@jbrowse/product-core 2.6.1 → 2.6.3

package/src/Session/Tracks.ts

@@ -1,72 +0,0 @@
-import { IAnyStateTreeNode, Instance, types } from 'mobx-state-tree'
-
-import PluginManager from '@jbrowse/core/PluginManager'
-import {
-  AnyConfiguration,
-  AnyConfigurationModel,
-} from '@jbrowse/core/configuration'
-import { BaseSessionModel, isBaseSession } from './BaseSession'
-import { ReferenceManagementSessionMixin } from './ReferenceManagement'
-
-/**
- * #stateModel TracksManagerSessionMixin
- * composed of
- * - BaseSessionModel
- * - ReferenceManagementSessionMixin
- */
-export function TracksManagerSessionMixin(pluginManager: PluginManager) {
-  return types
-    .compose(
-      'TracksManagerSessionMixin',
-      BaseSessionModel(pluginManager),
-      ReferenceManagementSessionMixin(pluginManager),
-    )
-    .views(self => ({
-      /**
-       * #getter
-       */
-      get tracks(): AnyConfigurationModel[] {
-        return self.jbrowse.tracks
-      },
-    }))
-    .actions(self => ({
-      /**
-       * #action
-       */
-      addTrackConf(trackConf: AnyConfiguration) {
-        return self.jbrowse.addTrackConf(trackConf)
-      },
-
-      /**
-       * #action
-       */
-      deleteTrackConf(trackConf: AnyConfigurationModel) {
-        const callbacksToDereferenceTrack: Function[] = []
-        const dereferenceTypeCount: Record<string, number> = {}
-        const referring = self.getReferring(trackConf)
-        self.removeReferring(
-          referring,
-          trackConf,
-          callbacksToDereferenceTrack,
-          dereferenceTypeCount,
-        )
-        callbacksToDereferenceTrack.forEach(cb => cb())
-        if (self.adminMode) {
-          return self.jbrowse.deleteTrackConf(trackConf)
-        }
-      },
-    }))
-}
-
-/** Session mixin MST type for a session that has tracks */
-export type SessionWithTracksType = ReturnType<typeof TracksManagerSessionMixin>
-
-/** Instance of a session that has tracks */
-export type SessionWithTracks = Instance<SessionWithTracksType>
-
-/** Type guard for SessionWithTracks */
-export function isSessionWithTracks(
-  thing: IAnyStateTreeNode,
-): thing is SessionWithTracks {
-  return isBaseSession(thing) && 'tracks' in thing
-}

package/src/Session/index.ts

@@ -1,10 +0,0 @@
-export * from './ReferenceManagement'
-export * from './Connections'
-export * from './DrawerWidgets'
-export * from './DialogQueue'
-export * from './Themes'
-export * from './Tracks'
-export * from './MultipleViews'
-export * from './BaseSession'
-export * from './SessionTracks'
-export * from './BaseSession'

package/src/index.ts

@@ -1,3 +0,0 @@
-export * from './RootModel'
-export * from './Session'
-export * from './ui'

package/src/ui/AboutDialog.tsx

@@ -1,31 +0,0 @@
-import React from 'react'
-import { AnyConfigurationModel } from '@jbrowse/core/configuration'
-import Dialog from '@jbrowse/core/ui/Dialog'
-import { getSession, getEnv } from '@jbrowse/core/util'
-import { getTrackName } from '@jbrowse/core/util/tracks'
-import AboutContents from './AboutDialogContents'
-
-export function AboutDialog({
-  config,
-  handleClose,
-}: {
-  config: AnyConfigurationModel
-  handleClose: () => void
-}) {
-  const session = getSession(config)
-  const trackName = getTrackName(config, session)
-  const { pluginManager } = getEnv(session)
-
-  const AboutComponent = pluginManager.evaluateExtensionPoint(
-    'Core-replaceAbout',
-    AboutContents,
-    { session, config },
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  ) as React.FC<any>
-
-  return (
-    <Dialog open onClose={handleClose} title={trackName} maxWidth="xl">
-      <AboutComponent config={config} />
-    </Dialog>
-  )
-}

package/src/ui/AboutDialogContents.tsx

@@ -1,88 +0,0 @@
-import React, { useState } from 'react'
-import copy from 'copy-to-clipboard'
-import { Button } from '@mui/material'
-import { makeStyles } from 'tss-react/mui'
-import {
-  getConf,
-  readConfObject,
-  AnyConfigurationModel,
-} from '@jbrowse/core/configuration'
-import { getSession, getEnv } from '@jbrowse/core/util'
-import {
-  BaseCard,
-  Attributes,
-} from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail'
-import FileInfoPanel from './FileInfoPanel'
-
-const useStyles = makeStyles()({
-  content: {
-    minWidth: 800,
-  },
-})
-
-export default function AboutContents({
-  config,
-}: {
-  config: AnyConfigurationModel
-}) {
-  const [copied, setCopied] = useState(false)
-  const conf = readConfObject(config)
-  const session = getSession(config)
-  const { classes } = useStyles()
-
-  const hideUris =
-    getConf(session, ['formatAbout', 'hideUris']) ||
-    readConfObject(config, ['formatAbout', 'hideUris'])
-
-  const { pluginManager } = getEnv(session)
-
-  const confPostExt = pluginManager.evaluateExtensionPoint(
-    'Core-customizeAbout',
-    {
-      config: {
-        ...conf,
-        ...getConf(session, ['formatAbout', 'config'], { config: conf }),
-        ...readConfObject(config, ['formatAbout', 'config'], { config: conf }),
-      },
-    },
-    { session, config },
-  ) as Record<string, unknown>
-
-  const ExtraPanel = pluginManager.evaluateExtensionPoint(
-    'Core-extraAboutPanel',
-    null,
-    { session, config },
-    // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  ) as { name: string; Component: React.FC<any> }
-
-  return (
-    <div className={classes.content}>
-      <BaseCard title="Configuration">
-        {!hideUris ? (
-          <Button
-            variant="contained"
-            style={{ float: 'right' }}
-            onClick={() => {
-              copy(JSON.stringify(conf, null, 2))
-              setCopied(true)
-              setTimeout(() => setCopied(false), 1000)
-            }}
-          >
-            {copied ? 'Copied to clipboard!' : 'Copy config'}
-          </Button>
-        ) : null}
-        <Attributes
-          attributes={confPostExt}
-          omit={['displays', 'baseUri', 'refNames', 'formatAbout']}
-          hideUris={hideUris}
-        />
-      </BaseCard>
-      {ExtraPanel ? (
-        <BaseCard title={ExtraPanel.name}>
-          <ExtraPanel.Component config={config} />
-        </BaseCard>
-      ) : null}
-      <FileInfoPanel config={config} />
-    </div>
-  )
-}

package/src/ui/FileInfoPanel.tsx

@@ -1,75 +0,0 @@
-import React, { useState, useEffect } from 'react'
-import { Typography } from '@mui/material'
-import {
-  readConfObject,
-  AnyConfigurationModel,
-} from '@jbrowse/core/configuration'
-import LoadingEllipses from '@jbrowse/core/ui/LoadingEllipses'
-import { getSession } from '@jbrowse/core/util'
-import {
-  BaseCard,
-  Attributes,
-} from '@jbrowse/core/BaseFeatureWidget/BaseFeatureDetail'
-
-type FileInfo = Record<string, unknown> | string
-
-export default function FileInfoPanel({
-  config,
-}: {
-  config: AnyConfigurationModel
-}) {
-  const [error, setError] = useState<unknown>()
-  const [info, setInfo] = useState<FileInfo>()
-  const session = getSession(config)
-  const { rpcManager } = session
-
-  useEffect(() => {
-    const aborter = new AbortController()
-    const { signal } = aborter
-    let cancelled = false
-    // eslint-disable-next-line @typescript-eslint/no-floating-promises
-    ;(async () => {
-      try {
-        const adapterConfig = readConfObject(config, 'adapter')
-        const result = await rpcManager.call(config.trackId, 'CoreGetInfo', {
-          adapterConfig,
-          signal,
-        })
-        if (!cancelled) {
-          setInfo(result as FileInfo)
-        }
-      } catch (e) {
-        if (!cancelled) {
-          console.error(e)
-          setError(e)
-        }
-      }
-    })()
-
-    return () => {
-      aborter.abort()
-      cancelled = true
-    }
-  }, [config, rpcManager])
-
-  const details =
-    typeof info === 'string'
-      ? {
-          header: `<pre>${info
-            .replaceAll('<', '&lt;')
-            .replaceAll('>', '&gt;')}</pre>`,
-        }
-      : info || {}
-
-  return info !== null ? (
-    <BaseCard title="File info">
-      {error ? (
-        <Typography color="error">{`${error}`}</Typography>
-      ) : info === undefined ? (
-        <LoadingEllipses message="Loading file data" />
-      ) : (
-        <Attributes attributes={details} />
-      )}
-    </BaseCard>
-  ) : null
-}

package/src/ui/index.ts

@@ -1 +0,0 @@
-export * from './AboutDialog'