Merge branch 'main' into staging

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>>;
@@ -7591,7 +7593,7 @@ 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']>;
@@ -13362,8 +13364,11 @@ export const VariantsMenuDocument = gql`
       hasPreviousPage
       hasNextPage
     }
-    nodes {
-      ...menuVariant
+    edges {
+      cursor
+      node {
+        ...menuVariant
+      }
     }
   }
 }

server/Gemfile.lock

@@ -83,25 +83,25 @@ GEM
       tzinfo (~> 2.0)
     addressable (2.8.6)
       public_suffix (>= 2.0.2, < 6.0)
-    airbrussh (1.5.1)
+    airbrussh (1.5.2)
       sshkit (>= 1.6.1, != 1.7.0)
     angular_rails_csrf (5.0.0)
       railties (>= 3, < 8)
     ast (2.4.2)
-    audited (5.4.3)
-      activerecord (>= 5.0, < 7.2)
-      request_store (~> 1.2)
+    audited (5.6.0)
+      activerecord (>= 5.2, < 7.2)
+      activesupport (>= 5.2, < 7.2)
     awesome_nested_set (3.6.0)
       activerecord (>= 4.0.0, < 7.2)
     aws-eventstream (1.3.0)
-    aws-partitions (1.900.0)
-    aws-sdk-core (3.191.4)
+    aws-partitions (1.922.0)
+    aws-sdk-core (3.194.0)
       aws-eventstream (~> 1, >= 1.3.0)
       aws-partitions (~> 1, >= 1.651.0)
       aws-sigv4 (~> 1.8)
       jmespath (~> 1, >= 1.6.1)
-    aws-sdk-kms (1.78.0)
-      aws-sdk-core (~> 3, >= 3.191.0)
+    aws-sdk-kms (1.80.0)
+      aws-sdk-core (~> 3, >= 3.193.0)
       aws-sigv4 (~> 1.1)
     aws-sdk-s3 (1.94.1)
       aws-sdk-core (~> 3, >= 3.112.0)
@@ -149,7 +149,7 @@ GEM
     diff-lcs (1.5.1)
     diffy (3.4.2)
     docile (1.4.0)
-    dockerfile-rails (1.6.7)
+    dockerfile-rails (1.6.10)
       rails (>= 3.0.0)
     drb (2.2.1)
     e2mmap (0.1.0)
@@ -191,8 +191,8 @@ GEM
     faraday-rack (1.0.0)
     faraday-retry (1.0.3)
     ffi (1.16.3)
-    fugit (1.10.1)
-      et-orbi (~> 1, >= 1.2.7)
+    fugit (1.11.0)
+      et-orbi (~> 1, >= 1.2.11)
       raabro (~> 1.4)
     globalid (1.2.1)
       activesupport (>= 6.1)
@@ -214,7 +214,7 @@ GEM
       reline (>= 0.4.2)
     jaro_winkler (1.5.6)
     jmespath (1.6.2)
-    json (2.7.1)
+    json (2.7.2)
     jwt (2.8.1)
       base64
     kaminari (1.2.2)
@@ -247,13 +247,14 @@ GEM
       net-smtp
     marcel (1.0.4)
     matrix (0.4.2)
-    method_source (1.0.0)
+    method_source (1.1.0)
     mini_magick (4.12.0)
     mini_mime (1.1.5)
     minitest (5.22.3)
     msgpack (1.7.2)
     multi_json (1.15.0)
-    multi_xml (0.6.0)
+    multi_xml (0.7.0)
+      bigdecimal (~> 3.1)
     multipart-post (2.4.0)
     mutex_m (0.2.0)
     net-ftp (0.3.4)
@@ -270,21 +271,21 @@ GEM
       net-ssh (>= 2.6.5, < 8.0.0)
     net-sftp (4.0.0)
       net-ssh (>= 5.0.0, < 8.0.0)
-    net-smtp (0.4.0.1)
+    net-smtp (0.5.0)
       net-protocol
-    net-ssh (7.2.1)
+    net-ssh (7.2.3)
     nio4r (2.7.1)
-    nokogiri (1.16.3-aarch64-linux)
+    nokogiri (1.16.4-aarch64-linux)
       racc (~> 1.4)
-    nokogiri (1.16.3-arm-linux)
+    nokogiri (1.16.4-arm-linux)
       racc (~> 1.4)
-    nokogiri (1.16.3-arm64-darwin)
+    nokogiri (1.16.4-arm64-darwin)
       racc (~> 1.4)
-    nokogiri (1.16.3-x86-linux)
+    nokogiri (1.16.4-x86-linux)
       racc (~> 1.4)
-    nokogiri (1.16.3-x86_64-darwin)
+    nokogiri (1.16.4-x86_64-darwin)
       racc (~> 1.4)
-    nokogiri (1.16.3-x86_64-linux)
+    nokogiri (1.16.4-x86_64-linux)
       racc (~> 1.4)
     oauth2 (1.4.11)
       faraday (>= 0.17.3, < 3.0)
@@ -317,7 +318,7 @@ GEM
       actionpack (>= 4.2)
       omniauth (~> 2.0)
     parallel (1.24.0)
-    parser (3.3.0.5)
+    parser (3.3.1.0)
       ast (~> 2.4.1)
       racc
     pg (1.5.6)
@@ -329,7 +330,7 @@ GEM
       pry (>= 0.10.4)
     psych (5.1.2)
       stringio
-    public_suffix (5.0.4)
+    public_suffix (5.0.5)
     puma (5.6.8)
       nio4r (~> 2.0)
     raabro (1.4.0)
@@ -381,25 +382,23 @@ GEM
       thor (~> 1.0, >= 1.2.2)
       zeitwerk (~> 2.6)
     rainbow (3.1.1)
-    rake (13.1.0)
+    rake (13.2.1)
     rb-fsevent (0.11.2)
     rb-inotify (0.10.1)
       ffi (~> 1.0)
     rbs (2.8.4)
     rdoc (6.6.3.1)
       psych (>= 4.0.0)
-    redis-client (0.21.1)
+    redis-client (0.22.1)
       connection_pool
     regexp_parser (2.9.0)
-    reline (0.5.0)
+    reline (0.5.4)
       io-console (~> 0.5)
-    request_store (1.6.0)
-      rack (>= 1.4)
     reverse_markdown (2.1.1)
       nokogiri
     rexml (3.2.6)
     rinku (2.0.6)
-    rubocop (1.62.1)
+    rubocop (1.63.4)
       json (~> 2.3)
       language_server-protocol (>= 3.17.0)
       parallel (~> 1.10)
@@ -410,8 +409,8 @@ GEM
       rubocop-ast (>= 1.31.1, < 2.0)
       ruby-progressbar (~> 1.7)
       unicode-display_width (>= 2.4.0, < 3.0)
-    rubocop-ast (1.31.2)
-      parser (>= 3.3.0.4)
+    rubocop-ast (1.31.3)
+      parser (>= 3.3.1.0)
     ruby-progressbar (1.13.0)
     ruby-vips (2.2.1)
       ffi (~> 1.12)
@@ -441,7 +440,7 @@ GEM
       activemodel (>= 6.1)
       hashie
     semantic_range (3.0.0)
-    sidekiq (7.2.2)
+    sidekiq (7.2.4)
       concurrent-ruby (< 2)
       connection_pool (>= 2.3.0)
       rack (>= 2.2.4)
@@ -485,7 +484,8 @@ GEM
       actionpack (>= 5.2)
       activesupport (>= 5.2)
       sprockets (>= 3.0.0)
-    sshkit (1.22.0)
+    sshkit (1.22.2)
+      base64
       mutex_m
       net-scp (>= 1.1.2)
       net-sftp (>= 2.1.2)

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