feat(shared-data, app, protocol-designer, api-client, api, robot-serv…

…er): schemaV7 migration (#13007) closes RAUT-515 and RAUT-272 and RQA-1128 --------- Co-authored-by: TamarZanzouri <[email protected]>
Opentrons · Jul 26, 2023 · 9f29c9d · 9f29c9d
1 parent a87555f
commit 9f29c9d
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diff --git a/api-client/src/maintenance_runs/createMaintenanceCommand.ts b/api-client/src/maintenance_runs/createMaintenanceCommand.ts
@@ -1,6 +1,6 @@
 import { POST, request } from '../request'
 
-import type { CreateCommand } from '@opentrons/shared-data/protocol/types/schemaV6'
+import type { CreateCommand } from '@opentrons/shared-data/protocol/types/schemaV7'
 import type { ResponsePromise } from '../request'
 import type { HostConfig } from '../types'
 import type { CommandData, CreateCommandParams } from '../runs/types'

diff --git a/api-client/src/protocols/utils.ts b/api-client/src/protocols/utils.ts
@@ -11,13 +11,13 @@ import type {
   LoadedLabware,
   LoadedModule,
 } from '@opentrons/shared-data'
-import type { RunTimeCommand } from '@opentrons/shared-data/protocol/types/schemaV6'
+import type { RunTimeCommand } from '@opentrons/shared-data/protocol/types/schemaV7'
 import type {
   LoadLabwareRunTimeCommand,
   LoadModuleRunTimeCommand,
   LoadPipetteRunTimeCommand,
   LoadLiquidRunTimeCommand,
-} from '@opentrons/shared-data/protocol/types/schemaV6/command/setup'
+} from '@opentrons/shared-data/protocol/types/schemaV7/command/setup'
 
 interface PipetteNamesByMount {
   left: PipetteName | null

diff --git a/api-client/src/runs/commands/createCommand.ts b/api-client/src/runs/commands/createCommand.ts
@@ -4,7 +4,7 @@ import type { ResponsePromise } from '../../request'
 import type { HostConfig } from '../../types'
 import type { CommandData } from '../types'
 import type { CreateCommandParams } from './types'
-import type { CreateCommand } from '@opentrons/shared-data/protocol/types/schemaV6'
+import type { CreateCommand } from '@opentrons/shared-data/protocol/types/schemaV7'
 
 export function createCommand(
   config: HostConfig,

diff --git a/api-client/src/runs/commands/createLiveCommand.ts b/api-client/src/runs/commands/createLiveCommand.ts
@@ -4,7 +4,7 @@ import type { ResponsePromise } from '../../request'
 import type { HostConfig } from '../../types'
 import type { CommandData } from '../types'
 import type { CreateCommandParams } from './types'
-import type { CreateCommand } from '@opentrons/shared-data/protocol/types/schemaV6'
+import type { CreateCommand } from '@opentrons/shared-data/protocol/types/schemaV7'
 
 export function createLiveCommand(
   config: HostConfig,

diff --git a/api/src/opentrons/protocol_reader/file_format_validator.py b/api/src/opentrons/protocol_reader/file_format_validator.py
@@ -7,7 +7,10 @@
 from pydantic import ValidationError as PydanticValidationError
 
 from opentrons_shared_data.labware.labware_definition import LabwareDefinition
-from opentrons_shared_data.protocol.models import ProtocolSchemaV6 as JsonProtocolV6
+from opentrons_shared_data.protocol.models import (
+    ProtocolSchemaV6 as JsonProtocolV6,
+    ProtocolSchemaV7 as JsonProtocolV7,
+)
 
 from opentrons.protocols.models import JsonProtocol as JsonProtocolUpToV5
 
@@ -57,7 +60,9 @@ def validate_sync() -> None:
 async def _validate_json_protocol(info: IdentifiedJsonMain) -> None:
     def validate_sync() -> None:
         try:
-            if info.schema_version == 6:
+            if info.schema_version == 7:
+                JsonProtocolV7.parse_obj(info.unvalidated_json)
+            elif info.schema_version == 6:
                 JsonProtocolV6.parse_obj(info.unvalidated_json)
             else:
                 JsonProtocolUpToV5.parse_obj(info.unvalidated_json)

diff --git a/api/src/opentrons/protocol_runner/json_file_reader.py b/api/src/opentrons/protocol_runner/json_file_reader.py
@@ -1,13 +1,23 @@
 """JSON file reading."""
+from typing import Union
 
 from opentrons_shared_data.protocol.models.protocol_schema_v6 import ProtocolSchemaV6
-from opentrons.protocol_reader import ProtocolSource
+from opentrons_shared_data.protocol.models.protocol_schema_v7 import ProtocolSchemaV7
+from opentrons.protocol_reader import ProtocolSource, JsonProtocolConfig
 
 
 class JsonFileReader:
     """Reads and parses JSON protocol files."""
 
     @staticmethod
-    def read(protocol_source: ProtocolSource) -> ProtocolSchemaV6:
+    def read(
+        protocol_source: ProtocolSource,
+    ) -> Union[ProtocolSchemaV6, ProtocolSchemaV7]:
         """Read and parse file into a JsonProtocol model."""
-        return ProtocolSchemaV6.parse_file(protocol_source.main_file)
+        if (
+            isinstance(protocol_source.config, JsonProtocolConfig)
+            and protocol_source.config.schema_version == 6
+        ):
+            return ProtocolSchemaV6.parse_file(protocol_source.main_file)
+        else:
+            return ProtocolSchemaV7.parse_file(protocol_source.main_file)
diff --git a/api/src/opentrons/protocol_runner/json_translator.py b/api/src/opentrons/protocol_runner/json_translator.py
@@ -1,9 +1,14 @@
 """Translation of JSON protocol commands into ProtocolEngine commands."""
-from typing import cast, List
+from typing import cast, List, Union
 from pydantic import parse_obj_as
 
 from opentrons_shared_data.pipette.dev_types import PipetteNameType
-from opentrons_shared_data.protocol.models import ProtocolSchemaV6, protocol_schema_v6
+from opentrons_shared_data.protocol.models import (
+    ProtocolSchemaV6,
+    protocol_schema_v6,
+    ProtocolSchemaV7,
+    protocol_schema_v7,
+)
 
 from opentrons.types import MountType
 from opentrons.protocol_engine import (
@@ -23,7 +28,8 @@ class CommandTranslatorError(Exception):
 
 
 def _translate_labware_command(
-    protocol: ProtocolSchemaV6, command: protocol_schema_v6.Command
+    protocol: ProtocolSchemaV6,
+    command: protocol_schema_v6.Command,
 ) -> pe_commands.LoadLabwareCreate:
     labware_id = command.params.labwareId
     # v6 data model supports all commands and therefor most props are optional.
@@ -49,8 +55,38 @@ def _translate_labware_command(
     return labware_command
 
 
+def _translate_v7_labware_command(
+    command: protocol_schema_v7.Command,
+) -> pe_commands.LoadLabwareCreate:
+    labware_id = command.params.labwareId
+    # v7 data model supports all commands and therefor most props are optional.
+    # load labware command must contain labware_id and definition_id.
+    assert labware_id is not None
+    assert command.params.version is not None
+    assert command.params.namespace is not None
+    assert command.params.loadName is not None
+
+    labware_command = pe_commands.LoadLabwareCreate(
+        params=pe_commands.LoadLabwareParams(
+            labwareId=command.params.labwareId,
+            displayName=command.params.displayName,
+            version=command.params.version,
+            namespace=command.params.namespace,
+            loadName=command.params.loadName,
+            location=parse_obj_as(
+                # https://github.com/samuelcolvin/pydantic/issues/1847
+                LabwareLocation,  # type: ignore[arg-type]
+                command.params.location,
+            ),
+        ),
+        key=command.key,
+    )
+    return labware_command
+
+
 def _translate_module_command(
-    protocol: ProtocolSchemaV6, command: protocol_schema_v6.Command
+    protocol: ProtocolSchemaV6,
+    command: protocol_schema_v6.Command,
 ) -> pe_commands.CommandCreate:
     module_id = command.params.moduleId
     modules = protocol.modules
@@ -69,8 +105,28 @@ def _translate_module_command(
     return translated_obj
 
 
+def _translate_v7_module_command(
+    command: protocol_schema_v7.Command,
+) -> pe_commands.CommandCreate:
+    module_id = command.params.moduleId
+    # v7 data model supports all commands and therefor most props are optional.
+    # load module command must contain module_id. modules cannot be None.
+    assert module_id is not None
+    assert command.params.model is not None
+    translated_obj = pe_commands.LoadModuleCreate(
+        params=pe_commands.LoadModuleParams(
+            model=ModuleModel(command.params.model),
+            location=DeckSlotLocation.parse_obj(command.params.location),
+            moduleId=command.params.moduleId,
+        ),
+        key=command.key,
+    )
+    return translated_obj
+
+
 def _translate_pipette_command(
-    protocol: ProtocolSchemaV6, command: protocol_schema_v6.Command
+    protocol: ProtocolSchemaV6,
+    command: protocol_schema_v6.Command,
 ) -> pe_commands.CommandCreate:
     pipette_id = command.params.pipetteId
     # v6 data model supports all commands and therefor most props are optional.
@@ -87,8 +143,27 @@ def _translate_pipette_command(
     return translated_obj
 
 
+def _translate_v7_pipette_command(
+    command: protocol_schema_v7.Command,
+) -> pe_commands.CommandCreate:
+    pipette_id = command.params.pipetteId
+    # v7 data model supports all commands and therefor most props are optional.
+    # load pipette command must contain pipette_id.
+    assert pipette_id is not None
+    assert command.params.pipetteName is not None
+    translated_obj = pe_commands.LoadPipetteCreate(
+        params=pe_commands.LoadPipetteParams(
+            pipetteName=PipetteNameType(command.params.pipetteName),
+            mount=MountType(command.params.mount),
+            pipetteId=command.params.pipetteId,
+        ),
+        key=command.key,
+    )
+    return translated_obj
+
+
 def _translate_simple_command(
-    command: protocol_schema_v6.Command,
+    command: Union[protocol_schema_v6.Command, protocol_schema_v7.Command]
 ) -> pe_commands.CommandCreate:
     dict_command = command.dict(exclude_none=True)
 
@@ -113,7 +188,9 @@ def _translate_simple_command(
 class JsonTranslator:
     """Class that translates commands/liquids from PD/JSON to ProtocolEngine."""
 
-    def translate_liquids(self, protocol: ProtocolSchemaV6) -> List[Liquid]:
+    def translate_liquids(
+        self, protocol: Union[ProtocolSchemaV6, ProtocolSchemaV7]
+    ) -> List[Liquid]:
         """Takes json protocol v6 and translates liquids->protocol engine liquids."""
         protocol_liquids = protocol.liquids or {}
 
@@ -130,6 +207,16 @@ def translate_liquids(self, protocol: ProtocolSchemaV6) -> List[Liquid]:
         ]
 
     def translate_commands(
+        self,
+        protocol: Union[ProtocolSchemaV7, ProtocolSchemaV6],
+    ) -> List[pe_commands.CommandCreate]:
+        """Takes json protocol and translates commands->protocol engine commands."""
+        if isinstance(protocol, ProtocolSchemaV6):
+            return self._translate_v6_commands(protocol)
+        else:
+            return self._translate_v7_commands(protocol)
+
+    def _translate_v6_commands(
         self,
         protocol: ProtocolSchemaV6,
     ) -> List[pe_commands.CommandCreate]:
@@ -146,3 +233,14 @@ def translate_commands(
                 translated_obj = _translate_simple_command(command)
             commands_list.append(translated_obj)
         return commands_list
+
+    def _translate_v7_commands(
+        self,
+        protocol: Union[ProtocolSchemaV7],
+    ) -> List[pe_commands.CommandCreate]:
+        """Takes json protocol v7 and translates commands->protocol engine commands."""
+        commands_list: List[pe_commands.CommandCreate] = []
+        for command in protocol.commands:
+            translated_obj = _translate_simple_command(command)
+            commands_list.append(translated_obj)
+        return commands_list
diff --git a/api/tests/opentrons/protocol_reader/test_file_format_validator.py b/api/tests/opentrons/protocol_reader/test_file_format_validator.py
@@ -27,7 +27,7 @@
         (4, "protocol/fixtures/4/simpleV4.json"),
         (5, "protocol/fixtures/5/simpleV5.json"),
         (6, "protocol/fixtures/6/simpleV6.json"),
-        # todo(mm, 2022-12-22): Add simpleV7 when we support that in production.
+        (7, "protocol/fixtures/7/simpleV7.json"),
     ],
 )
 async def test_valid_json_main_file(
@@ -73,9 +73,8 @@ async def test_valid_python_main_file() -> None:
 
 
 @pytest.mark.parametrize(
-    # todo(mm, 2022-12-22): Add v7+ when we support that in production.
     "identified_schema_version",
-    range(3, 7),
+    range(3, 8),
 )
 async def test_invalid_json_main(identified_schema_version: int) -> None:
     """It should raise when non-conforming JSON is provided as a main file."""

diff --git a/api/tests/opentrons/protocol_reader/test_file_identifier.py b/api/tests/opentrons/protocol_reader/test_file_identifier.py
@@ -157,7 +157,19 @@ class _ValidJsonProtocolSpec:
     "spec",
     [
         # Basic JSON protocols of various versions:
-        # todo(mm, 2022-12-22): Add a v7 protocol when we support that in production.
+        _ValidJsonProtocolSpec(
+            file_name="foo.json",
+            contents=load_shared_data("protocol/fixtures/7/simpleV7.json"),
+            expected_schema_version=7,
+            expected_robot_type="OT-2 Standard",
+            expected_metadata={
+                "protocolName": "Simple test protocol",
+                "author": "engineering <[email protected]>",
+                "description": "A short test protocol",
+                "created": 1223131231,
+                "tags": ["unitTest"],
+            },
+        ),
         _ValidJsonProtocolSpec(
             file_name="foo.json",
             contents=load_shared_data("protocol/fixtures/6/simpleV6.json"),