feat(agora): agora fixes (AG-1604) and Q4 2024 changes (AG-1605) (#2955)

apps/agora/api/src/components/genes.ts

@@ -164,7 +164,7 @@ export async function genesRoute(req: Request, res: Response, next: NextFunction
   try {
     const result = await getGenes(<string | string[]>req.query.ids);
     setHeaders(res);
-    res.json({ items: result });
+    res.json(result);
   } catch (err) {
     next(err);
   }

apps/agora/api/src/models/genes.ts

@@ -53,7 +53,7 @@ const DruggabilitySchema = new Schema<Druggability>({
   sm_druggability_bucket: { type: Number, required: true },
   safety_bucket: { type: Number, required: true },
   abability_bucket: { type: Number, required: true },
-  pharos_class: { type: String, required: true },
+  pharos_class: { type: [String], required: true },
   classification: { type: String, required: true },
   safety_bucket_definition: { type: String, required: true },
   abability_bucket_definition: { type: String, required: true },
@@ -67,6 +67,7 @@ const GeneSchema = new Schema<Gene>(
     summary: { type: String, required: true },
     hgnc_symbol: { type: String, required: true },
     alias: [{ type: String, required: true }],
+    uniprotkb_accessions: [{ type: String, required: true }],
     is_igap: { type: Boolean, required: true },
     is_eqtl: { type: Boolean, required: true },
     is_any_rna_changed_in_ad_brain: { type: Boolean, required: true },
@@ -75,7 +76,7 @@ const GeneSchema = new Schema<Gene>(
     protein_brain_change_studied: { type: Boolean, required: true },
     target_nominations: { type: [TargetNominationSchema], required: true },
     median_expression: { type: [MedianExpressionSchema], required: true },
-    druggability: { type: [DruggabilitySchema], required: true },
+    druggability: { type: DruggabilitySchema, required: true },
     total_nominations: { type: Number, required: true },
     ensembl_info: { type: EnsemblInfoSchema, required: true },
   },

apps/agora/app/src/app/app.component.html

@@ -6,4 +6,3 @@
   <agora-footer></agora-footer>
 </div>
 <p-toast class="global-toast" position="bottom-center"></p-toast>
-<agora-loading-overlay [isGlobal]="true"></agora-loading-overlay>

apps/agora/app/src/app/app.component.ts

@@ -1,17 +1,13 @@
 import { Component, inject, OnInit } from '@angular/core';
 import { Meta, Title } from '@angular/platform-browser';
 import { ActivatedRoute, NavigationEnd, Router, RouterModule } from '@angular/router';
-import {
-  FooterComponent,
-  HeaderComponent,
-  LoadingOverlayComponent,
-} from '@sagebionetworks/agora/ui';
+import { FooterComponent, HeaderComponent } from '@sagebionetworks/agora/ui';
 import { filter } from 'rxjs';
 import { ToastModule } from 'primeng/toast';
 import { MessageService } from 'primeng/api';
 
 @Component({
-  imports: [RouterModule, HeaderComponent, FooterComponent, LoadingOverlayComponent, ToastModule],
+  imports: [RouterModule, HeaderComponent, FooterComponent, ToastModule],
   providers: [MessageService],
   selector: 'app-root',
   templateUrl: './app.component.html',

apps/agora/app/src/app/app.routes.ts

@@ -60,20 +60,25 @@ export const routes: Route[] = [
       description: 'Nominate a gene as a new candidate for AD treatment or prevention.',
     },
   },
+  {
+    path: 'genes/:id/similar',
+    loadChildren: () =>
+      import('@sagebionetworks/agora/genes').then((routes) => routes.similarRoute),
+  },
   {
     path: 'genes/:id/:tab/:subtab',
     loadChildren: () =>
-      import('@sagebionetworks/agora/gene-details').then((routes) => routes.routes),
+      import('@sagebionetworks/agora/genes').then((routes) => routes.detailsRoute),
   },
   {
     path: 'genes/:id/:tab',
     loadChildren: () =>
-      import('@sagebionetworks/agora/gene-details').then((routes) => routes.routes),
+      import('@sagebionetworks/agora/genes').then((routes) => routes.detailsRoute),
   },
   {
     path: 'genes/:id',
     loadChildren: () =>
-      import('@sagebionetworks/agora/gene-details').then((routes) => routes.routes),
+      import('@sagebionetworks/agora/genes').then((routes) => routes.detailsRoute),
     data: {
       title: 'Agora | Gene Details',
       description: "View information and evidence about genes in Alzheimer's disease.",

apps/agora/app/src/config/config.json

@@ -3,5 +3,6 @@
   "appVersion": "4.0.0",
   "csrApiUrl": "http://localhost:3333/v1",
   "ssrApiUrl": "http://agora-api:3333/v1",
-  "rollbarToken": "e788198867474855a996485580b08d03"
+  "rollbarToken": "e788198867474855a996485580b08d03",
+  "tagName": "agora/v0.0.2"
 }

apps/agora/app/src/config/config.json.template

@@ -3,5 +3,6 @@
   "appVersion": "${APP_VERSION}",
   "csrApiUrl": "${CSR_API_URL}",
   "ssrApiUrl": "${SSR_API_URL}",
-  "rollbarToken": "${ROLLBAR_TOKEN}"
+  "rollbarToken": "${ROLLBAR_TOKEN}",
+  "tagName": "${TAG_NAME}"
 }

apps/agora/data/.env.example

@@ -7,6 +7,6 @@ DB_HOST="agora-mongo" # must match mongo service name
 
 # specifies data release manifest and team images folder
 DATA_FILE="syn13363290"
-DATA_VERSION="68"
+DATA_VERSION="71"
 TEAM_IMAGES_ID="syn12861877"
 SYNAPSE_AUTH_TOKEN="agora-service-user-pat-here"

libs/agora/api-client-angular/src/lib/.openapi-generator/FILES

@@ -25,6 +25,7 @@ model/gCTGeneNominations.ts
 model/gCTGeneTissue.ts
 model/gCTGenesList.ts
 model/gene.ts
+model/geneNetworkLinks.ts
 model/genesList.ts
 model/medianExpression.ts
 model/models.ts

libs/agora/api-client-angular/src/lib/model/druggability.ts

@@ -17,7 +17,7 @@ export interface Druggability {
   sm_druggability_bucket: number;
   safety_bucket: number;
   abability_bucket: number;
-  pharos_class: string;
+  pharos_class: Array<string>;
   classification: string;
   safety_bucket_definition: string;
   abability_bucket_definition: string;

libs/agora/api-client-angular/src/lib/model/gene.ts

@@ -14,6 +14,7 @@ import { ExperimentalValidation } from './experimentalValidation';
 import { EnsemblInfo } from './ensemblInfo';
 import { RnaDifferentialExpression } from './rnaDifferentialExpression';
 import { BioDomains } from './bioDomains';
+import { GeneNetworkLinks } from './geneNetworkLinks';
 import { TargetNomination } from './targetNomination';
 import { NeuropathologicCorrelation } from './neuropathologicCorrelation';
 import { SimilarGenesNetwork } from './similarGenesNetwork';
@@ -31,6 +32,7 @@ export interface Gene {
   summary: string;
   hgnc_symbol: string;
   alias: Array<string>;
+  uniprotkb_accessions?: Array<string>;
   is_igap: boolean;
   is_eqtl: boolean;
   is_any_rna_changed_in_ad_brain: boolean;
@@ -39,7 +41,7 @@ export interface Gene {
   protein_brain_change_studied: boolean;
   target_nominations: Array<TargetNomination> | null;
   median_expression: Array<MedianExpression>;
-  druggability: Array<Druggability>;
+  druggability: Druggability;
   total_nominations: number | null;
   is_adi?: boolean;
   is_tep?: boolean;
@@ -52,12 +54,12 @@ export interface Gene {
   overall_scores?: OverallScores;
   neuropathologic_correlations?: Array<NeuropathologicCorrelation> | null;
   experimental_validation?: Array<ExperimentalValidation> | null;
-  links?: { [key: string]: object } | null;
+  links?: { [key: string]: GeneNetworkLinks } | null;
   similar_genes_network?: SimilarGenesNetwork;
   ab_modality_display_value?: string | null;
   safety_rating_display_value?: string | null;
   sm_druggability_display_value?: string | null;
-  pharos_class_display_value?: string | null;
+  pharos_class_display_value?: Array<string> | null;
   is_any_rna_changed_in_ad_brain_display_value?: string | null;
   is_any_protein_changed_in_ad_brain_display_value?: string | null;
   nominated_target_display_value?: boolean | null;

libs/agora/api-client-angular/src/lib/model/geneNetworkLinks.ts

@@ -0,0 +1,37 @@
+/**
+ * Agora REST API
+ * No description provided (generated by Openapi Generator https://github.com/openapitools/openapi-generator)
+ *
+ * The version of the OpenAPI document: 1.0.0
+ *
+ *
+ * NOTE: This class is auto generated by OpenAPI Generator (https://openapi-generator.tech).
+ * https://openapi-generator.tech
+ * Do not edit the class manually.
+ */
+
+/**
+ * Gene Network Links
+ */
+export interface GeneNetworkLinks {
+  /**
+   * Ensembl gene ID for gene A
+   */
+  geneA_ensembl_gene_id: string;
+  /**
+   * Ensembl gene ID for gene B
+   */
+  geneB_ensembl_gene_id: string;
+  /**
+   * External gene name for gene A
+   */
+  geneA_external_gene_name: string;
+  /**
+   * External gene name for gene B
+   */
+  geneB_external_gene_name: string;
+  /**
+   * Associated brain region
+   */
+  brainRegion: string;
+}

libs/agora/api-client-angular/src/lib/model/models.ts

@@ -12,6 +12,7 @@ export * from './gCTGeneNominations';
 export * from './gCTGeneTissue';
 export * from './gCTGenesList';
 export * from './gene';
+export * from './geneNetworkLinks';
 export * from './genesList';
 export * from './medianExpression';
 export * from './neuropathologicCorrelation';

libs/agora/api-description/build/openapi.yaml

@@ -421,8 +421,9 @@ components:
           type: integer
           example: 3
         pharos_class:
-          type: string
-          example: Tclin
+          type: array
+          items:
+            type: string
         classification:
           type: string
           example: Enzyme
@@ -622,6 +623,31 @@ components:
         - reference_doi
         - date_report
         - abability_bucket_definition
+    GeneNetworkLinks:
+      type: object
+      description: Gene Network Links
+      properties:
+        geneA_ensembl_gene_id:
+          type: string
+          description: Ensembl gene ID for gene A
+        geneB_ensembl_gene_id:
+          type: string
+          description: Ensembl gene ID for gene B
+        geneA_external_gene_name:
+          type: string
+          description: External gene name for gene A
+        geneB_external_gene_name:
+          type: string
+          description: External gene name for gene B
+        brainRegion:
+          type: string
+          description: Associated brain region
+      required:
+        - geneA_ensembl_gene_id
+        - geneB_ensembl_gene_id
+        - geneA_external_gene_name
+        - geneB_external_gene_name
+        - brainRegion
     SimilarGenesNetworkNode:
       type: object
       description: SimilarGenesNetworkNode
@@ -730,6 +756,10 @@ components:
           type: array
           items:
             type: string
+        uniprotkb_accessions:
+          type: array
+          items:
+            type: string
         is_igap:
           type: boolean
         is_eqtl:
@@ -752,9 +782,7 @@ components:
           items:
             $ref: '#/components/schemas/MedianExpression'
         druggability:
-          type: array
-          items:
-            $ref: '#/components/schemas/Druggability'
+          $ref: '#/components/schemas/Druggability'
         total_nominations:
           type: integer
           nullable: true
@@ -805,7 +833,7 @@ components:
         links:
           type: object
           additionalProperties:
-            type: object
+            $ref: '#/components/schemas/GeneNetworkLinks'
           nullable: true
         similar_genes_network:
           $ref: '#/components/schemas/SimilarGenesNetwork'
@@ -820,7 +848,9 @@ components:
           type: string
           nullable: true
         pharos_class_display_value:
-          type: string
+          type: array
+          items:
+            type: string
           nullable: true
         is_any_rna_changed_in_ad_brain_display_value:
           type: string

libs/agora/api-description/src/components/schemas/Druggability.yaml

@@ -11,8 +11,9 @@ properties:
     type: integer
     example: 3
   pharos_class:
-    type: string
-    example: 'Tclin'
+    type: array
+    items:
+      type: string
   classification:
     type: string
     example: 'Enzyme'

libs/agora/api-description/src/components/schemas/Gene.yaml

@@ -15,6 +15,10 @@ properties:
     type: array
     items:
       type: string
+  uniprotkb_accessions:
+    type: array
+    items:
+      type: string
   is_igap:
     type: boolean
   is_eqtl:
@@ -37,9 +41,7 @@ properties:
     items:
       $ref: MedianExpression.yaml
   druggability:
-    type: array
-    items:
-      $ref: Druggability.yaml
+    $ref: Druggability.yaml
   total_nominations:
     type: integer
     nullable: true
@@ -90,7 +92,7 @@ properties:
   links:
     type: object
     additionalProperties:
-      type: object
+      $ref: GeneNetworkLinks.yaml
     nullable: true
   similar_genes_network:
     $ref: SimilarGenesNetwork.yaml
@@ -105,7 +107,9 @@ properties:
     type: string
     nullable: true
   pharos_class_display_value:
-    type: string
+    type: array
+    items:
+      type: string
     nullable: true
   is_any_rna_changed_in_ad_brain_display_value:
     type: string

libs/agora/api-description/src/components/schemas/GeneNetworkLinks.yaml

@@ -0,0 +1,24 @@
+type: object
+description: Gene Network Links
+properties:
+  geneA_ensembl_gene_id:
+    type: string
+    description: 'Ensembl gene ID for gene A'
+  geneB_ensembl_gene_id:
+    type: string
+    description: 'Ensembl gene ID for gene B'
+  geneA_external_gene_name:
+    type: string
+    description: 'External gene name for gene A'
+  geneB_external_gene_name:
+    type: string
+    description: 'External gene name for gene B'
+  brainRegion:
+    type: string
+    description: 'Associated brain region'
+required:
+  - geneA_ensembl_gene_id
+  - geneB_ensembl_gene_id
+  - geneA_external_gene_name
+  - geneB_external_gene_name
+  - brainRegion