@apollo-annotation/jbrowse-plugin-apollo 0.3.13 → 1.0.0

package/src/components/OpenLocalFile.tsx

@@ -1,189 +0,0 @@
-/* eslint-disable @typescript-eslint/no-unsafe-call */
-/* eslint-disable @typescript-eslint/unbound-method */
-/* eslint-disable @typescript-eslint/no-unnecessary-condition */
-/* eslint-disable @typescript-eslint/no-misused-promises */
-import { type AbstractSessionModel, isElectron } from '@jbrowse/core/util'
-import {
-  Button,
-  DialogActions,
-  DialogContent,
-  DialogContentText,
-  FormControl,
-  FormHelperText,
-  TextField,
-  useTheme,
-} from '@mui/material'
-import { nanoid } from 'nanoid'
-import React, { useState } from 'react'
-
-import type { InMemoryFileDriver } from '../BackendDrivers'
-import type { ApolloSessionModel } from '../session'
-import { loadAssemblyIntoClient } from '../util'
-
-import { Dialog } from './Dialog'
-
-interface OpenLocalFileProps {
-  session: ApolloSessionModel
-  handleClose(): void
-  inMemoryFileDriver: InMemoryFileDriver
-}
-
-export interface RefSeqInterface {
-  refName: string
-  uniqueId: string
-  aliases?: string[]
-}
-
-export function OpenLocalFile({ handleClose, session }: OpenLocalFileProps) {
-  const { apolloDataStore } = session
-  const { addAssembly, addSessionAssembly, assemblyManager, notify } =
-    session as unknown as AbstractSessionModel & {
-      // eslint-disable-next-line @typescript-eslint/no-unsafe-function-type
-      addSessionAssembly: Function
-    }
-
-  const [file, setFile] = useState<File | null>(null)
-  const [assemblyName, setAssemblyName] = useState('')
-  const [errorMessage, setErrorMessage] = useState('')
-  const [submitted, setSubmitted] = useState(false)
-  const theme = useTheme()
-
-  function handleChangeFile(e: React.ChangeEvent<HTMLInputElement>) {
-    const selectedFile = e.target.files?.item(0)
-    if (!selectedFile) {
-      return
-    }
-    setErrorMessage('')
-    setFile(selectedFile)
-    if (!assemblyName) {
-      const fileName = selectedFile.name
-      const lastDotIndex = fileName.lastIndexOf('.')
-      if (lastDotIndex === -1) {
-        setAssemblyName(fileName)
-      } else {
-        setAssemblyName(fileName.slice(0, lastDotIndex))
-      }
-    }
-  }
-
-  async function onSubmit(event: React.FormEvent<HTMLFormElement>) {
-    event.preventDefault()
-    setErrorMessage('')
-    setSubmitted(true)
-
-    if (!file) {
-      throw new Error('No file selected')
-    }
-
-    // Right now we are not using stream because there was a problem with 'pipe' in ReadStream
-    const fileData = await new Response(file).text()
-    const assemblyId = `${assemblyName}-${file.name}-${nanoid(8)}`
-    try {
-      await loadAssemblyIntoClient(assemblyId, fileData, apolloDataStore)
-    } catch (error) {
-      console.error(error)
-      notify(`Error loading GFF3 ${file.name}, ${String(error)}`, 'error')
-      handleClose()
-      return
-    }
-
-    const fileMetadata: { file?: string } = {}
-    if (isElectron) {
-      // eslint-disable-next-line @typescript-eslint/no-unsafe-assignment
-      const { webUtils } = globalThis.require('electron')
-      // eslint-disable-next-line @typescript-eslint/no-unsafe-member-access
-      fileMetadata.file = webUtils.getPathForFile(file) as string
-    }
-    const assemblyConfig = {
-      name: assemblyId,
-      aliases: [assemblyName],
-      displayName: assemblyName,
-      sequence: {
-        trackId: `sequenceConfigId-${assemblyName}`,
-        type: 'ReferenceSequenceTrack',
-        adapter: { type: 'ApolloSequenceAdapter', assemblyId },
-        metadata: { apollo: true, ...fileMetadata },
-      },
-    }
-
-    // Save assembly into session
-    await (isElectron
-      ? addAssembly?.(assemblyConfig)
-      : (addSessionAssembly || addAssembly)(assemblyConfig))
-    const a = await assemblyManager.waitForAssembly(assemblyConfig.name)
-    if (a) {
-      // @ts-expect-error MST type coercion problem?
-      session.addApolloTrackConfig(a)
-      notify(`Loaded GFF3 ${file.name}`, 'success')
-    } else {
-      notify(`Error loading GFF3 ${file.name}`, 'error')
-    }
-    handleClose()
-  }
-
-  function handleAssemblyNameChange(
-    event: React.ChangeEvent<HTMLInputElement>,
-  ) {
-    setAssemblyName(event.target.value)
-  }
-
-  return (
-    <Dialog
-      open
-      title="Open local GFF3 file"
-      handleClose={handleClose}
-      maxWidth={false}
-      data-testid="open-local-file"
-    >
-      <form onSubmit={onSubmit}>
-        <DialogContent style={{ display: 'flex', flexDirection: 'column' }}>
-          <FormControl>
-            <div style={{ flexDirection: 'row' }}>
-              <Button
-                variant="contained"
-                component="label"
-                style={{ marginRight: theme.spacing() }}
-              >
-                Choose File
-                <input
-                  type="file"
-                  required
-                  hidden
-                  onChange={handleChangeFile}
-                />
-              </Button>
-              {file ? file.name : 'No file chosen'}
-            </div>
-            <FormHelperText>
-              Make sure your GFF3 has an embedded FASTA section
-            </FormHelperText>
-          </FormControl>
-          <TextField
-            required
-            label="Assembly name"
-            value={assemblyName}
-            onChange={handleAssemblyNameChange}
-          />
-        </DialogContent>
-        <DialogActions>
-          <Button disabled={false} variant="contained" type="submit">
-            {submitted ? 'Submitting...' : 'Submit'}
-          </Button>
-          <Button
-            disabled={submitted}
-            variant="outlined"
-            type="submit"
-            onClick={handleClose}
-          >
-            Cancel
-          </Button>
-        </DialogActions>
-      </form>
-      {errorMessage ? (
-        <DialogContent>
-          <DialogContentText color="error">{errorMessage}</DialogContentText>
-        </DialogContent>
-      ) : null}
-    </Dialog>
-  )
-}

package/src/util/loadAssemblyIntoClient.ts

@@ -1,94 +0,0 @@
-import { type ClientDataStore, checkRegistry } from '@apollo-annotation/common'
-import type {
-  ApolloAssemblyI,
-  CheckResultSnapshot,
-} from '@apollo-annotation/mst'
-import { gff3ToAnnotationFeature } from '@apollo-annotation/shared'
-import {
-  type GFF3Comment,
-  type GFF3Feature,
-  type GFF3Sequence,
-  parseStringSync,
-} from '@gmod/gff'
-import { getSnapshot } from '@jbrowse/mobx-state-tree'
-
-export async function loadAssemblyIntoClient(
-  assemblyId: string,
-  gff3FileText: string,
-  apolloDataStore: ClientDataStore,
-) {
-  const featuresAndSequences: (GFF3Feature | GFF3Sequence | GFF3Comment)[] =
-    parseStringSync(gff3FileText, {
-      parseSequences: true,
-      parseComments: true,
-      parseDirectives: false,
-      parseFeatures: true,
-    })
-  if (featuresAndSequences.length === 0) {
-    throw new Error('No features found in GFF3 file')
-  }
-
-  let sequenceFeatureCount = 0
-  let assembly = apolloDataStore.assemblies.get(assemblyId)
-  if (!assembly) {
-    assembly = apolloDataStore.addAssembly(assemblyId, 'InMemoryFileDriver')
-  }
-
-  for (const seqLine of featuresAndSequences) {
-    if (Array.isArray(seqLine)) {
-      // regular feature
-      const feature = gff3ToAnnotationFeature(seqLine)
-
-      const ref =
-        assembly.refSeqs.get(feature.refSeq) ??
-        assembly.addRefSeq(feature.refSeq, feature.refSeq)
-      if (!ref.features.has(feature._id)) {
-        ref.addFeature(feature)
-      }
-    } else if ('comment' in seqLine) {
-      assembly.addComment(seqLine.comment)
-    } else {
-      sequenceFeatureCount++
-      // sequence feature
-      let ref = assembly.refSeqs.get(seqLine.id)
-      if (!ref) {
-        ref = assembly.addRefSeq(seqLine.id, seqLine.id, seqLine.description)
-      }
-      if (seqLine.description && !ref.description) {
-        ref.setDescription(seqLine.description)
-      }
-      ref.addSequence({
-        start: 0,
-        stop: seqLine.sequence.length,
-        sequence: seqLine.sequence,
-      })
-    }
-  }
-
-  if (sequenceFeatureCount === 0) {
-    throw new Error('No embedded FASTA section found in GFF3')
-  }
-
-  const checkResults: CheckResultSnapshot[] = await checkFeatures(assembly)
-  apolloDataStore.addCheckResults(checkResults)
-  return assembly
-}
-
-export async function checkFeatures(
-  assembly: ApolloAssemblyI,
-): Promise<CheckResultSnapshot[]> {
-  const checkResults: CheckResultSnapshot[] = []
-  for (const ref of assembly.refSeqs.values()) {
-    for (const feature of ref.features.values()) {
-      for (const check of checkRegistry.getChecks().values()) {
-        const result: CheckResultSnapshot[] = await check.checkFeature(
-          getSnapshot(feature),
-          (start: number, stop: number) =>
-            Promise.resolve(ref.getSequence(start, stop)),
-        )
-        checkResults.push(...result)
-      }
-    }
-  }
-  return checkResults
-}