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Add ability to define custom aliases for refSeq names (#419)
* refname alias UI * refname alias UI * refname alias UI * refname alias UI * cleanup * refname alias cli * update alias on client session * update alias on client session * refname alias editable row * Standardize AddRefSeqAliasesChange --------- Co-authored-by: Garrett Stevens <stevens.garrett.j@gmail.com>
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,102 @@ | ||
| import * as fs from 'node:fs' | ||
| import { Agent, RequestInit, Response, fetch } from 'undici' | ||
| import { Flags } from '@oclif/core' | ||
| import { BaseCommand } from '../../baseCommand.js' | ||
| import { | ||
| createFetchErrorMessage, | ||
| localhostToAddress, | ||
| queryApollo, | ||
| wrapLines, | ||
| } from '../../utils.js' | ||
| import { ConfigError } from '../../ApolloConf.js' | ||
|
|
||
| export default class AddRefNameAlias extends BaseCommand< | ||
| typeof AddRefNameAlias | ||
| > { | ||
| static summary = 'Add reference name aliases from a file' | ||
| static description = wrapLines( | ||
| 'Reference name aliasing is a process to make chromosomes that are named slightly differently but which refer to the same thing render properly. This command reads a file with reference name aliases and adds them to the database.', | ||
| ) | ||
|
|
||
| static examples = [ | ||
| { | ||
| description: 'Add reference name aliases:', | ||
| command: '<%= config.bin %> <%= command.id %> -i alias.txt -a myAssembly', | ||
| }, | ||
| ] | ||
|
|
||
| static flags = { | ||
| 'input-file': Flags.string({ | ||
| char: 'i', | ||
| description: 'Input refname alias file', | ||
| required: true, | ||
| }), | ||
| assembly: Flags.string({ | ||
| char: 'a', | ||
| description: 'Name for this assembly.', | ||
| required: true, | ||
| }), | ||
| } | ||
|
|
||
| async run(): Promise<void> { | ||
| const { flags } = await this.parse(AddRefNameAlias) | ||
|
|
||
| if (!fs.existsSync(flags['input-file'])) { | ||
| this.error(`File ${flags['input-file']} does not exist`) | ||
| } | ||
|
|
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| const access: { address: string; accessToken: string } = | ||
| await this.getAccess(flags['config-file'], flags.profile) | ||
| const filehandle = await fs.promises.open(flags['input-file']) | ||
| const fileContent = await filehandle.readFile({ encoding: 'utf8' }) | ||
| await filehandle.close() | ||
| const lines = fileContent.split('\n') | ||
|
|
||
| const refNameAliases = [] | ||
| for (const line of lines) { | ||
| const [refName, ...aliases] = line.split('\t') | ||
| refNameAliases.push({ refName, aliases }) | ||
| } | ||
|
|
||
| const assemblies: Response = await queryApollo( | ||
| access.address, | ||
| access.accessToken, | ||
| 'assemblies', | ||
| ) | ||
| const json = (await assemblies.json()) as object[] | ||
| const assembly = json.find((x) => 'name' in x && x.name === flags.assembly) | ||
| const assemblyId = assembly && '_id' in assembly ? assembly._id : undefined | ||
|
|
||
| if (!assemblyId) { | ||
| this.error(`Assembly ${flags.assembly} not found`) | ||
| } | ||
|
|
||
| const change = { | ||
| typeName: 'AddRefSeqAliasesChange', | ||
| assembly: assemblyId, | ||
| refSeqAliases: refNameAliases, | ||
| } | ||
|
|
||
| const auth: RequestInit = { | ||
| method: 'POST', | ||
| body: JSON.stringify(change), | ||
| headers: { | ||
| Authorization: `Bearer ${access.accessToken}`, | ||
| 'Content-Type': 'application/json', | ||
| }, | ||
| dispatcher: new Agent({ headersTimeout: 60 * 60 * 1000 }), | ||
| } | ||
| const url = new URL(localhostToAddress(`${access.address}/changes`)) | ||
| const response = await fetch(url, auth) | ||
| if (!response.ok) { | ||
| const errorMessage = await createFetchErrorMessage( | ||
| response, | ||
| 'Failed to add reference name aliases', | ||
| ) | ||
| throw new ConfigError(errorMessage) | ||
| } | ||
| this.log( | ||
| `Reference name aliases added successfully to assembly ${flags.assembly}`, | ||
| ) | ||
| } | ||
| } |
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,3 @@ | ||
| ctgA ctga CTGA | ||
| ctgB ctgb CTGB | ||
| ctgC ctgc CTGC |
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88 changes: 88 additions & 0 deletions
88
packages/apollo-shared/src/Changes/AddRefSeqAliasesChange.ts
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,88 @@ | ||
| import { | ||
| AssemblySpecificChange, | ||
| Change, | ||
| ChangeOptions, | ||
| ClientDataStore, | ||
| LocalGFF3DataStore, | ||
| SerializedAssemblySpecificChange, | ||
| ServerDataStore, | ||
| } from '@apollo-annotation/common' | ||
| import { getSession } from '@jbrowse/core/util' | ||
|
|
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| export interface SerializedRefSeqAliases { | ||
| refName: string | ||
| aliases: string[] | ||
| } | ||
|
|
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| export interface SerializedRefSeqAliasesChange | ||
| extends SerializedAssemblySpecificChange { | ||
| typeName: 'AddRefSeqAliasesChange' | ||
| refSeqAliases: SerializedRefSeqAliases[] | ||
| } | ||
|
|
||
| export class AddRefSeqAliasesChange extends AssemblySpecificChange { | ||
| typeName = 'AddRefSeqAliasesChange' as const | ||
| refSeqAliases: SerializedRefSeqAliases[] | ||
|
|
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| constructor(json: SerializedRefSeqAliasesChange, options?: ChangeOptions) { | ||
| super(json, options) | ||
| this.refSeqAliases = json.refSeqAliases | ||
| } | ||
|
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| executeOnClient(clientDataStore: ClientDataStore) { | ||
| const { assemblyManager } = getSession(clientDataStore) | ||
| const assembly = assemblyManager.get(this.assembly) | ||
| if (!assembly) { | ||
| throw new Error(`assembly ${this.assembly} not found`) | ||
| } | ||
| const sessionAliases = assembly.refNameAliases | ||
| const sessionLCAliases = assembly.lowerCaseRefNameAliases | ||
|
|
||
| if (!sessionAliases || !sessionLCAliases) { | ||
| throw new Error('Session refNameAliases not found in assembly') | ||
| } | ||
|
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| for (const refSeqAlias of this.refSeqAliases) { | ||
| const { aliases, refName } = refSeqAlias | ||
| for (const alias of aliases) { | ||
| sessionAliases[alias] = refName | ||
| sessionLCAliases[alias.toLowerCase()] = refName | ||
| } | ||
| } | ||
| assembly.setRefNameAliases(sessionAliases, sessionLCAliases) | ||
| return Promise.resolve() | ||
| } | ||
|
|
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| getInverse(): Change { | ||
| throw new Error('Method not implemented.') | ||
| } | ||
|
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| toJSON(): SerializedRefSeqAliasesChange { | ||
| const { assembly, refSeqAliases, typeName } = this | ||
| return { assembly, typeName, refSeqAliases } | ||
| } | ||
|
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| async executeOnServer(backend: ServerDataStore) { | ||
| const { refSeqModel, session } = backend | ||
| const { assembly, logger, refSeqAliases } = this | ||
|
|
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| for (const refSeqAlias of refSeqAliases) { | ||
| logger.debug?.( | ||
| `Updating Refname alias for assembly: ${assembly}, refSeqAlias: ${JSON.stringify(refSeqAlias)}`, | ||
| ) | ||
| const { aliases, refName } = refSeqAlias | ||
| await refSeqModel | ||
| .updateOne({ assembly, name: refName }, { $set: { aliases } }) | ||
| .session(session) | ||
| } | ||
| } | ||
|
|
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| executeOnLocalGFF3(_backend: LocalGFF3DataStore): Promise<unknown> { | ||
| throw new Error('Method not implemented.') | ||
| } | ||
|
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| // eslint-disable-next-line @typescript-eslint/class-literal-property-style | ||
| get notification(): string { | ||
| return 'RefSeq aliases have been added.' | ||
| } | ||
| } |
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