@jbrowse/plugin-spreadsheet-view 2.6.1 → 2.6.2

package/src/SpreadsheetView/index.ts

@@ -1,20 +0,0 @@
-import { lazy } from 'react'
-import { ViewType } from '@jbrowse/core/pluggableElementTypes'
-import PluginManager from '@jbrowse/core/PluginManager'
-import stateModel from './models/SpreadsheetView'
-
-export default (pluginManager: PluginManager) => {
-  pluginManager.addViewType(() => {
-    return new ViewType({
-      name: 'SpreadsheetView',
-      displayName: 'Spreadsheet view',
-      stateModel,
-      ReactComponent: lazy(() => import('./components/SpreadsheetView')),
-    })
-  })
-}
-
-export {
-  type SpreadsheetViewModel,
-  type SpreadsheetViewStateModel,
-} from './models/SpreadsheetView'

package/src/SpreadsheetView/models/ColumnDataTypes/LocEnd.ts

@@ -1,21 +0,0 @@
-import MakeSpreadsheetColumnType from './MakeSpreadsheetColumnType'
-import { FilterModelType as NumberFilterModel } from './Number'
-import { types } from 'mobx-state-tree'
-
-const FilterModelType = types.compose(
-  NumberFilterModel,
-  types.model({
-    type: types.literal('LocEnd'),
-  }),
-)
-
-const LocEnd = MakeSpreadsheetColumnType('LocEnd', {
-  categoryName: 'Location',
-  displayName: 'End',
-  compare(cellA: { text: string }, cellB: { text: string }) {
-    return parseFloat(cellA.text) - parseFloat(cellB.text)
-  },
-  FilterModelType,
-})
-
-export default LocEnd

package/src/SpreadsheetView/models/ColumnDataTypes/LocRef.ts

@@ -1,21 +0,0 @@
-import MakeSpreadsheetColumnType from './MakeSpreadsheetColumnType'
-import { FilterModelType as NumberFilterModel } from './Text'
-import { types } from 'mobx-state-tree'
-
-const FilterModelType = types.compose(
-  NumberFilterModel,
-  types.model({
-    type: types.literal('LocRef'),
-  }),
-)
-
-const LocRef = MakeSpreadsheetColumnType('LocRef', {
-  categoryName: 'Location',
-  displayName: 'Reference seq',
-  compare(cellA: { text: string }, cellB: { text: string }) {
-    return cellA.text.localeCompare(cellB.text)
-  },
-  FilterModelType,
-})
-
-export default LocRef

package/src/SpreadsheetView/models/ColumnDataTypes/LocStart.ts

@@ -1,21 +0,0 @@
-import MakeSpreadsheetColumnType from './MakeSpreadsheetColumnType'
-import { types } from 'mobx-state-tree'
-import { FilterModelType as NumberFilterModel } from './Number'
-
-const FilterModelType = types.compose(
-  NumberFilterModel,
-  types.model({
-    type: types.literal('LocStart'),
-  }),
-)
-
-const LocStart = MakeSpreadsheetColumnType('LocStart', {
-  categoryName: 'Location',
-  displayName: 'Start',
-  compare(cellA: { text: string }, cellB: { text: string }) {
-    return parseFloat(cellA.text) - parseFloat(cellB.text)
-  },
-  FilterModelType,
-})
-
-export default LocStart

package/src/SpreadsheetView/models/ColumnDataTypes/LocString.tsx

@@ -1,328 +0,0 @@
-import React from 'react'
-import {
-  IconButton,
-  TextField,
-  MenuItem,
-  InputAdornment,
-  Select,
-} from '@mui/material'
-import { makeStyles } from 'tss-react/mui'
-import { observer } from 'mobx-react'
-import { types, getParent, getPropertyMembers } from 'mobx-state-tree'
-
-// jbrowse imports
-import {
-  getPropertyType,
-  getEnumerationValues,
-  getSubType,
-} from '@jbrowse/core/util/mst-reflection'
-import { LinearGenomeViewModel } from '@jbrowse/plugin-linear-genome-view'
-import {
-  doesIntersect2,
-  isContainedWithin,
-  compareLocs,
-  getSession,
-  parseLocString,
-} from '@jbrowse/core/util'
-
-// icons
-import ClearIcon from '@mui/icons-material/Clear'
-
-// locals
-import MakeSpreadsheetColumnType from './MakeSpreadsheetColumnType'
-
-type LGV = LinearGenomeViewModel
-
-const useStyles = makeStyles()({
-  textFilterControlAdornment: { marginRight: '-18px' },
-  textFilterControl: {
-    '& .MuiInput-formControl': {
-      marginTop: 8,
-    },
-    '& .MuiInputLabel-formControl': {
-      top: '-7px',
-      '&.MuiInputLabel-shrink': {
-        top: '-3px',
-      },
-    },
-  },
-})
-
-// React component for the column filter control
-const FilterReactComponent = observer(function ({
-  filterModel,
-}: {
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  filterModel: any
-}) {
-  const { classes } = useStyles()
-  const operationChoices = getEnumerationValues(
-    getSubType(getPropertyType(getPropertyMembers(filterModel), 'operation')),
-  )
-  return (
-    <>
-      <Select
-        value={filterModel.operation}
-        onChange={event => filterModel.setOperation(String(event.target.value))}
-      >
-        {operationChoices.map(name => (
-          <MenuItem key={name} value={name}>
-            {name}
-          </MenuItem>
-        ))}
-      </Select>{' '}
-      <TextField
-        label="range"
-        placeholder="chr1:100-200"
-        error={filterModel.locStringIsInvalid}
-        value={filterModel.locString}
-        onChange={evt => filterModel.setLocString(evt.target.value)}
-        className={classes.textFilterControl}
-        InputProps={{
-          endAdornment: (
-            <InputAdornment
-              className={classes.textFilterControlAdornment}
-              position="end"
-            >
-              <IconButton
-                aria-label="clear filter"
-                onClick={() => filterModel.setLocString('')}
-              >
-                <ClearIcon />
-              </IconButton>
-            </InputAdornment>
-          ),
-        }}
-      />
-    </>
-  )
-})
-
-const OPERATIONS = [
-  'overlaps with',
-  'contained within',
-  'fully contains',
-  'does not overlap',
-  'not contained within',
-  'does not contain',
-]
-
-interface Loc {
-  start: number
-  end: number
-  refName: string
-}
-
-// NOTE: assembly names, if present, are ignored in all of these predicates
-const OPERATION_PREDICATES = {
-  'overlaps with': (cellLocation, specifiedLocation) => {
-    return (
-      cellLocation.refName === specifiedLocation.refName &&
-      doesIntersect2(
-        cellLocation.start,
-        cellLocation.end,
-        specifiedLocation.start,
-        specifiedLocation.end,
-      )
-    )
-  },
-  'contained within': (cellLocation, specifiedLocation) => {
-    return (
-      cellLocation.refName === specifiedLocation.refName &&
-      isContainedWithin(
-        cellLocation.start,
-        cellLocation.end,
-        specifiedLocation.start,
-        specifiedLocation.end,
-      )
-    )
-  },
-  'fully contains': (cellLocation, specifiedLocation) => {
-    return (
-      cellLocation.refName === specifiedLocation.refName &&
-      isContainedWithin(
-        specifiedLocation.start,
-        specifiedLocation.end,
-        cellLocation.start,
-        cellLocation.end,
-      )
-    )
-  },
-} as { [key: string]: (a: Loc, b: Loc) => boolean }
-
-OPERATION_PREDICATES['does not overlap'] = (
-  cellLocation,
-  specifiedLocation,
-) => {
-  return !OPERATION_PREDICATES['overlaps with'](cellLocation, specifiedLocation)
-}
-OPERATION_PREDICATES['not contained within'] = (
-  cellLocation,
-  specifiedLocation,
-) => {
-  return !OPERATION_PREDICATES['contained within'](
-    cellLocation,
-    specifiedLocation,
-  )
-}
-OPERATION_PREDICATES['does not contain'] = (
-  cellLocation,
-  specifiedLocation,
-) => {
-  return !OPERATION_PREDICATES['fully contains'](
-    cellLocation,
-    specifiedLocation,
-  )
-}
-
-// MST model for the column filter control
-const FilterModelType = types
-  .model('ColumnLocStringFilter', {
-    type: types.literal('LocString'),
-    columnNumber: types.integer,
-    locString: '',
-    operation: types.optional(types.enumeration(OPERATIONS), OPERATIONS[0]),
-  })
-  .views(self => ({
-    get locStringIsInvalid() {
-      if (self.locString) {
-        const parsed = this.parsedLocString
-        return (
-          !parsed ||
-          parsed.refName === '' ||
-          typeof parsed.start !== 'number' ||
-          typeof parsed.end !== 'number' ||
-          parsed.start > parsed.end
-        )
-      }
-      return false
-    },
-    get parsedLocString() {
-      const session = getSession(self)
-
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any
-      const model = getParent<any>(self, 3).spreadsheet
-      const { assemblyName } = model
-      try {
-        return parseLocString(self.locString, refName =>
-          session.assemblyManager.isValidRefName(refName, assemblyName),
-        )
-      } catch (e) {
-        return undefined
-      }
-    },
-  }))
-  .views(self => ({
-    // returns a function that tests the given row
-    get predicate() {
-      const {
-        locString,
-        locStringIsInvalid,
-        parsedLocString,
-        operation,
-        columnNumber,
-      } = self // avoid closing over self
-      if (!locString || locStringIsInvalid || !parsedLocString) {
-        return function alwaysTrue() {
-          return true
-        }
-      }
-
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any
-      return function stringPredicate(_sheet: any, row: any) {
-        const { cellsWithDerived: cells } = row
-        const cell = cells[columnNumber]
-
-        if (!cell || !cell.text || !cell.extendedData) {
-          return false
-        }
-        const parsedCellText = cell.extendedData
-        if (!parsedCellText.refName) {
-          return false
-        }
-
-        const predicate = OPERATION_PREDICATES[operation]
-        if (!predicate) {
-          throw new Error(`"${operation}" not implemented in location filter`)
-        }
-
-        return predicate(parsedCellText, parsedLocString as Loc)
-      }
-    },
-  }))
-  .actions(self => ({
-    setLocString(s: string) {
-      self.locString = s
-    },
-    setOperation(op: string) {
-      self.operation = op
-    },
-  }))
-  .volatile(() => ({ ReactComponent: FilterReactComponent }))
-
-// opens a new LGV at the location described in the locString in the cell text
-
-async function locationLinkClick(
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  spreadsheet: any,
-  _columnNumber: number,
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  cell: any,
-) {
-  const session = getSession(spreadsheet)
-  const { assemblyName } = spreadsheet
-
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  const { id } = getParent<any>(spreadsheet)
-
-  const newViewId = `${id}_${assemblyName}`
-  let view = session.views.find(v => v.id === newViewId) as LGV
-  if (!view) {
-    view = session.addView('LinearGenomeView', {
-      id: newViewId,
-    }) as LGV
-  }
-  await view.navToLocString(cell.text, assemblyName)
-}
-
-// eslint-disable-next-line @typescript-eslint/no-explicit-any
-type DataCell = any
-
-const DataCellReactComponent = observer(function ({
-  cell,
-  columnNumber,
-  spreadsheet,
-}: DataCell) {
-  return (
-    <a
-      onClick={async evt => {
-        evt.preventDefault()
-        const session = getSession(spreadsheet)
-        try {
-          await locationLinkClick(spreadsheet, columnNumber, cell)
-        } catch (e) {
-          console.error(e)
-          session.notify(`${e}`, 'error')
-        }
-      }}
-      title="open a new linear genome view here"
-      href="#link"
-    >
-      {cell.text}
-    </a>
-  )
-})
-
-const LocStringColumnType = MakeSpreadsheetColumnType('LocString', {
-  categoryName: 'Location',
-  displayName: 'Full location',
-
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  compare(cellA: { extendedData: any }, cellB: { extendedData: any }) {
-    return compareLocs(cellA.extendedData, cellB.extendedData)
-  },
-  FilterModelType,
-  DataCellReactComponent,
-})
-
-export default LocStringColumnType

package/src/SpreadsheetView/models/ColumnDataTypes/MakeSpreadsheetColumnType.tsx

@@ -1,38 +0,0 @@
-/* eslint-disable @typescript-eslint/no-explicit-any */
-import React from 'react'
-import { types } from 'mobx-state-tree'
-
-/** utility function for assembling the MST model of a column data type */
-export default function MakeSpreadsheetColumnType(
-  name: string,
-  {
-    DataCellReactComponent = null,
-    FilterModelType = null,
-    compare,
-    displayName = undefined,
-    categoryName = undefined,
-  }: {
-    compare?: any
-    DataCellReactComponent?: React.FC<any> | null
-    FilterModelType?: any
-    displayName?: string
-    categoryName?: string
-  },
-) {
-  return types
-    .model(`ColumnDataType${name}`, {
-      type: types.literal(name),
-    })
-    .volatile(() => ({
-      DataCellReactComponent,
-      FilterModelType: FilterModelType,
-      displayName: displayName || name,
-      categoryName,
-    }))
-    .views(() => ({
-      compare,
-      get hasFilter() {
-        return !!FilterModelType
-      },
-    }))
-}

package/src/SpreadsheetView/models/ColumnDataTypes/Number.tsx

@@ -1,177 +0,0 @@
-import React from 'react'
-import { types } from 'mobx-state-tree'
-import { observer } from 'mobx-react'
-import { MenuItem, Select, TextField } from '@mui/material'
-import { makeStyles } from 'tss-react/mui'
-import MakeSpreadsheetColumnType from './MakeSpreadsheetColumnType'
-
-const OPERATIONS = [
-  'equals',
-  'greater than',
-  'less than',
-  'between',
-  'not between',
-]
-
-// NOTE: assembly names, if present, are ignored in all of these predicates
-const OPERATION_PREDICATES = {
-  equals: (numberInCell, firstNumber) => {
-    return numberInCell === firstNumber
-  },
-  'greater than': (numberInCell, firstNumber) => {
-    return numberInCell > firstNumber
-  },
-  'less than': (numberInCell, firstNumber) => {
-    return numberInCell < firstNumber
-  },
-  between: (numberInCell, firstNumber, secondNumber) => {
-    return (
-      numberInCell > firstNumber &&
-      secondNumber !== undefined &&
-      numberInCell < secondNumber
-    )
-  },
-} as { [key: string]: (arg0: number, a: number, b?: number) => boolean }
-
-OPERATION_PREDICATES['not between'] = (
-  numberInCell,
-  firstNumber,
-  secondNumber,
-) => {
-  return !OPERATION_PREDICATES.between(numberInCell, firstNumber, secondNumber)
-}
-
-const useStyles = makeStyles()({
-  textFilterControlAdornment: { marginRight: '-18px' },
-  textFilterControl: {
-    '& .MuiInput-formControl': {
-      marginTop: 8,
-    },
-    '& .MuiInputLabel-formControl': {
-      top: '-7px',
-      '&.MuiInputLabel-shrink': {
-        top: '-3px',
-      },
-    },
-  },
-})
-
-// React component for the column filter control
-const FilterReactComponent = observer(
-  // eslint-disable-next-line @typescript-eslint/no-explicit-any
-  ({ filterModel }: { filterModel: any }) => {
-    const { classes } = useStyles()
-
-    const operationChoices = OPERATIONS
-
-    return (
-      <>
-        <Select
-          value={filterModel.operation}
-          onChange={e => filterModel.setOperation(String(e.target.value))}
-        >
-          {operationChoices.map(name => (
-            <MenuItem key={name} value={name}>
-              {name}
-            </MenuItem>
-          ))}
-        </Select>{' '}
-        <TextField
-          label="number"
-          placeholder="123"
-          type="number"
-          error={filterModel.firstNumberIsInvalid}
-          defaultValue={filterModel.firstNumber}
-          onChange={evt => {
-            filterModel.setFirstNumber(parseFloat(evt.target.value))
-          }}
-          className={classes.textFilterControl}
-        />
-        {filterModel.operation !== 'between' &&
-        filterModel.operation !== 'not between' ? null : (
-          <>
-            {' and '}
-            <TextField
-              label="number"
-              placeholder="456"
-              type="number"
-              error={filterModel.secondNumberIsInvalid}
-              defaultValue={filterModel.secondNumber}
-              onChange={evt =>
-                filterModel.setSecondNumber(parseFloat(evt.target.value))
-              }
-              className={classes.textFilterControl}
-            />
-          </>
-        )}
-      </>
-    )
-  },
-)
-
-// MST model for the column filter control
-const FilterModelType = types
-  .model('ColumnNumberFilter', {
-    type: types.literal('Number'),
-    columnNumber: types.integer,
-    firstNumber: types.maybe(types.number),
-    secondNumber: types.maybe(types.number),
-    operation: types.optional(types.enumeration(OPERATIONS), OPERATIONS[0]),
-  })
-  .views(self => ({
-    // returns a function that tests the given row
-    get predicate() {
-      if (typeof self.firstNumber !== 'number') {
-        return function alwaysTrue() {
-          return true
-        }
-      }
-
-      const { firstNumber, secondNumber, operation, columnNumber } = self // avoid closing over self
-
-      // eslint-disable-next-line @typescript-eslint/no-explicit-any
-      return function stringPredicate(_sheet: any, row: any) {
-        const { cellsWithDerived } = row
-        const cell = cellsWithDerived[columnNumber]
-
-        if (!cell || !cell.text) {
-          return false
-        }
-
-        const parsedCellText = parseFloat(cell.text)
-        if (typeof parsedCellText !== 'number') {
-          return false
-        }
-
-        const predicate = OPERATION_PREDICATES[operation]
-        if (!predicate) {
-          throw new Error(`"${operation}" not implemented in location filter`)
-        }
-
-        return predicate(parsedCellText, firstNumber, secondNumber)
-      }
-    },
-  }))
-  .actions(self => ({
-    setFirstNumber(n: number) {
-      self.firstNumber =
-        Number.isNaN(n) || typeof n !== 'number' ? undefined : n
-    },
-    setSecondNumber(n: number) {
-      self.secondNumber =
-        Number.isNaN(n) || typeof n !== 'number' ? undefined : n
-    },
-    setOperation(op: string) {
-      self.operation = op
-    },
-  }))
-  .volatile(() => ({ ReactComponent: FilterReactComponent }))
-
-const NumberColumn = MakeSpreadsheetColumnType('Number', {
-  compare(cellA: { text: string }, cellB: { text: string }) {
-    return parseFloat(cellA.text) - parseFloat(cellB.text)
-  },
-  FilterModelType,
-})
-
-export { NumberColumn, FilterModelType }