merged development_3.0

.github/workflows/codeql.yml

@@ -0,0 +1,66 @@
+name: "CodeQL-Advanced"
+
+on:
+  push:
+    branches: [ "development_3.0" ]
+  pull_request:
+    branches: [ "development_3.0" ]
+
+jobs:
+  analyze:
+    name: Analyze (${{ matrix.language }})
+    runs-on:
+      group: ncats-onprem-internal-runners
+    timeout-minutes: ${{ (matrix.language == 'swift' && 120) || 360 }}
+    permissions:
+      # required for all workflows
+      security-events: write
+
+      # required to fetch internal or private CodeQL packs
+      packages: read
+
+      # only required for workflows in private repositories
+      actions: read
+      contents: read
+
+    strategy:
+      fail-fast: false
+      matrix:
+        include:
+        - language: javascript-typescript
+          build-mode: none # This mode only analyzes Java. Set this to 'autobuild' or 'manual' to analyze Kotlin too.
+    steps:
+    - name: Checkout repository
+      uses: actions/checkout@v4
+
+    # Initializes the CodeQL tools for scanning.
+    - name: Initialize CodeQL
+      uses: github/codeql-action/init@v3
+      with:
+        languages: ${{ matrix.language }}
+        build-mode: ${{ matrix.build-mode }}
+    - if: matrix.build-mode == 'manual'
+      shell: bash
+      run: |
+        echo 'If you are using a "manual" build mode for one or more of the' \
+          'languages you are analyzing, replace this with the commands to build' \
+          'your code, for example:'
+        echo '  make bootstrap'
+        echo '  make release'
+        exit 1
+
+    - name: Perform CodeQL Analysis
+      uses: github/codeql-action/analyze@v3
+      with:
+        category: "/language:${{matrix.language}}"
+
+    - name: Generate Security Report
+      uses: rsdmike/[email protected]
+      with:
+          token: ${{ secrets.GITHUB_TOKEN }}
+
+    - name: Upload Artifacts
+      uses: actions/upload-artifact@v4
+      with: 
+          name: reports
+          path: ./*.pdf

.travis.yml

@@ -2,7 +2,7 @@ dist: trusty
 
 language: node_js
 node_js:
-  - 14.17.0
+  - 17.9.1
 
 
 install:
@@ -21,6 +21,9 @@ install:
   - npm install webpack
   - npm i --save webpack-sources --legacy-peer-deps
   - npm install -f @types/[email protected]
+  - npm install -g yarn
+  - npm uninstall undici
+  - npm install [email protected]
   - export NODE_OPTIONS="--max-old-space-size=8192"
 script:
   - npm run build:fda:prod

package.dev.json

@@ -70,7 +70,7 @@
     "zone.js": "0.11.4",
     "z-schema": "5.0.4",
     "jexl": "2.3.0",
-    "xlsx": "^0.18.5"
+    "xlsx": "0.18.5"
   },
   "devDependencies": {
     "@angular-devkit/build-angular": "13.2.1",
@@ -89,7 +89,7 @@
     "@types/node": "17.0.16",
     "@typescript-eslint/eslint-plugin": "5.11.0",
     "@typescript-eslint/parser": "5.11.0",
-    "cheerio": "^1.0.0-rc.2",
+    "cheerio": "1.0.0-rc.2",
     "codelyzer": "6.0.2",
     "cpx-fixed": "1.6.0",
     "eslint": "8.8.0",

package.real.json

@@ -78,7 +78,7 @@
     "z-schema": "4.2.2",
     "jexl": "2.3.0",
     "ngx-schema-form": "2.7.0",
-    "xlsx": "^0.18.5"
+    "xlsx": "0.18.5"
   },
   "devDependencies": {
     "@angular-devkit/build-angular": "13.2.1",
@@ -97,7 +97,7 @@
     "@types/node": "17.0.16",
     "@typescript-eslint/eslint-plugin": "5.11.0",
     "@typescript-eslint/parser": "5.11.0",
-    "cheerio": "^1.0.0-rc.2",
+    "cheerio": "1.0.0-rc.2",
     "codelyzer": "6.0.2",
     "cpx-fixed": "1.6.0",
     "eslint": "8.8.0",

projects/ketcher-wrapper/src/lib/ketcher-wrapper.component.ts

@@ -10,6 +10,7 @@ import { Ketcher } from './ketcher.model';
 export class KetcherWrapperComponent implements OnInit, AfterViewInit {
   @ViewChild('ketcherFrame', { static: true }) ketcherFrame: { nativeElement: HTMLIFrameElement };
   @Output() ketcherOnLoad = new EventEmitter<any>();
+  randomId: string;
   safeKetcherFilePath: SafeUrl;
   @ViewChild('ketcherBody') kBod: ElementRef;
   @ViewChild('ketcherFrame') iframe: ElementRef;
@@ -18,11 +19,10 @@ export class KetcherWrapperComponent implements OnInit, AfterViewInit {
     private sanitizer: DomSanitizer,
     private renderer: Renderer2
   ) {
-
+    this.randomId = Math.random().toString(36).replace('0.', '');
   }
 
   ngOnInit() {
-
 
   }
 
@@ -35,8 +35,8 @@ export class KetcherWrapperComponent implements OnInit, AfterViewInit {
     });
         
     //  let doc = this.iframe.nativeElement.contentDocument || this.iframe.nativeElement.contentWindow;
-    };
-   // this.renderer.listen(window, 'blur', () => this.onWindowBlur());*/
+    };*/
+    this.renderer.listen(window, 'blur', () => this.onWindowBlur());
   }
 
 
@@ -49,5 +49,36 @@ export class KetcherWrapperComponent implements OnInit, AfterViewInit {
         }
     }, interval);
 }
+@HostListener('mouseover')
+private onIframeMouseOver() {
+  this.iframeMouseOver = true;
+  this.resetFocusOnWindow();
+}
+
+@HostListener('mouseout')
+private onIframeMouseOut() {
+  this.iframeMouseOver = false;
+  this.resetFocusOnWindow();
+}
+
+@HostListener('click')
+private onClick() {
+ // this.iframeMouseOver = false;
+ setTimeout(() => {
+  this.resetFocusOnWindow();
+ }, 100);
+}
 
+private onWindowBlur() {
+  if (this.iframeMouseOver) {
+    this.resetFocusOnWindow();
+  }
+}
+
+private resetFocusOnWindow() {
+  setTimeout(() => {
+
+    window.focus();
+  }, 100);
+}
 }

projects/ketcher-wrapper/src/lib/ketcher.model.ts

@@ -6,7 +6,7 @@ export interface Ketcher {
     editor?: any;
     getSmiles: () => string;
     saveSmiles: () => Promise<any>;
-    getMolfile: () => string;
+    getMolfile: () => any;
     setMolecule: (molString: any) => void;
     addFragment: (molString: any) => void;
     showMolfile: (clientArea: any, molString: any, options: any) => any;

src/app/core/admin/fragment-wizard/fragment-wizard.component.ts

@@ -215,7 +215,6 @@ private overlayContainer: HTMLElement;
 
 
   getPossibleSmiles(smi) {
-    console.log(smi);
     function getMarkers(smi) {
       let temp = smi.replace(/@H/g, '').replace(/[^A-Z*]/g, '');
       var alias: any = {

src/app/core/app-routing.module.ts

@@ -126,7 +126,11 @@ const childRoutes: Routes = [
   {
     path: 'user-downloads/:id',
     component: UserDownloadsComponent
-  }
+  },
+  {
+    path: 'structure-features',
+    component: SubstanceFormComponent
+  },
 ];
 
 const routes: Routes = [

src/app/core/auth/auth.service.ts

@@ -1,7 +1,7 @@
 import { Injectable, PLATFORM_ID, Inject } from '@angular/core';
 import { ConfigService } from '../config/config.service';
 import { Auth, Role, UserGroup } from './auth.model';
-import { Observable, Subject } from 'rxjs';
+import { Observable, Subject, of } from 'rxjs';
 import { map, take, catchError } from 'rxjs/operators';
 import { HttpClient, HttpParams } from '@angular/common/http';
 import { isPlatformBrowser } from '@angular/common';
@@ -57,7 +57,11 @@ export class AuthService {
 
   public checkAuth(): Observable<Auth> {
     const url = `${(this.configService.configData && this.configService.configData.apiBaseUrl) || '/'}api/v1/`;
-    return this.http.get<any>(`${url}whoami`);
+    if (this.configService.configData && this.configService.configData.dummyWhoami) {
+      return of(this.configService.configData.dummyWhoami);
+    } else {
+      return this.http.get<any>(`${url}whoami`);
+    }
   }
 
   login(username: string, password: string): Observable<Auth> {
@@ -70,7 +74,12 @@ export class AuthService {
     };
 
     const url = `${(this.configService.configData && this.configService.configData.apiBaseUrl) || '/'}api/v1/`;
-    return this.http.get<Auth>(`${url}whoami`, options).pipe(
+
+    let obs = this.http.get<Auth>(`${url}whoami`, options);
+    if (this.configService.configData && this.configService.configData.dummyWhoami) {
+      obs = of(this.configService.configData.dummyWhoami);
+    }
+    return obs.pipe(
       map(auth => {
         if (auth && auth.computedToken) {
           this._auth = auth;
@@ -295,6 +304,9 @@ export class AuthService {
     return new Observable(observer => {
       this.configService.afterLoad().then(cd => {
         const url = `${(this.configService.configData && this.configService.configData.apiBaseUrl) || '/'}api/v1/`;
+        if (this.configService.configData && this.configService.configData.dummyWhoami) {
+          observer.next(this.configService.configData.dummyWhoami);
+        } else {
         this.http.get<Auth>(`${url}whoami`)
           .subscribe(
             auth => {
@@ -309,6 +321,7 @@ export class AuthService {
             },
             () => observer.complete()
           );
+        }
       });
     });
   }

src/app/core/config/config.model.ts

@@ -1,3 +1,5 @@
+import { Auth } from "@gsrs-core/auth";
+
 export interface Config {
     apiBaseUrl?: string;
     gsrsHomeBaseUrl?: string;
@@ -78,6 +80,9 @@ export interface Config {
     jsdrawLicense?: boolean;
     disableKetcher?: boolean;
     useApprovalAPI?: boolean;
+    dummyWhoami?: Auth;
+    enableStructureFeatures?: boolean;
+    structureEditSearch?: boolean;
 }
 
 export interface StagingAreaSettings {

src/app/core/structure-editor/structure-editor-implementation.model.ts

@@ -57,7 +57,7 @@ export class EditorImplementation implements Editor {
     getMolfile(): Observable<any> {
         return new Observable<any>(observer => {
         if (this.ketcher && this.ketcher != null) {
-            from(this.ketcher.getMolfile()).pipe(take(1)).subscribe(result => { 
+            this.ketcher.getMolfile().then(result => { 
                 let mfile = result;
 
                 observer.next(mfile);
@@ -96,8 +96,7 @@ export class EditorImplementation implements Editor {
 
     getSmiles(): Observable<string> {
         if (this.ketcher != null) {
-            return  from(this.ketcher.getSmiles()).pipe(switchMap(data => {
-                return data;}));
+        return from(this.ketcher.getSmiles());
         } else if (this.jsdraw != null) {
             return new Observable<string>(observer => {
                 observer.next(this.jsdraw.getSmiles());
@@ -144,6 +143,7 @@ export class EditorImplementation implements Editor {
     setMolecule(molfile: string): void {
         if (this.ketcher && this.ketcher != null) {
             this.ketcher.setMolecule(molfile);
+            this.ketcher.setMolecule(molfile);
         } else if (this.jsdraw && this.jsdraw != null) {
             // from simple tests, this should push the current molecule down
             // on the undo stack.
@@ -164,18 +164,17 @@ export class EditorImplementation implements Editor {
             } else if (this.ketcher != null) {
               this.ketcher.editor.subscribe('change',  operations => { 
                     if(!(operations.length == 1 && operations[0].operation == 'Load canvas')){
-                        from(this.ketcher.getMolfile()).pipe(take(1)).subscribe(result => { 
+                        this.ketcher.getMolfile().then(result => { 
                             observer.next(result);
                         });
                     } else {
                         this.getMolfile().pipe(take(1)).subscribe(result => { 
                             observer.next(result);
                         });
-                    //    observer.next(this.tempMol);
                     }
 
 
-                 });//*/
+                 });
 
             }
             else {

src/app/core/structure-editor/structure-editor.component.html

@@ -5,7 +5,7 @@
     <ncats-jsdraw-wrapper id = "jsdrawwrap" oncontextmenu="return false" (jsDrawOnLoad)="jsDrawOnLoad($event)" [hidden]="structureEditor === 'ketcher' && !firstload" style = "width:990px"></ncats-jsdraw-wrapper>
   </div>
   <div style = "width: 100%">
-    <ncats-ketcher-wrapper (ketcherOnLoad)="ketcherOnLoad($event)" [hidden]="structureEditor === 'jsdraw'">
+    <ncats-ketcher-wrapper id="ketcherwrapper" (ketcherOnLoad)="ketcherOnLoad($event)" [hidden]="structureEditor === 'jsdraw'">
     </ncats-ketcher-wrapper>
   </div>