sapiopycommons 2025.9.8a730__py3-none-any.whl → 2025.9.9a736__py3-none-any.whl

sapiopycommons/ai/tool_service_base.py

@@ -1,975 +0,0 @@
-from __future__ import annotations
-
-import base64
-import io
-import json
-import logging
-import re
-import traceback
-from abc import abstractmethod, ABC
-from logging import Logger
-from typing import Any, Iterable, Sequence, Mapping
-
-from grpc import ServicerContext
-from sapiopylib.rest.User import SapioUser, ensure_logger_initialized
-from sapiopylib.rest.pojo.datatype.FieldDefinition import AbstractVeloxFieldDefinition
-
-from sapiopycommons.ai.protoapi.fielddefinitions.fields_pb2 import FieldValueMapPbo, FieldValuePbo
-from sapiopycommons.ai.protoapi.fielddefinitions.velox_field_def_pb2 import VeloxFieldDefPbo, FieldTypePbo, \
-    SelectionPropertiesPbo, IntegerPropertiesPbo, DoublePropertiesPbo, BooleanPropertiesPbo, StringPropertiesPbo
-from sapiopycommons.ai.protoapi.plan.item.item_container_pb2 import ContentTypePbo
-from sapiopycommons.ai.protoapi.plan.tool.entry_pb2 import StepOutputBatchPbo, StepItemContainerPbo, \
-    StepBinaryContainerPbo, StepCsvContainerPbo, StepCsvHeaderRowPbo, StepCsvRowPbo, StepJsonContainerPbo, \
-    StepTextContainerPbo, StepInputBatchPbo
-from sapiopycommons.ai.protoapi.plan.tool.tool_pb2 import ToolDetailsRequestPbo, ToolDetailsResponsePbo, \
-    ToolDetailsPbo, ProcessStepRequestPbo, ProcessStepResponsePbo, ToolOutputDetailsPbo, ToolIoConfigBasePbo, \
-    ToolInputDetailsPbo, ExampleContainerPbo, ProcessStepResponseStatusPbo
-from sapiopycommons.ai.protoapi.plan.tool.tool_pb2_grpc import ToolServiceServicer
-from sapiopycommons.ai.protoapi.session.sapio_conn_info_pb2 import SapioUserSecretTypePbo, SapioConnectionInfoPbo
-from sapiopycommons.ai.protobuf_utils import ProtobufUtils
-from sapiopycommons.ai.test_client import ContainerType
-from sapiopycommons.files.file_util import FileUtil
-from sapiopycommons.files.temp_files import TempFileHandler
-from sapiopycommons.general.aliases import FieldMap, FieldValue
-
-
-# FR-47422: Created classes.
-class SapioToolResult(ABC):
-    """
-    A class representing a result from a Sapio tool. Instantiate one of the subclasses to create a result object.
-    """
-
-    @abstractmethod
-    def to_proto(self) -> StepOutputBatchPbo | list[FieldValueMapPbo]:
-        """
-        Convert this SapioToolResult object to a StepOutputBatchPbo or list of FieldValueMapPbo proto objects.
-        """
-        pass
-
-
-class BinaryResult(SapioToolResult):
-    """
-    A class representing binary results from a Sapio tool.
-    """
-    binary_data: list[bytes]
-    content_type: str
-    file_extensions: list[str]
-    name: str
-
-    def __init__(self, binary_data: list[bytes], content_type: str = "binary", file_extensions: list[str] = None,
-                 name: str | None = None):
-        """
-        :param binary_data: The binary data as a list of bytes.
-        :param content_type: The content type of the data.
-        :param file_extensions: A list of file extensions that this binary data can be saved as.
-        :param name: An optional identifying name for this result that will be accessible to the next tool.
-        """
-        self.binary_data = binary_data
-        self.content_type = content_type
-        self.file_extensions = file_extensions if file_extensions else []
-        self.name = name
-
-    def to_proto(self) -> StepOutputBatchPbo | list[FieldValueMapPbo]:
-        return StepOutputBatchPbo(
-            item_container=StepItemContainerPbo(
-                content_type=ContentTypePbo(name=self.content_type, extensions=self.file_extensions),
-                container_name=self.name,
-                binary_container=StepBinaryContainerPbo(items=self.binary_data)
-            )
-        )
-
-
-class CsvResult(SapioToolResult):
-    """
-    A class representing CSV results from a Sapio tool.
-    """
-    csv_data: list[dict[str, Any]]
-    content_type: str
-    file_extensions: list[str]
-    name: str
-
-    def __init__(self, csv_data: list[dict[str, Any]], content_type: str = "csv", file_extensions: list[str] = None,
-                 name: str | None = None):
-        """
-        :param csv_data: The list of CSV data results, provided as a list of dictionaries of column name to value.
-        :param content_type: The content type of the data.
-        :param file_extensions: A list of file extensions that this binary data can be saved as.
-        :param name: An optional identifying name for this result that will be accessible to the next tool.
-        """
-        self.csv_data = csv_data
-        self.content_type = content_type
-        self.file_extensions = file_extensions if file_extensions else ["csv"]
-        self.name = name
-
-    def to_proto(self) -> StepOutputBatchPbo | list[FieldValueMapPbo]:
-        return StepOutputBatchPbo(
-            item_container=StepItemContainerPbo(
-                content_type=ContentTypePbo(name=self.content_type, extensions=self.file_extensions),
-                container_name=self.name,
-                csv_container=StepCsvContainerPbo(
-                    header=StepCsvHeaderRowPbo(cells=self.csv_data[0].keys()),
-                    items=[StepCsvRowPbo(cells=[str(x) for x in row.values()]) for row in self.csv_data]
-                )
-            ) if self.csv_data else None
-        )
-
-
-class FieldMapResult(SapioToolResult):
-    """
-    A class representing field map results from a Sapio tool.
-    """
-    field_maps: list[FieldMap]
-
-    def __init__(self, field_maps: list[FieldMap]):
-        """
-        :param field_maps: A list of field maps, where each map is a dictionary of field names to values. Each entry
-            will create a new data record in the system, so long as the tool definition specifies an output data type
-            name.
-        """
-        self.field_maps = field_maps
-
-    def to_proto(self) -> StepOutputBatchPbo | list[FieldValueMapPbo]:
-        new_records: list[FieldValueMapPbo] = []
-        for field_map in self.field_maps:
-            fields: dict[str, FieldValuePbo] = {}
-            for field, value in field_map.items():
-                field_value = FieldValuePbo()
-                if isinstance(value, str):
-                    field_value.string_value = value
-                elif isinstance(value, int):
-                    field_value.int_value = value
-                elif isinstance(value, float):
-                    field_value.double_value = value
-                elif isinstance(value, bool):
-                    field_value.bool_value = value
-                fields[field] = field_value
-            new_records.append(FieldValueMapPbo(fields=fields))
-        return new_records
-
-
-class JsonResult(SapioToolResult):
-    """
-    A class representing JSON results from a Sapio tool.
-    """
-    json_data: list[Any]
-    content_type: str
-    file_extensions: list[str]
-    name: str
-
-    def __init__(self, json_data: list[Any], content_type: str = "json", file_extensions: list[str] = None,
-                 name: str | None = None):
-        """
-        :param json_data: The list of JSON data results. Each entry in the list represents a separate JSON object.
-            These entries must be able to be serialized to JSON using json.dumps().
-        :param content_type: The content type of the data.
-        :param file_extensions: A list of file extensions that this binary data can be saved as.
-        :param name: An optional identifying name for this result that will be accessible to the next tool.
-        """
-        self.json_data = json_data
-        self.content_type = content_type
-        self.file_extensions = file_extensions if file_extensions else ["json"]
-        self.name = name
-
-    def to_proto(self) -> StepOutputBatchPbo | list[FieldValueMapPbo]:
-        return StepOutputBatchPbo(
-            item_container=StepItemContainerPbo(
-                content_type=ContentTypePbo(name=self.content_type, extensions=self.file_extensions),
-                container_name=self.name,
-                json_container=StepJsonContainerPbo(items=[json.dumps(x) for x in self.json_data])
-            )
-        )
-
-
-class TextResult(SapioToolResult):
-    """
-    A class representing text results from a Sapio tool.
-    """
-    text_data: list[str]
-    content_type: str
-    file_extensions: list[str]
-    name: str
-
-    def __init__(self, text_data: list[str], content_type: str = "text", file_extensions: list[str] = None,
-                 name: str | None = None):
-        """
-        :param text_data: The text data as a list of strings.
-        :param content_type: The content type of the data.
-        :param file_extensions: A list of file extensions that this binary data can be saved as.
-        :param name: An optional identifying name for this result that will be accessible to the next tool.
-        """
-        self.text_data = text_data
-        self.content_type = content_type
-        self.file_extensions = file_extensions if file_extensions else ["txt"]
-        self.name = name
-
-    def to_proto(self) -> StepOutputBatchPbo | list[FieldValueMapPbo]:
-        return StepOutputBatchPbo(
-            item_container=StepItemContainerPbo(
-                content_type=ContentTypePbo(name=self.content_type, extensions=self.file_extensions),
-                container_name=self.name,
-                text_container=StepTextContainerPbo(items=self.text_data)
-            )
-        )
-
-
-class ToolServiceBase(ToolServiceServicer, ABC):
-    """
-    A base class for implementing a tool service. Subclasses should implement the register_tools method to register
-    their tools with the service.
-    """
-    debug_mode: bool = False
-
-    def GetToolDetails(self, request: ToolDetailsRequestPbo, context: ServicerContext) -> ToolDetailsResponsePbo:
-        try:
-            # Get the tool details from the registered tools.
-            details: list[ToolDetailsPbo] = []
-            for tool in self.register_tools():
-                details.append(tool().to_pbo())
-            if not details:
-                raise Exception("No tools registered with this service.")
-            return ToolDetailsResponsePbo(tool_framework_version=self.tool_version(), tool_details=details)
-        except Exception as e:
-            # Woe to you if you somehow cause an exception to be raised when just initializing your tools.
-            # There's no way to log this.
-            print(f"CRITICAL ERROR: {e}")
-            print(traceback.format_exc())
-            return ToolDetailsResponsePbo()
-
-    def ProcessData(self, request: ProcessStepRequestPbo, context: ServicerContext) -> ProcessStepResponsePbo:
-        try:
-            # Convert the SapioConnectionInfo proto object to a SapioUser object.
-            user = self._create_user(request.sapio_user)
-            # Get the tool results from the registered tool matching the request.
-            success, msg, results, logs = self.run(user, request, context)
-            # Convert the results to protobuf objects.
-            output_data: list[StepOutputBatchPbo] = []
-            new_records: list[FieldValueMapPbo] = []
-            for result in results:
-                data: StepOutputBatchPbo | list[FieldValueMapPbo] = result.to_proto()
-                if isinstance(data, StepOutputBatchPbo):
-                    output_data.append(data)
-                else:
-                    new_records.extend(data)
-            # Return a ProcessStepResponse proto object containing the results to the caller.
-            status = ProcessStepResponseStatusPbo.SUCCESS if success else ProcessStepResponseStatusPbo.FAILURE
-            return ProcessStepResponsePbo(status=status, status_message=msg, output=output_data, log=logs,
-                                          new_records=new_records)
-        except Exception as e:
-            # This try/except should never be needed, as the tool should handle its own exceptions, but better safe
-            # than sorry.
-            print(f"CRITICAL ERROR: {e}")
-            print(traceback.format_exc())
-            return ProcessStepResponsePbo(status=ProcessStepResponseStatusPbo.FAILURE,
-                                          status_message=f"CRITICAL ERROR: {e}",
-                                          log=[traceback.format_exc()])
-
-    @staticmethod
-    def _create_user(info: SapioConnectionInfoPbo, timeout_seconds: int = 60) -> SapioUser:
-        """
-        Create a SapioUser object from the given SapioConnectionInfo proto object.
-
-        :param info: The SapioConnectionInfo proto object.
-        :param timeout_seconds: The request timeout for calls made from this user object.
-        """
-        user = SapioUser(info.webservice_url, True, timeout_seconds, guid=info.app_guid)
-        match info.secret_type:
-            case SapioUserSecretTypePbo.SESSION_TOKEN:
-                user.api_token = info.secret
-            case SapioUserSecretTypePbo.PASSWORD:
-                secret: str = info.secret
-                if secret.startswith("Basic "):
-                    secret = secret[6:]
-                credentials: list[str] = base64.b64decode(secret).decode().split(":", 1)
-                user.username = credentials[0]
-                user.password = credentials[1]
-            case _:
-                raise Exception(f"Unexpected secret type: {info.secret_type}")
-        return user
-
-    @staticmethod
-    def tool_version() -> int:
-        """
-        :return: The version of this set of tools.
-        """
-        return 1
-
-    @abstractmethod
-    def register_tools(self) -> list[type[ToolBase]]:
-        """
-        Register tool types with this service. Provided tools should implement the ToolBase class.
-
-        :return: A list of tools to register to this service.
-        """
-        pass
-
-    def run(self, user: SapioUser, request: ProcessStepRequestPbo, context: ServicerContext) \
-            -> tuple[bool, str, list[SapioToolResult], list[str]]:
-        """
-        Execute a tool from this service.
-
-        :param user: A user object that can be used to initialize manager classes using DataMgmtServer to query the
-            system.
-        :param request: The request object containing the input data.
-        :param context: The gRPC context.
-        :return: Whether or not the tool succeeded, the status message, the results of the tool, and any logs
-            generated by the tool.
-        """
-        # Locate the tool named in the request.
-        find_tool: str = request.tool_name
-        registered_tools: dict[str, type[ToolBase]] = {t.name(): t for t in self.register_tools()}
-        if find_tool not in registered_tools:
-            # If the tool is not found, list all of the registered tools for this service so that the LLM can correct
-            # the tool it is requesting.
-            all_tool_names: str = "\n".join(registered_tools.keys())
-            msg: str = (f"Tool \"{find_tool}\" not found in the registered tools for this service. The registered "
-                        f"tools for this service are: \n{all_tool_names}")
-            return False, msg, [], []
-
-        # Instantiate the tool class.
-        tool: ToolBase = registered_tools[find_tool]()
-        try:
-            # Setup the tool with details from the request.
-            tool.setup(user, request, context, self.debug_mode)
-            # Validate that the provided inputs match the tool's expected inputs.
-            if len(request.input) != len(tool.input_configs):
-                msg: str = (f"Expected {len(tool.input_configs)} inputs for this tool, but got {len(request.input)} "
-                            f"instead.")
-            else:
-                msg: str = tool.validate_input()
-            # If there is no error message, then the inputs are valid.
-            success: bool = not bool(msg)
-            # If this is a dry run, then provide the fixed dry run output.
-            # Otherwise, if the inputs were successfully validated, then the tool is executed normally.
-            results: list[SapioToolResult] = []
-            if request.dry_run:
-                results = tool.dry_run_output()
-            elif success:
-                results = tool.run(user)
-                # Update the status message to reflect the successful execution of the tool.
-                msg = f"{tool.name()} successfully completed."
-            return success, msg, results, tool.logs
-        except Exception as e:
-            tool.log_exception("Exception occurred during tool execution.", e)
-            return False, str(e), [], tool.logs
-        finally:
-            # Clean up any temporary files created by the tool. If in debug mode, then log the files instead
-            # so that they can be manually inspected.
-            if self.debug_mode:
-                print("Temporary files/directories created during tool execution:")
-                for directory in tool.temp_data.directories:
-                    print(f"\tDirectory: {directory}")
-                for file in tool.temp_data.files:
-                    print(f"\tFile: {file}")
-            else:
-                tool.temp_data.cleanup()
-
-
-class ToolBase(ABC):
-    """
-    A base class for implementing a tool.
-    """
-    _name: str
-    _description: str
-    _data_type_name: str | None
-    input_configs: list[ToolInputDetailsPbo]
-    _input_container_types: list[ContainerType]
-    output_configs: list[ToolOutputDetailsPbo]
-    _output_container_types: list[ContainerType]
-    config_fields: list[VeloxFieldDefPbo]
-
-    logs: list[str]
-    logger: Logger
-    verbose_logging: bool
-    debug_mode: bool
-
-    temp_data: TempFileHandler
-
-    user: SapioUser
-    request: ProcessStepRequestPbo
-    context: ServicerContext
-
-    @staticmethod
-    @abstractmethod
-    def name() -> str:
-        """
-        :return: The name of the tool. This should be unique across all tools in the service.
-        """
-        pass
-
-    @staticmethod
-    @abstractmethod
-    def description() -> str:
-        """
-        :return: A description of the tool.
-        """
-        pass
-
-    @staticmethod
-    def data_type_name() -> str | None:
-        """
-        :return: The name of the output data type of this tool, if applicable. When this tool returns
-            FieldMapResult objects in its run method, this name will be used to set the data type of the output data.
-        """
-        return None
-
-    def __init__(self):
-        self._name = self.name()
-        self._description = self.description()
-        self._data_type_name = self.data_type_name()
-        self.input_configs = []
-        self._input_container_types = []
-        self.output_configs = []
-        self._output_container_types = []
-        self.config_fields = []
-        self.temp_data = TempFileHandler()
-        self.logs = []
-        self.logger = logging.getLogger(f"ToolBase.{self._name}")
-        ensure_logger_initialized(self.logger)
-
-    def setup(self, user: SapioUser, request: ProcessStepRequestPbo, context: ServicerContext, debug_mode: bool) -> None:
-        """
-        Setup the tool with the user, request, and context. This method can be overridden by subclasses to perform
-        additional setup.
-
-        :param user: A user object that can be used to initialize manager classes using DataMgmtServer to query the
-            system.
-        :param request: The request object containing the input data.
-        :param context: The gRPC context.
-        :param debug_mode: If true, the tool should run in debug mode, providing additional logging and not cleaning
-            up temporary files.
-        """
-        self.user = user
-        self.request = request
-        self.context = context
-        self.verbose_logging = request.verbose_logging
-        self.debug_mode = debug_mode
-
-    def add_input(self, container_type: ContainerType, content_type: str, display_name: str, description: str,
-                  structure_example: str | bytes | None = None, validation: str | None = None,
-                  input_count: tuple[int, int] | None = None, is_paged: bool = False,
-                  page_size: tuple[int, int] | None = None, max_request_bytes: int | None = None) -> None:
-        """
-        Add an input configuration to the tool. This determines how many inputs this tool will accept in the plan
-        manager, as well as what those inputs are. The IO number of the input will be set to the current number of
-        inputs. That is, the first time this is called, the IO number will be 0, the second time it is called, the IO
-        number will be 1, and so on.
-
-        :param container_type: The container type of the input.
-        :param content_type: The content type of the input.
-        :param display_name: The display name of the input.
-        :param description: The description of the input.
-        :param structure_example: An optional example of the structure of the input, such as how the structure of a
-            JSON output may look. This does not need to be an entirely valid example, and should often be truncated for
-            brevity.
-        :param validation: An optional validation string for the input.
-        :param input_count: A tuple of the minimum and maximum number of inputs allowed for this tool.
-        :param is_paged: If true, this input will be paged. If false, this input will not be paged.
-        :param page_size: A tuple of the minimum and maximum page size for this tool. The input must be paged in order
-            for this to have an effect.
-        :param max_request_bytes: The maximum request size in bytes for this tool.
-        """
-        structure: ExampleContainerPbo | None = None
-        if isinstance(structure_example, str):
-            structure = ExampleContainerPbo(text_example=structure_example)
-        elif isinstance(structure_example, bytes):
-            structure = ExampleContainerPbo(binary_example=structure_example)
-        self.input_configs.append(ToolInputDetailsPbo(
-            base_config=ToolIoConfigBasePbo(
-                io_number=len(self.input_configs),
-                content_type=content_type,
-                display_name=display_name,
-                description=description,
-                structure_example=structure
-            ),
-            validation=validation,
-            min_input_count=input_count[0] if input_count else None,
-            max_input_count=input_count[1] if input_count else None,
-            paged=is_paged,
-            min_page_size=page_size[0] if page_size else None,
-            max_page_size=page_size[1] if page_size else None,
-            max_request_bytes=max_request_bytes,
-        ))
-        self._input_container_types.append(container_type)
-
-    def add_output(self, container_type: ContainerType, content_type: str, display_name: str, description: str,
-                   testing_example: str | bytes, structure_example: str | bytes | None = None) -> None:
-        """
-        Add an output configuration to the tool. This determines how many inputs this tool will accept in the plan
-        manager, as well as what those inputs are. The IO number of the output will be set to the current number of
-        outputs. That is, the first time this is called, the IO number will be 0, the second time it is called, the IO
-        number will be 1, and so on.
-
-        :param container_type: The container type of the output.
-        :param content_type: The content type of the output.
-        :param display_name: The display name of the output.
-        :param description: The description of the output.
-        :param testing_example: An example of the input to be used when testing this tool in the system. This must be
-            an entirely valid example of what an output of this tool could look like so that it can be properly used
-            to run tests with. The provided example may be a string, such as for representing JSON or CSV outputs,
-            or bytes, such as for representing binary outputs like images or files.
-        :param structure_example: An optional example of the structure of the input, such as how the structure of a
-            JSON output may look. This does not need to be an entirely valid example, and should often be truncated for
-            brevity.
-        """
-        testing: ExampleContainerPbo | None = None
-        if isinstance(testing_example, str):
-            testing = ExampleContainerPbo(text_example=testing_example)
-        elif isinstance(testing_example, bytes):
-            testing = ExampleContainerPbo(binary_example=testing_example)
-
-        structure: ExampleContainerPbo | None = None
-        if isinstance(structure_example, str):
-            structure = ExampleContainerPbo(text_example=structure_example)
-        elif isinstance(structure_example, bytes):
-            structure = ExampleContainerPbo(binary_example=structure_example)
-
-        self.output_configs.append(ToolOutputDetailsPbo(
-            base_config=ToolIoConfigBasePbo(
-                io_number=len(self.output_configs),
-                content_type=content_type,
-                display_name=display_name,
-                description=description,
-                structure_example=structure,
-                testing_example=testing
-            )))
-        self._output_container_types.append(container_type)
-
-    def add_config_field(self, field: VeloxFieldDefPbo) -> None:
-        """
-        Add a configuration field to the tool. This field will be used to configure the tool in the plan manager.
-
-        :param field: The configuration field details.
-        """
-        self.config_fields.append(field)
-
-    def add_config_field_def(self, field: AbstractVeloxFieldDefinition) -> None:
-        """
-        Add a configuration field to the tool. This field will be used to configure the tool in the plan manager.
-
-        :param field: The configuration field details.
-        """
-        self.config_fields.append(ProtobufUtils.field_def_to_pbo(field))
-
-    def add_boolean_config_field(self, field_name: str, display_name: str, description: str,
-                                 default_value: bool | None = None, optional: bool = False) -> None:
-        """
-        Add a boolean configuration field to the tool. This field will be used to configure the tool in the plan
-        manager.
-
-        :param field_name: The name of the field.
-        :param display_name: The display name of the field.
-        :param description: The description of the field.
-        :param default_value: The default value of the field.
-        :param optional: If true, this field is optional. If false, this field is required.
-        """
-        self.config_fields.append(VeloxFieldDefPbo(
-            data_field_type=FieldTypePbo.BOOLEAN,
-            data_field_name=field_name,
-            display_name=display_name,
-            description=description,
-            required=not optional,
-            editable=True,
-            boolean_properties=BooleanPropertiesPbo(
-                default_value=default_value
-            )
-        ))
-
-    def add_double_config_field(self, field_name: str, display_name: str, description: str,
-                                default_value: float | None = None, min_value: float = -10.**120,
-                                max_value: float = 10.**120, precision: int = 2, optional: bool = False) -> None:
-        """
-        Add a double configuration field to the tool. This field will be used to configure the tool in the plan
-        manager.
-
-        :param field_name: The name of the field.
-        :param display_name: The display name of the field.
-        :param description: The description of the field.
-        :param default_value: The default value of the field.
-        :param min_value: The minimum value of the field.
-        :param max_value: The maximum value of the field.
-        :param precision: The precision of the field.
-        :param optional: If true, this field is optional. If false, this field is required.
-        """
-        self.config_fields.append(VeloxFieldDefPbo(
-            data_field_type=FieldTypePbo.DOUBLE,
-            data_field_name=field_name,
-            display_name=display_name,
-            description=description,
-            required=not optional,
-            editable=True,
-            double_properties=DoublePropertiesPbo(
-                default_value=default_value,
-                min_value=min_value,
-                max_value=max_value,
-                precision=precision
-            )
-        ))
-
-    def add_integer_config_field(self, field_name: str, display_name: str, description: str,
-                                 default_value: int | None = None, min_value: int = -2**31, max_value: int = 2**31-1,
-                                 optional: bool = False) -> None:
-        """
-        Add an integer configuration field to the tool. This field will be used to configure the tool in the plan
-        manager.
-
-        :param field_name: The name of the field.
-        :param display_name: The display name of the field.
-        :param description: The description of the field.
-        :param default_value: The default value of the field.
-        :param min_value: The minimum value of the field.
-        :param max_value: The maximum value of the field.
-        :param optional: If true, this field is optional. If false, this field is required.
-        """
-        self.config_fields.append(VeloxFieldDefPbo(
-            data_field_type=FieldTypePbo.INTEGER,
-            data_field_name=field_name,
-            display_name=display_name,
-            description=description,
-            required=not optional,
-            editable=True,
-            integer_properties=IntegerPropertiesPbo(
-                default_value=default_value,
-                min_value=min_value,
-                max_value=max_value
-            )
-        ))
-
-    def add_string_config_field(self, field_name: str, display_name: str, description: str,
-                                default_value: str | None = None, max_length: int = 1000, optional: bool = False) \
-            -> None:
-        """
-        Add a string configuration field to the tool. This field will be used to configure the tool in the plan
-        manager.
-
-        :param field_name: The name of the field.
-        :param display_name: The display name of the field.
-        :param description: The description of the field.
-        :param default_value: The default value of the field.
-        :param max_length: The maximum length of the field.
-        :param optional: If true, this field is optional. If false, this field is required.
-        """
-        self.config_fields.append(VeloxFieldDefPbo(
-            data_field_type=FieldTypePbo.STRING,
-            data_field_name=field_name,
-            display_name=display_name,
-            description=description,
-            required=not optional,
-            editable=True,
-            string_properties=StringPropertiesPbo(
-                default_value=default_value,
-                max_length=max_length
-            )
-        ))
-
-    def add_list_config_field(self, field_name: str, display_name: str, description: str,
-                              default_value: str | None = None, allowed_values: list[str] | None = None,
-                              direct_edit: bool = False, optional: bool = False) -> None:
-        """
-        Add a list configuration field to the tool. This field will be used to configure the tool in the plan
-        manager.
-
-        :param field_name: The name of the field.
-        :param display_name: The display name of the field.
-        :param description: The description of the field.
-        :param default_value: The default value of the field.
-        :param allowed_values: The list of allowed values for the field.
-        :param direct_edit: If true, the user can enter a value that is not in the list of allowed values. If false,
-            the user can only select from the list of allowed values.
-        :param optional: If true, this field is optional. If false, this field is required.
-        """
-        self.config_fields.append(VeloxFieldDefPbo(
-            data_field_type=FieldTypePbo.SELECTION,
-            data_field_name=field_name,
-            display_name=display_name,
-            description=description,
-            required=not optional,
-            editable=True,
-            selection_properties=SelectionPropertiesPbo(
-                default_value=default_value,
-                static_list_values=allowed_values,
-                direct_edit=direct_edit,
-            )
-        ))
-
-    def add_multi_list_config_field(self, field_name: str, display_name: str, description: str,
-                                    default_value: list[str] | None = None, allowed_values: list[str] | None = None,
-                                    direct_edit: bool = False, optional: bool = False) -> None:
-        """
-        Add a multi-select list configuration field to the tool. This field will be used to configure the tool in the
-        plan manager.
-
-        :param field_name: The name of the field.
-        :param display_name: The display name of the field.
-        :param description: The description of the field.
-        :param default_value: The default value of the field.
-        :param allowed_values: The list of allowed values for the field.
-        :param direct_edit: If true, the user can enter a value that is not in the list of allowed values. If false,
-            the user can only select from the list of allowed values.
-        :param optional: If true, this field is optional. If false, this field is required.
-        """
-        self.config_fields.append(VeloxFieldDefPbo(
-            data_field_type=FieldTypePbo.SELECTION,
-            data_field_name=field_name,
-            display_name=display_name,
-            description=description,
-            required=not optional,
-            editable=True,
-            selection_properties=SelectionPropertiesPbo(
-                default_value=",".join(default_value) if default_value else None,
-                static_list_values=allowed_values,
-                multi_select=True,
-                direct_edit=direct_edit,
-            )
-        ))
-
-    def to_pbo(self) -> ToolDetailsPbo:
-        """
-        :return: The ToolDetailsPbo proto object representing this tool.
-        """
-        return ToolDetailsPbo(
-            name=self._name,
-            description=self._description,
-            input_configs=self.input_configs,
-            output_configs=self.output_configs,
-            output_data_type_name=self._data_type_name,
-            config_fields=self.config_fields
-        )
-
-    @abstractmethod
-    def validate_input(self) -> str | None:
-        """
-        Validate the request given to this tool. If the request is validly formatted, this method should return None.
-        If the request is not valid, this method should return an error message indicating what is wrong with the
-        request.
-
-        This method should not perform any actual processing of the request. It should only validate the inputs and
-        configurations provided in the request.
-
-        The request inputs can be accessed using the self.get_input_*() methods.
-        The request settings can be accessed using the self.get_config_fields() method.
-        The request itself can be accessed using self.request.
-
-        :return: A tuple containing a boolean indicating whether the request is valid and a message describing the
-            result of the validation.
-        """
-        pass
-
-    def dry_run_output(self) -> list[SapioToolResult]:
-        """
-        Provide fixed results for a dry run of this tool. This method should not perform any actual processing of the
-        request. It should only return example outputs that can be used to test the next tool in the plan.
-
-        The default implementation of this method looks at the testing_example field of each output configuration
-        and returns a SapioToolResult object based on the content type of the output.
-
-        :return: A list of SapioToolResult objects containing example outputs for this tool. Each result in the list
-            corresponds to a separate output from the tool.
-        """
-        results: list[SapioToolResult] = []
-        for output, container_type in zip(self.output_configs, self._output_container_types):
-            config: ToolIoConfigBasePbo = output.base_config
-            example: ExampleContainerPbo = config.testing_example
-            content_type: str = config.content_type
-            match container_type:
-                case ContainerType.BINARY:
-                    example: bytes = example.binary_example
-                    results.append(BinaryResult(binary_data=[example], content_type=content_type))
-                case ContainerType.CSV:
-                    example: str = example.text_example
-                    results.append(CsvResult(FileUtil.tokenize_csv(example.encode())[0], content_type=content_type))
-                case ContainerType.JSON:
-                    # The example may be in the JSONL format instead of plain JSON, so we need to use Pandas to parse
-                    # the example into plain JSON.
-                    example: str = example.text_example
-                    # Format the JSONL in a way that Pandas likes. Collapse everything into a single line, and then
-                    # split it back into multiple lines where each line is a single JSON list or dictionary.
-                    example: str = re.sub("([]}])\s*([\[{])", r"\1\n\2", example.replace("\n", "")).strip()
-                    # Read the JSONL into a Pandas DataFrame and convert it back to plain JSON.
-                    import pandas as pd
-                    with io.StringIO(example) as stream:
-                        example: str = pd.read_json(path_or_buf=stream, lines=True).to_json()
-                    results.append(JsonResult(json_data=[json.loads(example)], content_type=content_type))
-                case ContainerType.TEXT:
-                    example: str = example.text_example
-                    results.append(TextResult(text_data=[example], content_type=content_type))
-        return results
-
-    @abstractmethod
-    def run(self, user: SapioUser) -> list[SapioToolResult]:
-        """
-        Execute this tool.
-
-        The request inputs can be accessed using the self.get_input_*() methods.
-        The request settings can be accessed using the self.get_config_fields() method.
-        The request itself can be accessed using self.request.
-
-        :param user: A user object that can be used to initialize manager classes using DataMgmtServer to query the
-            system.
-        :return: A list of SapioToolResult objects containing the response data. Each result in the list corresponds to
-            a separate output from the tool. Field map results do not appear as tool output in the plan manager, instead
-            appearing as records related to the plan step during the run.
-        """
-        pass
-
-    def log_info(self, message: str) -> None:
-        """
-        Log an info message for this tool. If verbose logging is enabled, this message will be included in the logs
-        returned to the caller. Empty/None inputs will not be logged.
-
-        :param message: The message to log.
-        """
-        if not message:
-            return
-        if self.verbose_logging:
-            self.logs.append(f"INFO: {self._name}: {message}")
-        self.logger.info(message)
-
-    def log_warning(self, message: str) -> None:
-        """
-        Log a warning message for this tool. This message will be included in the logs returned to the caller.
-        Empty/None inputs will not be logged.
-
-        :param message: The message to log.
-        """
-        if not message:
-            return
-        self.logs.append(f"WARNING: {self._name}: {message}")
-        self.logger.warning(message)
-
-    def log_error(self, message: str) -> None:
-        """
-        Log an error message for this tool. This message will be included in the logs returned to the caller.
-        Empty/None inputs will not be logged.
-
-        :param message: The message to log.
-        """
-        if not message:
-            return
-        self.logs.append(f"ERROR: {self._name}: {message}")
-        self.logger.error(message)
-
-    def log_exception(self, message: str, e: Exception) -> None:
-        """
-        Log an exception for this tool. This message will be included in the logs returned to the caller.
-        Empty/None inputs will not be logged.
-
-        :param message: The message to log.
-        :param e: The exception to log.
-        """
-        if not message and not e:
-            return
-        self.logs.append(f"EXCEPTION: {self._name}: {message} - {e}")
-        self.logger.error(f"{message}\n{traceback.format_exc()}")
-
-    def get_input_name(self, index: int = 0) -> str | None:
-        """
-        Get the name of the input from the request object.
-
-        :param index: The index of the input to parse. Defaults to 0. Used for tools that accept multiple inputs.
-        :return: The name of the input from the request object, or None if no name is set.
-        """
-        return self.request.input[index].item_container.container_name
-
-    def get_input_binary(self, index: int = 0) -> list[bytes]:
-        """
-        Get the binary data from the request object.
-
-        :param index: The index of the input to parse. Defaults to 0. Used for tools that accept multiple inputs.
-        :return: The binary data from the request object.
-        """
-        return list(self.request.input[index].item_container.binary_container.items)
-
-    def get_input_csv(self, index: int = 0) -> tuple[list[str], list[dict[str, str]]]:
-        """
-        Parse the CSV data from the request object.
-
-        :param index: The index of the input to parse. Defaults to 0. Used for tools that accept multiple inputs.
-        :return: A tuple containing the header row and the data rows. The header row is a list of strings representing
-            the column names, and the data rows are a list of dictionaries where each dictionary represents a row in the
-            CSV with the column names as keys and the corresponding values as strings.
-        """
-        input_data: Sequence[StepInputBatchPbo] = self.request.input
-        ret_val: list[dict[str, str]] = []
-        headers: Iterable[str] = input_data[index].item_container.csv_container.header.cells
-        for row in input_data[index].item_container.csv_container.items:
-            row_dict: dict[str, str] = {}
-            for header, value in zip(headers, row.cells):
-                row_dict[header] = value
-            ret_val.append(row_dict)
-        return list(headers), ret_val
-
-    def get_input_json(self, index: int = 0) -> list[list[Any]] | list[dict[str, Any]]:
-        """
-        Parse the JSON data from the request object.
-
-        :param index: The index of the input to parse. Defaults to 0. Used for tools that accept multiple inputs.
-        :return: A list of parsed JSON objects. Each entry in the list represents a separate JSON entry from the input.
-            Depending on this tool, this may be a list of dictionaries or a list of lists.
-        """
-        return [json.loads(x) for x in self.request.input[index].item_container.json_container.items]
-
-    def get_input_text(self, index: int = 0) -> list[str]:
-        """
-        Parse the text data from the request object.
-
-        :param index: The index of the input to parse. Defaults to 0. Used for tools that accept multiple inputs.
-        :return: A list of text data as strings.
-        """
-        return list(self.request.input[index].item_container.text_container.items)
-
-    def get_config_defs(self) -> dict[str, VeloxFieldDefPbo]:
-        """
-        Get the config field definitions for this tool.
-
-        :return: A dictionary of field definitions, where the keys are the field names and the values are the
-            VeloxFieldDefPbo objects representing the field definitions.
-        """
-        field_defs: dict[str, VeloxFieldDefPbo] = {}
-        for field_def in self.to_pbo().config_fields:
-            field_defs[field_def.data_field_name] = field_def
-        return field_defs
-
-    def get_config_fields(self) -> dict[str, FieldValue | list[str]]:
-        """
-        Get the configuration field values from the request object. If a field is not present in the request,
-        the default value from the config definition will be returned.
-
-        :return: A dictionary of configuration field names and their values. For multi-select selection list fields,
-            a list of strings will be returned. For all other field types, the value will match the field type
-            (bool for boolean fields, float for double fields, int for short, integer, long, and enum fields, and
-            string for everything else).
-        """
-        config_fields: dict[str, Any] = {}
-        raw_configs: Mapping[str, FieldValuePbo] = self.request.config_field_values
-        for field_name, field_def in self.get_config_defs().items():
-            field_value: FieldValue = None
-            # If the field is present in the request, convert the protobuf value to a Python value.
-            if field_name in raw_configs:
-                field_value = ProtobufUtils.field_pbo_to_value(raw_configs[field_name])
-            # If the field isn't present or is None, use the default value from the field definition.
-            if field_value is None:
-                field_value = ProtobufUtils.field_def_pbo_to_default_value(field_def)
-            # If the field is a multi-select selection list, split the value by commas and strip whitespace.
-            if field_def.data_field_type == FieldTypePbo.SELECTION and field_def.selection_properties.multi_select:
-                field_value: list[str] = [x.strip() for x in field_value.split(',') if x.strip()]
-            config_fields[field_name] = field_value
-        return config_fields
-
-    @staticmethod
-    def read_from_json(json_data: list[dict[str, Any]], key: str) -> list[Any]:
-        """
-        From a list of dictionaries, return a list of values for the given key from each dictionary. Skips null values.
-
-        :param json_data: The JSON data to read from.
-        :param key: The key to read the values from.
-        :return: A list of values corresponding to the given key in the JSON data.
-        """
-        ret_val: list[Any] = []
-        for entry in json_data:
-            if key in entry:
-                value = entry[key]
-                if isinstance(value, list):
-                    ret_val.extend(value)
-                elif value is not None:
-                    ret_val.append(value)
-        return ret_val