Save track data

GMOD · Jan 5, 2023 · 37df522 · 37df522
1 parent 45b7d35
commit 37df522
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Showing 4 changed files with 23 additions and 30 deletions.
diff --git a/packages/core/pluggableElementTypes/models/BaseTrackModel.ts b/packages/core/pluggableElementTypes/models/BaseTrackModel.ts
@@ -1,3 +1,4 @@
+import { lazy } from 'react'
 import { transaction } from 'mobx'
 import {
   getRoot,
@@ -16,10 +17,14 @@ import {
 } from '../../configuration'
 import PluginManager from '../../PluginManager'
 import { MenuItem } from '../../ui'
+import { Save } from '../../ui/Icons'
 import { getContainingView, getEnv, getSession } from '../../util'
 import { isSessionModelWithConfigEditing } from '../../util/types'
 import { ElementId } from '../../util/types/mst'
 
+// lazies
+const SaveTrackDataDlg = lazy(() => import('./components/SaveTrackData'))
+
 export function getCompatibleDisplays(self: IAnyStateTreeNode) {
   const { pluginManager } = getEnv(self)
   const view = getContainingView(self)
@@ -210,6 +215,17 @@ export function createBaseTrackModel(
 
         return [
           ...menuItems,
+          {
+            label: 'Save track data',
+            icon: Save,
+            onClick: () => {
+              getSession(self).queueDialog(handleClose => [
+                SaveTrackDataDlg,
+                // @ts-ignore
+                { model: self, handleClose },
+              ])
+            },
+          },
           ...(compatDisp.length > 1
             ? [
                 {

diff --git a/...BasicDisplay/components/SaveTrackData.tsx → ...Types/models/components/SaveTrackData.tsx b/...BasicDisplay/components/SaveTrackData.tsx → ...Types/models/components/SaveTrackData.tsx
@@ -4,20 +4,15 @@ import { Dialog, ErrorMessage } from '@jbrowse/core/ui'
 import {
   getSession,
   getContainingView,
-  getContainingTrack,
   Feature,
   Region,
 } from '@jbrowse/core/util'
 import { getConf } from '@jbrowse/core/configuration'
 import { makeStyles } from 'tss-react/mui'
-import {
-  BaseDisplayModel,
-  BaseTrackModel,
-} from '@jbrowse/core/pluggableElementTypes'
+import { BaseTrackModel } from '@jbrowse/core/pluggableElementTypes'
 import { observer } from 'mobx-react'
 
 // locals
-import { LinearGenomeViewModel } from '../../LinearGenomeView'
 import { stringifyGFF3 } from './util'
 
 const useStyles = makeStyles()(theme => ({
@@ -32,19 +27,12 @@ const useStyles = makeStyles()(theme => ({
   },
 }))
 
-type LGV = LinearGenomeViewModel
-
-/**
- * Fetches and returns a list features for a given list of regions
- */
 async function fetchFeatures(
   track: BaseTrackModel,
-  view: LGV,
   regions: Region[],
   signal?: AbortSignal,
 ) {
-  const session = getSession(view)
-  const { rpcManager } = session
+  const { rpcManager } = getSession(track)
   const adapterConfig = getConf(track, ['adapter'])
   const sessionId = 'getSequence'
   return rpcManager.call(sessionId, 'CoreGetFeatures', {
@@ -59,7 +47,7 @@ function SaveTrackDataDlg({
   model,
   handleClose,
 }: {
-  model: BaseDisplayModel
+  model: BaseTrackModel
   handleClose: () => void
 }) {
   const { classes } = useStyles()
@@ -70,11 +58,11 @@ function SaveTrackDataDlg({
     // eslint-disable-next-line @typescript-eslint/no-floating-promises
     ;(async () => {
       try {
-        const view = getContainingView(model) as LGV
-        const track = getContainingTrack(model) as BaseTrackModel
+        const view = getContainingView(model)
+        const track = model
         const regions = view.dynamicBlocks.contentBlocks
         setError(undefined)
-        const feats = await fetchFeatures(track, view, regions)
+        const feats = await fetchFeatures(track, regions)
         const ret = stringifyGFF3(feats)
         setFeatures(ret)
       } catch (e) {

diff --git a/...src/LinearBasicDisplay/components/util.ts → ...bleElementTypes/models/components/util.ts b/...src/LinearBasicDisplay/components/util.ts → ...bleElementTypes/models/components/util.ts
diff --git a/plugins/linear-genome-view/src/LinearBasicDisplay/model.ts b/plugins/linear-genome-view/src/LinearBasicDisplay/model.ts
@@ -13,10 +13,8 @@ import VisibilityIcon from '@mui/icons-material/Visibility'
 
 // locals
 import { BaseLinearDisplay } from '../BaseLinearDisplay'
-import { Save } from '@jbrowse/core/ui/Icons'
 
 const SetMaxHeightDlg = lazy(() => import('./components/SetMaxHeight'))
-const SaveTrackDataDlg = lazy(() => import('./components/SaveTrackData'))
 
 /**
  * #stateModel LinearBasicDisplay
@@ -175,16 +173,7 @@ function stateModelFactory(configSchema: AnyConfigurationSchemaType) {
               checked: self.showLabels,
               onClick: () => self.toggleShowLabels(),
             },
-            {
-              label: 'Save track data',
-              icon: Save,
-              onClick: () => {
-                getSession(self).queueDialog(handleClose => [
-                  SaveTrackDataDlg,
-                  { model: self, handleClose },
-                ])
-              },
-            },
+
             {
               label: 'Show descriptions',
               icon: VisibilityIcon,