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Simplify
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@cmdcolin
cmdcolin committed Nov 18, 2024
1 parent 764ac5e commit 228ca99
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Showing 6 changed files with 149 additions and 176 deletions.
6 changes: 5 additions & 1 deletion packages/core/rpc/BaseRpcDriver.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -133,7 +133,11 @@ export default abstract class BaseRpcDriver {
}
}

async remoteAbort(sessionId: string, functionName: string, stopTokenId: number) {
async remoteAbort(
sessionId: string,
functionName: string,
stopTokenId: number,
) {
const worker = await this.getWorker(sessionId)
await worker.call(
functionName,
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3 changes: 3 additions & 0 deletions packages/core/util/index.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -1009,6 +1009,9 @@ export async function updateStatus<U>(
cb('')
return res
}

// call statusCallback with current status and clear when finished, and check
// stopToken afterwards
export async function updateStatus2<U>(
msg: string,
cb: (arg: string) => void,
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4 changes: 4 additions & 0 deletions packages/core/util/stopToken.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -29,10 +29,14 @@
*/

export function createStopToken() {
// URL not available in jest and can't properly mock it
// eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
return URL.createObjectURL?.(new Blob()) || `${Math.random()}`
}

export function stopStopToken(stopToken: string) {
// URL not available in jest and can't properly mock it
// eslint-disable-next-line @typescript-eslint/no-unnecessary-condition
URL.revokeObjectURL?.(stopToken)
}

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145 changes: 62 additions & 83 deletions plugins/alignments/src/BamAdapter/BamAdapter.ts
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Original file line number Diff line number Diff line change
Expand Up @@ -7,15 +7,15 @@ import {
BaseOptions,
} from '@jbrowse/core/data_adapters/BaseAdapter'
import { Region } from '@jbrowse/core/util/types'
import { bytesForRegions, updateStatus2, Feature } from '@jbrowse/core/util'
import { bytesForRegions, updateStatus, Feature } from '@jbrowse/core/util'
import { openLocation } from '@jbrowse/core/util/io'
import { ObservableCreate } from '@jbrowse/core/util/rxjs'
import { checkStopToken } from '@jbrowse/core/util/stopToken'
import QuickLRU from '@jbrowse/core/util/QuickLRU'

// locals
import BamSlightlyLazyFeature from './BamSlightlyLazyFeature'
import { FilterBy } from '../shared/types'
import { checkStopToken } from '@jbrowse/core/util/stopToken'

interface Header {
idToName: string[]
Expand Down Expand Up @@ -78,23 +78,20 @@ export default class BamAdapter extends BaseFeatureDataAdapter {

async getHeader(_opts?: BaseOptions) {
const { bam } = await this.configure()
// TODO:ABORT
return bam.getHeaderText()
}

private async setupPre(opts?: BaseOptions) {
const { stopToken, statusCallback = () => {} } = opts || {}
const { statusCallback = () => {} } = opts || {}
const { bam } = await this.configure()
this.samHeader = await updateStatus2(
this.samHeader = await updateStatus(
'Downloading index',
statusCallback,
stopToken,
async () => {
// TODO:ABORT
const samHeader = await bam.getHeader()

// use the @SQ lines in the header to figure out the mapping between
// ref ref ID numbers and names
// use the @SQ lines in the header to figure out the
// mapping between ref ref ID numbers and names
const idToName: string[] = []
const nameToId: Record<string, number> = {}
samHeader
Expand Down Expand Up @@ -130,12 +127,7 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
return idToName
}

private async seqFetch(
refName: string,
start: number,
end: number,
opts?: { stopToken?: string },
) {
private async seqFetch(refName: string, start: number, end: number) {
const { sequenceAdapter } = await this.configure()
const refSeqStore = sequenceAdapter
if (!refSeqStore) {
Expand All @@ -145,15 +137,12 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
return undefined
}

const features = refSeqStore.getFeatures(
{
refName,
start,
end,
assemblyName: '',
},
opts,
)
const features = refSeqStore.getFeatures({
refName,
start,
end,
assemblyName: '',
})

const seqChunks = await firstValueFrom(features.pipe(toArray()))

Expand Down Expand Up @@ -191,80 +180,70 @@ export default class BamAdapter extends BaseFeatureDataAdapter {
const { refName, start, end, originalRefName } = region
const { stopToken, filterBy, statusCallback = () => {} } = opts || {}
return ObservableCreate<Feature>(async observer => {
checkStopToken(stopToken)
const { bam } = await this.configure()
await this.setup(opts)
checkStopToken(stopToken)

// TODO:ABORT
const records = await updateStatus2(
const records = await updateStatus(
'Downloading alignments',
statusCallback,
stopToken,
() => bam.getRecordsForRange(refName, start, end),
)
await updateStatus2(
'Processing alignments',
statusCallback,
stopToken,
async () => {
const {
flagInclude = 0,
flagExclude = 0,
tagFilter,
readName,
} = filterBy || {}
checkStopToken(stopToken)

for (const record of records) {
let ref: string | undefined
if (!record.tags.MD) {
ref = await this.seqFetch(
originalRefName || refName,
record.start,
record.end,
opts,
)
}
await updateStatus('Processing alignments', statusCallback, async () => {
const {
flagInclude = 0,
flagExclude = 0,
tagFilter,
readName,
} = filterBy || {}

for (const record of records) {
let ref: string | undefined
if (!record.tags.MD) {
ref = await this.seqFetch(
originalRefName || refName,
record.start,
record.end,
)
}

const flags = record.flags
const flags = record.flags
if ((flags & flagInclude) !== flagInclude && !(flags & flagExclude)) {
continue
}

if (tagFilter) {
const readVal = record.tags[tagFilter.tag]
const filterVal = tagFilter.value
if (
(flags & flagInclude) !== flagInclude &&
!(flags & flagExclude)
filterVal === '*'
? readVal === undefined
: `${readVal}` !== `${filterVal}`
) {
continue
}
}

if (tagFilter) {
const readVal = record.tags[tagFilter.tag]
const filterVal = tagFilter.value
if (
filterVal === '*'
? readVal === undefined
: `${readVal}` !== `${filterVal}`
) {
continue
}
}

if (readName && record.name !== readName) {
continue
}
if (readName && record.name !== readName) {
continue
}

// retrieve a feature from our feature cache if it is available, the
// features in the cache have pre-computed mismatches objects that
// can be re-used across blocks
const ret = this.ultraLongFeatureCache.get(`${record.id}`)
if (!ret) {
const elt = new BamSlightlyLazyFeature(record, this, ref)
this.ultraLongFeatureCache.set(`${record.id}`, elt)
observer.next(elt)
} else {
observer.next(ret)
}
// retrieve a feature from our feature cache if it is available, the
// features in the cache have pre-computed mismatches objects that
// can be re-used across blocks
const ret = this.ultraLongFeatureCache.get(`${record.id}`)
if (!ret) {
const elt = new BamSlightlyLazyFeature(record, this, ref)
this.ultraLongFeatureCache.set(`${record.id}`, elt)
observer.next(elt)
} else {
observer.next(ret)
}
},
)
observer.complete()
}, stopToken)
}
observer.complete()
})
})
}

async getMultiRegionFeatureDensityStats(
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