@apollo-annotation/jbrowse-plugin-apollo 0.3.5 → 0.3.7

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/AddAssemblyAliases.tsx

@@ -0,0 +1,114 @@
+import { AddAssemblyAliasesChange } from '@apollo-annotation/shared'
+import { Box, DialogContent, DialogContentText } from '@mui/material'
+import { DataGrid, type GridColDef, type GridRowModel } from '@mui/x-data-grid'
+import React from 'react'
+
+import {
+  type ApolloInternetAccount,
+  type CollaborationServerDriver,
+} from '../BackendDrivers'
+import { type ChangeManager } from '../ChangeManager'
+import { type ApolloSessionModel } from '../session'
+
+import { Dialog } from './Dialog'
+
+interface AddAssemblyAliasProps {
+  session: ApolloSessionModel
+  handleClose: () => void
+  changeManager: ChangeManager
+}
+
+const columns: GridColDef[] = [
+  {
+    field: 'name',
+    headerName: 'Assembly Name',
+    width: 150,
+    editable: false,
+  },
+  {
+    field: 'aliases',
+    headerName: 'Aliases',
+    width: 300,
+    editable: true,
+  },
+]
+
+interface AssemblyAlias {
+  id: string
+  name: string
+  aliases: string
+}
+
+export function AddAssemblyAliases({
+  changeManager,
+  handleClose,
+  session,
+}: AddAssemblyAliasProps) {
+  const { apolloDataStore } = session
+  const { collaborationServerDriver } = apolloDataStore as {
+    collaborationServerDriver: CollaborationServerDriver
+    getInternetAccount(
+      assemblyName?: string,
+      internetAccountId?: string,
+    ): ApolloInternetAccount
+  }
+  const assemblies = collaborationServerDriver.getAssemblies()
+
+  const rows: AssemblyAlias[] = assemblies.map((assembly) => {
+    return {
+      id: assembly.name,
+      name: assembly.displayName ?? assembly.name,
+      aliases: assembly.aliases.join(', '),
+    } as AssemblyAlias
+  })
+
+  const [errorMessage, setErrorMessage] = React.useState('')
+
+  const processRowUpdate = (newRow: GridRowModel, _oldRow: GridRowModel) => {
+    const change = new AddAssemblyAliasesChange({
+      typeName: 'AddAssemblyAliasesChange',
+      assembly: newRow.id as string,
+      aliases: (newRow.aliases as string).split(','),
+    })
+    void changeManager.submit(change).catch(() => {
+      setErrorMessage('Error submitting change')
+    })
+    handleClose()
+    return newRow
+  }
+
+  return (
+    <Dialog
+      open
+      title="Add assembly aliases"
+      handleClose={handleClose}
+      maxWidth={'sm'}
+      data-testid="add-assembly-alias"
+      fullWidth
+    >
+      <DialogContent style={{ display: 'flex', flexDirection: 'column' }}>
+        <Box sx={{ height: 400, width: '100%' }}>
+          <DataGrid
+            rows={rows}
+            columns={columns}
+            initialState={{
+              pagination: {
+                paginationModel: {
+                  pageSize: 5,
+                },
+              },
+            }}
+            pageSizeOptions={[5]}
+            processRowUpdate={processRowUpdate}
+            disableRowSelectionOnClick
+          />
+        </Box>
+      </DialogContent>
+      {errorMessage ? (
+        <DialogContent>
+          <DialogContentText color="error">{errorMessage}</DialogContentText>
+        </DialogContent>
+      ) : null}
+    </Dialog>
+  )
+}

package/src/components/AddChildFeature.tsx

@@ -1,8 +1,7 @@
 /* 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 {
   Button,
   DialogActions,
@@ -13,11 +12,12 @@ 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'
 
@@ -36,7 +36,6 @@ export function AddChildFeature({
   sourceAssemblyId,
   sourceFeature,
 }: AddChildFeatureProps) {
-  const { notify } = session as unknown as AbstractSessionModel
   const [end, setEnd] = useState(String(sourceFeature.max))
   const [start, setStart] = useState(String(sourceFeature.min + 1))
   const [type, setType] = useState('')
@@ -62,7 +61,7 @@ export function AddChildFeature({
     return terms
   }
 
-  async function onSubmit(event: React.FormEvent<HTMLFormElement>) {
+  function onSubmit(event: React.FormEvent<HTMLFormElement>) {
     event.preventDefault()
     setErrorMessage('')
     const change = new AddFeatureChange({
@@ -78,8 +77,7 @@ export function AddChildFeature({
       },
       parentFeatureId: sourceFeature._id,
     })
-    await changeManager.submit(change)
-    notify('Feature added successfully', 'success')
+    void changeManager.submit(change)
     handleClose()
     event.preventDefault()
   }