From e39eebe4ac12f37cd8087f473f2a07cf4d88f730 Mon Sep 17 00:00:00 2001
From: Srujithchaithanya1 <srujithchaithanya@gmail.com>
Date: Sat, 28 Mar 2026 16:58:31 +0530
Subject: [PATCH 1/3] handled deleted Instances

---
 .../src/app/search/search.component.html      | 22 ++++++++++--
 .../src/app/search/search.component.scss      |  6 ++++
 .../src/app/search/search.component.ts        | 34 +++++++++++++++++--
 .../src/services/search.service.ts            |  1 +
 4 files changed, 59 insertions(+), 4 deletions(-)

diff --git a/projects/website-angular/src/app/search/search.component.html b/projects/website-angular/src/app/search/search.component.html
index b77b750..1ec5204 100644
--- a/projects/website-angular/src/app/search/search.component.html
+++ b/projects/website-angular/src/app/search/search.component.html
@@ -281,8 +281,26 @@ <h2>{{ group.typeName }} ({{ group.entriesCount }})</h2>
                           @for (entry of group.entries; track entry.dbId) {
                             <div class="search-entry">
                               <div class="entry-header">
-                                <a class="entry-name" [routerLink]="getDetailLink(entry)" [innerHTML]="entry.name"></a>
-                                <span class="entry-id">{{ entry.stId }}</span>
+                                @if (entry.deleted) {
+                                  <span>❌</span>
+                                  <span class="deleted" [innerHTML]="entry.stId"></span>
+                                  @if (entry.replacementStIds?.length) {
+                                    ⇒
+                                    <a
+                                      [routerLink]="['/content/detail', entry.replacementStIds[0]]"
+                                      title="Go to replacement">
+                                      {{ entry.replacementStIds[0] }}
+                                    </a>
+                                  }
+
+                                } @else {
+                                  <a class="entry-name"
+                                    [routerLink]="getDetailLink(entry)"
+                                    [innerHTML]="entry.name">
+                                  </a>
+                                  <span class="entry-id">{{ entry.stId }}</span>
+                                }
+
                               </div>
                               @if (entry.species?.length) {
                                 <div class="entry-species">
diff --git a/projects/website-angular/src/app/search/search.component.scss b/projects/website-angular/src/app/search/search.component.scss
index ed74920..261fce0 100644
--- a/projects/website-angular/src/app/search/search.component.scss
+++ b/projects/website-angular/src/app/search/search.component.scss
@@ -73,6 +73,12 @@ $border-radius: 8px;
   align-items: flex-start;
 }
 
+.deleted {
+  text-decoration: line-through;
+  color: #555;
+}
+
+
 // Facet sidebar
 .facet-sidebar {
   width: 260px;
diff --git a/projects/website-angular/src/app/search/search.component.ts b/projects/website-angular/src/app/search/search.component.ts
index 8f8abb4..54cfaad 100644
--- a/projects/website-angular/src/app/search/search.component.ts
+++ b/projects/website-angular/src/app/search/search.component.ts
@@ -199,7 +199,26 @@ export class SearchComponent implements OnInit, OnDestroy, AfterViewInit {
           this.hasNoResults = false;
         } else {
           // Successful API response - check if we have results
-          this.results = results as SearchResult;
+          const res = results as SearchResult;
+          const hasNonDeleted = res.results?.some(group =>
+            group.entries.some(e => !e.deleted)
+          );
+          res.results = res.results?.map(group => {
+            const entries = hasNonDeleted
+              ? group.entries.filter(e => !e.deleted)
+              : group.entries;
+
+            return {
+              ...group,
+              entries,
+              entriesCount: entries.length
+            };
+          }).filter(group => group.entries.length > 0) || [];
+          res.numberOfMatches = res.results.reduce(
+            (sum, g) => sum + g.entries.length,
+            0
+          );
+          this.results = res;
           this.facets = facets;
           this.totalPages = Math.ceil(((results as SearchResult).numberOfMatches || 0) / this.pageSize);
           this.hasNoResults = ((results as SearchResult).numberOfMatches || 0) === 0;
@@ -233,7 +252,7 @@ export class SearchComponent implements OnInit, OnDestroy, AfterViewInit {
 
   get allEntries(): SearchEntry[] {
     if (!this.results?.results) return [];
-    return this.results.results.flatMap(g => g.entries);
+    return this.results.results.flatMap(g => this.filterDeletedEntries(g.entries));
   }
 
   toggleFacet(category: string, value: string): void {
@@ -272,6 +291,17 @@ export class SearchComponent implements OnInit, OnDestroy, AfterViewInit {
     this.advancedMode = !this.advancedMode;
   }
 
+  private filterDeletedEntries(entries: SearchEntry[]): SearchEntry[] {
+    if (!entries?.length) return [];
+
+    const nonDeleted = entries.filter(e => !e.deleted);
+    if (nonDeleted.length > 0) {
+      return nonDeleted;
+    }
+
+    return entries;
+  }
+
   private updateQueryParams(params: Record<string, string | string[] | null>): void {
     this.router.navigate([], {
       relativeTo: this.route,
diff --git a/projects/website-angular/src/services/search.service.ts b/projects/website-angular/src/services/search.service.ts
index 2f51072..f3c4650 100644
--- a/projects/website-angular/src/services/search.service.ts
+++ b/projects/website-angular/src/services/search.service.ts
@@ -16,6 +16,7 @@ export interface SearchEntry {
   referenceIdentifier: string;
   databaseName: string;
   referenceURL: string;
+  deleted: string;
 }
 
 export interface ResultGroup {

From 98f485759ede2d0bbde378986c8034d94882b555 Mon Sep 17 00:00:00 2001
From: Srujithchaithanya1 <srujithchaithanya@gmail.com>
Date: Sat, 28 Mar 2026 16:59:18 +0530
Subject: [PATCH 2/3] changed interface

---
 .../src/app/viewport/search/search.component.ts                | 3 ++-
 1 file changed, 2 insertions(+), 1 deletion(-)

diff --git a/projects/pathway-browser/src/app/viewport/search/search.component.ts b/projects/pathway-browser/src/app/viewport/search/search.component.ts
index 57fa02e..60e6dad 100644
--- a/projects/pathway-browser/src/app/viewport/search/search.component.ts
+++ b/projects/pathway-browser/src/app/viewport/search/search.component.ts
@@ -487,7 +487,8 @@ export namespace Search {
       isDisease: boolean;
       hasEHLD?: boolean;
       hasReferenceEntity: boolean;
-      disease: boolean
+      disease: boolean;
+      deleted: boolean;
     }
 
     export interface EntryResult {

From fab89a9c3c147d5edc6bf94061870c34179f195c Mon Sep 17 00:00:00 2001
From: Srujithchaithanya1 <srujithchaithanya@gmail.com>
Date: Sat, 28 Mar 2026 17:34:06 +0530
Subject: [PATCH 3/3] added deleted date and fixes Deleted Instance Handling in
 Search Fixes #35

---
 .../src/app/viewport/search/search.component.ts             | 1 +
 .../website-angular/src/app/search/search.component.html    | 6 ++++++
 projects/website-angular/src/app/search/search.component.ts | 3 ++-
 projects/website-angular/src/services/search.service.ts     | 3 ++-
 4 files changed, 11 insertions(+), 2 deletions(-)

diff --git a/projects/pathway-browser/src/app/viewport/search/search.component.ts b/projects/pathway-browser/src/app/viewport/search/search.component.ts
index 60e6dad..d9185f4 100644
--- a/projects/pathway-browser/src/app/viewport/search/search.component.ts
+++ b/projects/pathway-browser/src/app/viewport/search/search.component.ts
@@ -489,6 +489,7 @@ export namespace Search {
       hasReferenceEntity: boolean;
       disease: boolean;
       deleted: boolean;
+      date: number;
     }
 
     export interface EntryResult {
diff --git a/projects/website-angular/src/app/search/search.component.html b/projects/website-angular/src/app/search/search.component.html
index 1ec5204..7e2993e 100644
--- a/projects/website-angular/src/app/search/search.component.html
+++ b/projects/website-angular/src/app/search/search.component.html
@@ -302,6 +302,12 @@ <h2>{{ group.typeName }} ({{ group.entriesCount }})</h2>
                                 }
 
                               </div>
+                              @if (entry.deleted && entry.date) {
+                                <div class="deleted-date">
+                                  <b>Deleted on</b>
+                                  {{ entry.date | date:'MMM d, y, h:mm:ss a' }}
+                                </div>
+                              }
                               @if (entry.species?.length) {
                                 <div class="entry-species">
                                   @for (sp of entry.species; track sp; let last = $last) {
diff --git a/projects/website-angular/src/app/search/search.component.ts b/projects/website-angular/src/app/search/search.component.ts
index 54cfaad..fcb62c9 100644
--- a/projects/website-angular/src/app/search/search.component.ts
+++ b/projects/website-angular/src/app/search/search.component.ts
@@ -15,11 +15,12 @@ import {
   SearchFilters,
   FacetCount,
 } from '../../services/search.service';
+import { DatePipe } from '@angular/common';
 
 @Component({
   selector: 'app-search',
   standalone: true,
-  imports: [PageLayoutComponent, TileComponent, RouterLink, SearchBarComponent, FormsModule],
+  imports: [PageLayoutComponent, TileComponent, RouterLink, SearchBarComponent, FormsModule, DatePipe],
   templateUrl: './search.component.html',
   styleUrl: './search.component.scss',
 })
diff --git a/projects/website-angular/src/services/search.service.ts b/projects/website-angular/src/services/search.service.ts
index f3c4650..0c35f90 100644
--- a/projects/website-angular/src/services/search.service.ts
+++ b/projects/website-angular/src/services/search.service.ts
@@ -16,7 +16,8 @@ export interface SearchEntry {
   referenceIdentifier: string;
   databaseName: string;
   referenceURL: string;
-  deleted: string;
+  deleted: boolean;
+  date: number;
 }
 
 export interface ResultGroup {