@apollo-annotation/shared 0.3.12 → 1.0.0

package/package.json

@@ -1,6 +1,11 @@
 {
   "name": "@apollo-annotation/shared",
-  "version": "0.3.12",
+  "version": "1.0.0",
+  "repository": {
+    "type": "git",
+    "url": "https://github.com/GMOD/Apollo3.git",
+    "directory": "packages/apollo-shared"
+  },
   "sideEffects": false,
   "type": "module",
   "exports": "./dist/index.js",
@@ -12,9 +17,9 @@
     "test:ci": "NODE_V8_COVERAGE=./coverage glob -c \"tsx --test --test-reporter spec --experimental-test-coverage \" \"**/*.test.ts\""
   },
   "dependencies": {
-    "@apollo-annotation/common": "^0.3.12",
-    "@apollo-annotation/mst": "^0.3.12",
-    "@apollo-annotation/schemas": "^0.3.12",
+    "@apollo-annotation/common": "^1.0.0",
+    "@apollo-annotation/mst": "^1.0.0",
+    "@apollo-annotation/schemas": "^1.0.0",
     "@gmod/gff": "^2.1.0",
     "@gmod/indexedfasta": "^5.0.2",
     "@jbrowse/core": "^4.1.1",

package/src/Changes/{DeleteFeatureChange.ts → AddAndDeleteFeatureChanges.ts}

@@ -1,18 +1,36 @@
 /* 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 { AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
 import type { Feature } from '@apollo-annotation/schemas'
 
-import { AddFeatureChange } from './AddFeatureChange.js'
+interface SerializedAddFeatureChangeBase extends SerializedFeatureChange {
+  typeName: 'AddFeatureChange'
+}
+
+export interface AddFeatureChangeDetails {
+  addedFeature: AnnotationFeatureSnapshot
+  parentFeatureId?: string // Parent feature to where feature will be added
+  copyFeature?: boolean // Are we copying or adding a new child feature
+  allIds?: string[]
+}
+
+interface SerializedAddFeatureChangeSingle
+  extends SerializedAddFeatureChangeBase,
+    AddFeatureChangeDetails {}
+
+interface SerializedAddFeatureChangeMultiple
+  extends SerializedAddFeatureChangeBase {
+  changes: AddFeatureChangeDetails[]
+}
+
+export type SerializedAddFeatureChange =
+  | SerializedAddFeatureChangeSingle
+  | SerializedAddFeatureChangeMultiple
 
 interface SerializedDeleteFeatureChangeBase extends SerializedFeatureChange {
   typeName: 'DeleteFeatureChange'
@@ -36,130 +54,82 @@ export type SerializedDeleteFeatureChange =
   | SerializedDeleteFeatureChangeSingle
   | SerializedDeleteFeatureChangeMultiple
 
-export class DeleteFeatureChange extends FeatureChange {
-  typeName = 'DeleteFeatureChange' as const
-  changes: DeleteFeatureChangeDetails[]
+export class AddFeatureChange extends FeatureChange {
+  typeName = 'AddFeatureChange' as const
+  changes: AddFeatureChangeDetails[]
 
-  constructor(json: SerializedDeleteFeatureChange, options?: ChangeOptions) {
+  constructor(json: SerializedAddFeatureChange, options?: ChangeOptions) {
     super(json, options)
     this.changes = 'changes' in json ? json.changes : [json]
   }
   // eslint-disable-next-line @typescript-eslint/class-literal-property-style
   get notification() {
-    return 'Feature deleted successfully'
+    return 'Feature added successfully'
   }
 
-  toJSON(): SerializedDeleteFeatureChange {
+  toJSON(): SerializedAddFeatureChange {
     const { assembly, changedIds, changes, typeName } = this
     if (changes.length === 1) {
-      const [{ deletedFeature, parentFeatureId }] = changes
-      return { typeName, changedIds, assembly, deletedFeature, parentFeatureId }
+      const [{ addedFeature, allIds, copyFeature, parentFeatureId }] = changes
+      return {
+        typeName,
+        changedIds,
+        assembly,
+        addedFeature,
+        parentFeatureId,
+        copyFeature,
+        allIds,
+      }
     }
     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 { INDEXED_IDS } = process.env
-    let idsToIndex: string[] | undefined
-    if (INDEXED_IDS) {
-      idsToIndex = INDEXED_IDS.split(',')
-    }
+  getInverse() {
+    const { assembly, changedIds, changes, logger } = this
+    const inverseChangedIds = [...changedIds].reverse()
+    const inverseChanges = [...changes].reverse().map((addFeatureChange) => ({
+      deletedFeature: addFeatureChange.addedFeature,
+      parentFeatureId: addFeatureChange.parentFeatureId,
+    }))
 
-    // Loop the changes
-    for (const change of changes) {
-      const { deletedFeature, parentFeatureId } = change
-
-      // Search feature
-      const featureDoc = await featureModel
-        .findOne({ allIds: deletedFeature._id })
-        .session(session)
-        .exec()
-      if (!featureDoc) {
-        const errMsg = `*** ERROR: The following featureId was not found in database ='${deletedFeature._id}'`
-        logger.error(errMsg)
-        throw new Error(errMsg)
-      }
+    return new DeleteFeatureChange(
+      {
+        changedIds: inverseChangedIds,
+        typeName: 'DeleteFeatureChange',
+        changes: inverseChanges,
+        assembly,
+      },
+      { logger },
+    )
+  }
+}
 
-      // Check if feature is on top level, then simply delete the whole document (i.e. not just sub-feature inside document)
-      if (featureDoc._id.equals(deletedFeature._id)) {
-        if (parentFeatureId) {
-          throw new Error(
-            `Feature "${deletedFeature._id}" is top-level, but received a parent feature ID`,
-          )
-        }
-        await featureModel.findByIdAndDelete(featureDoc._id)
-        logger.debug?.(
-          `Feature "${deletedFeature._id}" deleted from document "${featureDoc._id}". Whole document deleted.`,
-        )
-        continue
-      }
+export function isAddFeatureChange(
+  change: unknown,
+): change is AddFeatureChange {
+  return (change as AddFeatureChange).typeName === 'AddFeatureChange'
+}
 
-      const deletedIds = findAndDeleteChildFeature(
-        featureDoc,
-        deletedFeature._id,
-        this,
-      )
-      deletedIds.push(deletedFeature._id)
-      featureDoc.allIds = featureDoc.allIds.filter(
-        (id) => !deletedIds.includes(id),
-      )
-      const indexedIds = this.getIndexedIds(featureDoc, idsToIndex)
-      if (featureDoc.indexedIds) {
-        if (indexedIds.length > 0) {
-          featureDoc.indexedIds = indexedIds
-        } else {
-          delete featureDoc.indexedIds
-        }
-      } else {
-        if (indexedIds.length > 0) {
-          featureDoc.indexedIds = indexedIds
-        }
-      }
-      // Save updated document in Mongo
-      featureDoc.markModified('children') // Mark as modified. Without this save() -method is not updating data in database
-      try {
-        await featureDoc.save()
-      } catch (error) {
-        logger.debug?.(`*** FAILED: ${error}`)
-        throw error
-      }
+export class DeleteFeatureChange extends FeatureChange {
+  typeName = 'DeleteFeatureChange' as const
+  changes: DeleteFeatureChangeDetails[]
 
-      logger.debug?.(
-        `Feature "${deletedFeature._id}" deleted from document "${featureDoc._id}"`,
-      )
-    }
+  constructor(json: SerializedDeleteFeatureChange, options?: ChangeOptions) {
+    super(json, options)
+    this.changes = 'changes' in json ? json.changes : [json]
   }
-
-  async executeOnLocalGFF3(_backend: LocalGFF3DataStore) {
-    throw new Error('executeOnLocalGFF3 not implemented')
+  // eslint-disable-next-line @typescript-eslint/class-literal-property-style
+  get notification() {
+    return 'Feature deleted successfully'
   }
 
-  async executeOnClient(dataStore: ClientDataStore) {
-    if (!dataStore) {
-      throw new Error('No data store')
-    }
-    for (const change of this.changes) {
-      const { deletedFeature, parentFeatureId } = change
-      if (parentFeatureId) {
-        const parentFeature = dataStore.getFeature(parentFeatureId)
-        if (!parentFeature) {
-          throw new Error(`Could not find parent feature "${parentFeatureId}"`)
-        }
-        parentFeature.deleteChild(deletedFeature._id)
-      } else {
-        if (dataStore.getFeature(deletedFeature._id)) {
-          dataStore.deleteFeature(deletedFeature._id)
-        }
-      }
+  toJSON(): SerializedDeleteFeatureChange {
+    const { assembly, changedIds, changes, typeName } = this
+    if (changes.length === 1) {
+      const [{ deletedFeature, parentFeatureId }] = changes
+      return { typeName, changedIds, assembly, deletedFeature, parentFeatureId }
     }
+    return { typeName, changedIds, assembly, changes }
   }
 
   getInverse() {

package/src/Changes/AddAssemblyAliasesChange.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 SerializedAssemblyAliasesChange
   extends SerializedAssemblySpecificChange {
@@ -27,16 +20,6 @@ export class AddAssemblyAliasesChange extends AssemblySpecificChange {
     this.aliases = json.aliases
   }
 
-  executeOnClient(clientDataStore: ClientDataStore) {
-    const { assemblyManager } = getSession(clientDataStore)
-    const assembly = assemblyManager.get(this.assembly)
-    if (!assembly) {
-      throw new Error(`assembly ${this.assembly} not found`)
-    }
-    assembly.configuration.aliases.set(this.aliases)
-    return Promise.resolve()
-  }
-
   getInverse(): Change {
     throw new Error('Method not implemented.')
   }
@@ -46,24 +29,6 @@ export class AddAssemblyAliasesChange extends AssemblySpecificChange {
     return { assembly, typeName, aliases }
   }
 
-  async executeOnServer(backend: ServerDataStore) {
-    const { assemblyModel } = backend
-    const { assembly, logger, aliases } = this
-    logger.debug?.(
-      `Updating assembly aliases for assembly: ${assembly}, aliases: ${JSON.stringify(aliases)}`,
-    )
-    const asm = await assemblyModel.findById(assembly)
-    if (!asm) {
-      throw new Error(`Assembly with ID ${assembly} not found`)
-    }
-    asm.aliases = aliases
-    await asm.save()
-  }
-
-  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 'Assembly aliases have been added.'

package/src/Changes/AddAssemblyAndFeaturesFromFileChange.ts

@@ -1,19 +1,9 @@
-/* eslint-disable @typescript-eslint/no-unsafe-member-access */
-/* eslint-disable @typescript-eslint/no-unsafe-argument */
-/* eslint-disable @typescript-eslint/no-unsafe-call */
-/* 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 { FromFileBaseChange } from './FromFileBaseChange.js'
-
 export interface SerializedAddAssemblyAndFeaturesFromFileChangeBase
   extends SerializedAssemblySpecificChange {
   typeName: 'AddAssemblyAndFeaturesFromFileChange'
@@ -38,7 +28,7 @@ export type SerializedAddAssemblyAndFeaturesFromFileChange =
   | SerializedAddAssemblyAndFeaturesFromFileChangeSingle
   | SerializedAddAssemblyAndFeaturesFromFileChangeMultiple
 
-export class AddAssemblyAndFeaturesFromFileChange extends FromFileBaseChange {
+export class AddAssemblyAndFeaturesFromFileChange extends AssemblySpecificChange {
   typeName = 'AddAssemblyAndFeaturesFromFileChange' as const
   changes: AddAssemblyAndFeaturesFromFileChangeDetails[]
 
@@ -63,99 +53,6 @@ export class AddAssemblyAndFeaturesFromFileChange extends FromFileBaseChange {
     return { typeName, assembly, changes }
   }
 
-  /**
-   * Applies the required change to database
-   * @param backend - parameters from backend
-   * @returns
-   */
-  async executeOnServer(backend: ServerDataStore) {
-    const { assemblyModel, checkModel, fileModel, filesService, user } = backend
-    const { assembly, changes, logger } = this
-    for (const change of changes) {
-      const { assemblyName, fileIds, parseOptions } = change
-      const fileId = fileIds.fa
-
-      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 "${fileDoc.checksum}"`)
-
-      // Check and add new assembly
-      const assemblyDoc = await assemblyModel
-        .findOne({ name: assemblyName })
-        .exec()
-      if (assemblyDoc) {
-        throw new Error(`Assembly "${assemblyName}" already exists`)
-      }
-      // get checks
-      const checkDocs = await checkModel.find({ isDefault: true }).exec()
-
-      const checks = checkDocs.map((checkDoc) => checkDoc._id.toHexString())
-      // Add assembly
-      const [newAssemblyDoc] = await assemblyModel.create([
-        { _id: assembly, name: assemblyName, user, status: -1, fileId, checks },
-      ])
-      logger.debug?.(
-        `Added new assembly "${assemblyName}", docId "${newAssemblyDoc._id.toHexString()}"`,
-      )
-      logger.debug?.(`File type: "${fileDoc.type}"`)
-
-      // 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,
-      )
-
-      const { bufferSize = 10_000, strict = true } = parseOptions ?? {}
-      const featureStream = filesService.parseGFF3(
-        filesService.getFileStream(fileDoc),
-        { bufferSize },
-      )
-      let featureCount = 0
-      let errorCount = 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
-          }
-          if (errorCount <= 99) {
-            logger.warn('Error parsing feature')
-            logger.warn(error)
-            if (errorCount === 99) {
-              logger.warn(
-                'Reached 100 parsing errors, omitting further warnings from log',
-              )
-            }
-          }
-          errorCount++
-        }
-        featureCount++
-        if (featureCount % 1000 === 0) {
-          logger.debug?.(`Processed ${featureCount} features`)
-        }
-      }
-    }
-  }
-
-  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 AddAssemblyAndFeaturesFromFileChange(

package/src/Changes/AddAssemblyFromExternalChange.ts

@@ -1,18 +1,8 @@
-/* eslint-disable @typescript-eslint/no-unsafe-member-access */
-/* eslint-disable @typescript-eslint/no-unsafe-assignment */
-/* eslint-disable @typescript-eslint/no-unnecessary-condition */
-
-/* eslint-disable @typescript-eslint/require-await */
 import {
   AssemblySpecificChange,
   type ChangeOptions,
-  type ClientDataStore,
-  type LocalGFF3DataStore,
   type SerializedAssemblySpecificChange,
-  type ServerDataStore,
 } from '@apollo-annotation/common'
-import { BgzipIndexedFasta, IndexedFasta } from '@gmod/indexedfasta'
-import { RemoteFile } from 'generic-filehandle2'
 
 export interface SerializedAddAssemblyFromExternalChangeBase
   extends SerializedAssemblySpecificChange {
@@ -62,83 +52,6 @@ export class AddAssemblyFromExternalChange extends AssemblySpecificChange {
     return { typeName, assembly, changes }
   }
 
-  /**
-   * Applies the required change to database
-   * @param backend - parameters from backend
-   * @returns
-   */
-  async executeOnServer(backend: ServerDataStore) {
-    const { assemblyModel, checkModel, refSeqModel, user } = backend
-    const { assembly, changes, logger } = this
-    const { CHUNK_SIZE } = process.env
-    const customChunkSize = CHUNK_SIZE && Number(CHUNK_SIZE)
-
-    for (const change of changes) {
-      const { assemblyName, externalLocation } = change
-      const { fa, fai, gzi } = externalLocation
-      const sequenceAdapter = gzi
-        ? new BgzipIndexedFasta({
-            fasta: new RemoteFile(fa, { fetch }),
-            fai: new RemoteFile(fai, { fetch }),
-            gzi: new RemoteFile(gzi, { fetch }),
-          })
-        : new IndexedFasta({
-            fasta: new RemoteFile(fa, { fetch }),
-            fai: new RemoteFile(fai, { fetch }),
-          })
-      const allSequenceSizes = await sequenceAdapter.getSequenceSizes()
-
-      if (!allSequenceSizes) {
-        throw new Error('No data read from indexed fasta getSequenceSizes')
-      }
-
-      const assemblyDoc = await assemblyModel
-        .findOne({ name: assemblyName })
-        .exec()
-      if (assemblyDoc) {
-        throw new Error(`Assembly "${assemblyName}" already exists`)
-      }
-      const checkDocs = await checkModel.find({ default: true }).exec()
-      const checks = checkDocs.map((checkDoc) => checkDoc._id.toHexString())
-      const [newAssemblyDoc] = await assemblyModel.create([
-        {
-          _id: assembly,
-          name: assemblyName,
-          user,
-          status: -1,
-          externalLocation,
-          checks,
-        },
-      ])
-      logger.debug?.(
-        `Added new assembly "${assemblyName}", docId "${newAssemblyDoc._id}"`,
-      )
-
-      for (const sequenceName in allSequenceSizes) {
-        const [newRefSeqDoc] = await refSeqModel.create([
-          {
-            name: sequenceName,
-            assembly: newAssemblyDoc._id,
-            length: allSequenceSizes[sequenceName],
-            ...(customChunkSize ? { chunkSize: customChunkSize } : null),
-            user,
-            status: -1,
-          },
-        ])
-        logger.debug?.(
-          `Added new refSeq "${sequenceName}", docId "${newRefSeqDoc._id}"`,
-        )
-      }
-    }
-  }
-
-  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 AddAssemblyFromExternalChange(