@jbrowse/plugin-spreadsheet-view 2.6.1 → 2.6.3

package/src/SpreadsheetView/models/Spreadsheet.ts

@@ -1,209 +0,0 @@
-import { stringToJexlExpression } from '@jbrowse/core/util/jexlStrings'
-import { getSession, getEnv } from '@jbrowse/core/util'
-import { autorun } from 'mobx'
-import {
-  addDisposer,
-  types,
-  getParent,
-  SnapshotIn,
-  Instance,
-} from 'mobx-state-tree'
-
-// locals
-import { ColumnTypes, AnyColumnType } from './ColumnDataTypes'
-import StaticRowSetModel from './StaticRowSet'
-import RowModel from './Row'
-
-type Row = Instance<typeof RowModel>
-
-const ColumnDefinition = types
-  .model('ColumnDefinition', {
-    name: types.maybe(types.string),
-    dataType: types.optional(AnyColumnType, () => ({
-      type: 'Text',
-    })),
-    // set to true if column is derived from other columns
-    // if the column is derived, each cell will have a
-    // `derivationFunction` that is called to get its value
-    isDerived: false,
-    // if this cell is derived from other cells, execute this function to get
-    // the value
-    derivationFunctionText: types.maybe(types.string),
-  })
-  .views(self => ({
-    get expr() {
-      if (self.isDerived) {
-        // compile this as a jexl expression
-        return stringToJexlExpression(
-          String(self.derivationFunctionText),
-          getEnv(self).pluginManager.jexl,
-        )
-      }
-      return undefined
-    },
-  }))
-
-type RowMenuPosition = { anchorEl: Element; rowNumber: string } | null
-
-/**
- * #stateModel SpreadsheetViewSpreadsheet
- * #category view
- */
-function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
-
-const Spreadsheet = types
-  .model('Spreadsheet', {
-    /**
-     * #property
-     */
-    rowSet: types.optional(StaticRowSetModel, () => StaticRowSetModel.create()),
-    /**
-     * #property
-     */
-    columns: types.array(ColumnDefinition),
-    /**
-     * #property
-     */
-    columnDisplayOrder: types.array(types.number),
-    /**
-     * #property
-     */
-    hasColumnNames: false,
-    /**
-     * #property
-     */
-    sortColumns: types.array(
-      types
-        .model('SortColumns', {
-          columnNumber: types.number,
-          descending: false,
-        })
-        .actions(self => ({
-          switchDirection() {
-            self.descending = !self.descending
-          },
-        })),
-    ),
-
-    assemblyName: types.maybe(types.string),
-  })
-  .volatile(() => ({
-    defaultDataType: ColumnTypes.Text,
-    rowMenuPosition: null as RowMenuPosition,
-    isLoaded: false,
-  }))
-  .views(self => ({
-    /**
-     * #getter
-     */
-    get initialized() {
-      const session = getSession(self)
-      const name = self.assemblyName
-      return name ? session.assemblyManager.get(name)?.initialized : false
-    },
-    /**
-     * #getter
-     */
-    get hideRowSelection() {
-      // just delegates to parent
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any
-      return getParent<any>(self).hideRowSelection
-    },
-
-    /**
-     * #getter
-     * list of data type names to be made available in the column
-     * dropdown menu
-     */
-    get dataTypeChoices() {
-      const typeNames = Object.keys(ColumnTypes) as (keyof typeof ColumnTypes)[]
-      return typeNames.map(typeName => {
-        const dataType = ColumnTypes[typeName].create({ type: typeName })
-        const { displayName, categoryName } = dataType
-        return { typeName, displayName, categoryName }
-      })
-    },
-
-    /**
-     * #method
-     */
-    rowSortingComparisonFunction(rowA: Row, rowB: Row) {
-      for (let i = 0; i < self.sortColumns.length; i += 1) {
-        const { columnNumber, descending } = self.sortColumns[i]
-        const { dataType } = self.columns[columnNumber]
-        const result = dataType.compare(
-          rowA.cellsWithDerived[columnNumber],
-          rowB.cellsWithDerived[columnNumber],
-        )
-        if (result) {
-          return descending ? -result : result
-        }
-      }
-      return 0
-    },
-  }))
-  .actions(self => ({
-    afterAttach() {
-      addDisposer(
-        self,
-        autorun(async () => {
-          const session = getSession(self)
-          const { assemblyManager } = session
-          try {
-            if (self.assemblyName) {
-              await assemblyManager.waitForAssembly(self.assemblyName)
-              this.setLoaded(true)
-            }
-          } catch (error) {
-            session.notify(
-              `failed to load assembly ${self.assemblyName} ${error}`,
-              'error',
-            )
-          }
-        }),
-      )
-    },
-
-    /**
-     * #action
-     */
-    setLoaded(flag: boolean) {
-      self.isLoaded = flag
-    },
-
-    /**
-     * #action
-     */
-    setRowMenuPosition(newPosition: RowMenuPosition) {
-      self.rowMenuPosition = newPosition
-    },
-
-    /**
-     * #action
-     */
-    setSortColumns(newSort: NonNullable<SnapshotIn<typeof self.sortColumns>>) {
-      if (newSort) {
-        // @ts-expect-error
-        self.sortColumns = newSort
-      }
-    },
-
-    /**
-     * #action
-     */
-    setColumnType(columnNumber: number, newTypeName: string) {
-      self.columns[columnNumber].dataType = { type: newTypeName }
-    },
-
-    /**
-     * #action
-     */
-    unselectAll() {
-      return self.rowSet.unselectAll()
-    },
-  }))
-
-export type SpreadsheetStateModel = typeof Spreadsheet
-export type SpreadsheetModel = Instance<SpreadsheetStateModel>
-
-export default Spreadsheet

package/src/SpreadsheetView/models/SpreadsheetView.test.ts

@@ -1,8 +0,0 @@
-import SpreadsheetView from './SpreadsheetView'
-
-describe('Spreadsheet View mst model', () => {
-  it('can instantiate with empty args', () => {
-    const view = SpreadsheetView.create({ type: 'SpreadsheetView' })
-    expect(view).toBeTruthy()
-  })
-})

package/src/SpreadsheetView/models/SpreadsheetView.ts

@@ -1,243 +0,0 @@
-import {
-  types,
-  getParent,
-  getEnv,
-  cast,
-  SnapshotIn,
-  Instance,
-} from 'mobx-state-tree'
-import { BaseViewModel } from '@jbrowse/core/pluggableElementTypes/models'
-import { readConfObject } from '@jbrowse/core/configuration'
-import { MenuItem } from '@jbrowse/core/ui'
-import { getSession } from '@jbrowse/core/util'
-
-// icons
-import DoneIcon from '@mui/icons-material/Done'
-import FolderOpenIcon from '@mui/icons-material/FolderOpen'
-
-import SpreadsheetModel from './Spreadsheet'
-import ImportWizardModel from './ImportWizard'
-import FilterControlsModel from './FilterControls'
-
-type Spreadsheet = Instance<typeof SpreadsheetModel>
-
-export type MenuItemWithDisabledCallback = MenuItem & {
-  disabled?:
-    | boolean
-    | ((
-        viewModel: unknown,
-        spreadsheetModel: Spreadsheet,
-        rowNumber: number,
-        row: Spreadsheet['rowSet']['rows'][0],
-      ) => boolean)
-}
-
-const defaultRowMenuItems: MenuItemWithDisabledCallback[] = [
-  {
-    label: 'Toggle select',
-    icon: DoneIcon,
-    onClick(_view: unknown, spreadsheet: Spreadsheet) {
-      const rowNumber = spreadsheet.rowMenuPosition?.rowNumber
-      if (rowNumber !== undefined) {
-        spreadsheet.rowSet.rows[+rowNumber - 1].toggleSelect()
-      }
-    },
-  },
-]
-
-const minHeight = 40
-const defaultHeight = 440
-
-/**
- * #stateModel SpreadsheetView
- * #category view
- */
-function x() {} // eslint-disable-line @typescript-eslint/no-unused-vars
-
-const model = types
-  .model('SpreadsheetView', {
-    /**
-     * #property
-     */
-    type: types.literal('SpreadsheetView'),
-    /**
-     * #property
-     */
-    offsetPx: 0,
-    /**
-     * #property
-     */
-    height: types.optional(
-      types.refinement(
-        'SpreadsheetViewHeight',
-        types.number,
-        n => n >= minHeight,
-      ),
-      defaultHeight,
-    ),
-    /**
-     * #property
-     */
-    hideVerticalResizeHandle: false,
-    /**
-     * #property
-     */
-    hideFilterControls: false,
-    /**
-     * #property
-     */
-    filterControls: types.optional(FilterControlsModel, () =>
-      FilterControlsModel.create({}),
-    ),
-    /**
-     * #property
-     * switch specifying whether we are showing the import wizard or the
-     * spreadsheet in our viewing area
-     */
-    mode: types.optional(
-      types.enumeration('SpreadsheetViewMode', ['import', 'display']),
-      'import',
-    ),
-    /**
-     * #property
-     */
-    importWizard: types.optional(ImportWizardModel, () =>
-      ImportWizardModel.create(),
-    ),
-    /**
-     * #property
-     */
-    spreadsheet: types.maybe(SpreadsheetModel),
-  })
-  .volatile(() => ({
-    width: 400,
-    rowMenuItems: defaultRowMenuItems,
-  }))
-  .views(self => ({
-    /**
-     * #getter
-     */
-    get readyToDisplay() {
-      return !!self.spreadsheet && self.spreadsheet.isLoaded
-    },
-    /**
-     * #getter
-     */
-    get hideRowSelection() {
-      return !!getEnv(self).hideRowSelection
-    },
-    /**
-     * #getter
-     */
-    get outputRows() {
-      if (self.spreadsheet && self.spreadsheet.rowSet.isLoaded) {
-        const selected = self.spreadsheet.rowSet.selectedFilteredRows
-        if (selected.length) {
-          return selected
-        }
-        return self.spreadsheet.rowSet.sortedFilteredRows
-      }
-      return undefined
-    },
-    /**
-     * #getter
-     */
-    get assembly() {
-      const name = self.spreadsheet?.assemblyName
-      if (name) {
-        const assemblies = getSession(self).assemblies
-        return assemblies?.find(asm => readConfObject(asm, 'name') === name)
-      }
-      return undefined
-    },
-  }))
-  .actions(self => ({
-    /**
-     * #action
-     */
-    setRowMenuItems(newItems: MenuItem[]) {
-      self.rowMenuItems = newItems
-    },
-    /**
-     * #action
-     */
-    setWidth(newWidth: number) {
-      self.width = newWidth
-      return self.width
-    },
-    /**
-     * #action
-     */
-    setHeight(newHeight: number) {
-      self.height = newHeight > minHeight ? newHeight : minHeight
-      return self.height
-    },
-    /**
-     * #action
-     */
-    resizeHeight(distance: number) {
-      const oldHeight = self.height
-      const newHeight = this.setHeight(self.height + distance)
-      return newHeight - oldHeight
-    },
-    /**
-     * #action
-     */
-    resizeWidth(distance: number) {
-      const oldWidth = self.width
-      const newWidth = this.setWidth(self.width + distance)
-      return newWidth - oldWidth
-    },
-
-    /**
-     * #action
-     * load a new spreadsheet and set our mode to display it
-     */
-    displaySpreadsheet(spreadsheet: SnapshotIn<typeof SpreadsheetModel>) {
-      self.filterControls.clearAllFilters()
-      self.spreadsheet = cast(spreadsheet)
-      self.mode = 'display'
-    },
-    /**
-     * #action
-     */
-    setImportMode() {
-      self.mode = 'import'
-    },
-    /**
-     * #action
-     */
-    setDisplayMode() {
-      if (self.readyToDisplay) {
-        self.mode = 'display'
-      }
-    },
-    /**
-     * #action
-     */
-    closeView() {
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any
-      getParent<any>(self, 2).removeView(self)
-    },
-  }))
-  .views(self => ({
-    /**
-     * #method
-     */
-    menuItems() {
-      return [
-        {
-          label: 'Return to import form',
-          onClick: () => self.setImportMode(),
-          icon: FolderOpenIcon,
-        },
-      ]
-    },
-  }))
-
-const SpreadsheetView = types.compose(BaseViewModel, model)
-
-export type SpreadsheetViewStateModel = typeof SpreadsheetView
-export type SpreadsheetViewModel = Instance<SpreadsheetViewStateModel>
-
-export default SpreadsheetView

package/src/SpreadsheetView/models/StaticRowSet.ts

@@ -1,65 +0,0 @@
-import RowModel from './Row'
-import { types, getParent } from 'mobx-state-tree'
-
-const StaticRowModel = types
-  .model('StaticRowSet', {
-    isLoaded: types.literal(true),
-    rows: types.array(RowModel),
-  })
-  .views(self => ({
-    get count() {
-      return self.rows.length
-    },
-
-    get passingFiltersCount() {
-      return this.sortedFilteredRows.length
-    },
-
-    get selectedCount() {
-      return this.selectedRows.length
-    },
-
-    get selectedAndPassingFiltersCount() {
-      return this.selectedFilteredRows.length
-    },
-
-    get sortedRows() {
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any
-      const parent = getParent<any>(self)
-      return [...self.rows].sort(parent.rowSortingComparisonFunction)
-    },
-
-    get selectedRows() {
-      return self.rows.filter(r => r.isSelected)
-    },
-
-    get selectedFilteredRows() {
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any
-      const sheet = getParent<any>(self)
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any
-      const view = getParent<any>(sheet)
-      const { filterControls } = view
-      return this.selectedRows.filter(row =>
-        filterControls.rowPassesFilters(sheet, row),
-      )
-    },
-
-    // the set of all rows that pass the filters, sorted
-    get sortedFilteredRows() {
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any
-      const sheet = getParent<any>(self)
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any
-      const view = getParent<any>(sheet)
-      const { filterControls } = view
-      return self.rows
-        .filter(row => filterControls.rowPassesFilters(sheet, row))
-        .sort(sheet.rowSortingComparisonFunction)
-    },
-  }))
-  .actions(self => ({
-    unselectAll() {
-      self.rows.forEach(row => row.unSelect())
-    },
-  }))
-
-export default StaticRowModel