Avoid any

packages/app-core/src/ui/App/ViewMenu.tsx

@@ -4,7 +4,7 @@ import {
   IconButtonProps as IconButtonPropsType,
 } from '@mui/material'
 import { observer } from 'mobx-react'
-import { getSession } from '@jbrowse/core/util'
+import { AbstractSessionModel, getSession } from '@jbrowse/core/util'
 import CascadingMenuButton from '@jbrowse/core/ui/CascadingMenuButton'
 import { IBaseViewModel } from '@jbrowse/core/pluggableElementTypes/models'
 
@@ -22,7 +22,10 @@ const ViewMenu = observer(function ({
   IconProps: SvgIconProps
 }) {
   const { menuItems } = model
-  const session = getSession(model)
+  const session = getSession(model) as AbstractSessionModel & {
+    moveViewDown: (arg: string) => void
+    moveViewUp: (arg: string) => void
+  }
 
   const items = [
     ...(session.views.length > 1

packages/core/pluggableElementTypes/models/BaseTrackModel.ts

@@ -116,9 +116,8 @@ export function createBaseTrackModel(
         return (
           isSessionModelWithConfigEditing(session) &&
           (adminMode ||
-            sessionTracks.find(
-              (track: { trackId: string }) =>
-                track.trackId === self.configuration?.trackId,
+            sessionTracks?.find(
+              track => track.trackId === self.configuration?.trackId,
             ))
         )
       },
@@ -130,21 +129,6 @@ export function createBaseTrackModel(
       setMinimized(flag: boolean) {
         self.minimized = flag
       },
-      /**
-       * #action
-       */
-      activateConfigurationUI() {
-        const session = getSession(self)
-        const view = getContainingView(self)
-        if (isSessionModelWithConfigEditing(session)) {
-          // @ts-expect-error
-          const trackConf = session.editTrackConfiguration(self.configuration)
-          if (trackConf && trackConf !== self.configuration) {
-            view.hideTrack(self.configuration)
-            view.showTrack(trackConf)
-          }
-        }
-      },
 
       /**
        * #action

packages/core/util/index.ts

@@ -208,7 +208,7 @@ export function springAnimate(
 export function findParentThatIs<T extends (a: IAnyStateTreeNode) => boolean>(
   node: IAnyStateTreeNode,
   predicate: T,
-): TypeTestedByPredicate<T> & IAnyStateTreeNode {
+): TypeTestedByPredicate<T> {
   return findParentThat(node, predicate)
 }
 
@@ -1141,6 +1141,7 @@ export function getTickDisplayStr(totalBp: number, bpPerPx: number) {
 }
 
 export function getViewParams(model: IAnyStateTreeNode, exportSVG?: boolean) {
+  // @ts-expect-error
   const { dynamicBlocks, staticBlocks, offsetPx } = getContainingView(model)
   const b = dynamicBlocks?.contentBlocks[0] || {}
   const staticblock = staticBlocks?.contentBlocks[0] || {}

packages/core/util/types/index.ts

@@ -22,6 +22,7 @@ import {
 import RpcManager from '../../rpc/RpcManager'
 import { Feature } from '../simpleFeature'
 import { BaseInternetAccountModel } from '../../pluggableElementTypes/models'
+import { ThemeOptions } from '@mui/material'
 
 export * from './util'
 
@@ -82,16 +83,26 @@ export type DialogComponentType =
 
 /** minimum interface that all session state models must implement */
 export interface AbstractSessionModel extends AbstractViewContainer {
+  jbrowse: IAnyStateTreeNode
   drawerPosition?: string
-  setSelection(feature: Feature): void
-  clearSelection(): void
   configuration: AnyConfigurationModel
   rpcManager: RpcManager
   assemblyNames: string[]
   assemblies: AnyConfigurationModel[]
   selection?: unknown
-  duplicateCurrentSession?(): void
-  notify(message: string, level?: NotificationLevel, action?: SnackAction): void
+  focusedViewId?: string
+  themeName?: string
+  setFocusedViewId?: (id: string) => void
+  allThemes?: () => Record<string, ThemeOptions | undefined>
+  setSelection: (feature: Feature) => void
+  setSession?: (arg: { name: string; [key: string]: unknown }) => void
+  clearSelection: () => void
+  duplicateCurrentSession?: () => void
+  notify: (
+    message: string,
+    level?: NotificationLevel,
+    action?: SnackAction,
+  ) => void
   assemblyManager: AssemblyManager
   version: string
   getTrackActionMenuItems?: Function
@@ -100,13 +111,20 @@ export interface AbstractSessionModel extends AbstractViewContainer {
   textSearchManager?: TextSearchManager
   connections: AnyConfigurationModel[]
   deleteConnection?: Function
+  temporaryAssemblies?: unknown[]
+  addTemporaryAssembly?: (arg: Record<string, unknown>) => void
+  removeTemporaryAssembly?: (arg: string) => void
   sessionConnections?: AnyConfigurationModel[]
+  sessionTracks?: AnyConfigurationModel[]
   connectionInstances?: {
     name: string
     tracks: AnyConfigurationModel[]
     configuration: AnyConfigurationModel
   }[]
   makeConnection?: Function
+  breakConnection?: Function
+  // eslint-disable-next-line @typescript-eslint/no-explicit-any
+  prepareToBreakConnection?: (arg: AnyConfigurationModel) => any
   adminMode?: boolean
   showWidget?: Function
   addWidget?: Function
@@ -155,6 +173,16 @@ export function isSessionWithAddTracks(
   )
 }
 
+/** abstract interface for a session allows adding tracks */
+export interface SessionWithShareURL extends AbstractSessionModel {
+  shareURL: string
+}
+export function isSessionWithShareURL(
+  thing: unknown,
+): thing is SessionWithShareURL {
+  return isSessionModel(thing) && 'shareURL' in thing && !!thing.shareURL
+}
+
 export interface Widget {
   type: string
   id: string

plugins/alignments/src/shared/BaseDisplayComponent.tsx

@@ -1,6 +1,9 @@
 import React from 'react'
 import { LoadingEllipses } from '@jbrowse/core/ui'
-import { BlockMsg } from '@jbrowse/plugin-linear-genome-view'
+import {
+  BlockMsg,
+  LinearGenomeViewModel,
+} from '@jbrowse/plugin-linear-genome-view'
 import { makeStyles } from 'tss-react/mui'
 import { observer } from 'mobx-react'
 
@@ -56,7 +59,7 @@ const DataDisplay = observer(function ({
   children?: React.ReactNode
 }) {
   const { drawn, loading } = model
-  const view = getContainingView(model)
+  const view = getContainingView(model) as LinearGenomeViewModel
   const left = (model.lastDrawnOffsetPx || 0) - view.offsetPx
   return (
     // this data-testid is located here because changing props on the canvas

plugins/alignments/src/shared/fetchChains.ts

@@ -41,6 +41,7 @@ export interface ChainData {
 export async function fetchChains(
   self: LinearReadArcsDisplayModel | LinearReadCloudDisplayModel,
 ) {
+  // @ts-expect-error
   const { rpcSessionId: sessionId } = getContainingTrack(self)
   const { rpcManager } = getSession(self)
   const view = getContainingView(self) as LGV

plugins/circular-view/src/BaseChordDisplay/models/renderReaction.ts

@@ -1,10 +1,11 @@
 import clone from 'clone'
 import { getRpcSessionId } from '@jbrowse/core/util/tracks'
 import { getSession, getContainingView } from '@jbrowse/core/util'
+import { CircularViewModel } from '../../CircularView/models/CircularView'
 
 // eslint-disable-next-line @typescript-eslint/no-explicit-any
 export function renderReactionData(self: any) {
-  const view = getContainingView(self)
+  const view = getContainingView(self) as CircularViewModel
   const { rendererType } = self
   const { rpcManager } = getSession(view)
 

plugins/data-management/src/AddConnectionWidget/components/AddConnectionWidget.tsx

@@ -1,6 +1,6 @@
 import React, { useMemo, useState } from 'react'
 import { Button, Step, StepContent, StepLabel, Stepper } from '@mui/material'
-import { getSession, getEnv } from '@jbrowse/core/util'
+import { getSession, getEnv, isSessionModelWithWidgets } from '@jbrowse/core/util'
 import { makeStyles } from 'tss-react/mui'
 import { observer } from 'mobx-react'
 import { ConnectionType } from '@jbrowse/core/pluggableElementTypes'
@@ -98,7 +98,10 @@ const AddConnectionWidget = observer(function ({ model }: { model: unknown }) {
                         session.notify('No config model to add')
                       }
 
+                      if(isSessionModelWithWidgets(session)) {
+
                       session.hideWidget(model)
+                      }
                     } else {
                       setActiveStep(activeStep + 1)
                     }

plugins/data-management/src/AddTrackWidget/components/DefaultAddTrackWorkflow.tsx

@@ -14,6 +14,8 @@ import { getRoot } from 'mobx-state-tree'
 import {
   getSession,
   isElectron,
+  isSessionModelWithWidgets,
+  isSessionWithAddTracks,
   isSupportedIndexingAdapter,
 } from '@jbrowse/core/util'
 import { getConf } from '@jbrowse/core/configuration'
@@ -90,7 +92,10 @@ const DefaultAddTrackWorkflow = observer(function ({
     ].join('')
 
     const assemblyInstance = session.assemblyManager.get(assembly)
-
+    if (!isSessionWithAddTracks(session)) {
+      setTrackErrorMessage('Unable to add tracks to this model')
+      return
+    }
     if (assemblyInstance && trackAdapter && trackAdapter.type !== 'UNKNOWN') {
       session.addTrackConf({
         trackId,
@@ -102,40 +107,40 @@ const DefaultAddTrackWorkflow = observer(function ({
           sequenceAdapter: getConf(assemblyInstance, ['sequence', 'adapter']),
         },
       })
-      if (model.view) {
-        model.view.showTrack(trackId)
-        if (
-          isElectron &&
-          textIndexTrack &&
-          isSupportedIndexingAdapter(trackAdapter.type)
-        ) {
-          const attr = textIndexingConf || {
-            attributes: ['Name', 'ID'],
-            exclude: ['CDS', 'exon'],
-          }
-          const indexName = trackName + '-index'
-          const newEntry = {
-            indexingParams: {
-              ...attr,
-              assemblies: [assembly],
-              tracks: [trackId],
-              indexType: 'perTrack',
-              name: indexName,
-              timestamp: new Date().toISOString(),
-            },
+      model.view.showTrack?.(trackId)
+      if (
+        isElectron &&
+        textIndexTrack &&
+        isSupportedIndexingAdapter(trackAdapter.type)
+      ) {
+        const attr = textIndexingConf || {
+          attributes: ['Name', 'ID'],
+          exclude: ['CDS', 'exon'],
+        }
+        const indexName = trackName + '-index'
+        const newEntry = {
+          indexingParams: {
+            ...attr,
+            assemblies: [assembly],
+            tracks: [trackId],
+            indexType: 'perTrack',
             name: indexName,
-            cancelCallback: () => jobsManager.abortJob(),
-          }
-          jobsManager.queueJob(newEntry)
+            timestamp: new Date().toISOString(),
+          },
+          name: indexName,
+          cancelCallback: () => jobsManager.abortJob(),
         }
+        jobsManager.queueJob(newEntry)
       } else {
         session.notify(
           'Open a new view, or use the track selector in an existing view, to view this track',
           'info',
         )
       }
       model.clearData()
-      session.hideWidget(model)
+      if (isSessionModelWithWidgets(session)) {
+        session.hideWidget(model)
+      }
     } else {
       setTrackErrorMessage(
         'Failed to add track.\nThe configuration of this file is not currently supported.',

plugins/data-management/src/AddTrackWidget/components/PasteConfigWorkflow.tsx

@@ -2,7 +2,11 @@ import React, { useState } from 'react'
 import { Button, TextField } from '@mui/material'
 import { ErrorMessage } from '@jbrowse/core/ui'
 import { makeStyles } from 'tss-react/mui'
-import { getSession } from '@jbrowse/core/util'
+import {
+  getSession,
+  isSessionModelWithWidgets,
+  isSessionWithAddTracks,
+} from '@jbrowse/core/util'
 import { observer } from 'mobx-react'
 
 // locals
@@ -51,10 +55,15 @@ const PasteConfigAddTrackWorkflow = observer(function ({
             const session = getSession(model)
             const conf = JSON.parse(val)
             const confs = Array.isArray(conf) ? conf : [conf]
-            confs.forEach(c => session.addTrackConf(c))
-            confs.forEach(c => c.trackId)
-            model.clearData()
-            session.hideWidget(model)
+            if (
+              isSessionWithAddTracks(session) &&
+              isSessionModelWithWidgets(session)
+            ) {
+              confs.forEach(c => session.addTrackConf(c))
+              confs.forEach(c => model.view.showTrack(c.trackId))
+              model.clearData()
+              session.hideWidget(model)
+            }
           } catch (e) {
             console.error(e)
             setError(e)

plugins/data-management/src/HierarchicalTrackSelectorWidget/components/tree/HamburgerMenu.tsx

@@ -61,7 +61,7 @@ const HamburgerMenu = observer(function ({
     deletingConnection?: boolean,
   ) {
     const name = readConfObject(connectionConf, 'name')
-    const result = session.prepareToBreakConnection(connectionConf)
+    const result = session.prepareToBreakConnection?.(connectionConf)
     if (result) {
       const [safelyBreakConnection, dereferenceTypeCount] = result
       if (Object.keys(dereferenceTypeCount).length > 0) {

plugins/data-management/src/PluginStoreWidget/components/InstalledPlugin.tsx

@@ -46,11 +46,12 @@ const InstalledPlugin = observer(function ({
   const [dialogPlugin, setDialogPlugin] = useState<string>()
   const { pluginManager } = getEnv(model)
   const session = getSession(model)
-  const { jbrowse, adminMode, sessionPlugins } = session
-  const isSessionPlugin = sessionPlugins?.some(
-    (p: { url: string }) =>
-      pluginManager.pluginMetadata[plugin.name].url === p.url,
-  )
+  const { jbrowse, adminMode } = session
+  const isSessionPlugin = isSessionWithSessionPlugins(session)
+    ? session.sessionPlugins?.some(
+        p => pluginManager.pluginMetadata[plugin.name].url === p.url,
+      )
+    : false
 
   return (
     <>
@@ -76,7 +77,6 @@ const InstalledPlugin = observer(function ({
       <ListItem key={plugin.name}>
         {adminMode || isSessionPlugin ? (
           <IconButton
-            aria-label="removePlugin"
             data-testid={`removePlugin-${plugin.name}`}
             onClick={() => setDialogPlugin(plugin.name)}
           >

plugins/data-management/src/ucsc-trackhub/model.ts

@@ -104,7 +104,7 @@ export default function UCSCTrackHubConnection(pluginManager: PluginManager) {
             `There was a problem connecting to the UCSC Track Hub "${self.configuration.name}". Please make sure you have entered a valid hub.txt file. The error that was thrown is: "${e}"`,
             'error',
           )
-          session.breakConnection(self.configuration)
+          session.breakConnection?.(self.configuration)
         }
       },
     }))

plugins/dotplot-view/src/DotplotDisplay/stateModelFactory.tsx

@@ -54,10 +54,10 @@ export function stateModelFactory(configSchema: AnyConfigurationSchemaType) {
     )
     .views(self => ({
       get shouldDisplay() {
-        const view = getContainingView(self)
+        const { vview, hview } = getContainingView(self) as DotplotViewModel
         return (
-          view.vview.bpPerPx === self.data.bpPerPxY &&
-          view.hview.bpPerPx === self.data.bpPerPxX
+          vview.bpPerPx === self.data.bpPerPxY &&
+          hview.bpPerPx === self.data.bpPerPxX
         )
       },
       /**

plugins/dotplot-view/src/DotplotView/components/ImportSyntenyTrackSelector.tsx

@@ -38,7 +38,10 @@ const Selector = observer(
   }) => {
     const session = getSession(model)
     const { tracks, sessionTracks } = session
-    const allTracks = [...tracks, ...sessionTracks] as AnyConfigurationModel[]
+    const allTracks = [
+      ...tracks,
+      ...(sessionTracks || []),
+    ] as AnyConfigurationModel[]
     const filteredTracks = allTracks.filter(t => f(t, assembly2, assembly1))
     const resetTrack = filteredTracks[0]?.trackId || ''
     const [value, setValue] = useState(resetTrack)