Add support for additional ClinGen/ACMG code modifiers

client/src/app/forms2/types/acmg-code-select/acmg-code-select.type.html

@@ -15,7 +15,7 @@
   (cvcOnModelChange)="props.change && props.change(field, $event)">
 </cvc-entity-select>
 
- 
+
 <!--  <nz-select
   [nzMode]="props.isMultiSelect ? 'multiple' : 'default'"
   [nzCustomTemplate]="selectedTemplate"

client/src/app/forms2/types/acmg-code-select/acmg-code-select.type.ts

@@ -208,7 +208,7 @@ export class CvcAcmgCodeSelectField
         else if (requiresAcmgCode) {
           this.props.required = true
           this.props.disabled = false
-          this.props.description = 'Please provide evidence criteria from the standards and guidelines for interpretation of sequence variants from ACMG/AMP in <a href="https://pubmed.ncbi.nlm.nih.gov/25741868/" target="_blank">Richards et. al. 2015</a>.',
+          this.props.description = 'Please provide evidence criteria from the standards and guidelines for interpretation of sequence variants from ACMG/AMP in <a href="https://pubmed.ncbi.nlm.nih.gov/25741868/" target="_blank">Richards et. al. 2015</a>. Review all codes and select each one that applies. If a code is not applied, it is inferred to not be met.',
           this.props.extraType = 'description'
         }
         // field currently has a value, but state indicates no ACMG Code is required, or no type is provided && type is required, so reset field

client/src/app/forms2/types/clingen-code-select/clingen-code-select.type.ts

@@ -161,7 +161,7 @@ export class CvcClingenCodeSelectField
         } else {
           this.exclusiveSelected = false
         }
-      } 
+      }
       if(this.previousDescription && !this.exclusiveSelected) {
           this.props.description = this.previousDescription
           this.props.extraType = this.previousDescriptionType
@@ -235,7 +235,7 @@ export class CvcClingenCodeSelectField
         else if (requiresClingenCode) {
           this.props.required = true
           this.props.disabled = false
-          this.props.description = 'Please provide the evidence classifications from the Standards for the classification of pathogenicity of somatic variants in cancer (oncogenicity) in <a href="https://pubmed.ncbi.nlm.nih.gov/25741868/" target="_blank">Horak et. al. 2022.</a>.'
+          this.props.description = 'Please provide the evidence classifications from the Standards for the classification of pathogenicity of somatic variants in cancer (oncogenicity) in <a href="https://pubmed.ncbi.nlm.nih.gov/25741868/" target="_blank">Horak et. al. 2022.</a>. Review all codes and select each one that applies. If a code is not applied, it is inferred to not be met.'
           this.props.extraType = 'description'
         }
         // field currently has a value, but state indicates no ClinGen Code is required, or no type is provided && type is required, so reset field

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

@@ -95,15 +95,29 @@
             </nz-descriptions-item>
 
             <!-- ACMG Codes -->
-            <nz-descriptions-item nzTitle="ACMG Codes">
+            <nz-descriptions-item [nzSpan]='2' [nzTitle]="acmgTitle">
+              <ng-template #acmgTitle>
+                ACMG Codes
+                <span nz-typography
+                  nzType="secondary">
+                  <i nz-icon
+                    nzType="info-circle"
+                    nz-tooltip
+                    nzTooltipTitle="All codes are reviewed during acceptance. Absence of a code implies it is not met."
+                    >
+                  </i>
+                </span>
+              </ng-template>
               <ng-container *ngIf="assertionRules.requiresAcmgCodes(assertion.assertionType); else valueNotApplicable">
                 <ng-container *ngIf="assertion.acmgCodes.length > 0">
-                  <nz-tag
-                    nz-tooltip
-                    [nzTooltipTitle]="code.description"
-                    *ngFor="let code of assertion.acmgCodes"
-                    >{{ code.code }}</nz-tag
-                  >
+                  <cvc-tag-list>
+                    <nz-tag
+                      nz-tooltip
+                      [nzTooltipTitle]="code.description"
+                      *ngFor="let code of assertion.acmgCodes"
+                      >{{ code.code }}</nz-tag
+                    >
+                  </cvc-tag-list>
                 </ng-container>
                 <ng-container *ngIf="assertion.acmgCodes.length == 0">
                   <span
@@ -116,15 +130,29 @@
             </nz-descriptions-item>
 
             <!-- ClinGen Codes -->
-            <nz-descriptions-item nzTitle="ClinGen/CGC/VICC Codes">
+            <nz-descriptions-item [nzSpan]='2' [nzTitle]="clingenTitle">
+              <ng-template #clingenTitle>
+                ClinGen/CGC/VICC Codes
+                <span nz-typography
+                  nzType="secondary">
+                  <i nz-icon
+                    nzType="info-circle"
+                    nz-tooltip
+                    nzTooltipTitle="All codes are reviewed during acceptance. Absence of a code implies it is not met."
+                    >
+                  </i>
+                </span>
+              </ng-template>
               <ng-container
                 *ngIf="assertionRules.requiresClingenCodes(assertion.assertionType); else valueNotApplicable">
                 <ng-container *ngIf="assertion.clingenCodes.length > 0">
-                  <nz-tag
-                    nz-tooltip
-                    [nzTooltipTitle]="code.description"
-                    *ngFor="let code of assertion.clingenCodes"
-                    >{{ code.code }}</nz-tag>
+                  <cvc-tag-list>
+                    <nz-tag
+                      nz-tooltip
+                      [nzTooltipTitle]="code.description"
+                      *ngFor="let code of assertion.clingenCodes"
+                      >{{ code.code }}</nz-tag>
+                  </cvc-tag-list>
                 </ng-container>
                 <ng-container *ngIf="assertion.clingenCodes.length == 0">
                   <span

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

@@ -13,4 +13,4 @@ nz-space-item {
 .summary-block {
   max-height: 200px;
   overflow-y: auto;
-}
+}

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

@@ -15,7 +15,6 @@ import { startWith } from 'rxjs/operators'
 import { pluck } from 'rxjs-etc/operators'
 import { Observable } from 'rxjs'
 import { AssertionState } from '@app/forms/config/states/assertion.state'
-import { tag } from 'rxjs-spy/cjs/operators'
 
 @Component({
   selector: 'cvc-assertion-summary',

server/app/admin/acmg_codes_admin.rb

@@ -0,0 +1,33 @@
+Trestle.resource(:acmg_codes) do
+  collection do
+    AcmgCode.all.order(code: :asc)
+  end
+
+  search do |q|
+    q ? collection.where("acmg_codes.code ILIKE ? OR acmg_codes.description ILIKE ?", "%#{q}%", "%#{q}%") : collection
+  end
+
+  remove_action :destroy, :new
+
+  menu do
+    item :acmg_codes, icon: "fas fa-project-diagram", priority: :last
+  end
+
+  scope :all
+
+  # Customize the table columns shown on the index view.
+  table do
+    column :code
+    column :description, truncate: false
+  end
+
+  # Customize the form fields shown on the new/edit views.
+  form do |code|
+      row do
+        col(sm: 2) { static_field :code }
+      end
+
+      text_area :description
+    end
+  end
+

server/app/admin/clingen_codes_admin.rb

@@ -0,0 +1,33 @@
+Trestle.resource(:clingen_codes) do
+  collection do
+    ClingenCode.all.order(code: :asc)
+  end
+
+  search do |q|
+    q ? collection.where("clingen_codes.code ILIKE ? OR clingen_codes.description ILIKE ?", "%#{q}%", "%#{q}%") : collection
+  end
+
+  remove_action :destroy, :new
+
+  menu do
+    item :clingen_codes, icon: "fas fa-project-diagram", priority: :last
+  end
+
+  scope :all
+
+  # Customize the table columns shown on the index view.
+  table do
+    column :code
+    column :description, truncate: false
+  end
+
+  # Customize the form fields shown on the new/edit views.
+  form do |code|
+      row do
+        col(sm: 2) { static_field :code }
+      end
+
+      text_area :description
+    end
+  end
+

server/db/migrate/20230830152401_add_new_codes.rb

@@ -0,0 +1,35 @@
+class AddNewCodes < ActiveRecord::Migration[6.1]
+  def up
+
+    #Add tiering for Clingen Codes. Issue#873
+    ClingenCode.where.not(code: ['OP3', 'OM3', 'OS3', 'N/A']).find_each do |code|
+      modifiers = [
+        'Very-strong',
+        'Strong',
+        'Moderate',
+        'Supporting',
+      ]
+
+      if code.code =~ /VS\d/
+        modifiers.delete('Very-strong')
+      elsif code.code =~ /S\d/
+        modifiers.delete('Strong')
+      elsif code.code =~ /M\d/
+        modifiers.delete('Moderate')
+      elsif code.code =~ /P\d/
+        modifiers.delete('Supporting')
+      end
+
+      modifiers.each do |m|
+        ClingenCode.create!(code: "#{code.code}_#{m}", description: '')
+      end
+    end
+
+    ClingenCode.create!(code: "OS3_Very-strong", description: '')
+
+  end
+
+  def down
+    ClingenCode.where("code LIKE '%^_%' ESCAPE '^'").destroy_all
+  end
+end

server/db/schema.rb

@@ -10,7 +10,7 @@
 #
 # It's strongly recommended that you check this file into your version control system.
 
-ActiveRecord::Schema.define(version: 2023_06_22_140624) do
+ActiveRecord::Schema.define(version: 2023_08_31_142739) do
 
   # These are extensions that must be enabled in order to support this database
   enable_extension "plpgsql"
@@ -56,6 +56,31 @@
     t.index ["blob_id", "variation_digest"], name: "index_active_storage_variant_records_uniqueness", unique: true
   end
 
+  create_table "activities", force: :cascade do |t|
+    t.text "type", null: false
+    t.bigint "user_id", null: false
+    t.bigint "organization_id"
+    t.string "subject_type", null: false
+    t.bigint "subject_id", null: false
+    t.datetime "created_at", precision: 6, null: false
+    t.datetime "updated_at", precision: 6, null: false
+    t.text "verbiage"
+    t.index ["organization_id"], name: "index_activities_on_organization_id"
+    t.index ["subject_type", "subject_id"], name: "index_activities_on_subject"
+    t.index ["type"], name: "index_activities_on_type"
+    t.index ["user_id"], name: "index_activities_on_user_id"
+  end
+
+  create_table "activity_linked_entities", force: :cascade do |t|
+    t.string "entity_type", null: false
+    t.bigint "entity_id", null: false
+    t.bigint "activity_id", null: false
+    t.datetime "created_at", precision: 6, null: false
+    t.datetime "updated_at", precision: 6, null: false
+    t.index ["activity_id"], name: "index_activity_linked_entities_on_activity_id"
+    t.index ["entity_type", "entity_id"], name: "index_activity_linked_entities_on_entity"
+  end
+
   create_table "advanced_searches", id: :serial, force: :cascade do |t|
     t.datetime "created_at"
     t.datetime "updated_at"
@@ -358,6 +383,7 @@
     t.text "user_role"
     t.string "originating_object_type"
     t.bigint "originating_object_id"
+    t.integer "activity_id"
     t.index ["organization_id"], name: "index_events_on_organization_id"
     t.index ["originating_object_id", "originating_object_type"], name: "idx_event_originating_obj"
     t.index ["originating_object_type", "originating_object_id"], name: "index_events_on_originating_object"
@@ -643,11 +669,11 @@
     t.text "journal"
     t.string "full_journal_title"
     t.text "title"
-    t.text "status", default: "fully curated", null: false
     t.boolean "is_review"
     t.integer "source_type", null: false
     t.integer "asco_abstract_id"
     t.text "asco_presenter"
+    t.boolean "fully_curated", default: false, null: false
     t.index ["asco_abstract_id"], name: "index_sources_on_asco_abstract_id"
     t.index ["asco_presenter"], name: "index_sources_on_asco_presenter"
     t.index ["citation_id"], name: "index_sources_on_citation_id"
@@ -857,6 +883,8 @@
   add_foreign_key "acmg_codes_assertions", "assertions"
   add_foreign_key "active_storage_attachments", "active_storage_blobs", column: "blob_id"
   add_foreign_key "active_storage_variant_records", "active_storage_blobs", column: "blob_id"
+  add_foreign_key "activities", "organizations"
+  add_foreign_key "activities", "users"
   add_foreign_key "assertions", "nccn_guidelines"
   add_foreign_key "assertions_clingen_codes", "assertions"
   add_foreign_key "assertions_clingen_codes", "clingen_codes"
@@ -880,6 +908,7 @@
   add_foreign_key "disease_aliases_diseases", "diseases"
   add_foreign_key "domain_expert_tags", "users"
   add_foreign_key "entity_mentions", "comments"
+  add_foreign_key "events", "activities"
   add_foreign_key "events", "organizations"
   add_foreign_key "events", "users", column: "originating_user_id"
   add_foreign_key "evidence_items", "diseases"