@jbrowse/plugin-grid-bookmark 2.5.0 → 2.6.2

package/src/GridBookmarkWidget/model.ts

@@ -1,66 +0,0 @@
-import { types, cast, Instance } from 'mobx-state-tree'
-import PluginManager from '@jbrowse/core/PluginManager'
-import { Region } from '@jbrowse/core/util/types'
-import { Region as RegionModel, ElementId } from '@jbrowse/core/util/types/mst'
-
-const LabeledRegionModel = types
-  .compose(
-    RegionModel,
-    types.model('Label', { label: types.optional(types.string, '') }),
-  )
-  .actions(self => ({
-    setLabel(label: string) {
-      self.label = label
-    },
-  }))
-
-export default function f(pluginManager: PluginManager) {
-  return types
-    .model('GridBookmarkModel', {
-      id: ElementId,
-      type: types.literal('GridBookmarkWidget'),
-      view: types.safeReference(
-        pluginManager.pluggableMstType('view', 'stateModel'),
-      ),
-      bookmarkedRegions: types.array(LabeledRegionModel),
-      modelSelectedAssembly: '',
-    })
-    .actions(self => ({
-      importBookmarks(regions: Region[]) {
-        self.bookmarkedRegions = cast([...self.bookmarkedRegions, ...regions])
-      },
-      addBookmark(region: Region) {
-        self.bookmarkedRegions.push(region)
-      },
-      removeBookmark(index: number) {
-        self.bookmarkedRegions.splice(index, 1)
-      },
-      clearAllBookmarks() {
-        self.bookmarkedRegions.clear()
-      },
-      updateBookmarkLabel(index: number, label: string) {
-        self.bookmarkedRegions[index]?.setLabel(label)
-      },
-      setSelectedAssembly(assembly: string) {
-        self.modelSelectedAssembly = assembly
-      },
-    }))
-    .views(self => ({
-      get selectedAssembly() {
-        return (
-          self.modelSelectedAssembly ||
-          (self.bookmarkedRegions.length
-            ? self.bookmarkedRegions[0].assemblyName
-            : '')
-        )
-      },
-      get assemblies() {
-        return [
-          ...new Set(self.bookmarkedRegions.map(region => region.assemblyName)),
-        ]
-      },
-    }))
-}
-
-export type GridBookmarkStateModel = ReturnType<typeof f>
-export type GridBookmarkModel = Instance<GridBookmarkStateModel>

package/src/GridBookmarkWidget/types.ts

@@ -1,5 +0,0 @@
-import { Region } from '@jbrowse/core/util/types'
-
-export interface LabeledRegion extends Region {
-  label: string
-}

package/src/GridBookmarkWidget/utils.ts

@@ -1,90 +0,0 @@
-import { saveAs } from 'file-saver'
-import { getSession, assembleLocString } from '@jbrowse/core/util'
-import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
-import { AbstractViewModel } from '@jbrowse/core/util/types'
-
-// locals
-import { GridBookmarkModel } from './model'
-import { LabeledRegion } from './types'
-
-type LGV = LinearGenomeViewModel
-
-type MaybeLGV = LGV | undefined
-
-export async function navToBookmark(
-  locString: string,
-  views: AbstractViewModel[],
-  model: GridBookmarkModel,
-) {
-  const session = getSession(model)
-  try {
-    // search for exact match to an lgv that this bookmark widget launched, or
-    // any lgv that looks like it is relevant to what we are browsing
-    const { selectedAssembly } = model
-    const newViewId = `${model.id}_${selectedAssembly}`
-    let view = (views.find(
-      v => v.type === 'LinearGenomeView' && v.id === newViewId,
-    ) ||
-      views.find(
-        v =>
-          v.type === 'LinearGenomeView' &&
-          // @ts-expect-error
-          v.assemblyNames[0] === selectedAssembly,
-      )) as MaybeLGV
-
-    if (!view) {
-      view = session.addView('LinearGenomeView', {
-        id: newViewId,
-      }) as LGV
-    }
-    await view.navToLocString(locString, selectedAssembly)
-  } catch (e) {
-    console.error(e)
-    session.notify(`${e}`, 'error')
-  }
-}
-
-export function downloadBookmarkFile(
-  bookmarkedRegions: LabeledRegion[],
-  fileFormat: string,
-  model: GridBookmarkModel,
-) {
-  const { selectedAssembly } = model
-  const fileHeader =
-    fileFormat === 'TSV'
-      ? 'chrom\tstart\tend\tlabel\tassembly_name\tcoord_range\n'
-      : ''
-
-  const fileContents = bookmarkedRegions
-    .map(b => {
-      const { label } = b
-      const labelVal = label === '' ? '.' : label
-      const locString = assembleLocString(b)
-
-      if (fileFormat === 'BED') {
-        if (b.assemblyName === selectedAssembly || selectedAssembly === 'all') {
-          return `${b.refName}\t${b.start}\t${b.end}\t${labelVal}\n`
-        }
-        return ''
-      } else {
-        return `${b.refName}\t${b.start + 1}\t${b.end}\t${labelVal}\t${
-          b.assemblyName
-        }\t${locString}\n`
-      }
-    })
-    .reduce((a, b) => a + b, fileHeader)
-
-  const blob = new Blob([fileContents || ''], {
-    type:
-      fileFormat === 'BED'
-        ? 'text/x-bed;charset=utf-8'
-        : 'text/tab-separated-values;charset=utf-8',
-  })
-
-  const fileName =
-    fileFormat === 'BED'
-      ? `jbrowse_bookmarks_${selectedAssembly}.bed`
-      : 'jbrowse_bookmarks.tsv'
-
-  saveAs(blob, fileName)
-}

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

@@ -1,3 +0,0 @@
-// Jest Snapshot v1, https://goo.gl/fbAQLP
-
-exports[`adds grid bookmark widget 1`] = `{}`;

package/src/index.test.ts

@@ -1,26 +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 grid bookmark widget', () => {
-  const GridBookmarkWidget = pluginManager.getWidgetType('GridBookmarkWidget')
-  const config = GridBookmarkWidget.configSchema.create({
-    type: 'GridBookmarkWidget',
-  })
-  expect(getSnapshot(config)).toMatchSnapshot()
-})

package/src/index.ts

@@ -1,137 +0,0 @@
-import Plugin from '@jbrowse/core/Plugin'
-import PluginManager from '@jbrowse/core/PluginManager'
-import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
-import { getSession, isSessionModelWithWidgets } from '@jbrowse/core/util'
-import {
-  PluggableElementType,
-  ViewType,
-} from '@jbrowse/core/pluggableElementTypes'
-
-// icons
-import BookmarkIcon from '@mui/icons-material/Bookmark'
-import BookmarksIcon from '@mui/icons-material/Bookmarks'
-
-import GridBookmarkWidgetF from './GridBookmarkWidget'
-
-export default class extends Plugin {
-  name = 'GridBookmarkPlugin'
-
-  install(pluginManager: PluginManager) {
-    GridBookmarkWidgetF(pluginManager)
-
-    pluginManager.addToExtensionPoint(
-      'Core-extendPluggableElement',
-      (pluggableElement: PluggableElementType) => {
-        if (pluggableElement.name === 'LinearGenomeView') {
-          const { stateModel } = pluggableElement as ViewType
-          const newStateModel = stateModel.extend(
-            (self: LinearGenomeViewModel) => {
-              const superMenuItems = self.menuItems
-              const superRubberBandMenuItems = self.rubberBandMenuItems
-              return {
-                actions: {
-                  activateBookmarkWidget() {
-                    const session = getSession(self)
-                    if (isSessionModelWithWidgets(session)) {
-                      let bookmarkWidget = session.widgets.get('GridBookmark')
-                      if (!bookmarkWidget) {
-                        bookmarkWidget = session.addWidget(
-                          'GridBookmarkWidget',
-                          'GridBookmark',
-                          { view: self },
-                        )
-                      }
-
-                      session.showWidget(bookmarkWidget)
-                      return bookmarkWidget
-                    }
-
-                    throw new Error('Could not open bookmark widget')
-                  },
-
-                  bookmarkCurrentRegion() {
-                    const selectedRegions = self.getSelectedRegions(
-                      self.leftOffset,
-                      self.rightOffset,
-                    )
-                    const firstRegion = selectedRegions[0]
-                    const session = getSession(self)
-                    if (isSessionModelWithWidgets(session)) {
-                      const { widgets } = session
-                      let bookmarkWidget = widgets.get('GridBookmark')
-                      if (!bookmarkWidget) {
-                        this.activateBookmarkWidget()
-                        bookmarkWidget = widgets.get('GridBookmark')
-                      }
-                      // @ts-expect-error
-                      bookmarkWidget.addBookmark(firstRegion)
-                    }
-                  },
-                },
-                views: {
-                  menuItems() {
-                    const newMenuItems = [
-                      ...superMenuItems(),
-                      { type: 'divider' },
-                      {
-                        label: 'Open bookmark widget',
-                        icon: BookmarksIcon,
-                        // @ts-expect-error
-                        onClick: self.activateBookmarkWidget,
-                      },
-                      {
-                        label: 'Bookmark current region',
-                        icon: BookmarkIcon,
-                        // @ts-expect-error
-                        onClick: self.bookmarkCurrentRegion,
-                      },
-                    ]
-
-                    return newMenuItems
-                  },
-
-                  rubberBandMenuItems() {
-                    const newRubberBandMenuItems = [
-                      ...superRubberBandMenuItems(),
-                      {
-                        label: 'Bookmark region',
-                        icon: BookmarkIcon,
-                        onClick: () => {
-                          const { leftOffset, rightOffset } = self
-                          const selectedRegions = self.getSelectedRegions(
-                            leftOffset,
-                            rightOffset,
-                          )
-                          const firstRegion = selectedRegions[0]
-                          const session = getSession(self)
-                          if (isSessionModelWithWidgets(session)) {
-                            const { widgets } = session
-                            let bookmarkWidget = widgets.get('GridBookmark')
-                            if (!bookmarkWidget) {
-                              // @ts-expect-error
-                              self.activateBookmarkWidget()
-                              bookmarkWidget = widgets.get('GridBookmark')
-                            }
-                            // @ts-expect-error
-                            bookmarkWidget.addBookmark(firstRegion)
-                          }
-                        },
-                      },
-                    ]
-
-                    return newRubberBandMenuItems
-                  },
-                },
-              }
-            },
-          )
-
-          ;(pluggableElement as ViewType).stateModel = newStateModel
-        }
-        return pluggableElement
-      },
-    )
-  }
-
-  configure(_pluginManager: PluginManager) {}
-}