feat(protocol-designer): save v3 protocols (#3588)

Closes #3336 and closes #3414

- change command creators to match v3 protocol schema
- deep refactor of test fixtures, too many hard-coded strings etc, to allow testing flow rates and offsets somewhat sanely
- remove vestigal `defaultValues` access in APIv1 executor for JSON v3 protocols
- minor changes to v3 protocol schema
- for consolidate and transfer, make touch tip happen after the destination well's inner mix, do not touch tip between the dispense and the inner mix
- redo shared-data schemaV1/schemaV3 imports - `import {NameOfType} from '@opentrons/shared-data/path/to/schemaV3` vs `import {NameOfTypeV3} from '@opentrons/shared-data'`

api/src/opentrons/protocols/execute_v3.py

@@ -29,7 +29,7 @@ def load_labware(protocol_data):
     for labware_id, props in data.items():
         slot = props['slot']
         definition_id = props['definitionId']
-        definition = defs[definition_id]
+        definition = defs.get(definition_id)
         if not definition:
             raise RuntimeError(
                 'No definition under def id {}'.format(definition_id))
@@ -52,7 +52,7 @@ def load_labware(protocol_data):
     return loaded_labware
 
 
-def _get_location(loaded_labware, command_type, params, default_values):
+def _get_location(loaded_labware, command_type, params):
     labwareId = params.get('labware')
     if not labwareId:
         # not all commands use labware param
@@ -64,23 +64,10 @@ def _get_location(loaded_labware, command_type, params, default_values):
             'Command tried to use labware "{}", but that ID does not exist ' +
             'in protocol\'s "labware" section'.format(labwareId))
 
-    # default offset from bottom for aspirate/dispense commands
-    offset_default = default_values.get(
-        '{}MmFromBottom'.format(command_type))
-
-    # optional command-specific value, fallback to default
-    offset_from_bottom = params.get(
-        'offsetFromBottomMm', offset_default)
+    offset_from_bottom = params.get('offsetFromBottomMm')
 
     if offset_from_bottom is None:
-        # not all commands use offsets
-
-        # touch-tip uses offset from top, not bottom, as default
-        # when offsetFromBottomMm command-specific value is unset
-        if command_type == 'touchTip':
-            return lw.wells(well).top(
-                z=default_values['touchTipMmFromTop'])
-
+        # not all commands use offsets (eg pick up tip / drop tip)
         return lw.wells(well)
 
     return lw.wells(well).bottom(offset_from_bottom)
@@ -94,41 +81,21 @@ def _get_pipette(command_params, loaded_pipettes):
 # TODO (Ian 2018-08-22) once Pipette has more sensible way of managing
 # flow rate value (eg as an argument in aspirate/dispense fns), remove this
 def _set_flow_rate(
-        pipette_name, pipette, command_type, params, default_values):
+        pipette_name, pipette, command_type, params):
     """
-    Set flow rate in uL/mm, to value obtained from command's params,
-    or if unspecified in command params, then from protocol's "defaultValues".
+    Set flow rate in uL/mm, to value obtained from command's params
     """
-    default_aspirate = default_values.get(
-        'aspirateFlowRate', {}).get(pipette_name)
-
-    default_dispense = default_values.get(
-        'dispenseFlowRate', {}).get(pipette_name)
-
     flow_rate_param = params.get('flowRate')
 
-    if flow_rate_param is not None:
-        if command_type == 'aspirate':
-            pipette.set_flow_rate(
-                aspirate=flow_rate_param,
-                dispense=default_dispense)
-            return
-        if command_type == 'dispense':
-            pipette.set_flow_rate(
-                aspirate=default_aspirate,
-                dispense=flow_rate_param)
-            return
-
     pipette.set_flow_rate(
-        aspirate=default_aspirate,
-        dispense=default_dispense
-    )
+        aspirate=flow_rate_param,
+        dispense=flow_rate_param)
+    return
 
 
 # C901 code complexity is due to long elif block, ok in this case (Ian+Ben)
 def dispatch_commands(protocol_data, loaded_pipettes, loaded_labware):  # noqa: C901 E501
     commands = protocol_data['commands']
-    default_values = protocol_data.get('defaultValues', {})
 
     for command_item in commands:
         command_type = command_item['command']
@@ -141,7 +108,7 @@ def dispatch_commands(protocol_data, loaded_pipettes, loaded_labware):  # noqa:
         pipette_name = protocol_pipette_data.get('name')
 
         location = _get_location(
-            loaded_labware, command_type, params, default_values)
+            loaded_labware, command_type, params)
         volume = params.get('volume')
 
         if pipette:
@@ -150,7 +117,7 @@ def dispatch_commands(protocol_data, loaded_pipettes, loaded_labware):  # noqa:
             # Flow rate is persisted inside the Pipette object
             # and is settable but not easily gettable
             _set_flow_rate(
-                pipette_name, pipette, command_type, params, default_values)
+                pipette_name, pipette, command_type, params)
 
         if command_type == 'delay':
             wait = params.get('wait')
@@ -188,8 +155,7 @@ def dispatch_commands(protocol_data, loaded_pipettes, loaded_labware):  # noqa:
             (well_object, loc_tuple) = location
 
             # Use the offset baked into the well_object.
-            # Do not allow API to apply its v_offset kwarg default value,
-            # and do not apply the JSON protocol's default offset.
+            # Do not allow API to apply its v_offset kwarg default value
             z_from_bottom = loc_tuple[2]
             offset_from_top = (
                 well_object.properties['depth'] - z_from_bottom) * -1

api/tests/opentrons/protocols/test_execute_v3.py

@@ -32,10 +32,6 @@ def test_get_location():
     plate = labware.load("96-flat", 1)
     well = "B2"
 
-    default_values = {
-        'aspirateMmFromBottom': 2
-    }
-
     loaded_labware = {
         "someLabwareId": plate
     }
@@ -48,20 +44,9 @@ def test_get_location():
             "offsetFromBottomMm": offset
         }
         result = execute_v3._get_location(
-            loaded_labware, command_type, command_params, default_values)
+            loaded_labware, command_type, command_params)
         assert result == plate.well(well).bottom(offset)
 
-    command_params = {
-        "labware": "someLabwareId",
-        "well": well
-    }
-
-    # no command-specific offset, use default
-    result = execute_v3._get_location(
-        loaded_labware, command_type, command_params, default_values)
-    assert result == plate.well(well).bottom(
-        default_values['aspirateMmFromBottom'])
-
 
 def test_load_labware(get_labware_fixture):
     robot.reset()
@@ -148,6 +133,9 @@ def mock_set_flow_rate(aspirate, dispense):
     monkeypatch.setattr(pipette, 'set_flow_rate', mock_set_flow_rate)
     monkeypatch.setattr(execute_v3, '_sleep', mock_sleep)
 
+    aspirateOffset = 12.1
+    dispenseOffset = 12.2
+
     protocol_data = {
         "defaultValues": {
             "aspirateFlowRate": {
@@ -171,7 +159,8 @@ def mock_set_flow_rate(aspirate, dispense):
                     "labware": "sourcePlateId",
                     "well": "A1",
                     "volume": 5,
-                    "flowRate": 123
+                    "flowRate": 123,
+                    "offsetFromBottomMm": aspirateOffset
                 }
             },
             {
@@ -186,7 +175,9 @@ def mock_set_flow_rate(aspirate, dispense):
                     "pipette": "pipetteId",
                     "labware": "destPlateId",
                     "well": "B1",
-                    "volume": 4.5
+                    "volume": 4.5,
+                    "flowRate": 3.5,
+                    "offsetFromBottomMm": dispenseOffset
                 }
             },
         ]
@@ -196,12 +187,12 @@ def mock_set_flow_rate(aspirate, dispense):
         protocol_data, loaded_pipettes, loaded_labware)
 
     assert cmd == [
-        ("aspirate", 5, source_plate['A1']),
+        ("aspirate", 5, source_plate['A1'].bottom(aspirateOffset)),
         ("sleep", 42),
-        ("dispense", 4.5, dest_plate['B1'])
+        ("dispense", 4.5, dest_plate['B1'].bottom(dispenseOffset))
     ]
 
     assert flow_rates == [
-        (123, 102),
-        (101, 102)
+        (123, 123),
+        (3.5, 3.5)
     ]

app/src/protocol/types.js

@@ -1,9 +1,7 @@
 // @flow
 // protocol type defs
-import type {
-  SchemaV1ProtocolFile,
-  SchemaV3ProtocolFile,
-} from '@opentrons/shared-data'
+import type { ProtocolFile as SchemaV1ProtocolFile } from '@opentrons/shared-data/protocol/flowTypes/schemaV1'
+import type { ProtocolFile as SchemaV3ProtocolFile } from '@opentrons/shared-data/protocol/flowTypes/schemaV3'
 
 // data may be a full JSON protocol or just a metadata dict from Python
 export type ProtocolData =

protocol-designer/src/components/FileSidebar/ConnectedFileSidebar.js

@@ -33,7 +33,7 @@ export default connect<Props, {||}, SP, {||}, _, _>(
 
 function mapStateToProps(state: BaseState): SP {
   const protocolName =
-    fileDataSelectors.getFileMetadata(state)['protocol-name'] || 'untitled'
+    fileDataSelectors.getFileMetadata(state).protocolName || 'untitled'
   const fileData = fileDataSelectors.createFile(state)
   const canDownload = selectors.getCurrentPage(state) !== 'file-splash'
 

protocol-designer/src/components/StepEditForm/fields/TipPosition/TipPositionModal.js

@@ -34,7 +34,7 @@ const DECIMALS_ALLOWED = 1
 
 type OP = {|
   mmFromBottom: number,
-  wellHeightMM: number,
+  wellDepthMm: number,
   isOpen: boolean,
   closeModal: () => mixed,
   fieldName: TipOffsetFields,
@@ -57,7 +57,7 @@ class TipPositionModal extends React.Component<Props, State> {
     this.state = { value: initialValue }
   }
   componentDidUpdate(prevProps: Props) {
-    if (prevProps.wellHeightMM !== this.props.wellHeightMM) {
+    if (prevProps.wellDepthMm !== this.props.wellDepthMm) {
       this.setState({ value: roundValue(this.props.mmFromBottom) })
     }
   }
@@ -67,21 +67,21 @@ class TipPositionModal extends React.Component<Props, State> {
     this.props.closeModal()
   }
   getDefaultMmFromBottom = (): number => {
-    const { fieldName, wellHeightMM } = this.props
-    return utils.getDefaultMmFromBottom({ fieldName, wellHeightMM })
+    const { fieldName, wellDepthMm } = this.props
+    return utils.getDefaultMmFromBottom({ fieldName, wellDepthMm })
   }
   getMinMaxMmFromBottom = (): {
     maxMmFromBottom: number,
     minMmFromBottom: number,
   } => {
     if (getIsTouchTipField(this.props.fieldName)) {
       return {
-        maxMmFromBottom: roundValue(this.props.wellHeightMM),
-        minMmFromBottom: roundValue(this.props.wellHeightMM / 2),
+        maxMmFromBottom: roundValue(this.props.wellDepthMm),
+        minMmFromBottom: roundValue(this.props.wellDepthMm / 2),
       }
     }
     return {
-      maxMmFromBottom: roundValue(this.props.wellHeightMM * 2),
+      maxMmFromBottom: roundValue(this.props.wellDepthMm * 2),
       minMmFromBottom: 0,
     }
   }
@@ -139,7 +139,7 @@ class TipPositionModal extends React.Component<Props, State> {
   render() {
     if (!this.props.isOpen) return null
     const { value } = this.state
-    const { fieldName, wellHeightMM } = this.props
+    const { fieldName, wellDepthMm } = this.props
     const { maxMmFromBottom, minMmFromBottom } = this.getMinMaxMmFromBottom()
 
     return (
@@ -209,7 +209,7 @@ class TipPositionModal extends React.Component<Props, State> {
                     mmFromBottom={
                       value != null ? value : this.getDefaultMmFromBottom()
                     }
-                    wellHeightMM={wellHeightMM}
+                    wellDepthMm={wellDepthMm}
                   />
                 </div>
               </div>

protocol-designer/src/components/StepEditForm/fields/TipPosition/TipPositionZAxisViz.js

@@ -11,15 +11,15 @@ const WELL_HEIGHT_PIXELS = 48
 const PIXEL_DECIMALS = 2
 type Props = {
   mmFromBottom: number,
-  wellHeightMM: number,
+  wellDepthMm: number,
 }
 
 const TipPositionZAxisViz = (props: Props) => {
-  const fractionOfWellHeight = props.mmFromBottom / props.wellHeightMM
+  const fractionOfWellHeight = props.mmFromBottom / props.wellDepthMm
   const pixelsFromBottom =
     Number(fractionOfWellHeight) * WELL_HEIGHT_PIXELS - WELL_HEIGHT_PIXELS
   const roundedPixelsFromBottom = round(pixelsFromBottom, PIXEL_DECIMALS)
-  const bottomPx = props.wellHeightMM
+  const bottomPx = props.wellDepthMm
     ? roundedPixelsFromBottom
     : props.mmFromBottom - WELL_HEIGHT_PIXELS
   return (
@@ -29,8 +29,8 @@ const TipPositionZAxisViz = (props: Props) => {
         className={styles.pipette_tip_image}
         style={{ bottom: `${bottomPx}px` }}
       />
-      {props.wellHeightMM !== null && (
-        <span className={styles.well_height_label}>{props.wellHeightMM}mm</span>
+      {props.wellDepthMm !== null && (
+        <span className={styles.well_height_label}>{props.wellDepthMm}mm</span>
       )}
       <img
         src={WELL_CROSS_SECTION_IMAGE}

protocol-designer/src/components/StepEditForm/fields/TipPosition/index.js

@@ -2,6 +2,7 @@
 import * as React from 'react'
 import { connect } from 'react-redux'
 import { HoverTooltip, FormGroup, InputField } from '@opentrons/components'
+import { getWellsDepth } from '@opentrons/shared-data'
 import i18n from '../../../../localization'
 import { selectors as stepFormSelectors } from '../../../../step-forms'
 import { getDisabledFields } from '../../../../steplist/formLevel'
@@ -32,7 +33,7 @@ type OP = {| fieldName: TipOffsetFields, className?: string |}
 type SP = {|
   disabled: boolean,
   mmFromBottom: ?string,
-  wellHeightMM: ?number,
+  wellDepthMm: ?number,
 |}
 
 type Props = { ...OP, ...SP }
@@ -43,7 +44,7 @@ class TipPositionInput extends React.Component<Props, TipPositionInputState> {
   state: TipPositionInputState = { isModalOpen: false }
 
   handleOpen = () => {
-    if (this.props.wellHeightMM) {
+    if (this.props.wellDepthMm) {
       this.setState({ isModalOpen: true })
     }
   }
@@ -52,7 +53,7 @@ class TipPositionInput extends React.Component<Props, TipPositionInputState> {
   }
 
   render() {
-    const { disabled, fieldName, mmFromBottom, wellHeightMM } = this.props
+    const { disabled, fieldName, mmFromBottom, wellDepthMm } = this.props
     const isTouchTipField = getIsTouchTipField(this.props.fieldName)
 
     const Wrapper = ({ children, hoverTooltipHandlers }) =>
@@ -70,12 +71,12 @@ class TipPositionInput extends React.Component<Props, TipPositionInputState> {
       )
 
     let value = ''
-    if (wellHeightMM != null) {
+    if (wellDepthMm != null) {
       // show default value for field in parens if no mmFromBottom value is selected
       value =
         mmFromBottom != null
           ? mmFromBottom
-          : getDefaultMmFromBottom({ fieldName, wellHeightMM })
+          : getDefaultMmFromBottom({ fieldName, wellDepthMm })
     }
 
     return (
@@ -87,7 +88,7 @@ class TipPositionInput extends React.Component<Props, TipPositionInputState> {
             <TipPositionModal
               fieldName={fieldName}
               closeModal={this.handleClose}
-              wellHeightMM={wellHeightMM}
+              wellDepthMm={wellDepthMm}
               // $FlowFixMe: mmFromBottom is typed as a number in TipPositionModal
               mmFromBottom={mmFromBottom}
               isOpen={this.state.isModalOpen}
@@ -113,20 +114,20 @@ const mapSTP = (state: BaseState, ownProps: OP): SP => {
     ownProps.fieldName
   )
 
-  let wellHeightMM = null
+  let wellDepthMm = null
   const labwareId: ?string = rawForm && rawForm[labwareFieldName]
   if (labwareId != null) {
     const labwareDef = stepFormSelectors.getLabwareEntities(state)[labwareId]
       .def
 
     // NOTE: only taking depth of first well in labware def, UI not currently equipped for multiple depths
     const firstWell = labwareDef.wells['A1']
-    if (firstWell) wellHeightMM = firstWell.depth
+    if (firstWell) wellDepthMm = getWellsDepth(labwareDef, ['A1'])
   }
 
   return {
     disabled: rawForm ? getDisabledFields(rawForm).has(fieldName) : false,
-    wellHeightMM,
+    wellDepthMm,
     mmFromBottom: rawForm && rawForm[fieldName],
   }
 }