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Add API and CLI command for getting by indexed id
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‎.github/workflows/pull_request.yml‎

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@@ -46,7 +46,7 @@ jobs:
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- name: Start apollo
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run: |
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yarn --cwd packages/apollo-shared start &
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ALLOW_ROOT_USER=true ROOT_USER_PASSWORD=pass yarn --cwd packages/apollo-collaboration-server start &
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yarn --cwd packages/apollo-collaboration-server test:cli:start &
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- name: Run CLI tests
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run: yarn test:cli
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working-directory: packages/apollo-cli

‎packages/apollo-cli/README.md‎

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@@ -48,6 +48,7 @@ USAGE
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- [`apollo feature edit-type`](#apollo-feature-edit-type)
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- [`apollo feature get`](#apollo-feature-get)
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- [`apollo feature get-id`](#apollo-feature-get-id)
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- [`apollo feature get-indexed-id ID`](#apollo-feature-get-indexed-id-id)
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- [`apollo feature import INPUT-FILE`](#apollo-feature-import-input-file)
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- [`apollo feature search`](#apollo-feature-search)
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- [`apollo file delete`](#apollo-file-delete)
@@ -705,6 +706,38 @@ EXAMPLES
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_See code:
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[src/commands/feature/get-id.ts](https://github.com/GMOD/Apollo3/blob/v0.3.9/packages/apollo-cli/src/commands/feature/get-id.ts)_
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## `apollo feature get-indexed-id ID`
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Get features given an indexed identifier
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```
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USAGE
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$ apollo feature get-indexed-id ID [--profile <value>] [--config-file <value>] [-a <value>] [--topLevel]
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ARGUMENTS
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ID Indexed identifier to search for
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FLAGS
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-a, --assembly=<value>... Assembly names or IDs to search; use "-" to read it from stdin. If omitted search all
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assemblies
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--config-file=<value> Use this config file (mostly for testing)
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--profile=<value> Use credentials from this profile
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--topLevel Return the top-level parent of the feature instead of the feature itself
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DESCRIPTION
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Get features given an indexed identifier
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Get features that match a given indexed identifier, such as the ID of a feature from an imported GFF3 file
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EXAMPLES
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Get features for this indexed identifier:
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$ apollo feature get-indexed-id -i abc...zyz def...foo
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```
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_See code:
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[src/commands/feature/get-indexed-id.ts](https://github.com/GMOD/Apollo3/blob/v0.3.9/packages/apollo-cli/src/commands/feature/get-indexed-id.ts)_
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## `apollo feature import INPUT-FILE`
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Import features from local gff file

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

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@@ -0,0 +1,96 @@
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import { Args, Flags } from '@oclif/core'
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import { fetch } from 'undici'
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import { BaseCommand } from '../../baseCommand.js'
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import {
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convertAssemblyNameToId,
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createFetchErrorMessage,
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idReader,
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localhostToAddress,
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} from '../../utils.js'
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export default class Get extends BaseCommand<typeof Get> {
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static summary = 'Get features given an indexed identifier'
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static description =
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'Get features that match a given indexed identifier, such as the ID of a feature from an imported GFF3 file'
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static examples = [
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{
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description: 'Get features for this indexed identifier:',
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command: '<%= config.bin %> <%= command.id %> -i abc...zyz def...foo',
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},
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]
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static args = {
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id: Args.string({
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description: 'Indexed identifier to search for',
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required: true,
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}),
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}
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static flags = {
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assembly: Flags.string({
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char: 'a',
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multiple: true,
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description:
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'Assembly names or IDs to search; use "-" to read it from stdin. If omitted search all assemblies',
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}),
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topLevel: Flags.boolean({
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description:
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'Return the top-level parent of the feature instead of the feature itself',
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}),
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}
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public async run(): Promise<void> {
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const { args, flags } = await this.parse(Get)
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const access = await this.getAccess()
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const { topLevel } = flags
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const { id } = args
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const assembly = flags.assembly && (await idReader(flags.assembly))
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const assemblyIds =
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assembly &&
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(await convertAssemblyNameToId(
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access.address,
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access.accessToken,
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assembly,
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))
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if (assemblyIds?.length === 0) {
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this.log(JSON.stringify([], null, 2))
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this.exit(0)
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}
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const url = new URL(
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localhostToAddress(`${access.address}/features/getByIndexedId`),
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)
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const searchParams = new URLSearchParams({ id })
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if (assemblyIds) {
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searchParams.append('assemblies', assemblyIds.join(','))
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}
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if (topLevel) {
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searchParams.append('topLevel', 'true')
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}
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url.search = searchParams.toString()
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const uri = url.toString()
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const auth = {
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headers: {
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authorization: `Bearer ${access.accessToken}`,
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'Content-Type': 'application/json',
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},
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}
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const response = await fetch(uri, auth)
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if (!response.ok) {
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const errorMessage = await createFetchErrorMessage(
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response,
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'Failed to access Apollo with the current address and/or access token\nThe server returned:\n',
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)
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throw new Error(errorMessage)
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}
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const results = (await response.json()) as object
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this.log(JSON.stringify(results, null, 2))
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}
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}

‎packages/apollo-cli/src/test/test.ts‎

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@@ -774,6 +774,56 @@ void describe('Test CLI', () => {
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assert.ok(p.stdout.includes('"Q"'))
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})
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void globalThis.itName('Get feature by indexed ID', () => {
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new Shell(
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`${apollo} assembly add-from-gff ${P} test_data/tiny.fasta.gff3 -a vv1 -f`,
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)
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new Shell(
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`${apollo} assembly add-from-gff ${P} test_data/tiny.fasta.gff3 -a vv2 -f`,
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)
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// Search multiple assemblies
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let p = new Shell(`${apollo} feature get-indexed-id ${P} MyGene -a vv1 vv2`)
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let out = JSON.parse(p.stdout)
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assert.strictEqual(out.length, 2)
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assert.ok(p.stdout.includes('MyGene'))
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// Specifying no assembly defaults to searching all assemblies
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p = new Shell(`${apollo} feature get-indexed-id ${P} MyGene`)
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out = JSON.parse(p.stdout)
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assert.strictEqual(out.length, 2)
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assert.ok(p.stdout.includes('MyGene'))
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// Search single assembly
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p = new Shell(`${apollo} feature get-indexed-id ${P} MyGene -a vv1`)
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out = JSON.parse(p.stdout)
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assert.strictEqual(out.length, 1)
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assert.ok(p.stdout.includes('MyGene'))
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// Warn on unknown assembly
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p = new Shell(`${apollo} feature get-indexed-id ${P} EDEN -a foobar`)
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assert.strictEqual('[]', p.stdout.trim())
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assert.ok(p.stderr.includes('Warning'))
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// Return empty array with no matches
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p = new Shell(`${apollo} feature get-indexed-id ${P} foobarspam -a vv1`)
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assert.deepStrictEqual(p.stdout.trim(), '[]')
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// Gets subfeature
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p = new Shell(`${apollo} feature get-indexed-id ${P} myCDS.1 -a vv1`)
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out = JSON.parse(p.stdout)
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assert.strictEqual(out.length, 1)
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assert.ok(out.at(0)?.type === 'CDS')
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// Gets top-level feature from subfeature id
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p = new Shell(
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`${apollo} feature get-indexed-id ${P} myCDS.1 -a vv1 --topLevel`,
821+
)
822+
out = JSON.parse(p.stdout)
823+
assert.strictEqual(out.length, 1)
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assert.ok(out.at(0)?.type === 'gene')
825+
})
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777827
void globalThis.itName('Delete features', () => {
778828
new Shell(
779829
`${apollo} assembly add-from-gff ${P} test_data/tiny.fasta.gff3 -a vv1 -f`,

‎packages/apollo-collaboration-server/src/features/dto/feature.dto.ts‎

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@@ -4,3 +4,9 @@ export interface FeatureCountRequest {
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start?: number
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end?: number
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}
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export interface GetByIndexedIdRequest {
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id: string
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assemblies?: string
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topLevel?: boolean
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}

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

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@@ -11,7 +11,7 @@ import { FeatureRangeSearchDto } from '../entity/gff3Object.dto'
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import { Role } from '../utils/role/role.enum'
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import { Validations } from '../utils/validation/validatation.decorator'
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14-
import { FeatureCountRequest } from './dto/feature.dto'
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import { FeatureCountRequest, GetByIndexedIdRequest } from './dto/feature.dto'
1515
import { FeaturesService } from './features.service'
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1717
@Validations(Role.ReadOnly)
@@ -55,6 +55,11 @@ export class FeaturesController {
5555
return { count }
5656
}
5757

58+
@Get('getByIndexedId')
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async getById(@Query() getByIndexedIdRequest: GetByIndexedIdRequest) {
60+
return this.featuresService.getByIndexedId(getByIndexedIdRequest)
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}
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/**
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* 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.
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* @param featureid - featureId

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

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@@ -15,7 +15,7 @@ import { ChecksService } from '../checks/checks.service'
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import { FeatureRangeSearchDto } from '../entity/gff3Object.dto'
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import { OperationsService } from '../operations/operations.service'
1717

18-
import { FeatureCountRequest } from './dto/feature.dto'
18+
import { FeatureCountRequest, GetByIndexedIdRequest } from './dto/feature.dto'
1919

2020
@Injectable()
2121
export class FeaturesService {
@@ -70,6 +70,53 @@ export class FeaturesService {
7070
return count
7171
}
7272

73+
async getByIndexedId(getByIndexedIdRequest: GetByIndexedIdRequest) {
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const { assemblies, id, topLevel } = getByIndexedIdRequest
75+
const refSeqsQuery: { refSeq?: RefSeqDocument[] } = {}
76+
if (assemblies) {
77+
const assemblyIds = assemblies.split(',')
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const refSeqs = await this.refSeqModel
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.find({ assembly: assemblyIds })
80+
.exec()
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refSeqsQuery.refSeq = refSeqs
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}
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const topLevelFeatures = await this.featureModel
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.find({ indexedIds: id, ...refSeqsQuery })
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.exec()
86+
if (topLevelFeatures.length === 0) {
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return []
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}
89+
if (topLevel) {
90+
return topLevelFeatures
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}
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return topLevelFeatures
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.map((topLevelFeature) => this.findIndexedId(id, topLevelFeature))
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.filter((feature): feature is Feature => feature !== undefined)
95+
}
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findIndexedId(id: string, feature: FeatureDocument): Feature | undefined {
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const { attributes } = feature.toObject({
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flattenMaps: true,
100+
})
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if (attributes) {
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for (const attributeValue of Object.values(attributes)) {
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if (attributeValue.includes(id)) {
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return feature
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}
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}
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}
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if (!feature.children) {
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return
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}
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for (const [, childFeature] of feature.children) {
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const subFeature = this.findIndexedId(id, childFeature as FeatureDocument)
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if (subFeature) {
114+
return subFeature
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}
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}
117+
return
118+
}
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/**
74121
* 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.
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* @param featureId - featureId

‎packages/website/docs/admin/cli/feature.md‎

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@@ -12,6 +12,7 @@ Commands to manage features
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- [`apollo feature edit-type`](#apollo-feature-edit-type)
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- [`apollo feature get`](#apollo-feature-get)
1414
- [`apollo feature get-id`](#apollo-feature-get-id)
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- [`apollo feature get-indexed-id ID`](#apollo-feature-get-indexed-id-id)
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- [`apollo feature import INPUT-FILE`](#apollo-feature-import-input-file)
1617
- [`apollo feature search`](#apollo-feature-search)
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@@ -336,6 +337,38 @@ EXAMPLES
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_See code:
337338
[src/commands/feature/get-id.ts](https://github.com/GMOD/Apollo3/blob/v0.3.9/packages/apollo-cli/src/commands/feature/get-id.ts)_
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340+
## `apollo feature get-indexed-id ID`
341+
342+
Get features given an indexed identifier
343+
344+
```
345+
USAGE
346+
$ apollo feature get-indexed-id ID [--profile <value>] [--config-file <value>] [-a <value>] [--topLevel]
347+
348+
ARGUMENTS
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ID Indexed identifier to search for
350+
351+
FLAGS
352+
-a, --assembly=<value>... Assembly names or IDs to search; use "-" to read it from stdin. If omitted search all
353+
assemblies
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--config-file=<value> Use this config file (mostly for testing)
355+
--profile=<value> Use credentials from this profile
356+
--topLevel Return the top-level parent of the feature instead of the feature itself
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358+
DESCRIPTION
359+
Get features given an indexed identifier
360+
361+
Get features that match a given indexed identifier, such as the ID of a feature from an imported GFF3 file
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363+
EXAMPLES
364+
Get features for this indexed identifier:
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366+
$ apollo feature get-indexed-id -i abc...zyz def...foo
367+
```
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369+
_See code:
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[src/commands/feature/get-indexed-id.ts](https://github.com/GMOD/Apollo3/blob/v0.3.9/packages/apollo-cli/src/commands/feature/get-indexed-id.ts)_
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## `apollo feature import INPUT-FILE`
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Import features from local gff file

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