Save track data

Author: cmdcolin

packages/core/package.json

@@ -46,6 +46,7 @@
     "dompurify": "^3.2.0",
     "escape-html": "^1.0.3",
     "fast-deep-equal": "^3.1.3",
+    "file-saver": "^2.0.0",
     "generic-filehandle": "^3.0.0",
     "is-object": "^1.0.1",
     "jexl": "^2.3.0",

packages/core/pluggableElementTypes/models/BaseTrackModel.ts

@@ -1,8 +1,15 @@
+import { lazy } from 'react'
+
 import { transaction } from 'mobx'
 import { getRoot, resolveIdentifier, types } from 'mobx-state-tree'
 
+import { Save } from '@mui/icons-material'
+
 import { ConfigurationReference, getConf } from '../../configuration'
 import { getContainingView, getEnv, getSession } from '../../util'
+import { stringifyBED } from './saveTrackFileTypes/bed'
+import { stringifyGBK } from './saveTrackFileTypes/genbank'
+import { stringifyGFF3 } from './saveTrackFileTypes/gff3'
 import { isSessionModelWithConfigEditing } from '../../util/types'
 import { ElementId } from '../../util/types/mst'
 
@@ -14,6 +21,9 @@ import type {
 import type { MenuItem } from '../../ui'
 import type { IAnyStateTreeNode, Instance } from 'mobx-state-tree'
 
+// lazies
+const SaveTrackDataDlg = lazy(() => import('./components/SaveTrackData'))
+
 export function getCompatibleDisplays(self: IAnyStateTreeNode) {
   const { pluginManager } = getEnv(self)
   const view = getContainingView(self)
@@ -177,6 +187,27 @@ export function createBaseTrackModel(
         })
       },
     }))
+    .views(() => ({
+      saveTrackFileFormatOptions() {
+        return {
+          gff3: {
+            name: 'GFF3',
+            extension: 'gff3',
+            callback: stringifyGFF3,
+          },
+          genbank: {
+            name: 'GenBank',
+            extension: 'gbk',
+            callback: stringifyGBK,
+          },
+          bed: {
+            name: 'BED',
+            extension: 'bed',
+            callback: stringifyBED,
+          },
+        }
+      },
+    }))
     .views(self => ({
       /**
        * #method
@@ -190,6 +221,19 @@ export function createBaseTrackModel(
 
         return [
           ...menuItems,
+          {
+            label: 'Save track data',
+            icon: Save,
+            onClick: () => {
+              getSession(self).queueDialog(handleClose => [
+                SaveTrackDataDlg,
+                {
+                  model: self,
+                  handleClose,
+                },
+              ])
+            },
+          },
           ...(compatDisp.length > 1
             ? [
                 {

packages/core/pluggableElementTypes/models/components/SaveTrackData.tsx

@@ -0,0 +1,200 @@
+import React, { useEffect, useState } from 'react'
+
+import { getConf } from '@jbrowse/core/configuration'
+import { Dialog, ErrorMessage } from '@jbrowse/core/ui'
+import { getContainingView, getSession } from '@jbrowse/core/util'
+import GetAppIcon from '@mui/icons-material/GetApp'
+import {
+  Button,
+  DialogActions,
+  DialogContent,
+  FormControl,
+  FormControlLabel,
+  FormLabel,
+  Radio,
+  RadioGroup,
+  TextField,
+  Typography,
+} from '@mui/material'
+import { saveAs } from 'file-saver'
+import { observer } from 'mobx-react'
+import { makeStyles } from 'tss-react/mui'
+
+import type {
+  AbstractSessionModel,
+  AbstractTrackModel,
+  Feature,
+  Region,
+} from '@jbrowse/core/util'
+import type { IAnyStateTreeNode } from 'mobx-state-tree'
+
+// icons
+
+const useStyles = makeStyles()({
+  root: {
+    width: '80em',
+  },
+  textAreaFont: {
+    fontFamily: 'Courier New',
+  },
+})
+
+async function fetchFeatures(
+  track: IAnyStateTreeNode,
+  regions: Region[],
+  signal?: AbortSignal,
+) {
+  const { rpcManager } = getSession(track)
+  const adapterConfig = getConf(track, ['adapter'])
+  const sessionId = 'getFeatures'
+  return rpcManager.call(sessionId, 'CoreGetFeatures', {
+    adapterConfig,
+    regions,
+    sessionId,
+    signal,
+  }) as Promise<Feature[]>
+}
+interface FileTypeExporter {
+  name: string
+  extension: string
+  callback: (arg: {
+    features: Feature[]
+    session: AbstractSessionModel
+    assemblyName: string
+  }) => Promise<string> | string
+}
+const SaveTrackDataDialog = observer(function ({
+  model,
+  handleClose,
+}: {
+  model: AbstractTrackModel & {
+    saveTrackFileFormatOptions: () => Record<string, FileTypeExporter>
+  }
+  handleClose: () => void
+}) {
+  const options = model.saveTrackFileFormatOptions()
+  const { classes } = useStyles()
+  const [error, setError] = useState<unknown>()
+  const [features, setFeatures] = useState<Feature[]>()
+  const [type, setType] = useState(Object.keys(options)[0])
+  const [str, setStr] = useState('')
+
+  useEffect(() => {
+    // eslint-disable-next-line @typescript-eslint/no-floating-promises
+    ;(async () => {
+      try {
+        const view = getContainingView(model) as { visibleRegions?: Region[] }
+        setError(undefined)
+        setFeatures(await fetchFeatures(model, view.visibleRegions || []))
+      } catch (e) {
+        console.error(e)
+        setError(e)
+      }
+    })()
+  }, [model])
+
+  useEffect(() => {
+    // eslint-disable-next-line @typescript-eslint/no-floating-promises
+    ;(async () => {
+      try {
+        const { visibleRegions } = getContainingView(model) as {
+          visibleRegions?: Region[]
+        }
+        const session = getSession(model)
+        if (!features || !visibleRegions?.length || !type) {
+          return
+        }
+        const generator = options[type] || {
+          callback: () => 'Unknown',
+        }
+        setStr(
+          await generator.callback({
+            features,
+            session,
+            assemblyName: visibleRegions[0]!.assemblyName,
+          }),
+        )
+      } catch (e) {
+        setError(e)
+      }
+    })()
+  }, [type, features, options, model])
+
+  const loading = !features
+  return (
+    <Dialog maxWidth="xl" open onClose={handleClose} title="Save track data">
+      <DialogContent className={classes.root}>
+        {error ? <ErrorMessage error={error} /> : null}
+        {features && !features.length ? (
+          <Typography>No features found</Typography>
+        ) : null}
+
+        <FormControl>
+          <FormLabel>File type</FormLabel>
+          <RadioGroup
+            value={type}
+            onChange={e => {
+              setType(e.target.value)
+            }}
+          >
+            {Object.entries(options).map(([key, val]) => (
+              <FormControlLabel
+                key={key}
+                value={key}
+                control={<Radio />}
+                label={val.name}
+              />
+            ))}
+          </RadioGroup>
+        </FormControl>
+        <TextField
+          variant="outlined"
+          multiline
+          minRows={5}
+          maxRows={15}
+          fullWidth
+          value={
+            loading
+              ? 'Loading...'
+              : str.length > 100_000
+                ? 'Too large to view here, click "Download" to results to file'
+                : str
+          }
+          InputProps={{
+            readOnly: true,
+            classes: {
+              input: classes.textAreaFont,
+            },
+          }}
+        />
+      </DialogContent>
+      <DialogActions>
+        <Button
+          onClick={() => {
+            if (!type) {
+              return
+            }
+            const ext = options[type]?.extension || 'unknown'
+            const blob = new Blob([str], { type: 'text/plain;charset=utf-8' })
+            saveAs(blob, `jbrowse_track_data.${ext}`)
+          }}
+          startIcon={<GetAppIcon />}
+        >
+          Download
+        </Button>
+
+        <Button
+          variant="contained"
+          type="submit"
+          onClick={() => {
+            handleClose()
+          }}
+        >
+          Close
+        </Button>
+      </DialogActions>
+    </Dialog>
+  )
+})
+
+export default SaveTrackDataDialog

packages/core/pluggableElementTypes/models/saveTrackFileTypes/bed.ts

@@ -0,0 +1,13 @@
+import type { Feature } from '@jbrowse/core/util'
+
+export function stringifyBED({ features }: { features: Feature[] }) {
+  const fields = ['refName', 'start', 'end', 'name', 'score', 'strand']
+  return features
+    .map(feature =>
+      fields
+        .map(field => feature.get(field))
+        .join('\t')
+        .trim(),
+    )
+    .join('\n')
+}