address pr comments

api/src/opentrons/protocol_api/_parameter_context.py

@@ -19,7 +19,7 @@
 from opentrons.protocol_engine.types import (
     RunTimeParameter,
     PrimitiveRunTimeParamValuesType,
-    CsvRunTimeParamFilesType,
+    CSVRunTimeParamFilesType,
     FileInfo,
 )
 
@@ -218,7 +218,7 @@ def set_parameters(
                 parameter.value = validated_value
 
     def initialize_csv_files(
-        self, run_time_param_file_overrides: CsvRunTimeParamFilesType
+        self, run_time_param_file_overrides: CSVRunTimeParamFilesType
     ) -> None:
         """Initializes the files for CSV parameters.
 

api/src/opentrons/protocol_engine/types.py

@@ -1068,4 +1068,4 @@ class CSVParameter(RTPBase):
     StrictStr, Union[StrictInt, StrictFloat, StrictBool, StrictStr]
 ]  # update value types as more RTP types are added
 
-CsvRunTimeParamFilesType = Mapping[StrictStr, StrictStr]
+CSVRunTimeParamFilesType = Mapping[StrictStr, StrictStr]

api/src/opentrons/protocol_runner/protocol_runner.py

@@ -44,7 +44,7 @@
     DeckConfigurationType,
     RunTimeParameter,
     PrimitiveRunTimeParamValuesType,
-    CsvRunTimeParamFilesType,
+    CSVRunTimeParamFilesType,
 )
 from ..protocols.types import PythonProtocol
 
@@ -186,7 +186,7 @@ async def load(
         protocol_source: ProtocolSource,
         python_parse_mode: PythonParseMode,
         run_time_param_values: Optional[PrimitiveRunTimeParamValuesType],
-        run_time_param_files: Optional[CsvRunTimeParamFilesType],
+        run_time_param_files: Optional[CSVRunTimeParamFilesType],
     ) -> None:
         """Load a Python or JSONv5(& older) ProtocolSource into managed ProtocolEngine."""
         labware_definitions = await protocol_reader.extract_labware_definitions(
@@ -254,7 +254,7 @@ async def run(  # noqa: D102
         deck_configuration: DeckConfigurationType,
         protocol_source: Optional[ProtocolSource] = None,
         run_time_param_values: Optional[PrimitiveRunTimeParamValuesType] = None,
-        run_time_param_files: Optional[CsvRunTimeParamFilesType] = None,
+        run_time_param_files: Optional[CSVRunTimeParamFilesType] = None,
         python_parse_mode: PythonParseMode = PythonParseMode.NORMAL,
     ) -> RunResult:
         # TODO(mc, 2022-01-11): move load to runner creation, remove from `run`

api/src/opentrons/protocol_runner/python_protocol_wrappers.py

@@ -15,7 +15,7 @@
 from opentrons.protocol_engine import ProtocolEngine
 from opentrons.protocol_engine.types import (
     PrimitiveRunTimeParamValuesType,
-    CsvRunTimeParamFilesType,
+    CSVRunTimeParamFilesType,
 )
 from opentrons.protocol_reader import ProtocolSource, ProtocolFileRole
 from opentrons.util.broker import Broker
@@ -165,7 +165,7 @@ def extract_run_parameters(
         protocol: PythonProtocol,
         parameter_context: ParameterContext,
         run_time_param_overrides: Optional[PrimitiveRunTimeParamValuesType],
-        run_time_param_file_overrides: Optional[CsvRunTimeParamFilesType],
+        run_time_param_file_overrides: Optional[CSVRunTimeParamFilesType],
     ) -> Optional[Parameters]:
         """Extract the parameters defined in the protocol, overridden with values for the run."""
         return exec_add_parameters(

api/src/opentrons/protocol_runner/run_orchestrator.py

@@ -32,7 +32,7 @@
     DeckConfigurationType,
     RunTimeParameter,
     PrimitiveRunTimeParamValuesType,
-    CsvRunTimeParamFilesType,
+    CSVRunTimeParamFilesType,
 )
 from ..protocol_reader import JsonProtocolConfig, PythonProtocolConfig, ProtocolSource
 from ..protocols.parse import PythonParseMode
@@ -325,7 +325,7 @@ async def load(
         self,
         protocol_source: ProtocolSource,
         run_time_param_values: Optional[PrimitiveRunTimeParamValuesType],
-        run_time_param_files: Optional[CsvRunTimeParamFilesType],
+        run_time_param_files: Optional[CSVRunTimeParamFilesType],
         parse_mode: ParseMode,
     ) -> None:
         """Load a json/python protocol."""

api/src/opentrons/protocols/execution/execute_python.py

@@ -12,7 +12,7 @@
 from opentrons.protocols.types import PythonProtocol, MalformedPythonProtocolError
 from opentrons.protocol_engine.types import (
     PrimitiveRunTimeParamValuesType,
-    CsvRunTimeParamFilesType,
+    CSVRunTimeParamFilesType,
 )
 
 
@@ -71,7 +71,7 @@ def _raise_pretty_protocol_error(exception: Exception, filename: str) -> None:
 def _parse_and_set_parameters(
     parameter_context: ParameterContext,
     run_time_param_overrides: Optional[PrimitiveRunTimeParamValuesType],
-    run_time_param_file_overrides: Optional[CsvRunTimeParamFilesType],
+    run_time_param_file_overrides: Optional[CSVRunTimeParamFilesType],
     new_globs: Dict[Any, Any],
     filename: str,
 ) -> Parameters:
@@ -111,7 +111,7 @@ def exec_add_parameters(
     protocol: PythonProtocol,
     parameter_context: ParameterContext,
     run_time_param_overrides: Optional[PrimitiveRunTimeParamValuesType],
-    run_time_param_file_overrides: Optional[CsvRunTimeParamFilesType],
+    run_time_param_file_overrides: Optional[CSVRunTimeParamFilesType],
 ) -> Optional[Parameters]:
     """Exec the add_parameters function and get the final run time parameters with overrides."""
     new_globs: Dict[Any, Any] = {}

robot-server/robot_server/protocols/analyses_manager.py

@@ -5,7 +5,7 @@
 
 from opentrons.protocol_engine.types import (
     PrimitiveRunTimeParamValuesType,
-    CsvRunTimeParamFilesType,
+    CSVRunTimeParamFilesType,
 )
 from opentrons.protocol_engine.errors import ErrorOccurrence
 
@@ -40,7 +40,7 @@ async def initialize_analyzer(
         analysis_id: str,
         protocol_resource: ProtocolResource,
         run_time_param_values: Optional[PrimitiveRunTimeParamValuesType],
-        run_time_param_files: Optional[CsvRunTimeParamFilesType],
+        run_time_param_files: Optional[CSVRunTimeParamFilesType],
     ) -> protocol_analyzer.ProtocolAnalyzer:
         """Initialize the protocol analyzer with protocol resource and run time parameter values & fileIds.
 

robot-server/robot_server/protocols/analysis_models.py

@@ -5,7 +5,7 @@
 from opentrons.protocol_engine.types import (
     RunTimeParameter,
     PrimitiveRunTimeParamValuesType,
-    CsvRunTimeParamFilesType,
+    CSVRunTimeParamFilesType,
 )
 from opentrons_shared_data.robot.dev_types import RobotType
 from pydantic import BaseModel, Field
@@ -56,7 +56,7 @@ class AnalysisRequest(BaseModel):
         default={},
         description="Key-value pairs of primitive run-time parameters defined in a protocol.",
     )
-    runTimeParameterFiles: CsvRunTimeParamFilesType = Field(
+    runTimeParameterFiles: CSVRunTimeParamFilesType = Field(
         default={},
         description="Key-fileId pairs of CSV run-time parameters defined in a protocol.",
     )

robot-server/robot_server/protocols/completed_analysis_store.py

@@ -299,7 +299,7 @@ def get_csv_rtps_by_analysis_id(
         with self._sql_engine.begin() as transaction:
             results = transaction.execute(statement).all()
 
-        csv_rtps: Dict[str, Union[str, None]] = {}
+        csv_rtps: Dict[str, Optional[str]] = {}
         for row in results:
             param = CsvParameterResource.from_sql_row(row)
             csv_rtps.update({param.parameter_variable_name: param.file_id})
@@ -349,7 +349,6 @@ async def make_room_and_add(
         with self._sql_engine.begin() as transaction:
             transaction.execute(delete_primitive_rtp_statement)
             transaction.execute(delete_csv_rtp_statement)
-            transaction.execute(delete_csv_rtp_statement)
             transaction.execute(delete_statement)
             transaction.execute(insert_statement)
             for param in primitive_rtp_resources:

robot-server/robot_server/protocols/protocol_analyzer.py

@@ -10,7 +10,7 @@
 from opentrons.protocol_engine.types import (
     PrimitiveRunTimeParamValuesType,
     RunTimeParameter,
-    CsvRunTimeParamFilesType,
+    CSVRunTimeParamFilesType,
 )
 import opentrons.util.helpers as datetime_helper
 from opentrons.protocol_runner import (
@@ -53,7 +53,7 @@ def get_verified_run_time_parameters(self) -> List[RunTimeParameter]:
     async def load_orchestrator(
         self,
         run_time_param_values: Optional[PrimitiveRunTimeParamValuesType],
-        run_time_param_files: Optional[CsvRunTimeParamFilesType],
+        run_time_param_files: Optional[CSVRunTimeParamFilesType],
     ) -> None:
         """Load runner with the protocol and run time parameter values.
 

robot-server/robot_server/protocols/router.py

@@ -9,7 +9,7 @@
 
 from opentrons.protocol_engine.types import (
     PrimitiveRunTimeParamValuesType,
-    CsvRunTimeParamFilesType,
+    CSVRunTimeParamFilesType,
 )
 from opentrons_shared_data.robot import user_facing_robot_type
 from opentrons.util.performance_helpers import TrackingFunctions
@@ -434,7 +434,7 @@ async def _start_new_analysis_if_necessary(
     analysis_id: str,
     force_analyze: bool,
     rtp_values: PrimitiveRunTimeParamValuesType,
-    rtp_files: CsvRunTimeParamFilesType,
+    rtp_files: CSVRunTimeParamFilesType,
     protocol_resource: ProtocolResource,
     analysis_store: AnalysisStore,
     analyses_manager: AnalysesManager,

robot-server/robot_server/protocols/rtp_resources.py

@@ -4,7 +4,7 @@
 import sqlalchemy
 
 from dataclasses import dataclass
-from typing import Dict, Callable, Union
+from typing import Dict, Callable, Union, Optional
 
 from opentrons.protocols.parameters.types import PrimitiveAllowedTypes
 
@@ -74,7 +74,7 @@ class CsvParameterResource:
 
     analysis_id: str
     parameter_variable_name: str
-    file_id: Union[str, None]
+    file_id: Optional[str]
 
     def to_sql_values(self) -> Dict[str, object]:
         """Return this data as a dict that can be passed to an SQLAlchemy insert."""

robot-server/tests/protocols/test_protocols_router.py

@@ -12,7 +12,7 @@
     PrimitiveRunTimeParamValuesType,
     NumberParameter,
     CSVParameter,
-    CsvRunTimeParamFilesType,
+    CSVRunTimeParamFilesType,
     FileInfo,
 )
 from opentrons.protocols.api_support.types import APIVersion
@@ -1654,7 +1654,7 @@ async def test_update_protocol_analyses_with_new_rtp_values(
         "dry_run": True,
         "mount": "left",
     }
-    rtp_files: CsvRunTimeParamFilesType = {
+    rtp_files: CSVRunTimeParamFilesType = {
         "csv_param": "file-id",
     }
     protocol_source = ProtocolSource(