Enable unicorn consistent-destructuring

.eslintrc.js

@@ -76,12 +76,11 @@ module.exports = {
     // eslint-plugin-tsdoc rules
     'tsdoc/syntax': 'warn',
     // eslint-plugin-unicorn rules (override recommended)
-    'unicorn/consistent-destructuring': 'off',
-    'unicorn/filename-case': 'off',
+    'unicorn/filename-case': 'off', // Doesn't match our file naming, maybe can be configured later
     'unicorn/no-empty-file': 'off', // False positives
-    'unicorn/no-null': 'off',
+    'unicorn/no-null': 'off', // A lot of null in React and other libraries
     'unicorn/prefer-module': 'off', // Cypress and apollo-collaboration-server need this
-    'unicorn/prevent-abbreviations': 'off',
+    'unicorn/prevent-abbreviations': 'off', // Doesn't guess a lot of abbreviations correctly
     // Special case @typescript-eslint/eslint-plugin rule
     // Will be part of "plugin:@typescript-eslint/recommended-type-checked" when
     // that extension is enabled. Remove from here at that time.

packages/apollo-collaboration-server/src/operations/operations.service.ts

@@ -47,24 +47,36 @@ export class OperationsService {
   async executeOperation<T extends Operation>(
     serializedOperation: ReturnType<T['toJSON']>,
   ): Promise<ReturnType<T['executeOnServer']>> {
-    const { logger } = this
+    const {
+      assemblyModel,
+      connection,
+      countersService,
+      featureModel,
+      fileModel,
+      filesService,
+      logger,
+      pluginsService,
+      refSeqChunkModel,
+      refSeqModel,
+      userModel,
+    } = this
     const OperationType = operationRegistry.getOperationType(
       serializedOperation.typeName,
     )
     const operation = new OperationType(serializedOperation, { logger })
-    const session = await this.connection.startSession()
+    const session = await connection.startSession()
     const result = (await operation.execute({
       typeName: 'Server',
-      featureModel: this.featureModel,
-      assemblyModel: this.assemblyModel,
-      refSeqModel: this.refSeqModel,
-      refSeqChunkModel: this.refSeqChunkModel,
-      fileModel: this.fileModel,
-      userModel: this.userModel,
+      featureModel,
+      assemblyModel,
+      refSeqModel,
+      refSeqChunkModel,
+      fileModel,
+      userModel,
       session,
-      filesService: this.filesService,
-      counterService: this.countersService,
-      pluginsService: this.pluginsService,
+      filesService,
+      counterService: countersService,
+      pluginsService,
       user: '',
     })) as ReturnType<T['executeOnServer']>
     await session.endSession()

packages/apollo-common/src/AssemblySpecificChange.ts

@@ -125,19 +125,19 @@ export abstract class AssemblySpecificChange extends Change {
           if (!refSeqDoc) {
             throw new Error('No refSeq document found')
           }
-          const { chunkSize } = refSeqDoc
+          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 ${chunkIndex} of "${refSeqDoc._id}"`,
+              `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: refSeqDoc._id,
+                refSeq: _id,
                 n: chunkIndex,
                 sequence,
                 user,

packages/apollo-shared/src/Changes/AddFeatureChange.ts

@@ -86,7 +86,7 @@ export class AddFeatureChange extends FeatureChange {
     for (const change of changes) {
       logger.debug?.(`change: ${JSON.stringify(change)}`)
       const { addedFeature, allIds, copyFeature, parentFeatureId } = change
-      const { refSeq } = addedFeature
+      const { _id, refSeq } = addedFeature
       const refSeqDoc = await refSeqModel
         .findById(refSeq)
         .session(session)
@@ -111,7 +111,7 @@ export class AddFeatureChange extends FeatureChange {
         )
         featureCnt++
       } else {
-        addedFeature.gffId = addedFeature._id // User added manually new feature so then gffId = _id
+        addedFeature.gffId = _id // User added manually new feature so then gffId = _id
         // Adding new child feature
         if (parentFeatureId) {
           const topLevelFeature = await featureModel
@@ -146,19 +146,19 @@ export class AddFeatureChange extends FeatureChange {
             }
             parentFeature.attributes = attributes
           }
-          parentFeature.children.set(addedFeature._id, {
+          parentFeature.children.set(_id, {
             allIds: [],
             ...addedFeature,
             // eslint-disable-next-line @typescript-eslint/ban-ts-comment
             // @ts-expect-error
-            _id: addedFeature._id,
+            _id,
           })
           const childIds = this.getChildFeatureIds(addedFeature)
-          topLevelFeature.allIds.push(addedFeature._id, ...childIds)
+          topLevelFeature.allIds.push(_id, ...childIds)
           await topLevelFeature.save()
         } else {
           const childIds = this.getChildFeatureIds(addedFeature)
-          const allIdsV2 = [addedFeature._id, ...childIds]
+          const allIdsV2 = [_id, ...childIds]
           const [newFeatureDoc] = await featureModel.create(
             [{ allIds: allIdsV2, ...addedFeature }],
             { session },

packages/apollo-shared/src/Changes/DeleteAssemblyChange.ts

@@ -64,7 +64,7 @@ export class DeleteAssemblyChange extends AssemblySpecificChange {
     await refSeqModel.deleteMany({ assembly }).exec()
     await assemblyModel.findByIdAndDelete(assembly).exec()
 
-    this.logger.debug?.(`Assembly "${assembly}" deleted from database.`)
+    logger.debug?.(`Assembly "${assembly}" deleted from database.`)
   }
 
   async executeOnLocalGFF3(_backend: LocalGFF3DataStore) {

packages/apollo-shared/src/Changes/DeleteFeatureChange.ts

@@ -132,7 +132,7 @@ export class DeleteFeatureChange extends FeatureChange {
     if (!feature.children) {
       throw new Error(`Feature ${feature._id} has no children`)
     }
-    const { children } = feature
+    const { _id, children } = feature
     const child = children.get(featureIdToDelete)
     if (child) {
       const deletedIds = this.getChildFeatureIds(child)
@@ -147,9 +147,7 @@ export class DeleteFeatureChange extends FeatureChange {
       }
     }
 
-    throw new Error(
-      `Feature "${featureIdToDelete}" not found in ${feature._id}`,
-    )
+    throw new Error(`Feature "${featureIdToDelete}" not found in ${_id}`)
   }
 
   async executeOnLocalGFF3(_backend: LocalGFF3DataStore) {

packages/jbrowse-plugin-apollo/src/ApolloInternetAccount/model.ts

@@ -230,11 +230,11 @@ const stateModelFactory = (
             'No LastChangeSequence stored in session. Please, refresh you browser to get last updates from server',
           )
         }
-        const { baseURL } = self
+        const { baseURL, lastChangeSequenceNumber } = self
 
         const url = new URL('changes', baseURL)
         const searchParams = new URLSearchParams({
-          since: String(self.lastChangeSequenceNumber),
+          since: String(lastChangeSequenceNumber),
           sort: '1',
         })
         url.search = searchParams.toString()
@@ -319,7 +319,7 @@ const stateModelFactory = (
               'label' in menuItem && menuItem.label === 'Add Assembly',
           )
         ) {
-          pluginManager.rootModel.insertInMenu(
+          rootModel.insertInMenu(
             'Apollo',
             {
               label: 'Add Assembly',
@@ -339,7 +339,7 @@ const stateModelFactory = (
             },
             0,
           )
-          pluginManager.rootModel.insertInMenu(
+          rootModel.insertInMenu(
             'Apollo',
             {
               label: 'Delete Assembly',
@@ -359,7 +359,7 @@ const stateModelFactory = (
             },
             1,
           )
-          pluginManager.rootModel.insertInMenu(
+          rootModel.insertInMenu(
             'Apollo',
             {
               label: 'Import Features',
@@ -379,7 +379,7 @@ const stateModelFactory = (
             },
             2,
           )
-          pluginManager.rootModel.insertInMenu(
+          rootModel.insertInMenu(
             'Apollo',
             {
               label: 'Manage Users',
@@ -399,7 +399,7 @@ const stateModelFactory = (
             },
             9,
           )
-          pluginManager.rootModel.insertInMenu(
+          rootModel.insertInMenu(
             'Apollo',
             {
               label: 'Undo',
@@ -555,8 +555,11 @@ const stateModelFactory = (
     }))
     .actions((self) => {
       const {
+        authType,
         getFetcher: superGetFetcher,
         getPreAuthorizationInformation: superGetPreAuthorizationInformation,
+        googleAuthInternetAccount,
+        microsoftAuthInternetAccount,
         retrieveToken: superRetrieveToken,
       } = self
       let authTypePromise: Promise<AuthType> | undefined
@@ -574,16 +577,16 @@ const stateModelFactory = (
           }
         },
         retrieveToken() {
-          if (self.authType === 'google') {
-            return self.googleAuthInternetAccount.retrieveToken()
+          if (authType === 'google') {
+            return googleAuthInternetAccount.retrieveToken()
           }
-          if (self.authType === 'microsoft') {
-            return self.microsoftAuthInternetAccount.retrieveToken()
+          if (authType === 'microsoft') {
+            return microsoftAuthInternetAccount.retrieveToken()
           }
-          if (self.authType === 'guest') {
+          if (authType === 'guest') {
             return superRetrieveToken()
           }
-          throw new Error(`Unknown authType "${self.authType}"`)
+          throw new Error(`Unknown authType "${authType}"`)
         },
         getFetcher(
           location?: UriLocation,
@@ -593,6 +596,7 @@ const stateModelFactory = (
             init?: RequestInit,
           ): Promise<Response> => {
             let { authType } = self
+            const { googleClientId, microsoftClientId } = self
             if (!authType) {
               if (!authTypePromise) {
                 if (location?.internetAccountPreAuthorization) {
@@ -624,8 +628,8 @@ const stateModelFactory = (
                           }
                           doneCallback()
                         },
-                        google: Boolean(self.googleClientId),
-                        microsoft: Boolean(self.microsoftClientId),
+                        google: Boolean(googleClientId),
+                        microsoft: Boolean(microsoftClientId),
                         allowGuestUser,
                       },
                     ])

packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/components/LinearApolloDisplay.tsx

@@ -37,6 +37,7 @@ export const LinearApolloDisplay = observer(function LinearApolloDisplay(
     contextMenuItems: getContextMenuItems,
     cursor,
     featuresHeight,
+    isShown,
     onMouseDown,
     onMouseLeave,
     onMouseMove,
@@ -54,7 +55,7 @@ export const LinearApolloDisplay = observer(function LinearApolloDisplay(
   const [contextCoord, setContextCoord] = useState<Coord>()
   const [contextMenuItems, setContextMenuItems] = useState<MenuItem[]>([])
   const message = regionCannotBeRendered()
-  if (!model.isShown) {
+  if (!isShown) {
     return null
   }
   return (