sapiopycommons 2025.10.1a772__py3-none-any.whl → 2025.10.9a776__py3-none-any.whl

sapiopycommons/ai/agent_service_base.py

@@ -0,0 +1,1114 @@
+from __future__ import annotations
+
+import base64
+import io
+import json
+import logging
+import re
+import subprocess
+import traceback
+from abc import abstractmethod, ABC
+from logging import Logger
+from os import PathLike
+from subprocess import CompletedProcess
+from typing import Any, Iterable, Mapping, Sequence
+
+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, \
+    FieldValidatorPbo
+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
+from sapiopycommons.ai.protoapi.plan.tool.tool_pb2 import ToolDetailsRequestPbo, ToolDetailsResponsePbo, \
+    ToolDetailsPbo, ProcessStepRequestPbo, ProcessStepResponsePbo, ToolOutputDetailsPbo, ToolIoConfigBasePbo, \
+    ToolInputDetailsPbo, ExampleContainerPbo, ProcessStepResponseStatusPbo, ToolCitationPbo
+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 SapioAgentResult(ABC):
+    """
+    A class representing a result from a Sapio agent. Instantiate one of the subclasses to create a result object.
+    """
+
+    @abstractmethod
+    def to_proto(self) -> StepOutputBatchPbo | list[FieldValueMapPbo]:
+        """
+        Convert this SapioAgentResult object to a StepOutputBatchPbo or list of FieldValueMapPbo proto objects.
+        """
+        pass
+
+
+class BinaryResult(SapioAgentResult):
+    """
+    A class representing binary results from a Sapio agent.
+    """
+    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 agent.
+        """
+        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(SapioAgentResult):
+    """
+    A class representing CSV results from a Sapio agent.
+    """
+    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 agent.
+        """
+        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(SapioAgentResult):
+    """
+    A class representing field map results from a Sapio agent.
+    """
+    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 agent 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(SapioAgentResult):
+    """
+    A class representing JSON results from a Sapio agent.
+    """
+    json_data: list[dict[str, Any]]
+    content_type: str
+    file_extensions: list[str]
+    name: str
+
+    def __init__(self, json_data: list[dict[str, 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 agent.
+        """
+        # Verify that the given json_data is actually a list of dictionaries.
+        if not isinstance(json_data, list) or not all(isinstance(x, dict) for x in json_data):
+            raise ValueError("json_data must be a list of dictionaries.")
+        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(SapioAgentResult):
+    """
+    A class representing text results from a Sapio agent.
+    """
+    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 agent.
+        """
+        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 AgentServiceBase(ToolServiceServicer, ABC):
+    """
+    A base class for implementing an agent service. Subclasses should implement the register_agents method to register
+    their agents with the service.
+    """
+    debug_mode: bool = False
+
+    def GetToolDetails(self, request: ToolDetailsRequestPbo, context: ServicerContext) -> ToolDetailsResponsePbo:
+        try:
+            # Get the agent details from the registered agents.
+            details: list[ToolDetailsPbo] = []
+            for agent in self.register_agents():
+                details.append(agent().to_pbo())
+            if not details:
+                raise Exception("No agents registered with this service.")
+            return ToolDetailsResponsePbo(tool_framework_version=self.server_version(), tool_details=details)
+        except Exception as e:
+            # Woe to you if you somehow cause an exception to be raised when just initializing your agents.
+            # 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 agent results from the registered agent 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 agent 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 server_version() -> int:
+        """
+        :return: The version of this set of .
+        """
+        return 1
+
+    @abstractmethod
+    def register_agents(self) -> list[type[AgentBase]]:
+        """
+        Register agent types with this service. Provided agents should implement the AgentBase class.
+
+        :return: A list of agents to register to this service.
+        """
+        pass
+
+    def run(self, user: SapioUser, request: ProcessStepRequestPbo, context: ServicerContext) \
+            -> tuple[bool, str, list[SapioAgentResult], list[str]]:
+        """
+        Execute an agent 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 agent succeeded, the status message, the results of the agent, and any logs
+            generated by the agent.
+        """
+        # Locate the agent named in the request.
+        find_agent: str = request.tool_name
+        registered_agents: dict[str, type[AgentBase]] = {t.name(): t for t in self.register_agents()}
+        if find_agent not in registered_agents:
+            # If the agent is not found, list all of the registered agents for this service so that the LLM can correct
+            # the agent it is requesting.
+            all_agent_names: str = "\n".join(registered_agents.keys())
+            msg: str = (f"Agent \"{find_agent}\" not found in the registered agents for this service. The registered "
+                        f"agents for this service are: \n{all_agent_names}")
+            return False, msg, [], []
+
+        # Instantiate the agent class.
+        agent: AgentBase = registered_agents[find_agent]()
+        try:
+            # Setup the agent with details from the request.
+            agent.setup(user, request, context, self.debug_mode)
+            # Validate that the provided inputs match the agent's expected inputs.
+            msg: str = ""
+            if len(request.input) != len(agent.input_configs):
+                msg = f"Expected {len(agent.input_configs)} inputs for this agent, but got {len(request.input)} instead."
+            else:
+                errors: list[str] = agent.validate_input()
+                if errors:
+                    msg = "\n".join(errors)
+            # 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 agent is executed normally.
+            results: list[SapioAgentResult] = []
+            if request.dry_run:
+                results = agent.dry_run_output()
+            elif success:
+                results = agent.run(user)
+                # Update the status message to reflect the successful execution of the agent.
+                msg = f"{agent.name()} successfully completed."
+            return success, msg, results, agent.logs
+        except Exception as e:
+            agent.log_exception("Exception occurred during agent execution.", e)
+            return False, str(e), [], agent.logs
+        finally:
+            # Clean up any temporary files created by the agent. 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 agent execution:")
+                for directory in agent.temp_data.directories:
+                    print(f"\tDirectory: {directory}")
+                for file in agent.temp_data.files:
+                    print(f"\tFile: {file}")
+            else:
+                agent.temp_data.cleanup()
+
+
+class AgentBase(ABC):
+    """
+    A base class for implementing an agent.
+    """
+    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
+
+    temp_data: TempFileHandler
+
+    user: SapioUser
+    request: ProcessStepRequestPbo
+    context: ServicerContext
+    debug_mode: bool
+
+    @classmethod
+    @abstractmethod
+    def identifier(cls):
+        """
+        :return: The unique identifier of the agent. This is used by the system to determine which agent should be
+            updated if an agent is re-imported. This should not be changed after the first time that an agent is
+            imported, otherwise a duplicate agent will be created.
+        """
+        pass
+
+    @staticmethod
+    @abstractmethod
+    def name() -> str:
+        """
+        :return: The display name of the agent. This should be unique across all agents in the service.
+        """
+        pass
+
+    @staticmethod
+    @abstractmethod
+    def category() -> str:
+        """
+        :return: The category of the agent. This is used to group similar agents together in the plan manager.
+        """
+        pass
+
+    @staticmethod
+    @abstractmethod
+    def description() -> str:
+        """
+        :return: A description of the agent.
+        """
+        pass
+
+    @staticmethod
+    @abstractmethod
+    def citations() -> dict[str, str]:
+        """
+        :return: Any citations or references for this agent, as a dictionary of citation name to URL.
+        """
+        pass
+
+    @staticmethod
+    def data_type_name() -> str | None:
+        """
+        :return: The name of the output data type of this agent, if applicable. When this agent returns
+            FieldMapResult objects in its run method, this name will be used to set the data type of the output data.
+        """
+        return None
+
+    @staticmethod
+    def license_flag() -> str | None:
+        """
+        :return: The license flag for this agent. The system must have this license in order to use this agent.
+            If None, the agent is not license locked.
+        """
+        return None
+
+    def __init__(self):
+        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"AgentBase.{self.name()}")
+        ensure_logger_initialized(self.logger)
+
+    def setup(self, user: SapioUser, request: ProcessStepRequestPbo, context: ServicerContext, debug_mode: bool) -> None:
+        """
+        Setup the agent 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 agent 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 agent. This determines how many inputs this agent 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. This must be provided for any container type other than BINARY.
+        :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 agent.
+        :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 agent. 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 agent.
+        """
+        if container_type != ContainerType.BINARY and structure_example is None:
+            raise ValueError("structure_example must be provided for inputs with a container_type other than BINARY.")
+        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,
+                # The testing example on the input is never used, hence why it can't be set by this function.
+                # The testing example is only used during dry runs, in which the testing_example of the output
+                # of the previous step is what gets passed to the next step's input validation.
+                testing_example=None
+            ),
+            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 agent. This determines how many inputs this agent 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 agent in the system. This must be
+            an entirely valid example of what an output of this agent 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. This must be provided for any container type other than BINARY.
+        """
+        if not testing_example:
+            raise ValueError("A testing_example must be provided for the output.")
+        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)
+
+        if container_type != ContainerType.BINARY and structure_example is None:
+            raise ValueError("structure_example must be provided for inputs with a container_type other than BINARY.")
+        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 agent. This field will be used to configure the agent 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 agent. This field will be used to configure the agent 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 agent. This field will be used to configure the agent 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 agent. This field will be used to configure the agent 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 agent. This field will be used to configure the agent 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,
+                                validation_regex: str | None = None, error_msg: str | None = None) -> None:
+        """
+        Add a string configuration field to the agent. This field will be used to configure the agent 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.
+        :param validation_regex: An optional regex that the field value must match.
+        :param error_msg: An optional error message to display if the field value does not match the regex.
+        """
+        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,
+                field_validator=FieldValidatorPbo(validation_regex=validation_regex, error_message=error_msg) if validation_regex else None
+            )
+        ))
+
+    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,
+                              validation_regex: str | None = None, error_msg: str | None = None) -> None:
+        """
+        Add a list configuration field to the agent. This field will be used to configure the agent 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.
+        :param validation_regex: An optional regex that the field value must match.
+        :param error_msg: An optional error message to display if the field value does not match the regex.
+        """
+        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,
+                field_validator=FieldValidatorPbo(validation_regex=validation_regex, error_message=error_msg) if validation_regex else None
+            )
+        ))
+
+    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,
+                                    validation_regex: str | None = None, error_msg: str | None = None) -> None:
+        """
+        Add a multi-select list configuration field to the agent. This field will be used to configure the agent 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.
+        :param validation_regex: An optional regex that the field value must match.
+        :param error_msg: An optional error message to display if the field value does not match the regex.
+        """
+        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,
+                field_validator=FieldValidatorPbo(validation_regex=validation_regex, error_message=error_msg) if validation_regex else None
+            )
+        ))
+
+    def to_pbo(self) -> ToolDetailsPbo:
+        """
+        :return: The ToolDetailsPbo proto object representing this agent.
+        """
+        return ToolDetailsPbo(
+            import_id=self.identifier(),
+            name=self.name(),
+            description=self.description(),
+            category=self.category(),
+            citation=[ToolCitationPbo(title=x, url=y) for x, y in self.citations().items()],
+            input_configs=self.input_configs,
+            output_configs=self.output_configs,
+            output_data_type_name=self.data_type_name(),
+            config_fields=self.config_fields,
+            license_info=self.license_flag(),
+        )
+
+    @abstractmethod
+    def validate_input(self) -> list[str] | None:
+        """
+        Validate the request given to this agent. 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 list of the error messages if the request is not valid. If the request is valid, return an empty
+            list or None.
+        """
+        pass
+
+    def dry_run_output(self) -> list[SapioAgentResult]:
+        """
+        Provide fixed results for a dry run of this agent. 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 agent in the plan.
+
+        The default implementation of this method looks at the testing_example field of each output configuration
+        and returns a SapioAgentResult object based on the content type of the output.
+
+        :return: A list of SapioAgentResult objects containing example outputs for this agent. Each result in the list
+            corresponds to a separate output from the agent.
+        """
+        results: list[SapioAgentResult] = []
+        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()
+                    data = json.loads(example)
+                    if not isinstance(data, list):
+                        data = [data]
+                    results.append(JsonResult(json_data=data, 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[SapioAgentResult]:
+        """
+        Execute this agent.
+
+        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 SapioAgentResult objects containing the response data. Each result in the list corresponds to
+            a separate output from the agent. Field map results do not appear as agent output in the plan manager,
+            instead appearing as records related to the plan step during the run.
+        """
+        pass
+
+    def call_subprocess(self,
+                        args: str | bytes | PathLike[str] | PathLike[bytes] | Sequence[str | bytes | PathLike[str] | PathLike[bytes]],
+                        cwd: str | bytes | PathLike[str] | PathLike[bytes] | None = None,
+                        **kwargs) -> CompletedProcess[str]:
+        """
+        Call a subprocess with the given arguments, logging the command and any errors that occur.
+        This function will raise an exception if the return code of the subprocess is non-zero. The output of the
+        subprocess will be captured and returned as part of the CompletedProcess object.
+
+        :param args: The list of arguments to pass to the subprocess.
+        :param cwd: The working directory to run the subprocess in. If None, the current working directory is used.
+        :param kwargs: Additional keyword arguments to pass to subprocess.run().
+        :return: The CompletedProcess object returned by subprocess.run().
+        """
+        try:
+            self.log_info(f"Running subprocess with command: {' '.join(args)}")
+            return subprocess.run(args, check=True, capture_output=True, text=True, cwd=cwd, **kwargs)
+        except subprocess.CalledProcessError as e:
+            self.log_error(f"Error running subprocess. Return code: {e.returncode}")
+            self.log_error(f"STDOUT: {e.stdout}")
+            self.log_error(f"STDERR: {e.stderr}")
+            raise
+
+    def log_info(self, message: str) -> None:
+        """
+        Log an info message for this agent. 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 agent. 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 agent. 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 agent. 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 is_input_partial(self, index: int = 0) -> bool:
+        """
+        Check if the input at the given index is marked as partial.
+
+        :param index: The index of the input to check. Defaults to 0. Used for agents that accept multiple inputs.
+        :return: True if the input is marked as partial, False otherwise.
+        """
+        return self.request.input[index].is_partial
+
+    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 agents 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_content_type(self, index: int = 0) -> ContentTypePbo:
+        """
+        Get the content type of the input from the request object.
+
+        :param index: The index of the input to parse. Defaults to 0. Used for agents that accept multiple inputs.
+        :return: The content type of the input from the request object.
+        """
+        return self.request.input[index].item_container.content_type
+
+    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 agents that accept multiple inputs.
+        :return: The binary data from the request object.
+        """
+        container: StepItemContainerPbo = self.request.input[index].item_container
+        if not container.HasField("binary_container"):
+            raise Exception(f"Input {index} does not contain a binary container.")
+        return list(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 agents 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.
+        """
+        container: StepItemContainerPbo = self.request.input[index].item_container
+        if not container.HasField("csv_container"):
+            raise Exception(f"Input {index} does not contain a CSV container.")
+        ret_val: list[dict[str, str]] = []
+        headers: Iterable[str] = container.csv_container.header.cells
+        for row in 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[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 agents that accept multiple inputs.
+        :return: A list of parsed JSON objects, which are represented as dictionaries.
+        """
+        container: StepItemContainerPbo = self.request.input[index].item_container
+        if not container.HasField("json_container"):
+            raise Exception(f"Input {index} does not contain a JSON container.")
+        input_json: list[Any] = [json.loads(x) for x in container.json_container.items]
+        # Verify that the given JSON actually is a list of dictionaries. If they aren't then the previous step provided
+        # bad input. Agents are enforced to result in a list of dictionaries when returning JSON data, so this is likely
+        # an error caused by a script or static input step.
+        for i, entry in enumerate(input_json):
+            if not isinstance(entry, dict):
+                raise Exception(f"Element {i} of input {index} is not a dictionary object. All top-level JSON inputs "
+                                f"are expected to be dictionaries.")
+        return input_json
+
+    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 agents that accept multiple inputs.
+        :return: A list of text data as strings.
+        """
+        container: StepItemContainerPbo = self.request.input[index].item_container
+        if not container.HasField("text_container"):
+            raise Exception(f"Input {index} does not contain a text container.")
+        return list(container.text_container.items)
+
+    def get_config_defs(self) -> dict[str, VeloxFieldDefPbo]:
+        """
+        Get the config field definitions for this agent.
+
+        :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
+
+    @staticmethod
+    def flatten_text(text_data: list[str]) -> list[str]:
+        """
+        From a list of strings that come from a text input, flatten the list by splitting each string on newlines and
+        stripping whitespace. Empty lines will be removed.
+
+        :param text_data: The text data to flatten.
+        :return: A flattened list of strings.
+        """
+        ret_val: list[str] = []
+        for entry in text_data:
+            lines: list[str] = [x.strip() for x in entry.splitlines() if x.strip()]
+            ret_val.extend(lines)
+        return ret_val