@apollo-annotation/jbrowse-plugin-apollo 0.3.5 → 0.3.6

package/src/OntologyManager/OntologyStore/indexeddb-storage.ts

@@ -1,17 +1,23 @@
 /* eslint-disable @typescript-eslint/no-unnecessary-condition */
 import { openLocation } from '@jbrowse/core/util/io'
 import equal from 'fast-deep-equal/es6'
-import { IDBPDatabase, IDBPTransaction, openDB } from 'idb/with-async-ittr'
+import {
+  type IDBPDatabase,
+  type IDBPTransaction,
+  openDB,
+} from 'idb/with-async-ittr'
+
+import { defaultTextIndexFields } from '..'
 
 import { PREFIXED_ID_PATH, getWords } from './fulltext'
 import {
-  OntologyDB,
+  type OntologyDB,
   isOntologyDBEdge,
   isOntologyDBNode,
 } from './indexeddb-schema'
-import { GraphDocument } from './obo-graph-json-schema'
-import OntologyStore from '.'
-import { defaultTextIndexFields } from '..'
+import { type GraphDocument } from './obo-graph-json-schema'
+
+import type OntologyStore from '.'
 
 /** schema version we are currently on, used for the IndexedDB schema open call */
 const schemaVersion = 2

package/src/OntologyManager/index.ts

@@ -1,5 +1,5 @@
 import {
-  AnyConfigurationModel,
+  type AnyConfigurationModel,
   ConfigurationSchema,
   readConfObject,
 } from '@jbrowse/core/configuration'
@@ -10,18 +10,20 @@ import {
 } from '@jbrowse/core/util/types/mst'
 import { autorun } from 'mobx'
 import {
-  Instance,
+  type Instance,
   addDisposer,
   flow,
   getRoot,
   getSnapshot,
   types,
 } from 'mobx-state-tree'
-import OntologyStore, { OntologyStoreOptions } from './OntologyStore'
-import { OntologyDBNode } from './OntologyStore/indexeddb-schema'
+
+import type ApolloPluginConfigurationSchema from '../config'
+import { type ApolloRootModel } from '../types'
+
+import OntologyStore, { type OntologyStoreOptions } from './OntologyStore'
+import { type OntologyDBNode } from './OntologyStore/indexeddb-schema'
 import { applyPrefixes, expandPrefixes } from './OntologyStore/prefixes'
-import ApolloPluginConfigurationSchema from '../config'
-import { ApolloRootModel } from '../types'
 
 export { isDeprecated } from './OntologyStore/indexeddb-schema'
 

package/src/OntologyManager/util.ts

@@ -1,6 +1,7 @@
-import { AnnotationFeature } from '@apollo-annotation/mst'
+import { type AnnotationFeature } from '@apollo-annotation/mst'
+
+import type OntologyStore from './OntologyStore'
 
-import OntologyStore from './OntologyStore'
 import { isOntologyClass } from '.'
 
 export async function fetchValidDescendantTerms(

package/src/TabularEditor/HybridGrid/ChangeHandling.ts

@@ -1,11 +1,11 @@
-import type { AnnotationFeature } from '@apollo-annotation/mst'
+import { type AnnotationFeature } from '@apollo-annotation/mst'
 import {
   LocationEndChange,
   LocationStartChange,
   TypeChange,
 } from '@apollo-annotation/shared'
 
-import type { ChangeManager } from '../../ChangeManager'
+import { type ChangeManager } from '../../ChangeManager'
 
 export function handleFeatureTypeChange(
   changeManager: ChangeManager,

package/src/TabularEditor/HybridGrid/Feature.tsx

@@ -1,25 +1,26 @@
 /* eslint-disable unicorn/no-nested-ternary */
 /* eslint-disable @typescript-eslint/unbound-method */
 
-import { AnnotationFeature } from '@apollo-annotation/mst'
-import { AbstractSessionModel } from '@jbrowse/core/util'
+import { type AnnotationFeature } from '@apollo-annotation/mst'
+import { type AbstractSessionModel } from '@jbrowse/core/util'
 import { observer } from 'mobx-react'
 import React from 'react'
 import { makeStyles } from 'tss-react/mui'
 
-import { OntologyTermAutocomplete } from '../../components/OntologyTermAutocomplete'
 import { isOntologyClass } from '../../OntologyManager'
-import OntologyStore from '../../OntologyManager/OntologyStore'
-import { DisplayStateModel } from '../types'
+import type OntologyStore from '../../OntologyManager/OntologyStore'
+import { OntologyTermAutocomplete } from '../../components/OntologyTermAutocomplete'
+import { type DisplayStateModel } from '../types'
+
 import {
   handleFeatureEndChange,
   handleFeatureStartChange,
   handleFeatureTypeChange,
 } from './ChangeHandling'
 import { FeatureAttributes } from './FeatureAttributes'
-import { featureContextMenuItems } from './featureContextMenuItems'
-import type { ContextMenuState } from './HybridGrid'
+import { type ContextMenuState } from './HybridGrid'
 import { NumberCell } from './NumberCell'
+import { featureContextMenuItems } from './featureContextMenuItems'
 
 const useStyles = makeStyles()((theme) => ({
   typeContent: {
@@ -132,6 +133,7 @@ export const Feature = observer(function Feature({
           displayState.setApolloHover({
             feature,
             topLevelFeature: getTopLevelFeature(feature),
+            // @ts-expect-error TODO fix in future when moving hover logic to session.
             glyph: displayState.getGlyph(getTopLevelFeature(feature)),
           })
         }}

package/src/TabularEditor/HybridGrid/FeatureAttributes.tsx

@@ -1,5 +1,5 @@
 /* eslint-disable @typescript-eslint/restrict-template-expressions */
-import { AnnotationFeature } from '@apollo-annotation/mst'
+import { type AnnotationFeature } from '@apollo-annotation/mst'
 import { observer } from 'mobx-react'
 import { getSnapshot } from 'mobx-state-tree'
 import React from 'react'

package/src/TabularEditor/HybridGrid/HybridGrid.tsx

@@ -1,10 +1,11 @@
-import { Menu, MenuItem } from '@jbrowse/core/ui'
+import { Menu, type MenuItem } from '@jbrowse/core/ui'
 import { useTheme } from '@mui/material'
 import { observer } from 'mobx-react'
 import React, { useEffect, useRef, useState } from 'react'
 import { makeStyles } from 'tss-react/mui'
 
-import { DisplayStateModel } from '../types'
+import { type DisplayStateModel } from '../types'
+
 import { Feature } from './Feature'
 
 const useStyles = makeStyles()((theme) => ({

package/src/TabularEditor/HybridGrid/ToolBar.tsx

@@ -6,7 +6,7 @@ import { observer } from 'mobx-react'
 import React from 'react'
 import { makeStyles } from 'tss-react/mui'
 
-import { DisplayStateModel } from '../types'
+import { type DisplayStateModel } from '../types'
 
 const useStyles = makeStyles()({
   toolbar: {

package/src/TabularEditor/HybridGrid/featureContextMenuItems.ts

@@ -1,14 +1,14 @@
-import { AnnotationFeature } from '@apollo-annotation/mst'
-import { MenuItem } from '@jbrowse/core/ui'
+import { type AnnotationFeature } from '@apollo-annotation/mst'
+import { type MenuItem } from '@jbrowse/core/ui'
 import {
-  AbstractSessionModel,
-  SessionWithWidgets,
+  type AbstractSessionModel,
+  type SessionWithWidgets,
   isSessionModelWithWidgets,
 } from '@jbrowse/core/util'
 
-import { ChangeManager } from '../../ChangeManager'
+import { type ChangeManager } from '../../ChangeManager'
 import { AddChildFeature, CopyFeature, DeleteFeature } from '../../components'
-import { ApolloSessionModel } from '../../session'
+import { type ApolloSessionModel } from '../../session'
 import { getApolloInternetAccount } from '../../util'
 
 export function featureContextMenuItems(

package/src/TabularEditor/TabularEditorPane.tsx

@@ -3,7 +3,7 @@ import React from 'react'
 
 import HybridGrid from './HybridGrid'
 import { ToolBar } from './HybridGrid/ToolBar'
-import { DisplayStateModel } from './types'
+import { type DisplayStateModel } from './types'
 
 function stopPropagation(e: React.MouseEvent) {
   e.stopPropagation()

package/src/TabularEditor/model.ts

@@ -1,6 +1,6 @@
-import { Instance, getParent, types } from 'mobx-state-tree'
+import { type Instance, getParent, types } from 'mobx-state-tree'
 
-import { DisplayStateModel } from './types'
+import { type DisplayStateModel } from './types'
 
 export const TabularEditorStateModelType = types
   .model('TabularEditor', {

package/src/TabularEditor/types.ts

@@ -1,3 +1,6 @@
-import { LinearApolloDisplay } from '../LinearApolloDisplay/stateModel'
+import { type LinearApolloDisplay } from '../LinearApolloDisplay/stateModel'
+import { type LinearApolloSixFrameDisplay } from '../LinearApolloSixFrameDisplay/stateModel'
 
-export type DisplayStateModel = LinearApolloDisplay
+export type DisplayStateModel =
+  | LinearApolloDisplay
+  | LinearApolloSixFrameDisplay

package/src/components/AddAssembly.tsx

@@ -9,49 +9,46 @@ import {
   AddAssemblyFromFileChange,
 } from '@apollo-annotation/shared'
 import { readConfObject } from '@jbrowse/core/configuration'
-import { AbstractSessionModel } from '@jbrowse/core/util'
+import { type AbstractSessionModel } from '@jbrowse/core/util'
+import InfoIcon from '@mui/icons-material/Info'
+import LinkIcon from '@mui/icons-material/Link'
+import RadioButtonCheckedIcon from '@mui/icons-material/RadioButtonChecked'
+import RadioButtonUncheckedIcon from '@mui/icons-material/RadioButtonUnchecked'
 import {
+  Accordion,
+  AccordionDetails,
+  AccordionSummary,
+  Box,
   Button,
+  Checkbox,
   DialogActions,
   DialogContent,
   DialogContentText,
-  Accordion,
-  AccordionSummary,
-  AccordionDetails,
-  Typography,
-  Box,
-  FormGroup,
   FormControlLabel,
-  Checkbox,
-  LinearProgress,
-  TextField,
-  Tooltip,
+  FormGroup,
   IconButton,
+  InputAdornment,
+  LinearProgress,
   Table,
-  TableCell,
   TableBody,
-  InputAdornment,
+  TableCell,
   TableRow,
+  TextField,
+  Tooltip,
+  Typography,
 } from '@mui/material'
-
-import { makeStyles } from 'tss-react/mui'
-
 import ObjectID from 'bson-objectid'
 import { getRoot } from 'mobx-state-tree'
 import React, { useEffect, useState } from 'react'
+import { makeStyles } from 'tss-react/mui'
 
-import { ApolloInternetAccountModel } from '../ApolloInternetAccount/model'
-import { ChangeManager } from '../ChangeManager'
-import { ApolloSessionModel } from '../session'
-import { ApolloRootModel } from '../types'
+import { type ApolloInternetAccountModel } from '../ApolloInternetAccount/model'
+import { type ChangeManager } from '../ChangeManager'
+import { type ApolloSessionModel } from '../session'
+import { type ApolloRootModel } from '../types'
 import { createFetchErrorMessage } from '../util'
-import { Dialog } from './Dialog'
 
-import RadioButtonUncheckedIcon from '@mui/icons-material/RadioButtonUnchecked'
-import RadioButtonCheckedIcon from '@mui/icons-material/RadioButtonChecked'
-
-import InfoIcon from '@mui/icons-material/Info'
-import LinkIcon from '@mui/icons-material/Link'
+import { Dialog } from './Dialog'
 
 interface AddAssemblyProps {
   session: ApolloSessionModel
@@ -518,164 +515,170 @@ export function AddAssembly({
                 fileType === FileType.GFF3 ? (
                   <Table size="small" sx={{ mt: 2 }}>
                     <TableBody>
-                      <TableRow />
-                      <TableCell style={{ borderBottomWidth: 0 }}>
-                        <Box display="flex" alignItems="center">
-                          <span>FASTA</span>
-                          <Tooltip title='Unless "Store sequence in database" enabled, FASTA input must be compressed with bgzip and indexed with samtools faidx (or equivalent). Compression is optional for sequences stored in the database.'>
-                            <IconButton size="small">
-                              <InfoIcon sx={{ fontSize: 18 }} />
-                            </IconButton>
-                          </Tooltip>
-                        </Box>
-                      </TableCell>
-                      <TableCell style={{ borderBottomWidth: 0 }}>
-                        <input
-                          data-testid="fasta-input-file"
-                          type="file"
-                          onChange={(
-                            e: React.ChangeEvent<HTMLInputElement>,
-                          ) => {
-                            setFastaFile(e.target.files?.item(0) ?? null)
-                          }}
-                          disabled={submitted && !errorMessage}
-                        />
-                      </TableCell>
-
-                      <TableRow />
-                      <TableCell style={{ borderBottomWidth: 0 }}>
-                        FASTA index (.fai)
-                      </TableCell>
-                      <TableCell style={{ borderBottomWidth: 0 }}>
-                        <input
-                          data-testid="fai-input-file"
-                          type="file"
-                          onChange={(
-                            e: React.ChangeEvent<HTMLInputElement>,
-                          ) => {
-                            setFastaIndexFile(e.target.files?.item(0) ?? null)
-                          }}
-                          disabled={
-                            (submitted && !errorMessage) || sequenceIsEditable
-                          }
-                        />
-                      </TableCell>
-
-                      <TableRow />
-                      <TableCell style={{ borderBottomWidth: 0 }}>
-                        FASTA binary index (.gzi)
-                      </TableCell>
-                      <TableCell style={{ borderBottomWidth: 0 }}>
-                        <input
-                          data-testid="gzi-input-file"
-                          type="file"
-                          onChange={(
-                            e: React.ChangeEvent<HTMLInputElement>,
-                          ) => {
-                            setFastaGziIndexFile(
-                              e.target.files?.item(0) ?? null,
-                            )
-                          }}
-                          disabled={
-                            (submitted && !errorMessage) || sequenceIsEditable
-                          }
-                        />
-                      </TableCell>
+                      <TableRow>
+                        <TableCell style={{ borderBottomWidth: 0 }}>
+                          <Box display="flex" alignItems="center">
+                            <span>FASTA</span>
+                            <Tooltip title='Unless "Store sequence in database" enabled, FASTA input must be compressed with bgzip and indexed with samtools faidx (or equivalent). Compression is optional for sequences stored in the database.'>
+                              <IconButton size="small">
+                                <InfoIcon sx={{ fontSize: 18 }} />
+                              </IconButton>
+                            </Tooltip>
+                          </Box>
+                        </TableCell>
+                        <TableCell style={{ borderBottomWidth: 0 }}>
+                          <input
+                            data-testid="fasta-input-file"
+                            type="file"
+                            onChange={(
+                              e: React.ChangeEvent<HTMLInputElement>,
+                            ) => {
+                              setFastaFile(e.target.files?.item(0) ?? null)
+                            }}
+                            disabled={submitted && !errorMessage}
+                          />
+                        </TableCell>
+                      </TableRow>
+
+                      <TableRow>
+                        <TableCell style={{ borderBottomWidth: 0 }}>
+                          FASTA index (.fai)
+                        </TableCell>
+                        <TableCell style={{ borderBottomWidth: 0 }}>
+                          <input
+                            data-testid="fai-input-file"
+                            type="file"
+                            onChange={(
+                              e: React.ChangeEvent<HTMLInputElement>,
+                            ) => {
+                              setFastaIndexFile(e.target.files?.item(0) ?? null)
+                            }}
+                            disabled={
+                              (submitted && !errorMessage) || sequenceIsEditable
+                            }
+                          />
+                        </TableCell>
+                      </TableRow>
+
+                      <TableRow>
+                        <TableCell style={{ borderBottomWidth: 0 }}>
+                          FASTA binary index (.gzi)
+                        </TableCell>
+                        <TableCell style={{ borderBottomWidth: 0 }}>
+                          <input
+                            data-testid="gzi-input-file"
+                            type="file"
+                            onChange={(
+                              e: React.ChangeEvent<HTMLInputElement>,
+                            ) => {
+                              setFastaGziIndexFile(
+                                e.target.files?.item(0) ?? null,
+                              )
+                            }}
+                            disabled={
+                              (submitted && !errorMessage) || sequenceIsEditable
+                            }
+                          />
+                        </TableCell>
+                      </TableRow>
                     </TableBody>
                   </Table>
                 ) : (
                   <Table size="small" sx={{ mt: 2 }}>
                     <TableBody>
-                      <TableRow />
-                      <TableCell style={{ borderBottomWidth: 0 }}>
-                        <Box display="flex" alignItems="center">
-                          <span>FASTA</span>
-                          <Tooltip title="Remote FASTA input must be compressed with bgzip and indexed with samtools faidx (or equivalent)">
-                            <IconButton size="small">
-                              <InfoIcon sx={{ fontSize: 18 }} />
-                            </IconButton>
-                          </Tooltip>
-                        </Box>
-                      </TableCell>
-                      <TableCell style={{ borderBottomWidth: 0 }}>
-                        <TextField
-                          data-testid="fasta-input-url"
-                          variant="outlined"
-                          value={fastaUrl}
-                          error={!validFastaUrl}
-                          onChange={(
-                            e: React.ChangeEvent<HTMLInputElement>,
-                          ) => {
-                            setFastaUrl(e.target.value)
-                          }}
-                          disabled={submitted && !errorMessage}
-                          slotProps={{
-                            input: {
-                              startAdornment: (
-                                <InputAdornment position="start">
-                                  <LinkIcon />
-                                </InputAdornment>
-                              ),
-                            },
-                          }}
-                        />
-                      </TableCell>
-
-                      <TableRow />
-                      <TableCell style={{ borderBottomWidth: 0 }}>
-                        FASTA index (.fai)
-                      </TableCell>
-                      <TableCell style={{ borderBottomWidth: 0 }}>
-                        <TextField
-                          data-testid="fai-input-url"
-                          variant="outlined"
-                          value={fastaIndexUrl}
-                          error={!validFastaIndexUrl}
-                          onChange={(
-                            e: React.ChangeEvent<HTMLInputElement>,
-                          ) => {
-                            setFastaIndexUrl(e.target.value)
-                          }}
-                          disabled={submitted && !errorMessage}
-                          slotProps={{
-                            input: {
-                              startAdornment: (
-                                <InputAdornment position="start">
-                                  <LinkIcon />
-                                </InputAdornment>
-                              ),
-                            },
-                          }}
-                        />
-                      </TableCell>
-
-                      <TableRow />
-                      <TableCell style={{ borderBottomWidth: 0 }}>
-                        FASTA binary index (.gzi)
-                      </TableCell>
-                      <TableCell style={{ borderBottomWidth: 0 }}>
-                        <TextField
-                          data-testid="gzi-input-url"
-                          variant="outlined"
-                          value={fastaGziIndexUrl}
-                          error={!validFastaGziIndexUrl}
-                          onChange={(
-                            e: React.ChangeEvent<HTMLInputElement>,
-                          ) => {
-                            setFastaGziIndexUrl(e.target.value)
-                          }}
-                          disabled={submitted && !errorMessage}
-                          slotProps={{
-                            input: {
-                              startAdornment: (
-                                <InputAdornment position="start">
-                                  <LinkIcon />
-                                </InputAdornment>
-                              ),
-                            },
-                          }}
-                        />
-                      </TableCell>
+                      <TableRow>
+                        <TableCell style={{ borderBottomWidth: 0 }}>
+                          <Box display="flex" alignItems="center">
+                            <span>FASTA</span>
+                            <Tooltip title="Remote FASTA input must be compressed with bgzip and indexed with samtools faidx (or equivalent)">
+                              <IconButton size="small">
+                                <InfoIcon sx={{ fontSize: 18 }} />
+                              </IconButton>
+                            </Tooltip>
+                          </Box>
+                        </TableCell>
+                        <TableCell style={{ borderBottomWidth: 0 }}>
+                          <TextField
+                            data-testid="fasta-input-url"
+                            variant="outlined"
+                            value={fastaUrl}
+                            error={!validFastaUrl}
+                            onChange={(
+                              e: React.ChangeEvent<HTMLInputElement>,
+                            ) => {
+                              setFastaUrl(e.target.value)
+                            }}
+                            disabled={submitted && !errorMessage}
+                            slotProps={{
+                              input: {
+                                startAdornment: (
+                                  <InputAdornment position="start">
+                                    <LinkIcon />
+                                  </InputAdornment>
+                                ),
+                              },
+                            }}
+                          />
+                        </TableCell>
+                      </TableRow>
+
+                      <TableRow>
+                        <TableCell style={{ borderBottomWidth: 0 }}>
+                          FASTA index (.fai)
+                        </TableCell>
+                        <TableCell style={{ borderBottomWidth: 0 }}>
+                          <TextField
+                            data-testid="fai-input-url"
+                            variant="outlined"
+                            value={fastaIndexUrl}
+                            error={!validFastaIndexUrl}
+                            onChange={(
+                              e: React.ChangeEvent<HTMLInputElement>,
+                            ) => {
+                              setFastaIndexUrl(e.target.value)
+                            }}
+                            disabled={submitted && !errorMessage}
+                            slotProps={{
+                              input: {
+                                startAdornment: (
+                                  <InputAdornment position="start">
+                                    <LinkIcon />
+                                  </InputAdornment>
+                                ),
+                              },
+                            }}
+                          />
+                        </TableCell>
+                      </TableRow>
+
+                      <TableRow>
+                        <TableCell style={{ borderBottomWidth: 0 }}>
+                          FASTA binary index (.gzi)
+                        </TableCell>
+                        <TableCell style={{ borderBottomWidth: 0 }}>
+                          <TextField
+                            data-testid="gzi-input-url"
+                            variant="outlined"
+                            value={fastaGziIndexUrl}
+                            error={!validFastaGziIndexUrl}
+                            onChange={(
+                              e: React.ChangeEvent<HTMLInputElement>,
+                            ) => {
+                              setFastaGziIndexUrl(e.target.value)
+                            }}
+                            disabled={submitted && !errorMessage}
+                            slotProps={{
+                              input: {
+                                startAdornment: (
+                                  <InputAdornment position="start">
+                                    <LinkIcon />
+                                  </InputAdornment>
+                                ),
+                              },
+                            }}
+                          />
+                        </TableCell>
+                      </TableRow>
                     </TableBody>
                   </Table>
                 )}

package/src/components/AddChildFeature.tsx

@@ -1,8 +1,8 @@
 /* eslint-disable @typescript-eslint/unbound-method */
 /* eslint-disable @typescript-eslint/no-misused-promises */
-import { AnnotationFeature } from '@apollo-annotation/mst'
+import { type AnnotationFeature } from '@apollo-annotation/mst'
 import { AddFeatureChange } from '@apollo-annotation/shared'
-import { AbstractSessionModel } from '@jbrowse/core/util'
+import { type AbstractSessionModel } from '@jbrowse/core/util'
 import {
   Button,
   DialogActions,
@@ -13,11 +13,12 @@ import {
 import ObjectID from 'bson-objectid'
 import React, { useState } from 'react'
 
-import { ChangeManager } from '../ChangeManager'
+import { type ChangeManager } from '../ChangeManager'
 import { isOntologyClass } from '../OntologyManager'
-import OntologyStore from '../OntologyManager/OntologyStore'
+import type OntologyStore from '../OntologyManager/OntologyStore'
 import { fetchValidDescendantTerms } from '../OntologyManager/util'
-import { ApolloSessionModel } from '../session'
+import { type ApolloSessionModel } from '../session'
+
 import { Dialog } from './Dialog'
 import { OntologyTermAutocomplete } from './OntologyTermAutocomplete'