JBrowse 4.3.0 dependency upgrade

.github/workflows/cypress_debug.yml

@@ -19,7 +19,7 @@ jobs:
         run: yarn --immutable
 
       - name: Get latest JBrowse
-        run: yarn run jbrowse create --nightly .jbrowse
+        run: yarn run jbrowse create .jbrowse
         working-directory: packages/jbrowse-plugin-apollo
 
       - name: Start MongoDB

.github/workflows/pull_request.yml

@@ -42,7 +42,7 @@ jobs:
 
       # Cypress tests
       - name: Get latest JBrowse
-        run: yarn run jbrowse create --nightly .jbrowse
+        run: yarn run jbrowse create .jbrowse
         working-directory: packages/jbrowse-plugin-apollo
       - name: Start MongoDB
         uses: supercharge/mongodb-github-action@1.12.1

packages/apollo-collaboration-server/package.json

@@ -46,9 +46,9 @@
     "@emotion/styled": "^11.10.6",
     "@gmod/gff": "^2.1.0",
     "@gmod/indexedfasta": "^5.0.2",
-    "@jbrowse/core": "^4.1.1",
-    "@jbrowse/mobx-state-tree": "^5.5.0",
-    "@mui/material": "^7.3.7",
+    "@jbrowse/core": "^4.3.0",
+    "@jbrowse/mobx-state-tree": "^5.8.7",
+    "@mui/material": "^7.3.11",
     "@nestjs/common": "^10.1.0",
     "@nestjs/config": "^3.0.0",
     "@nestjs/core": "^10.1.0",

packages/apollo-common/package.json

@@ -14,7 +14,7 @@
   },
   "dependencies": {
     "@apollo-annotation/schemas": "workspace:^",
-    "@jbrowse/core": "^4.1.1",
+    "@jbrowse/core": "^4.3.0",
     "bson-objectid": "^2.0.4",
     "tslib": "^2.3.1"
   },
@@ -29,8 +29,8 @@
     "typescript": "^5.5.3"
   },
   "peerDependencies": {
-    "@jbrowse/mobx-state-tree": "^5.5.0",
-    "@mui/material": "^7.3.7",
+    "@jbrowse/mobx-state-tree": "^5.8.7",
+    "@mui/material": "^7.3.11",
     "@mui/x-data-grid": "^8.0.0",
     "mobx": "^6.6.1",
     "mobx-react": "^7.2.1",

packages/apollo-mst/package.json

@@ -13,8 +13,8 @@
     "build": "tsc"
   },
   "dependencies": {
-    "@jbrowse/core": "^4.1.1",
-    "@jbrowse/mobx-state-tree": "^5.5.0",
+    "@jbrowse/core": "^4.3.0",
+    "@jbrowse/mobx-state-tree": "^5.8.7",
     "mobx": "^6.6.1",
     "react-dom": "^18.2.0",
     "rxjs": "^7.4.0",

packages/apollo-shared/package.json

@@ -22,14 +22,14 @@
     "@apollo-annotation/schemas": "workspace:^",
     "@gmod/gff": "^2.1.0",
     "@gmod/indexedfasta": "^5.0.2",
-    "@jbrowse/core": "^4.1.1",
+    "@jbrowse/core": "^4.3.0",
     "bson-objectid": "^2.0.4",
     "generic-filehandle2": "^2.0.18",
     "jwt-decode": "^3.1.2",
     "tslib": "^2.3.1"
   },
   "devDependencies": {
-    "@jbrowse/mobx-state-tree": "^5.5.0",
+    "@jbrowse/mobx-state-tree": "^5.8.7",
     "@nestjs/common": "^10.1.0",
     "@nestjs/core": "^10.1.0",
     "@types/chai": "^4.3.19",
@@ -46,8 +46,8 @@
     "typescript": "^5.5.3"
   },
   "peerDependencies": {
-    "@jbrowse/mobx-state-tree": "^5.5.0",
-    "@mui/material": "^7.3.7",
+    "@jbrowse/mobx-state-tree": "^5.8.7",
+    "@mui/material": "^7.3.11",
     "@mui/x-data-grid": "^8.0.0",
     "mobx": "^6.6.1",
     "mobx-react": "^7.2.1",

packages/jbrowse-plugin-apollo/package.json

@@ -52,9 +52,9 @@
     "@emotion/react": "^11.10.6",
     "@emotion/styled": "^11.10.6",
     "@gmod/gff": "^2.1.0",
-    "@jbrowse/plugin-authentication": "^4.1.1",
-    "@jbrowse/plugin-linear-genome-view": "^4.1.1",
-    "@mui/icons-material": "^7.3.7",
+    "@jbrowse/plugin-authentication": "^4.3.0",
+    "@jbrowse/plugin-linear-genome-view": "^4.3.0",
+    "@mui/icons-material": "^7.3.11",
     "@types/jsonpath": "^0.2.0",
     "autosuggest-highlight": "^3.3.4",
     "bson-objectid": "^2.0.4",
@@ -72,12 +72,12 @@
     "@babel/core": "^7.28.6",
     "@babel/plugin-proposal-class-properties": "^7.18.6",
     "@babel/preset-env": "^7.28.6",
-    "@jbrowse/cli": "^4.1.1",
-    "@jbrowse/core": "^4.1.1",
+    "@jbrowse/cli": "^4.3.0",
+    "@jbrowse/core": "^4.3.0",
     "@jbrowse/development-tools": "^2.2.1",
-    "@jbrowse/mobx-state-tree": "^5.5.0",
+    "@jbrowse/mobx-state-tree": "^5.8.7",
     "@jest/globals": "^29.0.3",
-    "@mui/material": "^7.3.7",
+    "@mui/material": "^7.3.11",
     "@mui/x-data-grid": "^8.0.0",
     "@rollup/plugin-babel": "^6.1.0",
     "@rollup/plugin-commonjs": "^29.0.0",
@@ -133,9 +133,9 @@
     "typescript": "^5.5.3"
   },
   "peerDependencies": {
-    "@jbrowse/core": "^4.1.1",
-    "@jbrowse/mobx-state-tree": "^5.5.0",
-    "@mui/material": "^7.3.7",
+    "@jbrowse/core": "^4.3.0",
+    "@jbrowse/mobx-state-tree": "^5.8.7",
+    "@mui/material": "^7.3.11",
     "mobx": "^6.6.1",
     "mobx-react": "^9.0.0",
     "prop-types": "^15.8.1",

packages/jbrowse-plugin-apollo/src/ApolloJobModel.ts

@@ -1,4 +1,3 @@
-/* eslint-disable @typescript-eslint/no-unsafe-assignment */
 /* eslint-disable @typescript-eslint/no-confusing-void-expression */
 import {
   type SessionWithWidgets,

packages/jbrowse-plugin-apollo/src/ApolloTextSearchAdapter/ApolloTextSearchAdapter.ts

@@ -78,7 +78,7 @@ export class ApolloTextSearchAdapter
     const { assemblyManager } = session as unknown as AbstractSessionModel
     for (const assemblyName of this.assemblyNames) {
       const backendDriver = apolloDataStore.getBackendDriver(assemblyName)
-      const assembly = assemblyManager.get(assemblyName)
+      const assembly = assemblyManager.get(assemblyName) as Assembly | undefined
       if (!(backendDriver && assembly)) {
         continue
       }

packages/jbrowse-plugin-apollo/src/BackendDrivers/LocalDriver/LocalDriver.ts

@@ -74,7 +74,9 @@ export class LocalDriver extends BackendDriver {
   async getSequence(region: Region): Promise<{ seq: string; refSeq: string }> {
     const session = getSession(this.clientStore)
     const { assemblyManager } = session
-    const assembly = await assemblyManager.waitForAssembly(region.assemblyName)
+    const assembly = (await assemblyManager.waitForAssembly(
+      region.assemblyName,
+    )) as Assembly | undefined
     if (!assembly) {
       throw new Error(`Assembly not found: "${region.assemblyName}"`)
     }
@@ -109,7 +111,9 @@ export class LocalDriver extends BackendDriver {
   async getRegions(assemblyName: string): Promise<Region[]> {
     const session = getSession(this.clientStore)
     const { assemblyManager } = session
-    const assembly = await assemblyManager.waitForAssembly(assemblyName)
+    const assembly = (await assemblyManager.waitForAssembly(assemblyName)) as
+      | Assembly
+      | undefined
     if (!assembly) {
       throw new Error(`Assembly not found: "${assemblyName}"`)
     }
@@ -127,7 +131,9 @@ export class LocalDriver extends BackendDriver {
   async getRefNameAliases(assemblyName: string): Promise<RefNameAliases[]> {
     const session = getSession(this.clientStore)
     const { assemblyManager } = session
-    const assembly = await assemblyManager.waitForAssembly(assemblyName)
+    const assembly = (await assemblyManager.waitForAssembly(assemblyName)) as
+      | Assembly
+      | undefined
     if (!assembly) {
       throw new Error(`Assembly not found: "${assemblyName}"`)
     }

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

@@ -1,4 +1,5 @@
 import type { CheckResultI } from '@apollo-annotation/mst'
+import type { Assembly } from '@jbrowse/core/assemblyManager/assembly'
 import { type AbstractSessionModel, doesIntersect2 } from '@jbrowse/core/util'
 import ErrorIcon from '@mui/icons-material/Error'
 import { Avatar, Badge, Box, Tooltip } from '@mui/material'
@@ -23,7 +24,9 @@ export const CheckResultWarnings = observer(function CheckResultWarnings({
   }
   return lgv.dynamicBlocks.contentBlocks.map((block) => {
     const widthBp = lgv.bpPerPx * apolloRowHeight
-    const assembly = assemblyManager.get(block.assemblyName)
+    const assembly = assemblyManager.get(block.assemblyName) as
+      | Assembly
+      | undefined
     if (!assembly) {
       return null
     }

packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/ExonGlyph.ts

@@ -106,7 +106,7 @@ function getContextMenuItems(
     session,
   } = display
   const [region] = regions
-  const currentAssemblyId = display.getAssemblyId(region.assemblyName)
+  const currentAssemblyId = display.getAssemblyId(region.assemblyName) as string
   const role = internetAccount ? internetAccount.role : 'admin'
   const admin = role === 'admin'
   const menuItems: MenuItem[] = []

packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/glyphs/TranscriptGlyph.ts

@@ -205,7 +205,7 @@ function getContextMenuItems(
 ): MenuItem[] {
   const { changeManager, regions, selectedFeature, session } = display
   const [region] = regions
-  const currentAssemblyId = display.getAssemblyId(region.assemblyName)
+  const currentAssemblyId = display.getAssemblyId(region.assemblyName) as string
   const menuItems: MenuItem[] = []
   if (isSessionModelWithWidgets(session)) {
     menuItems.splice(1, 0, {

packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/base.ts

@@ -5,6 +5,7 @@
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 import type { AnnotationFeature } from '@apollo-annotation/mst'
 import type PluginManager from '@jbrowse/core/PluginManager'
+import type { Assembly } from '@jbrowse/core/assemblyManager/assembly'
 import {
   type AnyConfigurationSchemaType,
   ConfigurationReference,
@@ -137,7 +138,9 @@ export function baseModelFactory(
         const { assemblyName } = region
         const { assemblyManager } =
           self.session as unknown as AbstractSessionModel
-        const assembly = assemblyManager.get(assemblyName)
+        const assembly = assemblyManager.get(assemblyName) as
+          | Assembly
+          | undefined
         if (!assembly) {
           throw new Error(`No assembly found with name ${assemblyName}`)
         }

packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/layouts.ts

@@ -2,6 +2,7 @@
 
 import type { AnnotationFeature } from '@apollo-annotation/mst'
 import type PluginManager from '@jbrowse/core/PluginManager'
+import type { Assembly } from '@jbrowse/core/assemblyManager/assembly'
 import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration'
 import { type AbstractSessionModel, doesIntersect2 } from '@jbrowse/core/util'
 import { addDisposer, isAlive } from '@jbrowse/mobx-state-tree'
@@ -72,7 +73,9 @@ export function layoutsModelFactory(
       getCanonicalRefName(assemblyName: string, refSeq: string) {
         const { assemblyManager } =
           self.session as unknown as AbstractSessionModel
-        const assembly = assemblyManager.get(assemblyName)
+        const assembly = assemblyManager.get(assemblyName) as
+          | Assembly
+          | undefined
         if (!assembly) {
           throw new Error('no assembly in layout')
         }

packages/jbrowse-plugin-apollo/src/LinearApolloDisplay/stateModel/mouseEvents.ts

@@ -4,6 +4,7 @@ import {
   LocationStartChange,
 } from '@apollo-annotation/shared'
 import type PluginManager from '@jbrowse/core/PluginManager'
+import type { Assembly } from '@jbrowse/core/assemblyManager/assembly'
 import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration'
 import type { MenuItem } from '@jbrowse/core/ui'
 import { doesIntersect2 } from '@jbrowse/core/util'
@@ -189,7 +190,9 @@ export function mouseEventsModelFactory(
           }
           const { displayedRegions } = self.lgv
           const region = displayedRegions[start.regionNumber]
-          const assembly = self.getAssemblyId(region.assemblyName)
+          const assembly = self.getAssemblyId(region.assemblyName) as
+            | Assembly
+            | undefined
           const changes = getPropagatedLocationChanges(
             feature,
             current.bp,

packages/jbrowse-plugin-apollo/src/LinearApolloReferenceSequenceDisplay/stateModel/base.ts

@@ -5,6 +5,7 @@
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 import type { AnnotationFeature } from '@apollo-annotation/mst'
 import type PluginManager from '@jbrowse/core/PluginManager'
+import type { Assembly } from '@jbrowse/core/assemblyManager/assembly'
 import {
   type AnyConfigurationSchemaType,
   ConfigurationReference,
@@ -115,7 +116,9 @@ export function baseModelFactory(
         const { assemblyName } = region
         const { assemblyManager } =
           self.session as unknown as AbstractSessionModel
-        const assembly = assemblyManager.get(assemblyName)
+        const assembly = assemblyManager.get(assemblyName) as
+          | Assembly
+          | undefined
         if (!assembly) {
           throw new Error(`No assembly found with name ${assemblyName}`)
         }

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

@@ -3,6 +3,7 @@
 /* eslint-disable @typescript-eslint/no-misused-promises */
 
 import type { CheckResultI } from '@apollo-annotation/mst'
+import type { Assembly } from '@jbrowse/core/assemblyManager/assembly'
 import { Menu, type MenuItem } from '@jbrowse/core/ui'
 import {
   type AbstractSessionModel,
@@ -157,7 +158,9 @@ export const LinearApolloSixFrameDisplay = observer(
               />
               {lgv.displayedRegions.flatMap((region, idx) => {
                 const widthBp = lgv.bpPerPx * apolloRowHeight
-                const assembly = assemblyManager.get(region.assemblyName)
+                const assembly = assemblyManager.get(region.assemblyName) as
+                  | Assembly
+                  | undefined
                 if (showCheckResults) {
                   const filteredCheckResults = [
                     ...session.apolloDataStore.checkResults.values(),

packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/glyphs/GeneGlyph.ts

@@ -856,7 +856,7 @@ function getContextMenuItems(
     session,
   } = display
   const [region] = regions
-  const currentAssemblyId = display.getAssemblyId(region.assemblyName)
+  const currentAssemblyId = display.getAssemblyId(region.assemblyName) as string
   const menuItems: MenuItem[] = []
   const role = internetAccount ? internetAccount.role : 'admin'
   const readOnly = !(role && ['admin', 'user'].includes(role))

packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/base.ts

@@ -5,6 +5,7 @@
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 import type { AnnotationFeature } from '@apollo-annotation/mst'
 import type PluginManager from '@jbrowse/core/PluginManager'
+import type { Assembly } from '@jbrowse/core/assemblyManager/assembly'
 import {
   type AnyConfigurationSchemaType,
   ConfigurationReference,
@@ -128,7 +129,9 @@ export function baseModelFactory(
         const { assemblyName } = region
         const { assemblyManager } =
           self.session as unknown as AbstractSessionModel
-        const assembly = assemblyManager.get(assemblyName)
+        const assembly = assemblyManager.get(assemblyName) as
+          | Assembly
+          | undefined
         if (!assembly) {
           throw new Error(`No assembly found with name ${assemblyName}`)
         }

packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/layouts.ts

@@ -2,6 +2,7 @@
 
 import type { AnnotationFeature } from '@apollo-annotation/mst'
 import type PluginManager from '@jbrowse/core/PluginManager'
+import type { Assembly } from '@jbrowse/core/assemblyManager/assembly'
 import type { AnyConfigurationSchemaType } from '@jbrowse/core/configuration'
 import {
   type AbstractSessionModel,
@@ -45,7 +46,9 @@ export function layoutsModelFactory(
         const { assemblyManager } =
           self.session as unknown as AbstractSessionModel
         return self.lgv.displayedRegions.map((region) => {
-          const assembly = assemblyManager.get(region.assemblyName)
+          const assembly = assemblyManager.get(region.assemblyName) as
+            | Assembly
+            | undefined
           let min: number | undefined
           let max: number | undefined
           const { end, refName, start } = region
@@ -101,7 +104,9 @@ export function layoutsModelFactory(
         const { assemblyManager } =
           self.session as unknown as AbstractSessionModel
         return self.lgv.displayedRegions.map((region, idx) => {
-          const assembly = assemblyManager.get(region.assemblyName)
+          const assembly = assemblyManager.get(region.assemblyName) as
+            | Assembly
+            | undefined
           const featureLayout = new Map<number, LayoutRow[]>()
           const minMax = self.featuresMinMax[idx]
           if (!minMax) {

packages/jbrowse-plugin-apollo/src/LinearApolloSixFrameDisplay/stateModel/mouseEvents.ts

@@ -202,7 +202,7 @@ export function mouseEventsModelFactory(
         }
         const { displayedRegions } = self.lgv
         const region = displayedRegions[start.regionNumber]
-        const assembly = self.getAssemblyId(region.assemblyName)
+        const assembly = self.getAssemblyId(region.assemblyName) as string
         const changes = getPropagatedLocationChanges(
           feature,
           current.bp,