@apollo-annotation/common 0.3.10 → 0.3.12

package/package.json

@@ -1,40 +1,43 @@
 {
   "name": "@apollo-annotation/common",
-  "version": "0.3.10",
+  "version": "0.3.12",
   "repository": {
     "type": "git",
     "url": "https://github.com/GMOD/Apollo3.git",
     "directory": "packages/apollo-common"
   },
-  "main": "./dist/index.js",
+  "sideEffects": false,
+  "type": "module",
+  "exports": "./dist/index.js",
   "scripts": {
-    "build": "tsc"
+    "build": "tsc --build"
   },
   "dependencies": {
-    "@apollo-annotation/schemas": "^0.3.10",
-    "@jbrowse/core": "^3.6.5",
+    "@apollo-annotation/schemas": "^0.3.12",
+    "@jbrowse/core": "^4.1.1",
     "bson-objectid": "^2.0.4",
     "tslib": "^2.3.1"
   },
   "devDependencies": {
-    "@apollo-annotation/mst": "^0.3.10",
-    "@gmod/gff": "^2.0.0",
+    "@apollo-annotation/mst": "^0.3.12",
+    "@gmod/gff": "^2.1.0",
     "@nestjs/common": "^10.1.0",
     "@nestjs/core": "^10.1.0",
-    "@types/node": "^20.19.15",
-    "generic-filehandle": "^3.0.0",
+    "@types/node": "^24.10.9",
+    "generic-filehandle2": "^2.0.18",
     "mongoose": "^6.12.0",
     "typescript": "^5.5.3"
   },
   "peerDependencies": {
-    "@mui/material": "^7.0.0",
+    "@jbrowse/mobx-state-tree": "^5.5.0",
+    "@mui/material": "^7.3.7",
     "@mui/x-data-grid": "^8.0.0",
     "mobx": "^6.6.1",
     "mobx-react": "^7.2.1",
-    "mobx-state-tree": "^5.4.0",
     "prop-types": "^15.8.1",
     "react": "^18.2.0",
     "react-dom": "^18.2.0",
+    "reflect-metadata": "^0.1.13",
     "rxjs": "^7.4.0",
     "tss-react": "^4.6.1"
   },

package/src/AssemblySpecificChange.ts

@@ -1,12 +1,13 @@
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
-import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
+import type { AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
+import type { Feature } from '@apollo-annotation/schemas'
 
 import {
   Change,
   type ChangeOptions,
   type SerializedChange,
   isChange,
-} from './Change'
+} from './Change.js'
 
 export interface SerializedAssemblySpecificChange extends SerializedChange {
   assembly: string
@@ -30,18 +31,27 @@ export abstract class AssemblySpecificChange extends Change {
   }
 
   getIndexedIds(
-    feature: AnnotationFeatureSnapshot,
+    feature: AnnotationFeatureSnapshot | Feature,
     idsToIndex: string[] | undefined,
   ): string[] {
     const indexedIds: string[] = []
     for (const additionalId of idsToIndex ?? []) {
-      const idValue = feature.attributes?.[additionalId]
-      if (idValue) {
+      const { attributes } = feature
+      // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment
+      const idValue: string[] =
+        attributes instanceof Map
+          ? attributes.get(additionalId)
+          : attributes?.[additionalId]
+      if (idValue?.[0]) {
         indexedIds.push(idValue[0])
       }
     }
     if (feature.children) {
-      for (const child of Object.values(feature.children)) {
+      const childrenIterable =
+        feature.children instanceof Map
+          ? feature.children.values()
+          : Object.values(feature.children)
+      for (const child of childrenIterable) {
         const childIndexedIds = this.getIndexedIds(child, idsToIndex)
         indexedIds.push(...childIndexedIds)
       }

package/src/Change.ts

@@ -1,22 +1,22 @@
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 /* eslint-disable @typescript-eslint/restrict-template-expressions */
-import {
-  type AnnotationFeature,
-  type AnnotationFeatureSnapshot,
-  type ApolloAssemblyI,
-  type BackendDriverType,
-  type CheckResultI,
-  type CheckResultSnapshot,
+import type {
+  AnnotationFeature,
+  AnnotationFeatureSnapshot,
+  ApolloAssemblyI,
+  BackendDriverType,
+  CheckResultI,
+  CheckResultSnapshot,
 } from '@apollo-annotation/mst'
-import { type AppRootModel, type Region } from '@jbrowse/core/util'
+import type { AppRootModel, Region } from '@jbrowse/core/util'
 
-import { changeRegistry } from './ChangeTypeRegistry'
+import { changeRegistry } from './ChangeTypeRegistry.js'
 import {
   type BackendDataStore,
   Operation,
   type OperationOptions,
   type SerializedOperation,
-} from './Operation'
+} from './Operation.js'
 
 export interface ClientDataStore {
   typeName: 'Client'

package/src/ChangeTypeRegistry.ts

@@ -1,4 +1,4 @@
-import { type Change } from './Change'
+import type { Change } from './Change.js'
 
 // eslint-disable-next-line @typescript-eslint/no-explicit-any
 type ChangeType = new (...args: any[]) => Change

package/src/Check.ts

@@ -1,6 +1,6 @@
-import {
-  type AnnotationFeatureSnapshot,
-  type CheckResultSnapshot,
+import type {
+  AnnotationFeatureSnapshot,
+  CheckResultSnapshot,
 } from '@apollo-annotation/mst'
 
 export abstract class Check {

package/src/CheckRegistry.ts

@@ -1,4 +1,4 @@
-import { type Check } from './Check'
+import type { Check } from './Check.js'
 
 class CheckRegistry {
   checks = new Map<string, Check>()

package/src/FeatureChange.ts

@@ -1,16 +1,16 @@
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 /* eslint-disable @typescript-eslint/no-unsafe-argument */
-import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
-import { type Feature } from '@apollo-annotation/schemas'
+import type { AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
+import type { Feature } from '@apollo-annotation/schemas'
 import ObjectID from 'bson-objectid'
-import { type Types } from 'mongoose'
+import type { Types } from 'mongoose'
 
 import {
   AssemblySpecificChange,
   type SerializedAssemblySpecificChange,
   isAssemblySpecificChange,
-} from './AssemblySpecificChange'
-import { type ChangeOptions } from './Change'
+} from './AssemblySpecificChange.js'
+import type { ChangeOptions } from './Change.js'
 
 export interface SerializedFeatureChange
   extends SerializedAssemblySpecificChange {

package/src/Operation.ts

@@ -1,22 +1,22 @@
 /* eslint-disable @typescript-eslint/no-confusing-void-expression */
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 /* eslint-disable @typescript-eslint/restrict-template-expressions */
-import { type FileHandle } from 'node:fs/promises'
+import type { FileHandle } from 'node:fs/promises'
 
-import {
-  type AssemblyDocument,
-  type CheckDocument,
-  type FeatureDocument,
-  type FileDocument,
-  type JBrowseConfigDocument,
-  type RefSeqChunkDocument,
-  type RefSeqDocument,
-  type UserDocument,
+import type {
+  AssemblyDocument,
+  CheckDocument,
+  FeatureDocument,
+  FileDocument,
+  JBrowseConfigDocument,
+  RefSeqChunkDocument,
+  RefSeqDocument,
+  UserDocument,
 } from '@apollo-annotation/schemas'
-import { type GFF3Feature } from '@gmod/gff'
-import { type LoggerService } from '@nestjs/common'
-import { type GenericFilehandle } from 'generic-filehandle'
-import { type ClientSession, type Model } from 'mongoose'
+import type { GFF3Feature } from '@gmod/gff'
+import type { LoggerService } from '@nestjs/common'
+import type { GenericFilehandle } from 'generic-filehandle2'
+import type { ClientSession, Model } from 'mongoose'
 
 export interface LocalGFF3DataStore {
   typeName: 'LocalGFF3'
@@ -47,7 +47,10 @@ export interface ServerDataStore {
     getFileHandle(file: FileDocument): GenericFilehandle
     parseGFF3(
       stream: ReadableStream<Uint8Array>,
-      parseOptions?: { bufferSize?: number },
+      parseOptions?: {
+        bufferSize?: number
+        errorCallback?(errorMessage: string): void
+      },
     ): ReadableStream<GFF3Feature>
     create(createFileDto: CreateFileDto): void
     remove(id: string): void

package/src/OperationTypeRegistry.ts

@@ -1,4 +1,4 @@
-import { type Operation } from './Operation'
+import type { Operation } from './Operation.js'
 
 // eslint-disable-next-line @typescript-eslint/no-explicit-any
 type OperationType = new (...args: any[]) => Operation

package/src/Validation.ts

@@ -1,10 +1,10 @@
 /* eslint-disable @typescript-eslint/require-await */
-import { type FeatureDocument } from '@apollo-annotation/schemas'
-import { type ExecutionContext } from '@nestjs/common'
-import { type Reflector } from '@nestjs/core'
-import { type ClientSession, type Model } from 'mongoose'
+import type { FeatureDocument } from '@apollo-annotation/schemas'
+import type { ExecutionContext } from '@nestjs/common'
+import type { Reflector } from '@nestjs/core'
+import type { ClientSession, Model } from 'mongoose'
 
-import { type Change, type ClientDataStore } from './Change'
+import type { Change, ClientDataStore } from './Change.js'
 
 export interface Context {
   context: ExecutionContext

package/src/declare.d.ts

@@ -0,0 +1,29 @@
+declare module 'bson-objectid' {
+  import type { Buffer } from 'node:buffer'
+
+  export default ObjectID
+
+  declare const ObjectID: ObjectIDCtor
+
+  declare interface ObjectID {
+    readonly id: string
+    readonly str: string
+
+    toHexString(): string
+    equals(other: ObjectID): boolean
+    getTimestamp(): Date
+  }
+
+  declare interface ObjectIDCtor {
+    (hexStringOrIdStringOrArrayOrBuffer?: string | number[] | Buffer): ObjectID
+
+    new (
+      hexStringOrIdStringOrArrayOrBuffer?: string | number[] | Buffer,
+    ): ObjectID
+
+    createFromTime(time: number): ObjectID
+    createFromHexString(hexString: string): ObjectID
+    isValid(hexStringOrObjectID: string | ObjectID): boolean
+    toString(): string
+  }
+}

package/src/index.ts

@@ -1,10 +1,10 @@
-export * from './ApolloPlugin'
-export * from './AssemblySpecificChange'
-export * from './Change'
-export * from './ChangeTypeRegistry'
-export * from './Check'
-export * from './CheckRegistry'
-export * from './FeatureChange'
-export * from './Operation'
-export * from './OperationTypeRegistry'
-export * from './Validation'
+export * from './ApolloPlugin.js'
+export * from './AssemblySpecificChange.js'
+export * from './Change.js'
+export * from './ChangeTypeRegistry.js'
+export * from './Check.js'
+export * from './CheckRegistry.js'
+export * from './FeatureChange.js'
+export * from './Operation.js'
+export * from './OperationTypeRegistry.js'
+export * from './Validation.js'

package/tsconfig.json

@@ -1,17 +1,14 @@
 {
-  "extends": "../../tsconfig-base.json",
+  "extends": "../../tsconfig",
   "compilerOptions": {
     "composite": true,
     "incremental": true,
     "outDir": "./dist",
     "rootDir": "./src",
-    "target": "ES2019",
-    "lib": ["ES2019", "DOM"],
-    "module": "CommonJS",
     "tsBuildInfoFile": "./dist/tsconfig.tsbuildinfo",
-    "experimentalDecorators": true,
-    "emitDecoratorMetadata": true,
-    "strictPropertyInitialization": false,
+    // For nodejs:
+    "lib": ["esnext"],
+    "types": ["node"],
   },
   "include": ["./src"],
   "references": [{ "path": "../apollo-schemas" }, { "path": "../apollo-mst" }],