@apollo-annotation/jbrowse-plugin-apollo 0.3.4 → 0.3.6

package/package.json

@@ -1,6 +1,6 @@
 {
   "name": "@apollo-annotation/jbrowse-plugin-apollo",
-  "version": "0.3.4",
+  "version": "0.3.6",
   "description": "Apollo plugin for JBrowse 2",
   "keywords": [
     "jbrowse",
@@ -48,9 +48,9 @@
     }
   },
   "dependencies": {
-    "@apollo-annotation/common": "^0.3.4",
-    "@apollo-annotation/mst": "^0.3.4",
-    "@apollo-annotation/shared": "^0.3.4",
+    "@apollo-annotation/common": "^0.3.6",
+    "@apollo-annotation/mst": "^0.3.6",
+    "@apollo-annotation/shared": "^0.3.6",
     "@emotion/react": "^11.10.6",
     "@emotion/styled": "^11.10.6",
     "@gmod/gff": "1.2.0",

package/src/ApolloInternetAccount/addMenuItems.ts

@@ -1,4 +1,7 @@
-import { AbstractMenuManager, AbstractSessionModel } from '@jbrowse/core/util'
+import {
+  type AbstractMenuManager,
+  type AbstractSessionModel,
+} from '@jbrowse/core/util'
 
 import {
   AddAssembly,
@@ -7,7 +10,7 @@ import {
   ImportFeatures,
   ManageUsers,
 } from '../components'
-import { ApolloSessionModel } from '../session'
+import { type ApolloSessionModel } from '../session'
 
 export function addMenuItems(rootModel: AbstractMenuManager) {
   rootModel.appendToMenu('Apollo', {

package/src/ApolloInternetAccount/components/AuthTypeSelector.tsx

@@ -12,6 +12,7 @@ import { makeStyles } from 'tss-react/mui'
 
 import { Dialog } from '../../components/Dialog'
 import { createFetchErrorMessage } from '../../util'
+
 import { GoogleButton, GuestButton, MicrosoftButton } from './LoginButtons'
 
 const useStyles = makeStyles()((theme) => ({

package/src/ApolloInternetAccount/components/LoginButtons.tsx

@@ -1,5 +1,5 @@
 import AccountCircleIcon from '@mui/icons-material/AccountCircle'
-import { Button, ButtonProps } from '@mui/material'
+import { Button, type ButtonProps } from '@mui/material'
 import React from 'react'
 import { makeStyles } from 'tss-react/mui'
 

package/src/ApolloInternetAccount/components/LoginIcons.tsx

@@ -1,4 +1,4 @@
-import { SvgIcon, SvgIconProps } from '@mui/material'
+import { SvgIcon, type SvgIconProps } from '@mui/material'
 import React from 'react'
 
 // Icon source: https://developers.google.com/identity/branding-guidelines

package/src/ApolloInternetAccount/configSchema.ts

@@ -1,6 +1,6 @@
 import { ConfigurationSchema } from '@jbrowse/core/configuration'
 import { BaseInternetAccountConfig } from '@jbrowse/core/pluggableElementTypes'
-import { Instance } from 'mobx-state-tree'
+import { type Instance } from 'mobx-state-tree'
 
 const ApolloConfigSchema = ConfigurationSchema(
   'ApolloInternetAccount',

package/src/ApolloInternetAccount/model.ts

@@ -7,31 +7,32 @@
 /* eslint-disable @typescript-eslint/no-misused-promises */
 import { Change } from '@apollo-annotation/common'
 import {
-  ChangeMessage,
-  CheckResultUpdate,
-  RequestUserInformationMessage,
-  UserLocation,
-  UserLocationMessage,
+  type ChangeMessage,
+  type CheckResultUpdate,
+  type RequestUserInformationMessage,
+  type UserLocation,
+  type UserLocationMessage,
   getDecodedToken,
   makeUserSessionId,
 } from '@apollo-annotation/shared'
 import { ConfigurationReference, getConf } from '@jbrowse/core/configuration'
 import { InternetAccount } from '@jbrowse/core/pluggableElementTypes'
 import {
-  AbstractSessionModel,
+  type AbstractSessionModel,
   isAbstractMenuManager,
   isElectron,
 } from '@jbrowse/core/util'
 import { autorun } from 'mobx'
-import { Instance, flow, getRoot, types } from 'mobx-state-tree'
+import { type Instance, flow, getRoot, types } from 'mobx-state-tree'
 import { io } from 'socket.io-client'
 
-import { Collaborator } from '../session'
-import { ApolloRootModel } from '../types'
+import { type Collaborator } from '../session'
+import { type ApolloRootModel } from '../types'
 import { createFetchErrorMessage } from '../util'
+
 import { addMenuItems } from './addMenuItems'
 import { AuthTypeSelector } from './components/AuthTypeSelector'
-import { ApolloInternetAccountConfigModel } from './configSchema'
+import { type ApolloInternetAccountConfigModel } from './configSchema'
 
 type AuthType = 'google' | 'microsoft' | 'guest'
 

package/src/ApolloJobModel.ts

@@ -1,7 +1,7 @@
 /* eslint-disable @typescript-eslint/no-unsafe-assignment */
 /* eslint-disable @typescript-eslint/no-confusing-void-expression */
 import {
-  SessionWithWidgets,
+  type SessionWithWidgets,
   getSession,
   isSessionModelWithWidgets,
 } from '@jbrowse/core/util'

package/src/ApolloRefNameAliasAdapter/ApolloRefNameAliasAdapter.ts

@@ -1,13 +1,15 @@
-import { RefNameAliases } from './../BackendDrivers/BackendDriver'
+import { readConfObject } from '@jbrowse/core/configuration'
 import {
-  BaseRefNameAliasAdapter,
   BaseAdapter,
+  type BaseRefNameAliasAdapter,
 } from '@jbrowse/core/data_adapters/BaseAdapter'
-import { readConfObject } from '@jbrowse/core/configuration'
-import { ApolloSessionModel } from '../session'
-import { BackendDriver } from '../BackendDrivers'
+import type RpcServer from 'librpc-web-mod/dist/server'
 import { nanoid } from 'nanoid'
-import RpcServer from 'librpc-web-mod/dist/server'
+
+import { type BackendDriver } from '../BackendDrivers'
+import { type ApolloSessionModel } from '../session'
+
+import { type RefNameAliases } from './../BackendDrivers/BackendDriver'
 
 declare global {
   const rpcServer: RpcServer

package/src/ApolloRefNameAliasAdapter/index.ts

@@ -1,8 +1,8 @@
+import type PluginManager from '@jbrowse/core/PluginManager'
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'
-import PluginManager from '@jbrowse/core/PluginManager'
 
-import configSchema from './configSchema'
 import ApolloRefNameAliasAdapter from './ApolloRefNameAliasAdapter'
+import configSchema from './configSchema'
 
 export function installApolloRefNameAliasAdapter(pluginManager: PluginManager) {
   pluginManager.addAdapterType(

package/src/ApolloSequenceAdapter/ApolloSequenceAdapter.ts

@@ -6,12 +6,12 @@
 import { readConfObject } from '@jbrowse/core/configuration'
 import { BaseSequenceAdapter } from '@jbrowse/core/data_adapters/BaseAdapter'
 import { ObservableCreate } from '@jbrowse/core/util/rxjs'
-import SimpleFeature, { Feature } from '@jbrowse/core/util/simpleFeature'
-import { NoAssemblyRegion, Region } from '@jbrowse/core/util/types'
+import SimpleFeature, { type Feature } from '@jbrowse/core/util/simpleFeature'
+import { type NoAssemblyRegion, type Region } from '@jbrowse/core/util/types'
 import { nanoid } from 'nanoid'
 
-import { BackendDriver } from '../BackendDrivers'
-import { ApolloSessionModel } from '../session'
+import { type BackendDriver } from '../BackendDrivers'
+import { type ApolloSessionModel } from '../session'
 
 // declare global {
 //   var rpcServer: import('librpc-web-mod').RpcServer
@@ -127,6 +127,19 @@ export class ApolloSequenceAdapter extends BaseSequenceAdapter {
         const backendDriver = dataStore.getBackendDriver(
           assemblyId,
         ) as BackendDriver
+        const regions = await backendDriver.getRegions(
+          regionWithAssemblyName.assemblyName,
+        )
+        const region = regions.find(
+          (region) => region.refName === regionWithAssemblyName.refName,
+        )
+        if (!region) {
+          observer.error('Cannot get region')
+          return
+        }
+        if (regionWithAssemblyName.end > region.end) {
+          regionWithAssemblyName.end = region.end
+        }
         const { seq } = await backendDriver.getSequence(regionWithAssemblyName)
         observer.next(
           new SimpleFeature({

package/src/ApolloSequenceAdapter/index.ts

@@ -1,5 +1,5 @@
+import type PluginManager from '@jbrowse/core/PluginManager'
 import AdapterType from '@jbrowse/core/pluggableElementTypes/AdapterType'
-import PluginManager from '@jbrowse/core/PluginManager'
 
 import { ApolloSequenceAdapter } from './ApolloSequenceAdapter'
 import configSchema from './configSchema'

package/src/ApolloTextSearchAdapter/ApolloTextSearchAdapter.ts

@@ -1,14 +1,15 @@
-import { AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
+import { type AnnotationFeatureSnapshot } from '@apollo-annotation/mst'
+import BaseResult from '@jbrowse/core/TextSearch/BaseResults'
+import { type Assembly } from '@jbrowse/core/assemblyManager/assembly'
 import { readConfObject } from '@jbrowse/core/configuration'
 import {
   BaseAdapter,
-  BaseTextSearchAdapter,
-  BaseTextSearchArgs,
+  type BaseTextSearchAdapter,
+  type BaseTextSearchArgs,
 } from '@jbrowse/core/data_adapters/BaseAdapter'
-import BaseResult from '@jbrowse/core/TextSearch/BaseResults'
-import { AbstractSessionModel, UriLocation } from '@jbrowse/core/util'
-import { ApolloSessionModel } from '../session'
-import { Assembly } from '@jbrowse/core/assemblyManager/assembly'
+import { type AbstractSessionModel, type UriLocation } from '@jbrowse/core/util'
+
+import { type ApolloSessionModel } from '../session'
 
 export class ApolloTextSearchAdapter
   extends BaseAdapter

package/src/ApolloTextSearchAdapter/index.ts

@@ -1,5 +1,5 @@
+import type PluginManager from '@jbrowse/core/PluginManager'
 import { TextSearchAdapterType } from '@jbrowse/core/pluggableElementTypes'
-import PluginManager from '@jbrowse/core/PluginManager'
 
 import { ApolloTextSearchAdapter } from './ApolloTextSearchAdapter'
 import configSchema from './configSchema'

package/src/BackendDrivers/BackendDriver.ts

@@ -1,13 +1,13 @@
-import { Change, ClientDataStore } from '@apollo-annotation/common'
+import { type Change, type ClientDataStore } from '@apollo-annotation/common'
 import {
-  AnnotationFeatureSnapshot,
-  CheckResultSnapshot,
+  type AnnotationFeatureSnapshot,
+  type CheckResultSnapshot,
 } from '@apollo-annotation/mst'
-import { ValidationResultSet } from '@apollo-annotation/shared'
-import { Assembly } from '@jbrowse/core/assemblyManager/assembly'
-import { Region } from '@jbrowse/core/util'
+import { type ValidationResultSet } from '@apollo-annotation/shared'
+import { type Assembly } from '@jbrowse/core/assemblyManager/assembly'
+import { type Region } from '@jbrowse/core/util'
 
-import { SubmitOpts } from '../ChangeManager'
+import { type SubmitOpts } from '../ChangeManager'
 
 export interface RefNameAliases {
   refName: string

package/src/BackendDrivers/CollaborationServerDriver.ts

@@ -4,21 +4,25 @@
 /* eslint-disable @typescript-eslint/no-unsafe-member-access */
 /* eslint-disable @typescript-eslint/no-unsafe-call */
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
-import { AssemblySpecificChange, Change } from '@apollo-annotation/common'
+import { type AssemblySpecificChange, Change } from '@apollo-annotation/common'
 import {
-  AnnotationFeatureSnapshot,
-  ApolloRefSeqI,
-  CheckResultSnapshot,
+  type AnnotationFeatureSnapshot,
+  type ApolloRefSeqI,
+  type CheckResultSnapshot,
 } from '@apollo-annotation/mst'
-import { ChangeMessage, ValidationResultSet } from '@apollo-annotation/shared'
+import {
+  type ChangeMessage,
+  ValidationResultSet,
+} from '@apollo-annotation/shared'
 import { getConf } from '@jbrowse/core/configuration'
-import { BaseInternetAccountModel } from '@jbrowse/core/pluggableElementTypes'
-import { Region, getSession } from '@jbrowse/core/util'
-import { Socket } from 'socket.io-client'
+import { type BaseInternetAccountModel } from '@jbrowse/core/pluggableElementTypes'
+import { type Region, getSession } from '@jbrowse/core/util'
+import { type Socket } from 'socket.io-client'
 
-import { ChangeManager, SubmitOpts } from '../ChangeManager'
+import { ChangeManager, type SubmitOpts } from '../ChangeManager'
 import { createFetchErrorMessage } from '../util'
-import { BackendDriver, RefNameAliases } from './BackendDriver'
+
+import { BackendDriver, type RefNameAliases } from './BackendDriver'
 
 export interface ApolloRefSeqResponse {
   _id: string

package/src/BackendDrivers/DesktopFileDriver.ts

@@ -1,25 +1,26 @@
 /* eslint-disable @typescript-eslint/require-await */
 import {
-  AssemblySpecificChange,
-  Change,
+  type AssemblySpecificChange,
+  type Change,
   isAssemblySpecificChange,
 } from '@apollo-annotation/common'
 import {
-  AnnotationFeatureSnapshot,
-  CheckResultSnapshot,
+  type AnnotationFeatureSnapshot,
+  type CheckResultSnapshot,
 } from '@apollo-annotation/mst'
 import {
-  annotationFeatureToGFF3,
   ValidationResultSet,
+  annotationFeatureToGFF3,
   splitStringIntoChunks,
 } from '@apollo-annotation/shared'
-import gff, { GFF3Item } from '@gmod/gff'
+import gff, { type GFF3Item } from '@gmod/gff'
 import { getConf } from '@jbrowse/core/configuration'
-import { Region, getSession } from '@jbrowse/core/util'
+import { type Region, getSession } from '@jbrowse/core/util'
 import { getSnapshot } from 'mobx-state-tree'
 
 import { checkFeatures, loadAssemblyIntoClient } from '../util'
-import { BackendDriver, RefNameAliases } from './BackendDriver'
+
+import { BackendDriver, type RefNameAliases } from './BackendDriver'
 
 export class DesktopFileDriver extends BackendDriver {
   async loadAssembly(assemblyName: string) {
@@ -32,7 +33,7 @@ export class DesktopFileDriver extends BackendDriver {
       file: string
     }
 
-    // eslint-disable-next-line @typescript-eslint/no-require-imports
+    // eslint-disable-next-line @typescript-eslint/no-require-imports, @typescript-eslint/consistent-type-imports
     const fs = require('node:fs') as typeof import('fs')
     const fileContents = await fs.promises.readFile(file, 'utf8')
     return loadAssemblyIntoClient(assemblyName, fileContents, this.clientStore)
@@ -166,7 +167,7 @@ export class DesktopFileDriver extends BackendDriver {
 
     const gff3Contents = gff.formatSync(gff3Items)
 
-    // eslint-disable-next-line @typescript-eslint/no-require-imports
+    // eslint-disable-next-line @typescript-eslint/no-require-imports, @typescript-eslint/consistent-type-imports
     const fs = require('node:fs') as typeof import('fs')
     await fs.promises.writeFile(file, gff3Contents, 'utf8')
 

package/src/BackendDrivers/InMemoryFileDriver.ts

@@ -1,17 +1,21 @@
 /* eslint-disable @typescript-eslint/require-await */
-import { AssemblySpecificChange, Change } from '@apollo-annotation/common'
 import {
-  AnnotationFeatureSnapshot,
-  CheckResultSnapshot,
+  type AssemblySpecificChange,
+  type Change,
+} from '@apollo-annotation/common'
+import {
+  type AnnotationFeatureSnapshot,
+  type CheckResultSnapshot,
 } from '@apollo-annotation/mst'
 import { ValidationResultSet } from '@apollo-annotation/shared'
 import { getConf } from '@jbrowse/core/configuration'
-import { Region, getSession } from '@jbrowse/core/util'
+import { type Region, getSession } from '@jbrowse/core/util'
 
-import { SubmitOpts } from '../ChangeManager'
-import { BackendDriver, RefNameAliases } from './BackendDriver'
+import { type SubmitOpts } from '../ChangeManager'
 import { checkFeatures } from '../util'
 
+import { BackendDriver, type RefNameAliases } from './BackendDriver'
+
 export class InMemoryFileDriver extends BackendDriver {
   async getFeatures(): Promise<
     [AnnotationFeatureSnapshot[], CheckResultSnapshot[]]

package/src/ChangeManager.ts

@@ -2,18 +2,18 @@
 /* eslint-disable @typescript-eslint/no-unsafe-call */
 /* eslint-disable @typescript-eslint/no-unsafe-member-access */
 import {
-  Change,
-  ClientDataStore,
+  type Change,
+  type ClientDataStore,
   isAssemblySpecificChange,
 } from '@apollo-annotation/common'
 import {
-  ValidationResultSet,
+  type ValidationResultSet,
   validationRegistry,
 } from '@apollo-annotation/shared'
 import { getSession } from '@jbrowse/core/util'
-import { IAnyStateTreeNode } from 'mobx-state-tree'
+import { type IAnyStateTreeNode } from 'mobx-state-tree'
 
-import { ApolloSessionModel } from './session'
+import { type ApolloSessionModel } from './session'
 
 export interface SubmitOpts {
   /** defaults to true */

package/src/FeatureDetailsWidget/ApolloFeatureDetailsWidget.tsx

@@ -1,14 +1,22 @@
 import { getSession } from '@jbrowse/core/util'
+import ExpandMoreIcon from '@mui/icons-material/ExpandMore'
+import {
+  Accordion,
+  AccordionDetails,
+  AccordionSummary,
+  Typography,
+} from '@mui/material'
 import { observer } from 'mobx-react'
-import React from 'react'
+import React, { useEffect, useState } from 'react'
 import { makeStyles } from 'tss-react/mui'
 
-import { ApolloSessionModel } from '../session'
+import { type ApolloSessionModel } from '../session'
+
 import { Attributes } from './Attributes'
 import { BasicInformation } from './BasicInformation'
-import { ApolloFeatureDetailsWidget as ApolloFeatureDetails } from './model'
-import { Sequence } from './Sequence'
 import { FeatureDetailsNavigation } from './FeatureDetailsNavigation'
+import { Sequence } from './Sequence'
+import { type ApolloFeatureDetailsWidget as ApolloFeatureDetails } from './model'
 
 const useStyles = makeStyles()((theme) => ({
   root: {
@@ -24,6 +32,12 @@ export const ApolloFeatureDetailsWidget = observer(
     const currentAssembly = session.apolloDataStore.assemblies.get(assembly)
     const { classes } = useStyles()
 
+    const [panelState, setPanelState] = useState<string[]>(['attributes'])
+
+    useEffect(() => {
+      setPanelState(['attributes'])
+    }, [feature])
+
     if (!(feature && currentAssembly)) {
       return null
     }
@@ -39,6 +53,14 @@ export const ApolloFeatureDetailsWidget = observer(
       ])
     }
 
+    function handlePanelChange(expanded: boolean, panel: string) {
+      if (expanded) {
+        setPanelState([...panelState, panel])
+      } else {
+        setPanelState(panelState.filter((p) => p !== panel))
+      }
+    }
+
     return (
       <div className={classes.root}>
         <BasicInformation
@@ -46,22 +68,72 @@ export const ApolloFeatureDetailsWidget = observer(
           session={session}
           assembly={currentAssembly._id}
         />
-        <hr />
-        <Attributes
-          feature={feature}
-          session={session}
-          assembly={currentAssembly._id}
-          editable={true}
-        />
-        <hr />
-        <Sequence
-          feature={feature}
-          session={session}
-          assembly={currentAssembly._id}
-          refName={refName}
-        />
-        <hr />
-        <FeatureDetailsNavigation model={model} feature={feature} />
+        <Accordion
+          style={{ marginTop: 10 }}
+          expanded={panelState.includes('attributes')}
+          onChange={(e, expanded) => {
+            handlePanelChange(expanded, 'attributes')
+          }}
+        >
+          <AccordionSummary
+            expandIcon={<ExpandMoreIcon style={{ color: 'white' }} />}
+            aria-controls="panel1-content"
+            id="panel1-header"
+          >
+            <Typography component="span">Attributes</Typography>
+          </AccordionSummary>
+          <AccordionDetails>
+            <Attributes
+              feature={feature}
+              session={session}
+              assembly={currentAssembly._id}
+              editable={true}
+            />
+          </AccordionDetails>
+        </Accordion>
+        <Accordion
+          style={{ marginTop: 10 }}
+          expanded={panelState.includes('sequence')}
+          onChange={(e, expanded) => {
+            handlePanelChange(expanded, 'sequence')
+          }}
+        >
+          <AccordionSummary
+            expandIcon={<ExpandMoreIcon style={{ color: 'white' }} />}
+            aria-controls="panel2-content"
+            id="panel2-header"
+          >
+            <Typography component="span">Sequence</Typography>
+          </AccordionSummary>
+          <AccordionDetails>
+            {panelState.includes('sequence') && (
+              <Sequence
+                feature={feature}
+                session={session}
+                assembly={currentAssembly._id}
+                refName={refName}
+              />
+            )}
+          </AccordionDetails>
+        </Accordion>
+        <Accordion
+          style={{ marginTop: 10 }}
+          expanded={panelState.includes('related_features')}
+          onChange={(e, expanded) => {
+            handlePanelChange(expanded, 'related_features')
+          }}
+        >
+          <AccordionSummary
+            expandIcon={<ExpandMoreIcon style={{ color: 'white' }} />}
+            aria-controls="panel3-content"
+            id="panel3-header"
+          >
+            <Typography component="span">Related features</Typography>
+          </AccordionSummary>
+          <AccordionDetails>
+            <FeatureDetailsNavigation model={model} feature={feature} />
+          </AccordionDetails>
+        </Accordion>
       </div>
     )
   },