From 4824933514639625aacd134639caffe3b28d39ab Mon Sep 17 00:00:00 2001 From: Kyosti Sutinen Date: Fri, 8 Sep 2023 11:50:12 +0300 Subject: [PATCH] Ready for draft PR --- packages/apollo-mst/src/index.ts | 5 +- .../src/BackendDrivers/DesktopFileDriver.ts | 575 +----------------- .../src/components/OpenLocalFile.tsx | 12 +- .../src/session/ClientDataStore.ts | 27 +- 4 files changed, 44 insertions(+), 575 deletions(-) diff --git a/packages/apollo-mst/src/index.ts b/packages/apollo-mst/src/index.ts index 33ad871ff..fd3e307b1 100644 --- a/packages/apollo-mst/src/index.ts +++ b/packages/apollo-mst/src/index.ts @@ -14,12 +14,14 @@ export const Sequence = types.model({ start: types.number, stop: types.number, sequence: types.string, + description: types.string, }) interface SequenceSnapshot { start: number stop: number sequence: string + description: string } export const ApolloRefSeq = types @@ -28,7 +30,6 @@ export const ApolloRefSeq = types name: types.string, features: types.map(AnnotationFeature), sequence: types.array(Sequence), - description: '', }) .actions((self) => ({ addFeature(feature: AnnotationFeatureSnapshot) { @@ -46,11 +47,13 @@ export const ApolloRefSeq = types start: s.start, stop: s.stop, sequence: s.sequence, + description: s.description, })) newSequences.push({ start: seq.start, stop: seq.stop, sequence: seq.sequence, + description: seq.description, }) newSequences.sort((s1, s2) => s1.start - s2.start) const consolidatedSequences = newSequences.reduce((result, current) => { diff --git a/packages/jbrowse-plugin-apollo/src/BackendDrivers/DesktopFileDriver.ts b/packages/jbrowse-plugin-apollo/src/BackendDrivers/DesktopFileDriver.ts index d0985fd72..4c60a92c7 100644 --- a/packages/jbrowse-plugin-apollo/src/BackendDrivers/DesktopFileDriver.ts +++ b/packages/jbrowse-plugin-apollo/src/BackendDrivers/DesktopFileDriver.ts @@ -1,23 +1,14 @@ /* eslint-disable @typescript-eslint/no-explicit-any */ -import gff, { - GFF3Feature, - GFF3FeatureLine, - GFF3FeatureLineWithRefs, - GFF3Sequence, -} from '@gmod/gff' -import { GFF3Attributes, GFF3Item } from '@gmod/gff/dist/util' +import gff, { GFF3FeatureLineWithRefs, GFF3Sequence } from '@gmod/gff' import { getConf } from '@jbrowse/core/configuration' import { BaseInternetAccountModel } from '@jbrowse/core/pluggableElementTypes' -import { Region, getSession, isElectron } from '@jbrowse/core/util' -import { AssemblySpecificChange, Change, SerializedChange } from 'apollo-common' +import { getSession } from '@jbrowse/core/util' +import { AssemblySpecificChange, Change } from 'apollo-common' import { AnnotationFeatureI, AnnotationFeatureSnapshot } from 'apollo-mst' import { ValidationResultSet } from 'apollo-shared' import { values } from 'mobx' -import { nanoid } from 'nanoid' import { Socket } from 'socket.io-client' -import { ChangeManager, SubmitOpts } from '../ChangeManager' -import { ApolloSession } from '../session' import { createFetchErrorMessage } from '../util' import { BackendDriver } from './BackendDriver' @@ -28,176 +19,6 @@ export interface ApolloInternetAccount extends BaseInternetAccountModel { getMissingChanges(): void } -function createFeature(gff3Feature: GFF3Feature): AnnotationFeatureSnapshot { - const [firstFeature] = gff3Feature - const { - seq_id: refName, - type, - start, - end, - strand, - score, - phase, - child_features: childFeatures, - source, - attributes, - } = firstFeature - if (!refName) { - throw new Error( - `feature does not have seq_id: ${JSON.stringify(firstFeature)}`, - ) - } - if (!type) { - throw new Error( - `feature does not have type: ${JSON.stringify(firstFeature)}`, - ) - } - if (start === null) { - throw new Error( - `feature does not have start: ${JSON.stringify(firstFeature)}`, - ) - } - if (end === null) { - throw new Error( - `feature does not have end: ${JSON.stringify(firstFeature)}`, - ) - } - const feature: AnnotationFeatureSnapshot = { - _id: nanoid(), - gffId: '', - refSeq: refName, - type, - start, - end, - } - if (gff3Feature.length > 1) { - feature.discontinuousLocations = gff3Feature.map((f) => { - const { start: subStart, end: subEnd, phase: locationPhase } = f - if (subStart === null || subEnd === null) { - throw new Error( - `feature does not have start and/or end: ${JSON.stringify(f)}`, - ) - } - let parsedPhase: 0 | 1 | 2 | undefined = undefined - if (locationPhase) { - if (locationPhase === '0') { - parsedPhase = 0 - } else if (locationPhase === '1') { - parsedPhase = 1 - } else if (locationPhase === '2') { - parsedPhase = 2 - } else { - throw new Error(`Unknown phase: "${locationPhase}"`) - } - } - return { start: subStart, end: subEnd, phase: parsedPhase } - }) - } - if (strand) { - if (strand === '+') { - feature.strand = 1 - } else if (strand === '-') { - feature.strand = -1 - } else { - throw new Error(`Unknown strand: "${strand}"`) - } - } - if (score !== null) { - feature.score = score - } - if (phase) { - if (phase === '0') { - feature.phase = 0 - } else if (phase === '1') { - feature.phase = 1 - } else if (phase === '2') { - feature.phase = 2 - } else { - throw new Error(`Unknown phase: "${phase}"`) - } - } - - if (childFeatures?.length) { - const children: Record = {} - for (const childFeature of childFeatures) { - const child = createFeature(childFeature) - children[child._id] = child - // Add value to gffId - child.attributes?._id - ? (child.gffId = child.attributes?._id.toString()) - : (child.gffId = child._id) - } - feature.children = children - } - if (source ?? attributes) { - const attrs: Record = {} - if (source) { - attrs.source = [source] - } - if (attributes) { - Object.entries(attributes).forEach(([key, val]) => { - if (val) { - const newKey = key.toLowerCase() - if (newKey !== 'parent') { - // attrs[key.toLowerCase()] = val - switch (key) { - case 'ID': - attrs._id = val - break - case 'Name': - attrs.gff_name = val - break - case 'Alias': - attrs.gff_alias = val - break - case 'Target': - attrs.gff_target = val - break - case 'Gap': - attrs.gff_gap = val - break - case 'Derives_from': - attrs.gff_derives_from = val - break - case 'Note': - attrs.gff_note = val - break - case 'Dbxref': - attrs.gff_dbxref = val - break - case 'Ontology_term': { - const goTerms: string[] = [] - const otherTerms: string[] = [] - val.forEach((v) => { - if (v.startsWith('GO:')) { - goTerms.push(v) - } else { - otherTerms.push(v) - } - }) - if (goTerms.length) { - attrs['Gene Ontology'] = goTerms - } - if (otherTerms.length) { - attrs.gff_ontology_term = otherTerms - } - break - } - case 'Is_circular': - attrs.gff_is_circular = val - break - default: - attrs[key.toLowerCase()] = val - } - } - } - }) - } - feature.attributes = attrs - } - return feature -} - export class DesktopFileDriver extends BackendDriver { private async fetch( internetAccount: ApolloInternetAccount, @@ -236,89 +57,18 @@ export class DesktopFileDriver extends BackendDriver { return response.json() as Promise } - async getFeatures(region: Region) { + async getFeatures() { return [] } - /** - * Checks if there is assembly-refSeq specific socket. If not, it opens one - * @param assembly - assemblyId - * @param refSeq - refSeqName - * @param internetAccount - internet account - */ - async checkSocket( - assembly: string, - refSeq: string, - internetAccount: ApolloInternetAccount, - ) { - const { socket } = internetAccount - const token = internetAccount.retrieveToken() - const channel = `${assembly}-${refSeq}` - const changeManager = new ChangeManager(this.clientStore) - const session = getSession(this.clientStore) - const { notify } = session - - if (!socket.hasListeners(channel)) { - socket.on( - channel, - async (message: { - changeSequence: string - userToken: string - channel: string - changeInfo: SerializedChange - userName: string - }) => { - // Save server last change sequnece into session storage - internetAccount.setLastChangeSequenceNumber( - Number(message.changeSequence), - ) - if (message.userToken !== token && message.channel === channel) { - const change = Change.fromJSON(message.changeInfo) - await changeManager.submit(change, { submitToBackend: false }) - } - }, - ) - socket.on('reconnect', () => { - notify('You are re-connected to the Apollo server.', 'success') - internetAccount.getMissingChanges() - }) - socket.on('disconnect', () => { - notify('You are disconnected from the Apollo server.', 'error') - }) - } - } - /** * Call backend endpoint to get sequence by criteria * @param region - Searchable region containing refSeq, start and end * @returns */ - async getSequence(region: Region): Promise<{ seq: string; refSeq: string }> { - console.log('**** IT NEVER COMES HERE TO READ SEQUENCE **** ') - const { assemblyName, refName, start, end } = region - const { assemblyManager } = getSession(this.clientStore) - const assembly = assemblyManager.get(assemblyName) - if (!assembly) { - throw new Error(`Could not find assembly with name "${assemblyName}"`) - } - const { file } = getConf(assembly, ['sequence', 'metadata']) as { - file: string - } - // eslint-disable-next-line @typescript-eslint/no-var-requires - const fs = require('fs') - const filePath = - '/Users/kyosti/src/Apollo/Assembly_files/volvox.sort.fasta.gff3' - - const fileData = (await fs.promises.readFile(filePath, 'utf-8') - .text) as string - const featuresAndSequences = gff.parseStringSync(fileData, { - parseSequences: true, - parseComments: false, - parseDirectives: false, - parseFeatures: false, - }) - const result = { seq: fileData, refSeq: refName } - return { seq: fileData, refSeq: refName } + // async getSequence(region: Region): Promise<{ seq: string; refSeq: string }> { + async getSequence() { + return { seq: '', refSeq: '' } } async getRefSeqs() { @@ -346,10 +96,7 @@ export class DesktopFileDriver extends BackendDriver { }) } - async submitChange( - change: Change | AssemblySpecificChange, - opts: SubmitOpts = {}, - ) { + async submitChange(change: Change | AssemblySpecificChange) { const tmpObj = JSON.parse(JSON.stringify(change.toJSON())) const { assemblyManager } = getSession(this.clientStore) const assembly = assemblyManager.get(tmpObj.assembly) @@ -361,161 +108,37 @@ export class DesktopFileDriver extends BackendDriver { } // eslint-disable-next-line @typescript-eslint/no-var-requires const fs = require('fs') - const newFileName = `${file}_001.gff3` + const newFileName = `${file}_exported.gff3` // *** HERE WE MUST USE NAME OF ORIGINAL FILE. THIS IS ONLY FOR TEST PURPOSE let commentsOfGFF3 = '' let headersOfGFF3 = '##gff-version 3\n' let featuresOfGFF3 = '' let fastaOfGFF3 = '##FASTA\n' let wholeGFF3 = '' - const gff3Items: GFF3Item[] = [{ directive: 'gff-version', value: '3' }] const assemblyName = this.clientStore.assemblies - // console.log(`*** ASSEMBLY DATA: ${JSON.stringify(assemblyName)}`) - const { util } = gff - assemblyName.forEach((valueAssembly, keyAssembly) => { + assemblyName.forEach((valueAssembly) => { if (valueAssembly.comments) { commentsOfGFF3 += `${valueAssembly.comments}\n` } - valueAssembly.refSeqs.forEach((valRefSeq, keyRefSeq) => { + valueAssembly.refSeqs.forEach((valRefSeq) => { const refSeqName = valRefSeq.name - valRefSeq.features.forEach((valFeature, keyFeature) => { - // console.log(`Feature: ${JSON.stringify(val2)}`) - const attr: GFF3Attributes = {} - // let sourceValue = '' - // valFeature.attributes.forEach((valAttribute, keyAttribute) => { - // // console.log(`Attribute KEY: "${keyAttr}", VALUE: "${valAttr}"`) - // switch (keyAttribute) { - // case '_id': - // keyAttribute = 'ID' - // break - // case 'gff_name': - // keyAttribute = 'Name' - // break - // case 'gff_alias': - // keyAttribute = 'Alias' - // break - // case 'gff_target': - // keyAttribute = 'Target' - // break - // case 'gff_gap': - // keyAttribute = 'Gap' - // break - // case 'gff_derives_from': - // keyAttribute = 'Derives_from' - // break - // case 'gff_note': - // keyAttribute = 'Note' - // break - // case 'gff_dbxref': - // keyAttribute = 'Dbxref' - // break - // case 'gff_is_circular': - // keyAttribute = 'Is_circular' - // break - // default: - // break - // } - // if (keyAttribute.toUpperCase() === 'SOURCE') { - // sourceValue = valAttribute as unknown as string - // } else { - // attr[keyAttribute] = valAttribute - // } - // }) - let strand: string | null = null - if (valFeature.strand) { - if (valFeature.strand === 1) { - strand = '+' - } else if (valFeature.strand === -1) { - strand = '-' - } - } - let score: number | null = null - if (valFeature.score) { - score = valFeature.score - } - const phase: string | null = valFeature.phase - ? (valFeature.phase as unknown as string) - : null - - // const locations = valFeature.discontinuousLocations?.length - // ? valFeature.discontinuousLocations - // : [ - // { - // start: valFeature.start, - // end: valFeature.end, - // phase, - // }, - // ] - // ******* - - // ******* - // console.log(`ATTRIBUTES: ${JSON.stringify(valFeature.attributes)}`) - // // *** TÄHÄN EHKÄ PITÄÄ LAITTAA FUNKTIO KUTSUÖ makeGFF3Feature() niinkuin "features.services.ts" luokassa - const featureLine0 = this.makeGFF3Feature( - valFeature, - // valFeature.refSeq, - ) - gff3Items.push(this.makeGFF3Feature(valFeature, )) - // const featureLine: GFF3FeatureLineWithRefs = { - // seq_id: valFeature.refSeq, - // start: valFeature.start, - // source: sourceValue, - // type: valFeature.type, - // end: valFeature.end, - // score, - // strand, - // phase, - // attributes: attr, - // child_features: valFeature.children as unknown as GFF3Feature[], - // derived_features: - // valFeature.discontinuousLocations as unknown as GFF3Feature[], - // // derived_features: ** EMPTY ARRAY **/valFeature.discontinuousLocations as unknown as GFF3Feature[] - // } + valRefSeq.features.forEach((valFeature) => { + const featureLine = this.makeGFF3Feature(valFeature) + const featureLineAsString = util.formatFeature(featureLine) - // const featureLine01 = this.makeGFF3Feature( - // featureLine, - // valFeature.refSeq, - // ) - // const featureLineAsString = util.formatFeature([featureLine]) // SHOULD WE USE formatFeature or formatItem ??? - // const featureLineAsString = util.formatFeature([featureLine]) - const featureLineAsString = util.formatFeature(featureLine0) - if (valFeature.start > 17399 && valFeature.end < 23001) { - console.log(`Feature line: ${JSON.stringify(valFeature)}`) - console.log(`A Feature line: ${JSON.stringify(featureLine0)}`) - console.log( - `B Feature line: ${JSON.stringify( - util.formatFeature(featureLine0), - )}`, - ) - console.log( - `C Feature line: ${JSON.stringify( - util.formatItem(featureLine0), - )}`, - ) - console.log(`D Feature line: ${featureLineAsString}`) - console.log( - `discontinuousLocations: ${JSON.stringify( - valFeature.discontinuousLocations, - )}`, - ) - } - // const featureLineAsString = util.formatFeature([featureLine01]) featuresOfGFF3 += featureLineAsString - // console.log(`Feature line: ${featureLineAsString}`) }) - valRefSeq.sequence.forEach((valSeq, keySeq) => { + valRefSeq.sequence.forEach((valSeq) => { headersOfGFF3 += `##sequence-region ${refSeqName} 1 ${valSeq.stop}\n` const gff3Seq: GFF3Sequence = { id: refSeqName, - description: refSeqName, + description: valSeq.description, sequence: valSeq.sequence, } fastaOfGFF3 += util.formatSequence(gff3Seq) }) }) }) - const gff3 = gff.formatSync(gff3Items) - // console.log(`RESULT: ${JSON.stringify(gff3)}`) if (commentsOfGFF3) { const parts = commentsOfGFF3.split(',') const resultString = parts.map((part) => `# ${part}`).join('\n') @@ -531,116 +154,8 @@ export class DesktopFileDriver extends BackendDriver { return results } - // makeGFF3Feature1( - // feature: AnnotationFeatureI, - // parentId?: string, - // ): GFF3Feature { - // const locations = feature.discontinuousLocations?.length - // ? feature.discontinuousLocations - // : [ - // { - // start: feature.start, - // end: feature.end, - // phase: feature.phase, - // }, - // ] - // const attributes: Record = { - // ...(feature.attributes ? getSnapshot(feature.attributes) : {}), - // } - // const ontologyTerms: string[] = [] - // const source = feature.attributes?.get('source')?.[0] ?? null - // delete attributes.source - // if (parentId) { - // attributes.Parent = [parentId] - // } - // if (attributes._id) { - // attributes.ID = attributes._id - // delete attributes._id - // } - // if (attributes.gff_name) { - // attributes.Name = attributes.gff_name - // delete attributes.gff_name - // } - // if (attributes.gff_alias) { - // attributes.Alias = attributes.gff_alias - // delete attributes.gff_alias - // } - // if (attributes.gff_target) { - // attributes.Target = attributes.gff_target - // delete attributes.gff_target - // } - // if (attributes.gff_gap) { - // attributes.Gap = attributes.gff_gap - // delete attributes.gff_gap - // } - // if (attributes.gff_derives_from) { - // attributes.Derives_from = attributes.gff_derives_from - // delete attributes.gff_derives_from - // } - // if (attributes.gff_note) { - // attributes.Note = attributes.gff_note - // delete attributes.gff_note - // } - // if (attributes.gff_dbxref) { - // attributes.Dbxref = attributes.gff_dbxref - // delete attributes.gff_dbxref - // } - // if (attributes.gff_is_circular) { - // attributes.Is_circular = attributes.gff_is_circular - // delete attributes.gff_is_circular - // } - // if (attributes.gff_ontology_term) { - // ontologyTerms.push(...attributes.gff_ontology_term) - // delete attributes.gff_ontology_term - // } - // if (attributes['Gene Ontology']) { - // ontologyTerms.push(...attributes['Gene Ontology']) - // delete attributes['Gene Ontology'] - // } - // if (attributes['Sequence Ontology']) { - // ontologyTerms.push(...attributes['Sequence Ontology']) - // delete attributes['Sequence Ontology'] - // } - // if (ontologyTerms.length) { - // attributes.Ontology_term = ontologyTerms - // } - // return locations.map((location) => { - // const featureLine: GFF3FeatureLineWithRefs = { - // start: location.start, - // end: location.end, - // seq_id: feature.refSeq, - // source, - // type: feature.type, - // score: feature.score ?? null, - // strand: feature.strand ? (feature.strand === 1 ? '+' : '-') : null, - // phase: - // location.phase === 0 - // ? '0' - // : location.phase === 1 - // ? '1' - // : location.phase === 2 - // ? '2' - // : null, - // attributes: Object.keys(attributes).length ? attributes : null, - // derived_features: [], - // child_features: [], - // } - // if (feature.children && feature.children.size > 0) { - // featureLine.child_features = values(feature.children).map((child) => { - // return makeGFF3Feature1( - // child as unknown as AnnotationFeatureI, - // attributes.ID[0], - // ) - // }) - // } - // return featureLine - // }) - // } - makeGFF3Feature( - // eslint-disable-next-line @typescript-eslint/no-explicit-any featureDocument: any, - // refSeqName: string, parentId?: string, ): GFF3FeatureLineWithRefs[] { const locations = featureDocument.discontinuousLocations?.length @@ -657,32 +172,15 @@ export class DesktopFileDriver extends BackendDriver { ? JSON.parse(JSON.stringify(featureDocument.attributes)) : {} - // console.log(`GFF ATTRIBUTE _id: ${JSON.stringify(attributes._id)}`) const ontologyTerms: string[] = [] - // const source = featureDocument.attributes?.source?.[0] ?? null let source: any = null - // let parentId: any = null - if (featureDocument.attributes) { - source = JSON.parse(JSON.stringify(featureDocument.attributes)).source?.[0] - } if (featureDocument.attributes) { - console.log(`*** PARENT: ${JSON.parse(JSON.stringify(featureDocument.attributes)).parent?.[0]}`) - } - if (parentId) { - console.log(`*** PARENTTI OLI: ${parentId}`) + source = JSON.parse(JSON.stringify(featureDocument.attributes)) + .source?.[0] } let featId = '' if (featureDocument.attributes) { - featId = JSON.parse(JSON.stringify(featureDocument.attributes))._id?.[0] - console.log(`*** FEATURE ID ${featId}`) - } - // const source = featureDocument.attributes?.source?.[0] ?? null - - if (featureDocument.start > 17399 && featureDocument.end < 23001) { - console.log(`1 attributes: ${JSON.stringify(featureDocument.attributes)}`) - console.log(`2 locations: ${JSON.stringify(locations)}`) - console.log(`3 children: ${JSON.stringify(featureDocument.children)}`) - console.log(`4 source: ${source}`) + featId = JSON.parse(JSON.stringify(featureDocument.attributes))._id?.[0] } delete attributes.source @@ -740,39 +238,6 @@ export class DesktopFileDriver extends BackendDriver { if (ontologyTerms.length) { attributes.Ontology_term = ontologyTerms } - - // return locations.map( - // // eslint-disable-next-line @typescript-eslint/no-explicit-any - // (location: any) => ({ - // start: location.start, - // end: location.end, - // seq_id: refSeqName, - // source, - // type: featureDocument.type, - // score: featureDocument.score ?? null, - // strand: featureDocument.strand - // ? featureDocument.strand === 1 - // ? '+' - // : '-' - // : null, - // phase: - // location.phase === 0 - // ? '0' - // : location.phase === 1 - // ? '1' - // : location.phase === 2 - // ? '2' - // : null, - // attributes: Object.keys(attributes).length ? attributes : null, - // derived_features: [], - // // child_features: featureDocument.children - // // ? Object.values(featureDocument.children).map((child) => - // // this.makeGFF3Feature(child, refSeqName, attributes.ID[0]), - // // ) - // // : [], - // }), - // ) - // eslint-disable-next-line @typescript-eslint/no-explicit-any return locations.map((location: any) => { const featureLine: GFF3FeatureLineWithRefs = { start: location.start, @@ -799,13 +264,11 @@ export class DesktopFileDriver extends BackendDriver { child_features: [], } if (featureDocument.children && featureDocument.children.size > 0) { - // eslint-disable-next-line @typescript-eslint/no-explicit-any featureLine.child_features = values(featureDocument.children).map( (child: any) => { return this.makeGFF3Feature( child as unknown as AnnotationFeatureI, featId, - // attributes.ID[0], ) }, ) diff --git a/packages/jbrowse-plugin-apollo/src/components/OpenLocalFile.tsx b/packages/jbrowse-plugin-apollo/src/components/OpenLocalFile.tsx index 6c4ee46da..2296d9d75 100644 --- a/packages/jbrowse-plugin-apollo/src/components/OpenLocalFile.tsx +++ b/packages/jbrowse-plugin-apollo/src/components/OpenLocalFile.tsx @@ -144,13 +144,13 @@ export function OpenLocalFile({ session, handleClose }: OpenLocalFileProps) { seq: seqLine.sequence, }) if (!ref) { - ref = assembly.addRefSeq(seqLine.id, seqLine.id) + ref = assembly.addRefSeq(seqLine.id, seqLine.description) } ref.addSequence({ start: 0, stop: seqLine.sequence.length, sequence: seqLine.sequence, - description: seqLine.description, + description: seqLine.description ? seqLine.description : '', }) } } @@ -267,13 +267,7 @@ export function OpenLocalFile({ session, handleClose }: OpenLocalFileProps) { /> -