import { getAdapter } from '@jbrowse/core/data_adapters/dataAdapterCache'
import RpcMethodTypeWithFiltersAndRenameRegions from '@jbrowse/core/pluggableElementTypes/RpcMethodTypeWithFiltersAndRenameRegions'
import { firstValueFrom, toArray } from 'rxjs'

import { processFeaturesToFasta } from '../util/fastaUtils'

import type { Sample } from '../types'
import type { AnyConfigurationModel } from '@jbrowse/core/configuration'
import type { BaseFeatureDataAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'
import type { Region } from '@jbrowse/core/util'

export default class MafGetSequences extends RpcMethodTypeWithFiltersAndRenameRegions {
  name = 'MafGetSequences'

  async execute(
    args: {
      adapterConfig: AnyConfigurationModel
      samples: Sample[]
      stopToken?: string
      sessionId: string
      headers?: Record<string, string>
      regions: Region[]
      showAllLetters: boolean
      includeInsertions?: boolean
    },
    rpcDriverClassName: string,
  ) {
    const deserializedArgs = await this.deserializeArguments(
      args,
      rpcDriverClassName,
    )
    const {
      samples,
      regions,
      adapterConfig,
      sessionId,
      showAllLetters,
      includeInsertions,
    } = deserializedArgs
    const dataAdapter = (
      await getAdapter(this.pluginManager, sessionId, adapterConfig)
    ).dataAdapter as BaseFeatureDataAdapter

    const features = await firstValueFrom(
      dataAdapter.getFeatures(regions[0]!, deserializedArgs).pipe(toArray()),
    )
    return processFeaturesToFasta({
      features: new Map(features.map(f => [f.id(), f])),
      samples,
      regions,
      showAllLetters,
      includeInsertions,
    })
  }
}