Merge pull request #720 from griffithlab/source_link

Add sources as a supported entity to tag linking in comments

client/src/app/components/comments/comment-body/comment-body.component.html

@@ -32,6 +32,9 @@
             <span *ngSwitchCase="'MOLECULAR_PROFILE'">
                 <cvc-molecular-profile-tag [molecularProfile]="{id: c.entityId, name: c.displayName, link: c.link, deprecated: c.deprecated}"></cvc-molecular-profile-tag>
             </span>
+            <span *ngSwitchCase="'SOURCE'">
+                <cvc-source-tag [source]="{id: c.entityId, displayName: c.displayName, link: c.link}"></cvc-source-tag>
+            </span>
             <span *ngSwitchCase="'ROLE'">
                 <nz-tag><i nz-icon
                     nzType="civic-{{c.displayName.slice(0, -1)}}" nzTheme="twotone" nzTwotoneColor="#A0D8F5"></i> {{c.displayName}}</nz-tag>

client/src/app/components/comments/comment-body/comment-body.module.ts

@@ -12,6 +12,7 @@ import { CvcOrganizationTagModule } from '@app/components/organizations/organiza
 import { NzTagModule } from 'ng-zorro-antd/tag';
 import { NzIconModule } from 'ng-zorro-antd/icon';
 import { CvcMolecularProfileTagModule } from '@app/components/molecular-profiles/molecular-profile-tag/molecular-profile-tag.module';
+import { CvcSourceTagModule } from '@app/components/sources/source-tag/source-tag.module';
 
 @NgModule({
   declarations: [CvcCommentBodyComponent],
@@ -27,7 +28,8 @@ import { CvcMolecularProfileTagModule } from '@app/components/molecular-profiles
     CvcGeneTagModule,
     CvcUserTagModule,
     CvcOrganizationTagModule,
-    CvcMolecularProfileTagModule
+    CvcMolecularProfileTagModule,
+    CvcSourceTagModule,
   ],
   exports: [CvcCommentBodyComponent]
 })

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

@@ -36,6 +36,9 @@ export class IconNameForSubscribableEntity implements PipeTransform {
       case 'MOLECULAR_PROFILE':
       case 'MolecularProfile':
         return 'civic-molecularprofile';
+      case 'SOURCE':
+      case 'Source':
+        return 'civic-source';
       default:
         console.log('String No icon name found for ' + e);
         return 'border-outer';

client/src/app/forms/comment-input/comment-input.form.ts

@@ -120,6 +120,8 @@ export class CvcCommentInputForm implements OnDestroy, OnChanges {
         return `RID${id}`;
       case TaggableEntity.MolecularProfile:
         return `MPID${id}`
+      case TaggableEntity.Source:
+        return `SID${id}`
       case TaggableEntity.Role:
         return Object.keys(UserRole)[id];
     }

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

@@ -4389,6 +4389,7 @@ export enum TaggableEntity {
   MolecularProfile = 'MOLECULAR_PROFILE',
   Revision = 'REVISION',
   Role = 'ROLE',
+  Source = 'SOURCE',
   Variant = 'VARIANT',
   VariantGroup = 'VARIANT_GROUP'
 }

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

@@ -7246,6 +7246,7 @@ enum TaggableEntity {
   MOLECULAR_PROFILE
   REVISION
   ROLE
+  SOURCE
   VARIANT
   VARIANT_GROUP
 }

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

@@ -30827,6 +30827,12 @@
               "description": null,
               "isDeprecated": false,
               "deprecationReason": null
+            },
+            {
+              "name": "SOURCE",
+              "description": null,
+              "isDeprecated": false,
+              "deprecationReason": null
             }
           ],
           "possibleTypes": null

server/app/graphql/types/commentable/taggable_entity.rb

@@ -8,5 +8,6 @@ class TaggableEntity < Types::BaseEnum
     value 'REVISION'
     value 'ROLE'
     value 'MOLECULAR_PROFILE'
+    value 'SOURCE'
   end
 end

server/app/graphql/types/commentable/taggable_entity_input_type.rb

@@ -23,6 +23,8 @@ def prepare
         Revision
       when 'MOLECULAR_PROFILE'
         MolecularProfile
+      when 'SOURCE'
+        Source
       else
         #it was a role
         nil

server/app/graphql/types/queries/typeahead_queries.rb

@@ -41,7 +41,7 @@ def self.included(klass)
         description "Retrieve entity type typeahead fields for a entity mention search term."
         argument :query_term, GraphQL::Types::String, required: true
       end
-      
+
       klass.field :acmg_codes_typeahead, [Types::Entities::AcmgCodeType], null: false do
         description "Retrieve ACMG Code options as a typeahead"
         argument :query_term, GraphQL::Types::String, required: true

server/app/models/actions/extract_references.rb

@@ -53,7 +53,7 @@ def self.status_value_for_referenced_entity(item)
         nil
       end
     end
-    
+
     def self.deprecation_value_for_referenced_entity(item)
       if item.is_a?(Variant) || item.is_a?(MolecularProfile)
         item.deprecated
@@ -72,7 +72,7 @@ def self.typeahead_matches(query_term)
             display_name: referenced_item.respond_to?(:display_name) ? referenced_item.display_name : referenced_item.name,
             tag_type: tag_type,
             status: status_value_for_referenced_entity(referenced_item),
-            deprecated: self.class.deprecation_value_for_referenced_entity(referenced_item),
+            deprecated: deprecation_value_for_referenced_entity(referenced_item),
           }
           end
         else
@@ -99,15 +99,17 @@ def self.extract_type(type)
         [Assertion, 'ASSERTION']
       when 'MP'
         [MolecularProfile, 'MOLECULAR_PROFILE']
+      when 'S'
+        [Source, 'SOURCE']
       end
     end
 
     def self.split_regex
-      @split_regex ||= Regexp.new(/\s*(#(?:a|v|g|vg|e|r|mp)(?:id)?\d+)\b/i)
+      @split_regex ||= Regexp.new(/\s*(#(?:a|v|g|vg|e|r|mp|s)(?:id)?\d+)\b/i)
     end
 
     def self.scan_regex
-      @scan_regex ||= Regexp.new(/#(?<type>a|v|g|vg|e|r|mp)(?:id)?(?<id>\d+)\b/i)
+      @scan_regex ||= Regexp.new(/#(?<type>a|v|g|vg|e|r|mp|s)(?:id)?(?<id>\d+)\b/i)
     end
   end
 end