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Fix upper case querying of jbrowse 1 text search store #3548

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merged 1 commit into from
Feb 24, 2023
Merged

Fix upper case querying of jbrowse 1 text search store #3548

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103 changes: 71 additions & 32 deletions plugins/legacy-jbrowse/src/JBrowse1TextSearchAdapter/JBrowse1TextSearchAdapter.test.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -6,59 +6,98 @@ import last from '../../test_data/names/f.json'
import Adapter from './JBrowse1TextSearchAdapter'
import configSchema from './configSchema'

test('adapter can fetch files from names index', async () => {
function mockFetch(url: string): Promise<Response> {
let response = {}
if (url.includes('names/meta.json')) {
response = meta
}
if (url.includes('names/0.json')) {
response = first
}
if (url.includes('names/f.json')) {
response = last
}
return Promise.resolve(new Response(JSON.stringify(response)))
function mockFetch(url: string) {
let response = {}
if (url.includes('names/meta.json')) {
response = meta
}
if (url.includes('names/0.json')) {
response = first
}
if (url.includes('names/f.json')) {
response = last
}
return Promise.resolve(new Response(JSON.stringify(response)))
}

const rootTemplate = path
.join(__dirname, '..', '..', '..', '..', 'test_data', 'names')
.replace(/\\/g, '\\\\')
const rootTemplate = path
.join(__dirname, '..', '..', '..', '..', 'test_data', 'names')
.replace(/\\/g, '\\\\')

test('search upper case', async () => {
const spy = jest.spyOn(global, 'fetch')
// eslint-disable-next-line @typescript-eslint/no-explicit-any
spy.mockImplementation(mockFetch as any)

const urlPath = decodeURI(new URL(`file://${rootTemplate}`).href)
const args = {
type: 'JBrowse1TextSearchAdapter',
textSearchAdapterId: 'JBrowse1GenerateNamesAdapterTest',
namesIndexLocation: {
uri: urlPath,
locationType: 'UriLocation',
},
}
// create adapter
const adapter = new Adapter(configSchema.create(args))
// prefix search
const adapter = new Adapter(
configSchema.create({
type: 'JBrowse1TextSearchAdapter',
textSearchAdapterId: 'JBrowse1GenerateNamesAdapterTest',
namesIndexLocation: {
uri: decodeURI(new URL(`file://${rootTemplate}`).href),
locationType: 'UriLocation',
},
}),
)
const results = await adapter.searchIndex({
searchType: 'prefix',
queryString: 'Apple',
})
// check results are of type BaseResult for prefix search
expect(results.length).toBeGreaterThan(0)
expect(results[0] instanceof BaseResult).toBeTruthy()
expect(results[0].getLabel()).toEqual('Apple1')
expect(results[1].getLabel()).toEqual('Apple2')
expect(results[2].getLabel()).toEqual('Apple3')

// exact search
const results2 = await adapter.searchIndex({
searchType: 'exact',
queryString: 'Apple3',
})
// check results are of type location for exact search
expect(results2.length).toEqual(5)
expect(results2.length).toBeGreaterThan(0)
expect(results2[0] instanceof BaseResult).toBeTruthy()
expect(results2[0].getLabel()).toEqual('Apple3')
expect(results2[0].getLocation()).toEqual('ctgA:17399-23000')
})

test('search lower case', async () => {
const spy = jest.spyOn(global, 'fetch')
// eslint-disable-next-line @typescript-eslint/no-explicit-any
spy.mockImplementation(mockFetch as any)

const adapter = new Adapter(
configSchema.create({
type: 'JBrowse1TextSearchAdapter',
textSearchAdapterId: 'JBrowse1GenerateNamesAdapterTest',
namesIndexLocation: {
uri: decodeURI(new URL(`file://${rootTemplate}`).href),
locationType: 'UriLocation',
},
}),
)
const results = await adapter.searchIndex({
searchType: 'prefix',
queryString: 'apple',
})
// check results are of type BaseResult for prefix search
expect(results.length).toBeGreaterThan(0)
expect(results[0] instanceof BaseResult).toBeTruthy()
expect(results[0].getLabel()).toEqual('Apple1')
expect(results[1].getLabel()).toEqual('Apple2')
expect(results[2].getLabel()).toEqual('Apple3')

// exact search
const results2 = await adapter.searchIndex({
searchType: 'exact',
queryString: 'apple3',
})
// check results are of type location for exact search
expect(results2.length).toEqual(5)
const test2 = results2[0]
expect(test2 instanceof BaseResult).toBeTruthy()
expect(test2.getLabel()).toEqual('Apple3')
expect(test2.getLocation()).toEqual('ctgA:17399-23000')
expect(results2.length).toBeGreaterThan(0)
expect(results2[0] instanceof BaseResult).toBeTruthy()
expect(results2[0].getLabel()).toEqual('Apple3')
expect(results2[0].getLocation()).toEqual('ctgA:17399-23000')
})
49 changes: 24 additions & 25 deletions plugins/legacy-jbrowse/src/JBrowse1TextSearchAdapter/JBrowse1TextSearchAdapter.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -4,9 +4,10 @@ import {
BaseAdapter,
} from '@jbrowse/core/data_adapters/BaseAdapter'
import BaseResult from '@jbrowse/core/TextSearch/BaseResults'
import { Instance } from 'mobx-state-tree'
import { readConfObject } from '@jbrowse/core/configuration'
import MyConfigSchema from './configSchema'
import {
AnyConfigurationModel,
readConfObject,
} from '@jbrowse/core/configuration'
import HttpMap from './HttpMap'
import PluginManager from '@jbrowse/core/PluginManager'
import { getSubAdapterType } from '@jbrowse/core/data_adapters/dataAdapterCache'
Expand All @@ -23,7 +24,8 @@ interface SearchResults {

export type NamesIndexRecord = string | Array<string | number>

// Jbrowse1 text search adapter
type IndexFile = Record<string, SearchResults>

// Uses index built by generate-names.pl
export default class JBrowse1TextSearchAdapter
extends BaseAdapter
Expand All @@ -34,19 +36,15 @@ export default class JBrowse1TextSearchAdapter
tracksNames?: string[]

constructor(
config: Instance<typeof MyConfigSchema>,
config: AnyConfigurationModel,
getSubAdapter?: getSubAdapterType,
pluginManager?: PluginManager,
) {
super(config, getSubAdapter, pluginManager)
const namesIndexLocation = readConfObject(config, 'namesIndexLocation')
if (!namesIndexLocation) {
throw new Error('must provide namesIndexLocation')
}
const namesIndex = readConfObject(config, 'namesIndexLocation')
const { baseUri, uri } = namesIndex
this.httpMap = new HttpMap({
url: namesIndexLocation.baseUri
? new URL(namesIndexLocation.uri, namesIndexLocation.baseUri).href
: namesIndexLocation.uri,
url: baseUri ? new URL(uri, baseUri).href : uri,
})
}

Expand All @@ -55,30 +53,31 @@ export default class JBrowse1TextSearchAdapter
* else it returns empty
* @param query - string query
*/
async loadIndexFile(query: string): Promise<Record<string, SearchResults>> {
async loadIndexFile(query: string): Promise<IndexFile> {
return this.httpMap.getBucket(query)
}

async searchIndex(args: BaseArgs) {
const { searchType, queryString } = args
const tracks = this.tracksNames || (await this.httpMap.getTrackNames())
const entries = await this.loadIndexFile(queryString.toLowerCase())
if (entries[queryString]) {
return this.formatResults(entries[queryString], tracks, searchType)
}
return []
const str = queryString.toLowerCase()
const entries = await this.loadIndexFile(str)
return entries[str]
? this.formatResults(entries[str], tracks, searchType)
: []
}
formatResults(results: SearchResults, tracks: string[], searchType?: string) {
return [
...(searchType === 'exact'
? []
: results.prefix.map(result => {
return new BaseResult({
label: typeof result === 'object' ? result.name : result,
matchedAttribute: 'name',
matchedObject: { result: result },
})
})),
: results.prefix.map(
result =>
new BaseResult({
label: typeof result === 'object' ? result.name : result,
matchedAttribute: 'name',
matchedObject: { result: result },
}),
)),
...results.exact.map(result => {
const name = result[0]
const trackIndex = result[1]
Expand Down