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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,138 @@ | ||
| import { HubFile, SingleFileHub } from '@gmod/ucsc-hub' | ||
| import { | ||
| generateTracks, | ||
| fetchGenomesFile, | ||
| fetchTrackDbFile, | ||
| } from './ucscTrackHub' | ||
|
|
||
| import { getConf } from '@jbrowse/core/configuration' | ||
| import { FileLocation, getSession } from '@jbrowse/core/util' | ||
| import { openLocation } from '@jbrowse/core/util/io' | ||
| import { nanoid } from '@jbrowse/core/util/nanoid' | ||
|
|
||
| function resolve(uri: string, baseUri: string) { | ||
| return new URL(uri, baseUri).href | ||
| } | ||
|
|
||
| // eslint-disable-next-line @typescript-eslint/no-explicit-any | ||
| export async function doConnect(self: any) { | ||
| const session = getSession(self) | ||
| const notLoadedAssemblies = [] as string[] | ||
| try { | ||
| const hubFileLocation = getConf(self, 'hubTxtLocation') as FileLocation | ||
| const hubFileText = await openLocation(hubFileLocation).readFile('utf8') | ||
| const hubUri = resolve(hubFileLocation.uri, hubFileLocation.baseUri) | ||
| const { assemblyManager } = session | ||
| if (hubFileText.includes('useOneFile on')) { | ||
| const hub = new SingleFileHub(hubFileText) | ||
| const { genome, tracks } = hub | ||
| const genomeName = genome.name! | ||
|
|
||
| const asm = assemblyManager.get(genomeName) | ||
| if (!asm) { | ||
| console.log({ genome }, genome.data.twoBitPath) | ||
| // @ts-expect-error | ||
| session.addAssemblyConf({ | ||
| name: genomeName, | ||
| sequence: { | ||
| type: 'ReferenceSequenceTrack', | ||
| trackId: `${genomeName}-${nanoid()}`, | ||
| adapter: { | ||
| type: 'TwoBitAdapter', | ||
| twoBitLocation: { | ||
| uri: resolve(genome.data.twoBitPath, hubUri), | ||
| }, | ||
| chromSizesLocation: { | ||
| uri: resolve(genome.data.chromSizes, hubUri), | ||
| }, | ||
| }, | ||
| }, | ||
| }) | ||
| } | ||
| const asm2 = assemblyManager.get(genomeName) | ||
| const sequenceAdapter = getConf(asm2!, ['sequence', 'adapter']) | ||
| const tracksNew = generateTracks({ | ||
| trackDb: tracks, | ||
| trackDbLoc: hubFileLocation, | ||
| assemblyName: genomeName, | ||
| sequenceAdapter, | ||
| }) | ||
| self.addTrackConfs(tracksNew) | ||
| } else { | ||
| const hubFile = new HubFile(hubFileText) | ||
| const genomeFile = hubFile.data.genomesFile | ||
| if (!genomeFile) { | ||
| throw new Error('genomesFile not found on hub') | ||
| } | ||
|
|
||
| // @ts-expect-error | ||
| const hubUri = resolve(hubFileLocation.uri, hubFileLocation.baseUri) | ||
| const genomesFileLocation = hubUri | ||
| ? { | ||
| uri: resolve(genomeFile, hubUri), | ||
| locationType: 'UriLocation' as const, | ||
| } | ||
| : { | ||
| localPath: genomeFile, | ||
| locationType: 'LocalPathLocation' as const, | ||
| } | ||
| const genomesFile = await fetchGenomesFile(genomesFileLocation) | ||
| const map = {} as Record<string, number> | ||
| for (const [genomeName, genome] of Object.entries(genomesFile.data)) { | ||
| const assemblyNames = getConf(self, 'assemblyNames') | ||
| if (assemblyNames.length > 0 && !assemblyNames.includes(genomeName)) { | ||
| continue | ||
| } | ||
|
|
||
| const asm = assemblyManager.get(genomeName) | ||
| if (!asm) { | ||
| notLoadedAssemblies.push(genomeName) | ||
| continue | ||
| } | ||
|
|
||
| // @ts-expect-error | ||
| const db = genome.data.trackDb | ||
| if (!db) { | ||
| throw new Error('genomesFile not found on hub') | ||
| } | ||
| const base = new URL(genomeFile, hubUri) | ||
| const loc = hubUri | ||
| ? { | ||
| uri: new URL(db, base).href, | ||
| locationType: 'UriLocation' as const, | ||
| } | ||
| : { | ||
| localPath: db, | ||
| locationType: 'LocalPathLocation' as const, | ||
| } | ||
| const trackDb = await fetchTrackDbFile(loc) | ||
| const sequenceAdapter = getConf(asm, ['sequence', 'adapter']) | ||
| const tracks = generateTracks({ | ||
| trackDb, | ||
| trackDbLoc: loc, | ||
| assemblyName: genomeName, | ||
| sequenceAdapter, | ||
| }) | ||
| self.addTrackConfs(tracks) | ||
| map[genomeName] = tracks.length | ||
| } | ||
|
|
||
| const loadedAssemblies = Object.entries(map) | ||
| const str1 = loadedAssemblies.length | ||
| ? `Loaded data from these assemblies: ${loadedAssemblies | ||
| .map(([key, val]) => `${key} (${val} tracks)`) | ||
| .join(', ')}` | ||
| : '' | ||
| const str2 = notLoadedAssemblies.length | ||
| ? `Skipped data from these assemblies: ${notLoadedAssemblies.join( | ||
| ', ', | ||
| )}` | ||
| : '' | ||
| session.notify([str1, str2].filter(f => !!f).join('. '), 'success') | ||
| } | ||
| } catch (e) { | ||
| console.error(e) | ||
| session.notify(`${getConf(self, 'name')}: "${e}"`, 'error') | ||
| session.breakConnection?.(self.configuration) | ||
| } | ||
| } | ||
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -0,0 +1,7 @@ | ||
| <!doctype html> | ||
| <html> | ||
| <body> | ||
| <p>Hello world!</p> | ||
| <p>Volvox single file trackhub</p> | ||
| </body> | ||
| </html> |
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