@jbrowse/plugin-data-management 2.5.0 → 2.6.2

package/src/PluginStoreWidget/index.ts

@@ -1,19 +0,0 @@
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-import { WidgetType } from '@jbrowse/core/pluggableElementTypes'
-import PluginManager from '@jbrowse/core/PluginManager'
-import { lazy } from 'react'
-
-import stateModelFactory from './model'
-const configSchema = ConfigurationSchema('PluginStoreWidget', {})
-
-export default (pluginManager: PluginManager) => {
-  pluginManager.addWidgetType(() => {
-    return new WidgetType({
-      name: 'PluginStoreWidget',
-      heading: 'Plugin store',
-      configSchema,
-      stateModel: stateModelFactory(pluginManager),
-      ReactComponent: lazy(() => import('./components/PluginStoreWidget')),
-    })
-  })
-}

package/src/PluginStoreWidget/model.test.tsx

@@ -1,15 +0,0 @@
-import { createTestSession } from '@jbrowse/web/src/rootModel'
-jest.mock('@jbrowse/web/src/makeWorkerInstance', () => () => {})
-
-describe('PluginStoreModel', () => {
-  it('filters plugins correctly', () => {
-    const session = createTestSession()
-    const model = session.addWidget('PluginStoreWidget', 'pluginStoreWidget')
-
-    model.setFilterText('Foo')
-    expect(model.filterText).toEqual('Foo')
-
-    model.clearFilterText()
-    expect(model.filterText).toEqual('')
-  })
-})

package/src/PluginStoreWidget/model.ts

@@ -1,26 +0,0 @@
-import { types, Instance } from 'mobx-state-tree'
-import PluginManager from '@jbrowse/core/PluginManager'
-import { ElementId } from '@jbrowse/core/util/types/mst'
-
-export default function f(pluginManager: PluginManager) {
-  return types
-    .model('PluginStoreModel', {
-      id: ElementId,
-      type: types.literal('PluginStoreWidget'),
-      filterText: '',
-      view: types.safeReference(
-        pluginManager.pluggableMstType('view', 'stateModel'),
-      ),
-    })
-    .actions(self => ({
-      clearFilterText() {
-        self.filterText = ''
-      },
-      setFilterText(newText: string) {
-        self.filterText = newText
-      },
-    }))
-}
-
-export type PluginStoreStateModel = ReturnType<typeof f>
-export type PluginStoreModel = Instance<PluginStoreStateModel>

package/src/SetDefaultSession/SetDefaultSession.test.tsx

@@ -1,59 +0,0 @@
-import React from 'react'
-import { fireEvent, render } from '@testing-library/react'
-import SetDefaultSession from './SetDefaultSession'
-
-const mockRootModel = {
-  jbrowse: {
-    assemblies: [
-      {
-        name: 'testAssembly',
-        sequence: {
-          type: 'testSequenceTrack',
-          trackId: '',
-          adapter: {
-            type: 'testSeqAdapter',
-            twoBitLocation: {
-              uri: 'test.2bit',
-              locationType: 'UriLocation',
-            },
-          },
-        },
-      },
-    ],
-    setDefaultSessionConf: jest.fn(),
-  },
-  session: {
-    savedSessions: [],
-    notify: jest.fn(),
-  },
-}
-
-describe('SetDefaultSession GUI', () => {
-  it('closes when the return button is clicked', () => {
-    const onClose = jest.fn()
-    const { getByText } = render(
-      <SetDefaultSession rootModel={mockRootModel} onClose={onClose} />,
-    )
-    fireEvent.click(getByText('Cancel'))
-    expect(onClose).toHaveBeenCalled()
-  })
-
-  it('unsets to the default session with reset button', () => {
-    const MockSession = {
-      ...mockRootModel,
-      session: {
-        ...mockRootModel.session,
-        name: `Moo session`,
-        savedSessions: [],
-        notify: jest.fn(),
-      },
-    }
-    const { getByText } = render(
-      <SetDefaultSession rootModel={MockSession} onClose={() => {}} />,
-    )
-    fireEvent.click(getByText('Clear default session'))
-    expect(MockSession.jbrowse.setDefaultSessionConf).toHaveBeenCalledWith({
-      name: `New session`,
-    })
-  })
-})

package/src/SetDefaultSession/SetDefaultSession.tsx

@@ -1,76 +0,0 @@
-import React from 'react'
-import { observer } from 'mobx-react'
-import {
-  Dialog,
-  DialogTitle,
-  DialogContent,
-  DialogActions,
-  Button,
-  Typography,
-} from '@mui/material'
-
-function canSetDefaultSession(obj: unknown): obj is {
-  jbrowse: { setDefaultSessionConf: Function }
-  session: unknown
-} {
-  return typeof obj === 'object' && !!obj && 'jbrowse' in obj
-}
-
-const SetDefaultSession = observer(
-  ({ 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 onClose={onClose}>
-        <DialogTitle>Set default session</DialogTitle>
-        <DialogContent>
-          <Typography>
-            Select &quot;Set current session as default&quot; to make your
-            current session saved to the config file. You can also hit
-            &quot;Clear default session&quot;, 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={() => {
-              jbrowse.setDefaultSessionConf(session)
-              onClose()
-            }}
-          >
-            Set current session as default
-          </Button>
-        </DialogActions>
-      </Dialog>
-    )
-  },
-)
-
-export default SetDefaultSession

package/src/SetDefaultSession/index.ts

@@ -1 +0,0 @@
-export { default } from './SetDefaultSession'

package/src/__snapshots__/index.test.ts.snap

@@ -1,9 +0,0 @@
-// Jest Snapshot v1, https://goo.gl/fbAQLP
-
-exports[`adds config editor widget 1`] = `{}`;
-
-exports[`adds connection add widget 1`] = `{}`;
-
-exports[`adds hierarchical track selector 1`] = `{}`;
-
-exports[`adds track add widget 1`] = `{}`;

package/src/index.test.ts

@@ -1,54 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager'
-import Config from '@jbrowse/plugin-config'
-import { getSnapshot } from 'mobx-state-tree'
-import ThisPlugin from '.'
-
-let pluginManager: PluginManager
-
-beforeAll(() => {
-  pluginManager = new PluginManager([new ThisPlugin(), new Config()])
-  pluginManager.createPluggableElements()
-  pluginManager.configure()
-})
-
-test("won't add if already added", () => {
-  expect(() => pluginManager.addPlugin(new ThisPlugin())).toThrow(
-    /JBrowse already configured, cannot add plugins/,
-  )
-})
-
-test('adds track add widget', () => {
-  const AddTrackWidget = pluginManager.getWidgetType('AddTrackWidget')
-  const config = AddTrackWidget.configSchema.create({
-    type: 'AddTrackWidget',
-  })
-  expect(getSnapshot(config)).toMatchSnapshot()
-})
-
-test('adds config editor widget', () => {
-  const ConfigurationEditorWidget = pluginManager.getWidgetType(
-    'ConfigurationEditorWidget',
-  )
-  const config = ConfigurationEditorWidget.configSchema.create({
-    type: 'ConfigurationEditorWidget',
-  })
-  expect(getSnapshot(config)).toMatchSnapshot()
-})
-
-test('adds connection add widget', () => {
-  const AddConnectionWidget = pluginManager.getWidgetType('AddConnectionWidget')
-  const config = AddConnectionWidget.configSchema.create({
-    type: 'AddConnectionWidget',
-  })
-  expect(getSnapshot(config)).toMatchSnapshot()
-})
-
-test('adds hierarchical track selector', () => {
-  const HierarchicalTrackSelectorWidget = pluginManager.getWidgetType(
-    'HierarchicalTrackSelectorWidget',
-  )
-  const config = HierarchicalTrackSelectorWidget.configSchema.create({
-    type: 'HierarchicalTrackSelectorWidget',
-  })
-  expect(getSnapshot(config)).toMatchSnapshot()
-})

package/src/index.ts

@@ -1,37 +0,0 @@
-import { lazy } from 'react'
-import Plugin from '@jbrowse/core/Plugin'
-import PluginManager from '@jbrowse/core/PluginManager'
-import UCSCTrackHubConnectionF from './ucsc-trackhub'
-import AddTrackWidgetF from './AddTrackWidget'
-
-import AddConnectionWidgetF from './AddConnectionWidget'
-import PluginStoreWidgetF from './PluginStoreWidget'
-import HierarchicalTrackSelectorWidgetF from './HierarchicalTrackSelectorWidget'
-
-const SetDefaultSession = lazy(() => import('./SetDefaultSession'))
-
-const AssemblyManager = lazy(() => import('./AssemblyManager'))
-
-export default class extends Plugin {
-  name = 'DataManagementPlugin'
-
-  exports = {
-    AssemblyManager,
-    SetDefaultSession,
-  }
-
-  install(pluginManager: PluginManager) {
-    UCSCTrackHubConnectionF(pluginManager)
-    AddTrackWidgetF(pluginManager)
-    HierarchicalTrackSelectorWidgetF(pluginManager)
-    AddConnectionWidgetF(pluginManager)
-    PluginStoreWidgetF(pluginManager)
-  }
-
-  configure(_pluginManager: PluginManager) {}
-}
-
-export { AssemblyManager, SetDefaultSession }
-
-export { type AddTrackModel } from './AddTrackWidget/model'
-export { type HierarchicalTrackSelectorModel } from './HierarchicalTrackSelectorWidget'

package/src/ucsc-trackhub/configSchema.ts

@@ -1,41 +0,0 @@
-import { baseConnectionConfig } from '@jbrowse/core/pluggableElementTypes/models'
-import { ConfigurationSchema } from '@jbrowse/core/configuration'
-
-/**
- * #config UCSCTrackHubConnection
- */
-function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
-
-const UCSCTrackHubConnection = ConfigurationSchema(
-  'UCSCTrackHubConnection',
-  {
-    /**
-     * #slot
-     */
-    hubTxtLocation: {
-      type: 'fileLocation',
-      defaultValue: {
-        uri: 'http://mysite.com/path/to/hub.txt',
-        locationType: 'UriLocation',
-      },
-      description: 'location of the hub file (usually called hub.txt)',
-    },
-    /**
-     * #slot
-     */
-    assemblyNames: {
-      type: 'stringArray',
-      defaultValue: [],
-      description:
-        'optional list of genomes to import from this track hub, if empty all genomes will be imported',
-    },
-  },
-  {
-    /**
-     * #baseConfiguration
-     */
-    baseConfiguration: baseConnectionConfig,
-  },
-)
-
-export default UCSCTrackHubConnection

package/src/ucsc-trackhub/index.ts

@@ -1,19 +0,0 @@
-import { ConnectionType } from '@jbrowse/core/pluggableElementTypes'
-import PluginManager from '@jbrowse/core/PluginManager'
-
-import stateModelFactory from './model'
-import configSchema from './configSchema'
-
-export default (pluginManager: PluginManager) => {
-  pluginManager.addConnectionType(
-    () =>
-      new ConnectionType({
-        name: 'UCSCTrackHubConnection',
-        configSchema,
-        stateModel: stateModelFactory(pluginManager),
-        displayName: 'UCSC Track Hub',
-        description: 'A track or assembly hub in the Track Hub format',
-        url: '//genome.ucsc.edu/goldenPath/help/hgTrackHubHelp.html#Intro',
-      }),
-  )
-}

package/src/ucsc-trackhub/model.ts

@@ -1,107 +0,0 @@
-import PluginManager from '@jbrowse/core/PluginManager'
-import { BaseConnectionModelFactory } from '@jbrowse/core/pluggableElementTypes/models'
-import {
-  ConfigurationReference,
-  readConfObject,
-  getConf,
-} from '@jbrowse/core/configuration'
-import { getSession } from '@jbrowse/core/util'
-import { types } from 'mobx-state-tree'
-
-// locals
-import configSchema from './configSchema'
-import {
-  fetchGenomesFile,
-  fetchHubFile,
-  fetchTrackDbFile,
-  generateTracks,
-} from './ucscTrackHub'
-
-export default function UCSCTrackHubConnection(pluginManager: PluginManager) {
-  return types
-    .compose(
-      'UCSCTrackHubConnection',
-      BaseConnectionModelFactory(pluginManager),
-      types.model({
-        configuration: ConfigurationReference(configSchema),
-        type: types.literal('UCSCTrackHubConnection'),
-      }),
-    )
-    .actions(self => ({
-      async connect() {
-        const session = getSession(self)
-        try {
-          const connectionName = getConf(self, 'name') // NOTE: name comes from the base configuration
-          const hubFileLocation = getConf(self, 'hubTxtLocation')
-          const hubFile = await fetchHubFile(hubFileLocation)
-          const genomeFile = hubFile.get('genomesFile')
-          if (!genomeFile) {
-            throw new Error('genomesFile not found on hub')
-          }
-
-          const hubUri = new URL(hubFileLocation.uri, hubFileLocation.baseUri)
-          const genomesFileLocation = hubUri
-            ? {
-                uri: new URL(genomeFile, hubUri).href,
-                locationType: 'UriLocation' as const,
-              }
-            : {
-                localPath: genomeFile,
-                locationType: 'LocalPathLocation' as const,
-              }
-          const genomesFile = await fetchGenomesFile(genomesFileLocation)
-          const trackDbData = []
-          for (const [genomeName, genome] of genomesFile) {
-            const assemblyNames = getConf(self, 'assemblyNames')
-            if (
-              assemblyNames.length > 0 &&
-              !assemblyNames.includes(genomeName)
-            ) {
-              continue
-            }
-
-            const conf = session.assemblyManager.get(genomeName)?.configuration
-            if (!conf) {
-              throw new Error(
-                `Cannot find assembly for "${genomeName}" from the genomes file for connection "${connectionName}"`,
-              )
-            }
-            const db = genome.get('trackDb')
-            if (!db) {
-              throw new Error('genomesFile not found on hub')
-            }
-            const base = new URL(genomeFile, hubUri)
-            const trackDbLoc = hubUri
-              ? {
-                  uri: new URL(db, base).href,
-                  locationType: 'UriLocation' as const,
-                }
-              : {
-                  localPath: db,
-                  locationType: 'LocalPathLocation' as const,
-                }
-            const trackDb = await fetchTrackDbFile(trackDbLoc)
-            trackDbData.push([trackDbLoc, trackDb, genomeName, conf] as const)
-          }
-          for (const [
-            trackDbLoc,
-            trackDbFile,
-            genomeName,
-            conf,
-          ] of trackDbData) {
-            const seqAdapter = readConfObject(conf, ['sequence', 'adapter'])
-            self.addTrackConfs(
-              generateTracks(trackDbFile, trackDbLoc, genomeName, seqAdapter),
-            )
-          }
-        } catch (e) {
-          console.error(e)
-          session.notify(
-            `There was a problem connecting to the UCSC Track Hub "${self.configuration.name}". Please make sure you have entered a valid hub.txt file. The error that was thrown is: "${e}"`,
-            'error',
-          )
-          session.breakConnection(self.configuration)
-        }
-      },
-    }))
-}

package/src/ucsc-trackhub/ucscAssemblies.ts

@@ -1,201 +0,0 @@
-// These are the assemblies for which there is a sequence file located at
-// http://hgdownload.soe.ucsc.edu/goldenPath/${assemblyName}/bigZips/${assemblyName}.2bit
-// This list was generated by `getUcscAssemblies.js`
-
-export default `ailMel1
-allMis1
-anoCar1
-anoCar2
-anoGam1
-anoGam3
-apiMel1
-apiMel2
-aplCal1
-aptMan1
-aquChr2
-balAcu1
-bisBis1
-bosTau2
-bosTau3
-bosTau4
-bosTau6
-bosTau7
-bosTau8
-braFlo1
-caeJap1
-caePb1
-caePb2
-caeRem2
-caeRem3
-calJac1
-calJac3
-calMil1
-canFam1
-canFam3
-cavPor3
-cb3
-ce10
-ce11
-ce2
-ce4
-ce6
-cerSim1
-chlSab2
-choHof1
-chrPic1
-ci1
-ci2
-ci3
-criGri1
-criGriChoV1
-danRer10
-danRer11
-danRer3
-danRer4
-danRer5
-danRer6
-danRer7
-dasNov3
-dipOrd1
-dm1
-dm2
-dm3
-dm6
-dp2
-dp3
-droAna1
-droAna2
-droEre1
-droGri1
-droMoj1
-droMoj2
-droPer1
-droSec1
-droSim1
-droVir1
-droVir2
-droYak1
-droYak2
-eboVir3
-echTel1
-echTel2
-equCab1
-equCab2
-eriEur1
-eriEur2
-felCat3
-felCat4
-felCat5
-felCat8
-fr1
-fr2
-fr3
-gadMor1
-galGal2
-galGal3
-galGal4
-galGal5
-galGal6
-galVar1
-gasAcu1
-geoFor1
-gorGor3
-gorGor4
-gorGor5
-hetGla1
-hetGla2
-hg16
-hg18
-hg19
-hg38
-latCha1
-loxAfr3
-macEug2
-macFas5
-manPen1
-melGal1
-melGal5
-melUnd1
-micMur1
-micMur2
-mm10
-mm7
-mm8
-mm9
-monDom2
-monDom4
-monDom5
-musFur1
-myoLuc2
-nanPar1
-nasLar1
-nomLeu1
-nomLeu2
-nomLeu3
-ochPri2
-ochPri3
-oreNil2
-ornAna1
-ornAna2
-oryCun2
-oryLat2
-otoGar3
-oviAri1
-oviAri3
-oviAri4
-panPan1
-panPan2
-panTro1
-panTro2
-panTro3
-panTro4
-panTro5
-panTro6
-papAnu2
-papHam1
-petMar1
-petMar2
-ponAbe2
-ponAbe3
-priPac1
-proCap1
-pteVam1
-rheMac2
-rheMac3
-rheMac8
-rhiRox1
-rn4
-rn5
-rn6
-sacCer1
-sacCer2
-sacCer3
-saiBol1
-sarHar1
-sorAra1
-sorAra2
-speTri2
-strPur1
-strPur2
-susScr11
-susScr2
-susScr3
-taeGut1
-taeGut2
-tarSyr1
-tarSyr2
-tetNig1
-tetNig2
-thaSir1
-triMan1
-tupBel1
-turTru2
-venter1
-vicPac1
-vicPac2
-xenLae2
-xenTro1
-xenTro2
-xenTro3
-xenTro7
-xenTro9`.split(/\r?\n/)