@apollo-annotation/shared 0.3.13 → 1.0.0

package/src/Changes/AddAssemblyFromFileChange.ts

@@ -1,18 +1,8 @@
-/* eslint-disable @typescript-eslint/no-unsafe-call */
-/* eslint-disable @typescript-eslint/no-unsafe-argument */
-/* eslint-disable @typescript-eslint/no-unsafe-member-access */
-/* eslint-disable @typescript-eslint/no-unsafe-assignment */
-/* eslint-disable @typescript-eslint/require-await */
-import type {
-  ChangeOptions,
-  ClientDataStore,
-  LocalGFF3DataStore,
-  SerializedAssemblySpecificChange,
-  ServerDataStore,
+import {
+  AssemblySpecificChange,
+  type ChangeOptions,
+  type SerializedAssemblySpecificChange,
 } from '@apollo-annotation/common'
-import { BgzipIndexedFasta } from '@gmod/indexedfasta'
-
-import { FromFileBaseChange } from './FromFileBaseChange.js'
 
 export interface SerializedAddAssemblyFromFileChangeBase
   extends SerializedAssemblySpecificChange {
@@ -37,7 +27,7 @@ export type SerializedAddAssemblyFromFileChange =
   | SerializedAddAssemblyFromFileChangeSingle
   | SerializedAddAssemblyFromFileChangeMultiple
 
-export class AddAssemblyFromFileChange extends FromFileBaseChange {
+export class AddAssemblyFromFileChange extends AssemblySpecificChange {
   typeName = 'AddAssemblyFromFileChange' as const
   changes: AddAssemblyFromFileChangeDetails[]
 
@@ -62,160 +52,6 @@ export class AddAssemblyFromFileChange extends FromFileBaseChange {
     return { typeName, assembly, changes }
   }
 
-  /**
-   * Applies the required change to database
-   * @param backend - parameters from backend
-   * @returns
-   */
-  async executeOnServer(backend: ServerDataStore) {
-    const { changes } = this
-    for (const change of changes) {
-      const { assemblyName, fileIds } = change
-      await ('gzi' in fileIds
-        ? this.executeOnServerIndexed(backend, assemblyName, fileIds)
-        : this.executeOnServerFasta(backend, assemblyName, fileIds.fa))
-    }
-  }
-
-  async executeOnServerIndexed(
-    backend: ServerDataStore,
-    assemblyName: string,
-    fileIds: { fa: string; fai: string; gzi: string },
-  ) {
-    const { CHUNK_SIZE } = process.env
-    const customChunkSize = CHUNK_SIZE && Number(CHUNK_SIZE)
-
-    const { FILE_UPLOAD_FOLDER } = process.env
-    if (!FILE_UPLOAD_FOLDER) {
-      throw new Error('No FILE_UPLOAD_FOLDER found in .env file')
-    }
-
-    const { fa: faId, fai: faiId, gzi: gziId } = fileIds
-    const {
-      assemblyModel,
-      checkModel,
-      fileModel,
-      filesService,
-      refSeqModel,
-      user,
-    } = backend
-
-    const faDoc = await fileModel.findById(faId)
-    const faChecksum = faDoc?.checksum
-    if (!faChecksum) {
-      throw new Error(`No checksum for file document ${faDoc?.id}`)
-    }
-
-    const faiDoc = await fileModel.findById(faiId)
-    const faiChecksum = faiDoc?.checksum
-    if (!faiChecksum) {
-      throw new Error(`No checksum for file document ${faiDoc?.id}`)
-    }
-
-    const gziDoc = await fileModel.findById(gziId)
-    const gziChecksum = gziDoc?.checksum
-    if (!gziChecksum) {
-      throw new Error(`No checksum for file document ${gziDoc?.id}`)
-    }
-
-    const fasta = filesService.getFileHandle(faDoc)
-    const fai = filesService.getFileHandle(faiDoc)
-    const gzi = filesService.getFileHandle(gziDoc)
-    const sequenceAdapter = new BgzipIndexedFasta({ fasta, fai, gzi })
-    const allSequenceSizes = await sequenceAdapter.getSequenceSizes()
-    await Promise.all([fasta.close(), fai.close(), gzi.close()])
-
-    const assemblyDoc = await assemblyModel
-      .findOne({ name: assemblyName })
-      .exec()
-    if (assemblyDoc) {
-      throw new Error(`Assembly "${assemblyName}" already exists`)
-    }
-    const checkDocs = await checkModel.find({ isDefault: true }).exec()
-    const checks = checkDocs.map((checkDoc) => checkDoc._id.toHexString())
-    const [newAssemblyDoc] = await assemblyModel.create([
-      {
-        _id: this.assembly,
-        name: assemblyName,
-        user,
-        status: -1,
-        fileIds,
-        checks,
-      },
-    ])
-    this.logger.debug?.(
-      `Added new assembly "${assemblyName}", docId "${newAssemblyDoc._id}"`,
-    )
-
-    for (const sequenceName in allSequenceSizes) {
-      const [newRefSeqDoc] = await refSeqModel.create([
-        {
-          name: sequenceName,
-          assembly: newAssemblyDoc._id,
-          length: allSequenceSizes[sequenceName],
-          ...(customChunkSize ? { chunkSize: customChunkSize } : null),
-          user,
-          status: -1,
-        },
-      ])
-      this.logger.debug?.(
-        `Added new refSeq "${sequenceName}", docId "${newRefSeqDoc._id}"`,
-      )
-    }
-  }
-
-  async executeOnServerFasta(
-    backend: ServerDataStore,
-    assemblyName: string,
-    fileId: string,
-  ) {
-    const { assemblyModel, checkModel, fileModel, user } = backend
-    // Get file checksum
-    const fileDoc = await fileModel.findById(fileId).exec()
-    if (!fileDoc) {
-      throw new Error(`File "${fileId}" not found in Mongo`)
-    }
-    this.logger.debug?.(`FileId "${fileId}", checksum "${fileDoc.checksum}"`)
-
-    // Check and add new assembly
-    const assemblyDoc = await assemblyModel
-      .findOne({ name: assemblyName })
-      .exec()
-    if (assemblyDoc) {
-      throw new Error(`Assembly "${assemblyName}" already exists`)
-    }
-    const checkDocs = await checkModel.find({ default: true }).exec()
-    const checks = checkDocs.map((checkDoc) => checkDoc._id.toHexString())
-    // Add assembly
-    const [newAssemblyDoc] = await assemblyModel.create([
-      {
-        _id: this.assembly,
-        name: assemblyName,
-        user,
-        status: -1,
-        fileIds: { fa: fileId },
-        checks,
-      },
-    ])
-    this.logger.debug?.(
-      `Added new assembly "${assemblyName}", docId "${newAssemblyDoc._id}"`,
-    )
-    this.logger.debug?.(
-      `File type: "${fileDoc.type}", assemblyId: "${newAssemblyDoc._id}"`,
-    )
-
-    // Add refSeqs
-    // We cannot use Mongo 'session' / transaction here because Mongo has 16 MB limit for transaction
-    await this.addRefSeqIntoDb(fileDoc, newAssemblyDoc._id.toString(), backend)
-  }
-
-  async executeOnLocalGFF3(_backend: LocalGFF3DataStore) {
-    throw new Error('executeOnLocalGFF3 not implemented')
-  }
-
-  // eslint-disable-next-line @typescript-eslint/no-empty-function
-  async executeOnClient(_dataStore: ClientDataStore) {}
-
   getInverse() {
     const { assembly, changes, logger, typeName } = this
     return new AddAssemblyFromFileChange(

package/src/Changes/AddFeaturesFromFileChange.ts

@@ -1,14 +1,9 @@
-/* eslint-disable @typescript-eslint/require-await */
-import type {
-  ChangeOptions,
-  ClientDataStore,
-  LocalGFF3DataStore,
-  SerializedAssemblySpecificChange,
-  ServerDataStore,
+import {
+  AssemblySpecificChange,
+  type ChangeOptions,
+  type SerializedAssemblySpecificChange,
 } from '@apollo-annotation/common'
 
-import { FromFileBaseChange } from './FromFileBaseChange.js'
-
 export interface SerializedAddFeaturesFromFileChangeBase
   extends SerializedAssemblySpecificChange {
   typeName: 'AddFeaturesFromFileChange'
@@ -33,7 +28,7 @@ export type SerializedAddFeaturesFromFileChange =
   | SerializedAddFeaturesFromFileChangeSingle
   | SerializedAddFeaturesFromFileChangeMultiple
 
-export class AddFeaturesFromFileChange extends FromFileBaseChange {
+export class AddFeaturesFromFileChange extends AssemblySpecificChange {
   typeName = 'AddFeaturesFromFileChange' as const
   changes: AddFeaturesFromFileChangeDetails[]
   deleteExistingFeatures = false
@@ -61,82 +56,6 @@ export class AddFeaturesFromFileChange extends FromFileBaseChange {
     return { typeName, assembly, changes, deleteExistingFeatures }
   }
 
-  /**
-   * Applies the required change to database
-   * @param backend - parameters from backend
-   * @returns
-   */
-  async executeOnServer(backend: ServerDataStore) {
-    const { fileModel, filesService } = backend
-    const { changes, deleteExistingFeatures, logger } = this
-
-    if (deleteExistingFeatures) {
-      await this.removeExistingFeatures(backend)
-    }
-
-    for (const change of changes) {
-      const { fileId, parseOptions } = change
-
-      const { FILE_UPLOAD_FOLDER } = process.env
-      if (!FILE_UPLOAD_FOLDER) {
-        throw new Error('No FILE_UPLOAD_FOLDER found in .env file')
-      }
-      // Get file checksum
-      const fileDoc = await fileModel.findById(fileId).exec()
-      if (!fileDoc) {
-        throw new Error(`File "${fileId}" not found in Mongo`)
-      }
-      logger.debug?.(`FileId "${fileId}", checksum "${fileDoc.checksum}"`)
-
-      let errorCount = 0
-      // eslint-disable-next-line unicorn/consistent-function-scoping
-      const errorLogger = (error: unknown) => {
-        if (errorCount <= 99) {
-          logger.warn('Error parsing or adding feature')
-          logger.warn(error)
-          if (errorCount === 99) {
-            logger.warn(
-              'Reached 100 feature errors, omitting further warnings from log',
-            )
-          }
-        }
-        errorCount++
-      }
-
-      // Read data from compressed file and parse the content
-      const { bufferSize = 10_000, strict = true } = parseOptions ?? {}
-      const featureStream = filesService.parseGFF3(
-        filesService.getFileStream(fileDoc),
-        { bufferSize, errorCallback: strict ? undefined : errorLogger },
-      )
-      let featureCount = 0
-      for await (const gff3Feature of featureStream) {
-        // Add new feature into database
-        try {
-          await this.addFeatureIntoDb(gff3Feature, backend)
-        } catch (error) {
-          // if the first feature is an error, assume the file isn't valid and throw
-          if (strict || featureCount === 0) {
-            throw error
-          }
-          errorLogger(error)
-        }
-        featureCount++
-        if (featureCount % 1000 === 0) {
-          logger.debug?.(`Processed ${featureCount} features`)
-        }
-      }
-    }
-    logger.debug?.('New features added into database!')
-  }
-
-  async executeOnLocalGFF3(_backend: LocalGFF3DataStore) {
-    throw new Error('executeOnLocalGFF3 not implemented')
-  }
-
-  // eslint-disable-next-line @typescript-eslint/no-empty-function
-  async executeOnClient(_dataStore: ClientDataStore) {}
-
   getInverse() {
     const { assembly, changes, logger, typeName } = this
     return new AddFeaturesFromFileChange(

package/src/Changes/AddRefSeqAliasesChange.ts

@@ -1,16 +1,9 @@
-/* eslint-disable @typescript-eslint/no-unsafe-member-access */
-/* eslint-disable @typescript-eslint/no-unsafe-call */
-/* eslint-disable @typescript-eslint/no-unsafe-assignment */
 import {
   AssemblySpecificChange,
   type Change,
   type ChangeOptions,
-  type ClientDataStore,
-  type LocalGFF3DataStore,
   type SerializedAssemblySpecificChange,
-  type ServerDataStore,
 } from '@apollo-annotation/common'
-import { getSession } from '@jbrowse/core/util'
 
 export interface SerializedRefSeqAliases {
   refName: string
@@ -32,24 +25,6 @@ export class AddRefSeqAliasesChange extends AssemblySpecificChange {
     this.refSeqAliases = json.refSeqAliases
   }
 
-  executeOnClient(clientDataStore: ClientDataStore) {
-    const { assemblyManager } = getSession(clientDataStore)
-    const assembly = assemblyManager.get(this.assembly)
-    if (!assembly) {
-      throw new Error(`assembly ${this.assembly} not found`)
-    }
-    const sessionAliases = assembly.refNameAliases ?? {}
-
-    for (const refSeqAlias of this.refSeqAliases) {
-      const { aliases, refName } = refSeqAlias
-      for (const alias of aliases) {
-        sessionAliases[alias] = refName
-      }
-    }
-    assembly.setRefNameAliases(sessionAliases)
-    return Promise.resolve()
-  }
-
   getInverse(): Change {
     throw new Error('Method not implemented.')
   }
@@ -59,25 +34,6 @@ export class AddRefSeqAliasesChange extends AssemblySpecificChange {
     return { assembly, typeName, refSeqAliases }
   }
 
-  async executeOnServer(backend: ServerDataStore) {
-    const { refSeqModel, session } = backend
-    const { assembly, logger, refSeqAliases } = this
-
-    for (const refSeqAlias of refSeqAliases) {
-      logger.debug?.(
-        `Updating Refname alias for assembly: ${assembly}, refSeqAlias: ${JSON.stringify(refSeqAlias)}`,
-      )
-      const { aliases, refName } = refSeqAlias
-      await refSeqModel
-        .updateOne({ assembly, name: refName }, { $set: { aliases } })
-        .session(session)
-    }
-  }
-
-  executeOnLocalGFF3(_backend: LocalGFF3DataStore): Promise<unknown> {
-    throw new Error('Method not implemented.')
-  }
-
   // eslint-disable-next-line @typescript-eslint/class-literal-property-style
   get notification(): string {
     return 'RefSeq aliases have been added.'

package/src/Changes/DeleteAssemblyChange.ts

@@ -1,16 +1,7 @@
-/* eslint-disable @typescript-eslint/no-unsafe-assignment */
-/* eslint-disable @typescript-eslint/no-unsafe-return */
-/* eslint-disable @typescript-eslint/require-await */
-/* eslint-disable @typescript-eslint/no-unnecessary-condition */
-/* eslint-disable @typescript-eslint/no-unsafe-call */
 import {
   AssemblySpecificChange,
-  type ClientDataStore,
-  type LocalGFF3DataStore,
   type SerializedAssemblySpecificChange,
-  type ServerDataStore,
 } from '@apollo-annotation/common'
-import { getSession } from '@jbrowse/core/util'
 
 export interface SerializedDeleteAssemblyChange
   extends SerializedAssemblySpecificChange {
@@ -28,69 +19,6 @@ export class DeleteAssemblyChange extends AssemblySpecificChange {
     return { typeName, assembly }
   }
 
-  /**
-   * Applies the required change to database
-   * @param backend - parameters from backend
-   * @returns
-   */
-  async executeOnServer(backend: ServerDataStore) {
-    const {
-      assemblyModel,
-      featureModel,
-      refSeqChunkModel,
-      refSeqModel,
-      session,
-    } = backend
-    const { assembly, logger } = this
-
-    const assemblyDoc = await assemblyModel
-      .findById(assembly)
-      .session(session)
-      .exec()
-    if (!assemblyDoc) {
-      const errMsg = `*** ERROR: Assembly with id "${assembly}" not found`
-      logger.error(errMsg)
-      throw new Error(errMsg)
-    }
-
-    // We cannot use Mongo 'session' / transaction here because Mongo has 16 MB limit for transaction
-
-    // Get RefSeqs
-    const refSeqs = await refSeqModel.find({ assembly }).exec()
-    const refSeqIds = refSeqs.map((refSeq) => refSeq._id)
-
-    // Get and delete RefSeqChunks
-    await refSeqChunkModel.deleteMany({ refSeq: refSeqIds }).exec()
-
-    // Get and delete Features
-    await featureModel.deleteMany({ refSeq: refSeqIds }).exec()
-
-    // Delete RefSeqs and Assembly
-    await refSeqModel.deleteMany({ assembly }).exec()
-    await assemblyModel.findByIdAndDelete(assembly).exec()
-
-    logger.debug?.(`Assembly "${assembly}" deleted from database.`)
-  }
-
-  async executeOnLocalGFF3(_backend: LocalGFF3DataStore) {
-    throw new Error('executeOnLocalGFF3 not implemented')
-  }
-
-  async executeOnClient(dataStore: ClientDataStore) {
-    const { assembly } = this
-    if (!dataStore) {
-      throw new Error('No data store')
-    }
-    const session = getSession(dataStore)
-    // If assemblyId is not present in client data store
-    if (dataStore.assemblies.has(assembly)) {
-      dataStore.deleteAssembly(assembly)
-    }
-    await session.removeAssembly?.(assembly)
-    // @ts-expect-error this isn't on the AbstractSessionModel
-    await session.removeSessionAssembly?.(assembly)
-  }
-
   getInverse() {
     const { assembly, logger } = this
     return new DeleteAssemblyChange(

package/src/Changes/DeleteUserChange.ts

@@ -1,11 +1,7 @@
-/* eslint-disable @typescript-eslint/require-await */
 import {
   Change,
   type ChangeOptions,
-  type ClientDataStore,
-  type LocalGFF3DataStore,
   type SerializedChange,
-  type ServerDataStore,
 } from '@apollo-annotation/common'
 
 export interface SerializedDeleteUserChangeBase extends SerializedChange {
@@ -45,27 +41,6 @@ export class DeleteUserChange extends Change {
     return { typeName, userId }
   }
 
-  async executeOnServer(backend: ServerDataStore) {
-    const { session, userModel } = backend
-    const { logger, userId } = this
-    const user = await userModel
-      .findOneAndDelete({ _id: userId })
-      .session(session)
-      .exec()
-    if (!user) {
-      const errMsg = `*** ERROR: User with id "${userId}" not found`
-      logger.error(errMsg)
-      throw new Error(errMsg)
-    }
-  }
-
-  async executeOnLocalGFF3(_backend: LocalGFF3DataStore) {
-    throw new Error('executeOnLocalGFF3 not implemented')
-  }
-
-  // eslint-disable-next-line @typescript-eslint/no-empty-function
-  async executeOnClient(_dataStore: ClientDataStore) {}
-
   getInverse() {
     const { logger, typeName, userId } = this
     return new DeleteUserChange({ typeName, userId }, { logger })

package/src/Changes/FeatureAttributeChange.ts

@@ -1,15 +1,9 @@
-/* eslint-disable @typescript-eslint/restrict-template-expressions */
-/* eslint-disable @typescript-eslint/require-await */
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 import {
   type ChangeOptions,
-  type ClientDataStore,
   FeatureChange,
-  type LocalGFF3DataStore,
   type SerializedFeatureChange,
-  type ServerDataStore,
 } from '@apollo-annotation/common'
-import type { Feature, FeatureDocument } from '@apollo-annotation/schemas'
 
 interface SerializedFeatureAttributeChangeBase extends SerializedFeatureChange {
   typeName: 'FeatureAttributeChange'
@@ -59,104 +53,6 @@ export class FeatureAttributeChange extends FeatureChange {
     return { typeName, changedIds, assembly, changes }
   }
 
-  /**
-   * Applies the required change to database
-   * @param backend - parameters from backend
-   * @returns
-   */
-  async executeOnServer(backend: ServerDataStore) {
-    const { featureModel, session } = backend
-    const { changes, logger } = this
-
-    const featuresForChanges: {
-      feature: Feature
-      topLevelFeature: FeatureDocument
-    }[] = []
-    // Loop the changes and check that all features are found
-    for (const change of changes) {
-      const { featureId } = change
-
-      // Search correct feature
-      const topLevelFeature = await featureModel
-        .findOne({ allIds: featureId })
-        .session(session)
-        .exec()
-
-      if (!topLevelFeature) {
-        const errMsg = `*** ERROR: The following featureId was not found in database ='${featureId}'`
-        logger.error(errMsg)
-        throw new Error(errMsg)
-        // throw new NotFoundException(errMsg)  -- This is causing runtime error because Exception comes from @nestjs/common!!!
-      }
-      logger.debug?.(`*** Feature found: ${JSON.stringify(topLevelFeature)}`)
-
-      const foundFeature = this.getFeatureFromId(topLevelFeature, featureId)
-      if (!foundFeature) {
-        const errMsg = 'ERROR when searching feature by featureId'
-        logger.error(errMsg)
-        throw new Error(errMsg)
-      }
-      logger.debug?.(`*** Found feature: ${JSON.stringify(foundFeature)}`)
-      featuresForChanges.push({ feature: foundFeature, topLevelFeature })
-    }
-
-    const { INDEXED_IDS } = process.env
-    let idsToIndex: string[] | undefined
-    if (INDEXED_IDS) {
-      idsToIndex = INDEXED_IDS.split(',')
-    }
-    // Let's update objects
-    for (const [idx, change] of changes.entries()) {
-      const { newAttributes } = change
-      const { feature, topLevelFeature } = featuresForChanges[idx]
-      const indexedIdsChanged = idsToIndex?.some(
-        (id) => id in newAttributes || id in (feature?.attributes ?? {}),
-      )
-      feature.attributes = newAttributes
-      if (indexedIdsChanged) {
-        const indexedIds = this.getIndexedIds(topLevelFeature, idsToIndex)
-        topLevelFeature.indexedIds = indexedIds
-        topLevelFeature.markModified('indexedIds')
-      }
-      if (topLevelFeature._id.equals(feature._id)) {
-        topLevelFeature.markModified('attributes') // Mark as modified. Without this save() -method is not updating data in database
-      } else {
-        topLevelFeature.markModified('children') // Mark as modified. Without this save() -method is not updating data in database
-      }
-
-      try {
-        await topLevelFeature.save()
-      } catch (error) {
-        logger.debug?.(`*** FAILED: ${error}`)
-        throw error
-      }
-      logger.debug?.(
-        `*** Feature attributes modified (added, edited or deleted), docId: ${JSON.stringify(
-          topLevelFeature,
-        )}`,
-      )
-    }
-  }
-
-  async executeOnLocalGFF3(_backend: LocalGFF3DataStore) {
-    throw new Error('applyToLocalGFF3 not implemented')
-  }
-
-  async executeOnClient(dataStore: ClientDataStore) {
-    if (!dataStore) {
-      throw new Error('No data store')
-    }
-    for (const [idx, changedId] of this.changedIds.entries()) {
-      const feature = dataStore.getFeature(changedId)
-      if (!feature) {
-        throw new Error(`Could not find feature with identifier "${changedId}"`)
-      }
-      feature.setAttributes(
-        new Map(Object.entries(this.changes[idx].newAttributes)),
-      )
-    }
-  }
-
   getInverse() {
     const { assembly, changedIds, changes, logger } = this
     const inverseChangedIds = [...changedIds].reverse()

package/src/Changes/ImportJBrowseConfigChange.ts

@@ -1,11 +1,4 @@
-/* eslint-disable @typescript-eslint/require-await */
-import {
-  Change,
-  type ChangeOptions,
-  type ClientDataStore,
-  type LocalGFF3DataStore,
-  type ServerDataStore,
-} from '@apollo-annotation/common'
+import { Change, type ChangeOptions } from '@apollo-annotation/common'
 
 interface JBrowseAssembly {
   sequence: { adapter: { type: string } }
@@ -99,25 +92,6 @@ export class ImportJBrowseConfigChange extends Change {
     return { typeName, oldJBrowseConfig, newJBrowseConfig }
   }
 
-  async executeOnServer(backend: ServerDataStore) {
-    const { jbrowseConfigModel } = backend
-    const { logger, newJBrowseConfig } = this
-    await jbrowseConfigModel.deleteMany()
-    if (!newJBrowseConfig) {
-      return
-    }
-    const filteredConfig = filterJBrowseConfig(newJBrowseConfig)
-    await jbrowseConfigModel.create(filteredConfig)
-    logger.debug?.('Stored new JBrowse Config')
-  }
-
-  async executeOnLocalGFF3(_backend: LocalGFF3DataStore) {
-    throw new Error('executeOnLocalGFF3 not implemented')
-  }
-
-  // eslint-disable-next-line @typescript-eslint/no-empty-function
-  async executeOnClient(_dataStore: ClientDataStore) {}
-
   getInverse() {
     const { logger, newJBrowseConfig, oldJBrowseConfig } = this
     return new ImportJBrowseConfigChange(