Merge branch 'chore_release-8.0.0' into EXEC-504-get-error-list-route

api/src/opentrons/cli/analyze.py

@@ -248,7 +248,7 @@ async def _do_analyze(protocol_source: ProtocolSource) -> RunResult:
             protocol_source=protocol_source,
             parse_mode=ParseMode.NORMAL,
             run_time_param_values=None,
-            run_time_param_files=None,
+            run_time_param_paths=None,
         )
     except Exception as error:
         err_id = "analysis-setup-error"

api/src/opentrons/protocol_api/__init__.py

@@ -12,6 +12,7 @@
 from opentrons.protocols.parameters.exceptions import (
     RuntimeParameterRequired as RuntimeParameterRequiredError,
 )
+from opentrons.protocols.parameters.types import CSVParameter
 
 from .protocol_context import ProtocolContext
 from .deck import Deck
@@ -74,6 +75,7 @@
     "ALL",
     "OFF_DECK",
     "RuntimeParameterRequiredError",
+    "CSVParameter",
     # For internal Opentrons use only:
     "create_protocol_context",
     "ProtocolEngineCoreRequiredError",

api/src/opentrons/protocol_api/_parameter_context.py

@@ -1,5 +1,5 @@
 """Parameter context for python protocols."""
-
+import tempfile
 from typing import List, Optional, Union, Dict
 
 from opentrons.protocols.api_support.types import APIVersion
@@ -19,7 +19,7 @@
 from opentrons.protocol_engine.types import (
     RunTimeParameter,
     PrimitiveRunTimeParamValuesType,
-    CSVRunTimeParamFilesType,
+    CSVRuntimeParamPaths,
     FileInfo,
 )
 
@@ -218,15 +218,15 @@ def set_parameters(
                 parameter.value = validated_value
 
     def initialize_csv_files(
-        self, run_time_param_file_overrides: CSVRunTimeParamFilesType
+        self, run_time_param_file_overrides: CSVRuntimeParamPaths
     ) -> None:
         """Initializes the files for CSV parameters.
 
         :meta private:
 
         This is intended for Opentrons internal use only and is not a guaranteed API.
         """
-        for variable_name, file_id in run_time_param_file_overrides.items():
+        for variable_name, file_path in run_time_param_file_overrides.items():
             try:
                 parameter = self._parameters[variable_name]
             except KeyError:
@@ -240,11 +240,41 @@ def initialize_csv_files(
                     f"File Id was provided for the parameter '{variable_name}',"
                     f" but '{variable_name}' is not a CSV parameter."
                 )
+            # TODO(jbl 2024-08-02) This file opening should be moved elsewhere to provide more flexibility with files
+            #    that may be opened as non-text or non-UTF-8
+            # The parent folder in the path will be the file ID, so we can use that to resolve that here
+            file_id = file_path.parent.name
+            file_name = file_path.name
+
+            # Read the contents of the actual file
+            with file_path.open() as csv_file:
+                contents = csv_file.read()
+
+            # Open a temporary file with write permissions and write contents to that
+            temporary_file = tempfile.NamedTemporaryFile("r+")
+            temporary_file.write(contents)
+            temporary_file.flush()
+
+            # Open a new file handler for the temporary file with read-only permissions and close the other
+            parameter_file = open(temporary_file.name, "r")
+            temporary_file.close()
+
+            parameter.file_info = FileInfo(id=file_id, name=file_name)
+            parameter.value = parameter_file
+
+    def close_csv_files(self) -> None:
+        """Close all file handlers for CSV parameters.
 
-            parameter.file_info = FileInfo(id=file_id, name="")
-            # TODO (spp, 2024-07-16): set the file name and assign the file as parameter.value.
-            #  Most likely, we will be creating a temporary file copy of the original
-            #  to pass onto the protocol context
+        :meta private:
+
+        This is intended for Opentrons internal use only and is not a guaranteed API.
+        """
+        for parameter in self._parameters.values():
+            if (
+                isinstance(parameter, csv_parameter_definition.CSVParameterDefinition)
+                and parameter.value is not None
+            ):
+                parameter.value.close()
 
     def export_parameters_for_analysis(self) -> List[RunTimeParameter]:
         """Exports all parameters into a protocol engine models for reporting in analysis.