@jbrowse/product-core 2.6.1

package/src/Session/SessionTracks.ts

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+import { IAnyStateTreeNode, Instance, types } from 'mobx-state-tree'
+
+import PluginManager from '@jbrowse/core/PluginManager'
+import {
+  AnyConfiguration,
+  AnyConfigurationModel,
+} from '@jbrowse/core/configuration'
+
+// locals
+import { TracksManagerSessionMixin } from './Tracks'
+import { isBaseSession } from './BaseSession'
+
+/**
+ * #stateModel SessionTracksManagerSessionMixin
+ */
+export function SessionTracksManagerSessionMixin(pluginManager: PluginManager) {
+  return TracksManagerSessionMixin(pluginManager)
+    .named('SessionTracksManagerSessionMixin')
+    .props({
+      /**
+       * #property
+       */
+      sessionTracks: types.array(
+        pluginManager.pluggableConfigSchemaType('track'),
+      ),
+    })
+    .views(self => ({
+      /**
+       * #getter
+       */
+      get tracks(): AnyConfigurationModel[] {
+        return self.jbrowse.tracks
+      },
+    }))
+    .actions(self => {
+      const {
+        addTrackConf: superAddTrackConf,
+        deleteTrackConf: superDeleteTrackConf,
+      } = self
+      return {
+        /**
+         * #action
+         */
+        addTrackConf(trackConf: AnyConfiguration) {
+          if (self.adminMode) {
+            return superAddTrackConf(trackConf)
+          }
+          const { trackId, type } = trackConf as {
+            type: string
+            trackId: string
+          }
+          if (!type) {
+            throw new Error(`unknown track type ${type}`)
+          }
+          const track = self.sessionTracks.find(t => t.trackId === trackId)
+          if (track) {
+            return track
+          }
+          const length = self.sessionTracks.push(trackConf)
+          return self.sessionTracks[length - 1]
+        },
+
+        /**
+         * #action
+         */
+        deleteTrackConf(trackConf: AnyConfigurationModel) {
+          // try to delete it in the main config if in admin mode
+          const found = superDeleteTrackConf(trackConf)
+          if (found) {
+            return found
+          }
+          // if not found or not in admin mode, try to delete it in the
+          // sessionTracks
+          const { trackId } = trackConf
+          const idx = self.sessionTracks.findIndex(t => t.trackId === trackId)
+          if (idx === -1) {
+            return undefined
+          }
+          return self.sessionTracks.splice(idx, 1)
+        },
+      }
+    })
+}
+
+/** Session mixin MST type for a session that has `sessionTracks` */
+export type SessionWithSessionTracksType = ReturnType<
+  typeof SessionTracksManagerSessionMixin
+>
+
+/** Instance of a session that has `sessionTracks` */
+export type SessionWithSessionTracks = Instance<SessionWithSessionTracksType>
+
+/** Type guard for SessionWithSessionTracks */
+export function isSessionWithSessionTracks(
+  thing: IAnyStateTreeNode,
+): thing is SessionWithSessionTracks {
+  return isBaseSession(thing) && 'sessionTracks' in thing
+}

package/src/Session/Themes.ts

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+import {
+  IAnyStateTreeNode,
+  Instance,
+  addDisposer,
+  types,
+} from 'mobx-state-tree'
+
+import PluginManager from '@jbrowse/core/PluginManager'
+import { getConf } from '@jbrowse/core/configuration'
+import { createJBrowseTheme, defaultThemes } from '@jbrowse/core/ui'
+import { localStorageGetItem, localStorageSetItem } from '@jbrowse/core/util'
+import { ThemeOptions } from '@mui/material'
+import { autorun } from 'mobx'
+
+// locals
+import { BaseSession } from './BaseSession'
+
+type ThemeMap = { [key: string]: ThemeOptions }
+
+/**
+ * #stateModel ThemeManagerSessionMixin
+ */
+export function ThemeManagerSessionMixin(pluginManager: PluginManager) {
+  return types
+    .model({})
+    .volatile(() => ({
+      sessionThemeName: localStorageGetItem('themeName') || 'default',
+    }))
+    .views(s => ({
+      /**
+       * #method
+       */
+      allThemes(): ThemeMap {
+        const self = s as typeof s & BaseSession
+        const extraThemes = getConf(self.jbrowse, 'extraThemes')
+        return { ...defaultThemes, ...extraThemes }
+      },
+      /**
+       * #getter
+       */
+      get themeName() {
+        const { sessionThemeName } = s
+        const all = this.allThemes()
+        return all[sessionThemeName] ? sessionThemeName : 'default'
+      },
+      /**
+       * #getter
+       */
+      get theme() {
+        const self = s as typeof s & BaseSession
+        const configTheme = getConf(self.jbrowse, 'theme')
+        const all = this.allThemes()
+        return createJBrowseTheme(configTheme, all, this.themeName)
+      },
+    }))
+    .actions(self => ({
+      /**
+       * #action
+       */
+      setThemeName(name: string) {
+        self.sessionThemeName = name
+      },
+      afterAttach() {
+        addDisposer(
+          self,
+          autorun(() => {
+            localStorageSetItem('themeName', self.themeName)
+          }),
+        )
+      },
+    }))
+}
+
+/** Session mixin MST type for a session that supports theming */
+export type SessionWithThemesType = ReturnType<typeof ThemeManagerSessionMixin>
+
+/** Instance of a session that has theming support */
+export type SessionWithThemes = Instance<SessionWithThemesType>
+
+/** Type guard for SessionWithThemes */
+export function isSessionWithThemes(
+  session: IAnyStateTreeNode,
+): session is SessionWithThemes {
+  return 'theme' in session
+}

package/src/Session/Tracks.ts

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+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

@@ -0,0 +1,10 @@
+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

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

package/src/ui/AboutDialog.tsx

@@ -0,0 +1,31 @@
+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

@@ -0,0 +1,88 @@
+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

@@ -0,0 +1,75 @@
+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

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+export * from './AboutDialog'