fetch features by ids

Author: shashankbrgowda

packages/apollo-cli/README.md

@@ -16,7 +16,7 @@ $ npm install -g @apollo-annotation/cli
 $ apollo COMMAND
 running command...
 $ apollo (--version)
-@apollo-annotation/cli/0.3.9 linux-x64 node-v24.6.0
+@apollo-annotation/cli/0.3.9 darwin-x64 node-v20.19.0
 $ apollo --help [COMMAND]
 USAGE
   $ apollo COMMAND

packages/apollo-cli/src/commands/feature/get.ts

@@ -86,7 +86,9 @@ export default class Get extends BaseCommand<typeof Get> {
     start: number,
     end: number,
   ): Promise<Response> {
-    const url = new URL(localhostToAddress(`${address}/features/getFeatures`))
+    const url = new URL(
+      localhostToAddress(`${address}/features/getFeaturesByRange`),
+    )
     const searchParams = new URLSearchParams({
       refSeq,
       start: start.toString(),

packages/apollo-collaboration-server/src/entity/gff3Object.dto.ts

@@ -28,3 +28,8 @@ export interface FeatureRangeSearchDto {
   start: number
   end: number
 }
+
+export interface FeatureIdsSearchDto {
+  featureIds: string[]
+  topLevel?: boolean
+}

packages/apollo-collaboration-server/src/features/features.controller.ts

@@ -1,13 +1,18 @@
 import {
+  Body,
   Controller,
   Get,
   Logger,
   Param,
   ParseBoolPipe,
+  Post,
   Query,
 } from '@nestjs/common'
 
-import { FeatureRangeSearchDto } from '../entity/gff3Object.dto'
+import {
+  FeatureIdsSearchDto,
+  FeatureRangeSearchDto,
+} from '../entity/gff3Object.dto'
 import { Role } from '../utils/role/role.enum'
 import { Validations } from '../utils/validation/validatation.decorator'
 
@@ -36,15 +41,26 @@ export class FeaturesController {
    * @returns Return 'HttpStatus.OK' and array of features if search was successful
    * or if search data was not found or in case of error throw exception
    */
-  @Get('getFeatures')
-  getFeatures(@Query() request: FeatureRangeSearchDto) {
+  @Get('getFeaturesByRange')
+  getFeaturesByRange(@Query() request: FeatureRangeSearchDto) {
     this.logger.debug(
-      `getFeaturesByCriteria -method: refSeq: ${request.refSeq}, start: ${request.start}, end: ${request.end}`,
+      `getFeaturesByRange -method: refSeq: ${request.refSeq}, start: ${request.start}, end: ${request.end}`,
     )
 
     return this.featuresService.findByRange(request)
   }
 
+  @Post('getFeatures')
+  getFeatures(@Body() request: FeatureIdsSearchDto) {
+    this.logger.debug(
+      `getFeatures -method: featureIds: ${JSON.stringify(request.featureIds)}`,
+    )
+    return this.featuresService.findByFeatureIds(
+      request.featureIds,
+      request.topLevel,
+    )
+  }
+
   @Get('count')
   async getFeatureCount(@Query() featureCountRequest: FeatureCountRequest) {
     this.logger.debug(

packages/apollo-collaboration-server/src/features/features.service.ts

@@ -117,6 +117,26 @@ export class FeaturesService {
     return
   }
 
+  async findByFeatureIds(featureIds: string[], topLevel?: boolean) {
+    const foundFeatures: Feature[] = []
+    // all featureIds that have already been fetched
+    const fetchedFeatureIds = new Set<string>()
+
+    for (const featureId of featureIds) {
+      if (fetchedFeatureIds.has(featureId)) {
+        this.logger.debug(`FeatureId ${featureId} already fetched, skipping...`)
+        continue
+      }
+      const feature = await this.findById(featureId, topLevel)
+      foundFeatures.push(feature)
+
+      for (const id of feature.allIds) {
+        fetchedFeatureIds.add(id)
+      }
+    }
+    return foundFeatures
+  }
+
   /**
    * Get feature by featureId. When retrieving features by id, the features and any of its children are returned, but not any of its parent or sibling features.
    * @param featureId - featureId

packages/jbrowse-plugin-apollo/src/BackendDrivers/CollaborationServerDriver.ts

@@ -119,7 +119,7 @@ export class CollaborationServerDriver extends BackendDriver {
     ) as ApolloInternetAccount
     const { baseURL } = internetAccount
 
-    const url = new URL('features/getFeatures', baseURL)
+    const url = new URL('features/getFeaturesByRange', baseURL)
     const searchParams = new URLSearchParams({
       refSeq,
       start: String(start),