Merge branch 'main' into release

client/src/app/app.module.ts

@@ -21,7 +21,7 @@ import { GraphQLModule } from '@app/graphql/graphql.module'
 import { NzIconModule } from 'ng-zorro-antd/icon'
 import { CvcNetworkErrorAlertModule } from './components/app/network-error-alert/network-error-alert.module'
 import { Observable } from 'rxjs'
-import { AppLoadErrorHandler } from './core/utilities/app-reload-handler'
+import { AppErrorHandler } from './core/utilities/app-error-handler'
 import { CvcForms2Module } from '@app/forms/forms.module'
 
 registerLocaleData(en)
@@ -59,7 +59,7 @@ function initializeApiFactory(httpClient: HttpClient): () => Observable<any> {
     CookieService,
     {
       provide: ErrorHandler,
-      useClass: AppLoadErrorHandler,
+      useClass: AppErrorHandler,
     },
     { provide: NZ_I18N, useValue: en_US },
     {

client/src/app/components/variants/variants-menu/variants-menu.component.ts

@@ -86,8 +86,7 @@ export class CvcVariantsMenuComponent implements OnInit {
     )
 
     this.menuVariants$ = connection$.pipe(
-      map((c) => c.nodes),
-      filter(isNonNulled)
+      map((c) => c.edges.map((e) => e.node), filter(isNonNulled))
     )
 
     this.totalVariants$ = connection$.pipe(map((c) => c.totalCount))

client/src/app/components/variants/variants-menu/variants-menu.gql

@@ -27,8 +27,11 @@ query VariantsMenu(
       hasPreviousPage
       hasNextPage
     }
-    nodes {
-      ...menuVariant
+    edges{
+      cursor
+      node {
+        ...menuVariant
+      }
     }
   }
 }

client/src/app/core/utilities/app-error-handler.ts

@@ -0,0 +1,22 @@
+import { ErrorHandler, Injectable } from '@angular/core'
+import { environment } from 'environments/environment'
+
+@Injectable()
+export class AppErrorHandler implements ErrorHandler {
+  handleError(error: any): void {
+    if (environment.production) {
+      const chunkFailedMessage = /Loading chunk [\d]+ failed/
+      if (chunkFailedMessage.test(error.message)) {
+        if (
+          confirm(
+            'There is an updated version of CiVIC available. Click OK to reload.'
+          )
+        ) {
+          window.location.reload()
+        }
+      }
+    } else {
+      console.error(error)
+    }
+  }
+}

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

@@ -90,7 +90,7 @@ export type ActivityInterface = {
 /** The connection type for ActivityInterface. */
 export type ActivityInterfaceConnection = {
   __typename: 'ActivityInterfaceConnection';
-  /** List of activity types that have occured on this entity. */
+  /** List of activity types that have occurred on this entity. */
   activityTypes: Array<ActivityTypeInput>;
   /** A list of edges. */
   edges: Array<ActivityInterfaceEdge>;
@@ -1594,7 +1594,7 @@ export type EventConnection = {
   __typename: 'EventConnection';
   /** A list of edges. */
   edges: Array<EventEdge>;
-  /** List of event types that have occured on this entity. */
+  /** List of event types that have occurred on this entity. */
   eventTypes: Array<EventAction>;
   /** A list of nodes. */
   nodes: Array<Event>;
@@ -3305,7 +3305,7 @@ export enum MolecularProfileDisplayFilter {
   WithAccepted = 'WITH_ACCEPTED',
   /** Display only molecular profiles which have evidence in either an accepted or submitted state. */
   WithAcceptedOrSubmitted = '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. */
   WithSubmitted = 'WITH_SUBMITTED'
 }
 
@@ -3415,7 +3415,7 @@ export type Mutation = {
    */
   rejectRevisions?: Maybe<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.
    */
@@ -3448,7 +3448,7 @@ export type Mutation = {
   suggestVariantGroupRevision?: Maybe<SuggestVariantGroupRevisionPayload>;
   /** Unsubscribe from a CIViC entity to stop receiving notifications about it. */
   unsubscribe?: Maybe<UnsubscribePayload>;
-  /** Update the currentlly logged in User's Conflict of Interest statement */
+  /** Update the currently logged in User's Conflict of Interest statement */
   updateCoi?: Maybe<UpdateCoiPayload>;
   /** Mark one or more notifications as read/unread. The notification IDs provided must belong to the requesting user. */
   updateNotificationStatus?: Maybe<UpdateNotificationStatusPayload>;
@@ -3765,7 +3765,7 @@ export type NotificationConnection = {
   __typename: 'NotificationConnection';
   /** A list of edges. */
   edges: Array<NotificationEdge>;
-  /** List of event types that have occured on this entity. */
+  /** List of event types that have occurred on this entity. */
   eventTypes: Array<EventAction>;
   /** Users who have mentioned you. */
   mentioningUsers: Array<User>;
@@ -4265,6 +4265,8 @@ export type QueryActivitiesArgs = {
   first?: InputMaybe<Scalars['Int']>;
   last?: InputMaybe<Scalars['Int']>;
   mode?: InputMaybe<EventFeedMode>;
+  occuredAfter?: InputMaybe<Scalars['ISO8601DateTime']>;
+  occuredBefore?: InputMaybe<Scalars['ISO8601DateTime']>;
   organizationId?: InputMaybe<Array<Scalars['Int']>>;
   sortBy?: InputMaybe<DateSort>;
   subject?: InputMaybe<Array<SubscribableQueryInput>>;
@@ -7590,7 +7592,7 @@ export type VariantsMenuQueryVariables = Exact<{
 }>;
 
 
-export type VariantsMenuQuery = { __typename: 'Query', variants: { __typename: 'VariantInterfaceConnection', totalCount: number, pageInfo: { __typename: 'PageInfo', startCursor?: string | undefined, endCursor?: string | undefined, hasPreviousPage: boolean, hasNextPage: boolean }, nodes: Array<{ __typename: 'FactorVariant', id: number, name: string, link: string, flagged: boolean } | { __typename: 'GeneVariant', id: number, name: string, link: string, flagged: boolean } | { __typename: 'Variant', id: number, name: string, link: string, flagged: boolean }> } };
+export type VariantsMenuQuery = { __typename: 'Query', variants: { __typename: 'VariantInterfaceConnection', totalCount: number, pageInfo: { __typename: 'PageInfo', startCursor?: string | undefined, endCursor?: string | undefined, hasPreviousPage: boolean, hasNextPage: boolean }, edges: Array<{ __typename: 'VariantInterfaceEdge', cursor: string, node?: { __typename: 'FactorVariant', id: number, name: string, link: string, flagged: boolean } | { __typename: 'GeneVariant', id: number, name: string, link: string, flagged: boolean } | { __typename: 'Variant', id: number, name: string, link: string, flagged: boolean } | undefined }> } };
 
 export type VariantTypesForFeatureQueryVariables = Exact<{
   featureId?: InputMaybe<Scalars['Int']>;
@@ -13347,8 +13349,11 @@ export const VariantsMenuDocument = gql`
       hasPreviousPage
       hasNextPage
     }
-    nodes {
-      ...menuVariant
+    edges {
+      cursor
+      node {
+        ...menuVariant
+      }
     }
   }
 }

server/app/jobs/flag_duplicate_allele_registry_ids.rb

@@ -11,7 +11,7 @@ def perform
       variants = Variant.where(id: ids)
       variants.each do |variant|
         if variant.flags.select{|f| f.state == 'open' && f.open_activity.note =~ /This Variant may be a duplicate and may need to be deprecated/ && f.open_activity.user_id == 385}.count == 0
-          Activity::FlagEntity.new(
+          Activities::FlagEntity.new(
             flagging_user: civicbot_user,
             flaggable: variant,
             organization_id: nil,

server/app/lib/importer/disease_ontology_mirror.rb

@@ -142,8 +142,8 @@ def url_from_doid(doid)
     def add_flags(disease, text)
       civicbot_user = User.find(385)
       (disease.evidence_items + disease.assertions).each do |obj|
-        if obj.flags.select{|f| f.state == 'open' && f.open_activity.note == text && c.open_activity.user_id == 385}.count == 0
-          Activity::FlagEntity.new(
+        if obj.flags.select{|f| f.state == 'open' && f.open_activity.note == text && f.open_activity.user_id == 385}.count == 0
+          Activities::FlagEntity.new(
             flagging_user: civicbot_user,
             flaggable: obj,
             organization_id: nil,

server/app/lib/importer/sequence_ontology_mirror.rb

@@ -91,12 +91,12 @@ def process_obsolete_terms
               text += " Replaced by #{term['replaced_by']}."
             end
             obsolete_type.variants.each do |variant|
-              if variant.flags.select{|f| f.state == 'open' && f.comments.select{|c| c.text =~ /obsolete Sequence Ontology term/ && c.user_id == 385}.count > 0}.count == 0
-                Actions::FlagEntity.new(
+              if variant.flags.select{|f| f.state == 'open' && f.open_activity.note =~ /obsolete Sequence Ontology term/ && f.open_activity.user_id == 385}.count == 0
+                Activities::FlagEntity.new(
                   flagging_user: civicbot_user,
                   flaggable: variant,
                   organization_id: nil,
-                  comment: text
+                  note: text
                 ).perform
               end
             end

server/app/lib/scrapers/human_phenotype_ontology.rb

@@ -44,7 +44,7 @@ def self.update
                 civicbot_user = User.find(385)
                 (p.evidence_items + p.assertions).each do |obj|
                   if obj.flags.select{|f| f.state == 'open' && f.open_activity.note =~ /deprecated HPO term/ && f.open_activity.user_id == 385}.count == 0
-                    Activity::FlagEntity.new(
+                    Activities::FlagEntity.new(
                       flagging_user: civicbot_user,
                       flaggable: obj,
                       organization_id: nil,

server/config/initializers/sidekiq.rb

@@ -7,7 +7,7 @@
     config.on(:startup) do
       schedule_file = Rails.root.join("config", "scheduled_tasks.yml")
 
-      if File.exists?(schedule_file) && Rails.env.production?
+      if File.exist?(schedule_file) && Rails.env.production?
         Sidekiq::Cron::Job.load_from_hash YAML.load_file(schedule_file)
       end
     end