Merge pull request #543 from ncats/NAshorthand

fixing sitesshorthand bug, unused import cleanup
ncats · Aug 27, 2024 · 5e2e72a · 5e2e72a
2 parents c7a3282 + 96f76ee
commit 5e2e72a
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Showing 5 changed files with 55 additions and 24 deletions.
diff --git a/src/app/core/config/config.model.ts b/src/app/core/config/config.model.ts
@@ -82,6 +82,7 @@ export interface Config {
     useApprovalAPI?: boolean;
     dummyWhoami?: Auth;
     enableStructureFeatures?: boolean;
+    StructureFeaturePriority?: Array<string>;
     structureEditSearch?: boolean;
 }
 

diff --git a/src/app/core/substance-form/links/link-form.component.ts b/src/app/core/substance-form/links/link-form.component.ts
@@ -46,7 +46,9 @@ export class LinkFormComponent implements OnInit, OnDestroy {
 
   getStructure() {
     if (this.privateLink && this.privateLink.linkage){
-    this.smiles = this.vocabulary[this.privateLink.linkage];
+        if(this.vocabulary) {
+          this.smiles = this.vocabulary[this.privateLink.linkage];
+        } 
     if (this.smiles && this.smiles.fragmentStructure) {
       this.structure = this.cvService.getStructureUrlFragment(this.smiles.fragmentStructure);
     } else {

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
@@ -47,6 +47,16 @@ export class SubstanceFormStructureCardComponent extends SubstanceFormBase imple
   featuresOnly = false;
   hideFeaturesTable = false;
   structureEditSearch = true;
+  StructureFeaturePriority = [
+    'Category Score',
+    'Sum Of Scores',
+    'AI Limit (US)',
+    'Potency Category',
+    'Potency Score',
+    'type',
+    'Type',
+    'TYPE'
+  ];
   @ViewChild(StructureEditorComponent) structureEditorComponent!: StructureEditorComponent;
 
   constructor(
@@ -76,6 +86,13 @@ export class SubstanceFormStructureCardComponent extends SubstanceFormBase imple
         this.configService.configData.structureEditSearch !== null)) {
       this.structureEditSearch = this.configService.configData.structureEditSearch;
     }
+
+    if (this.configService.configData && 
+      (this.configService.configData.StructureFeaturePriority !== undefined && 
+        this.configService.configData.StructureFeaturePriority !== null)) {
+      this.StructureFeaturePriority = this.configService.configData.StructureFeaturePriority;
+    }
+
     if(this.activatedRoute.snapshot.routeConfig.path === 'structure-features') {
       this.featuresOnly = true;
     }
@@ -185,15 +202,27 @@ export class SubstanceFormStructureCardComponent extends SubstanceFormBase imple
     }
   }
 
+   featureSort(a: any, b: any): number {
+    const indexA = this.StructureFeaturePriority.indexOf(a.key);
+    const indexB =  this.StructureFeaturePriority.indexOf(b.key);
+
+
+    if (indexA !== -1 && indexB !== -1) {
+      return indexA - indexB;
+    } else if (indexA !== -1) {
+      return -1; // a comes first
+    } else if (indexB !== -1) {
+      return 1; // b comes first
+    } else {
+      return a.key.localeCompare(b.key);
+    }
+  }
+
   processStructurePostResponse(structurePostResponse?: InterpretStructureResponse): void {
     if (structurePostResponse && structurePostResponse.structure) {
       let customSort = (array: any[]): any[] => {
         return array.sort((a, b) => {
-          if (a.key === 'Category Score') return -1;
-          if (b.key === 'Category Score') return 1;
-          if (a.key === 'Sum Of Scores') return a.key === 'Category Score' ? 1 : -1;
-          if (b.key === 'Sum Of Scores') return b.key === 'Category Score' ? -1 : 1;
-          return a.key.localeCompare(b.key);
+          return this.featureSort(a, b);
         });
       };
 
@@ -219,6 +248,9 @@ export class SubstanceFormStructureCardComponent extends SubstanceFormBase imple
               if(key === 'sumOfScores'){
                 label = 'Sum Of Scores';
               }
+              if (key.toLowerCase() === 'type') {
+                label = 'Type';
+              }
               temp.push({'key': label,'value': structurePostResponse.featureList[type][0][key] });
             });
           }

diff --git a/src/app/core/substance-form/substance-form.service.ts b/src/app/core/substance-form/substance-form.service.ts
@@ -1423,6 +1423,7 @@ export class SubstanceFormService implements OnDestroy {
       });
     }
 
+    //TODO - recalculate sitesShorthand instead of deleting / determine when backend uses sitesShorthand over sites array
     if (this.privateSubstance.protein && this.privateSubstance.protein.disulfideLinks
       && this.privateSubstance.protein.disulfideLinks.length > 0) {
       for (let i = this.privateSubstance.protein.disulfideLinks.length -1; i >= 0; i--) {
@@ -1436,20 +1437,20 @@ export class SubstanceFormService implements OnDestroy {
           this.privateSubstance.protein.disulfideLinks.splice(i, 1);
         }
       }
+    }
 
-      if (this.privateSubstance.nucleicAcid) {
-        if (this.privateSubstance.nucleicAcid.linkages && this.privateSubstance.nucleicAcid.linkages.length > 0) {
-          for (let i = this.privateSubstance.nucleicAcid.linkages.length-1; i >= 0; i--) {
-            if (this.privateSubstance.nucleicAcid.linkages[i].sitesShorthand) {
-               delete this.privateSubstance.nucleicAcid.linkages[i].sitesShorthand;
-            }
+    if (this.privateSubstance.nucleicAcid) {
+      if (this.privateSubstance.nucleicAcid.linkages && this.privateSubstance.nucleicAcid.linkages.length > 0) {
+        for (let i = this.privateSubstance.nucleicAcid.linkages.length -1; i >= 0; i--) {
+          if (this.privateSubstance.nucleicAcid.linkages[i].sitesShorthand) {
+             delete this.privateSubstance.nucleicAcid.linkages[i].sitesShorthand;
           }
         }
-        if (this.privateSubstance.nucleicAcid.sugars && this.privateSubstance.nucleicAcid.sugars.length > 0) {
-          for (let i = this.privateSubstance.nucleicAcid.sugars.length-1; i >= 0; i--) {
-            if (this.privateSubstance.nucleicAcid.sugars[i].sitesShorthand) {
-               delete this.privateSubstance.nucleicAcid.sugars[i].sitesShorthand;
-            }
+      }
+      if (this.privateSubstance.nucleicAcid.sugars && this.privateSubstance.nucleicAcid.sugars.length > 0) {
+        for (let i = this.privateSubstance.nucleicAcid.sugars.length -1; i >= 0; i--) {
+          if (this.privateSubstance.nucleicAcid.sugars[i].sitesShorthand) {
+             delete this.privateSubstance.nucleicAcid.sugars[i].sitesShorthand;
           }
         }
       }

diff --git a/src/app/core/substance-ssg4m/ssg4m-scheme-view/ssg4m-scheme-view.component.ts b/src/app/core/substance-ssg4m/ssg4m-scheme-view/ssg4m-scheme-view.component.ts
@@ -3,17 +3,12 @@ import { Subscription } from 'rxjs';
 import { OverlayContainer } from '@angular/cdk/overlay';
 import { MatDialog } from '@angular/material/dialog';
 import { Environment } from 'src/environments/environment.model';
-import { ConfigService, LoadedComponents } from '@gsrs-core/config';
+import { ConfigService } from '@gsrs-core/config';
 import { UtilsService } from '@gsrs-core/utils';
-import { StructureImageModalComponent, StructureService } from '@gsrs-core/structure';
-import { SubstanceFormService } from '../../substance-form/substance-form.service';
+import { StructureImageModalComponent } from '@gsrs-core/structure';
 import { SubstanceFormSsg4mProcessService } from '../ssg4m-process/substance-form-ssg4m-process.service';
 import { SubstanceDetail, SpecifiedSubstanceG4mProcess, SubstanceAmount } from '@gsrs-core/substance/substance.model';
 import { SubstanceSsg4mService } from '../substance-ssg4m-form.service';
-import * as htmlToImage from 'html-to-image';
-import domToImage from 'dom-to-image';
-import jsPDF from 'jspdf';
-import * as moment from 'moment';
 
 @Component({
   selector: 'app-ssg4m-scheme-view',