Merge branch 'main' into release

.codespellignore

@@ -0,0 +1,2 @@
+iif
+mane

.codespellrc

@@ -0,0 +1,6 @@
+[codespell]
+# Ref: https://github.com/codespell-project/codespell#using-a-config-file
+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

.github/workflows/build_frontend.yml

@@ -21,7 +21,7 @@ jobs:
         with:
           working-directory: ./server
           bundler-cache: true
-          ruby-version: '3.0'
+          ruby-version: '3.3'
 
       - name: Setup node
         uses: actions/setup-node@v4

.github/workflows/codespell.yml

@@ -0,0 +1,25 @@
+# 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
+        with:
+          ignore_words_file: .codespellignore

.github/workflows/deploy.yml

@@ -37,7 +37,7 @@ jobs:
         uses: ruby/setup-ruby@v1
         with:
           working-directory: ./server
-          ruby-version: '3.0'
+          ruby-version: '3.3'
           bundler-cache: true
 
       - name: Deploy to production

.github/workflows/tests.yml

@@ -23,6 +23,9 @@ jobs:
       - name: 'Checkout code'
         uses: actions/checkout@v3
 
+      - name: 'Setup elasticsearch'
+        uses: ankane/setup-elasticsearch@v1
+
       - name: 'Setup Ruby'
         uses: ruby/setup-ruby@v1
         with:

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/generated/server.model.graphql

@@ -93,7 +93,7 @@ The connection type for ActivityInterface.
 """
 type ActivityInterfaceConnection {
   """
-  List of activity types that have occured on this entity.
+  List of activity types that have occurred on this entity.
   """
   activityTypes: [ActivityTypeInput!]!
 
@@ -2435,7 +2435,7 @@ type EventConnection {
   edges: [EventEdge!]!
 
   """
-  List of event types that have occured on this entity.
+  List of event types that have occurred on this entity.
   """
   eventTypes: [EventAction!]!
 
@@ -5124,7 +5124,7 @@ type LeaderboardUser {
     first: Int
 
     """
-    Filter the reponse to include only notifications generated by a particular subscription.
+    Filter the response to include only notifications generated by a particular subscription.
     """
     includeSeen: Boolean = false
 
@@ -5134,12 +5134,12 @@ type LeaderboardUser {
     last: Int
 
     """
-    Filter the response to include only notifications of a certaint type (ex: mentions).
+    Filter the response to include only notifications of a certain type (ex: mentions).
     """
     notificationType: NotificationReason
 
     """
-    Filter the reponse to include only notifications generated by a particular subscription.
+    Filter the response to include only notifications generated by a particular subscription.
     """
     subscriptionId: Int
   ): NotificationConnection
@@ -5759,7 +5759,7 @@ enum MolecularProfileDisplayFilter {
   WITH_ACCEPTED_OR_SUBMITTED
 
   """
-  Display molecular profiles which have at least one submited evidence item.
+  Display molecular profiles which have at least one submitted evidence item.
   """
   WITH_SUBMITTED
 }
@@ -6009,7 +6009,7 @@ type Mutation {
   ): RejectRevisionsPayload
 
   """
-  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.
   """
@@ -6161,7 +6161,7 @@ type Mutation {
   ): UnsubscribePayload
 
   """
-  Update the currentlly logged in User's Conflict of Interest statement
+  Update the currently logged in User's Conflict of Interest statement
   """
   updateCoi(
     """
@@ -6327,7 +6327,7 @@ type NotificationConnection {
   edges: [NotificationEdge!]!
 
   """
-  List of event types that have occured on this entity.
+  List of event types that have occurred on this entity.
   """
   eventTypes: [EventAction!]!
 
@@ -6889,6 +6889,8 @@ type Query {
     """
     last: Int
     mode: EventFeedMode
+    occuredAfter: ISO8601DateTime
+    occuredBefore: ISO8601DateTime
     organizationId: [Int!]
 
     """
@@ -10256,7 +10258,7 @@ type User {
     first: Int
 
     """
-    Filter the reponse to include only notifications generated by a particular subscription.
+    Filter the response to include only notifications generated by a particular subscription.
     """
     includeSeen: Boolean = false
 
@@ -10266,12 +10268,12 @@ type User {
     last: Int
 
     """
-    Filter the response to include only notifications of a certaint type (ex: mentions).
+    Filter the response to include only notifications of a certain type (ex: mentions).
     """
     notificationType: NotificationReason
 
     """
-    Filter the reponse to include only notifications generated by a particular subscription.
+    Filter the response to include only notifications generated by a particular subscription.
     """
     subscriptionId: Int
   ): NotificationConnection