@jbrowse/plugin-data-management 1.4.1 → 1.5.2

package/src/SetDefaultSession/SetDefaultSession.tsx

@@ -1,181 +1,70 @@
-import React, { useState } from 'react'
+import React from 'react'
 import { observer } from 'mobx-react'
-import Dialog from '@material-ui/core/Dialog'
-import { makeStyles } from '@material-ui/core/styles'
-import DialogTitle from '@material-ui/core/DialogTitle'
-import DialogContent from '@material-ui/core/DialogContent'
-import DialogActions from '@material-ui/core/DialogActions'
-import Button from '@material-ui/core/Button'
-import List from '@material-ui/core/List'
-import ListItem from '@material-ui/core/ListItem'
-import ListItemIcon from '@material-ui/core/ListItemIcon'
-import ListItemText from '@material-ui/core/ListItemText'
-import ListSubheader from '@material-ui/core/ListSubheader'
-import Paper from '@material-ui/core/Paper'
-import Typography from '@material-ui/core/Typography'
-import Radio from '@material-ui/core/Radio'
-import pluralize from 'pluralize'
-import { Grid } from '@material-ui/core'
+import {
+  Dialog,
+  DialogTitle,
+  DialogContent,
+  DialogActions,
+  Button,
+  Typography,
+} from '@material-ui/core'
 
-const useStyles = makeStyles(theme => ({
-  root: {
-    margin: theme.spacing(1),
-  },
-  message: {
-    padding: theme.spacing(3),
-  },
-  titleBox: {
-    color: '#fff',
-    backgroundColor: theme.palette.primary.main,
-    textAlign: 'center',
-  },
-  dialogContent: {
-    width: 600,
-  },
-  resetButton: {
-    justifyContent: 'center',
-    marginBottom: '6px',
-  },
-}))
-
-const CurrentSession = observer(
-  ({
-    session,
-    selectedDefault,
-    handleRadio,
-  }: {
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
-    session: any
-    selectedDefault: string
-    handleRadio: Function
-  }) => {
-    const classes = useStyles()
-
-    return (
-      <Paper className={classes.root}>
-        <List subheader={<ListSubheader>Currently open session</ListSubheader>}>
-          <ListItem>
-            <ListItemIcon>
-              <Radio
-                checked={session.name === selectedDefault}
-                onChange={() => handleRadio(session)}
-              />
-            </ListItemIcon>
-            <ListItemText primary={session.name} />
-          </ListItem>
-        </List>
-      </Paper>
-    )
-  },
-)
+function canSetDefaultSession(obj: unknown): obj is {
+  jbrowse: { setDefaultSessionConf: Function }
+  session: unknown
+} {
+  return typeof obj === 'object' && !!obj && 'jbrowse' in obj
+}
 
 const SetDefaultSession = observer(
-  ({
-    rootModel,
-    open,
-    onClose,
-    currentDefault,
-  }: {
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
-    rootModel: any
-    open: boolean
-    onClose: Function
-    currentDefault: string
-  }) => {
-    const classes = useStyles()
-    const { session } = rootModel
-    const [selectedDefault, setSelectedDefault] = useState(currentDefault)
-
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
-    function handleRadio(sessionSnapshot: any) {
-      setSelectedDefault(sessionSnapshot.name)
-      rootModel.jbrowse.setDefaultSessionConf(sessionSnapshot)
-      session.notify(
-        `Set default session to ${sessionSnapshot.name}`,
-        'success',
-      )
+  ({ rootModel, onClose }: { rootModel?: unknown; onClose: () => void }) => {
+    if (!rootModel) {
+      return null
     }
+    if (!canSetDefaultSession(rootModel)) {
+      console.error('Incorrect rootmodel')
+      return null
+    }
+    const { jbrowse, session } = rootModel
 
     return (
-      <Dialog open={open}>
-        <DialogTitle className={classes.titleBox}>
-          Set Default Session
-        </DialogTitle>
+      <Dialog open onClose={onClose}>
+        <DialogTitle>Set default session</DialogTitle>
         <DialogContent>
-          <Grid className={classes.resetButton} container>
-            <Grid item>
-              <Button
-                color="secondary"
-                variant="contained"
-                onClick={() => {
-                  setSelectedDefault('New session')
-                  rootModel.jbrowse.setDefaultSessionConf({
-                    name: `New session`,
-                  })
-                  session.notify('Reset default session', 'success')
-                }}
-              >
-                Clear default session
-              </Button>
-            </Grid>
-          </Grid>
-
-          <CurrentSession
-            session={session}
-            selectedDefault={selectedDefault}
-            handleRadio={handleRadio}
-          />
-          <Paper className={classes.root}>
-            <List subheader={<ListSubheader>Saved sessions</ListSubheader>}>
-              {session.savedSessions.length ? (
-                session.savedSessions.map(
-                  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-                  (sessionSnapshot: any) => {
-                    const { views = [] } = sessionSnapshot
-                    const totalTracks = views
-                      // eslint-disable-next-line @typescript-eslint/no-explicit-any
-                      .map((view: any) => view.tracks.length)
-                      .reduce((a: number, b: number) => a + b, 0)
-                    if (sessionSnapshot.name !== session.name) {
-                      return (
-                        <ListItem key={sessionSnapshot.name}>
-                          <ListItemIcon>
-                            <Radio
-                              checked={sessionSnapshot.name === selectedDefault}
-                              onChange={() => handleRadio(sessionSnapshot)}
-                            />
-                          </ListItemIcon>
-                          <ListItemText
-                            primary={sessionSnapshot.name}
-                            secondary={`${views.length} ${pluralize(
-                              'view',
-                              views.length,
-                            )}; ${totalTracks}
-                             open ${pluralize('track', totalTracks)}`}
-                          />
-                        </ListItem>
-                      )
-                    }
-                    return null
-                  },
-                )
-              ) : (
-                <Typography className={classes.message}>
-                  No saved sessions found
-                </Typography>
-              )}
-            </List>
-          </Paper>
+          <Typography>
+            Select "Set current session as default" to make your current session
+            saved to the config file. You can also hit "Clear default session",
+            which would remove the default session from the config.
+          </Typography>
         </DialogContent>
         <DialogActions>
+          <Button
+            variant="contained"
+            onClick={() => {
+              jbrowse.setDefaultSessionConf({
+                name: `New session`,
+              })
+              onClose()
+            }}
+          >
+            Clear default session
+          </Button>
           <Button
             color="secondary"
             variant="contained"
+            onClick={() => onClose()}
+          >
+            Cancel
+          </Button>
+          <Button
+            color="primary"
+            variant="contained"
             onClick={() => {
-              onClose(false)
+              jbrowse.setDefaultSessionConf(session)
+              onClose()
             }}
           >
-            Return
+            Set current session as default
           </Button>
         </DialogActions>
       </Dialog>

package/src/index.ts

@@ -3,10 +3,6 @@ import ConnectionType from '@jbrowse/core/pluggableElementTypes/ConnectionType'
 import WidgetType from '@jbrowse/core/pluggableElementTypes/WidgetType'
 import Plugin from '@jbrowse/core/Plugin'
 import PluginManager from '@jbrowse/core/PluginManager'
-import { SessionWithWidgets, isAbstractMenuManager } from '@jbrowse/core/util'
-import NoteAddIcon from '@material-ui/icons/NoteAdd'
-import InputIcon from '@material-ui/icons/Input'
-import ExtensionIcon from '@material-ui/icons/Extension'
 import {
   configSchema as ucscConfigSchema,
   modelFactory as ucscModelFactory,
@@ -105,53 +101,7 @@ export default class extends Plugin {
     })
   }
 
-  configure(pluginManager: PluginManager) {
-    if (isAbstractMenuManager(pluginManager.rootModel)) {
-      pluginManager.rootModel.appendToMenu('File', {
-        label: 'Open track',
-        icon: NoteAddIcon,
-        onClick: (session: SessionWithWidgets) => {
-          if (session.views.length === 0) {
-            session.notify('Please open a view to add a track first')
-          } else if (session.views.length >= 1) {
-            const widget = session.addWidget(
-              'AddTrackWidget',
-              'addTrackWidget',
-              { view: session.views[0].id },
-            )
-            session.showWidget(widget)
-            if (session.views.length > 1) {
-              session.notify(
-                `This will add a track to the first view. Note: if you want to open a track in a specific view open the track selector for that view and use the add track (plus icon) in the bottom right`,
-              )
-            }
-          }
-        },
-      })
-      pluginManager.rootModel.appendToMenu('File', {
-        label: 'Open connection',
-        icon: InputIcon,
-        onClick: (session: SessionWithWidgets) => {
-          const widget = session.addWidget(
-            'AddConnectionWidget',
-            'addConnectionWidget',
-          )
-          session.showWidget(widget)
-        },
-      })
-      pluginManager.rootModel.appendToMenu('File', {
-        label: 'Plugin store',
-        icon: ExtensionIcon,
-        onClick: (session: SessionWithWidgets) => {
-          const widget = session.addWidget(
-            'PluginStoreWidget',
-            'pluginStoreWidget',
-          )
-          session.showWidget(widget)
-        },
-      })
-    }
-  }
+  configure(pluginManager: PluginManager) {}
 }
 
 export { AssemblyManager, SetDefaultSession }

package/src/ucsc-trackhub/configSchema.js

@@ -6,7 +6,10 @@ export default ConfigurationSchema(
   {
     hubTxtLocation: {
       type: 'fileLocation',
-      defaultValue: { uri: 'http://mysite.com/path/to/hub.txt' },
+      defaultValue: {
+        uri: 'http://mysite.com/path/to/hub.txt',
+        locationType: 'UriLocation',
+      },
       description: 'location of the hub file (usually called hub.txt)',
     },
     assemblyNames: {

package/src/ucsc-trackhub/model.js

@@ -2,6 +2,7 @@ import { BaseConnectionModelFactory } from '@jbrowse/core/pluggableElementTypes/
 import {
   ConfigurationReference,
   readConfObject,
+  getConf,
 } from '@jbrowse/core/configuration'
 import { getSession } from '@jbrowse/core/util'
 import { types } from 'mobx-state-tree'
@@ -24,23 +25,23 @@ export default function UCSCTrackHubConnection(pluginManager) {
       })
       .actions(self => ({
         connect() {
-          const connectionName = readConfObject(self.configuration, 'name')
-          const hubFileLocation = readConfObject(
-            self.configuration,
-            'hubTxtLocation',
-          )
+          const connectionName = getConf(self, 'name')
+          const hubFileLocation = getConf(self, 'hubTxtLocation')
           const session = getSession(self)
           fetchHubFile(hubFileLocation)
             .then(hubFile => {
-              let genomesFileLocation
-              if (hubFileLocation.uri) {
-                genomesFileLocation = {
-                  uri: new URL(hubFile.get('genomesFile'), hubFileLocation.uri)
-                    .href,
-                }
-              } else {
-                genomesFileLocation = { localPath: hubFile.get('genomesFile') }
-              }
+              const genomesFileLocation = hubFileLocation.uri
+                ? {
+                    uri: new URL(
+                      hubFile.get('genomesFile'),
+                      hubFileLocation.uri,
+                    ).href,
+                    locationType: 'UriLocation',
+                  }
+                : {
+                    localPath: hubFile.get('genomesFile'),
+                    locationType: 'LocalPathLocation',
+                  }
               return Promise.all([
                 hubFile,
                 fetchGenomesFile(genomesFileLocation),
@@ -49,10 +50,7 @@ export default function UCSCTrackHubConnection(pluginManager) {
             .then(([hubFile, genomesFile]) => {
               const trackDbData = []
               for (const [genomeName, genome] of genomesFile) {
-                const assemblyNames = readConfObject(
-                  self.configuration,
-                  'assemblyNames',
-                )
+                const assemblyNames = getConf(self, 'assemblyNames')
                 if (
                   assemblyNames.length > 0 &&
                   !assemblyNames.includes(genomeName)
@@ -67,19 +65,21 @@ export default function UCSCTrackHubConnection(pluginManager) {
                     `Cannot find assembly for "${genomeName}" from the genomes file for connection "${connectionName}"`,
                   )
                 }
-                let trackDbFileLocation
-                if (hubFileLocation.uri) {
-                  trackDbFileLocation = {
-                    uri: new URL(
-                      genome.get('trackDb'),
-                      new URL(hubFile.get('genomesFile'), hubFileLocation.uri),
-                    ).href,
-                  }
-                } else {
-                  trackDbFileLocation = {
-                    localPath: genome.get('trackDb'),
-                  }
-                }
+                const trackDbFileLocation = hubFileLocation.uri
+                  ? {
+                      uri: new URL(
+                        genome.get('trackDb'),
+                        new URL(
+                          hubFile.get('genomesFile'),
+                          hubFileLocation.uri,
+                        ),
+                      ).href,
+                      locationType: 'UriLocation',
+                    }
+                  : {
+                      localPath: genome.get('trackDb'),
+                      locationType: 'LocalPathLocation',
+                    }
                 trackDbData.push(
                   Promise.all([
                     trackDbFileLocation,

package/src/ucsc-trackhub/ucscTrackHub.js

@@ -1,5 +1,4 @@
 import { objectHash } from '@jbrowse/core/util'
-import { GenomesFile, HubFile, TrackDbFile } from '@gmod/ucsc-hub'
 import { openLocation } from '@jbrowse/core/util/io'
 import {
   generateUnsupportedTrackConf,
@@ -12,6 +11,7 @@ export { ucscAssemblies }
 export async function fetchHubFile(hubFileLocation) {
   try {
     const hubFileText = await openLocation(hubFileLocation).readFile('utf8')
+    const { HubFile } = await import('@gmod/ucsc-hub')
     return new HubFile(hubFileText)
   } catch (error) {
     throw new Error(`Not a valid hub.txt file, got error: '${error}'`)
@@ -22,14 +22,14 @@ export async function fetchGenomesFile(genomesFileLocation) {
   const genomesFileText = await openLocation(genomesFileLocation).readFile(
     'utf8',
   )
+  const { GenomesFile } = await import('@gmod/ucsc-hub')
   return new GenomesFile(genomesFileText)
 }
 
 export async function fetchTrackDbFile(trackDbFileLocation) {
-  const trackDbFileText = await openLocation(trackDbFileLocation).readFile(
-    'utf8',
-  )
-  return new TrackDbFile(trackDbFileText)
+  const text = await openLocation(trackDbFileLocation).readFile('utf8')
+  const { TrackDbFile } = await import('@gmod/ucsc-hub')
+  return new TrackDbFile(text)
 }
 
 export function generateTracks(
@@ -101,9 +101,13 @@ function makeTrackConfig(
   if (trackDbFileLocation.uri) {
     bigDataLocation = {
       uri: new URL(track.get('bigDataUrl'), trackDbFileLocation.uri).href,
+      locationType: 'UriLocation',
     }
   } else {
-    bigDataLocation = { localPath: track.get('bigDataUrl') }
+    bigDataLocation = {
+      localPath: track.get('bigDataUrl'),
+      locationType: 'LocalPathLocation',
+    }
   }
   let bigDataIndexLocation
 
@@ -114,17 +118,25 @@ function makeTrackConfig(
           ? {
               uri: new URL(track.get('bigDataIndex'), trackDbFileLocation.uri)
                 .href,
+              locationType: 'UriLocation',
             }
           : {
               uri: new URL(
                 `${track.get('bigDataUrl')}.bai`,
                 trackDbFileLocation.uri,
               ).href,
+              locationType: 'UriLocation',
             }
       } else {
         bigDataIndexLocation = track.get('bigDataIndex')
-          ? { localPath: track.get('bigDataIndex') }
-          : { localPath: `${track.get('bigDataUrl')}.bai` }
+          ? {
+              localPath: track.get('bigDataIndex'),
+              locationType: 'LocalPathLocation',
+            }
+          : {
+              localPath: `${track.get('bigDataUrl')}.bai`,
+              locationType: 'LocalPathLocation',
+            }
       }
       return {
         type: 'AlignmentsTrack',
@@ -284,17 +296,25 @@ function makeTrackConfig(
           ? {
               uri: new URL(track.get('bigDataIndex'), trackDbFileLocation.uri)
                 .href,
+              locationType: 'UriLocation',
             }
           : {
               uri: new URL(
                 `${track.get('bigDataUrl')}.crai`,
                 trackDbFileLocation.uri,
               ).href,
+              locationType: 'UriLocation',
             }
       } else {
         bigDataIndexLocation = track.get('bigDataIndex')
-          ? { localPath: track.get('bigDataIndex') }
-          : { localPath: `${track.get('bigDataUrl')}.crai` }
+          ? {
+              localPath: track.get('bigDataIndex'),
+              locationType: 'LocalPathLocation',
+            }
+          : {
+              localPath: `${track.get('bigDataUrl')}.crai`,
+              locationType: 'LocalPathLocation',
+            }
       }
       return {
         type: 'AlignmentsTrack',
@@ -349,17 +369,25 @@ function makeTrackConfig(
           ? {
               uri: new URL(track.get('bigDataIndex'), trackDbFileLocation.uri)
                 .href,
+              locationType: 'UriLocation',
             }
           : {
               uri: new URL(
                 `${track.get('bigDataUrl')}.tbi`,
                 trackDbFileLocation.uri,
               ).href,
+              locationType: 'UriLocation',
             }
       } else {
         bigDataIndexLocation = track.get('bigDataIndex')
-          ? { localPath: track.get('bigDataIndex') }
-          : { localPath: `${track.get('bigDataUrl')}.tbi` }
+          ? {
+              localPath: track.get('bigDataIndex'),
+              locationType: 'LocalPathLocation',
+            }
+          : {
+              localPath: `${track.get('bigDataUrl')}.tbi`,
+              locationType: 'LocalPathLocation',
+            }
       }
       return {
         type: 'VariantTrack',