Merge branch 'main' into ruby-upgrade

.github/workflows/build_frontend.yml

@@ -12,7 +12,7 @@ jobs:
     runs-on: ubuntu-latest
     steps:
       - name: Checkout Code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
         with:
           ref: ${{ inputs.branch }}
 
@@ -24,9 +24,9 @@ jobs:
           ruby-version: '3.0'
 
       - name: Setup node
-        uses: actions/setup-node@v3
+        uses: actions/setup-node@v4
         with:
-          node-version: 16
+          node-version: 20
 
       - run: npm install -g yarn
         working-directory: ./client

client/angular.json

@@ -99,12 +99,12 @@
         "serve": {
           "builder": "@angular-devkit/build-angular:dev-server",
           "options": {
-            "browserTarget": "main:build",
-            "proxyConfig": "proxy.config.json"
+            "proxyConfig": "proxy.config.json",
+            "buildTarget": "main:build"
           },
           "configurations": {
             "production": {
-              "browserTarget": "main:build:production"
+              "buildTarget": "main:build:production"
             }
           }
         },

client/package.json

@@ -23,35 +23,35 @@
     "error-stack-parser": "2.0.6"
   },
   "dependencies": {
-    "@angular-devkit/schematics": "16.1.4",
-    "@angular/animations": "^16.1.5",
-    "@angular/common": "^16.1.5",
-    "@angular/compiler": "^16.1.5",
-    "@angular/core": "^16.1.5",
-    "@angular/forms": "^16.1.5",
-    "@angular/platform-browser": "^16.1.5",
-    "@angular/platform-browser-dynamic": "^16.1.5",
-    "@angular/router": "^16.1.5",
+    "@angular-devkit/schematics": "17.0.10",
+    "@angular/animations": "^17.0.9",
+    "@angular/common": "^17.0.9",
+    "@angular/compiler": "^17.0.9",
+    "@angular/core": "^17.0.9",
+    "@angular/forms": "^17.0.9",
+    "@angular/platform-browser": "^17.0.9",
+    "@angular/platform-browser-dynamic": "^17.0.9",
+    "@angular/router": "^17.0.9",
     "@apollo/client": "^3.7.17",
     "@ngneat/until-destroy": "^9.1.2",
-    "@ngrx/component": "^16.1.0",
+    "@ngrx/component": "^17.0.1",
     "@ngx-formly/core": "^6.2.2",
     "@ngx-formly/ng-zorro-antd": "^6.2.2",
     "apollo-angular": "^5.0.0",
-    "ng-zorro-antd": "^16.1.0",
+    "ng-zorro-antd": "17.0.0",
     "ngx-cookie-service": "^16.0.0",
     "rxjs": "^7.8.1",
     "rxjs-etc": "^10.6.2",
     "rxjs-spy": "^8.0.2",
     "ts-enum-util": "^4.0.2",
     "ts-mixin-extended": "^1.1.1",
-    "zone.js": "~0.13.1"
+    "zone.js": "0.14.3"
   },
   "devDependencies": {
-    "@angular-devkit/build-angular": "^16.1.4",
-    "@angular-eslint/schematics": "^16.1.0",
-    "@angular/cli": "^16.1.4",
-    "@angular/compiler-cli": "16.1.5",
+    "@angular-devkit/build-angular": "^17.0.10",
+    "@angular-eslint/schematics": "^16.1.2",
+    "@angular/cli": "^17.0.10",
+    "@angular/compiler-cli": "17.0.9",
     "@graphql-codegen/add": "^3.2.3",
     "@graphql-codegen/cli": "^2.16.4",
     "@graphql-codegen/fragment-matcher": "^3.3.3",
@@ -71,12 +71,12 @@
     "ts-node": "~10.9.1",
     "tslib": "^2.3.1",
     "tslint": "~6.1.0",
-    "typescript": "^4.9.4",
+    "typescript": "5.2.2",
     "webpack-bundle-analyzer": "^4.5.0"
   },
   "overrides": {
     "rxjs-spy": {
       "error-stack-parser": "2.0.6"
     }
   }
-}
+}

client/src/app/components/activities/activity-card/activity-card.module.ts

@@ -1,20 +1,20 @@
-import { CommonModule } from "@angular/common";
-import { NgModule } from "@angular/core";
-import { PushModule } from "@ngrx/component";
-import { NzCardModule } from "ng-zorro-antd/card";
-import { CvcActivityCardComponent } from "./activity-card.component";
-import { CvcCommentBodyModule } from "@app/components/comments/comment-body/comment-body.module";
-import { NzDividerModule } from "ng-zorro-antd/divider";
+import { CommonModule } from '@angular/common'
+import { NgModule } from '@angular/core'
+import { PushPipe } from '@ngrx/component'
+import { NzCardModule } from 'ng-zorro-antd/card'
+import { CvcActivityCardComponent } from './activity-card.component'
+import { CvcCommentBodyModule } from '@app/components/comments/comment-body/comment-body.module'
+import { NzDividerModule } from 'ng-zorro-antd/divider'
 
 @NgModule({
   declarations: [CvcActivityCardComponent],
   imports: [
     CommonModule,
-    PushModule,
+    PushPipe,
     NzCardModule,
     NzDividerModule,
-    CvcCommentBodyModule
+    CvcCommentBodyModule,
   ],
   exports: [CvcActivityCardComponent],
 })
-export class CvcActivityCardModule {}
+export class CvcActivityCardModule {}

client/src/app/components/activities/activity-feed/activity-feed.module.ts

@@ -1,7 +1,7 @@
 import { NgModule } from '@angular/core'
 import { CommonModule } from '@angular/common'
 import { CvcActivityFeedComponent } from './activity-feed.component'
-import { LetModule, PushModule } from '@ngrx/component'
+import { LetDirective, PushPipe } from '@ngrx/component'
 import { NzCardModule } from 'ng-zorro-antd/card'
 import { NzIconModule } from 'ng-zorro-antd/icon'
 import { NzFormModule } from 'ng-zorro-antd/form'
@@ -38,8 +38,8 @@ import { CvcCollapsibleCardModule } from '../collapsible-card/collapsible-card.m
   imports: [
     CommonModule,
     FormsModule,
-    LetModule,
-    PushModule,
+    LetDirective,
+    PushPipe,
     NzButtonModule,
     NzCardModule,
     NzIconModule,
@@ -69,7 +69,7 @@ import { CvcCollapsibleCardModule } from '../collapsible-card/collapsible-card.m
     CvcMolecularProfileTagModule,
     CvcRevisionTagModule,
     CvcActivityCardModule,
-    CvcCollapsibleCardModule
+    CvcCollapsibleCardModule,
   ],
   exports: [CvcActivityFeedComponent],
 })

client/src/app/components/activities/collapsible-card/collapsible-card.module.ts

@@ -1,21 +1,21 @@
-import { CommonModule } from "@angular/common";
-import { NgModule } from "@angular/core";
-import { LetModule, PushModule } from "@ngrx/component";
-import { NzCardModule } from "ng-zorro-antd/card";
-import { CvcCollapsibleCardComponent } from "./collapsible-card.component";
-import { NzButtonModule } from "ng-zorro-antd/button";
-import { NzIconModule } from "ng-zorro-antd/icon";
+import { CommonModule } from '@angular/common'
+import { NgModule } from '@angular/core'
+import { LetDirective, PushPipe } from '@ngrx/component'
+import { NzCardModule } from 'ng-zorro-antd/card'
+import { CvcCollapsibleCardComponent } from './collapsible-card.component'
+import { NzButtonModule } from 'ng-zorro-antd/button'
+import { NzIconModule } from 'ng-zorro-antd/icon'
 
 @NgModule({
   declarations: [CvcCollapsibleCardComponent],
   imports: [
     CommonModule,
-    PushModule,
-    LetModule,
+    PushPipe,
+    LetDirective,
     NzCardModule,
     NzButtonModule,
-    NzIconModule
+    NzIconModule,
   ],
   exports: [CvcCollapsibleCardComponent],
 })
-export class CvcCollapsibleCardModule {}
+export class CvcCollapsibleCardModule {}

client/src/app/forms/config/assertion-revise/assertion-revise.form.config.ts

@@ -76,15 +76,13 @@ const formFieldConfig: FormlyFieldConfig[] = [
                 type: 'direction-select',
                 props: {
                   required: true,
-                  formMode: 'revise',
                 },
               },
               {
                 key: 'significance',
                 type: 'significance-select',
                 props: {
                   required: true,
-                  formMode: 'revise',
                 },
               },
               {

client/src/app/forms/config/assertion-revise/assertion-revise.form.ts

@@ -1,22 +1,47 @@
-import { AfterViewInit, ChangeDetectionStrategy, ChangeDetectorRef, Component, Input, OnDestroy, OnInit } from '@angular/core'
+import {
+  AfterViewInit,
+  ChangeDetectionStrategy,
+  ChangeDetectorRef,
+  Component,
+  Input,
+  OnDestroy,
+  OnInit,
+} from '@angular/core'
 import { UntypedFormGroup } from '@angular/forms'
 import { NetworkErrorsService } from '@app/core/services/network-errors.service'
-import { MutationState, MutatorWithState } from '@app/core/utilities/mutation-state-wrapper'
-import { assertionReviseFormInitialModel, AssertionReviseModel } from '@app/forms/models/assertion-revise.model'
+import {
+  MutationState,
+  MutatorWithState,
+} from '@app/core/utilities/mutation-state-wrapper'
+import {
+  assertionReviseFormInitialModel,
+  AssertionReviseModel,
+} from '@app/forms/models/assertion-revise.model'
 import { AssertionState } from '@app/forms/states/assertion.state'
-import { AssertionRevisableFieldsGQL, Maybe, SuggestAssertionRevisionGQL, SuggestAssertionRevisionMutation, SuggestAssertionRevisionMutationVariables } from '@app/generated/civic.apollo'
+import {
+  AssertionRevisableFieldsGQL,
+  Maybe,
+  SuggestAssertionRevisionGQL,
+  SuggestAssertionRevisionMutation,
+  SuggestAssertionRevisionMutationVariables,
+} from '@app/generated/civic.apollo'
 import { UntilDestroy, untilDestroyed } from '@ngneat/until-destroy'
 import { FormlyFieldConfig, FormlyFormOptions } from '@ngx-formly/core'
 import { assertionReviseFields } from './assertion-revise.form.config'
-import { assertionFormModelToReviseInput, assertionToModelFields } from '@app/forms/utilities/assertion-to-model-fields'
+import {
+  assertionFormModelToReviseInput,
+  assertionToModelFields,
+} from '@app/forms/utilities/assertion-to-model-fields'
 
 @UntilDestroy()
 @Component({
   selector: 'cvc-assertion-revise-form',
   templateUrl: './assertion-revise.form.html',
   changeDetection: ChangeDetectionStrategy.OnPush,
 })
-export class CvcAssertionReviseForm implements OnInit, AfterViewInit, OnDestroy {
+export class CvcAssertionReviseForm
+  implements OnInit, AfterViewInit, OnDestroy
+{
   @Input() assertionId!: number
 
   model?: AssertionReviseModel
@@ -40,20 +65,25 @@ export class CvcAssertionReviseForm implements OnInit, AfterViewInit, OnDestroy
     private submitRevisionsGQL: SuggestAssertionRevisionGQL,
     private networkErrorService: NetworkErrorsService,
     private cdr: ChangeDetectorRef
-
   ) {
     this.form = new UntypedFormGroup({})
     this.fields = assertionReviseFields
     this.state = new AssertionState()
-    this.options = { formState: this.state}
+    this.state.formMode = 'revise'
+    this.options = { formState: this.state }
     this.reviseAssertionMutator = new MutatorWithState(networkErrorService)
   }
 
   onSubmit(model: AssertionReviseModel) {
-    if(!this.assertionId) { return }
+    if (!this.assertionId) {
+      return
+    }
     let input = assertionFormModelToReviseInput(this.assertionId, model)
     if (input) {
-      this.mutationState = this.reviseAssertionMutator.mutate(this.submitRevisionsGQL, {input: input })
+      this.mutationState = this.reviseAssertionMutator.mutate(
+        this.submitRevisionsGQL,
+        { input: input }
+      )
     }
   }
 
@@ -62,26 +92,27 @@ export class CvcAssertionReviseForm implements OnInit, AfterViewInit, OnDestroy
   }
 
   ngAfterViewInit(): void {
-    this.revisableFieldsGQL.fetch({assertionId: this.assertionId})
-    .pipe(untilDestroyed(this))
-    .subscribe({
-      next: ({data: { assertion }}) => {
-        if (assertion) {
-          this.model = {
-            id: assertion.id,
-            fields: assertionToModelFields(assertion)
+    this.revisableFieldsGQL
+      .fetch({ assertionId: this.assertionId })
+      .pipe(untilDestroyed(this))
+      .subscribe({
+        next: ({ data: { assertion } }) => {
+          if (assertion) {
+            this.model = {
+              id: assertion.id,
+              fields: assertionToModelFields(assertion),
+            }
+            this.cdr.detectChanges()
           }
-          this.cdr.detectChanges()
-        }
-      },
-      error: (error) => {
-        console.log("Error retrieving Assertion")
-        console.log(error)
-      },
-      complete: () => {
-        this.state.formReady$.next(true)
-      }
-    })
+        },
+        error: (error) => {
+          console.log('Error retrieving Assertion')
+          console.log(error)
+        },
+        complete: () => {
+          this.state.formReady$.next(true)
+        },
+      })
   }
 
   ngOnDestroy(): void {

client/src/app/forms/config/evidence-revise/evidence-revise.form.config.ts

@@ -3,16 +3,12 @@ import { CvcDirectionSelectFieldOptions } from '@app/forms/types/direction-selec
 import { CvcDiseaseSelectFieldOptions } from '@app/forms/types/disease-select/disease-select.type'
 import { CvcInteractionSelectFieldOptions } from '@app/forms/types/interaction-select/interaction-select.type'
 import { CvcLevelSelectFieldOptions } from '@app/forms/types/level-select/level-select.type'
-import { CvcMolecularProfileSelectFieldConfig } from '@app/forms/types/molecular-profile-select/molecular-profile-select.type'
 import { CvcOrgSubmitButtonFieldConfig } from '@app/forms/types/org-submit-button/org-submit-button.type'
 import { CvcOriginSelectFieldOptions } from '@app/forms/types/origin-select/origin-select.type'
 import { CvcPhenotypeSelectFieldOptions } from '@app/forms/types/phenotype-select/phenotype-select.type'
 import { CvcRatingFieldOptions } from '@app/forms/types/rating/rating.type'
 import { CvcSignificanceSelectFieldOptions } from '@app/forms/types/significance-select/significance-select.type'
-import {
-  CvcSourceSelectFieldConfig,
-  CvcSourceSelectFieldOptions,
-} from '@app/forms/types/source-select/source-select.type'
+import { CvcSourceSelectFieldConfig } from '@app/forms/types/source-select/source-select.type'
 import { CvcTherapySelectFieldOptions } from '@app/forms/types/therapy-select/therapy-select.type'
 import { CvcEntityTypeSelectFieldConfig } from '@app/forms/types/type-select/type-select.type'
 import assignFieldConfigDefaultValues from '@app/forms/utilities/assign-field-default-values'
@@ -22,7 +18,6 @@ import { CvcFormRowWrapperProps } from '@app/forms/wrappers/form-row/form-row.wr
 import { FormlyFieldConfig } from '@ngx-formly/core'
 
 const formFieldConfig: FormlyFieldConfig[] = [
-  // form-layout wrapper embeds the form in an nz-grid row, allowing the form to be placed adjacent to other controls or page elements. Currently, it provides a toggleable dev panel. Could be used to add a preview of the entity being added/edited, or more extensive feedback like lists of similar entities, etc.
   {
     wrappers: ['form-layout'],
     props: <CvcFormLayoutWrapperProps>{
@@ -87,15 +82,13 @@ const formFieldConfig: FormlyFieldConfig[] = [
                 type: 'direction-select',
                 props: {
                   required: true,
-                  formMode: 'revise',
                 },
               },
               <CvcSignificanceSelectFieldOptions>{
                 key: 'significance',
                 type: 'significance-select',
                 props: {
                   required: true,
-                  formMode: 'revise',
                 },
               },
               <CvcDiseaseSelectFieldOptions>{

client/src/app/forms/config/evidence-revise/evidence-revise.form.ts

@@ -62,6 +62,7 @@ export class CvcEvidenceReviseForm implements OnInit, AfterViewInit, OnDestroy {
     this.form = new UntypedFormGroup({})
     this.fields = evidenceReviseFields
     this.state = new EvidenceState()
+    this.state.formMode = 'revise'
     this.options = { formState: this.state }
     this.reviseEvidenceMutator = new MutatorWithState(networkErrorService)
   }