@apollo-annotation/common 0.3.5 → 0.3.7

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@apollo-annotation/common",
-  "version": "0.3.5",
+  "version": "0.3.7",
   "repository": {
     "type": "git",
     "url": "https://github.com/GMOD/Apollo3.git",
@@ -11,13 +11,13 @@
     "build": "tsc"
   },
   "dependencies": {
-    "@apollo-annotation/schemas": "^0.3.5",
+    "@apollo-annotation/schemas": "^0.3.7",
     "@jbrowse/core": "^3.0.1",
     "bson-objectid": "^2.0.4",
     "tslib": "^2.3.1"
   },
   "devDependencies": {
-    "@apollo-annotation/mst": "^0.3.5",
+    "@apollo-annotation/mst": "^0.3.7",
     "@nestjs/common": "^10.1.0",
     "@nestjs/core": "^10.1.0",
     "@types/node": "^18.14.2",

package/src/ApolloPlugin.ts

@@ -1,5 +1,5 @@
 import Plugin from '@jbrowse/core/Plugin'
-import PluginManager from '@jbrowse/core/PluginManager'
+import type PluginManager from '@jbrowse/core/PluginManager'
 
 export type ApolloPluginConstructor = new (...args: unknown[]) => ApolloPlugin
 

package/src/AssemblySpecificChange.ts

@@ -1,5 +1,10 @@
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
-import { Change, ChangeOptions, SerializedChange, isChange } from './Change'
+import {
+  Change,
+  type ChangeOptions,
+  type SerializedChange,
+  isChange,
+} from './Change'
 
 export interface SerializedAssemblySpecificChange extends SerializedChange {
   assembly: string

package/src/Change.ts

@@ -1,21 +1,21 @@
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 /* eslint-disable @typescript-eslint/restrict-template-expressions */
 import {
-  AnnotationFeature,
-  AnnotationFeatureSnapshot,
-  ApolloAssemblyI,
-  BackendDriverType,
-  CheckResultI,
-  CheckResultSnapshot,
+  type AnnotationFeature,
+  type AnnotationFeatureSnapshot,
+  type ApolloAssemblyI,
+  type BackendDriverType,
+  type CheckResultI,
+  type CheckResultSnapshot,
 } from '@apollo-annotation/mst'
-import { AppRootModel, Region } from '@jbrowse/core/util'
+import { type AppRootModel, type Region } from '@jbrowse/core/util'
 
 import { changeRegistry } from './ChangeTypeRegistry'
 import {
-  BackendDataStore,
+  type BackendDataStore,
   Operation,
-  OperationOptions,
-  SerializedOperation,
+  type OperationOptions,
+  type SerializedOperation,
 } from './Operation'
 
 export interface ClientDataStore {

package/src/ChangeTypeRegistry.ts

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

package/src/Check.ts

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

package/src/CheckRegistry.ts

@@ -1,4 +1,4 @@
-import { Check } from './Check'
+import { type Check } from './Check'
 
 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 { 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,
-  SerializedAssemblySpecificChange,
+  type SerializedAssemblySpecificChange,
   isAssemblySpecificChange,
 } from './AssemblySpecificChange'
-import { ChangeOptions } from './Change'
+import { type ChangeOptions } from './Change'
 
 export interface SerializedFeatureChange
   extends SerializedAssemblySpecificChange {
@@ -116,4 +116,69 @@ export abstract class FeatureChange extends AssemblySpecificChange {
       _id: newId,
     }
   }
+
+  addChild(parentFeature: Feature, child: AnnotationFeatureSnapshot) {
+    if (!parentFeature.attributes?._id) {
+      let { attributes } = parentFeature
+      if (!attributes) {
+        attributes = {}
+      }
+      // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment
+      attributes = {
+        _id: [parentFeature._id.toString()],
+        // eslint-disable-next-line unicorn/prefer-structured-clone
+        ...JSON.parse(JSON.stringify(attributes)),
+      }
+      parentFeature.attributes = attributes
+    }
+    const { _id } = child
+    if (!parentFeature.children) {
+      parentFeature.children = new Map()
+    }
+    parentFeature.children.set(_id, {
+      allIds: [],
+      ...child,
+      // eslint-disable-next-line @typescript-eslint/ban-ts-comment
+      // @ts-expect-error
+      _id,
+    })
+    // Child features should be sorted for click and drag of gene glyphs to work properly
+    parentFeature.children = new Map(
+      [...parentFeature.children.entries()].sort((a, b) => a[1].min - b[1].min),
+    )
+  }
+
+  /**
+   * Delete feature's subfeatures that match an ID and return the IDs of any
+   * sub-subfeatures that were deleted
+   * @param feature -
+   * @param featureIdToDelete -
+   * @returns - list of deleted feature IDs
+   */
+  findAndDeleteChildFeature(
+    feature: Feature,
+    featureIdToDelete: string,
+  ): string[] {
+    if (!feature.children) {
+      throw new Error(`Feature ${feature._id.toHexString()} has no children`)
+    }
+    const { _id, children } = feature
+    const child = children.get(featureIdToDelete)
+    if (child) {
+      const deletedIds = this.getChildFeatureIds(child)
+      children.delete(featureIdToDelete)
+      return deletedIds
+    }
+    for (const [, childFeature] of children) {
+      try {
+        return this.findAndDeleteChildFeature(childFeature, featureIdToDelete)
+      } catch {
+        // pass
+      }
+    }
+
+    throw new Error(
+      `Feature "${featureIdToDelete}" not found in ${_id.toHexString()}`,
+    )
+  }
 }

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 { ReadStream } from 'node:fs'
-import type { FileHandle } from 'node:fs/promises'
+import { type ReadStream } from 'node:fs'
+import { type FileHandle } from 'node:fs/promises'
 
 import {
-  AssemblyDocument,
-  FeatureDocument,
-  FileDocument,
-  RefSeqChunkDocument,
-  RefSeqDocument,
-  JBrowseConfigDocument,
-  UserDocument,
-  CheckDocument,
+  type AssemblyDocument,
+  type CheckDocument,
+  type FeatureDocument,
+  type FileDocument,
+  type JBrowseConfigDocument,
+  type RefSeqChunkDocument,
+  type RefSeqDocument,
+  type UserDocument,
 } from '@apollo-annotation/schemas'
-import type { LoggerService } from '@nestjs/common'
-import type { ClientSession, Model } from 'mongoose'
-import { GenericFilehandle } from 'generic-filehandle'
+import { type LoggerService } from '@nestjs/common'
+import { type GenericFilehandle } from 'generic-filehandle'
+import { type ClientSession, type Model } from 'mongoose'
 
 export interface LocalGFF3DataStore {
   typeName: 'LocalGFF3'

package/src/OperationTypeRegistry.ts

@@ -1,4 +1,4 @@
-import { Operation } from './Operation'
+import { type Operation } from './Operation'
 
 // 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 { FeatureDocument } from '@apollo-annotation/schemas'
-import type { ExecutionContext } from '@nestjs/common'
-import type { Reflector } from '@nestjs/core'
-import { ClientSession, 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, type Model } from 'mongoose'
 
-import { Change, ClientDataStore } from './Change'
+import { type Change, type ClientDataStore } from './Change'
 
 export interface Context {
   context: ExecutionContext