Merge pull request #454 from ncats/momentCheck

SR2 changes for staging area

package.dev.json

@@ -58,7 +58,7 @@
     "helmet": "3.21.2",
     "lodash": "4.17.21",
     "lucene-query-parser": "1.2.0",
-    "moment": "2.29.4",
+    "moment": "2.29.2",
     "ng-multiselect-dropdown": "0.2.10",
     "ngx-json-viewer": "2.4.0",
     "ngx-moment": "3.5.0",

package.json

@@ -62,7 +62,7 @@
     "ketcher-wrapper": "file:dist/ketcher-wrapper/ketcher-wrapper-0.0.1.tgz",
     "lodash": "4.17.21",
     "lucene-query-parser": "1.2.0",
-    "moment": "2.29.2",
+    "moment": "2.29.4",
     "ng-multiselect-dropdown": "0.2.10",
     "ngx-json-viewer": "2.4.0",
     "ngx-moment": "3.5.0",
@@ -106,7 +106,7 @@
     "husky": "7.0.4",
     "jasmine-core": "4.0.0",
     "jasmine-spec-reporter": "7.0.0",
-    "karma": "6.3.15",
+    "karma": "6.4.2",
     "karma-chrome-launcher": "3.1.0",
     "karma-coverage-istanbul-reporter": "3.0.3",
     "karma-jasmine": "4.0.1",

package.real.json

@@ -61,7 +61,7 @@
     "ketcher-wrapper": "file:dist/ketcher-wrapper/ketcher-wrapper-0.0.1.tgz",
     "lodash": "4.17.21",
     "lucene-query-parser": "1.2.0",
-    "moment": "2.29.4",
+    "moment": "2.29.2",
     "ng-multiselect-dropdown": "0.2.10",
     "ngx-json-viewer": "2.4.0",
     "ngx-moment": "3.5.0",

src/app/core/admin/import-browse/bulk-action-dialog/bulk-action-dialog.component.ts

@@ -3,6 +3,7 @@ import { ImportDialogComponent } from '@gsrs-core/admin/import-management/import
 import { MatDialogRef, MAT_DIALOG_DATA } from '@angular/material/dialog';
 import { LoadingService } from '@gsrs-core/loading';
 import { AdminService } from '@gsrs-core/admin/admin.service';
+import { ConfigService } from '@gsrs-core/config';
 
 @Component({
   selector: 'app-bulk-action-dialog',
@@ -21,11 +22,13 @@ export class BulkActionDialogComponent implements OnInit {
   deleteStaged = true;
   altStatusCount = 0;
   completedRecordCount = 0;
+  showMerge = false;
   constructor(
 
     public dialogRef: MatDialogRef<ImportDialogComponent>,
     public loadingService: LoadingService,
     private adminService: AdminService,
+    private configService: ConfigService,
 
 
     @Inject(MAT_DIALOG_DATA) public data: any
@@ -40,7 +43,12 @@ export class BulkActionDialogComponent implements OnInit {
       this.altStatusCount = 0;
     Object.keys(this.records).forEach(record => {
       if(this.records[record].checked) {
-        const temp = {"ID": record, "checked": true, "name": this.records[record].name};
+        let temp = {};
+        if (this.records[record].substance) {
+          temp = {"ID": record, "checked": true, "name": this.records[record].substance._name};
+        } else {
+          temp = {"ID": record, "checked": true, "name": this.records[record].name};
+        }
         this.filtered.push(temp);
         /*f (this.records[record].substance && this.records[record].substance._metadata && this.records[record].substance._metadata.importStatus
             && this.records[record].substance._metadata.importStatus !== 'staged') {
@@ -55,6 +63,11 @@ export class BulkActionDialogComponent implements OnInit {
 
 
   ngOnInit(): void {
+    if (this.configService.configData && this.configService.configData.stagingArea) {
+      if (this.configService.configData.stagingArea.mergeAction) {
+        this.showMerge = this.configService.configData.stagingArea.mergeAction
+      }
+    }
   }
 
   deleteStagedRecords(): void {

src/app/core/admin/import-browse/import-browse.component.ts

@@ -266,11 +266,10 @@ export class ImportBrowseComponent implements OnInit, AfterViewInit, OnDestroy {
         });
     } else {
       this.substances.forEach(record => {
-        console.log(record);
-          if (this.bulkList[record.id]) {
+          if (record.id && this.bulkList[record.id]) {
             this.bulkList[record.id].checked = true;
           } else {
-            this.bulkList[record.id.recordId] = {"checked": true, "name": record.name, "id": record.id};
+            this.bulkList[record.id] = {"checked": true, "name": record.name, "id": record.id};
           }
 
       });

src/app/core/admin/import-browse/import-summary/import-summary.component.html

@@ -367,7 +367,7 @@
               <span><a class ="action-button" color = "primary" [disabled] = "disabled"  mat-button mat-flat-button mat-primary-button 
                 [routerLink]="['/substances/register']"
               [queryParams]="{stagingID : substance._metadata.recordId}">Edit</a></span>
-            <span  ><button  class ="action-button" [disabled] = "disabled"  color = "primary" mat-button mat-flat-button mat-primary-button
+            <span  ><button *ngIf = "showMerge" class ="action-button" [disabled] = "disabled || !showMerge"  color = "primary" mat-button mat-flat-button mat-primary-button
                (click) = "openMergeModal()">Merge</button></span>
             <span><button class ="action-button" color = "primary" [disabled] = "disabled"  mat-button mat-flat-button mat-primary-button 
               (click) = "doAction('reject')">Reject</button></span>
@@ -411,7 +411,7 @@
                     </ng-container>-->
                     <ng-container matColumnDef="merge">
                       <th mat-header-cell *matHeaderCellDef>  </th>
-                      <td mat-cell *matCellDef="let record"> <span ><button class = "action-button" color = "primary" (click) = "openMergeModal(record)" mat-button mat-flat-button mat-primary-button  [disabled] = "disabled" >Merge</button></span></td>
+                      <td mat-cell *matCellDef="let record"> <span ><button class = "action-button" *ngIf = "showMerge" color = "primary" (click) = "openMergeModal(record)" mat-button mat-flat-button mat-primary-button  [disabled] = "disabled || !showMerge" >Merge</button></span></td>
                     </ng-container>
 
                     <tr mat-header-row *matHeaderRowDef="displayedColumns"></tr>

src/app/core/admin/import-browse/import-summary/import-summary.component.ts

@@ -75,6 +75,7 @@ export class ImportSummaryComponent implements OnInit {
   displayedColumns2 = ['type', 'message'];
   message = "";
   private privateMatches: any;
+  showMerge = false;
 
   disabled = false;
   performedAction: string;
@@ -130,11 +131,18 @@ export class ImportSummaryComponent implements OnInit {
     if (this.configService.configData && this.configService.configData.molWeightRounding) {
       this.rounding = '1.0-' + this.configService.configData.molWeightRounding;
     }
+
+    if (this.configService.configData && this.configService.configData.stagingArea) {
+      if (this.configService.configData.stagingArea.mergeAction) {
+        this.showMerge = this.configService.configData.stagingArea.mergeAction
+      }
+    }
   //  this.privateMatches = JSON.parse(JSON.stringify(this.substance.matchedRecords)).slice(0, 5);
   }
 
 
   matchFieldsToCount(matches: any) {
+    console.log(matches);
     matches.forEach(match => {
       let newArr: Array<any> = [];
       match.records.forEach(record => {
@@ -180,21 +188,34 @@ export class ImportSummaryComponent implements OnInit {
     return this.privateBulkAction;
   }
 
-  getMatchSummary() {
-    this.substance.matchedRecords.forEach(record => {
-      console.log(record);
+  changePage(event: PageEvent) {
+    this.pageSize = event.pageSize;
+    this.pageIndex = event.pageIndex;
+    const skip = event.pageSize * event.pageIndex;
+      this.privateMatches = JSON.parse(JSON.stringify(this.substance.matchedRecords)).slice(skip, (this.pageSize + skip));
+      this.matchFieldsToCount(this.privateMatches);
+
+      this.getMatchSummary();
+
+  }
+
+  getMatchSummary(skip?: any) {
+    if (!skip) {
+      this.privateMatches = JSON.parse(JSON.stringify(this.substance.matchedRecords)).slice(0, 5);
+      this.matchFieldsToCount(this.privateMatches);
+    }
+
+    this.privateMatches.forEach(record => {
       if (record.source && record.source === 'Staging Area'){
         this.adminService.GetStagedRecord(record.ID).subscribe(response => {
           record._name = response._name;
-          this.privateMatches = JSON.parse(JSON.stringify(this.substance.matchedRecords)).slice(0, 5);
         }, error => {
           console.log(error);
         })
       } else {
         this.substanceService.getSubstanceSummary(record.ID).subscribe(response => {
           record.uuid = response.uuid;
           record._name = response._name;
-          this.privateMatches = JSON.parse(JSON.stringify(this.substance.matchedRecords)).slice(0, 5);
         }, error => {
           console.log(error);
         });
@@ -284,14 +305,14 @@ export class ImportSummaryComponent implements OnInit {
   }
 
   doAction(action: string, mergeID?: string) {
-
+    console.log(action);
     this.displayAction = action;
     this.loadingService.setLoading(true);
     this.adminService.stagedRecordSingleAction(this.privateSubstance._metadata.recordId, action).subscribe(result => {
       if (result.jobStatus === 'completed') {
         this.loadingService.setLoading(false);
         this.doneAction.emit(this.privateSubstance.uuid);
-        this.message = "Record " + action + "  successful";
+        this.message = this.displayAction + " record action completed successfully";
         if (result) {
           this.disabled = true;
           this.performedAction = action;
@@ -328,8 +349,8 @@ export class ImportSummaryComponent implements OnInit {
       if (response.jobStatus === 'completed') {
              this.loadingService.setLoading(false);
               this.doneAction.emit(this.privateSubstance.uuid);
-      this.message = "Record " + action + "  successful";
-      if (result) {
+              this.message = this.displayAction + " record action completed successfully";
+              if (result) {
         this.disabled = true;
         this.performedAction = action;
       }
@@ -476,7 +497,8 @@ export class ImportSummaryComponent implements OnInit {
     const dialogRef = this.dialog.open(MergeActionDialogComponent, {
       minWidth: '50%',
       maxWidth: '90%',
-      height: '80%',
+      minHeight: '600px',
+      maxHeight: '90%',
       data: temp
     });
     this.overlayContainer.style.zIndex = '1002';
@@ -502,13 +524,7 @@ export class ImportSummaryComponent implements OnInit {
     this.showLessCodes = !this.showLessCodes;
   }
 
-  changePage(event: PageEvent) {
-    this.pageSize = event.pageSize;
-    this.pageIndex = event.pageIndex;
-    const skip = event.pageSize * event.pageIndex;
-      this.privateMatches = JSON.parse(JSON.stringify(this.substance.matchedRecords)).slice(skip, (this.pageSize + skip));
-
-  }
+
 
 
 }

src/app/core/admin/import-browse/merge-action-dialog/merge-action-dialog.component.html

@@ -1,5 +1,5 @@
-<h3 mat-dialog-header>Staging Record Merge</h3>
-<div mat-dialog-content style = "min-height:525px" >
+<h3 mat-dialog-header>Staging Record Merge <span class = "experimental-label">(experimental)</span></h3>
+<div mat-dialog-content style = "min-height:500px" >
     <div *ngIf = "!loading && !completed">
 <sf-form  [schema]="mergeSchema"  [model]="mergeModel" (onChange)="checkValue($event.value)" class = "top-margin"></sf-form>
 <div style = "margin-top:25px;" *ngIf = "!data.mergeRecord"><b>Select a record to merge into</b>
@@ -37,18 +37,18 @@ <h3 mat-dialog-header>Staging Record Merge</h3>
 </div>
 
 
-<div mat-dialog-actions style = "height: 50px;">
+<div mat-dialog-actions style = "min-height: 50px;">
      <div *ngIf = "success" style = "display:flex;width:100%">
             <span class = "middle-fill"></span> 
 
         <button  mat-button mat-flat-button color = "primary" [disabled] = "!(toMerge && toMerge !== null) || completed" (click) = "submit()">Submit</button> &nbsp; 
-        <button mat-button mat-flat-button color = "primary" mat-dialog-close>Cancel</button>
+        <button mat-button mat-flat-button color = "primary" mat-dialog-close (click) = "dialogRef.close()">Cancel</button>
      </div>
      <div *ngIf = "!success" style = "display:flex;width:100%">
             <button mat-button mat-flat-button color = "primary" (click) ="restart()" >Restart</button>
 
             <span class = "middle-fill"></span> 
 
-        <button mat-button mat-flat-button color = "primary" mat-dialog-close>Close</button>
+        <button mat-button mat-flat-button color = "primary" mat-dialog-close (click) = "dialogRef.close()">Close</button>
      </div>
     </div>

src/app/core/admin/import-browse/merge-action-dialog/merge-action-dialog.component.scss

@@ -5,6 +5,11 @@
     margin-top: 20px;
 }
 
+.experimental-action-label {
+    font-weight:500; 
+    margin-left: 25px;
+}
+
 .spinner {
     width: 100px !important;
 height: 100px !important;

src/app/core/admin/import-browse/merge-action-dialog/merge-action-dialog.component.ts

@@ -25,7 +25,6 @@ export class MergeActionDialogComponent implements OnInit {
   ) {
     console.log(data);
     if(data.recordId) {
-      console.log(data.recordId);
 
       this.entity = data.recordId;
       this.matches = data.matches;
@@ -47,7 +46,6 @@ export class MergeActionDialogComponent implements OnInit {
   getMergeSchema() {
     this.adminService.getMergeActionSchema().subscribe(response => {
       this.mergeSchema = response;
-      console.log(response);
     });
   }
 
@@ -77,8 +75,9 @@ export class MergeActionDialogComponent implements OnInit {
     refresh(id: string): void {
       this.adminService.processingstatus(id).subscribe(response => {
         if (response.results) {
+          this.success = response.completeSuccess;
           response.results.forEach(result => {
-            this.success = result.success;
+
 
             if(!this.success) {
               let temp = result.message;

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

@@ -55,6 +55,11 @@ export interface Config {
     bulkSearch?: any
     useDataUrl?: any;
     userProfile?: any;
+    stagingArea?: StagingAreaSettings;
+}
+
+export interface StagingAreaSettings {
+    mergeAction?: boolean;
 }
 
 export interface LoadedComponents {

src/app/core/home/home.component.html

@@ -79,8 +79,8 @@ <h2 class = "quick-links">Quick Links</h2>
                                     <a mat-list-item routerLink="/browse-adverse-events">
                                       <mat-icon matListIcon svgIcon="glasses"></mat-icon>
                                       Browse Adverse Events
-                                    </a>Other
-                                </span>Other
+                                    </a>
+                                </span>
                               <div *ngIf="adverseEventShOtherinyHomepageDisplay === true">
                                 <mat-divider></mat-divider>
                                 <a mat-list-item [href]="adverseEventShinyHomepageURL" target="_blank">
@@ -364,7 +364,7 @@ <h3 class = "resource-link">
         </div>
         <div mat-dialog-actions>
             <span class="middle-fill"></span>
-            <button class="mat-raised-button mat-primary" mat-dialog-close>Close</button>
+            <button class="mat-raised-button mat-primary" (click) = "dialogRef.close()" mat-dialog-close>Close</button>
         </div>
     </ng-template>
 

src/app/core/substance-details/substance-codes/substance-codes.component.html

@@ -91,7 +91,7 @@
     <ng-container matColumnDef="comments">
       <th mat-header-cell *matHeaderCellDef  mat-sort-header> Comments  </th>
       <td mat-cell *matCellDef="let code">
-          <button class = "mat-button mat-raised-button" color = "primary" (click)="openModal(commentTemplate)"
+          <button class = "mat-button mat-primary mat-raised-button" color = "primary" (click)="openModal(commentTemplate)"
             [ngClass] = "(!code.comments && !code.codeText) ? 'mat-button-disabled':''"
           [disabled] = "!code.comments && !code.codeText" >{{!code.comments && !code.codeText ? 'None' : 'View'}}</button>  
           <ng-template #commentTemplate>
@@ -108,7 +108,7 @@ <h2 mat-dialog-title>Code Comments</h2>
                </div>
               <div mat-dialog-actions>
                 <span class="middle-fill"></span>
-                <button class="mat-raised-button mat-primary" mat-dialog-close>Close</button>
+                <button class="mat-raised-button mat-primary" (click) = "close()" mat-dialog-close>Close</button>
               </div>
 
             </ng-template>

src/app/core/substance-form/substance-form.component.html

@@ -96,7 +96,7 @@
 
         <div mat-dialog-actions>
             <span class="middle-fill"></span>
-            <button class="mat-raised-button mat-primary" mat-dialog-close>Close</button>
+            <button class="mat-raised-button mat-primary" mat-dialog-close (click) = "dialogRef.close()">Close</button>
           </div>
       </ng-template>
 

src/app/core/substance-form/substance-form.component.ts

@@ -344,10 +344,14 @@ export class SubstanceFormComponent implements OnInit, AfterViewInit, OnDestroy
                   this.status = response.status;
                   this.substanceFormService.loadSubstance(response.substanceClass, response).pipe(take(1)).subscribe(() => {
                     this.setFormSections(formSections[response.substanceClass]);
+                    this.isLoading = false;
+                    this.loadingService.setLoading(false);
                   });
 
               }
             }, error => {
+              this.isLoading = false;
+              this.loadingService.setLoading(false);
               });  
        }  else {
           this.copy = this.activatedRoute.snapshot.queryParams['copy'] || null;

src/app/core/substance-form/substance-form.service.ts

@@ -1305,11 +1305,13 @@ export class SubstanceFormService implements OnDestroy {
             for (let i = 0; i < substanceCopy.modifications.physicalModifications.length; i++) {
               const prop = substanceCopy.modifications.physicalModifications[i];
               let present = false;
-              prop.parameters.forEach(param => {
-                if (param.parameterName) {
-                  present = true;
-                }
-              });
+              if (prop && prop.parameters){
+                prop.parameters.forEach(param => {
+                  if (param.parameterName) {
+                    present = true;
+                  }
+                });
+              }
 
               if (!prop.physicalModificationRole && !present) {
                 const invalidPropertyMessage: ValidationMessage = {