Merge pull request #623 from griffithlab/oncogenic-release

Add Support for Oncogenic Assertions and updated Oncogenic/Predisposing data model.
griffithlab · Sep 13, 2022 · 1d3ea49 · 1d3ea49
2 parents 4e616f0 + 289d8e3
commit 1d3ea49
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Showing 225 changed files with 12,110 additions and 14,000 deletions.
diff --git a/client/.eslintrc.json b/client/.eslintrc.json
@@ -0,0 +1,51 @@
+{
+  "root": true,
+  "ignorePatterns": [
+    "projects/**/*"
+  ],
+  "overrides": [
+    {
+      "files": [
+        "*.ts"
+      ],
+      "parserOptions": {
+        "project": [
+          "tsconfig.json",
+          "e2e/tsconfig.json"
+        ],
+        "createDefaultProgram": true
+      },
+      "extends": [
+        "plugin:@angular-eslint/recommended",
+        "plugin:@angular-eslint/template/process-inline-templates"
+      ],
+      "rules": {
+        "@angular-eslint/directive-selector": [
+          "error",
+          {
+            "type": "attribute",
+            "prefix": "cvc",
+            "style": "camelCase"
+          }
+        ],
+        "@angular-eslint/component-selector": [
+          "error",
+          {
+            "type": "element",
+            "prefix": "cvc",
+            "style": "kebab-case"
+          }
+        ]
+      }
+    },
+    {
+      "files": [
+        "*.html"
+      ],
+      "extends": [
+        "plugin:@angular-eslint/template/recommended"
+      ],
+      "rules": {}
+    }
+  ]
+}
diff --git a/client/.graphqlrc.yml b/client/.graphqlrc.yml
@@ -21,15 +21,15 @@ extensions:
         config:
           apolloClientVersion: 3
           nonOptionalTypename: true
-          futureProofUnions: true
-          futureProofEnums: true
+          futureProofUnions: false
+          futureProofEnums: false
           maybeValue: T | undefined
-      ./src/app/generated/server.possible-types.ts:
+      ./src/app/generated/civic.possible-types.ts:
         plugins:
           - fragment-matcher
         config:
-          apolloClientVersion: 2
-      ./src/app/generated/server.field-policies.ts:
+          apolloClientVersion: 3
+      ./src/app/generated/civic.apollo-helpers.ts:
         plugins:
           - typescript-apollo-client-helpers
         config:

diff --git a/client/angular.json b/client/angular.json
@@ -2,7 +2,8 @@
   "$schema": "./node_modules/@angular/cli/lib/config/schema.json",
   "version": 1,
   "cli": {
-    "packageManager": "yarn"
+    "packageManager": "yarn",
+    "defaultCollection": "@angular-eslint/schematics"
   },
   "newProjectRoot": "lib",
   "projects": {
@@ -138,6 +139,15 @@
               "devServerTarget": "main:serve:production"
             }
           }
+        },
+        "lint": {
+          "builder": "@angular-eslint/builder:lint",
+          "options": {
+            "lintFilePatterns": [
+              "src/**/*.ts",
+              "src/**/*.html"
+            ]
+          }
         }
       }
     }

diff --git a/client/package.json b/client/package.json
@@ -4,7 +4,9 @@
   "scripts": {
     "ng": "ng",
     "start": "ng serve",
-    "build": "ng build",
+    "build": "ng build --build-optimizer",
+    "build:stats": "ng build --stats-json",
+    "analyze": "webpack-bundle-analyzer ../server/public/stats.json",
     "test": "ng test",
     "lint": "ng lint",
     "e2e": "ng e2e",
@@ -14,68 +16,77 @@
     "generate-apollo:start": "graphql-codegen --watch"
   },
   "private": true,
+  "resolutions": {
+    "error-stack-parser": "2.0.6"
+  },
   "dependencies": {
-    "@angular/animations": "~13.1.3",
-    "@angular/common": "~13.1.3",
-    "@angular/compiler": "~13.1.3",
-    "@angular/core": "~13.1.3",
-    "@angular/forms": "~13.1.3",
-    "@angular/platform-browser": "~13.1.3",
-    "@angular/platform-browser-dynamic": "~13.1.3",
-    "@angular/router": "~13.1.3",
+    "@angular/animations": "~13.3.11",
+    "@angular/common": "~13.3.11",
+    "@angular/compiler": "~13.3.11",
+    "@angular/core": "~13.3.11",
+    "@angular/forms": "~13.3.11",
+    "@angular/platform-browser": "~13.3.11",
+    "@angular/platform-browser-dynamic": "~13.3.11",
+    "@angular/router": "~13.3.11",
     "@apollo/client": "^3.5.8",
+    "@ngneat/until-destroy": "^9.1.2",
     "@ngrx/component": "^12.5.1",
     "@ngx-formly/core": "^5.10.32",
     "@ngx-formly/ng-zorro-antd": "^0.0",
-    "apollo-angular": "^2.1.0",
-    "ng-zorro-antd": "^13.0.1",
+    "apollo-angular": "^3.0.1",
+    "ng-zorro-antd": "^13.3.2",
     "ngx-cookie-service": "^13.1.2",
     "ngx-logger": "^5.0.7",
     "ngx-timeago": "^2.0.0",
-    "rxjs": "~6.6.6",
+    "rxjs": "^6.5.3",
+    "rxjs-debug": "^1.3.0",
+    "rxjs-etc": "^10.6.2",
+    "rxjs-spy": "^7.5.3",
     "ts-enum-util": "^4.0.2",
     "tslib": "^2.3.1",
     "xstate": "^4.30.3",
     "xstate-angular": "^0.0.2",
     "zone.js": "~0.11.4"
   },
   "devDependencies": {
-    "@angular-devkit/build-angular": "~13.1.4",
-    "@angular-eslint/eslint-plugin": "^1.0.0",
-    "@angular-eslint/eslint-plugin-template": "^1.0.0",
-    "@angular-eslint/template-parser": "^1.0.0",
-    "@angular/cli": "^13.1.4",
-    "@angular/compiler-cli": "13.1.3",
+    "@angular-devkit/build-angular": "~13.3.8",
+    "@angular-eslint/builder": "13.2.1",
+    "@angular-eslint/eslint-plugin": "13.2.1",
+    "@angular-eslint/eslint-plugin-template": "13.2.1",
+    "@angular-eslint/schematics": "13.2.1",
+    "@angular-eslint/template-parser": "13.2.1",
+    "@angular/cli": "^13.3.8",
+    "@angular/compiler-cli": "13.3.11",
     "@angular/language-server": "^13.1.1",
-    "@graphql-codegen/add": "^2.0.2",
-    "@graphql-codegen/cli": "1.20.0",
-    "@graphql-codegen/fragment-matcher": "^2.0.1",
-    "@graphql-codegen/introspection": "^1.18.1",
-    "@graphql-codegen/typescript": "1.20.0",
-    "@graphql-codegen/typescript-apollo-angular": "2.2.1",
-    "@graphql-codegen/typescript-apollo-client-helpers": "^1.1.3",
-    "@graphql-codegen/typescript-operations": "^1.17.13",
-    "@graphql-eslint/eslint-plugin": "^0.7.1",
-    "@graphql-inspector/cli": "^2.3.0",
+    "@graphql-codegen/add": "3.1.1",
+    "@graphql-codegen/cli": "2.6.2",
+    "@graphql-codegen/fragment-matcher": "3.2.1",
+    "@graphql-codegen/introspection": "2.1.1",
+    "@graphql-codegen/typescript": "2.4.10",
+    "@graphql-codegen/typescript-apollo-angular": "3.4.9",
+    "@graphql-codegen/typescript-apollo-client-helpers": "2.1.17",
+    "@graphql-codegen/typescript-operations": "2.3.7",
+    "@graphql-eslint/eslint-plugin": "3.10.3",
+    "@graphql-inspector/cli": "3.1.2",
     "@ngx-formly/schematics": "^5.10.30",
     "@types/jasmine": "~3.6.0",
     "@types/node": "^12.11.1",
-    "@typescript-eslint/eslint-plugin": "^4.13.0",
+    "@typescript-eslint/eslint-plugin": "5.17.0",
     "@typescript-eslint/eslint-plugin-tslint": "^4.13.0",
-    "@typescript-eslint/parser": "^4.13.0",
+    "@typescript-eslint/parser": "5.17.0",
     "casual": "^1.6.2",
     "codelyzer": "^6.0.0",
-    "eslint": "^7.20.0",
+    "eslint": "^8.12.0",
     "eslint-plugin-import": "^2.22.1",
     "eslint-plugin-jsdoc": "^31.0.3",
     "eslint-plugin-prefer-arrow": "^1.2.2",
     "express": "^4.17.2",
     "express-graphql": "^0.12.0",
-    "graphql": "^15.4.0",
+    "graphql": "16.4.0",
     "graphql-cli": "^4.1.0",
-    "graphql-config": "^3.2.0",
-    "graphql-mock": "^1.3.0",
-    "graphql-schema-linter": "^2.0.1",
+    "graphql-config": "4.3.0",
+    "graphql-mock": "2.0.0",
+    "graphql-schema-linter": "3.0.0",
     "jasmine-core": "~3.6.0",
     "jasmine-spec-reporter": "~5.0.0",
     "karma": "~6.3.16",
@@ -87,7 +98,6 @@
     "patch-package": "^6.4.7",
     "prettier": "^2.5.1",
     "protractor": "~7.0.0",
-    "rxjs-spy": "^7.5.3",
     "svg-to-ts": "^6.0.0",
     "svgo": "^2.3.0",
     "ts-node": "~8.3.0",

diff --git a/client/src/app/app.component.ts b/client/src/app/app.component.ts
@@ -11,7 +11,7 @@ declare let gtag: Function;
 @Component({
   selector: 'app-root',
   templateUrl: './app.component.html',
-  styleUrls: ['./app.component.less']
+  styleUrls: ['./app.component.less'],
 })
 
 export class AppComponent {

diff --git a/client/src/app/components/assertions/assertion-card/assertion-card.component.ts b/client/src/app/components/assertions/assertion-card/assertion-card.component.ts
@@ -1,13 +1,13 @@
 import { Component, Input, OnInit } from "@angular/core";
-import { AssertionBrowseTableRowFieldsFragment } from "@app/generated/civic.apollo";
+import { AssertionBrowseFieldsFragment } from "@app/generated/civic.apollo";
 
 @Component({
     selector: 'cvc-assertion-card',
     templateUrl: './assertion-card.component.html',
     styleUrls: ['./assertion-card.component.less']
 })
 export class CvcAssertionCardComponent implements OnInit {
-    @Input() assertion!: AssertionBrowseTableRowFieldsFragment;
+    @Input() assertion!: AssertionBrowseFieldsFragment;
 
     ngOnInit(){
         if(this.assertion == undefined) {

diff --git a/client/src/app/components/assertions/assertions-popover/assertion-popover.component.html b/client/src/app/components/assertions/assertions-popover/assertion-popover.component.html
@@ -46,7 +46,7 @@
           {{ assertion.variantOrigin | evidenceEnumDisplay }}
         </nz-descriptions-item>
 
-        <nz-descriptions-item *ngIf="assertion.assertionType == 'PREDISPOSING' else ampLevel" nzTitle="ACMG Codes" nzSpan="2">
+        <nz-descriptions-item *ngIf="assertionRules.requiresAcmgCodes(assertion.assertionType)" nzTitle="ACMG Codes" nzSpan="2">
           <ng-container *ngIf="assertion.acmgCodes.length > 0; else noAcmg">
             <nz-tag nz-tooltip [nzTooltipTitle]="code.description" *ngFor="let code of assertion.acmgCodes">{{ code.code }}</nz-tag> 
           </ng-container>
@@ -55,11 +55,18 @@
           </ng-template>
         </nz-descriptions-item>
 
-        <ng-template #ampLevel>
-          <nz-descriptions-item nzTitle="AMP/ASCO/CAP Category">
-            {{ assertion.ampLevel | formatAmp: 'compact' | ifEmpty: '--' }}
-          </nz-descriptions-item>
-        </ng-template>
+        <nz-descriptions-item *ngIf="assertionRules.requiresClingenCodes(assertion.assertionType)" nzTitle="ClinGen/CGC/VICC Codes" nzSpan="2">
+          <ng-container *ngIf="assertion.clingenCodes.length > 0; else noClingen">
+            <nz-tag nz-tooltip [nzTooltipTitle]="code.description" *ngFor="let code of assertion.clingenCodes">{{ code.code }}</nz-tag> 
+          </ng-container>
+          <ng-template #noClingen>
+            --
+          </ng-template>
+        </nz-descriptions-item>
+
+        <nz-descriptions-item *ngIf="assertionRules.requiresAmpLevel(assertion.assertionType)" nzTitle="AMP/ASCO/CAP Category">
+          {{ assertion.ampLevel | formatAmp: 'compact' | ifEmpty: '--' }}
+        </nz-descriptions-item>
 
         <nz-descriptions-item nzTitle="Regulatory Approval">
           <i nz-icon *ngIf="assertion.regulatoryApproval" nzType="check-circle" nzTheme="twotone" nzTwotoneColor="#52c41a"></i>

diff --git a/client/src/app/components/assertions/assertions-popover/assertion-popover.component.ts b/client/src/app/components/assertions/assertions-popover/assertion-popover.component.ts
@@ -1,7 +1,9 @@
 import { Component, Input, OnInit } from "@angular/core";
 import { AssertionPopoverFragment, AssertionPopoverGQL, Maybe } from "@app/generated/civic.apollo";
-import { map } from 'rxjs/operators'
+import { filter, map } from 'rxjs/operators'
 import { Observable } from 'rxjs';
+import { isNonNulled } from "rxjs-etc";
+import { AssertionState } from "@app/forms/config/states/assertion.state";
 
 @Component({
   selector: 'cvc-assertion-popover',
@@ -13,6 +15,8 @@ export class CvcAssertionPopoverComponent implements OnInit {
 
   assertion$?: Observable<Maybe<AssertionPopoverFragment>>
 
+  assertionRules = new AssertionState()
+
   constructor(private gql: AssertionPopoverGQL) { }
 
   ngOnInit() {
@@ -21,6 +25,8 @@ export class CvcAssertionPopoverComponent implements OnInit {
     }
     this.assertion$ = this.gql.watch({ assertionId: this.assertionId })
       .valueChanges
-      .pipe(map(({ data }) => data.assertion))
+      .pipe(map(r => r.data),
+        filter(isNonNulled),
+        map(({ assertion }) => assertion));
   }
 }
diff --git a/client/src/app/components/assertions/assertions-popover/assertion-popover.query.gql b/client/src/app/components/assertions/assertions-popover/assertion-popover.query.gql
@@ -18,6 +18,10 @@ fragment assertionPopover on Assertion {
     code
     description
   }
+  clingenCodes {
+    code
+    description
+  }
   nccnGuideline {
     id
     name