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assembly.ts
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assembly.ts
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import jsonStableStringify from 'json-stable-stringify'
import { cast, getParent, IAnyType, types, Instance } from 'mobx-state-tree'
import AbortablePromiseCache from 'abortable-promise-cache'
import { readConfObject } from '../configuration'
import { Region } from '../util/types'
import { Region as MSTRegion } from '../util/types/mst'
import { makeAbortableReaction, when } from '../util'
import QuickLRU from '../util/QuickLRU'
// Based on the UCSC Genome Browser chromosome color palette:
// https://github.com/ucscGenomeBrowser/kent/blob/a50ed53aff81d6fb3e34e6913ce18578292bc24e/src/hg/inc/chromColors.h
// Some colors darkened to have at least a 3:1 contrast ratio on a white
// background
const refNameColors = [
'rgb(153, 102, 0)',
'rgb(102, 102, 0)',
'rgb(153, 153, 30)',
'rgb(204, 0, 0)',
'rgb(255, 0, 0)',
'rgb(255, 0, 204)',
'rgb(165, 132, 132)', // originally 'rgb(255, 204, 204)'
'rgb(204, 122, 0)', // originally rgb(255, 153, 0)'
'rgb(178, 142, 0)', // originally 'rgb(255, 204, 0)'
'rgb(153, 153, 0)', // originally 'rgb(255, 255, 0)'
'rgb(122, 153, 0)', // originally 'rgb(204, 255, 0)'
'rgb(0, 165, 0)', // originally 'rgb(0, 255, 0)'
'rgb(53, 128, 0)',
'rgb(0, 0, 204)',
'rgb(96, 145, 242)', // originally 'rgb(102, 153, 255)'
'rgb(107, 142, 178)', // originally 'rgb(153, 204, 255)'
'rgb(0, 165, 165)', // originally 'rgb(0, 255, 255)'
'rgb(122, 153, 153)', // originally 'rgb(204, 255, 255)'
'rgb(153, 0, 204)',
'rgb(204, 51, 255)',
'rgb(173, 130, 216)', // originally 'rgb(204, 153, 255)'
'rgb(102, 102, 102)',
'rgb(145, 145, 145)', // originally 'rgb(153, 153, 153)'
'rgb(142, 142, 142)', // originally 'rgb(204, 204, 204)'
'rgb(142, 142, 107)', // originally 'rgb(204, 204, 153)'
'rgb(96, 163, 48)', // originally 'rgb(121, 204, 61)'
]
async function loadRefNameMap(
assembly: Assembly,
adapterConf: unknown,
options: BaseOptions,
signal?: AbortSignal,
) {
const { sessionId } = options
await when(() => Boolean(assembly.regions && assembly.refNameAliases), {
signal,
name: 'when assembly ready',
})
const refNames = await assembly.rpcManager.call(
sessionId,
'CoreGetRefNames',
{
adapterConfig: adapterConf,
signal,
...options,
},
{ timeout: 1000000 },
)
const refNameMap: Record<string, string> = {}
const { refNameAliases } = assembly
if (!refNameAliases) {
throw new Error(`error loading assembly ${assembly.name}'s refNameAliases`)
}
refNames.forEach((refName: string) => {
checkRefName(refName)
const canon = assembly.getCanonicalRefName(refName)
if (canon) {
refNameMap[canon] = refName
}
})
// make the reversed map too
const reversed: Record<string, string> = {}
for (const [canonicalName, adapterName] of Object.entries(refNameMap)) {
reversed[adapterName] = canonicalName
}
return {
forwardMap: refNameMap,
reverseMap: reversed,
}
}
function checkRefName(refName: string) {
// Valid refName pattern from https://samtools.github.io/hts-specs/SAMv1.pdf
if (
!refName.match(
/[0-9A-Za-z!#$%&+./:;?@^_|~-][0-9A-Za-z!#$%&*+./:;=?@^_|~-]*/,
)
) {
throw new Error(`Encountered invalid refName: "${refName}"`)
}
}
function getAdapterId(adapterConf: unknown) {
return jsonStableStringify(adapterConf)
}
type RefNameAliases = Record<string, string>
export interface BaseOptions {
signal?: AbortSignal
sessionId: string
statusCallback?: Function
}
interface CacheData {
adapterConf: unknown
self: Assembly
sessionId: string
options: BaseOptions
}
export default function assemblyFactory(assemblyConfigType: IAnyType) {
const adapterLoads = new AbortablePromiseCache({
cache: new QuickLRU({ maxSize: 1000 }),
async fill(
args: CacheData,
abortSignal?: AbortSignal,
statusCallback?: Function,
) {
const { adapterConf, self, options } = args
return loadRefNameMap(
self,
adapterConf,
{ ...options, statusCallback },
abortSignal,
)
},
})
return types
.model({
configuration: types.safeReference(assemblyConfigType),
regions: types.maybe(types.array(MSTRegion)),
refNameAliases: types.maybe(types.map(types.string)),
})
.views(self => ({
get name(): string {
return readConfObject(self.configuration, 'name')
},
get aliases(): string[] {
return readConfObject(self.configuration, 'aliases')
},
get refNames() {
return self.regions && self.regions.map(region => region.refName)
},
get allRefNames() {
if (!(this.refNames && self.refNameAliases)) {
return undefined
}
let aliases: string[] = []
self.refNameAliases.forEach(aliasList => {
aliases = aliases.concat(aliasList)
})
return [...this.refNames, ...aliases]
},
get rpcManager() {
return getParent(self, 2).rpcManager
},
get refNameColors() {
const colors = readConfObject(
self.configuration,
'refNameColors',
) as string[]
if (colors.length === 0) {
return refNameColors
}
return colors
},
}))
.views(self => ({
getCanonicalRefName(refName: string) {
if (!self.refNameAliases) {
throw new Error(
'aliases not loaded, we expect them to be loaded before getCanonicalRefName can be called',
)
}
return self.refNameAliases.get(refName)
},
getRefNameColor(refName: string) {
const idx = self.refNames?.findIndex(r => r === refName)
if (idx === undefined || idx === -1) {
return undefined
}
return self.refNameColors[idx % self.refNameColors.length]
},
isValidRefName(refName: string) {
if (!self.refNameAliases)
throw new Error(
'isValidRefName cannot be called yet, the assembly has not finished loading',
)
return !!this.getCanonicalRefName(refName)
},
}))
.actions(self => ({
setLoading() {},
setLoaded({
adapterRegionsWithAssembly,
refNameAliases,
}: {
adapterRegionsWithAssembly: Region[]
refNameAliases: RefNameAliases
}) {
this.setRegions(adapterRegionsWithAssembly)
this.setRefNameAliases(refNameAliases)
},
setError(error: Error) {
if (!getParent(self, 3).isAssemblyEditing) {
getParent(self, 3).setError(error)
}
},
setRegions(regions: Region[]) {
self.regions = cast(regions)
},
setRefNameAliases(refNameAliases: RefNameAliases) {
self.refNameAliases = cast(refNameAliases)
},
afterAttach() {
makeAbortableReaction(
// eslint-disable-next-line @typescript-eslint/no-explicit-any
self as any,
// @ts-ignore
loadAssemblyData,
loadAssemblyReaction,
{ name: `${self.name} assembly loading`, fireImmediately: true },
this.setLoading,
this.setLoaded,
this.setError,
)
},
}))
.views(self => ({
getAdapterMapEntry(adapterConf: unknown, options: BaseOptions) {
const { signal, statusCallback, ...rest } = options
if (!options.sessionId) {
throw new Error('sessionId is required')
}
const adapterId = getAdapterId(adapterConf)
return adapterLoads.get(
adapterId,
{
adapterConf,
self: self as Assembly,
options: rest,
} as CacheData,
signal,
statusCallback,
)
},
/**
* get Map of `canonical-name -> adapter-specific-name`
*/
async getRefNameMapForAdapter(adapterConf: unknown, opts: BaseOptions) {
if (!opts || !opts.sessionId) {
throw new Error('sessionId is required')
}
const map = await this.getAdapterMapEntry(adapterConf, opts)
return map.forwardMap
},
/**
* get Map of `adapter-specific-name -> canonical-name`
*/
async getReverseRefNameMapForAdapter(
adapterConf: unknown,
opts: BaseOptions,
) {
const map = await this.getAdapterMapEntry(adapterConf, opts)
return map.reverseMap
},
}))
}
function loadAssemblyData(self: Assembly) {
if (self.configuration) {
const sequenceAdapterConfig = readConfObject(self.configuration, [
'sequence',
'adapter',
])
const adapterConfigId = getAdapterId(sequenceAdapterConfig)
const { rpcManager } = getParent(self, 2)
const refNameAliasesAdapterConfig =
self.configuration.refNameAliases &&
readConfObject(self.configuration, ['refNameAliases', 'adapter'])
return {
sequenceAdapterConfig,
adapterConfigId,
rpcManager,
assemblyName: self.name,
refNameAliasesAdapterConfig,
}
}
return undefined
}
async function loadAssemblyReaction(
props: ReturnType<typeof loadAssemblyData> | undefined,
signal: AbortSignal,
) {
if (!props) {
return
}
const {
sequenceAdapterConfig,
rpcManager,
assemblyName,
refNameAliasesAdapterConfig,
} = props
const sessionId = `assembly-${assemblyName}`
const adapterRegions = (await rpcManager.call(
sessionId,
'CoreGetRegions',
{ sessionId, adapterConfig: sequenceAdapterConfig, signal },
{ timeout: 1000000 },
)) as Region[]
const adapterRegionsWithAssembly = adapterRegions.map(adapterRegion => {
const { refName } = adapterRegion
checkRefName(refName)
return { ...adapterRegion, assemblyName }
})
const refNameAliases: RefNameAliases = {}
if (refNameAliasesAdapterConfig) {
const refNameAliasesAborter = new AbortController()
const refNameAliasesList = (await rpcManager.call(
sessionId,
'CoreGetRefNameAliases',
{
sessionId,
adapterConfig: refNameAliasesAdapterConfig,
signal: refNameAliasesAborter.signal,
},
{ timeout: 1000000 },
)) as {
refName: string
aliases: string[]
}[]
refNameAliasesList.forEach(({ refName, aliases }) => {
aliases.forEach(alias => {
checkRefName(alias)
refNameAliases[alias] = refName
refNameAliases[refName] = refName
})
})
}
// eslint-disable-next-line consistent-return
return { adapterRegionsWithAssembly, refNameAliases }
}
export type Assembly = Instance<ReturnType<typeof assemblyFactory>>