Upgrade transitive dependencies

.yarnrc.yml

@@ -21,9 +21,6 @@ packageExtensions:
   mongoose-id-validator@*:
     peerDependencies:
       mongoose: "*"
-  tss-react@*:
-    peerDependencies:
-      "@mui/material": "*"
 
 plugins:
   - path: .yarn/plugins/@yarnpkg/plugin-typescript.cjs

packages/apollo-collaboration-server/package.json

@@ -26,7 +26,7 @@
   "dependencies": {
     "@emotion/react": "^11.10.6",
     "@emotion/styled": "^11.10.6",
-    "@gmod/gff": "^1.2.0",
+    "@gmod/gff": "1.2.0",
     "@gmod/indexedfasta": "^2.0.4",
     "@jbrowse/core": "^2.7.0",
     "@mui/base": "^5.0.0-alpha.118",
@@ -57,7 +57,7 @@
     "mobx-state-tree": "^5.1.7",
     "mongoose": "^6.12.0",
     "mongoose-id-validator": "^0.6.0",
-    "multer": "^1.4.4",
+    "multer": "^1.4.5-lts.1",
     "node-fetch": "^2.6.7",
     "passport": "^0.5.0",
     "passport-google-oauth20": "^2.0.0",

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

@@ -66,9 +66,8 @@ export class ChangesService {
   async create(change: BaseChange, user: DecodedJWT) {
     this.logger.debug(`Requested change: ${JSON.stringify(change)}`)
 
-    const sequence = await this.countersService.getNextSequenceValue(
-      'changeCounter',
-    )
+    const sequence =
+      await this.countersService.getNextSequenceValue('changeCounter')
     const uniqUserId = `${user.email}-${sequence}` // Same user can upload data from more than one client
 
     const validationResult = await validationRegistry.backendPreValidate(change)

packages/apollo-collaboration-server/src/features/features.controller.ts

@@ -106,9 +106,8 @@ export class FeaturesController {
     this.logger.debug(
       `Get features count by ${JSON.stringify(featureCountRequest)}`,
     )
-    const count = await this.featuresService.getFeatureCount(
-      featureCountRequest,
-    )
+    const count =
+      await this.featuresService.getFeatureCount(featureCountRequest)
     return { count }
   }
 

packages/apollo-common/package.json

@@ -11,7 +11,7 @@
     "build": "tsc"
   },
   "dependencies": {
-    "@gmod/gff": "^1.2.0",
+    "@gmod/gff": "1.2.0",
     "@jbrowse/core": "^2.7.0",
     "apollo-schemas": "workspace:^",
     "bson-objectid": "^2.0.4",

packages/apollo-shared/package.json

@@ -8,7 +8,7 @@
     "clean": "rimraf dist"
   },
   "dependencies": {
-    "@gmod/gff": "^1.2.0",
+    "@gmod/gff": "1.2.0",
     "@gmod/indexedfasta": "^2.0.4",
     "@jbrowse/core": "^2.7.0",
     "apollo-common": "workspace:^",

packages/jbrowse-plugin-apollo/package.json

@@ -53,7 +53,7 @@
   "dependencies": {
     "@emotion/react": "^11.10.6",
     "@emotion/styled": "^11.10.6",
-    "@gmod/gff": "^1.2.0",
+    "@gmod/gff": "1.2.0",
     "@jbrowse/plugin-authentication": "^2.0.1",
     "@jbrowse/plugin-linear-genome-view": "^2.0.1",
     "@mui/icons-material": "^5.8.4",
@@ -99,7 +99,7 @@
     "@types/prop-types": "^15",
     "@types/react": "^17.0.34",
     "@types/react-dom": "^18",
-    "cypress": "^12.17.2",
+    "cypress": "12.17.3",
     "cypress-mongodb": "^6.2.0",
     "fake-indexeddb": "^4.0.2",
     "jest": "^29.6.2",

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

@@ -561,9 +561,8 @@ const stateModelFactory = (
       let authTypePromise: Promise<AuthType> | undefined
       return {
         async getPreAuthorizationInformation(location: UriLocation) {
-          const preAuthInfo = await superGetPreAuthorizationInformation(
-            location,
-          )
+          const preAuthInfo =
+            await superGetPreAuthorizationInformation(location)
           return {
             ...preAuthInfo,
             authInfo: {