@apollo-annotation/common 0.1.17 → 0.1.19

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@apollo-annotation/common",
-  "version": "0.1.17",
+  "version": "0.1.19",
   "repository": {
     "type": "git",
     "url": "https://github.com/GMOD/Apollo3.git",
@@ -11,9 +11,9 @@
     "build": "tsc"
   },
   "dependencies": {
-    "@apollo-annotation/schemas": "^0.1.17",
+    "@apollo-annotation/schemas": "^0.1.19",
     "@gmod/gff": "1.2.0",
-    "@jbrowse/core": "^2.7.0",
+    "@jbrowse/core": "^2.13.1",
     "bson-objectid": "^2.0.4",
     "tslib": "^2.3.1"
   },
@@ -30,12 +30,12 @@
     "tss-react": "^4.6.1"
   },
   "devDependencies": {
-    "@apollo-annotation/mst": "^0.1.17",
+    "@apollo-annotation/mst": "^0.1.19",
     "@nestjs/common": "^10.1.0",
     "@nestjs/core": "^10.1.0",
     "@types/node": "^18.14.2",
     "mongoose": "^6.12.0",
-    "typescript": "^5.1.6"
+    "typescript": "^5.5.3"
   },
   "publishConfig": {
     "access": "public"

package/src/AssemblySpecificChange.ts

@@ -1,16 +1,5 @@
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
-/* eslint-disable @typescript-eslint/no-unsafe-assignment */
-/* eslint-disable @typescript-eslint/no-unsafe-member-access */
-/* eslint-disable @typescript-eslint/no-unsafe-call */
-/* eslint-disable @typescript-eslint/no-unsafe-argument */
-/* eslint-disable @typescript-eslint/restrict-template-expressions */
-import type { AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
-import { FileDocument, RefSeqDocument } from '@apollo-annotation/schemas'
-import { GFF3Feature } from '@gmod/gff'
-import ObjectID from 'bson-objectid'
-
 import { Change, ChangeOptions, SerializedChange, isChange } from './Change'
-import { ServerDataStore } from './Operation'
 
 export interface SerializedAssemblySpecificChange extends SerializedChange {
   assembly: string
@@ -32,437 +21,4 @@ export abstract class AssemblySpecificChange extends Change {
     super(json, options)
     this.assembly = json.assembly
   }
-
-  async addRefSeqIntoDb(
-    fileDoc: FileDocument,
-    assembly: string,
-    backend: ServerDataStore,
-  ) {
-    const { logger } = this
-    const { filesService, refSeqChunkModel, refSeqModel, user } = backend
-    const { CHUNK_SIZE } = process.env
-    const customChunkSize = CHUNK_SIZE && Number(CHUNK_SIZE)
-    let chunkIndex = 0
-    let refSeqLen = 0
-    let refSeqDoc: RefSeqDocument | undefined
-    let fastaInfoStarted = fileDoc.type !== 'text/x-gff3'
-
-    // Read data from compressed file and parse the content
-    const sequenceStream = filesService.getFileStream(fileDoc)
-    let sequenceBuffer = ''
-    let incompleteLine = ''
-    let lastLineIsIncomplete = true
-    let parsingStarted = false
-    logger.debug?.('starting sequence stream')
-    for await (const data of sequenceStream) {
-      const chunk = data.toString()
-      lastLineIsIncomplete = !chunk.endsWith('\n')
-      // chunk is small enough that you can split the whole thing into lines without having to make it into smaller chunks first.
-      const lines = chunk.split(/\r?\n/)
-      if (incompleteLine) {
-        lines[0] = `${incompleteLine}${lines[0]}`
-        incompleteLine = ''
-      }
-      if (lastLineIsIncomplete) {
-        incompleteLine = lines.pop() || ''
-      }
-      for await (const line of lines) {
-        // In case of GFF3 file we start to read sequence after '##FASTA' is found
-        if (!fastaInfoStarted) {
-          if (line.trim() === '##FASTA') {
-            fastaInfoStarted = true
-          }
-          continue
-        }
-        const refSeqInfoLine = /^>\s*(\S+)\s*(.*)/.exec(line)
-        // Add new ref sequence info if we are reference seq info line
-        if (refSeqInfoLine) {
-          parsingStarted = true
-          logger.debug?.(
-            `Reference sequence information line "${refSeqInfoLine}"`,
-          )
-
-          // If there is sequence from previous reference sequence then we need to add it to previous ref seq
-          if (sequenceBuffer !== '') {
-            if (!refSeqDoc) {
-              throw new Error('No refSeq document found')
-            }
-            refSeqLen += sequenceBuffer.length
-            logger.debug?.(
-              `Creating refSeq chunk number ${chunkIndex} of "${refSeqDoc._id}"`,
-            )
-            // We cannot use Mongo 'session' / transaction here because Mongo has 16 MB limit for transaction
-            await refSeqChunkModel.create([
-              {
-                refSeq: refSeqDoc._id,
-                n: chunkIndex,
-                sequence: sequenceBuffer,
-                user,
-                status: -1,
-              },
-            ])
-            sequenceBuffer = ''
-          }
-          await refSeqDoc?.updateOne({ length: refSeqLen })
-          // await refSeqDoc?.updateOne({ length: refSeqLen }, { session })
-          refSeqLen = 0
-          chunkIndex = 0
-
-          const name = refSeqInfoLine[1].trim()
-          const description = refSeqInfoLine[2] ? refSeqInfoLine[2].trim() : ''
-
-          // We cannot use Mongo 'session' / transaction here because Mongo has 16 MB limit for transaction
-          const [newRefSeqDoc] = await refSeqModel.create([
-            {
-              name,
-              description,
-              assembly,
-              length: 0,
-              ...(customChunkSize ? { chunkSize: customChunkSize } : null),
-              user,
-              status: -1,
-            },
-          ])
-          logger.debug?.(
-            `Added new refSeq "${name}", desc "${description}", docId "${newRefSeqDoc._id}"`,
-          )
-          refSeqDoc = newRefSeqDoc
-        } else if (/\S/.test(line)) {
-          if (!refSeqDoc) {
-            throw new Error('No refSeq document found')
-          }
-          const { _id, chunkSize } = refSeqDoc
-          sequenceBuffer += line.replaceAll(/\s/g, '')
-          // If sequence block > chunk size then save chunk into Mongo
-          while (sequenceBuffer.length >= chunkSize) {
-            const sequence = sequenceBuffer.slice(0, chunkSize)
-            refSeqLen += sequence.length
-            logger.debug?.(
-              `Creating refSeq chunk number ${chunkIndex} of "${_id}"`,
-            )
-            // We cannot use Mongo 'session' / transaction here because Mongo has 16 MB limit for transaction
-            await refSeqChunkModel.create([
-              { refSeq: _id, n: chunkIndex, sequence, user, status: -1 },
-            ])
-            chunkIndex++
-            // Set remaining sequence
-            sequenceBuffer = sequenceBuffer.slice(chunkSize)
-            logger.debug?.(`Remaining sequence: "${sequenceBuffer}"`)
-          }
-        }
-      }
-    }
-    if (!parsingStarted) {
-      throw new Error('No reference sequences found in file')
-    }
-
-    if (sequenceBuffer || lastLineIsIncomplete) {
-      if (!refSeqDoc) {
-        throw new Error('No refSeq document found')
-      }
-      // If the file did not end with line break so the last line is incomplete
-      if (lastLineIsIncomplete) {
-        sequenceBuffer += incompleteLine
-      }
-      refSeqLen += sequenceBuffer.length
-      logger.verbose?.(
-        `*** Add the very last chunk to ref seq ("${refSeqDoc._id}", index ${chunkIndex} and total length for ref seq is ${refSeqLen}): "${sequenceBuffer}"`,
-      )
-      logger.debug?.(
-        `Creating refSeq chunk number ${chunkIndex} of "${refSeqDoc._id}"`,
-      )
-      // We cannot use Mongo 'session' / transaction here because Mongo has 16 MB limit for transaction
-      await refSeqChunkModel.create([
-        {
-          refSeq: refSeqDoc._id,
-          n: chunkIndex,
-          sequence: sequenceBuffer,
-          user,
-          status: -1,
-        },
-      ])
-      await refSeqDoc.updateOne({ length: refSeqLen })
-    }
-  }
-
-  private refSeqCache = new Map<string, RefSeqDocument>()
-
-  async removeExistingFeatures(backend: ServerDataStore) {
-    const { featureModel, refSeqModel } = backend
-    const { assembly, logger } = this
-    logger.debug?.(`Removing existing features for assembly = ${assembly}`)
-
-    const refSeqs: RefSeqDocument[] = await refSeqModel
-      .find({ assembly })
-      .exec()
-
-    for (const refSeq of refSeqs) {
-      await featureModel.deleteMany({ refSeq: refSeq._id })
-    }
-  }
-
-  async addFeatureIntoDb(gff3Feature: GFF3Feature, backend: ServerDataStore) {
-    const { featureModel, refSeqModel, user } = backend
-    const { assembly, logger, refSeqCache } = this
-
-    const [{ seq_id: refName }] = gff3Feature
-    if (!refName) {
-      throw new Error(
-        `Valid seq_id not found in feature ${JSON.stringify(gff3Feature)}`,
-      )
-    }
-    let refSeqDoc = refSeqCache.get(refName)
-    if (!refSeqDoc) {
-      refSeqDoc =
-        (await refSeqModel.findOne({ assembly, name: refName }).exec()) ??
-        undefined
-      if (refSeqDoc) {
-        refSeqCache.set(refName, refSeqDoc)
-      }
-    }
-    if (!refSeqDoc) {
-      throw new Error(
-        `RefSeq was not found by assembly "${assembly}" and seq_id "${refName}" not found`,
-      )
-    }
-    // Let's add featureId to parent feature
-    const featureIds: string[] = []
-
-    const newFeature = createFeature(gff3Feature, refSeqDoc._id, featureIds)
-    logger.debug?.(`So far feature ids are: ${featureIds.toString()}`)
-    // Add value to gffId
-    newFeature.attributes?._id
-      ? (newFeature.gffId = newFeature.attributes?._id.toString())
-      : (newFeature.gffId = newFeature._id)
-    logger.debug?.(
-      `********************* Assembly specific change create ${JSON.stringify(
-        newFeature,
-      )}`,
-    )
-
-    // Add into Mongo
-    // We cannot use Mongo 'session' / transaction here because Mongo has 16 MB limit for transaction
-    const [newFeatureDoc] = await featureModel.create([
-      { allIds: featureIds, ...newFeature, user, status: -1 },
-    ])
-    logger.verbose?.(`Added docId "${newFeatureDoc._id}"`)
-  }
-}
-
-function createFeature(
-  gff3Feature: GFF3Feature,
-  refSeq: string,
-  featureIds?: string[],
-): AnnotationFeatureSnapshot {
-  const [firstFeature] = gff3Feature
-  const {
-    attributes,
-    child_features: childFeatures,
-    end,
-    phase,
-    score,
-    seq_id: refName,
-    source,
-    start,
-    strand,
-    type,
-  } = 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: new ObjectID().toHexString(),
-    gffId: '',
-    refSeq,
-    type,
-    start: start - 1,
-    end,
-  }
-  if (gff3Feature.length > 1) {
-    const lastEnd = Math.max(
-      ...gff3Feature.map((f) => {
-        if (f.end === null) {
-          throw new Error(`feature does not have end: ${JSON.stringify(f)}`)
-        }
-        return f.end
-      }),
-    )
-    feature.end = lastEnd
-    feature.discontinuousLocations = gff3Feature.map((f) => {
-      const { end: subEnd, phase: locationPhase, start: subStart } = f
-      if (subStart === null || subEnd === null) {
-        throw new Error(
-          `feature does not have start and/or end: ${JSON.stringify(f)}`,
-        )
-      }
-      let parsedPhase: 0 | 1 | 2 | undefined
-      if (locationPhase) {
-        switch (locationPhase) {
-          case '0': {
-            parsedPhase = 0
-
-            break
-          }
-          case '1': {
-            parsedPhase = 1
-
-            break
-          }
-          case '2': {
-            parsedPhase = 2
-
-            break
-          }
-          default: {
-            throw new Error(`Unknown phase: "${locationPhase}"`)
-          }
-        }
-      }
-      return { start: subStart - 1, end: subEnd, phase: parsedPhase }
-    })
-  }
-  if (strand) {
-    if (strand === '+') {
-      feature.strand = 1
-    } else if (strand === '-') {
-      feature.strand = -1
-    } else {
-      throw new Error(`Unknown strand: "${strand}"`)
-    }
-  }
-  if (score !== null) {
-    feature.score = score
-  }
-  if (phase) {
-    switch (phase) {
-      case '0': {
-        feature.phase = 0
-
-        break
-      }
-      case '1': {
-        feature.phase = 1
-
-        break
-      }
-      case '2': {
-        feature.phase = 2
-
-        break
-      }
-      default: {
-        throw new Error(`Unknown phase: "${phase}"`)
-      }
-    }
-  }
-  if (featureIds) {
-    featureIds.push(feature._id)
-  }
-
-  if (childFeatures?.length) {
-    const children: Record<string, AnnotationFeatureSnapshot> = {}
-    for (const childFeature of childFeatures) {
-      const child = createFeature(childFeature, refSeq, featureIds)
-      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<string, string[]> = {}
-    if (source) {
-      attrs.source = [source]
-    }
-    if (attributes) {
-      for (const [key, val] of Object.entries(attributes)) {
-        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[] = []
-                for (const v of val) {
-                  if (v.startsWith('GO:')) {
-                    goTerms.push(v)
-                  } else {
-                    otherTerms.push(v)
-                  }
-                }
-                if (goTerms.length > 0) {
-                  attrs['Gene Ontology'] = goTerms
-                }
-                if (otherTerms.length > 0) {
-                  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
 }

package/src/Change.ts

@@ -1,9 +1,10 @@
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 /* eslint-disable @typescript-eslint/restrict-template-expressions */
 import {
-  AnnotationFeatureI,
+  AnnotationFeature,
   AnnotationFeatureSnapshot,
   ApolloAssemblyI,
+  BackendDriverType,
   CheckResultI,
   CheckResultSnapshot,
 } from '@apollo-annotation/mst'
@@ -28,12 +29,15 @@ export interface ClientDataStore {
   ): AppRootModel['internetAccounts'][0]
   loadFeatures(regions: Region[]): void
   loadRefSeq(regions: Region[]): void
-  getFeature(featureId: string): AnnotationFeatureI | undefined
+  getFeature(featureId: string): AnnotationFeature | undefined
   addFeature(assemblyId: string, feature: AnnotationFeatureSnapshot): void
   deleteFeature(featureId: string): void
   deleteAssembly(assemblyId: string): void
   addCheckResults(checkResults: CheckResultSnapshot[]): void
-  addAssembly(assemblyId: string): ApolloAssemblyI
+  addAssembly(
+    assemblyId: string,
+    backendDriverType?: BackendDriverType,
+  ): ApolloAssemblyI
 }
 
 export type SerializedChange = SerializedOperation

package/src/Operation.ts

@@ -10,6 +10,7 @@ import {
   FileDocument,
   RefSeqChunkDocument,
   RefSeqDocument,
+  JBrowseConfigDocument,
   UserDocument,
 } from '@apollo-annotation/schemas'
 import type { LoggerService } from '@nestjs/common'
@@ -36,6 +37,7 @@ export interface ServerDataStore {
   refSeqChunkModel: Model<RefSeqChunkDocument>
   fileModel: Model<FileDocument>
   userModel: Model<UserDocument>
+  jbrowseConfigModel: Model<JBrowseConfigDocument>
   session: ClientSession
   filesService: {
     getFileStream(file: FileDocument): ReadStream

package/tsconfig.json

@@ -14,7 +14,5 @@
     "strictPropertyInitialization": false,
   },
   "include": ["./src"],
-  "references": [
-    { "path": "../apollo-schemas"},
-  ]
+  "references": [{ "path": "../apollo-schemas" }, { "path": "../apollo-mst" }],
 }