render an entity tag in a column whos row[colKey] data
+// to render an entity tag in a column whose row[colKey] data
 // is not a LinkableEntity, e.g. evidence-manager table's 'id' col
 interface EntityTagConfig {
   showStatus?: boolean // display tag status indicator styles
@@ -314,7 +314,7 @@ export const colTypeGuards = {
 // These guard attributes on col options, currently not used
 // in the TypeGuard pipe,  but in logic that handles column options.
 // FIXME(?): I had hoped that the discriminated union type ColumnOptionType
-// above would have made guard functions like this unecessary, but I was unable to
+// above would have made guard functions like this unnecessary, but I was unable to
 // write some of the generic cols/prefs handling functions w/o them. Not
 // sure if this is bc the types are not constructed properly.
 export const hasSortOptions: TypeGuard<any, SortConfig> = (

client/src/app/forms/types/molecular-profile-select/mp-expression-editor/mp-expression-editor.component.ts

@@ -238,7 +238,7 @@ export class MpExpressionEditorComponent implements AfterViewInit, OnChanges {
       )
       .subscribe((res) => {
         // FIXME: this casting of 'res' is a total hack, need proper gate functions for this error/response
-        // logic, or refactor the parser to use rxjs error handling (which will also simplfy template logic)
+        // logic, or refactor the parser to use rxjs error handling (which will also simplify template logic)
         if (this.isMpParseError(res)) {
           const err = res as MpParseError
           this.expressionMessage$.next(undefined)

client/src/app/forms/types/org-submit-button/org-submit-button.type.ts

@@ -68,7 +68,7 @@ export class CvcOrgSubmitButtonComponent
   organizations$: Observable<Organization[]>
   mostRecentOrg$: Observable<Maybe<Organization>>
 
-  // these syncronize submit button & org dropdown button states, styles
+  // these synchronize submit button & org dropdown button states, styles
   isDisabled$: Subject<boolean>
   isHidden$: Subject<boolean>
   buttonClass$!: BehaviorSubject<string>

client/src/app/forms/types/variant-select/variant-manager/variant-manager.config.ts

@@ -41,7 +41,7 @@ export const columnKeyToQueryVariableMap: VariantManagerColQueryMap = {
   aliases: 'variantAlias'
 }
 
-// colum keys included here will be hidden in preference panel, preventing
+// column keys included here will be hidden in preference panel, preventing
 // defaults from being changed by the user
 export const omittedFromPrefs: VariantManagerColKey[] = ['selected', 'id']
 

client/src/app/forms/types/variant-select/variant-manager/variant-manager.types.ts

@@ -184,7 +184,7 @@ interface TagConfig {
 // most entity tag cols can be customized using TagConfig.
 // if showStatus set to true, tag will display status styles.
 // NOTE: use BaseColumnConfig's 'context' option if it's necessary
-// to render an entity tag in a column whos row[colKey] data
+// to render an entity tag in a column whose row[colKey] data
 // is not a LinkableEntity, e.g. variant-manager table's 'id' col
 interface EntityTagConfig {
   showStatus?: boolean // display tag status indicator styles
@@ -329,7 +329,7 @@ export const colTypeGuards = {
 // These guard attributes on col options, currently not used
 // in the TypeGuard pipe,  but in logic that handles column options.
 // FIXME(?): I had hoped that the discriminated union type ColumnOptionType
-// above would have made guard functions like this unecessary, but I was unable to
+// above would have made guard functions like this unnecessary, but I was unable to
 // write some of the generic cols/prefs handling functions w/o them. Not
 // sure if this is bc the types are not constructed properly.
 export const hasSortOptions: TypeGuard<any, SortConfig> = (

client/src/app/forms/wrappers/form-row/form-row.wrapper.ts

@@ -19,7 +19,7 @@ type ResponsiveColConfig = {
 type FormRowOptions = {
   // nz-row gutter
   gutter?: number | [number, number] | null
-  // NOTE: if gutter[1] (vertial gutter) is set to 0, row will receive no top margin (see mp-finder config)
+  // NOTE: if gutter[1] (vertical gutter) is set to 0, row will receive no top margin (see mp-finder config)
   // nz-col's nzSpan, nzXs - nzXXl config applied to every field
   span?: string | number | null
   responsive?: ResponsiveColConfig

client/src/app/views/assertions/assertions-detail/assertions-summary/assertions-summary.page.html

@@ -1,7 +1,7 @@
 <ng-container *ngIf="assertion$ | ngrxPush as assertion">
   <!-- page layout row -->
   <nz-row [nzGutter]="[8, 16]">
-    <!-- LEFT COLUMN: assertion summary, desciption, attributes -->
+    <!-- LEFT COLUMN: assertion summary, description, attributes -->
     <nz-col [nzSpan]="12">
       <!-- layout row for description blocks -->
       <nz-row [nzGutter]="[8, 8]">

client/src/app/views/features/features-home/features-home.page.html

@@ -23,7 +23,7 @@ <h2>Features</h2>
           nzExpandable
           [nzEllipsisRows]="2">
           CIViC Features include a feature-level summary, a link to the Drug
-          Gene Interation Database, and extensive gene details from MyGene.info.
+          Gene InteractionDatabase, and extensive gene details from MyGene.info.
         </p>
       </nz-col>
       <nz-col

client/src/app/views/releases/releases-main/releases-main.component.html

@@ -77,7 +77,7 @@ <h2>Data Releases</h2>
           dynamically obtained from resources external to CIViC (e.g.
           MyVariant.Info, MyGene.Info). Variant TSV releases only include
           variant records with accepted evidence records. Variant TSV releases
-          from before August 2020 include all variant records, irregardless of
+          from before August 2020 include all variant records, regardless of
           the status of the associated evidence items. Evidence TSV releases
           only include accepted evidence items and exclude pending or rejected
           evidence items. Assertion TSV releases only include accepted

client/src/app/views/variant-groups/variant-groups-detail/variant-groups-summary/variant-groups-summary.page.html

@@ -77,7 +77,7 @@
       <ng-container *ngrxLet="this.variantGroup$ as variantGroup">
         <cvc-variants-table
           [variantGroupId]="variantGroup?.id"
-          cvcTitle="Variants in Variant Groupt {{variantGroup?.name}}"></cvc-variants-table>
+          cvcTitle="Variants in Variant Group {{variantGroup?.name}}"></cvc-variants-table>
       </ng-container>
     </nz-col>
   </nz-row>

client/src/main.ts

@@ -8,7 +8,7 @@ import { environment } from './environments/environment'
 if (environment.production) {
   enableProdMode()
 } else {
-  // enable RXjs Spy on non production bulds only
+  // enable RXjs Spy on non production builds only
   const spy = create()
   // deactivate CyclePlugin, which spams console w/
   // an alert about a next cycle in table-scroll.directive.

client/src/themes/overrides/entity-page-header.overrides.less

@@ -31,7 +31,7 @@
     }
     .header-description {
       padding: @default-padding-sm;
-      // adjust headline and desctiption to fit nicely with
+      // adjust headline and description to fit nicely with
       // the larger icon
       h2 {
         color: #262626;

server/app/graphql/loaders/association_count_loader.rb

@@ -1,6 +1,6 @@
 module Loaders
   class AssociationCountLoader < GraphQL::Batch::Loader
-    def initialize(model, association: assocation)
+    def initialize(model, association: association)
       @model = model
       @association = association
     end

server/app/graphql/mutations/resolve_flag.rb

@@ -1,6 +1,6 @@
 class Mutations::ResolveFlag < Mutations::MutationWithOrg
   description  <<~DOC.strip
-    Resolve a flag on a CIViC entity indicating that it was either erronously flagged or the issue has been resolved.
+    Resolve a flag on a CIViC entity indicating that it was either erroneously flagged or the issue has been resolved.
     Any user may resolve their own flag however only editors with valid conflict of interest statements can resolve other flags.
   DOC
 

server/app/graphql/mutations/update_coi.rb

@@ -1,5 +1,5 @@
 class Mutations::UpdateCoi < Mutations::BaseMutation
-  description "Update the currentlly logged in User's Conflict of Interest statement"
+  description "Update the currently logged in User's Conflict of Interest statement"
 
   argument :coi_present, Boolean, required: true,
     description: 'Does the user report having a conflict of interest? Mark true if so.'

server/app/graphql/resolvers/activities.rb

@@ -46,7 +46,7 @@ class Activities < GraphQL::Schema::Resolver
     end
 
     option(:mode, type: Types::Events::EventFeedMode) do |_, _|
-      #accesed in connection, yuck
+      #accessed in connection, yuck
     end
   end
 end

server/app/graphql/resolvers/top_level_events.rb

@@ -44,6 +44,6 @@ class Resolvers::TopLevelEvents < GraphQL::Schema::Resolver
   end
 
   option(:mode, type: Types::Events::EventFeedMode) do |_, _|
-    #accesed in connection, yuck
+    #accessed in connection, yuck
   end
 end

server/app/graphql/types/connections/activities_connection.rb

@@ -12,7 +12,7 @@ class ActivitiesConnection < Types::BaseConnection
       description: 'When filtered on a subject, user, or organization, the total number of events for that subject/user/organization, irregardless of other filters.'
 
     field :activity_types, [Types::Activities::ActivityTypeInputType], null: false,
-      description: 'List of activity types that have occured on this entity.'
+      description: 'List of activity types that have occurred on this entity.'
 
     field :subject_types, [Types::Activities::ActivitySubjectInputType], null: false
 

server/app/graphql/types/connections/events_connection.rb

@@ -6,7 +6,7 @@ class EventsConnection < Types::BaseConnection
       description: 'List of all users that have generated an event on the subject entity.'
 
     field :event_types, [Types::Events::EventActionType], null: false,
-      description: 'List of event types that have occured on this entity.'
+      description: 'List of event types that have occurred on this entity.'
 
     field :participating_organizations, [Types::Entities::OrganizationType], null: false,
       description: 'List of all organizations who are involved in this event stream.'

server/app/graphql/types/connections/notifications_connection.rb

@@ -9,7 +9,7 @@ class NotificationsConnection < Types::BaseConnection
       description: 'Users who have performed an action (other than a mention) that created a notification.'
 
     field :event_types, [Types::Events::EventActionType], null: false,
-      description: 'List of event types that have occured on this entity.'
+      description: 'List of event types that have occurred on this entity.'
 
     field :organizations, [Types::Entities::OrganizationType], null: false,
       description: 'List of all organizations who are involved in this notification stream.'

server/app/graphql/types/entities/user_type.rb

@@ -41,8 +41,8 @@ def authorized?(object, args, context)
 
     field :notifications, Types::Entities::NotificationType.connection_type, null: true do
       description 'Filterable list of notifications for the logged in user.'
-      type_desc = 'Filter the response to include only notifications of a certaint type (ex: mentions).'
-      sub_desc = 'Filter the reponse to include only notifications generated by a particular subscription.'
+      type_desc = 'Filter the response to include only notifications of a certain type (ex: mentions).'
+      sub_desc = 'Filter the response to include only notifications generated by a particular subscription.'
       event_desc = 'Filter the response to include only notifications generated by certain actions (ex: commenting).'
 
       argument :notification_type, Types::NotificationReasonType, required: false, description: type_desc

server/app/graphql/types/molecular_profile_display_filter_type.rb

@@ -5,7 +5,7 @@ class MolecularProfileDisplayFilterType < Types::BaseEnum
     value 'WITH_ACCEPTED_OR_SUBMITTED',
       description: 'Display only molecular profiles which have evidence in either an accepted or submitted state.'
     value 'WITH_SUBMITTED',
-      description: 'Display molecular profiles which have at least one submited evidence item.'
+      description: 'Display molecular profiles which have at least one submitted evidence item.'
     value 'ALL',
       description: 'Display all molecular profiles regardless of attached evidence status.'
   end

server/app/lib/importer/disease_ontology_mirror.rb

@@ -79,7 +79,7 @@ def assign_synonyms(disease, synonyms)
     end
 
     def delete_unprocessed_diseases
-      #sanity check for the DOID api, bail early if we cant find "cancer"
+      #sanity check for the DOID api, bail early if we can't find "cancer"
       uri = URI(url_from_doid(162))
       resp = Net::HTTP.get_response(uri)
       if resp.code != '200'

server/app/models/my_chem_info.rb

@@ -22,7 +22,7 @@ def response
   def parse_response(resp)
     p = JSON.parse(resp)
     if p['hits'] && p['hits'].size > 1
-      return nil #it was ambiguous somehow, shouldnt happen with a NCIT
+      return nil #it was ambiguous somehow, shouldn't happen with a NCIT
     end
 
     if p['hits'] && p['hits'].size == 1

server/app/models/my_disease_info.rb

@@ -22,7 +22,7 @@ def response
   def parse_response(resp)
     p = JSON.parse(resp)
     if p['hits'] && p['hits'].size > 1
-      return nil #it was ambiguous somehow, shouldnt happen with a DOID
+      return nil #it was ambiguous somehow, shouldn't happen with a DOID
     end
 
     if p['hits'] && p['hits'].size == 1

server/config/initializers/trestle.rb

@@ -16,7 +16,7 @@
   #
   # config.site_logo_small = "logo-small.png"
 
-  # Speficy a favicon to be used within the admin.
+  # Specify a favicon to be used within the admin.
   #
   # config.favicon = "favicon.ico"