@opentrons/shared-data 0.0.1-alpha.20 → 0.1.0-alpha.0

package/js/helpers/getOccludedSlotCountForModule.ts

@@ -1,13 +0,0 @@
-import { OT2_ROBOT_TYPE, THERMOCYCLER_MODULE_TYPE } from '..'
-import type { ModuleType, RobotType } from '..'
-
-export function getOccludedSlotCountForModule(
-  moduleType: ModuleType,
-  robotType: RobotType
-): number {
-  if (moduleType === THERMOCYCLER_MODULE_TYPE) {
-    return robotType === OT2_ROBOT_TYPE ? 4 : 2
-  } else {
-    return 1
-  }
-}

package/js/helpers/getVectorDifference.ts

@@ -1,12 +0,0 @@
-import type { Coordinates } from '../types'
-
-export function getVectorDifference(
-  pointA: Coordinates,
-  pointB: Coordinates
-): Coordinates {
-  return {
-    x: pointA.x - pointB.x,
-    y: pointA.y - pointB.y,
-    z: pointA.z - pointB.z,
-  }
-}

package/js/helpers/getVectorSum.ts

@@ -1,12 +0,0 @@
-import type { Coordinates } from '../types'
-
-export function getVectorSum(
-  pointA: Coordinates,
-  pointB: Coordinates
-): Coordinates {
-  return {
-    x: pointA.x + pointB.x,
-    y: pointA.y + pointB.y,
-    z: pointA.z + pointB.z,
-  }
-}

package/js/helpers/getWellNamePerMultiTip.ts

@@ -1,86 +0,0 @@
-import range from 'lodash/range'
-import { get96Channel384WellPlateWells } from './get96Channel384WellPlateWells'
-import { getLabwareHasQuirk, orderWells, sortWells } from './index'
-import type { LabwareDefinition2 } from '../types'
-
-// TODO Ian 2018-03-13 pull pipette offsets/positions from some pipette definitions data
-const OFFSET_8_CHANNEL = 9 // offset in mm between tips
-
-const MULTICHANNEL_TIP_SPAN = OFFSET_8_CHANNEL * (8 - 1) // length in mm from first to last tip of multichannel
-
-export function findWellAt(
-  labwareDef: LabwareDefinition2,
-  x: number,
-  y: number
-): string | null | undefined {
-  return Object.keys(labwareDef.wells)
-    .sort(sortWells)
-    .find((wellName: string) => {
-      const well = labwareDef.wells[wellName]
-
-      if (well.shape === 'circular') {
-        return (
-          Math.sqrt(Math.pow(x - well.x, 2) + Math.pow(y - well.y, 2)) <
-          well.diameter / 2
-        )
-      }
-
-      // Not circular, must be a rectangular well
-      // For rectangular wells, (x, y) is at the center.
-      return (
-        Math.abs(x - well.x) < well.xDimension / 2 &&
-        Math.abs(y - well.y) < well.yDimension / 2
-      )
-    })
-}
-
-// "topWellName" means well at the "top" of the column we're accessing: usually A row, or B row for 384-format
-export function getWellNamePerMultiTip(
-  labwareDef: LabwareDefinition2,
-  topWellName: string,
-  channels: 8 | 96
-): string[] | null {
-  const topWell = labwareDef.wells[topWellName]
-  if (!topWell) {
-    console.warn(
-      `well "${topWellName}" does not exist in labware ${labwareDef?.namespace}/${labwareDef?.parameters?.loadName}, cannot getWellNamePerMultiTip`
-    )
-    return null
-  }
-
-  const { x, y } = topWell
-  let offsetYTipPositions: number[] = range(0, 8).map(
-    tipNo => y - tipNo * OFFSET_8_CHANNEL
-  )
-  const orderedWells = orderWells(labwareDef.ordering, 't2b', 'l2r')
-
-  if (getLabwareHasQuirk(labwareDef, 'centerMultichannelOnWells')) {
-    // move multichannel up in Y by half the pipette's tip span to center it in the well
-    offsetYTipPositions = offsetYTipPositions.map(
-      tipPosY => tipPosY + MULTICHANNEL_TIP_SPAN / 2
-    )
-  }
-  // Return null for containers with any undefined wells
-  const wellsAccessed = offsetYTipPositions.reduce(
-    (acc: string[] | null, tipPosY) => {
-      const wellForTip = findWellAt(labwareDef, x, tipPosY)
-      if (acc === null || !wellForTip) {
-        return null
-      }
-      return acc.concat(wellForTip)
-    },
-    []
-  )
-
-  let ninetySixChannelWells = orderedWells
-  //  special casing 384 well plates to be every other well
-  //  both on the x and y ases.
-  if (orderedWells.length === 384) {
-    ninetySixChannelWells = get96Channel384WellPlateWells(
-      orderedWells,
-      topWellName
-    )
-  }
-
-  return channels === 8 ? wellsAccessed : ninetySixChannelWells
-}

package/js/helpers/getWellTotalVolume.ts

@@ -1,16 +0,0 @@
-import type { LabwareDefinition2 } from '../types'
-export const getWellTotalVolume = (
-  labwareDef: LabwareDefinition2,
-  wellName: string
-): number | null | undefined => {
-  const well = labwareDef.wells[wellName]
-
-  if (!well) {
-    console.warn(
-      `No well "${wellName}" found for labware ${labwareDef?.namespace}/${labwareDef?.parameters?.loadName}/${labwareDef?.version}"`
-    )
-    return null
-  }
-
-  return well.totalLiquidVolume
-}

package/js/helpers/index.ts

@@ -1,347 +0,0 @@
-import assert from 'assert'
-import uniq from 'lodash/uniq'
-
-import { OPENTRONS_LABWARE_NAMESPACE } from '../constants'
-import standardOt2DeckDef from '../../deck/definitions/4/ot2_standard.json'
-import standardFlexDeckDef from '../../deck/definitions/4/ot3_standard.json'
-import type {
-  DeckDefinition,
-  LabwareDefinition2,
-  ModuleModel,
-  RobotType,
-  ThermalAdapterName,
-} from '../types'
-
-export { getWellNamePerMultiTip } from './getWellNamePerMultiTip'
-export { getWellTotalVolume } from './getWellTotalVolume'
-export { wellIsRect } from './wellIsRect'
-export { orderWells } from './orderWells'
-export { get96Channel384WellPlateWells } from './get96Channel384WellPlateWells'
-
-export * from './parseProtocolData'
-export * from './volume'
-export * from './wellSets'
-export * from './getModuleVizDims'
-export * from './getVectorDifference'
-export * from './getVectorSum'
-export * from './getLoadedLabwareDefinitionsByUri'
-export * from './getOccludedSlotCountForModule'
-export * from './labwareInference'
-export * from './getAddressableAreasInProtocol'
-
-export const getLabwareDefIsStandard = (def: LabwareDefinition2): boolean =>
-  def?.namespace === OPENTRONS_LABWARE_NAMESPACE
-
-export const getLabwareDefURI = (def: LabwareDefinition2): string =>
-  constructLabwareDefURI(
-    def.namespace,
-    def.parameters.loadName,
-    String(def.version)
-  )
-
-export const constructLabwareDefURI = (
-  namespace: string,
-  loadName: string,
-  version: string
-): string => `${namespace}/${loadName}/${version}`
-
-// Load names of "retired" labware
-// TODO(mc, 2019-12-3): how should this correspond to LABWAREV2_DO_NOT_LIST?
-// see shared-data/js/getLabware.js
-const RETIRED_LABWARE = [
-  'geb_96_tiprack_10ul',
-  'geb_96_tiprack_1000ul',
-  'opentrons_1_trash_850ml_fixed',
-  'opentrons_10_tuberack_falcon_4x50ml_6x15ml_conical_acrylic',
-  'opentrons_24_tuberack_eppendorf_2ml_safelock_snapcap_acrylic',
-  'opentrons_24_tuberack_generic_0.75ml_snapcap_acrylic',
-  'opentrons_40_aluminumblock_eppendorf_24x2ml_safelock_snapcap_generic_16x0.2ml_pcr_strip',
-  'opentrons_96_aluminumblock_biorad_wellplate_200ul',
-  'tipone_96_tiprack_200ul',
-  'eppendorf_96_tiprack_1000ul_eptips',
-  'eppendorf_96_tiprack_10ul_eptips',
-  // Replaced by opentrons_96_wellplate_200ul_pcr_full_skirt
-  // https://opentrons.atlassian.net/browse/RLAB-230
-  'armadillo_96_wellplate_200ul_pcr_full_skirt',
-]
-
-export const getLabwareDisplayName = (
-  labwareDef: LabwareDefinition2
-): string => {
-  const { displayName } = labwareDef.metadata
-
-  if (
-    getLabwareDefIsStandard(labwareDef) &&
-    RETIRED_LABWARE.includes(labwareDef.parameters.loadName)
-  ) {
-    return `(Retired) ${displayName}`
-  }
-
-  return displayName
-}
-
-export const getTiprackVolume = (labwareDef: LabwareDefinition2): number => {
-  assert(
-    labwareDef.parameters.isTiprack,
-    `getTiprackVolume expected a tiprack labware ${getLabwareDefURI(
-      labwareDef
-    )}, but 'isTiprack' isn't true`
-  )
-  // NOTE: Ian 2019-04-16 assuming all tips are the same volume across the rack
-  const volume = labwareDef.wells.A1.totalLiquidVolume
-  assert(
-    volume >= 0,
-    `getTiprackVolume expected tip volume to be at least 0, got ${volume}`
-  )
-  return volume
-}
-
-export function getLabwareHasQuirk(
-  labwareDef: LabwareDefinition2,
-  quirk: string
-): boolean {
-  const quirks = labwareDef.parameters.quirks
-  return quirks ? quirks.includes(quirk) : false
-}
-
-export const intToAlphabetLetter = (
-  i: number,
-  lowerCase: boolean = false
-): string => String.fromCharCode((lowerCase ? 96 : 65) + i)
-// These utils are great candidates for unit tests
-export const toWellName = ({
-  rowNum,
-  colNum,
-}: {
-  rowNum: number
-  colNum: number
-}): string => String.fromCharCode(rowNum + 65) + (colNum + 1)
-
-function _parseWell(well: string): [string, number] {
-  const res = well.match(/([A-Z]+)(\d+)/)
-  const letters = res && res[1]
-  const number = res && parseInt(res[2])
-
-  if (!letters || number == null || Number.isNaN(number)) {
-    console.warn(
-      `Could not parse well ${well}. Got letters: "${
-        letters || 'void'
-      }", number: "${number || 'void'}"`
-    )
-    return ['', NaN]
-  }
-
-  return [letters, number]
-}
-
-/** A compareFunction for sorting an array of well names
- * Goes down the columns (A1 to H1 on 96 plate)
- * Then L to R across rows (1 to 12 on 96 plate)
- */
-export function sortWells(a: string, b: string): number {
-  const [letterA, numberA] = _parseWell(a)
-
-  const [letterB, numberB] = _parseWell(b)
-
-  if (numberA !== numberB) {
-    return numberA > numberB ? 1 : -1
-  }
-
-  if (letterA.length !== letterB.length) {
-    // Eg 'B' vs 'AA'
-    return letterA.length > letterB.length ? 1 : -1
-  }
-
-  return letterA > letterB ? 1 : -1
-}
-
-export function splitWellsOnColumn(sortedArray: string[]): string[][] {
-  return sortedArray.reduce<string[][]>((acc, curr) => {
-    const lastColumn = acc.slice(-1)
-
-    if (lastColumn === undefined || lastColumn.length === 0) {
-      return [[curr]]
-    }
-
-    const lastEle = lastColumn[0].slice(-1)[0].slice(1)
-
-    if (Number(curr.slice(1)) > Number(lastEle)) {
-      return [...acc, [curr]]
-    } else {
-      return [...acc.slice(0, -1), [...lastColumn[0], curr]]
-    }
-  }, [])
-}
-
-export const getWellDepth = (
-  labwareDef: LabwareDefinition2,
-  well: string
-): number => labwareDef.wells[well].depth
-
-// NOTE: this is used in PD for converting "offset from top" to "mm from bottom".
-// Assumes all wells have same offset because multi-offset not yet supported.
-// TODO: Ian 2019-07-13 return {[string: well]: offset} to support multi-offset
-export const getWellsDepth = (
-  labwareDef: LabwareDefinition2,
-  wells: string[]
-): number => {
-  const offsets = wells.map(well => getWellDepth(labwareDef, well))
-
-  if (uniq(offsets).length !== 1) {
-    console.warn(
-      `expected wells ${JSON.stringify(
-        wells
-      )} to all have same offset, but they were different. Labware def is ${getLabwareDefURI(
-        labwareDef
-      )}`
-    )
-  }
-
-  return offsets[0]
-}
-
-export const getSlotHasMatingSurfaceUnitVector = (
-  deckDef: DeckDefinition,
-  addressableAreaName: string
-): boolean => {
-  const matingSurfaceUnitVector = deckDef.locations.addressableAreas.find(
-    aa => aa.id === addressableAreaName
-  )?.matingSurfaceUnitVector
-
-  return Boolean(matingSurfaceUnitVector)
-}
-
-export const getAreSlotsHorizontallyAdjacent = (
-  slotNameA?: string | null,
-  slotNameB?: string | null
-): boolean => {
-  if (slotNameA == null || slotNameB == null) {
-    return false
-  }
-  const slotANumber = parseInt(slotNameA)
-  const slotBNumber = parseInt(slotNameB)
-  if (isNaN(slotBNumber) || isNaN(slotANumber)) {
-    return false
-  }
-  const orderedSlots = standardOt2DeckDef.locations.cutouts
-  // intentionally not substracting by 1 because trash (slot 12) should not count
-  const numSlots = orderedSlots.length
-  if (slotBNumber > numSlots || slotANumber > numSlots) {
-    return false
-  }
-  const slotWidth = orderedSlots[1].position[0] - orderedSlots[0].position[0]
-  const slotAPosition = orderedSlots[slotANumber - 1].position
-  const slotBPosition = orderedSlots[slotBNumber - 1].position
-
-  const yPositionSlotA = slotAPosition[1]
-  const yPositionSlotB = slotBPosition[1]
-
-  const xPositionSlotA = slotAPosition[0]
-  const xPositionSlotB = slotBPosition[0]
-
-  const areSlotsHorizontallyAdjacent =
-    yPositionSlotA === yPositionSlotB &&
-    Math.abs(xPositionSlotA - xPositionSlotB) === slotWidth
-
-  return areSlotsHorizontallyAdjacent
-}
-export const getAreSlotsVerticallyAdjacent = (
-  slotNameA?: string | null,
-  slotNameB?: string | null
-): boolean => {
-  if (slotNameA == null || slotNameB == null) {
-    return false
-  }
-  const slotANumber = parseInt(slotNameA)
-  const slotBNumber = parseInt(slotNameB)
-
-  if (isNaN(slotBNumber) || isNaN(slotANumber)) {
-    return false
-  }
-  const orderedSlots = standardOt2DeckDef.locations.cutouts
-  // intentionally not substracting by 1 because trash (slot 12) should not count
-  const numSlots = orderedSlots.length
-
-  if (slotBNumber > numSlots || slotANumber > numSlots) {
-    return false
-  }
-  // take the y coord of slot 4, and subtact from y coord of slot 1
-  const slotHeight = orderedSlots[3].position[1] - orderedSlots[0].position[1]
-  const slotAPosition = orderedSlots[slotANumber - 1].position
-  const slotBPosition = orderedSlots[slotBNumber - 1].position
-
-  const yPositionSlotA = slotAPosition[1]
-  const yPositionSlotB = slotBPosition[1]
-
-  const xPositionSlotA = slotAPosition[0]
-  const xPositionSlotB = slotBPosition[0]
-
-  const areSlotsVerticallyAdjacent =
-    xPositionSlotA === xPositionSlotB &&
-    Math.abs(yPositionSlotA - yPositionSlotB) === slotHeight
-
-  return areSlotsVerticallyAdjacent
-}
-//  TODO(jr, 11/12/23): rename this utility to mention that it
-//  is only used in the OT-2, same with getAreSlotsHorizontallyAdjacent
-//  and getAreSlotsVerticallyAdjacent
-export const getAreSlotsAdjacent = (
-  slotNameA?: string | null,
-  slotNameB?: string | null
-): boolean =>
-  getAreSlotsHorizontallyAdjacent(slotNameA, slotNameB) ||
-  getAreSlotsVerticallyAdjacent(slotNameA, slotNameB)
-
-export const getIsLabwareAboveHeight = (
-  labwareDef: LabwareDefinition2,
-  height: number
-): boolean => labwareDef.dimensions.zDimension > height
-
-export const getAdapterName = (labwareLoadname: string): ThermalAdapterName => {
-  let adapterName: ThermalAdapterName = 'Universal Flat Adapter'
-
-  if (
-    labwareLoadname ===
-    'opentrons_96_pcr_adapter_nest_wellplate_100ul_pcr_full_skirt'
-  ) {
-    adapterName = 'PCR Adapter'
-  } else if (
-    labwareLoadname === 'opentrons_96_deep_well_adapter_nest_wellplate_2ml_deep'
-  ) {
-    adapterName = 'Deep Well Adapter'
-  } else if (
-    labwareLoadname ===
-    'opentrons_96_flat_bottom_adapter_nest_wellplate_200ul_flat'
-  ) {
-    adapterName = '96 Flat Bottom Adapter'
-  }
-
-  return adapterName
-}
-
-export const getCalibrationAdapterLoadName = (
-  moduleModel: ModuleModel
-): string | null => {
-  switch (moduleModel) {
-    case 'heaterShakerModuleV1':
-      return 'opentrons_calibration_adapter_heatershaker_module'
-    case 'temperatureModuleV2':
-      return 'opentrons_calibration_adapter_temperature_module'
-    case 'thermocyclerModuleV2':
-      return 'opentrons_calibration_adapter_thermocycler_module'
-    default:
-      console.error(
-        `${moduleModel} does not have an associated calibration adapter`
-      )
-      return null
-  }
-}
-
-export const getDeckDefFromRobotType = (
-  robotType: RobotType
-): DeckDefinition => {
-  // @ts-expect-error imported JSON not playing nice with TS. see https://github.com/microsoft/TypeScript/issues/32063
-  return robotType === 'OT-3 Standard'
-    ? standardFlexDeckDef
-    : standardOt2DeckDef
-}

package/js/helpers/labwareInference.ts

@@ -1,92 +0,0 @@
-import isEqual from 'lodash/isEqual'
-import uniqWith from 'lodash/uniqWith'
-import round from 'lodash/round'
-import sortedUniq from 'lodash/sortedUniq'
-import uniq from 'lodash/uniq'
-import type {
-  LabwareWell,
-  LabwareWellShapeProperties,
-  LabwareDefinition2,
-  LabwareWellGroupMetadata,
-  LabwareBrand,
-} from '../types'
-
-export interface LabwareWellGroupProperties {
-  xOffsetFromLeft: number
-  yOffsetFromTop: number
-  xSpacing: number | null
-  ySpacing: number | null
-  wellCount: number
-  shape: LabwareWellShapeProperties | null
-  depth: number | null
-  totalLiquidVolume: number | null
-  metadata: LabwareWellGroupMetadata
-  brand: LabwareBrand | null
-}
-const ROUNDING_PRECISION = 2
-
-export function getUniqueWellProperties(
-  definition: LabwareDefinition2
-): LabwareWellGroupProperties[] {
-  const { groups, wells, dimensions } = definition
-
-  return groups.map(group => {
-    const wellProps = group.wells.map(n => wells[n])
-
-    const wellDepths = wellProps.map<number>(w => w.depth)
-    const wellVolumes = wellProps.map<number>(w => w.totalLiquidVolume)
-    const wellShapes = wellProps.map<LabwareWellShapeProperties>(
-      (well: LabwareWell) =>
-        well.shape === 'circular'
-          ? { shape: well.shape, diameter: well.diameter }
-          : {
-              shape: well.shape,
-              xDimension: well.xDimension,
-              yDimension: well.yDimension,
-            }
-    )
-
-    const xStart = wellProps[0]?.x ?? 0
-    const yStart = wellProps[0]?.y ?? 0
-
-    return {
-      metadata: group.metadata,
-      brand: group.brand || null,
-      xSpacing: getSpacingIfUniform(wellProps, 'x'),
-      ySpacing: getSpacingIfUniform(wellProps, 'y'),
-      xOffsetFromLeft: xStart,
-      yOffsetFromTop: round(dimensions.yDimension - yStart, ROUNDING_PRECISION),
-      wellCount: wellProps.length,
-      depth: getIfConsistent(wellDepths),
-      totalLiquidVolume: getIfConsistent(wellVolumes),
-      shape: getIfConsistent(wellShapes),
-    }
-  })
-}
-
-export function getIfConsistent<T>(items: T[]): T | null {
-  return uniqWith(items, isEqual).length === 1 ? items[0] : null
-}
-
-// returning null means "spacing is irregular"; returning 0 means "there is only 1 well along the given axis"
-export function getSpacingIfUniform(
-  wells: LabwareWell[],
-  axis: 'x' | 'y'
-): number | null {
-  const wellPositions = sortedUniq(uniq(wells.map(well => well[axis])))
-  if (wellPositions.length < 2) return 0
-
-  const initialSpacing = round(
-    wellPositions[1] - wellPositions[0],
-    ROUNDING_PRECISION
-  )
-
-  for (let i = 2; i < wellPositions.length; i++) {
-    const pos = wellPositions[i]
-    const prevWellPos = wellPositions[i - 1]
-    const spacing = round(pos - prevWellPos, ROUNDING_PRECISION)
-    if (spacing !== initialSpacing) return null
-  }
-
-  return Math.abs(initialSpacing)
-}

package/js/helpers/orderWells.ts

@@ -1,69 +0,0 @@
-import zipWith from 'lodash/zipWith'
-import uniq from 'lodash/uniq'
-import compact from 'lodash/compact'
-import flatten from 'lodash/flatten'
-
-export type WellOrderOption = 'l2r' | 'r2l' | 't2b' | 'b2t'
-
-// labware definitions in shared-data have an ordering
-// attribute which is an Array of Arrays of wells. Each inner
-// Array represents a physical column of wells on the labware
-// this function takes that 2d Array of columns and returns
-// the same wells in a 2d Array where each inner Array represents
-// a physical row of wells on the labware.
-// e.g.
-// [                      \       [
-//   ['A1', 'B1'],     === \        ['A1', 'A2']
-//   ['A2', 'B2']      === /        ['B1', 'B2']
-// ]                      /       ]
-//
-const _orderingColsToRows = (ordering: string[][]): string[][] =>
-  zipWith(...ordering, (...col) => compact(uniq(col)))
-
-// given a default "ordering" 2d array from labware definitions
-// where each inner array represents a physical column of wells
-// and well order option selections (e.g. 'l2r', 'r2l', 't2b', 'b2t')
-// this function returns a 1d array of wells from the labware
-// ordered by the given traversal technique
-export const orderWells = (
-  defaultOrdering: string[][],
-  first: WellOrderOption,
-  second: WellOrderOption
-): string[] => {
-  let orderedWells: string[][] = []
-
-  if (first === 't2b') {
-    if (second === 'l2r') {
-      orderedWells = defaultOrdering
-    } else if (second === 'r2l') {
-      orderedWells = defaultOrdering.slice().reverse()
-    }
-  } else if (first === 'b2t') {
-    if (second === 'l2r') {
-      orderedWells = defaultOrdering.map(col => col.slice().reverse())
-    } else if (second === 'r2l') {
-      orderedWells = defaultOrdering
-        .slice()
-        .reverse()
-        .map(col => col.slice().reverse())
-    }
-  } else if (first === 'l2r') {
-    if (second === 't2b') {
-      orderedWells = _orderingColsToRows(defaultOrdering)
-    } else if (second === 'b2t') {
-      orderedWells = _orderingColsToRows(defaultOrdering).slice().reverse()
-    }
-  } else if (first === 'r2l') {
-    if (second === 't2b') {
-      orderedWells = _orderingColsToRows(defaultOrdering).map(col =>
-        col.slice().reverse()
-      )
-    } else if (second === 'b2t') {
-      orderedWells = _orderingColsToRows(defaultOrdering)
-        .slice()
-        .reverse()
-        .map(col => col.slice().reverse())
-    }
-  }
-  return flatten(orderedWells)
-}