Merge pull request #517 from ncats/ketcher_fixes

fixes to structure search import/export
ncats · Jun 21, 2024 · e6f528a · e6f528a
2 parents 3b0e4d1 + 4566909
commit e6f528a
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Showing 7 changed files with 134 additions and 76 deletions.
diff --git a/src/app/core/structure-editor/structure-editor.component.ts b/src/app/core/structure-editor/structure-editor.component.ts
@@ -95,6 +95,16 @@ export class StructureEditorComponent implements OnInit, AfterViewInit, OnDestro
     }
   }
 
+  @Input() setMolecule(structure: any){
+    if(this.structureEditor==="ketcher") {
+      this.structureService.interpretStructure(structure).subscribe(resp => {
+        this.ketcher.setMolecule(resp.structure.molfile);
+      });
+    } else {
+      this.editor.setMolecule(structure);
+    }
+  } 
+
   listener = ()  => {
     var elmR=document.getElementById("root");
     if(this.structureEditor==="ketcher"){
@@ -154,6 +164,7 @@ export class StructureEditorComponent implements OnInit, AfterViewInit, OnDestro
 
       this.structureEditor = environment.structureEditor;
       let pref = sessionStorage.getItem('gsrsStructureEditor');
+      console.log(pref);
       if (pref && this.enableJSDraw) {
         if (pref === 'ketcher') {
           this.structureEditor = 'ketcher';

diff --git a/src/app/core/structure-search/structure-search.component.ts b/src/app/core/structure-search/structure-search.component.ts
@@ -15,6 +15,7 @@ import { Title } from '@angular/platform-browser';
 import * as _ from 'lodash';
 import { pipeline } from 'stream';
 import { take } from 'rxjs';
+import { StructureEditorComponent } from '@gsrs-core/structure-editor';
 
 @Component({
   selector: 'app-structure-search',
@@ -29,6 +30,7 @@ export class StructureSearchComponent implements OnInit, AfterViewInit, OnDestro
   showSimilarityCutoff = false;
   searchTypeControl = new FormControl();
   @ViewChild('contentContainer', { static: true }) contentContainer;
+  @ViewChild(StructureEditorComponent) structureEditor!: StructureEditorComponent;
   private overlayContainer: HTMLElement;
 
   constructor(
@@ -187,7 +189,7 @@ export class StructureSearchComponent implements OnInit, AfterViewInit, OnDestro
       this.overlayContainer.style.zIndex = null;
 
       if (structurePostResponse && structurePostResponse.structure && structurePostResponse.structure.molfile) {
-        this.editor.setMolecule(structurePostResponse.structure.molfile);
+        this.structureEditor.setMolecule(structurePostResponse.structure.molfile);
       }
     }, () => {
       this.overlayContainer.style.zIndex = null;
@@ -203,7 +205,7 @@ export class StructureSearchComponent implements OnInit, AfterViewInit, OnDestro
       height: 'auto',
       width: '650px',
       data: {
-        molfile: this.editor.getMolfile(),
+        molfile: mol,
         smiles: this.editor.getSmiles()
       }
     });

diff --git a/src/app/core/substance-details/substance-overview/substance-overview.component.html b/src/app/core/substance-details/substance-overview/substance-overview.component.html
@@ -55,7 +55,8 @@
       {{substance.definitionLevel}} DEFINITION
     </span>
   </div>
-  <div>
+  <div class = "full-col">
+  <div class = "left-col">
     <div class="name-value">
       <div class="name">Substance Class</div>
       <div class="value blue-font">{{substance.substanceClass | classDisplay}}</div>
@@ -87,6 +88,52 @@
         <span class = "deprecated" *ngIf ="substance.deprecated">RECORD IS DEPRECATED</span>
       </div>
     </div>
+    <div *ngIf="!isAdmin && !substance.$$source" class="name-value">
+      <div class="name">Record Version</div>
+      <div class="value blue-font">{{substance.version}}</div>
+    </div>
+    <div *ngIf="isAdmin && !substance.$$source" class="name-value">
+      <div class="name">Record Version</div>
+      <mat-form-field class="version-dropdown">
+        <mat-select [formControl]="versionControl" class="version-select">
+          <mat-option *ngFor="let version of versions" [value]="version" class="version-option">
+            {{version}}
+          </mat-option>
+        </mat-select>
+      </mat-form-field>
+      <button *ngIf="substance.version != versionControl.value" mat-button
+        class="mat-raised-button mat-primary view-version" (click)='changeVersion()'>View</button>
+    </div>
+    <div *ngIf="substance.version != latestVersion  && !substance.$$source" class="indent">
+      This is an older version of this substance - Ver. {{this.substance.version}}
+      <button *ngIf="isAdmin" mat-button
+        class="mat-raised-button mat-primary view-version" (click)='restoreVersion()'>Restore this version</button>
+    </div>
+
+    <div class="name-value">
+        <div class="name">Definitional Access</div>
+        <div class="value blue-font">
+            <span *ngIf="(defAccess && defAccess.length > 0) else defIndicator">
+              <span>Not a public definition</span>&nbsp;
+              <mat-icon svgIcon="lock"></mat-icon>
+            </span>
+            <ng-template #defIndicator>
+              <span>Public definition</span>&nbsp;
+              <mat-icon svgIcon="lock_open"></mat-icon>
+            </ng-template>
+          </div>
+      <!--  <div class="value">
+          <span *ngIf = "!defAccess || defAccess.length === 0">Public</span>
+          <span *ngIf = "defAccess && defAccess.length > 0">
+            <span class = "pre" *ngFor ="let access of defAccess;last as islast">
+              {{access}}{{!islast? ', ':''}}
+            </span>
+          </span>
+
+        </div>-->
+      </div>
+  </div>
+  <div class = "right-col">
     <div *ngIf="substance.protein" class="diverseWrapper">
       <div class="name-value" *ngIf="substance.protein.proteinType">
         <div class="name">Protein Type</div>
@@ -220,71 +267,32 @@
         </div>
       </div>
     </div>
-    <div *ngIf="!isAdmin && !substance.$$source" class="name-value">
-      <div class="name">Record Version</div>
-      <div class="value blue-font">{{substance.version}}</div>
-    </div>
-    <div *ngIf="isAdmin && !substance.$$source" class="name-value">
-      <div class="name">Record Version</div>
-      <mat-form-field class="version-dropdown">
-        <mat-select [formControl]="versionControl" class="version-select">
-          <mat-option *ngFor="let version of versions" [value]="version" class="version-option">
-            {{version}}
-          </mat-option>
-        </mat-select>
-      </mat-form-field>
-      <button *ngIf="substance.version != versionControl.value" mat-button
-        class="mat-raised-button mat-primary view-version" (click)='changeVersion()'>View</button>
-    </div>
-    <div *ngIf="substance.version != latestVersion  && !substance.$$source" class="indent">
-      This is an older version of this substance - Ver. {{this.substance.version}}
-      <button *ngIf="isAdmin" mat-button
-        class="mat-raised-button mat-primary view-version" (click)='restoreVersion()'>Restore this version</button>
-    </div>
-    <div class="name-value">
-      <div class="name">Tags</div>
-      <div class="value">
-        <mat-chip-list #tagList aria-label="Tags" selectable="false">
-          <mat-chip
-            *ngFor="let tag of substance.tags"
-            removable="false">
-              {{tag}}
-          </mat-chip>
-        </mat-chip-list>
-      </div>
-    </div>
-    <div class="name-value" *ngIf="references?.length > 0">
-      <div class="name">
-        <a tabindex="0" role="link" (click)="toggleReferences()" class='blue-font references-link'>
-          <span>{{showDef === false ? 'Show' : 'Hide'}} Definitional References</span>
-          <mat-icon svgIcon="{{defIcon}}"></mat-icon>
-        </a>
-      </div>
-    </div>
-    <div [hidden]="!showDef">
-      <app-references-manager [substance]="substance" [references]="references"></app-references-manager>
-    </div>
-    <div class="name-value">
-        <div class="name">Definitional Access</div>
-        <div class="value blue-font">
-            <span *ngIf="(defAccess && defAccess.length > 0) else defIndicator">
-              <span>Not a public definition</span>&nbsp;
-              <mat-icon svgIcon="lock"></mat-icon>
-            </span>
-            <ng-template #defIndicator>
-              <span>Public definition</span>&nbsp;
-              <mat-icon svgIcon="lock_open"></mat-icon>
-            </ng-template>
-          </div>
-      <!--  <div class="value">
-          <span *ngIf = "!defAccess || defAccess.length === 0">Public</span>
-          <span *ngIf = "defAccess && defAccess.length > 0">
-            <span class = "pre" *ngFor ="let access of defAccess;last as islast">
-              {{access}}{{!islast? ', ':''}}
-            </span>
-          </span>
-
-        </div>-->
-      </div>
   </div>
+</div>
+<div class="name-value">
+  <div class="name">Tags</div>
+  <div class="value">
+    <mat-chip-list #tagList aria-label="Tags" selectable="false">
+      <mat-chip
+        *ngFor="let tag of substance.tags"
+        removable="false">
+          {{tag}}
+      </mat-chip>
+    </mat-chip-list>
+  </div>
+  <div *ngIf="substance.tags.length === 0">
+    <i>None</i>
+  </div>
+</div>
+<div class="name-value" *ngIf="references?.length > 0">
+  <div class="name">
+    <a tabindex="0" role="link" (click)="toggleReferences()" class='blue-font references-link'>
+      <span>{{showDef === false ? 'Show' : 'Hide'}} Definitional References</span>
+      <mat-icon svgIcon="{{defIcon}}"></mat-icon>
+    </a>
+  </div>
+</div>
+<div [hidden]="!showDef">
+  <app-references-manager [substance]="substance" [references]="references"></app-references-manager>
+</div>
 </div>
diff --git a/src/app/core/substance-details/substance-overview/substance-overview.component.scss b/src/app/core/substance-details/substance-overview/substance-overview.component.scss
@@ -2,6 +2,22 @@
   display: inline-flex;
   vertical-align: middle;
 }
+
+.left-col {
+  width:50%;
+
+}
+
+.right-col {
+  width: 50%;
+}
+
+.full-col {
+  width: 100%;
+  display:flex;
+  flex-direction: row;
+}
+
 .version-dropdown{
   width:50px;
   border:0px;

diff --git a/src/app/core/substance-form/access-manager/access-manager.component.ts b/src/app/core/substance-form/access-manager/access-manager.component.ts
@@ -44,6 +44,20 @@ export class AccessManagerComponent implements OnInit, AfterViewInit {
   getVocabularies(): void {
     this.cvService.getDomainVocabulary('ACCESS_GROUP').subscribe(response => {
       const accessOptions = response['ACCESS_GROUP'].list;
+      console.log(accessOptions);
+      let hasRep = false;
+      accessOptions.forEach(option => {
+        if (option.value.toLowerCase() === 'representative') {
+          hasRep = true;
+        }
+      });
+      if (!hasRep) {
+        accessOptions.push(
+          {display: 'representative',
+            value: 'representative'
+          }
+        )
+      }
       this.createAccessFromGroup(accessOptions);
       this.accessOptions = accessOptions;
       this.crosscheckAccesses();

diff --git a/src/app/core/substance-form/structure/substance-form-structure-card.component.ts b/src/app/core/substance-form/structure/substance-form-structure-card.component.ts
@@ -1,4 +1,4 @@
-import { Component, OnInit, AfterViewInit, OnDestroy } from '@angular/core';
+import { Component, OnInit, AfterViewInit, OnDestroy, ViewChild } from '@angular/core';
 import { SubstanceFormBase } from '../base-classes/substance-form-base';
 import { Editor } from '../../structure-editor/structure.editor.model';
 import { SubstanceStructure } from '@gsrs-core/substance/substance.model';
@@ -17,6 +17,7 @@ import { SubstanceService } from '@gsrs-core/substance/substance.service';
 import { SubstanceFormStructuralUnitsService } from '../structural-units/substance-form-structural-units.service';
 import { SubstanceFormStructureService } from './substance-form-structure.service';
 import { ActivatedRoute } from '@angular/router';
+import { StructureEditorComponent } from '@gsrs-core/structure-editor';
 
 @Component({
   selector: 'app-substance-form-structure-card',
@@ -35,6 +36,7 @@ export class SubstanceFormStructureCardComponent extends SubstanceFormBase imple
   private overlayContainer: HTMLElement;
   structureErrorsArray: Array<StructureDuplicationMessage>;
   subscriptions: Array<Subscription> = [];
+  @ViewChild(StructureEditorComponent) structureEditorComponent!: StructureEditorComponent;
 
   constructor(
     private substanceFormService: SubstanceFormService,
@@ -197,7 +199,7 @@ export class SubstanceFormStructureCardComponent extends SubstanceFormBase imple
       this.overlayContainer.style.zIndex = null;
       if (response != null) {
         if (response && response.structure && response.structure.molfile) {
-          this.structureEditor.setMolecule(response.structure.molfile);
+          this.structureEditorComponent.setMolecule(response.structure.molfile);
         }
         this.processStructurePostResponse(response);
       }
@@ -249,7 +251,7 @@ export class SubstanceFormStructureCardComponent extends SubstanceFormBase imple
       this.overlayContainer.style.zIndex = null;
       if (molfile != null && molfile !== '') {
         this.updateStructureForm(molfile);
-        this.structureEditor.setMolecule(molfile);
+        this.structureEditorComponent.setMolecule(molfile);
       }
     }, () => { });
   }

diff --git a/src/app/core/substance-form/substance-form.service.ts b/src/app/core/substance-form/substance-form.service.ts
@@ -140,10 +140,13 @@ export class SubstanceFormService implements OnDestroy {
             substanceClass: 'mixture',
             references: [],
             names: [],
-            mixture: {},
+            mixture: {
+              access: ['representative']
+            },
             codes: [],
             relationships: [],
-            properties: []
+            properties: [],
+            access: ['representative']
           };
         } else if (substanceClass === 'structurallyDiverse') {
           this.privateSubstance = {
@@ -224,11 +227,13 @@ export class SubstanceFormService implements OnDestroy {
             polymer: {
               idealizedStructure: {},
               monomers: [],
+              access: ['representative']
             },
             codes: [],
             moieties: [],
             relationships: [],
-            properties: []
+            properties: [],
+            access: ['representative']
           };
         } else {
           this.privateSubstance = {
@@ -242,7 +247,7 @@ export class SubstanceFormService implements OnDestroy {
 
         // TP: default to protected for root level record.
         // ***** AN: Adding this right now for SSG4m and G2 ******
-        if (substanceClass !== 'specifiedSubstanceG4m') {
+        if (substanceClass !== 'specifiedSubstanceG4m' && substanceClass !== 'mixture' && substanceClass !== 'polymer') {
           this.privateSubstance.access = ["protected"];
 
           if (substanceClass !== 'specifiedSubstanceG2') {